evaluating epistatic interaction: Topics by WorldWideScience.org

Sample records for evaluating epistatic interaction

Epistatic interactions on chromosome 14 influencing stillbirth in Fleckvieh cattle

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Gábor Mészáros

2016-09-01

Full Text Available Single nucleotide polymorphism (SNP data of 7384 Fleckvieh bulls was analyzed to identify epistatic interactions influencing stillbirth. Deregressed breeding values were used as phenotypes. The epistatic effects were identified as significant interaction terms from pairwise linear regressions performed for each SNP after accounting for multiple testing. Majority of the detected epistatic effects were located in the 9-31Mb region of chromosome 14, corresponding to the most significant region from the genome wide association. Additional epistatic SNPs at 50.5Mb and 80.5 Mb at the same chromosome were detected. The region around 25 Mb contained genes connected to height and body size such as PLAG1, CHCHD7, LYN, RDHE2 (SDR16C5 and PENK. The other interesting region at 50.5Mb contained the TRPS1 gene influencing bone malformations. Both regions have been identified as candidates influencing stillbirth.
bNEAT: a Bayesian network method for detecting epistatic interactions in genome-wide association studies

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Chen Xue-wen

2011-07-01

Full Text Available Abstract Background Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis and treatment of complex human diseases. A recent study in automatic detection of epistatic interactions shows that Markov Blanket-based methods are capable of finding genetic variants strongly associated with common diseases and reducing false positives when the number of instances is large. Unfortunately, a typical dataset from genome-wide association studies consists of very limited number of examples, where current methods including Markov Blanket-based method may perform poorly. Results To address small sample problems, we propose a Bayesian network-based approach (bNEAT to detect epistatic interactions. The proposed method also employs a Branch-and-Bound technique for learning. We apply the proposed method to simulated datasets based on four disease models and a real dataset. Experimental results show that our method outperforms Markov Blanket-based methods and other commonly-used methods, especially when the number of samples is small. Conclusions Our results show bNEAT can obtain a strong power regardless of the number of samples and is especially suitable for detecting epistatic interactions with slight or no marginal effects. The merits of the proposed approach lie in two aspects: a suitable score for Bayesian network structure learning that can reflect higher-order epistatic interactions and a heuristic Bayesian network structure learning method.
Mechanistic basis of an epistatic interaction reducing age at onset in hereditary spastic paraplegia.

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Newton, Timothy; Allison, Rachel; Edgar, James R; Lumb, Jennifer H; Rodger, Catherine E; Manna, Paul T; Rizo, Tania; Kohl, Zacharias; Nygren, Anders O H; Arning, Larissa; Schüle, Rebecca; Depienne, Christel; Goldberg, Lisa; Frahm, Christiane; Stevanin, Giovanni; Durr, Alexandra; Schöls, Ludger; Winner, Beate; Beetz, Christian; Reid, Evan

2018-05-01

Many genetic neurological disorders exhibit variable expression within affected families, often exemplified by variations in disease age at onset. Epistatic effects (i.e. effects of modifier genes on the disease gene) may underlie this variation, but the mechanistic basis for such epistatic interactions is rarely understood. Here we report a novel epistatic interaction between SPAST and the contiguous gene DPY30, which modifies age at onset in hereditary spastic paraplegia, a genetic axonopathy. We found that patients with hereditary spastic paraplegia caused by genomic deletions of SPAST that extended into DPY30 had a significantly younger age at onset. We show that, like spastin, the protein encoded by SPAST, the DPY30 protein controls endosomal tubule fission, traffic of mannose 6-phosphate receptors from endosomes to the Golgi, and lysosomal ultrastructural morphology. We propose that additive effects on this pathway explain the reduced age at onset of hereditary spastic paraplegia in patients who are haploinsufficient for both genes.
An empirical comparison of several recent epistatic interaction detection methods.

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Wang, Yue; Liu, Guimei; Feng, Mengling; Wong, Limsoon

2011-11-01

Many new methods have recently been proposed for detecting epistatic interactions in GWAS data. There is, however, no in-depth independent comparison of these methods yet. Five recent methods-TEAM, BOOST, SNPHarvester, SNPRuler and Screen and Clean (SC)-are evaluated here in terms of power, type-1 error rate, scalability and completeness. In terms of power, TEAM performs best on data with main effect and BOOST performs best on data without main effect. In terms of type-1 error rate, TEAM and BOOST have higher type-1 error rates than SNPRuler and SNPHarvester. SC does not control type-1 error rate well. In terms of scalability, we tested the five methods using a dataset with 100 000 SNPs on a 64 bit Ubuntu system, with Intel (R) Xeon(R) CPU 2.66 GHz, 16 GB memory. TEAM takes ~36 days to finish and SNPRuler reports heap allocation problems. BOOST scales up to 100 000 SNPs and the cost is much lower than that of TEAM. SC and SNPHarvester are the most scalable. In terms of completeness, we study how frequently the pruning techniques employed by these methods incorrectly prune away the most significant epistatic interactions. We find that, on average, 20% of datasets without main effect and 60% of datasets with main effect are pruned incorrectly by BOOST, SNPRuler and SNPHarvester. The software for the five methods tested are available from the URLs below. TEAM: http://csbio.unc.edu/epistasis/download.php BOOST: http://ihome.ust.hk/~eeyang/papers.html. SNPHarvester: http://bioinformatics.ust.hk/SNPHarvester.html. SNPRuler: http://bioinformatics.ust.hk/SNPRuler.zip. Screen and Clean: http://wpicr.wpic.pitt.edu/WPICCompGen/. wangyue@nus.edu.sg.
Understanding Epistatic Interactions between Genes Targeted by Non-coding Regulatory Elements in Complex Diseases

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Min Kyung Sung

2014-12-01

Full Text Available Genome-wide association studies have proven the highly polygenic architecture of complex diseases or traits; therefore, single-locus-based methods are usually unable to detect all involved loci, especially when individual loci exert small effects. Moreover, the majority of associated single-nucleotide polymorphisms resides in non-coding regions, making it difficult to understand their phenotypic contribution. In this work, we studied epistatic interactions associated with three common diseases using Korea Association Resource (KARE data: type 2 diabetes mellitus (DM, hypertension (HT, and coronary artery disease (CAD. We showed that epistatic single-nucleotide polymorphisms (SNPs were enriched in enhancers, as well as in DNase I footprints (the Encyclopedia of DNA Elements [ENCODE] Project Consortium 2012, which suggested that the disruption of the regulatory regions where transcription factors bind may be involved in the disease mechanism. Accordingly, to identify the genes affected by the SNPs, we employed whole-genome multiple-cell-type enhancer data which discovered using DNase I profiles and Cap Analysis Gene Expression (CAGE. Assigned genes were significantly enriched in known disease associated gene sets, which were explored based on the literature, suggesting that this approach is useful for detecting relevant affected genes. In our knowledge-based epistatic network, the three diseases share many associated genes and are also closely related with each other through many epistatic interactions. These findings elucidate the genetic basis of the close relationship between DM, HT, and CAD.
Hybrid male sterility in rice is due to epistatic interactions with a pollen killer locus.

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Kubo, Takahiko; Yoshimura, Atsushi; Kurata, Nori

2011-11-01

In intraspecific crosses between cultivated rice (Oryza sativa) subspecies indica and japonica, the hybrid male sterility gene S24 causes the selective abortion of male gametes carrying the japonica allele (S24-j) via an allelic interaction in the heterozygous hybrids. In this study, we first examined whether male sterility is due solely to the single locus S24. An analysis of near-isogenic lines (NIL-F(1)) showed different phenotypes for S24 in different genetic backgrounds. The S24 heterozygote with the japonica genetic background showed male semisterility, but no sterility was found in heterozygotes with the indica background. This result indicates that S24 is regulated epistatically. A QTL analysis of a BC(2)F(1) population revealed a novel sterility locus that interacts with S24 and is found on rice chromosome 2. The locus was named Epistatic Factor for S24 (EFS). Further genetic analyses revealed that S24 causes male sterility when in combination with the homozygous japonica EFS allele (efs-j). The results suggest that efs-j is a recessive sporophytic allele, while the indica allele (EFS-i) can dominantly counteract the pollen sterility caused by S24 heterozygosity. In summary, our results demonstrate that an additional epistatic locus is an essential element in the hybrid sterility caused by allelic interaction at a single locus in rice. This finding provides a significant contribution to our understanding of the complex molecular mechanisms underlying hybrid sterility and microsporogenesis.
Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

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Aditi Gupta

2016-03-01

Full Text Available Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1 using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient condition that detects epistasis in most cases. We analyze the "fossils" of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing
Stripe rust and leaf rust resistance QTL mapping, epistatic interactions, and co-localization with stem rust resistance loci in spring wheat evaluated over three continents.

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Singh, A; Knox, R E; DePauw, R M; Singh, A K; Cuthbert, R D; Campbell, H L; Shorter, S; Bhavani, S

2014-11-01

In wheat, advantageous gene-rich or pleiotropic regions for stripe, leaf, and stem rust and epistatic interactions between rust resistance loci should be accounted for in plant breeding strategies. Leaf rust (Puccinia triticina Eriks.) and stripe rust (Puccinia striiformis f. tritici Eriks) contribute to major production losses in many regions worldwide. The objectives of this research were to identify and study epistatic interactions of quantitative trait loci (QTL) for stripe and leaf rust resistance in a doubled haploid (DH) population derived from the cross of Canadian wheat cultivars, AC Cadillac and Carberry. The relationship of leaf and stripe rust resistance QTL that co-located with stem rust resistance QTL previously mapped in this population was also investigated. The Carberry/AC Cadillac population was genotyped with DArT(®) and simple sequence repeat markers. The parents and population were phenotyped for stripe rust severity and infection response in field rust nurseries in Kenya (Njoro), Canada (Swift Current), and New Zealand (Lincoln); and for leaf rust severity and infection response in field nurseries in Canada (Swift Current) and New Zealand (Lincoln). AC Cadillac was a source of stripe rust resistance QTL on chromosomes 2A, 2B, 3A, 3B, 5B, and 7B; and Carberry was a source of resistance on chromosomes 2B, 4B, and 7A. AC Cadillac contributed QTL for resistance to leaf rust on chromosome 2A and Carberry contributed QTL on chromosomes 2B and 4B. Stripe rust resistance QTL co-localized with previously reported stem rust resistance QTL on 2B, 3B, and 7B, while leaf rust resistance QTL co-localized with 4B stem rust resistance QTL. Several epistatic interactions were identified both for stripe and leaf rust resistance QTL. We have identified useful combinations of genetic loci with main and epistatic effects. Multiple disease resistance regions identified on chromosomes 2A, 2B, 3B, 4B, 5B, and 7B are prime candidates for further investigation and
Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis

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Collins, Ryan L; Hu, Ting; Wejse, Christian

2013-01-01

for this problem. The goal of the present study was to apply MDR to mining high-order epistatic interactions in a population-based genetic study of tuberculosis (TB). Results The study used a previously published data set consisting of 19 candidate single-nucleotide polymorphisms (SNPs) in 321 pulmonary TB cases...
Improved functional overview of protein complexes using inferred epistatic relationships

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Ryan, Colm

2011-05-23

Abstract Background Epistatic Miniarray Profiling(E-MAP) quantifies the net effect on growth rate of disrupting pairs of genes, often producing phenotypes that may be more (negative epistasis) or less (positive epistasis) severe than the phenotype predicted based on single gene disruptions. Epistatic interactions are important for understanding cell biology because they define relationships between individual genes, and between sets of genes involved in biochemical pathways and protein complexes. Each E-MAP screen quantifies the interactions between a logically selected subset of genes (e.g. genes whose products share a common function). Interactions that occur between genes involved in different cellular processes are not as frequently measured, yet these interactions are important for providing an overview of cellular organization. Results We introduce a method for combining overlapping E-MAP screens and inferring new interactions between them. We use this method to infer with high confidence 2,240 new strongly epistatic interactions and 34,469 weakly epistatic or neutral interactions. We show that accuracy of the predicted interactions approaches that of replicate experiments and that, like measured interactions, they are enriched for features such as shared biochemical pathways and knockout phenotypes. We constructed an expanded epistasis map for yeast cell protein complexes and show that our new interactions increase the evidence for previously proposed inter-complex connections, and predict many new links. We validated a number of these in the laboratory, including new interactions linking the SWR-C chromatin modifying complex and the nuclear transport apparatus. Conclusion Overall, our data support a modular model of yeast cell protein network organization and show how prediction methods can considerably extend the information that can be extracted from overlapping E-MAP screens.
The role of epistatic interactions underpinning resistance to parasitic Varroa mites in haploid honey bee (Apis mellifera) drones.

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Conlon, Benjamin H; Frey, Eva; Rosenkranz, Peter; Locke, Barbara; Moritz, Robin F A; Routtu, Jarkko

2018-06-01

The Red Queen hypothesis predicts that host-parasite coevolutionary dynamics can select for host resistance through increased genetic diversity, recombination and evolutionary rates. However, in haplodiploid organisms such as the honeybee (Apis mellifera), models suggest the selective pressure is weaker than in diploids. Haplodiploid sex determination, found in A. mellifera, can allow deleterious recessive alleles to persist in the population through the diploid sex with negative effects predominantly expressed in the haploid sex. To overcome these negative effects in haploid genomes, epistatic interactions have been hypothesized to play an important role. Here, we use the interaction between A. mellifera and the parasitic mite Varroa destructor to test epistasis in the expression of resistance, through the inhibition of parasite reproduction, in haploid drones. We find novel loci on three chromosomes which explain over 45% of the resistance phenotype. Two of these loci interact only additively, suggesting their expression is independent of each other, but both loci interact epistatically with the third locus. With drone offspring inheriting only one copy of the queen's chromosomes, the drones will only possess one of two queen alleles throughout the years-long lifetime of the honeybee colony. Varroa, in comparison, completes its highly inbred reproductive cycle in a matter of weeks, allowing it to rapidly evolve resistance. Faced with the rapidly evolving Varroa, a diversity of pathways and epistatic interactions for the inhibition of Varroa reproduction could therefore provide a selective advantage to the high levels of recombination seen in A. mellifera. This allows for the remixing of phenotypes despite a fixed queen genotype. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.
Epistatic association mapping in homozygous crop cultivars.

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Hai-Yan Lü

Full Text Available The genetic dissection of complex traits plays a crucial role in crop breeding. However, genetic analysis and crop breeding have heretofore been performed separately. In this study, we designed a new approach that integrates epistatic association analysis in crop cultivars with breeding by design. First, we proposed an epistatic association mapping (EAM approach in homozygous crop cultivars. The phenotypic values of complex traits, along with molecular marker information, were used to perform EAM. In our EAM, all the main-effect quantitative trait loci (QTLs, environmental effects, QTL-by-environment interactions and QTL-by-QTL interactions were included in a full model and estimated by empirical Bayes approach. A series of Monte Carlo simulations was performed to confirm the reliability of the new method. Next, the information from all detected QTLs was used to mine novel alleles for each locus and to design elite cross combination. Finally, the new approach was adopted to dissect the genetic basis of seed length in 215 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 19 main-effect QTLs and 3 epistatic QTLs were identified, more than 10 novel alleles were mined and 3 elite parental combinations, such as Daqingdou and Zhengzhou790034, were predicted.
Missing value imputation for epistatic MAPs

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Ryan, Colm

2010-04-20

Abstract Background Epistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. An effective method for imputing interactions would therefore increase the types of possible analysis, as well as increase the potential to identify novel functional interactions between gene pairs. Several methods have been developed to handle missing values in microarray data, but it is unclear how applicable these methods are to E-MAP data because of their pairwise nature and the significantly larger number of missing values. Here we evaluate four alternative imputation strategies, three local (Nearest neighbor-based) and one global (PCA-based), that have been modified to work with symmetric pairwise data. Results We identify different categories for the missing data based on their underlying cause, and show that values from the largest category can be imputed effectively. We compare local and global imputation approaches across a variety of distinct E-MAP datasets, showing that both are competitive and preferable to filling in with zeros. In addition we show that these methods are effective in an E-MAP from a different species, suggesting that pairwise imputation techniques will be increasingly useful as analogous epistasis mapping techniques are developed in different species. We show that strongly alleviating interactions are significantly more difficult to predict than strongly aggravating interactions. Finally we show that imputed interactions, generated using nearest neighbor methods, are enriched for annotations in the same manner as measured interactions. Therefore our method potentially
Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects

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Cia-Hin Lau

2012-01-01

Full Text Available Epistasis (gene-gene interaction is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G and RETN (SNP-420C > G and SNP+299G > A gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM and metabolic syndrome (MS were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.
QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits

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2013-01-01

Background Asparagus bean (Vigna. unguiculata. ssp sesquipedalis) is a subspecies and special vegetable type of cowpea (Vigna. unguiculata L. Walp.) important in Asia. Genetic basis of horticulturally important traits of asparagus bean is still poorly understood, hindering the utilization of targeted, DNA marker-assisted breeding in this crop. Here we report the identification of quantitative trait loci (QTLs) and epistatic interactions for four horticultural traits, namely, days to first flowering (FLD), nodes to first flower (NFF), leaf senescence (LS) and pod number per plant (PN) using a recombinant inbred line (RIL) population of asparagus bean. Results A similar genetic mode of one major QTL plus a few minor QTLs was found to dominate each of the four traits, with the number of QTLs for individual traits ranging from three to four. These QTLs were distributed on 7 of the 11 chromosomes. Major QTLs for FLD, NFF and LS were co-localized on LG 11, indicative of tight linkage. Genome wide epistasis analysis detected two and one interactive locus pairs that significantly affect FLD and LS, respectively, and the epistatic QTLs for FLD appeared to work in different ways. Synteny based comparison of QTL locations revealed conservation of chromosome regions controlling these traits in related legume crops. Conclusion Major, minor, and epistatic QTLs were found to contribute to the inheritance of the FLD, NFF, LS, and PN. Positions of many of these QTLs are conserved among closely related legume species, indicating common mechanisms they share. To our best knowledge, this is the first QTL mapping report using an asparagus bean × asparagus bean intervarietal population and provides marker-trait associations for marker-assisted approaches to selection. PMID:23375055
Multi-location wheat stripe rust QTL analysis: genetic background and epistatic interactions.

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Vazquez, M Dolores; Zemetra, Robert; Peterson, C James; Chen, Xianming M; Heesacker, Adam; Mundt, Christopher C

2015-07-01

Epistasis and genetic background were important influences on expression of stripe rust resistance in two wheat RIL populations, one with resistance conditioned by two major genes and the other conditioned by several minor QTL. Stripe rust is a foliar disease of wheat (Triticum aestivum L.) caused by the air-borne fungus Puccinia striiformis f. sp. tritici and is present in most regions around the world where commercial wheat is grown. Breeding for durable resistance to stripe rust continues to be a priority, but also is a challenge due to the complexity of interactions among resistance genes and to the wide diversity and continuous evolution of the pathogen races. The goal of this study was to detect chromosomal regions for resistance to stripe rust in two winter wheat populations, 'Tubbs'/'NSA-98-0995' (T/N) and 'Einstein'/'Tubbs' (E/T), evaluated across seven environments and mapped with diversity array technology and simple sequence repeat markers covering polymorphic regions of ≈1480 and 1117 cM, respectively. Analysis of variance for phenotypic data revealed significant (P located in chromosomes 2AS and 6AL, with epistatic interaction between them, were responsible for the main phenotypic response. For the T/N population, eight QTL were identified, with those in chromosomes 2AL and 2BL accounting for the largest percentage of the phenotypic variance.
Epigenetic and epistatic interactions between serotonin transporter and brain-derived neurotrophic factor genetic polymorphism: insights in depression.

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Ignácio, Z M; Réus, G Z; Abelaira, H M; Quevedo, J

2014-09-05

Epidemiological studies have shown significant results in the interaction between the functions of brain-derived neurotrophic factor (BDNF) and 5-HT in mood disorders, such as major depressive disorder (MDD). The latest research has provided convincing evidence that gene transcription of these molecules is a target for epigenetic changes, triggered by stressful stimuli that starts in early childhood and continues throughout life, which are subsequently translated into structural and functional phenotypes culminating in depressive disorders. The short variants of 5-HTTLPR and BDNF-Met are seen as forms which are predisposed to epigenetic aberrations, which leads individuals to a susceptibility to environmental adversities, especially when subjected to stress in early life. Moreover, the polymorphic variants also feature epistatic interactions in directing the functional mechanisms elicited by stress and underlying the onset of depressive disorders. Also emphasized are works which show some mediators between stress and epigenetic changes of the 5-HTT and BDNF genes, such as the hypothalamic-pituitary-adrenal (HPA) axis and the cAMP response element-binding protein (CREB), which is a cellular transcription factor. Both the HPA axis and CREB are also involved in epistatic interactions between polymorphic variants of 5-HTTLPR and Val66Met. This review highlights some research studying changes in the epigenetic patterns intrinsic to genes of 5-HTT and BDNF, which are related to lifelong environmental adversities, which in turn increases the risks of developing MDD. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.
An information-gain approach to detecting three-way epistatic interactions in genetic association studies

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Hu, Ting; Chen, Yuanzhu; Kiralis, Jeff W

2013-01-01

Background Epistasis has been historically used to describe the phenomenon that the effect of a given gene on a phenotype can be dependent on one or more other genes, and is an essential element for understanding the association between genetic and phenotypic variations. Quantifying epistasis......-way epistasis. Methods Such a measure is based on information gain, and is able to separate all lower order effects from pure three-way epistasis. Results Our method was verified on synthetic data and applied to real data from a candidate-gene study of tuberculosis in a West African population....... In the tuberculosis data, we found a statistically significant pure three-way epistatic interaction effect that was stronger than any lower-order associations. Conclusion Our study provides a methodological basis for detecting and characterizing high-order gene-gene interactions in genetic association studies....
Genomic value prediction for quantitative traits under the epistatic model

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Xu Shizhong

2011-01-01

Full Text Available Abstract Background Most quantitative traits are controlled by multiple quantitative trait loci (QTL. The contribution of each locus may be negligible but the collective contribution of all loci is usually significant. Genome selection that uses markers of the entire genome to predict the genomic values of individual plants or animals can be more efficient than selection on phenotypic values and pedigree information alone for genetic improvement. When a quantitative trait is contributed by epistatic effects, using all markers (main effects and marker pairs (epistatic effects to predict the genomic values of plants can achieve the maximum efficiency for genetic improvement. Results In this study, we created 126 recombinant inbred lines of soybean and genotyped 80 makers across the genome. We applied the genome selection technique to predict the genomic value of somatic embryo number (a quantitative trait for each line. Cross validation analysis showed that the squared correlation coefficient between the observed and predicted embryo numbers was 0.33 when only main (additive effects were used for prediction. When the interaction (epistatic effects were also included in the model, the squared correlation coefficient reached 0.78. Conclusions This study provided an excellent example for the application of genome selection to plant breeding.
PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

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Wenchao Zhang

2016-05-01

Full Text Available The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS, for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/.

PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

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Zhang, Wenchao; Dai, Xinbin; Wang, Qishan; Xu, Shizhong; Zhao, Patrick X

2016-05-01

The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS), for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/.
Phenotypic and epistatic grouping of hypo- and hyper-rec mus mutants in Aspergillus.

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Kafer, E; Chae, S K

1994-03-01

The mutants musK to musS of Aspergillus nidulans are sensitive to methyl-methanesulfonate (MMS) and several of them are meiotic-defective and alter mitotic recombination frequencies. All were found to be cross-sensitive to 4-nitro-quinoline-N-oxide (4-NQO) but unexpectedly none of them was hypersensitive to gamma-rays and few to UV light. Double mus; uvs mutants were constructed to test for interactions with uvs mutations of the four epistatic groups of Aspergillus, "UvsF", "UvsC", "UvsI", and "UvsB". All meiotic-defective mus mutations caused some lethal interactions, usually with uvsF. None of them showed epistasis with UvsF or UvsB group mutants and one, musO, may represent a new group. Three mus mutations that affect recombination were assigned to the UvsC group, namely musN and K, and also musL which is recombination-defective and closely resembles uvsC. While uvsC mutants are mutators and lack UV-mutagenesis, most mus mutants had no effects on mutation. Only musR, which appeared epistatic with uvsI, showed reduced UV-reversion frequencies similar to uvsI. The recombination-proficient mus mutants appeared to be epistatic with more than one group, but in several cases sensitivities were slight and overlaps insufficient to obtain corroborating results with MMS and 4-NQO.
Epistatic adaptive evolution of human color vision.

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Shozo Yokoyama

2014-12-01

Full Text Available Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV-free retinal environment, the short wavelength-sensitive (SWS1 visual pigment in human (human S1 switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45-30 million years ago, the middle and long wavelength-sensitive (MWS/LWS pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

LENUS (Irish Health Repository)

Casey, Fergal

2011-08-22

Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.
Epistatic effects contribute to variation in BMD in Fischer 344 x Lewis F2 rats.

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Koller, Daniel L; Liu, Lixiang; Alam, Imranul; Sun, Qiwei; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

2008-01-01

To further delineate the factors underlying the complex genetic architecture of BMD in the rat model, a genome screen for epistatic interactions was conducted. Several significant interactions were identified, involving both previously identified and novel QTLs. The variation in several of the risk factors for osteoporotic fracture, including BMD, has been shown to be caused largely by genetic differences. However, the genetic architecture of BMD is complex in both humans and in model organisms. We have previously reported quantitative trait locus (QTL) results for BMD from a genome screen of 595 female F(2) progeny of Fischer 344 and Lewis rats. These progeny also provide an excellent opportunity to search for epistatic effects, or interaction between genetic loci, that contribute to fracture risk. Microsatellite marker data from a 20-cM genome screen was analyzed along with weight-adjusted BMD (DXA and pQCT) phenotypic data using the R/qtl software package. Genotype and phenotype data were permuted to determine a genome-wide significance threshold for the epistasis or interaction LOD score corresponding to an alpha level of 0.01. Novel loci on chromosomes 12 and 15 showed a strong epistatic effect on total BMD at the femoral midshaft by pQCT (LOD = 5.4). A previously reported QTL on chromosome 7 was found to interact with a novel locus on chromosome 20 to affect whole lumbar BMD by pQCT (LOD = 6.2). These results provide new information regarding the mode of action of previously identified rat QTLs, as well as identifying novel loci that act in combination with known QTLs or with other novel loci to contribute to the risk factors for osteoporotic fracture.
A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.).

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Kubo, Takahiko; Yamagata, Yoshiyuki; Eguchi, Maki; Yoshimura, Atsushi

2008-12-01

Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice (Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid sterility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) segments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 heterozygous plants, indicating that the sterility phenotype due to S35 was dependent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-ir/S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice.
Inference of epistatic effects in a key mitochondrial protein

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Nelson, Erik D.; Grishin, Nick V.

2018-06-01

We use Potts model inference to predict pair epistatic effects in a key mitochondrial protein—cytochrome c oxidase subunit 2—for ray-finned fishes. We examine the effect of phylogenetic correlations on our predictions using a simple exact fitness model, and we find that, although epistatic effects are underpredicted, they maintain a roughly linear relationship to their true (model) values. After accounting for this correction, epistatic effects in the protein are still relatively weak, leading to fitness valleys of depth 2 N s ≃-5 in compensatory double mutants. Interestingly, positive epistasis is more pronounced than negative epistasis, and the strongest positive effects capture nearly all sites subject to positive selection in fishes, similar to virus proteins evolving under selection pressure in the context of drug therapy.
Epistatic Effects Contribute to Variation in BMD in Fischer 344 × Lewis F2 Rats

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Koller, Daniel L; Liu, Lixiang; Alam, Imranul; Sun, Qiwei; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

2008-01-01

To further delineate the factors underlying the complex genetic architecture of BMD in the rat model, a genome screen for epistatic interactions was conducted. Several significant interactions were identified, involving both previously identified and novel QTLs. Introduction The variation in several of the risk factors for osteoporotic fracture, including BMD, has been shown to be caused largely by genetic differences. However, the genetic architecture of BMD is complex in both humans and in model organisms. We have previously reported quantitative trait locus (QTL) results for BMD from a genome screen of 595 female F2 progeny of Fischer 344 and Lewis rats. These progeny also provide an excellent opportunity to search for epistatic effects, or interaction between genetic loci, that contribute to fracture risk. Materials and Methods Microsatellite marker data from a 20-cM genome screen was analyzed along with weight-adjusted BMD (DXA and pQCT) phenotypic data using the R/qtl software package. Genotype and phenotype data were permuted to determine a genome-wide significance threshold for the epistasis or interaction LOD score corresponding to an α level of 0.01. Results and Conclusions Novel loci on chromosomes 12 and 15 showed a strong epistatic effect on total BMD at the femoral midshaft by pQCT (LOD = 5.4). A previously reported QTL on chromosome 7 was found to interact with a novel locus on chromosome 20 to affect whole lumbar BMD by pQCT (LOD = 6.2). These results provide new information regarding the mode of action of previously identified rat QTLs, as well as identifying novel loci that act in combination with known QTLs or with other novel loci to contribute to the risk factors for osteoporotic fracture. PMID:17907919
uvsI mutants defective in UV mutagenesis define a fourth epistatic group of uvs genes in Aspergillus.

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Chae, S K; Kafer, E

1993-01-01

Three UV-sensitive mutations of A. nidulans, uvsI, uvsJ and uvsA, were tested for epistatic relationships with members of the previously established groups, here called the "UvsF", "UvsC", and "UvsB" groups. uvsI mutants are defective for spontaneous and induced reversion of certain point mutations and differ also for other properties from previously analyzed uvs types. They are very sensitive to the killing effects of UV-light and 4-NQO (4-nitro-quinoline-N-oxide) but not to MMS (methylmethane sulfonate). When double- and single-mutant uvs strains were compared for sensitivity to these three agents, synergistic or additive effects were found for uvsI with all members of the three groups. The uvsI gene may therefore represent a fourth epistatic group, possibly involved in mutagenic repair. On the other hand, uvsJ was clearly epistatic with members of the UvsF group and fitted well into this group also by phenotype. The uvsA gene was tentatively assigned to the UvsC group. uvsA showed epistatic interactions with uvsC in all tests, and like UvsC-group mutants is UV-sensitive mainly in dividing cells. However, the uvsA mutation does not cause the defects in recombination and UV mutagenesis typical for this group.
Fitness ranking of individual mutants drives patterns of epistatic interactions in HIV-1.

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Javier P Martínez

Full Text Available Fitness interactions between mutations, referred to as epistasis, can strongly impact evolution. For RNA viruses and retroviruses with their high mutation rates, epistasis may be particularly important to overcome fitness losses due to the accumulation of deleterious mutations and thus could influence the frequency of mutants in a viral population. As human immunodeficiency virus type 1 (HIV-1 resistance to azidothymidine (AZT requires selection of sequential mutations, it is a good system to study the impact of epistasis. Here we present a thorough analysis of a classical AZT-resistance pathway (the 41-215 cluster of HIV-1 variants by fitness measurements in single round infection assays covering physiological drug concentrations ex vivo. The sign and value of epistasis varied and did not predict the epistatic effect on the mutant frequency. This complex behavior is explained by the fitness ranking of the variants that strongly depends on environmental factors, i.e., the presence and absence of drugs and the host cells used. Although some interactions compensate fitness losses, the observed small effect on the relative mutant frequencies suggests that epistasis might be inefficient as a buffering mechanism for fitness losses in vivo. While the use of epistasis-based hypotheses to make general assumptions on the evolutionary dynamics of viral populations is appealing, our data caution their interpretation without further knowledge on the characteristics of the viral mutant spectrum under different environmental conditions.
An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility.

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Iñigo Landa

Full Text Available Papillary Thyroid Cancer (PTC is a heterogeneous and complex disease; susceptibility to PTC is influenced by the joint effects of multiple common, low-penetrance genes, although relatively few have been identified to date. Here we applied a rigorous combined approach to assess both the individual and epistatic contributions of genetic factors to PTC susceptibility, based on one of the largest series of thyroid cancer cases described to date. In addition to identifying the involvement of TSHR variation in classic PTC, our pioneer study of epistasis revealed a significant interaction between variants in STK17B and PAX8. The interaction was detected by MD-MBR (p = 0.00010 and confirmed by other methods, and then replicated in a second independent series of patients (MD-MBR p = 0.017. Furthermore, we demonstrated an inverse correlation between expression of PAX8 and STK17B in a set of cell lines derived from human thyroid carcinomas. Overall, our work sheds additional light on the genetic basis of thyroid cancer susceptibility, and suggests a new direction for the exploration of the inherited genetic contribution to disease using association studies.
Spatiotemporal dynamics and epistatic interaction sites in dengue virus type 1: a comprehensive sequence-based analysis.

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Pei-Yu Chu

Full Text Available The continuing threat of dengue fever necessitates a comprehensive characterisation of its epidemiological trends. Phylogenetic and recombination events were reconstructed based on 100 worldwide dengue virus (DENV type 1 genome sequences with an outgroup (prototypes of DENV2-4. The phylodynamic characteristics and site-specific variation were then analysed using data without the outgroup. Five genotypes (GI-GV and a ladder-like structure with short terminal branch topology were observed in this study. Apparently, the transmission of DENV1 was geographically random before gradual localising with human activity as GI-GIII in South Asia, GIV in the South Pacific, and GV in the Americas. Genotypes IV and V have recently shown higher population densities compared to older genotypes. All codon regions and all tree branches were skewed toward a negative selection, which indicated that their variation was restricted by protein function. Notably, multi-epistatic interaction sites were found in both PrM 221 and NS3 1730. Recombination events accumulated in regions E, NS3-NS4A, and particularly in region NS5. The estimated coevolution pattern also highlights the need for further study of the biological role of protein PrM 221 and NS3 1730. The recent transmission of emergent GV sublineages into Central America and Europe mandates closely monitoring of genotype interaction and succession.
Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus.

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Holtz, Yan; Bonnefoy, Michel; Viader, Véronique; Ardisson, Morgane; Rode, Nicolas O; Poux, Gérard; Roumet, Pierre; Marie-Jeanne, Véronique; Ranwez, Vincent; Santoni, Sylvain; Gouache, David; David, Jacques L

2017-07-01

The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.
Molecular signature of epistatic selection: interrogating genetic interactions in the sex-ratio meiotic drive of Drosophila simulans.

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Chevin, Luis-Miguel; Bastide, Héloïse; Montchamp-Moreau, Catherine; Hospital, Frédéric

2009-06-01

Fine scale analyses of signatures of selection allow assessing quantitative aspects of a species' evolutionary genetic history, such as the strength of selection on genes. When several selected loci lie in the same genomic region, their epistatic interactions may also be investigated. Here, we study how the neutral polymorphism pattern was shaped by two close recombining loci that cause 'sex-ratio' meiotic drive in Drosophila simulans, as an example of strong selection with potentially strong epistasis. We compare the polymorphism data observed in a natural population with the results of forward stochastic simulations under several contexts of epistasis between the candidate loci for the drive. We compute the likelihood of different possible scenarios, in order to determine which configuration is most consistent with the data. Our results highlight that fine scale analyses of well-chosen candidate genomic regions provide information-rich data that can be used to investigate the genotype-phenotype-fitness map, which can hardly be studied in genome-wide analyses. We also emphasize that initial conditions and time of observation (here, time after the interruption of a partial selective sweep) are crucial parameters in the interpretation of real data, while these are often overlooked in theoretical studies.
Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations.

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Wang, D; Salah El-Basyoni, I; Stephen Baenziger, P; Crossa, J; Eskridge, K M; Dweikat, I

2012-11-01

Though epistasis has long been postulated to have a critical role in genetic regulation of important pathways as well as provide a major source of variation in the process of speciation, the importance of epistasis for genomic selection in the context of plant breeding is still being debated. In this paper, we report the results on the prediction of genetic values with epistatic effects for 280 accessions in the Nebraska Wheat Breeding Program using adaptive mixed least absolute shrinkage and selection operator (LASSO). The development of adaptive mixed LASSO, originally designed for association mapping, for the context of genomic selection is reported. The results show that adaptive mixed LASSO can be successfully applied to the prediction of genetic values while incorporating both marker main effects and epistatic effects. Especially, the prediction accuracy is substantially improved by the inclusion of two-locus epistatic effects (more than onefold in some cases as measured by cross-validation correlation coefficient), which is observed for multiple traits and planting locations. This points to significant potential in using non-additive genetic effects for genomic selection in crop breeding practices.
Both epistatic and additive effects of QTLs are involved in polygenic induced resistance to disease: a case study, the interaction pepper - Phytophthora capsici Leonian.

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Lefebvre, V; Palloix, A

1996-09-01

To study the resistance of pepper to Phytophthora capsici, we analyzed 94 doubled-haploid (DH) lines derived from the intraspecific F1 hybrid obtained from a cross between Perennial, an Indian pungent resistant line, and Yolo Wonder, an American bell-pepper susceptible line, with 119 DNA markers. Four different criteria were used to evaluate the resistance, corresponding to different steps or mechanisms of the host-pathogen interaction: root-rot index, receptivity, inducibility and stability. Three distinct ANOVA models between DNA marker genotypes and the four disease criteria identified 13 genomic regions, distributed across several linkage groups or unlinked markers, affecting the resistance of pepper to P. capsici. Some QTLs were criterion specific, whereas others affect several criteria, so that the four resistance criteria were controlled by different combinations of QTLs. The QTLs were very different in their quantitative effect (R(2) values), including major QTLs which explained 41-55% of the phenotypic variance, intermediate QTLs with additive or/and epistatic action (17-28% of the variance explained) and minor QTLs. Favourable alleles of some minor QTLs were carried in the susceptible parent. The total phenotypic variation accounted for by QTLs reached up to 90% for receptivity, with an important part due to epistasis effects between QTLs (with or without additive effects). The relative impact of resistance QTLs in disease response is discussed.
Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

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Trey K Sato

2016-10-01

Full Text Available The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3, a component of MAP Kinase (MAPK signaling (HOG1, a regulator of Protein Kinase A (PKA signaling (IRA2, and a scaffolding protein for mitochondrial iron-sulfur (Fe-S cluster biogenesis (ISU1. Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism.
Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

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Sato, Trey K; Tremaine, Mary; Parreiras, Lucas S; Hebert, Alexander S; Myers, Kevin S; Higbee, Alan J; Sardi, Maria; McIlwain, Sean J; Ong, Irene M; Breuer, Rebecca J; Avanasi Narasimhan, Ragothaman; McGee, Mick A; Dickinson, Quinn; La Reau, Alex; Xie, Dan; Tian, Mingyuan; Reed, Jennifer L; Zhang, Yaoping; Coon, Joshua J; Hittinger, Chris Todd; Gasch, Audrey P; Landick, Robert

2016-10-01

The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3), a component of MAP Kinase (MAPK) signaling (HOG1), a regulator of Protein Kinase A (PKA) signaling (IRA2), and a scaffolding protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis (ISU1). Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism.
Progeny-testing of full-sibs IBD in a SSC2 QTL region highlights epistatic interactions for fatness traits in pigs

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Iannuccelli Nathalie

2011-10-01

Full Text Available Abstract Background Many QTL have been detected in pigs, but very few of them have been fine-mapped up to the causal mutation. On SSC2, the IGF2-intron3-G3072A mutation has been described as the causative polymorphism for a QTL underlying muscle mass and backfat deposition, but further studies have demonstrated that at least one additional QTL should segregate downstream of this mutation. A marker-assisted backcrossing design was set up in order to confirm the segregation of this second locus, reduce its confidence interval and better understand its mode of segregation. Results Five recombinant full-sibs, with genotype G/G at the IGF2 mutation, were progeny-tested. Only two of them displayed significant QTL for fatness traits although four inherited the same paternal and maternal chromosomes, thus exhibiting the same haplotypic contrast in the QTL region. The hypothesis of an interaction with another region in the genome was proposed to explain these discrepancies and after a genome scan, four different regions were retained as potential interacting regions with the SSC2 QTL. A candidate interacting region on SSC13 was confirmed by the analysis of an F2 pedigree, and in the backcross pedigree one haplotype in this region was found to mask the SSC2 QTL effect. Conclusions Assuming the hypothesis of interactions with other chromosomal regions, the QTL could be unambiguously mapped to a 30 cM region delimited by recombination points. The marker-assisted backcrossing design was successfully used to confirm the segregation of a QTL on SSC2 and, because full-sibs that inherited the same alleles from their two parents were analysed, the detection of epistatic interactions could be performed between alleles and not between breeds as usually done with the traditional Line-Cross model. Additional analyses of other recombinant sires should provide more information to further improve the fine-mapping of this locus, and confirm or deny the interaction
A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

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Bidanel Jean P

2009-12-01

Full Text Available Abstract Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA and total number of piglets born (TNB in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P SSC17 (P P P P P Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17, dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

Modularization and epistatic hierarchy determine homeostatic actions of multiple blood pressure quantitative trait loci.

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Chauvet, Cristina; Crespo, Kimberley; Ménard, Annie; Roy, Julie; Deng, Alan Y

2013-11-15

Hypertension, the most frequently diagnosed clinical condition world-wide, predisposes individuals to morbidity and mortality, yet its underlying pathological etiologies are poorly understood. So far, a large number of quantitative trait loci (QTLs) have been identified in both humans and animal models, but how they function together in determining overall blood pressure (BP) in physiological settings is unknown. Here, we systematically and comprehensively performed pair-wise comparisons of individual QTLs to create a global picture of their functionality in an inbred rat model. Rather than each of numerous QTLs contributing to infinitesimal BP increments, a modularized pattern arises: two epistatic 'blocks' constitute basic functional 'units' for nearly all QTLs, designated as epistatic module 1 (EM1) and EM2. This modularization dictates the magnitude and scope of BP effects. Any EM1 member can contribute to BP additively to that of EM2, but not to those of the same module. Members of each EM display epistatic hierarchy, which seems to reflect a related functional pathway. Rat homologues of 11 human BP QTLs belong to either EM1 or EM2. Unique insights emerge into the novel genetic mechanism and hierarchy determining BP in the Dahl salt-sensitive SS/Jr (DSS) rat model that implicate a portion of human QTLs. Elucidating the pathways underlying EM1 and EM2 may reveal the genetic regulation of BP.
The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions

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Pool, John E.

2015-01-01

North American populations of Drosophila melanogaster derive from both European and African source populations, but despite their importance for genetic research, patterns of ancestry along their genomes are largely undocumented. Here, I infer geographic ancestry along genomes of the Drosophila Genetic Reference Panel (DGRP) and the D. melanogaster reference genome, which may have implications for reference alignment, association mapping, and population genomic studies in Drosophila. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Combining my estimate of admixture timing with historical records, I provide the first estimate of natural generation time for this species (approximately 15 generations per year). Ancestry levels were found to vary strikingly across the genome, with less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes (e.g., circadian rhythm). An important role for natural selection during the admixture process was further supported by evidence that many unlinked pairs of loci showed a deficiency of Africa–Europe allele combinations between them. Numerous epistatic fitness interactions may therefore exist between African and European genotypes, leading to ongoing selection against incompatible variants. By focusing on hubs in this network of fitness interactions, I identified a set of interacting loci that include genes with roles in sensation and neuropeptide/hormone reception. These findings suggest that admixed D. melanogaster samples could become an important study system for the genetics of early-stage isolation between populations. PMID:26354524
Genetics of simple and complex host-parasite interactions

International Nuclear Information System (INIS)

Sidhu, G.S.; Webster, J.M.

1977-01-01

In nature a host plant can be viewed as a miniature replica of an ecological system where true and incidental parasites share the same habitat. Consequently, they influence each other's presence directly by interspecific interaction, and indirectly by inducing changes in the host's physiology and so form disease complexes. Since all physiological phenomena have their counterpart in the respective genetic systems of interacting organisms, valuable genetic information can be derived from the analysis of complex parasitic systems. Disease complexes may be classified according to the nature of interaction between various parasites on the same host. One parasite may nullify the host's resistance to another (e.g. Tomato - Meloidogyne incognita + Fusarium oxysporum lycopersici system). Conversely, a parasite may invoke resistance in the host against another parasite (e.g. Tomato - Fusarium oxysporum lycopersici + Verticillium albo atrum system). From the study of simple parasitic systems we know that resistance versus susceptibility against a single parasite is normally monogenically controlled. However, when more than one parasite interacts to invoke or nullify each other's responses on the same host plant, the genetic results suggest epistatic ratios. Nevertheless, epistatic ratios have been obtained also from simple parasitic systems owing to gene interaction. The epistatic ratios obtained from complex and simple parasitic systems are contrasted and compared. It is suggested that epistatic ratios obtained from simple parasitic systems may, in fact, be artifacts resulting from complex parasitic associations that often occur in nature. Polygenic inheritance and the longevity of a cultivar is also discussed briefly in relation to complex parasitic associations. Induced mutations can play a significant role in the study of complex parasitic associations, and thus can be very useful in controlling plant diseases
The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions.

Science.gov (United States)

Pool, John E

2015-12-01

North American populations of Drosophila melanogaster derive from both European and African source populations, but despite their importance for genetic research, patterns of ancestry along their genomes are largely undocumented. Here, I infer geographic ancestry along genomes of the Drosophila Genetic Reference Panel (DGRP) and the D. melanogaster reference genome, which may have implications for reference alignment, association mapping, and population genomic studies in Drosophila. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Combining my estimate of admixture timing with historical records, I provide the first estimate of natural generation time for this species (approximately 15 generations per year). Ancestry levels were found to vary strikingly across the genome, with less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes (e.g., circadian rhythm). An important role for natural selection during the admixture process was further supported by evidence that many unlinked pairs of loci showed a deficiency of Africa-Europe allele combinations between them. Numerous epistatic fitness interactions may therefore exist between African and European genotypes, leading to ongoing selection against incompatible variants. By focusing on hubs in this network of fitness interactions, I identified a set of interacting loci that include genes with roles in sensation and neuropeptide/hormone reception. These findings suggest that admixed D. melanogaster samples could become an important study system for the genetics of early-stage isolation between populations. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Identification of quantitative trait loci underlying seed protein content of soybean including main, epistatic, and QTL × environment effects in different regions of Northeast China.

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Teng, Weili; Li, Wen; Zhang, Qi; Wu, Depeng; Zhao, Xue; Li, Haiyan; Han, Yingpeng; Li, Wenbin

2017-08-01

The objective here was to identify QTL underlying soybean protein content (PC), and to evaluate the additive and epistatic effects of the QTLs. A mapping population, consisting of 129 recombinant inbred lines (RILs), was created by crossing 'Dongnong 46' and 'L-100'. Phenotypic data of the parents and RILs were collected for 4 years in three locations of Heilongjiang Province of China. A total of 213 SSR markers were used to construct a genetic linkage map. Eight QTLs, located on seven chromosomes (Chr), were identified to be associated with PC among the 10 tested environments. Of the seven QTLs, five QTLs, qPR-2 (Satt710, on Chr9), qPR-3 (Sat_122, on Chr12), qPR-5 (Satt543, on Chr17), qPR-7 (Satt163, on Chr18), and qPR-8 (Satt614, on Chr20), were detected in six, seven, seven, six, and seven environments, respectively, implying relatively stable QTLs. qPR-3 could explain 3.33%-11.26% of the phenotypic variation across eight tested environments. qPR-5 and qPR-8 explained 3.64%-10.1% and 11.86%-18.40% of the phenotypic variation, respectively, across seven tested environments. Eight QTLs associated with PC exhibited additive and (or) additive × environment interaction effects. The results showed that environment-independent QTLs often had higher additive effects. Moreover, five epistatic pairwise QTLs were identified in the 10 environments.
The binary response of the GAL/MEL genetic switch of Saccharomyces cerevisiae is critically dependent on Gal80p-Gal4p interaction.

Science.gov (United States)

Das Adhikari, Akshay Kumar; Bhat, Paike Jayadeva

2016-09-01

Studies on the Saccharomyces cerevisiae GAL/MEL genetic switch have revealed that its bistability is dependent on ultrasensitivity that can be altered or abolished by disabling different combinations of nested feedback loops. In contrast, we have previously demonstrated that weakening of the interaction between Gal80p and Gal4p alone is sufficient to abolish the ultrasensitivity (Das Adhikari et al. 2014). Here, we demonstrate that altering the epistatic interaction between Gal80p and Gal4p also abolishes the bistability, and the switch response to galactose becomes graded instead of binary. However, the GAL/MEL switch of wild-type and epistatically altered strains responded in a graded fashion to melibiose. The properties of the epistatically altered strain resemble Kluyveromyces lactis, which separated from the Saccharomyces lineage 100 mya before whole-genome duplication (WGD). Based on the results reported here, we propose that epistatic interactions played a crucial role in the evolution of the fine regulation of S. cerevisiae GAL/MEL switch following WGD. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Epistasis × environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field.

Science.gov (United States)

Kerwin, Rachel E; Feusier, Julie; Muok, Alise; Lin, Catherine; Larson, Brandon; Copeland, Daniel; Corwin, Jason A; Rubin, Matthew J; Francisco, Marta; Li, Baohua; Joseph, Bindu; Weinig, Cynthia; Kliebenstein, Daniel J

2017-08-01

Despite the growing number of studies showing that genotype × environment and epistatic interactions control fitness, the influences of epistasis × environment interactions on adaptive trait evolution remain largely uncharacterized. Across three field trials, we quantified aliphatic glucosinolate (GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation. We found that aliphatic GSL accumulation was primarily influenced by additive and epistatic genetic variation, leaf damage was primarily influenced by environmental variation and relative fitness was primarily influenced by epistasis and epistasis × environment interactions. Epistasis × environment interactions accounted for up to 48% of the relative fitness variation in the field. At a single field site, the impact of epistasis on relative fitness varied significantly over 2 yr, showing that epistasis × environment interactions within a location can be temporally dynamic. These results suggest that the environmental dependency of epistasis can profoundly influence the response to selection, shaping the adaptive trajectories of natural populations in complex ways, and deserves further consideration in future evolutionary studies. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

Science.gov (United States)

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.
A developmental systems perspective on epistasis: computational exploration of mutational interactions in model developmental regulatory networks.

Directory of Open Access Journals (Sweden)

Jayson Gutiérrez

2009-09-01

Full Text Available The way in which the information contained in genotypes is translated into complex phenotypic traits (i.e. embryonic expression patterns depends on its decoding by a multilayered hierarchy of biomolecular systems (regulatory networks. Each layer of this hierarchy displays its own regulatory schemes (i.e. operational rules such as +/- feedback and associated control parameters, resulting in characteristic variational constraints. This process can be conceptualized as a mapping issue, and in the context of highly-dimensional genotype-phenotype mappings (GPMs epistatic events have been shown to be ubiquitous, manifested in non-linear correspondences between changes in the genotype and their phenotypic effects. In this study I concentrate on epistatic phenomena pervading levels of biological organization above the genetic material, more specifically the realm of molecular networks. At this level, systems approaches to studying GPMs are specially suitable to shed light on the mechanistic basis of epistatic phenomena. To this aim, I constructed and analyzed ensembles of highly-modular (fully interconnected networks with distinctive topologies, each displaying dynamic behaviors that were categorized as either arbitrary or functional according to early patterning processes in the Drosophila embryo. Spatio-temporal expression trajectories in virtual syncytial embryos were simulated via reaction-diffusion models. My in silico mutational experiments show that: 1 the average fitness decay tendency to successively accumulated mutations in ensembles of functional networks indicates the prevalence of positive epistasis, whereas in ensembles of arbitrary networks negative epistasis is the dominant tendency; and 2 the evaluation of epistatic coefficients of diverse interaction orders indicates that, both positive and negative epistasis are more prevalent in functional networks than in arbitrary ones. Overall, I conclude that the phenotypic and fitness effects of
CRISPR Perturbation of Gene Expression Alters Bacterial Fitness under Stress and Reveals Underlying Epistatic Constraints.

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Otoupal, Peter B; Erickson, Keesha E; Escalas-Bordoy, Antoni; Chatterjee, Anushree

2017-01-20

The evolution of antibiotic resistance has engendered an impending global health crisis that necessitates a greater understanding of how resistance emerges. The impact of nongenetic factors and how they influence the evolution of resistance is a largely unexplored area of research. Here we present a novel application of CRISPR-Cas9 technology for investigating how gene expression governs the adaptive pathways available to bacteria during the evolution of resistance. We examine the impact of gene expression changes on bacterial adaptation by constructing a library of deactivated CRISPR-Cas9 synthetic devices to tune the expression of a set of stress-response genes in Escherichia coli. We show that artificially inducing perturbations in gene expression imparts significant synthetic control over fitness and growth during stress exposure. We present evidence that these impacts are reversible; strains with synthetically perturbed gene expression regained wild-type growth phenotypes upon stress removal, while maintaining divergent growth characteristics under stress. Furthermore, we demonstrate a prevailing trend toward negative epistatic interactions when multiple gene perturbations are combined simultaneously, thereby posing an intrinsic constraint on gene expression underlying adaptive trajectories. Together, these results emphasize how CRISPR-Cas9 can be employed to engineer gene expression changes that shape bacterial adaptation, and present a novel approach to synthetically control the evolution of antimicrobial resistance.
Epistatic interaction between haplotypes of the ghrelin ligand and receptor genes influence susceptibility to myocardial infarction and coronary artery disease.

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Baessler, Andrea; Fischer, Marcus; Mayer, Bjoern; Koehler, Martina; Wiedmann, Silke; Stark, Klaus; Doering, Angela; Erdmann, Jeanette; Riegger, Guenter; Schunkert, Heribert; Kwitek, Anne E; Hengstenberg, Christian

2007-04-15

Data from both experimental models and humans provide evidence that ghrelin and its receptor, the growth hormone secretagogue receptor (ghrelin receptor, GHSR), possess a variety of cardiovascular effects. Thus, we hypothesized that genetic variants within the ghrelin system (ligand ghrelin and its receptor GHSR) are associated with susceptibility to myocardial infarction (MI) and coronary artery disease (CAD). Seven single nucleotide polymorphisms (SNPs) covering the GHSR region as well as eight SNPs across the ghrelin gene (GHRL) region were genotyped in index MI patients (864 Caucasians, 'index MI cases') from the German MI family study and in matched controls without evidence of CAD (864 Caucasians, 'controls', MONICA Augsburg). In addition, siblings of these MI patients with documented severe CAD (826 'affected sibs') were matched likewise with controls (n = 826 Caucasian 'controls') and used for verification. The effect of interactions between genetic variants of both genes of the ghrelin system was explored by conditional classification tree models. We found association of several GHSR SNPs with MI [best SNP odds ratio (OR) 1.7 (1.2-2.5); P = 0.002] using a recessive model. Moreover, we identified a common GHSR haplotype which significantly increases the risk for MI [multivariate adjusted OR for homozygous carriers 1.6 (1.1-2.5) and CAD OR 1.6 (1.1-2.5)]. In contrast, no relationship between genetic variants and the disease could be revealed for GHRL. However, the increase in MI/CAD frequency related to the susceptible GHSR haplotype was abolished when it coincided with a common GHRL haplotype. Multivariate adjustments as well as permutation-based methods conveyed the same results. These data are the first to demonstrate an association of SNPs and haplotypes within important genes of the ghrelin system and the susceptibility to MI, whereas association with MI/CAD could be identified for genetic variants across GHSR, no relationship could be revealed for GHRL
Epistasis × environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field

DEFF Research Database (Denmark)

Kerwin, Rachel E.; Feusier, Julie; Muok, Alise

2017-01-01

(GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation. We found that aliphatic GSL accumulation...
Assessing SNP-SNP interactions among DNA repair, modification and metabolism related pathway genes in breast cancer susceptibility.

Directory of Open Access Journals (Sweden)

Yadav Sapkota

Full Text Available Genome-wide association studies (GWASs have identified low-penetrance common variants (i.e., single nucleotide polymorphisms, SNPs associated with breast cancer susceptibility. Although GWASs are primarily focused on single-locus effects, gene-gene interactions (i.e., epistasis are also assumed to contribute to the genetic risks for complex diseases including breast cancer. While it has been hypothesized that moderately ranked (P value based weak single-locus effects in GWASs could potentially harbor valuable information for evaluating epistasis, we lack systematic efforts to investigate SNPs showing consistent associations with weak statistical significance across independent discovery and replication stages. The objectives of this study were i to select SNPs showing single-locus effects with weak statistical significance for breast cancer in a GWAS and/or candidate-gene studies; ii to replicate these SNPs in an independent set of breast cancer cases and controls; and iii to explore their potential SNP-SNP interactions contributing to breast cancer susceptibility. A total of 17 SNPs related to DNA repair, modification and metabolism pathway genes were selected since these pathways offer a priori knowledge for potential epistatic interactions and an overall role in breast carcinogenesis. The study design included predominantly Caucasian women (2,795 cases and 4,505 controls from Alberta, Canada. We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 and MDM2-rs769412 in logistic regression that conferred elevated risks for breast cancer (P(interaction<7.3 × 10(-3. Logic regression identified an interaction involving four SNPs (MBD2-rs4041245, MLH1-rs1799977, MDM2-rs769412, BRCA2-rs1799943 (P(permutation = 2.4 × 10(-3. SNPs involved in SNP-SNP interactions also showed single-locus effects with weak statistical significance, while BRCA2-rs1799943 showed stronger statistical significance (P
Exploitation of genetic interaction network topology for the prediction of epistatic behavior

KAUST Repository

Alanis Lobato, Gregorio

2013-10-01

Genetic interaction (GI) detection impacts the understanding of human disease and the ability to design personalized treatment. The mapping of every GI in most organisms is far from complete due to the combinatorial amount of gene deletions and knockdowns required. Computational techniques to predict new interactions based only on network topology have been developed in network science but never applied to GI networks.We show that topological prediction of GIs is possible with high precision and propose a graph dissimilarity index that is able to provide robust prediction in both dense and sparse networks.Computational prediction of GIs is a strong tool to aid high-throughput GI determination. The dissimilarity index we propose in this article is able to attain precise predictions that reduce the universe of candidate GIs to test in the lab. © 2013 Elsevier Inc.
Exploitation of genetic interaction network topology for the prediction of epistatic behavior

KAUST Repository

Alanis Lobato, Gregorio; Cannistraci, Carlo; Ravasi, Timothy

2013-01-01

Genetic interaction (GI) detection impacts the understanding of human disease and the ability to design personalized treatment. The mapping of every GI in most organisms is far from complete due to the combinatorial amount of gene deletions and knockdowns required. Computational techniques to predict new interactions based only on network topology have been developed in network science but never applied to GI networks.We show that topological prediction of GIs is possible with high precision and propose a graph dissimilarity index that is able to provide robust prediction in both dense and sparse networks.Computational prediction of GIs is a strong tool to aid high-throughput GI determination. The dissimilarity index we propose in this article is able to attain precise predictions that reduce the universe of candidate GIs to test in the lab. © 2013 Elsevier Inc.
Inferring genetic interactions from comparative fitness data.

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Crona, Kristina; Gavryushkin, Alex; Greene, Devin; Beerenwinkel, Niko

2017-12-20

Darwinian fitness is a central concept in evolutionary biology. In practice, however, it is hardly possible to measure fitness for all genotypes in a natural population. Here, we present quantitative tools to make inferences about epistatic gene interactions when the fitness landscape is only incompletely determined due to imprecise measurements or missing observations. We demonstrate that genetic interactions can often be inferred from fitness rank orders, where all genotypes are ordered according to fitness, and even from partial fitness orders. We provide a complete characterization of rank orders that imply higher order epistasis. Our theory applies to all common types of gene interactions and facilitates comprehensive investigations of diverse genetic interactions. We analyzed various genetic systems comprising HIV-1, the malaria-causing parasite Plasmodium vivax , the fungus Aspergillus niger , and the TEM-family of β-lactamase associated with antibiotic resistance. For all systems, our approach revealed higher order interactions among mutations.
Interactions of checkpoint-genes RAD9, RAD17, RAD24 and RAD53 determining radioresistance of Yeast Saccharomyces Cerevisiae

International Nuclear Information System (INIS)

Koltovaya, N.A.; Nikulushkina, Yu.V.; Roshchina, M.P.; Devin, A.B.

2007-01-01

The mechanisms of genetic control of progress through the division cell cycle (checkpoint-control) in yeast Saccharomyces cerevisiae have been studied intensively. To investigate the role of checkpoint-genes RAD9, RAD17, RAD24, RAD53 in cell radioresistance we have investigated cell sensitivity of double mutants to γ-ray. Double mutants involving various combinations with rad9Δ show epistatic interactions, i.e. the sensitivity of the double mutants to γ-ray was no greater than that of more sensitive of the two single mutants. This suggests that all these genes govern the same pathway. This group of genes was named RAD9-epistasis group. It is interesting to note that the genes RAD9 and RAD53 have positive effect but RAD17 and RAD24 have negative effect on radiosensitivity of yeast cells. Interactions between mutations may differ depending on the agent γ-ray or UV-light, for example mutations rad9Δ and rad24Δ show additive effect for γ-ray and epistatic effect for UV-light
A Simple and Computationally Efficient Approach to Multifactor Dimensionality Reduction Analysis of Gene-Gene Interactions for Quantitative Traits

OpenAIRE

Gui, Jiang; Moore, Jason H.; Williams, Scott M.; Andrews, Peter; Hillege, Hans L.; van der Harst, Pim; Navis, Gerjan; Van Gilst, Wiek H.; Asselbergs, Folkert W.; Gilbert-Diamond, Diane

2013-01-01

We present an extension of the two-class multifactor dimensionality reduction (MDR) algorithm that enables detection and characterization of epistatic SNP-SNP interactions in the context of a quantitative trait. The proposed Quantitative MDR (QMDR) method handles continuous data by modifying MDR's constructive induction algorithm to use a T-test. QMDR replaces the balanced accuracy metric with a T-test statistic as the score to determine the best interaction model. We used a simulation to ide...
LEAP: biomarker inference through learning and evaluating association patterns.

Science.gov (United States)

Jiang, Xia; Neapolitan, Richard E

2015-03-01

Single nucleotide polymorphism (SNP) high-dimensional datasets are available from Genome Wide Association Studies (GWAS). Such data provide researchers opportunities to investigate the complex genetic basis of diseases. Much of genetic risk might be due to undiscovered epistatic interactions, which are interactions in which combination of several genes affect disease. Research aimed at discovering interacting SNPs from GWAS datasets proceeded in two directions. First, tools were developed to evaluate candidate interactions. Second, algorithms were developed to search over the space of candidate interactions. Another problem when learning interacting SNPs, which has not received much attention, is evaluating how likely it is that the learned SNPs are associated with the disease. A complete system should provide this information as well. We develop such a system. Our system, called LEAP, includes a new heuristic search algorithm for learning interacting SNPs, and a Bayesian network based algorithm for computing the probability of their association. We evaluated the performance of LEAP using 100 1,000-SNP simulated datasets, each of which contains 15 SNPs involved in interactions. When learning interacting SNPs from these datasets, LEAP outperformed seven others methods. Furthermore, only SNPs involved in interactions were found to be probable. We also used LEAP to analyze real Alzheimer's disease and breast cancer GWAS datasets. We obtained interesting and new results from the Alzheimer's dataset, but limited results from the breast cancer dataset. We conclude that our results support that LEAP is a useful tool for extracting candidate interacting SNPs from high-dimensional datasets and determining their probability. © 2015 The Authors. *Genetic Epidemiology published by Wiley Periodicals, Inc.
The origin of human complex diversity: Stochastic epistatic modules and the intrinsic compatibility between distributional robustness and phenotypic changeability.

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Ijichi, Shinji; Ijichi, Naomi; Ijichi, Yukina; Imamura, Chikako; Sameshima, Hisami; Kawaike, Yoichi; Morioka, Hirofumi

2018-01-01

The continuing prevalence of a highly heritable and hypo-reproductive extreme tail of a human neurobehavioral quantitative diversity suggests the possibility that the reproductive majority retains the genetic mechanism for the extremes. From the perspective of stochastic epistasis, the effect of an epistatic modifier variant can randomly vary in both phenotypic value and effect direction among the careers depending on the genetic individuality, and the modifier careers are ubiquitous in the population distribution. The neutrality of the mean genetic effect in the careers warrants the survival of the variant under selection pressures. Functionally or metabolically related modifier variants make an epistatic network module and dozens of modules may be involved in the phenotype. To assess the significance of stochastic epistasis, a simplified module-based model was employed. The individual repertoire of the modifier variants in a module also participates in the genetic individuality which determines the genetic contribution of each modifier in the career. Because the entire contribution of a module to the phenotypic outcome is consequently unpredictable in the model, the module effect represents the total contribution of the related modifiers as a stochastic unit in the simulations. As a result, the intrinsic compatibility between distributional robustness and quantitative changeability could mathematically be simulated using the model. The artificial normal distribution shape in large-sized simulations was preserved in each generation even if the lowest fitness tail was un-reproductive. The robustness of normality beyond generations is analogous to the real situations of human complex diversity including neurodevelopmental conditions. The repeated regeneration of the un-reproductive extreme tail may be inevitable for the reproductive majority's competence to survive and change, suggesting implications of the extremes for others. Further model-simulations to

Epistatic and Independent Effects on Schizophrenia-Related Phenotypes Following Co-disruption of the Risk Factors Neuregulin-1 × DISC1.

Science.gov (United States)

O'Tuathaigh, Colm M P; Fumagalli, Fabio; Desbonnet, Lieve; Perez-Branguli, Francesc; Moloney, Gerard; Loftus, Samim; O'Leary, Claire; Petit, Emilie; Cox, Rachel; Tighe, Orna; Clarke, Gerard; Lai, Donna; Harvey, Richard P; Cryan, John F; Mitchell, Kevin J; Dinan, Timothy G; Riva, Marco A; Waddington, John L

2017-01-01

Few studies have addressed likely gene × gene (ie, epistatic) interactions in mediating risk for schizophrenia. Using a preclinical genetic approach, we investigated whether simultaneous disruption of the risk factors Neuregulin-1 (NRG1) and Disrupted-in-schizophrenia 1 (DISC1) would produce a disease-relevant phenotypic profile different from that observed following disruption to either gene alone. NRG1 heterozygotes exhibited hyperactivity and disruption to prepulse inhibition, both reversed by antipsychotic treatment, and accompanied by reduced striatal dopamine D2 receptor protein expression, impaired social cognition, and altered glutamatergic synaptic protein expression in selected brain areas. Single gene DISC1 mutants demonstrated a disruption in social cognition and nest-building, altered brain 5-hydroxytryptamine levels and hippocampal ErbB4 expression, and decreased cortical expression of the schizophrenia-associated microRNA miR-29b. Co-disruption of DISC1 and NRG1, indicative of epistasis, evoked an impairment in sociability and enhanced self-grooming, accompanied by changes in hypothalamic oxytocin/vasopressin gene expression. The findings indicate specific behavioral correlates and underlying cellular pathways downstream of main effects of DNA variation in the schizophrenia-associated genes NRG1 and DISC1. © The Author 2016. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models.

Science.gov (United States)

Moran, Paula; Stokes, Jennifer; Marr, Julia; Bock, Gavin; Desbonnet, Lieve; Waddington, John; O'Tuathaigh, Colm

2016-01-01

The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia.
Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models

Science.gov (United States)

Marr, Julia; Bock, Gavin; Desbonnet, Lieve; Waddington, John

2016-01-01

The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia. PMID:27725886
A map of directional genetic interactions in a metazoan cell.

Science.gov (United States)

Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

2015-03-06

Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.
AprioriGWAS, a new pattern mining strategy for detecting genetic variants associated with disease through interaction effects.

Science.gov (United States)

Zhang, Qingrun; Long, Quan; Ott, Jurg

2014-06-01

Identifying gene-gene interaction is a hot topic in genome wide association studies. Two fundamental challenges are: (1) how to smartly identify combinations of variants that may be associated with the trait from astronomical number of all possible combinations; and (2) how to test epistatic interaction when all potential combinations are available. We developed AprioriGWAS, which brings two innovations. (1) Based on Apriori, a successful method in field of Frequent Itemset Mining (FIM) in which a pattern growth strategy is leveraged to effectively and accurately reduce search space, AprioriGWAS can efficiently identify genetically associated genotype patterns. (2) To test the hypotheses of epistasis, we adopt a new conditional permutation procedure to obtain reliable statistical inference of Pearson's chi-square test for the [Formula: see text] contingency table generated by associated variants. By applying AprioriGWAS to age-related macular degeneration (AMD) data, we found that: (1) angiopoietin 1 (ANGPT1) and four retinal genes interact with Complement Factor H (CFH). (2) GO term "glycosaminoglycan biosynthetic process" was enriched in AMD interacting genes. The epistatic interactions newly found by AprioriGWAS on AMD data are likely true interactions, since genes interacting with CFH are retinal genes, and GO term enrichment also verified that interaction between glycosaminoglycans (GAGs) and CFH plays an important role in disease pathology of AMD. By applying AprioriGWAS on Bipolar disorder in WTCCC data, we found variants without marginal effect show significant interactions. For example, multiple-SNP genotype patterns inside gene GABRB2 and GRIA1 (AMPA subunit 1 receptor gene). AMPARs are found in many parts of the brain and are the most commonly found receptor in the nervous system. The GABRB2 mediates the fastest inhibitory synaptic transmission in the central nervous system. GRIA1 and GABRB2 are relevant to mental disorders supported by multiple
Evaluation of drug interaction microcomputer software: Dambro's Drug Interactions.

Science.gov (United States)

Poirier, T I; Giudici, R A

1990-01-01

Dambro's Drug Interactions was evaluated using general and specific criteria. The installation process, ease of learning and use were rated excellent. The user documentation and quality of the technical support were good. The scope of coverage, clinical documentation, frequency of updates, and overall clinical performance were fair. The primary advantages of the program are the quick searching and detection of drug interactions, and the attempt to provide useful interaction data, i.e., significance and reference. The disadvantages are the lack of current drug interaction information, outdated references, lack of evaluative drug interaction information, and the inability to save or print patient profiles. The program is not a good value for the pharmacist but has limited use as a quick screening tool.
Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models

Directory of Open Access Journals (Sweden)

Paula Moran

2016-01-01

Full Text Available The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia.
An ancestry-based approach for detecting interactions.

Science.gov (United States)

Park, Danny S; Eskin, Itamar; Kang, Eun Yong; Gamazon, Eric R; Eng, Celeste; Gignoux, Christopher R; Galanter, Joshua M; Burchard, Esteban; Ye, Chun J; Aschard, Hugues; Eskin, Eleazar; Halperin, Eran; Zaitlen, Noah

2018-02-01

Epistasis and gene-environment interactions are known to contribute significantly to variation of complex phenotypes in model organisms. However, their identification in human association studies remains challenging for myriad reasons. In the case of epistatic interactions, the large number of potential interacting sets of genes presents computational, multiple hypothesis correction, and other statistical power issues. In the case of gene-environment interactions, the lack of consistently measured environmental covariates in most disease studies precludes searching for interactions and creates difficulties for replicating studies. In this work, we develop a new statistical approach to address these issues that leverages genetic ancestry, defined as the proportion of ancestry derived from each ancestral population (e.g., the fraction of European/African ancestry in African Americans), in admixed populations. We applied our method to gene expression and methylation data from African American and Latino admixed individuals, respectively, identifying nine interactions that were significant at Pancestry can be a useful proxy for unknown and unmeasured covariates in the search for interaction effects. These results have important implications for our understanding of the genetic architecture of complex traits. © 2017 WILEY PERIODICALS, INC.
Epistatic Interaction of CYP1A1 and COMT Polymorphisms in Cervical Cancer

Directory of Open Access Journals (Sweden)

Andreia Matos

2016-01-01

Full Text Available There is a clear association between the excessive and cumulative exposure to estrogens and the development of cancer in hormone-sensitive tissues, such as the cervix. We studied the association of CYP1A1 M1 (rs4646903 and COMT (rs4680 polymorphisms in 130 cervical cancer cases (c-cancer and 179 controls. The CYP1A1 TT genotype was associated with a lower risk for c-cancer (OR = 0.39, p=0.002. The allele C of CYP1A1 was a risk for c-cancer (OR = 2.29, p=0.002. Women with COMT LL genotype had a higher risk of developing c-cancer (OR = 4.83, p<0.001. For the interaction of the CYP1A1&COMT, we observed that TC&HL genotypes had a greater risk for c-cancer (OR = 6.07, p=0.006 and TT&HL genotypes had a protection effect (OR = 0.24, p<0.001. The CYP1A1 TT and COMT LL genotypes had higher estradiol levels in c-cancer (p<0.001 and p=0.037, resp.. C-cancer is associated with less production of 2-methoxy-estradiol resultant of functional polymorphisms of CYP1A1 and COMT, separately. CYP1A1 and COMT work in a metabolic sequence and their interaction could lead to an alternative pathway of estrogen metabolism with production of 16-OH-estrone that is more proliferative.
A kernel regression approach to gene-gene interaction detection for case-control studies.

Science.gov (United States)

Larson, Nicholas B; Schaid, Daniel J

2013-11-01

Gene-gene interactions are increasingly being addressed as a potentially important contributor to the variability of complex traits. Consequently, attentions have moved beyond single locus analysis of association to more complex genetic models. Although several single-marker approaches toward interaction analysis have been developed, such methods suffer from very high testing dimensionality and do not take advantage of existing information, notably the definition of genes as functional units. Here, we propose a comprehensive family of gene-level score tests for identifying genetic elements of disease risk, in particular pairwise gene-gene interactions. Using kernel machine methods, we devise score-based variance component tests under a generalized linear mixed model framework. We conducted simulations based upon coalescent genetic models to evaluate the performance of our approach under a variety of disease models. These simulations indicate that our methods are generally higher powered than alternative gene-level approaches and at worst competitive with exhaustive SNP-level (where SNP is single-nucleotide polymorphism) analyses. Furthermore, we observe that simulated epistatic effects resulted in significant marginal testing results for the involved genes regardless of whether or not true main effects were present. We detail the benefits of our methods and discuss potential genome-wide analysis strategies for gene-gene interaction analysis in a case-control study design. © 2013 WILEY PERIODICALS, INC.
The Spiral-Interactive Program Evaluation Model.

Science.gov (United States)

Khaleel, Ibrahim Adamu

1988-01-01

Describes the spiral interactive program evaluation model, which is designed to evaluate vocational-technical education programs in secondary schools in Nigeria. Program evaluation is defined; utility oriented and process oriented models for evaluation are described; and internal and external evaluative factors and variables that define each…
Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation.

Science.gov (United States)

Roso, V M; Schenkel, F S; Miller, S P; Schaeffer, L R

2005-08-01

Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE and are sensitive to changes in the data file and to the addition or deletion of variables in the model. Generalized ridge regression methods were applied to obtain stable estimates of direct and maternal breed additive, dominance, and epistatic loss effects in the presence of multicollinearity among predictor variables. Preweaning weight gains of beef calves in Ontario, Canada, from 1986 to 1999 were analyzed. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effect. The degree and the nature of the multicollinearity were identified and ridge regression methods were used as an alternative to ordinary least squares (LS). Ridge parameters were obtained using two different objective methods: 1) generalized ridge estimator of Hoerl and Kennard (R1); and 2) bootstrap in combination with cross-validation (R2). Both ridge regression methods outperformed the LS estimator with respect to mean squared error of predictions (MSEP) and variance inflation factors (VIF) computed over 100 bootstrap samples. The MSEP of R1 and R2 were similar, and they were 3% less than the MSEP of LS. The average VIF of LS, R1, and R2 were equal to 26.81, 6.10, and 4.18, respectively. Ridge regression methods were particularly effective in decreasing the multicollinearity involving predictor variables of breed additive effects. Because of a high degree of confounding between estimates of maternal
Analysis of heterosis and quantitative trait loci for kernel shape related traits using triple testcross population in maize.

Directory of Open Access Journals (Sweden)

Lu Jiang

Full Text Available Kernel shape related traits (KSRTs have been shown to have important influences on grain yield. The previous studies that emphasize kernel length (KL and kernel width (KW lack a comprehensive evaluation of characters affecting kernel shape. In this study, materials of the basic generations (B73, Mo17, and B73 × Mo17, 82 intermated B73 × Mo17 (IBM individuals, and the corresponding triple testcross (TTC populations were used to evaluate heterosis, investigate correlations, and characterize the quantitative trait loci (QTL for six KSRTs: KL, KW, length to width ratio (LWR, perimeter length (PL, kernel area (KA, and circularity (CS. The results showed that the mid-parent heterosis (MPH for most of the KSRTs was moderate. The performance of KL, KW, PL, and KA exhibited significant positive correlation with heterozygosity but their Pearson's R values were low. Among KSRTs, the strongest significant correlation was found between PL and KA with R values was up to 0.964. In addition, KW, PL, KA, and CS were shown to be significant positive correlation with 100-kernel weight (HKW. 28 QTLs were detected for KSRTs in which nine were augmented additive, 13 were augmented dominant, and six were dominance × additive epistatic. The contribution of a single QTL to total phenotypic variation ranged from 2.1% to 32.9%. Furthermore, 19 additive × additive digenic epistatic interactions were detected for all KSRTs with the highest total R2 for KW (78.8%, and nine dominance × dominance digenic epistatic interactions detected for KL, LWR, and CS with the highest total R2 (55.3%. Among significant digenic interactions, most occurred between genomic regions not mapped with main-effect QTLs. These findings display the complexity of the genetic basis for KSRTs and enhance our understanding on heterosis of KSRTs from the quantitative genetic perspective.
Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing.

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Branham, Sandra E; Stansell, Zachary J; Couillard, David M; Farnham, Mark W

2017-03-01

Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information. A doubled haploid (DH) broccoli population segregating for heat tolerance was evaluated for head quality in three summer fields in Charleston, SC, USA. Multiple quantitative trait loci (QTL) mapping of 1,423 single nucleotide polymorphisms developed through genotyping-by-sequencing identified five QTL and one positive epistatic interaction that explained 62.1% of variation in heat tolerance. The QTL identified here can be used to develop markers for marker-assisted selection and to increase our understanding of the molecular mechanisms underlying plant response to heat stress.
Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

DEFF Research Database (Denmark)

Joseph, Bindu; Corwin, Jason A.; Li, Baohua

2013-01-01

Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes...... was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation...... in metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural variation....
Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1

Energy Technology Data Exchange (ETDEWEB)

Jenson, Justin M.; Ryan, Jeremy A.; Grant, Robert A.; Letai, Anthony; Keating, Amy E. (DFCI); (MIT)

2017-06-08

Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.
Physical interaction between components of DNA mismatch repair and nucleotide excision repair

International Nuclear Information System (INIS)

Bertrand, P.; Tishkoff, D.X.; Filosi, N.; Dasgupta, R.; Kolodner, R.D.

1998-01-01

Nucleotide excision repair (NER) and DNA mismatch repair are required for some common processes although the biochemical basis for this requirement is unknown. Saccharomyces cerevisiae RAD14 was identified in a two-hybrid screen using MSH2 as 'bait,' and pairwise interactions between MSH2 and RAD1, RAD2, RAD3, RAD10, RAD14, and RAD25 subsequently were demonstrated by two-hybrid analysis. MSH2 coimmunoprecipitated specifically with epitope-tagged versions of RAD2, RAD10, RAD14, and RAD25. MSH2 and RAD10 were found to interact in msh3 msh6 and mlh1 pms1 double mutants, suggesting a direct interaction with MSH2. Mutations in MSH2 increased the UV sensitivity of NER-deficient yeast strains, and msh2 mutations were epistatic to the mutator phenotype observed in NER-deficient strains. These data suggest that MSH2 and possibly other components of DNA mismatch repair exist in a complex with NER proteins, providing a biochemical and genetical basis for these proteins to function in common processes
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses.

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Thomer, Annika; Gottschalk, Maren; Christmann, Anna; Naccache, Fanny; Jung, Klaus; Hewicker-Trautwein, Marion; Distl, Ottmar; Metzger, Julia

2018-04-23

Curly coat represents an extraordinary type of coat in horses, particularly seen in American Bashkir Curly Horses and Missouri Foxtrotters. In some horses with curly coat, a hypotrichosis of variable extent was observed, making the phenotype appear more complex. In our study, we aimed at investigating the genetic background of curly coat with and without hypotrichosis using high density bead chip genotype and next generation sequencing data. Genome-wide association analysis detected significant signals (p = 1.412 × 10 -05 -1.102 × 10 -08 ) on horse chromosome 11 at 22-35 Mb. In this significantly associated region, six missense variants were filtered out from whole-genome sequencing data of three curly coated horses of which two variants within KRT25 and SP6 could explain all hair phenotypes. Horses heterozygous or homozygous only for KRT25 variant showed curly coat and hypotrichosis, whereas horses with SP6 variant only, exhibited curly coat without hypotrichosis. Horses with mutant alleles in both variants developed curly hair and hypotrichosis. Thus, mutant KRT25 allele is masking SP6 allele effect, indicative for epistasis of KRT25 variant over SP6 variant. In summary, genetic variants in two different genes, KRT25 and SP6, are responsible for curly hair. All horses with KRT25 variant are additionally hypotrichotic due to the KRT25 epistatic effect on SP6.
Universality Classes of Interaction Structures for NK Fitness Landscapes

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Hwang, Sungmin; Schmiegelt, Benjamin; Ferretti, Luca; Krug, Joachim

2018-02-01

Kauffman's NK-model is a paradigmatic example of a class of stochastic models of genotypic fitness landscapes that aim to capture generic features of epistatic interactions in multilocus systems. Genotypes are represented as sequences of L binary loci. The fitness assigned to a genotype is a sum of contributions, each of which is a random function defined on a subset of k ≤ L loci. These subsets or neighborhoods determine the genetic interactions of the model. Whereas earlier work on the NK model suggested that most of its properties are robust with regard to the choice of neighborhoods, recent work has revealed an important and sometimes counter-intuitive influence of the interaction structure on the properties of NK fitness landscapes. Here we review these developments and present new results concerning the number of local fitness maxima and the statistics of selectively accessible (that is, fitness-monotonic) mutational pathways. In particular, we develop a unified framework for computing the exponential growth rate of the expected number of local fitness maxima as a function of L, and identify two different universality classes of interaction structures that display different asymptotics of this quantity for large k. Moreover, we show that the probability that the fitness landscape can be traversed along an accessible path decreases exponentially in L for a large class of interaction structures that we characterize as locally bounded. Finally, we discuss the impact of the NK interaction structures on the dynamics of evolution using adaptive walk models.
Mapping Haplotype-haplotype Interactions with Adaptive LASSO

Directory of Open Access Journals (Sweden)

Li Ming

2010-08-01

Full Text Available Abstract Background The genetic etiology of complex diseases in human has been commonly viewed as a complex process involving both genetic and environmental factors functioning in a complicated manner. Quite often the interactions among genetic variants play major roles in determining the susceptibility of an individual to a particular disease. Statistical methods for modeling interactions underlying complex diseases between single genetic variants (e.g. single nucleotide polymorphisms or SNPs have been extensively studied. Recently, haplotype-based analysis has gained its popularity among genetic association studies. When multiple sequence or haplotype interactions are involved in determining an individual's susceptibility to a disease, it presents daunting challenges in statistical modeling and testing of the interaction effects, largely due to the complicated higher order epistatic complexity. Results In this article, we propose a new strategy in modeling haplotype-haplotype interactions under the penalized logistic regression framework with adaptive L1-penalty. We consider interactions of sequence variants between haplotype blocks. The adaptive L1-penalty allows simultaneous effect estimation and variable selection in a single model. We propose a new parameter estimation method which estimates and selects parameters by the modified Gauss-Seidel method nested within the EM algorithm. Simulation studies show that it has low false positive rate and reasonable power in detecting haplotype interactions. The method is applied to test haplotype interactions involved in mother and offspring genome in a small for gestational age (SGA neonates data set, and significant interactions between different genomes are detected. Conclusions As demonstrated by the simulation studies and real data analysis, the approach developed provides an efficient tool for the modeling and testing of haplotype interactions. The implementation of the method in R codes can be

Drug interactions evaluation: An integrated part of risk assessment of therapeutics

International Nuclear Information System (INIS)

Zhang, Lei; Reynolds, Kellie S.; Zhao, Ping; Huang, Shiew-Mei

2010-01-01

Pharmacokinetic drug interactions can lead to serious adverse events or decreased drug efficacy. The evaluation of a new molecular entity's (NME's) drug-drug interaction potential is an integral part of risk assessment during drug development and regulatory review. Alteration of activities of enzymes or transporters involved in the absorption, distribution, metabolism, or excretion of a new molecular entity by concomitant drugs may alter drug exposure, which can impact response (safety or efficacy). The recent Food and Drug Administration (FDA) draft drug interaction guidance ( (http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm072101.pdf)) highlights the methodologies and criteria that may be used to guide drug interaction evaluation by industry and regulatory agencies and to construct informative labeling for health practitioner and patients. In addition, the Food and Drug Administration established a 'Drug Development and Drug Interactions' website to provide up-to-date information regarding evaluation of drug interactions ( (http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugInteractionsLabeling/ucm080499.htm)). This review summarizes key elements in the FDA drug interaction guidance and new scientific developments that can guide the evaluation of drug-drug interactions during the drug development process.
In vitro evaluation of the interaction between methanol extract of ...

African Journals Online (AJOL)

Antimicrobial interaction studies between methanol extract of lichen (Ramalina farinacea (I) ach. (Fam: Ramalinacea) and tetracycline, against clinical isolates of Staphylococcus aureus was evaluated. Preliminary antimicrobial properties of the extract were evaluated. Antimicrobial interaction studies between the methanol ...
Age Differences in Voice Evaluation: From Auditory-Perceptual Evaluation to Social Interactions

Science.gov (United States)

Lortie, Catherine L.; Deschamps, Isabelle; Guitton, Matthieu J.; Tremblay, Pascale

2018-01-01

Purpose: The factors that influence the evaluation of voice in adulthood, as well as the consequences of such evaluation on social interactions, are not well understood. Here, we examined the effect of listeners' age and the effect of talker age, sex, and smoking status on the auditory-perceptual evaluation of voice, voice-related psychosocial…
DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1.

Science.gov (United States)

Kim, Sang-Hoon; Kim, Hani; Chung, Sunglan; Lee, Jae-Hoon

2017-09-16

Although DWD HYPERSENSITIVE TO UV-B 1 (DHU1) is reported to be a negative regulator in UV-B mediated cellular responses, its detailed role in UV-B signaling is still elusive. To further understand the action mechanism of DHU1 in UV-B response, physical and genetic interactions of DHU1 with various UV-B signaling components were investigated. Yeast two hybrid assay results suggested that DHU1 directly interacts with COP1 and RUP1, implying a functional connection with both COP1 and RUP1. In spite of the physical association between DHU1 and COP1, loss of DHU1 did not affect protein stability of COP1. Epistatic analysis showed that the functional loss of both DHU1 and UVR8 leads to alleviation of UV-B hypersensitivity displayed in dhu1-1. Moreover, phenotypic studies with dhu1-1 cop1-6 and dhu1-1 hy5-215 revealed that COP1 and HY5 are epistatic to DHU1, indicating that UV-B hypersensitivity of dhu1-1 requires both COP1 and HY5. In the case of dhu1-1 rup1-1, UV-B responsiveness was similar to that of both dhu1-1 and rup1-1, implying that DHU1 and RUP1 are required for each other's function. Collectively, these results show that the role of DHU1 as a negative regulator in UV-B response may be derived from its direct interaction with COP1 by sequestering COP1 from the active UVR8-COP1 complex, resulting in a decrease in the COP1 population that positively participates in UV-B signaling together with UVR8. Furthermore, this inhibitory role of DHU1 in UV-B signaling is likely to be functionally connected to RUP1. This study will serve as a platform to further understand more detailed action mechanism of DHU1 in UV-B response and DHU1-mediated core UV-B signaling in Arabidopsis. Copyright © 2017 Elsevier Inc. All rights reserved.
2nd Workshop on Evaluating Child Robot Interaction

NARCIS (Netherlands)

Zaga, Cristina; Lohse, M.; Charisi, Vasiliki; Evers, Vanessa; Neerincx, Marc; Kanda, Takayuki; Leite, Iolanda

Many researchers have started to explore natural interaction scenarios for children. No matter if these children are normally developing or have special needs, evaluating Child-Robot Interaction (CRI) is a challenge. To find methods that work well and provide reliable data is difficult, for example
Evaluation of self-interaction parameters from binary phase diagrams

International Nuclear Information System (INIS)

Ellison, T.L.

1977-10-01

The feasibility of calculating Wagner self-interaction parameters from binary phase diagrams was examined. The self-interaction parameters of 22 non-ferrous liquid solutions were calculated utilizing an equation based on the equality of the chemical potentials of a component in two equilibrium phases. Utilization of the equation requires the evaluation of the first and second derivatives of various liquidus and solidus data at infinite dilution of the solute component. Several numerical methods for evaluating the derivatives of tabular data were examined. A method involving power series curve fitting and subsequent differentiation of the power series was found to be the most suitable for the interaction parameter calculations. Comparison of the calculated self-interaction parameters with values obtained from thermodynamic measurements indicates that the Wagner self-interaction parameter can be successfully calculated from binary phase diagrams
Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes MdSAUR37, MdPP2CH and MdALMTII.

Science.gov (United States)

Jia, Dongjie; Shen, Fei; Wang, Yi; Wu, Ting; Xu, Xuefeng; Zhang, Xinzhong; Han, Zhenhai

2018-05-11

Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H + -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the physiological fundamentals of quantitative genetics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Questionnaires for eliciting evaluation data from users of interactive question answering

Energy Technology Data Exchange (ETDEWEB)

Kelly, Diane; Kantor, Paul B.; Morse, Emile; Scholtz, Jean; Sun, Y.

2009-01-01

Evaluating interactive question answering (QA) systems with real users can be challenging because traditional evaluation measures based on the relevance of items returned are difficult to employ since relevance judgments can be unstable in multi-user evaluations. The work reported in this paper evaluates, in distinguishing among a set of interactive QA systems, the effectiveness of three questionnaires: a Cognitive Workload Questionnaire (NASA TLX), and Task and System Questionnaires customized to a specific interactive QA application. These Questionnaires were evaluated with four systems, seven analysts, and eight scenarios during a 2-week workshop. Overall, results demonstrate that all three Questionnaires are effective at distinguishing among systems, with the Task Questionnaire being the most sensitive. Results also provide initial support for the validity and reliability of the Questionnaires.
Teaching Program Evaluation on Interactive Television.

Science.gov (United States)

McNeil, Keith; Steinhauser, Jim; Newman, Isadore

This paper describes a five-session course entitled "Program Evaluation," which was taught via interactive television in the summer of 2002 to 68 doctoral and master's students in 5 of 6 locations throughout New Mexico. Students received a 4-hour lecture and then participated in off-line activities directed by the instructor. Problems in distance…
The influence of intention and outcome on evaluations of social interaction.

Science.gov (United States)

Wu, Xiaoying; Hua, Rui; Yang, Zhangxiang; Yin, Jun

2018-01-01

Reading and making sense of social interactions between individuals is an important part of our daily social lives. Given that actions tend to be interpreted in terms of intent within the observed outcome, we investigated how intent and outcome interactively influence evaluations of social interactions. Through visual animations, intent was operationalized as an agent's (i.e., actor's) act intentionally or unintentionally having an influence on another agent (i.e., affectee). In Experiment 1, the act was helpful and the consequences brought small or great benefits to the affectee. In Experiment 2, the act was harmful and brought small or great losses to the affectee. We found that for both helpful and harmful contexts, social interaction evaluations were influenced by an interaction between the intent and outcome of the act. Specifically, great help/harm (i.e., the great-benefits or great-losses condition) was rated as a stronger social interaction than small help/harm, and the difference was larger in the intentional condition than in the unintentional condition. Furthermore, regardless of the interaction valence, the effect of the intent was larger than the effect of the outcome when evaluating social interaction. This result suggests that observers consider the intent and outcome jointly when evaluating a given social interaction, and the intent has a privileged role in this process. These findings are consistent with the idea that the intent is often deemed to be the cause driving the effect of outcome, and they help us to understand how social interactions are constructed within the action understanding system. Copyright © 2017 Elsevier B.V. All rights reserved.
Development and Evaluation of an Interactive Pen

Directory of Open Access Journals (Sweden)

Froilan G. Destreza

2015-11-01

Full Text Available Technologies have reached the classroom. It is one of the means of teaching strategies nowadays. Multimedia projectors have become one of the teaching tools the teacher cannot bear without it. The concept of making this tool to be interactive and easier to use was far conceived by the researcher. The researcher’s objective was to develop such tool and evaluate it according to its portability, simplicity, robustness, user-friendliness, effectiveness and efficiency. The respondents of the project were both the students and teachers of Batangas State University ARASOF-Nasugbu. The researcher has developed different prototypes for the interactive pen and tested in different environment and demonstrated the “know-how” of the project. The project was built using a simple infrared light emitting diode (IR LED, infrared tracker, and software which computes, detects and interact with the application program. Evaluation of the project followed the demonstration. The project got a high acceptance according to its portability, simplicity, robustness, user-friendliness, effectiveness and efficiency. The researcher is recommending the full implementation of the project in the Batangas State University ARASOF- Nasugbu and for better enhancement of the project by eliminating the pen.
Variants of SCARB1 and VDR Involved in Complex Genetic Interactions May Be Implicated in the Genetic Susceptibility to Clear Cell Renal Cell Carcinoma

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Ewelina Pośpiech

2015-01-01

Full Text Available The current data are still inconclusive in terms of a genetic component involved in the susceptibility to renal cell carcinoma. Our aim was to evaluate 40 selected candidate polymorphisms for potential association with clear cell renal cell carcinoma (ccRCC based on independent group of 167 patients and 200 healthy controls. The obtained data were searched for independent effects of particular polymorphisms as well as haplotypes and genetic interactions. Association testing implied position rs4765623 in the SCARB1 gene (OR=1.688, 95% CI: 1.104–2.582, P=0.016 and a haplotype in VDR comprising positions rs739837, rs731236, rs7975232, and rs1544410 (P=0.012 to be the risk factors in the studied population. The study detected several epistatic effects contributing to the genetic susceptibility to ccRCC. Variation in GNAS1 was implicated in a strong synergistic interaction with BIRC5. This effect was part of a model suggested by multifactor dimensionality reduction method including also a synergy between GNAS1 and SCARB1 (P=0.036. Significance of GNAS1-SCARB1 interaction was further confirmed by logistic regression (P=0.041, which also indicated involvement of SCARB1 in additional interaction with EPAS1 (P=0.008 as well as revealing interactions between GNAS1 and EPAS1 (P=0.016, GNAS1 and MC1R (P=0.031, GNAS1 and VDR (P=0.032, and MC1R and VDR (P=0.035.
Rice-arsenate interactions in hydroponics: a three-gene model for tolerance.

Science.gov (United States)

Norton, Gareth J; Nigar, Meher; Williams, Paul N; Dasgupta, Tapash; Meharg, Andrew A; Price, Adam H

2008-01-01

In this study, the genetic mapping of the tolerance of root growth to 13.3 muM arsenate [As(V)] using the BalaxAzucena population is improved, and candidate genes for further study are identified. A remarkable three-gene model of tolerance is advanced, which appears to involve epistatic interaction between three major genes, two on chromosome 6 and one on chromosome 10. Any combination of two of these genes inherited from the tolerant parent leads to the plant having tolerance. Lists of potential positional candidate genes are presented. These are then refined using whole genome transcriptomics data and bioinformatics. Physiological evidence is also provided that genes related to phosphate transport are unlikely to be behind the genetic loci conferring tolerance. These results offer testable hypotheses for genes related to As(V) tolerance that might offer strategies for mitigating arsenic (As) accumulation in consumed rice.
Rice–arsenate interactions in hydroponics: a three-gene model for tolerance

Science.gov (United States)

Norton, Gareth J.; Nigar, Meher; Dasgupta, Tapash; Meharg, Andrew A.; Price, Adam H.

2008-01-01

In this study, the genetic mapping of the tolerance of root growth to 13.3 μM arsenate [As(V)] using the Bala×Azucena population is improved, and candidate genes for further study are identified. A remarkable three-gene model of tolerance is advanced, which appears to involve epistatic interaction between three major genes, two on chromosome 6 and one on chromosome 10. Any combination of two of these genes inherited from the tolerant parent leads to the plant having tolerance. Lists of potential positional candidate genes are presented. These are then refined using whole genome transcriptomics data and bioinformatics. Physiological evidence is also provided that genes related to phosphate transport are unlikely to be behind the genetic loci conferring tolerance. These results offer testable hypotheses for genes related to As(V) tolerance that might offer strategies for mitigating arsenic (As) accumulation in consumed rice. PMID:18453529
Alleles versus genotypes: Genetic interactions and the dynamics of selection in sexual populations

Science.gov (United States)

Neher, Richard

2010-03-01

Physical interactions between amino-acids are essential for protein structure and activity, while protein-protein interactions and regulatory interactions are central to cellular function. As a consequence of these interactions, the combined effect of two mutations can differ from the sum of the individual effects of the mutations. This phenomenon of genetic interaction is known as epistasis. However, the importance of epistasis and its effects on evolutionary dynamics are poorly understood, especially in sexual populations where recombination breaks up existing combinations of alleles to produce new ones. Here, we present a computational model of selection dynamics involving many epistatic loci in a recombining population. We demonstrate that a large number of polymorphic interacting loci can, despite frequent recombination, exhibit cooperative behavior that locks alleles into favorable genotypes leading to a population consisting of a set of competing clones. As the recombination rate exceeds a certain critical value this ``genotype selection'' phase disappears in an abrupt transition giving way to ``allele selection'' - the phase where different loci are only weakly correlated as expected in sexually reproducing populations. Clustering of interacting sets of genes on a chromosome leads to the emergence of an intermediate regime, where localized blocks of cooperating alleles lock into genetic modules. Large populations attain highest fitness at a recombination rate just below critical, suggesting that natural selection might tune recombination rates to balance the beneficial aspect of exploration of genotype space with the breaking up of synergistic allele combinations.
Learning Predictive Interactions Using Information Gain and Bayesian Network Scoring.

Directory of Open Access Journals (Sweden)

Xia Jiang

Full Text Available The problems of correlation and classification are long-standing in the fields of statistics and machine learning, and techniques have been developed to address these problems. We are now in the era of high-dimensional data, which is data that can concern billions of variables. These data present new challenges. In particular, it is difficult to discover predictive variables, when each variable has little marginal effect. An example concerns Genome-wide Association Studies (GWAS datasets, which involve millions of single nucleotide polymorphism (SNPs, where some of the SNPs interact epistatically to affect disease status. Towards determining these interacting SNPs, researchers developed techniques that addressed this specific problem. However, the problem is more general, and so these techniques are applicable to other problems concerning interactions. A difficulty with many of these techniques is that they do not distinguish whether a learned interaction is actually an interaction or whether it involves several variables with strong marginal effects.We address this problem using information gain and Bayesian network scoring. First, we identify candidate interactions by determining whether together variables provide more information than they do separately. Then we use Bayesian network scoring to see if a candidate interaction really is a likely model. Our strategy is called MBS-IGain. Using 100 simulated datasets and a real GWAS Alzheimer's dataset, we investigated the performance of MBS-IGain.When analyzing the simulated datasets, MBS-IGain substantially out-performed nine previous methods at locating interacting predictors, and at identifying interactions exactly. When analyzing the real Alzheimer's dataset, we obtained new results and results that substantiated previous findings. We conclude that MBS-IGain is highly effective at finding interactions in high-dimensional datasets. This result is significant because we have increasingly
Psychometric evaluation of the Social Interaction Phobia Scale.

Science.gov (United States)

Reilly, Alison R; Carleton, R Nicholas; Weeks, Justin W

2012-01-01

The present study evaluated the psychometric properties of a novel measure of social anxiety symptoms, the Social Interaction Phobia Scale (SIPS), as a stand-alone item set, using an undergraduate sample (N=512). The 14-item SIPS has three subscales assessing Social Interaction Anxiety, Fear of Overt Evaluation, and Fear of Attracting Attention. Confirmatory factor analyses replicated the three-factor structure for the SIPS originally reported by Carleton et al. All SIPS scores demonstrated good internal consistency. The convergent validity of the SIPS was supported by strong and positive correlations between all SIPS scores and measures of social anxiety and fear of evaluation; the finding that the relationships between all SIPS scores and a social anxiety measure were stronger than relationships between all SIPS scores and measures of other constructs supported the discriminant validity of the SIPS. Results suggest that the SIPS possesses excellent psychometric properties.
QTL Information Table: 87 [Q-TARO

Lifescience Database Archive (English)

Full Text Available n effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110, 1445-1452. ...
Evaluation of Interactive Website Design Indicators for e-Entrepreneurship

OpenAIRE

Chih-Chao Chung; Li-Chung Chao; Chin-Hui Chen; Shi-Jer Lou

2016-01-01

Using an analytic network process (ANP) as an analytical tool, this study aims to construct an ANP evaluation model of interactive website design indicators. Through a review of the literature, interactive website design of e-entrepreneurship is generalized to the following dimensions: (1) Design; (2) Checking; (3) Service; (4) Interactive; and (5) Promotion, including 19 design indicators. The research is conducted for a case company. According to the findings, the model helps the case compa...
Using Affinity Diagrams to Evaluate Interactive Prototypes

DEFF Research Database (Denmark)

Lucero, Andrés

2015-01-01

our particular use of affinity diagramming in prototype evaluations. We reflect on a decade’s experience using affinity diagramming across a number of projects, both in industry and academia. Our affinity diagramming process in interaction design has been tailored and consists of four stages: creating...

Budding yeast mms4 is epistatic with rad52 and the function of Mms4 can be replaced by a bacterial Holliday junction resolvase.

Science.gov (United States)

Odagiri, Nao; Seki, Masayuki; Onoda, Fumitoshi; Yoshimura, Akari; Watanabe, Sei; Enomoto, Takemi

2003-03-01

MMS4 of Saccharomyces cerevisiae was originally identified as the gene responsible for one of the collection of methyl methanesulfonate (MMS)-sensitive mutants, mms4. Recently it was identified as a synthetic lethal gene with an SGS1 mutation. Epistatic analyses revealed that MMS4 is involved in a pathway leading to homologous recombination requiring Rad52 or in the recombination itself, in which SGS1 is also involved. MMS sensitivity of mms4 but not sgs1, was suppressed by introducing a bacterial Holliday junction (HJ) resolvase, RusA. The frequencies of spontaneously occurring unequal sister chromatid recombination (SCR) and loss of marker in the rDNA in haploid mms4 cells and interchromosomal recombination between heteroalleles in diploid mms4 cells were essentially the same as those of wild-type cells. Although UV- and MMS-induced interchromosomal recombination was defective in sgs1 diploid cells, hyper-induction of interchromosomal recombination was observed in diploid mms4 cells, indicating that the function of Mms4 is dispensable for this type of recombination.
Natural selection interacts with recombination to shape the evolution of hybrid genomes.

Science.gov (United States)

Schumer, Molly; Xu, Chenling; Powell, Daniel L; Durvasula, Arun; Skov, Laurits; Holland, Chris; Blazier, John C; Sankararaman, Sriram; Andolfatto, Peter; Rosenthal, Gil G; Przeworski, Molly

2018-05-11

To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
A Markov blanket-based method for detecting causal SNPs in GWAS

Directory of Open Access Journals (Sweden)

Han Bing

2010-04-01

Full Text Available Abstract Background Detecting epistatic interactions associated with complex and common diseases can help to improve prevention, diagnosis and treatment of these diseases. With the development of genome-wide association studies (GWAS, designing powerful and robust computational method for identifying epistatic interactions associated with common diseases becomes a great challenge to bioinformatics society, because the study of epistatic interactions often deals with the large size of the genotyped data and the huge amount of combinations of all the possible genetic factors. Most existing computational detection methods are based on the classification capacity of SNP sets, which may fail to identify SNP sets that are strongly associated with the diseases and introduce a lot of false positives. In addition, most methods are not suitable for genome-wide scale studies due to their computational complexity. Results We propose a new Markov Blanket-based method, DASSO-MB (Detection of ASSOciations using Markov Blanket to detect epistatic interactions in case-control GWAS. Markov blanket of a target variable T can completely shield T from all other variables. Thus, we can guarantee that the SNP set detected by DASSO-MB has a strong association with diseases and contains fewest false positives. Furthermore, DASSO-MB uses a heuristic search strategy by calculating the association between variables to avoid the time-consuming training process as in other machine-learning methods. We apply our algorithm to simulated datasets and a real case-control dataset. We compare DASSO-MB to other commonly-used methods and show that our method significantly outperforms other methods and is capable of finding SNPs strongly associated with diseases. Conclusions Our study shows that DASSO-MB can identify a minimal set of causal SNPs associated with diseases, which contains less false positives compared to other existing methods. Given the huge size of genomic dataset
Cockpit design and evaluation using interactive graphics

Science.gov (United States)

Evans, S. M.

1975-01-01

A general overview of the characteristics of an interactive graphics system which was developed to assist cockpit engineers design and evaluate work stations was presented. The manikin used in this COMputerized BIomechanical MAN-model (COMBIMAN) was described, as are provisions for generating work stations and assessing interactions between man and environment. The applications of the present system are explained, and critiques of COMBIMAN are presented. The limitations of the existing programs and the requirements of the designers necessitate future revisions and additions to the biomechanical and erogonomic properties of COMBIMAN. Some of these enhancements are discussed.
Bacteria Hunt: Evaluating multi-paradigm BCI interaction

NARCIS (Netherlands)

Mühl, C.; Gürkök, Hayrettin; Plass - Oude Bos, D.; Thurlings, Marieke E.; Scherffig, Lasse; Duvinage, Matthieu; Elbakyan, Alexandra A.; Kang, SungWook; Poel, Mannes; Heylen, Dirk K.J.

The multimodal, multi-paradigm brain-computer interfacing (BCI) game Bacteria Hunt was used to evaluate two aspects of BCI interaction in a gaming context. One goal was to examine the effect of feedback on the ability of the user to manipulate his mental state of relaxation. This was done by having
Evaluation of Interactive Website Design Indicators for e-Entrepreneurship

Directory of Open Access Journals (Sweden)

Chih-Chao Chung

2016-04-01

Full Text Available Using an analytic network process (ANP as an analytical tool, this study aims to construct an ANP evaluation model of interactive website design indicators. Through a review of the literature, interactive website design of e-entrepreneurship is generalized to the following dimensions: (1 Design; (2 Checking; (3 Service; (4 Interactive; and (5 Promotion, including 19 design indicators. The research is conducted for a case company. According to the findings, the model helps the case company review its current execution of interactive website design indicators and the experts’ opinions of the importance of interactive website design indicators. In addition, by comprehensive comparison, it confirms key design indicators and analyzes the managerial implications to help the case company set up precise strategic planning and resource distribution to enhance corporate operational performance and competitiveness.
Sex-specific asymmetry in eye development in interspecific hybrids ...

Indian Academy of Sciences (India)

hybrids having D. pseudoananassae as one of the parental species. One of them was the .... that recessive epistatic X-autosomal interactions are involved as none of the ... The X chromosome of the maternal species,. D. pseudoananassae ...
Crossbreeding Holstein-Friesian with Ethiopian Boran cattle in a ...

African Journals Online (AJOL)

Unknown

Friesian with Boran (unselected for milk), the epistatic interaction genes might have been lost due to the free recombination process during meiosis. Similar negative recombination effects on milk yield were reported even for crossing between two B.
Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

Directory of Open Access Journals (Sweden)

Mohan Babu

2014-02-01

Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.
Variability in working memory performance explained by epistasis vs polygenic scores in the ZNF804A pathway

NARCIS (Netherlands)

Nicodemus, Kristin K.; Hargreaves, April; Morris, Derek; Anney, Richard; Gill, Michael; Corvin, Aiden; Donohoe, Gary; Ripke, Stephan; Sanders, Alan R.; Kendler, Kenneth S.; Levinson, Douglas F.; Sklar, Pamela; Holmans, Peter A.; Lin, Dan-Yu; Duan, Jubao; Ophoff, Roel A.; Andreassen, Ole A.; Scolnick, Edward; Cichon, Sven; St Clair, David; Gurling, Hugh; Werge, Thomas; Rujescu, Dan; Blackwood, Douglas H. R.; Pato, Carlos N.; Malhotra, Anil K.; Purcell, Shaun; Dudbridge, Frank; Neale, Benjamin M.; Rossin, Lizzy; Visscher, Peter M.; Posthuma, Danielle; Ruderfer, Douglas M.; Fanous, Ayman; Stefansson, Hreinn; Steinberg, Stacy; Mowry, Bryan J.; Golimbet, Vera; de Hert, Marc; Jönsson, Erik G.; Bitter, István; Pietiläinen, Olli P. H.; Collier, David A.; Tosato, Sarah; Agartz, Ingrid; Albus, Margot; Alexander, Madeline; Amdur, Richard L.; de Haan, Lieuwe; Linszen, Don H.

2014-01-01

We investigated the variation in neuropsychological function explained by risk alleles at the psychosis susceptibility gene ZNF804A and its interacting partners using single nucleotide polymorphisms (SNPs), polygenic scores, and epistatic analyses. Of particular importance was the relative
Variability in working memory performance explained by epistasis vs polygenic scores in the ZNF804A pathway.

NARCIS (Netherlands)

Nicodemus, K.K.; Hargreaves, A.; Morris, D.; Anney, R.; Gill, M.; Corvin, A.; Posthuma, D.; Donohoe, G.

2014-01-01

IMPORTANCE We investigated the variation in neuropsychological function explained by risk alleles at the psychosis susceptibility gene ZNF804A and its interacting partners using single nucleotide polymorphisms (SNPs), polygenic scores, and epistatic analyses. Of particular importance was the
A Balanced Accuracy Fitness Function Leads to Robust Analysis Using Grammatical Evolution Neural Networks in the Case of Class Imbalance

Science.gov (United States)

The identification and characterization of genetic and environmental factors that predict common, complex disease is a major goal of human genetics. The ubiquitous nature of epistatic interaction in the underlying genetic etiology of such disease presents a difficult analytical ...
Using GOMS and NASA-TLX to Evaluate Human-Computer Interaction Process in Interactive Segmentation

NARCIS (Netherlands)

Ramkumar, A.; Stappers, P.J.; Niessen, W.J.; Adebahr, S; Schimek-Jasch, T; Nestle, U; Song, Y.

2016-01-01

HCI plays an important role in interactive medical image segmentation. The Goals, Operators, Methods, and Selection rules (GOMS) model and the National Aeronautics and Space Administration Task Load Index (NASA-TLX) questionnaire are different methods that are often used to evaluate the HCI
Soil-structure interaction - an engineering evaluation

International Nuclear Information System (INIS)

Hadjian, A.H.

1976-01-01

The two methods of analysis for structure interaction, the impedance and the finite element methods, are reviewed with regard to their present capabilities to address the significant factors of the problem. The objective of the paper is to evaluate if an adequate engineering solution to the problem is provided by either approach. Questions related to the reduction of seismic motions with depth scattering of incident waves, the three-dimensionality of the real problem, soil damping, strain dependency of soil properties and the uncertainties associated with all of the above are discussed in sufficient detail. All conclusions made are based on referenced material. It appears that both methods as presently practised have not yet completely solved the problem, the impedance approach has come closer to addressing the more significant issues. Because of this finding, in addition to its simplicity and low cost, the impedance approach is the perfect engineering method for soil-structure interaction. (Auth.)
Transcriptional robustness and protein interactions are associated in yeast

Directory of Open Access Journals (Sweden)

Conant Gavin C

2011-05-01

Full Text Available Abstract Background Robustness to insults, both external and internal, is a characteristic feature of life. One level of biological organization for which noise and robustness have been extensively studied is gene expression. Cells have a variety of mechanisms for buffering noise in gene expression, but it is not completely clear what rules govern whether or not a given gene uses such tools to maintain appropriate expression. Results Here, we show a general association between the degree to which yeast cells have evolved mechanisms to buffer changes in gene expression and whether they possess protein-protein interactions. We argue that this effect bears an affinity to epistasis, because yeast appears to have evolved regulatory mechanisms such that distant changes in gene copy number for a protein-protein interaction partner gene can alter a gene's expression. This association is not unexpected given recent work linking epistasis and the deleterious effects of changes in gene dosage (i.e., the dosage balance hypothesis. Using gene expression data from artificial aneuploid strains of bakers' yeast, we found that genes coding for proteins that physically interact with other proteins show less expression variation in response to aneuploidy than do other genes. This effect is even more pronounced for genes whose products interact with proteins encoded on aneuploid chromosomes. We further found that genes targeted by transcription factors encoded on aneuploid chromosomes were more likely to change in expression after aneuploidy. Conclusions We suggest that these observations can be best understood as resulting from the higher fitness cost of misexpression in epistatic genes and a commensurate greater regulatory control of them.
No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation.

Science.gov (United States)

Etges, William J

2014-01-01

Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors. © The American Genetic Association. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Combinations of Methods for Collaborative Evaluation of the Usability of Interactive Software Systems

Directory of Open Access Journals (Sweden)

Andrés Solano

2016-01-01

Full Text Available Usability is a fundamental quality characteristic for the success of an interactive system. It is a concept that includes a set of metrics and methods in order to obtain easy-to-learn and easy-to-use systems. Usability Evaluation Methods, UEM, are quite diverse; their application depends on variables such as costs, time availability, and human resources. A large number of UEM can be employed to assess interactive software systems, but questions arise when deciding which method and/or combination of methods gives more (relevant information. We propose Collaborative Usability Evaluation Methods, CUEM, following the principles defined by the Collaboration Engineering. This paper analyzes a set of CUEM conducted on different interactive software systems. It proposes combinations of CUEM that provide more complete and comprehensive information about the usability of interactive software systems than those evaluation methods conducted independently.
Evolution of genetic architecture under directional selection.

Science.gov (United States)

Hansen, Thomas F; Alvarez-Castro, José M; Carter, Ashley J R; Hermisson, Joachim; Wagner, Günter P

2006-08-01

We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis.
Evaluation of potential interactions between mycophenolic acid derivatives and proton pump inhibitors.

Science.gov (United States)

Gabardi, Steven; Olyaei, Ali

2012-01-01

To evaluate the incidence of gastrointestinal (GI) complications in solid organ transplant (SOT) recipients, impact of the complications on transplant outcomes, and the potential interactions between mycophenolic acid (MPA) derivatives and proton pump inhibitors (PPIs). An unrestricted literature search (1980-January 2012) was performed with MEDLINE and EMBASE using the following key words: drug-drug interaction, enteric-coated mycophenolic acid, GI complications, mycophenolate mofetil, solid organ transplant, and proton pump inhibitor, including individual agents within the class. Abstracts from scientific meetings were also evaluated. Additionally, reference citations from identified publications were reviewed. Relevant English-language, original research articles and review articles were evaluated if they focused on any of the topics identified in the search or included substantial content addressing GI complications in SOT recipients or drug interactions. GI complications are frequent among SOT recipients, with some studies showing prevalence rates as high as 70%. Transplant outcomes among renal transplant recipients are significantly impacted by GI complications, especially in patients requiring immunosuppressant dosage reductions or premature discontinuation. To this end, PPI use among patients receiving transplants is common. Recent data demonstrate that PPIs significantly reduce the overall exposure to MPA after oral administration of mycophenolate mofetil. Similar studies show this interaction does not exist between PPIs and enteric-coated mycophenolic acid (EC-MPA). Unfortunately, most of the available data evaluating this interaction are pharmacokinetic analyses that do not investigate the clinical impact of this interaction. A significant interaction exists between PPIs and mycophenolate mofetil secondary to reduced dissolution of mycophenolate mofetil in higher pH environments. EC-MPA is not absorbed in the stomach; therefore, low intragastric acidity
Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter.

Directory of Open Access Journals (Sweden)

Jakub Otwinowski

Full Text Available Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of high-throughput sequence data from the 75 base pairs long mutagenized E. coli lac promoter region, where each sequence is associated with its phenotype, the induced transcriptional activity measured by a fluorescent reporter. We find that the additive (non-epistatic contributions of individual mutations account for about two-thirds of the explainable phenotype variance, while pairwise epistasis explains about 7% of the variance for the full mutagenized sequence and about 15% for the subsequence associated with protein binding sites. Surprisingly, there is no evidence for third order epistatic contributions, and our inferred fitness landscape is essentially single peaked, with a small amount of antagonistic epistasis. There is a significant selective pressure on the wild type, which we deduce to be multi-objective optimal for gene expression in environments with different nutrient sources. We identify transcription factor (CRP and RNA polymerase binding sites in the promotor region and their interactions without difficult optimization steps. In particular, we observe evidence for previously unexplored genetic regulatory mechanisms, possibly kinetic in nature. We conclude with a cautionary note that inferred properties of fitness landscapes may be severely influenced by biases in the sequence data.

Studying Interaction in Undergraduate Tutorials: Results from a Small-Scale Evaluation

Science.gov (United States)

Shaw, Lorraine; Carey, Phil; Mair, Michael

2008-01-01

This article reports on an observation-based evaluation of student-tutor interaction in first-year undergraduate tutorials. Using a single case analysis, the paper looks at how tutors and students built and maintained relationships through two different though interlinked forms of interaction--storytelling and the use of classroom space for…
Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication.

Science.gov (United States)

Doust, Andrew N; Lukens, Lewis; Olsen, Kenneth M; Mauro-Herrera, Margarita; Meyer, Ann; Rogers, Kimberly

2014-04-29

Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-by-environment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.
Nuclear interactive evaluations on distributed processors

International Nuclear Information System (INIS)

Dix, G.E.; Congdon, S.P.

1988-01-01

BWR [boiling water reactor] nuclear design is a complicated process, involving trade-offs among a variety of conflicting objectives. Complex computer calculations and usually required for each design iteration. GE Nuclear Energy has implemented a system where the evaluations are performed interactively on a large number of small microcomputers. This approach minimizes the time it takes to carry out design iterations even through the processor speeds are low compared with modern super computers. All of the desktop microcomputers are linked to a common data base via an ethernet communications system so that design data can be shared and data quality can be maintained
Pre-evaluation and interactive editing of B-spline and GERBS curves and surfaces

Science.gov (United States)

Laksâ, Arne

2017-12-01

Interactive computer based geometry editing is very useful for designers and artists. Our goal has been to develop useful tools for geometry editing in a way that increases the ability for creative design. When we interactively editing geometry, we want to see the change happening gradually and smoothly on the screen. Pre-evaluation is a tool for increasing the speed of the graphics when doing interactive affine operation on control points and control surfaces. It is then possible to add details on surfaces, and change shape in a smooth and continuous way. We use pre-evaluation on basis functions, on blending functions and on local surfaces. Pre-evaluation can be made hierarchi-cally and is thus useful for local refinements. Sampling and plotting of curves, surfaces and volumes can today be handled by the GPU and it is therefore important to have a structured organization and updating system to be able to make interactive editing as smooth and user friendly as possible. In the following, we will show a structure for pre-evaluation and an optimal organisation of the computation and we will show the effect of implementing both of these techniques.
Development and Evaluation of an Interactive WebQuest Environment: "Web Macerasi"

Science.gov (United States)

Gulbahar, Yasemin; Madran, R. Orcun; Kalelioglu, Filiz

2010-01-01

This study was conducted to develop a web-based interactive system, Web Macerasi, for teaching-learning and evaluation purposes, and to find out the possible effects of this system. The study has two stages. In the first stage, a WebQuest site was designed as an interactive system in which various Internet and web technologies were used for…
Evaluation Criteria for Interactive E-Books for Open and Distance Learning

Science.gov (United States)

Bozkurt, Aras; Bozkaya, Mujgan

2015-01-01

The aim of this mixed method study is to identify evaluation criteria for interactive e-books. To find answers for the research questions of the study, both quantitative and qualitative data were collected through a four-round Delphi study with a panel consisting of 30 experts. After that, a total of 20 interactive e-books were examined with…
Evaluation of drug-drug interactions among patients with chronic ...

African Journals Online (AJOL)

Introduction: The risk of drug-drug interactions (DDIs) is high in patients with chronic kidney disease (CKD) necessitating dose adjustments or the avoidance of drug combinations. This study aimed to evaluate DDIs among patients with CKD in the University of Nigeria Teaching Hospital (UNTH), Enugu, South-East Nigeria.
Genetic control of soybean seed oil: II. QTL and genes that increase oil concentration without decreasing protein or with increased seed yield.

Science.gov (United States)

Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

2013-06-01

Soybean [Glycine max (L.) Merrill] seed oil is the primary global source of edible oil and a major renewable and sustainable feedstock for biodiesel production. Therefore, increasing the relative oil concentration in soybean is desirable; however, that goal is complex due to the quantitative nature of the oil concentration trait and possible effects on major agronomic traits such as seed yield or protein concentration. The objectives of the present study were to study the relationship between seed oil concentration and important agronomic and seed quality traits, including seed yield, 100-seed weight, protein concentration, plant height, and days to maturity, and to identify oil quantitative trait loci (QTL) that are co-localized with the traits evaluated. A population of 203 F4:6 recombinant inbred lines, derived from a cross between moderately high oil soybean genotypes OAC Wallace and OAC Glencoe, was developed and grown across multiple environments in Ontario, Canada, in 2009 and 2010. Among the 11 QTL associated with seed oil concentration in the population, which were detected using either single-factor ANOVA or multiple QTL mapping methods, the number of QTL that were co-localized with other important traits QTL were six for protein concentration, four for seed yield, two for 100-seed weight, one for days to maturity, and one for plant height. The oil-beneficial allele of the QTL tagged by marker Sat_020 was positively associated with seed protein concentration. The oil favorable alleles of markers Satt001 and GmDGAT2B were positively correlated with seed yield. In addition, significant two-way epistatic interactions, where one of the interacting markers was solely associated with seed oil concentration, were identified for the selected traits in this study. The number of significant epistatic interactions was seven for yield, four for days to maturity, two for 100-seed weight, one for protein concentration, and one for plant height. The identified molecular
Evaluation of clustering algorithms for protein-protein interaction networks

Directory of Open Access Journals (Sweden)

van Helden Jacques

2006-11-01

Full Text Available Abstract Background Protein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the whole network of protein interactions for a given organism. In 2002, the yeast interactome was estimated to contain up to 80,000 potential interactions. This estimate is based on the integration of data sets obtained by various methods (mass spectrometry, two-hybrid methods, genetic studies. High-throughput methods are known, however, to yield a non-negligible rate of false positives, and to miss a fraction of existing interactions. The interactome can be represented as a graph where nodes correspond with proteins and edges with pairwise interactions. In recent years clustering methods have been developed and applied in order to extract relevant modules from such graphs. These algorithms require the specification of parameters that may drastically affect the results. In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL, Restricted Neighborhood Search Clustering (RNSC, Super Paramagnetic Clustering (SPC, and Molecular Complex Detection (MCODE. Results A test graph was built on the basis of 220 complexes annotated in the MIPS database. To evaluate the robustness to false positives and false negatives, we derived 41 altered graphs by randomly removing edges from or adding edges to the test graph in various proportions. Each clustering algorithm was applied to these graphs with various parameter settings, and the clusters were compared with the annotated complexes. We analyzed the sensitivity of the algorithms to the parameters and determined their optimal parameter values. We also evaluated their robustness to alterations of the test graph. We then applied the four algorithms to six graphs obtained from high-throughput experiments and compared the resulting clusters with the annotated complexes. Conclusion This
Network clustering analysis using mixture exponential-family random graph models and its application in genetic interaction data.

Science.gov (United States)

Wang, Yishu; Zhao, Hongyu; Deng, Minghua; Fang, Huaying; Yang, Dejie

2017-08-24

Epistatic miniarrary profile (EMAP) studies have enabled the mapping of large-scale genetic interaction networks and generated large amounts of data in model organisms. It provides an incredible set of molecular tools and advanced technologies that should be efficiently understanding the relationship between the genotypes and phenotypes of individuals. However, the network information gained from EMAP cannot be fully exploited using the traditional statistical network models. Because the genetic network is always heterogeneous, for example, the network structure features for one subset of nodes are different from those of the left nodes. Exponentialfamily random graph models (ERGMs) are a family of statistical models, which provide a principled and flexible way to describe the structural features (e.g. the density, centrality and assortativity) of an observed network. However, the single ERGM is not enough to capture this heterogeneity of networks. In this paper, we consider a mixture ERGM (MixtureEGRM) networks, which model a network with several communities, where each community is described by a single EGRM.
Thermodynamic and kinetic approaches for evaluation of monoclonal antibody - Lipoprotein interactions.

Science.gov (United States)

Multia, Evgen; Sirén, Heli; Andersson, Karl; Samuelsson, Jörgen; Forssén, Patrik; Fornstedt, Torgny; Öörni, Katariina; Jauhiainen, Matti; Riekkola, Marja-Liisa

2017-02-01

Two complementary instrumental techniques were used, and the data generated was processed with advanced numerical tools to investigate the interactions between anti-human apoB-100 monoclonal antibody (anti-apoB-100 Mab) and apoB-100 containing lipoproteins. Partial Filling Affinity Capillary Electrophoresis (PF-ACE) combined with Adsorption Energy Distribution (AED) calculations provided information on the heterogeneity of the interactions without any a priori model assumptions. The AED calculations evidenced a homogenous binding site distribution for the interactions. Quartz Crystal Microbalance (QCM) studies were used to evaluate thermodynamics and kinetics of the Low-Density Lipoprotein (LDL) and anti-apoB-100 Mab interactions. High affinity and selectivity were observed, and the emerging data sets were analysed with so called Interaction Maps. In thermodynamic studies, the interaction between LDL and anti-apoB-100 Mab was found to be predominantly enthalpy driven. Both techniques were also used to study antibody interactions with Intermediate-Density (IDL) and Very Low-Density (VLDL) Lipoproteins. By screening affinity constants for IDL-VLDL sample in a single injection we were able to distinguish affinity constants for both subpopulations using the numerical Interaction Map tool. Copyright © 2016 Elsevier Inc. All rights reserved.
Simplified Human-Robot Interaction: Modeling and Evaluation

Directory of Open Access Journals (Sweden)

Balazs Daniel

2013-10-01

Full Text Available In this paper a novel concept of human-robot interaction (HRI modeling is proposed. Including factors like trust in automation, situational awareness, expertise and expectations a new user experience framework is formed for industrial robots. Service Oriented Robot Operation, proposed in a previous paper, creates an abstract level in HRI and it is also included in the framework. This concept is evaluated with exhaustive tests. Results prove that significant improvement in task execution may be achieved and the new system is more usable for operators with less experience with robotics; personnel specific for small and medium enterprises (SMEs.
SecondLife as an Evaluation Platform for Multiagent Systems Featuring Social Interactions

DEFF Research Database (Denmark)

Rehm, Matthias; Rosina, Peter

2008-01-01

In this paper we propose to use SecondLife as an evaluation environment for multiagent systems that model social group dynamics and social interactions. To this end we developed a control interface for NPCs in SecondLife that allows for running supervised or unsupervised long-term evaluations. Thus...
Associations of Polymorphisms in WNT9B and PBX1 with Mayer-Rokitansky-Kuster-Hauser Syndrome in Chinese Han.

Directory of Open Access Journals (Sweden)

Wenqing Ma

Full Text Available Mayer-Rokitansky-Küster-Hauser (MRKH syndrome is a rare syndrome that is characterized by congenital aplasia of the uterus and the upper portion (2/3 of the vagina. Previous attempts to identify causal mutations of MRKH syndrome have primarily resulted in negative outcomes. We investigated whether these reported variants are associated with MRKH syndrome (types I and II in a relatively large sample size of Chinese Han patients, and whether any gene-gene epistatic interactions exist among these variants.This study included 182 unrelated Chinese women with MRKH syndrome (155 with type I and 27 with type II and 228 randomized female controls. Seventeen candidate loci in the AMH, PBX1, WNT4, WNT7A, WNT9B, HOXA10, HOXA11, LHXA1 and GALT genes were genotyped using the Sequenom MassARRAY iPLEX platform. Single-marker association, additive effects and multifactor interactions were investigated.The gene frequency distributions of MRKH type 1 and type 2 were similar. Rs34072914 in WNT9B was found to be associated with MRKH syndrome (P = 0.024, OR = 2.65, 95%CI = 1.14-6.17. The dominant models of rs34072914 and rs2275558 in WNT9B and PBX1, respectively, were significantly associated with MRKH syndrome risk in the Chinese Han patients. Additive gene-gene interaction analyses indicated a significant synergetic interaction between WNT9B and PBX1 (RERI = 1.397, AP = 0.493, SI = 4.204. Multifactor dimensionality reduction (MDR analysis revealed novel dimensional epistatic four-gene effects (AMH, PBX1, WNT7A and WNT9B in MRKH syndrome.This association study successfully identified two susceptibility SNPs (WNT9B and PBX1 associated with MRKH syndrome risk, both separately and interactively. The discovery of a four-gene epistatic effect (AMH, PBX1, WNT7A and WNT9B in MRKH syndrome provides novel information for the elucidation of the genetic mechanism underlying the etiology of MRKH syndrome.
Dissecting quantitative trait loci for boron efficiency across multiple environments in Brassica napus.

Directory of Open Access Journals (Sweden)

Zunkang Zhao

Full Text Available High yield is the most important goal in crop breeding, and boron (B is an essential micronutrient for plants. However, B deficiency, leading to yield decreases, is an agricultural problem worldwide. Brassica napus is one of the most sensitive crops to B deficiency, and considerable genotypic variation exists among different cultivars in response to B deficiency. To dissect the genetic basis of tolerance to B deficiency in B. napus, we carried out QTL analysis for seed yield and yield-related traits under low and normal B conditions using the double haploid population (TNDH by two-year and the BQDH population by three-year field trials. In total, 80 putative QTLs and 42 epistatic interactions for seed yield, plant height, branch number, pod number, seed number, seed weight and B efficiency coefficient (BEC were identified under low and normal B conditions, singly explaining 4.15-23.16% and 0.53-14.38% of the phenotypic variation. An additive effect of putative QTLs was a more important controlling factor than the additive-additive effect of epistatic interactions. Four QTL-by-environment interactions and 7 interactions between epistatic interactions and the environment contributed to 1.27-4.95% and 1.17-3.68% of the phenotypic variation, respectively. The chromosome region on A2 of SYLB-A2 for seed yield under low B condition and BEC-A2 for BEC in the two populations was equivalent to the region of a reported major QTL, BE1. The B. napus homologous genes of Bra020592 and Bra020595 mapped to the A2 region and were speculated to be candidate genes for B efficiency. These findings reveal the complex genetic basis of B efficiency in B. napus. They provide a basis for the fine mapping and cloning of the B efficiency genes and for breeding B-efficient cultivars by marker-assisted selection (MAS.
Quantitative Trait Locus Analysis of seed germination and seedling vigour in Brassica rapa reveals QTL hotspots and epistatic interactions

NARCIS (Netherlands)

Basnet, R.K.; Duwal, A.; Tiwari, D.N.; Xiao, D.; Monakhos, S.; Bucher, J.; Visser, R.G.F.; Groot, S.P.C.; Bonnema, A.B.; Maliepaard, C.A.

2015-01-01

The genetic basis of seed germination and seedling vigour is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded
[An ADAA model and its analysis method for agronomic traits based on the double-cross mating design].

Science.gov (United States)

Xu, Z C; Zhu, J

2000-01-01

According to the double-cross mating design and using principles of Cockerham's general genetic model, a genetic model with additive, dominance and epistatic effects (ADAA model) was proposed for the analysis of agronomic traits. Components of genetic effects were derived for different generations. Monte Carlo simulation was conducted for analyzing the ADAA model and its reduced AD model by using different generations. It was indicated that genetic variance components could be estimated without bias by MINQUE(1) method and genetic effects could be predicted effectively by AUP method; at least three generations (including parent, F1 of single cross and F1 of double-cross) were necessary for analyzing the ADAA model and only two generations (including parent and F1 of double-cross) were enough for the reduced AD model. When epistatic effects were taken into account, a new approach for predicting the heterosis of agronomic traits of double-crosses was given on the basis of unbiased prediction of genotypic merits of parents and their crosses. In addition, genotype x environment interaction effects and interaction heterosis due to G x E interaction were discussed briefly.
Microarrays for the evaluation of cell-biomaterial surface interactions

Science.gov (United States)

Thissen, H.; Johnson, G.; McFarland, G.; Verbiest, B. C. H.; Gengenbach, T.; Voelcker, N. H.

2007-01-01

The evaluation of cell-material surface interactions is important for the design of novel biomaterials which are used in a variety of biomedical applications. While traditional in vitro test methods have routinely used samples of relatively large size, microarrays representing different biomaterials offer many advantages, including high throughput and reduced sample handling. Here, we describe the simultaneous cell-based testing of matrices of polymeric biomaterials, arrayed on glass slides with a low cell-attachment background coating. Arrays were constructed using a microarray robot at 6 fold redundancy with solid pins having a diameter of 375 Î¼m. Printed solutions contained at least one monomer, an initiator and a bifunctional crosslinker. After subsequent UV polymerisation, the arrays were washed and characterised by X-ray photoelectron spectroscopy. Cell culture experiments were carried out over 24 hours using HeLa cells. After labelling with CellTracker Â® Green for the final hour of incubation and subsequent fixation, the arrays were scanned. In addition, individual spots were also viewed by fluorescence microscopy. The evaluation of cell-surface interactions in high-throughput assays as demonstrated here is a key enabling technology for the effective development of future biomaterials.
Role of polymerase η in mitochondrial mutagenesis of Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Chatterjee, Nimrat; Pabla, Ritu [Dept. of Cell Biology and Anatomy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States); Siede, Wolfram, E-mail: wolfram.siede@unthsc.edu [Dept. of Cell Biology and Anatomy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States)

2013-02-08

Highlights: ► DNA polymerase η is detectable in mitochondria of budding yeast. ► Pol η reduces UV-induced mitochondrial base pair substitutions and frameshifts. ► For UV-induced base pair substitutions, Pol η and Pol ζ interact epistatically. -- Abstract: DNA polymerase η mostly catalyzes an error-free bypass of the most frequent UV lesions, pyrimidine dimers of the cyclobutane-type. In addition to its nuclear localization, we show here for the first time its mitochondrial localization in budding yeast. In mitochondria, this polymerase improves bypass replication fidelity opposite UV damage as shown in base pair substitution and frameshift assays. For base pair substitutions, polymerase η appears to be related in function and epistatic to DNA polymerase ζ which, however, plays the opposite role in the nucleus.
Reliability evaluation of containments including soil-structure interaction

International Nuclear Information System (INIS)

Pires, J.; Hwang, H.; Reich, M.

1985-12-01

Soil-structure interaction effects on the reliability assessment of containment structures are examined. The probability-based method for reliability evaluation of nuclear structures developed at Brookhaven National Laboratory is extended to include soil-structure interaction effects. In this method, reliability of structures is expressed in terms of limit state probabilities. Furthermore, random vibration theory is utilized to calculate limit state probabilities under random seismic loads. Earthquake ground motion is modeled by a segment of a zero-mean, stationary, filtered Gaussian white noise random process, represented by its power spectrum. All possible seismic hazards at a site, represented by a hazard curve, are also included in the analysis. The soil-foundation system is represented by a rigid surface foundation on an elastic halfspace. Random and other uncertainties in the strength properties of the structure, in the stiffness and internal damping of the soil, are also included in the analysis. Finally, a realistic reinforced concrete containment is analyzed to demonstrate the application of the method. For this containment, the soil-structure interaction effects on; (1) limit state probabilities, (2) structural fragility curves, (3) floor response spectra with probabilistic content, and (4) correlation coefficients for total acceleration response at specified structural locations, are examined in detail. 25 refs., 21 figs., 12 tabs

Identification of QTLs with main, epistatic and QTL by environment ...

Indian Academy of Sciences (India)

interaction effects for seed shape and hundred-seed weight in soybean ... worldwide. It provides about 69 and 30% of dietary protein ... as main component of plants is affected by seed shape. ... In this analysis, in 2010–2012, seed shape and.
Exploring Action Research as an Approach to Interactive (Participatory) Evaluation

Science.gov (United States)

Chaudary, Imran Anjum; Imran, Shahida

2012-01-01

This investigation seeks to understand "action research" as an approach to "interactive form of evaluation". The first half of the investigation illuminates the approach with the help of the selective body of literature and the second half draws attention to its application in the field with the help of an authentic evaluation…
Roles of biomarkers in evaluating interactions among mixtures of lead, cadmium and arsenic

International Nuclear Information System (INIS)

Wang Gensheng; Fowler, Bruce A.

2008-01-01

Human exposure to environmental chemicals is most correctly characterized as exposure to mixtures of these agents. The metals/metalloids, lead (Pb), cadmium (Cd), and arsenic (As), are among the leading toxic agents detected in the environment. Exposure to these elements, particularly at chronic low dose levels, is still a major public health concern. Concurrent exposure to Pb, Cd, or As may produce additive or synergistic interactions or even new effects that are not seen in single component exposures. Evaluating these interactions on a mechanistic basis is essential for risk assessment and management of metal/metalloid mixtures. This paper will review a number of individual studies that addressed interactions of these metals/metalloids in both experimental and human exposure studies with particular emphasis on biomarkers. In general, co-exposure to metal/metalloid mixtures produced more severe effects at both relatively high dose and low dose levels in a biomarker-specific manner. These effects were found to be mediated by dose, duration of exposure and genetic factors. While traditional endpoints, such as morphological changes and biochemical parameters for target organ toxicity, were effective measures for evaluating the toxicity of high dose metal/metalloid mixtures, biomarkers for oxidative stress, altered heme biosynthesis parameters, and stress proteins showed clear responses in evaluating toxicity of low dose metal/metalloid mixtures. Metallothionein, heat shock proteins, and glutathione are involved in regulating interactive effects of metal/metalloid mixtures at low dose levels. These findings suggest that further studies on interactions of these metal/metalloid mixtures utilizing biomarker endpoints are highly warranted
Genetic Analysis of Reduced γ-Tocopherol Content in Ethiopian Mustard Seeds.

Science.gov (United States)

García-Navarro, Elena; Fernández-Martínez, José M; Pérez-Vich, Begoña; Velasco, Leonardo

2016-01-01

Ethiopian mustard (Brassica carinata A. Braun) line BCT-6, with reduced γ-tocopherol content in the seeds, has been previously developed. The objective of this research was to conduct a genetic analysis of seed tocopherols in this line. BCT-6 was crossed with the conventional line C-101 and the F1, F2, and BC plant generations were analyzed. Generation mean analysis using individual scaling tests indicated that reduced γ-tocopherol content fitted an additive-dominant genetic model with predominance of additive effects and absence of epistatic interactions. This was confirmed through a joint scaling test and additional testing of the goodness of fit of the model. Conversely, epistatic interactions were identified for total tocopherol content. Estimation of the minimum number of genes suggested that both γ- and total tocopherol content may be controlled by two genes. A positive correlation between total tocopherol content and the proportion of γ-tocopherol was identified in the F2 generation. Additional research on the feasibility of developing germplasm with high tocopherol content and reduced concentration of γ-tocopherol is required.
Genetic Analysis of Reduced γ-Tocopherol Content in Ethiopian Mustard Seeds

Directory of Open Access Journals (Sweden)

Elena García-Navarro

2016-01-01

Full Text Available Ethiopian mustard (Brassica carinata A. Braun line BCT-6, with reduced γ-tocopherol content in the seeds, has been previously developed. The objective of this research was to conduct a genetic analysis of seed tocopherols in this line. BCT-6 was crossed with the conventional line C-101 and the F1, F2, and BC plant generations were analyzed. Generation mean analysis using individual scaling tests indicated that reduced γ-tocopherol content fitted an additive-dominant genetic model with predominance of additive effects and absence of epistatic interactions. This was confirmed through a joint scaling test and additional testing of the goodness of fit of the model. Conversely, epistatic interactions were identified for total tocopherol content. Estimation of the minimum number of genes suggested that both γ- and total tocopherol content may be controlled by two genes. A positive correlation between total tocopherol content and the proportion of γ-tocopherol was identified in the F2 generation. Additional research on the feasibility of developing germplasm with high tocopherol content and reduced concentration of γ-tocopherol is required.
Detection of epistatic effects with logic regression and a classical linear regression model.

Science.gov (United States)

Malina, Magdalena; Ickstadt, Katja; Schwender, Holger; Posch, Martin; Bogdan, Małgorzata

2014-02-01

To locate multiple interacting quantitative trait loci (QTL) influencing a trait of interest within experimental populations, usually methods as the Cockerham's model are applied. Within this framework, interactions are understood as the part of the joined effect of several genes which cannot be explained as the sum of their additive effects. However, if a change in the phenotype (as disease) is caused by Boolean combinations of genotypes of several QTLs, this Cockerham's approach is often not capable to identify them properly. To detect such interactions more efficiently, we propose a logic regression framework. Even though with the logic regression approach a larger number of models has to be considered (requiring more stringent multiple testing correction) the efficient representation of higher order logic interactions in logic regression models leads to a significant increase of power to detect such interactions as compared to a Cockerham's approach. The increase in power is demonstrated analytically for a simple two-way interaction model and illustrated in more complex settings with simulation study and real data analysis.
Evaluation of virtual environment as a form of interactive resuscitation exam

Science.gov (United States)

Leszczyński, Piotr; Charuta, Anna; Kołodziejczak, Barbara; Roszak, Magdalena

2017-10-01

There is scientific evidence confirming the effectiveness of e-learning within resuscitation, however, there is not enough research on modern examination techniques within the scope. The aim of the pilot research is to compare the exam results in the field of Advanced Life Support in a traditional (paper) and interactive (computer) form as well as to evaluate satisfaction of the participants. A survey was conducted which meant to evaluate satisfaction of exam participants. Statistical analysis of the collected data was conducted at a significance level of α = 0.05 using STATISTICS v. 12. Final results of the traditional exam (67.5% ± 15.8%) differed significantly (p test. Significant differences between the results of a traditional test and the one supported by Computer Based Learning system showed the possibility of achieving a more detailed competence verification in the field of resuscitation thanks to interactive solutions.
Order effect in interactive information retrieval evaluation

DEFF Research Database (Denmark)

Clemmensen, Melanie Landvad; Borlund, Pia

2016-01-01

, and the good-subject effect shed light on how and why order effect may affect test participants’ IR system interaction and search behaviour. Research limitations/implications – Insight about order effect has implications for test design of IIR studies and hence the knowledge base generated on the basis...... of such studies. Due to the limited sample of 20 test participants (Library and Information Science (LIS) students) inference statistics is not applicable; hence conclusions can be drawn from this sample of test participants only. Originality/value – Only few studies in LIS focus on order effect and none from...... the perspective of IIR. Keywords Evaluation, Research methods, Information retrieval, User studies, Searching, Information searches...
Predictable Phenotypes of Antibiotic Resistance Mutations.

Science.gov (United States)

Knopp, M; Andersson, D I

2018-05-15

Antibiotic-resistant bacteria represent a major threat to our ability to treat bacterial infections. Two factors that determine the evolutionary success of antibiotic resistance mutations are their impact on resistance level and the fitness cost. Recent studies suggest that resistance mutations commonly show epistatic interactions, which would complicate predictions of their stability in bacterial populations. We analyzed 13 different chromosomal resistance mutations and 10 host strains of Salmonella enterica and Escherichia coli to address two main questions. (i) Are there epistatic interactions between different chromosomal resistance mutations? (ii) How does the strain background and genetic distance influence the effect of chromosomal resistance mutations on resistance and fitness? Our results show that the effects of combined resistance mutations on resistance and fitness are largely predictable and that epistasis remains rare even when up to four mutations were combined. Furthermore, a majority of the mutations, especially target alteration mutations, demonstrate strain-independent phenotypes across different species. This study extends our understanding of epistasis among resistance mutations and shows that interactions between different resistance mutations are often predictable from the characteristics of the individual mutations. IMPORTANCE The spread of antibiotic-resistant bacteria imposes an urgent threat to public health. The ability to forecast the evolutionary success of resistant mutants would help to combat dissemination of antibiotic resistance. Previous studies have shown that the phenotypic effects (fitness and resistance level) of resistance mutations can vary substantially depending on the genetic context in which they occur. We conducted a broad screen using many different resistance mutations and host strains to identify potential epistatic interactions between various types of resistance mutations and to determine the effect of strain
Evaluating the Effects of Immersive Embodied Interaction on Cognition in Virtual Reality

Science.gov (United States)

Parmar, Dhaval

Virtual reality is on its advent of becoming mainstream household technology, as technologies such as head-mounted displays, trackers, and interaction devices are becoming affordable and easily available. Virtual reality (VR) has immense potential in enhancing the fields of education and training, and its power can be used to spark interest and enthusiasm among learners. It is, therefore, imperative to evaluate the risks and benefits that immersive virtual reality poses to the field of education. Research suggests that learning is an embodied process. Learning depends on grounded aspects of the body including action, perception, and interactions with the environment. This research aims to study if immersive embodiment through the means of virtual reality facilitates embodied cognition. A pedagogical VR solution which takes advantage of embodied cognition can lead to enhanced learning benefits. Towards achieving this goal, this research presents a linear continuum for immersive embodied interaction within virtual reality. This research evaluates the effects of three levels of immersive embodied interactions on cognitive thinking, presence, usability, and satisfaction among users in the fields of science, technology, engineering, and mathematics (STEM) education. Results from the presented experiments show that immersive virtual reality is greatly effective in knowledge acquisition and retention, and highly enhances user satisfaction, interest and enthusiasm. Users experience high levels of presence and are profoundly engaged in the learning activities within the immersive virtual environments. The studies presented in this research evaluate pedagogical VR software to train and motivate students in STEM education, and provide an empirical analysis comparing desktop VR (DVR), immersive VR (IVR), and immersive embodied VR (IEVR) conditions for learning. This research also proposes a fully immersive embodied interaction metaphor (IEIVR) for learning of computational
Evaluating display fidelity and interaction fidelity in a virtual reality game.

Science.gov (United States)

McMahan, Ryan P; Bowman, Doug A; Zielinski, David J; Brady, Rachael B

2012-04-01

In recent years, consumers have witnessed a technological revolution that has delivered more-realistic experiences in their own homes through high-definition, stereoscopic televisions and natural, gesture-based video game consoles. Although these experiences are more realistic, offering higher levels of fidelity, it is not clear how the increased display and interaction aspects of fidelity impact the user experience. Since immersive virtual reality (VR) allows us to achieve very high levels of fidelity, we designed and conducted a study that used a six-sided CAVE to evaluate display fidelity and interaction fidelity independently, at extremely high and low levels, for a VR first-person shooter (FPS) game. Our goal was to gain a better understanding of the effects of fidelity on the user in a complex, performance-intensive context. The results of our study indicate that both display and interaction fidelity significantly affect strategy and performance, as well as subjective judgments of presence, engagement, and usability. In particular, performance results were strongly in favor of two conditions: low-display, low-interaction fidelity (representative of traditional FPS games) and high-display, high-interaction fidelity (similar to the real world).
Subjective evaluation of physical and mental workload interactions across different muscle groups.

Science.gov (United States)

Mehta, Ranjana K; Agnew, Michael J

2015-01-01

Both physical and mental demands, and their interactions, have been shown to increase biomechanical loading and physiological reactivity as well as impair task performance. Because these interactions have shown to be muscle-dependent, the aim of this study was to determine the sensitivity of the NASA Task Load Index (NASA TLX) and Ratings of Perceived Exertion (RPE) to evaluate physical and mental workload during muscle-specific tasks. Twenty-four participants performed upper extremity and low back exertions at three physical workload levels in the absence and presence of a mental stressor. Outcome measures included RPE and NASA TLX (six sub-scales) ratings. The findings indicate that while both RPEs and NASA TLX ratings were sensitive to muscle-specific changes in physical demand, only an additional mental stressor and its interaction with either physical demand or muscle groups influenced the effort sub-scale and overall workload scores of the NASA TLX. While additional investigations in actual work settings are warranted, the NASA TLX shows promise in evaluating perceived workload that is sensitive not only to physical and mental demands but also sensitive in determining workload for tasks that employ different muscle groups.
GIS-Based Evaluation of Spatial Interactions by Geographic Disproportionality of Industrial Diversity

Directory of Open Access Journals (Sweden)

Jemyung Lee

2017-11-01

Full Text Available Diversity of regional industry is regarded as a key factor for regional development, as it has a positive relationship with economic stability, which attracts population. This paper focuses on how the spatial imbalance of industrial diversity contributes to the population change caused by inter-regional migration. This paper introduces a spatial interaction model for the Geographic Information System (GIS-based simulation of the spatial interactions to evaluate the demographic attraction force. The proposed model adopts the notions of gravity, entropy, and virtual work. An industrial classification by profit level is introduced and its diversity is quantified with the entropy of information theory. The introduced model is applied to the cases of 207 regions in South Korea. Spatial interactions are simulated with an optimized model and their resultant forces, the demographic attraction forces, are compared with observed net migration for verification. The results show that the evaluated attraction forces from industrial diversity have a very significant, positive, and moderate relationship with net migration, while other conventional factors of industry, population, economy, and the job market do not. This paper concludes that the geographical quality of industrial diversity has positive and significant effects on population change by migration.
Survival dimensionality reduction (SDR: development and clinical application of an innovative approach to detect epistasis in presence of right-censored data

Directory of Open Access Journals (Sweden)

Beretta Lorenzo

2010-08-01

Full Text Available Abstract Background Epistasis is recognized as a fundamental part of the genetic architecture of individuals. Several computational approaches have been developed to model gene-gene interactions in case-control studies, however, none of them is suitable for time-dependent analysis. Herein we introduce the Survival Dimensionality Reduction (SDR algorithm, a non-parametric method specifically designed to detect epistasis in lifetime datasets. Results The algorithm requires neither specification about the underlying survival distribution nor about the underlying interaction model and proved satisfactorily powerful to detect a set of causative genes in synthetic epistatic lifetime datasets with a limited number of samples and high degree of right-censorship (up to 70%. The SDR method was then applied to a series of 386 Dutch patients with active rheumatoid arthritis that were treated with anti-TNF biological agents. Among a set of 39 candidate genes, none of which showed a detectable marginal effect on anti-TNF responses, the SDR algorithm did find that the rs1801274 SNP in the FcγRIIa gene and the rs10954213 SNP in the IRF5 gene non-linearly interact to predict clinical remission after anti-TNF biologicals. Conclusions Simulation studies and application in a real-world setting support the capability of the SDR algorithm to model epistatic interactions in candidate-genes studies in presence of right-censored data. Availability: http://sourceforge.net/projects/sdrproject/
TCS1, a Microtubule-Binding Protein, Interacts with KCBP/ZWICHEL to Regulate Trichome Cell Shape in Arabidopsis thaliana.

Directory of Open Access Journals (Sweden)

Liangliang Chen

2016-10-01

Full Text Available How cell shape is controlled is a fundamental question in developmental biology, but the genetic and molecular mechanisms that determine cell shape are largely unknown. Arabidopsis trichomes have been used as a good model system to investigate cell shape at the single-cell level. Here we describe the trichome cell shape 1 (tcs1 mutants with the reduced trichome branch number in Arabidopsis. TCS1 encodes a coiled-coil domain-containing protein. Pharmacological analyses and observations of microtubule dynamics show that TCS1 influences the stability of microtubules. Biochemical analyses and live-cell imaging indicate that TCS1 binds to microtubules and promotes the assembly of microtubules. Further results reveal that TCS1 physically associates with KCBP/ZWICHEL, a microtubule motor involved in the regulation of trichome branch number. Genetic analyses indicate that kcbp/zwi is epistatic to tcs1 with respect to trichome branch number. Thus, our findings define a novel genetic and molecular mechanism by which TCS1 interacts with KCBP to regulate trichome cell shape by influencing the stability of microtubules.
On the practice of ignoring center-patient interactions in evaluating hospital performance.

Science.gov (United States)

Varewyck, Machteld; Vansteelandt, Stijn; Eriksson, Marie; Goetghebeur, Els

2016-01-30

We evaluate the performance of medical centers based on a continuous or binary patient outcome (e.g., 30-day mortality). Common practice adjusts for differences in patient mix through outcome regression models, which include patient-specific baseline covariates (e.g., age and disease stage) besides center effects. Because a large number of centers may need to be evaluated, the typical model postulates that the effect of a center on outcome is constant over patient characteristics. This may be violated, for example, when some centers are specialized in children or geriatric patients. Including interactions between certain patient characteristics and the many fixed center effects in the model increases the risk for overfitting, however, and could imply a loss of power for detecting centers with deviating mortality. Therefore, we assess how the common practice of ignoring such interactions impacts the bias and precision of directly and indirectly standardized risks. The reassuring conclusion is that the common practice of working with the main effects of a center has minor impact on hospital evaluation, unless some centers actually perform substantially better on a specific group of patients and there is strong confounding through the corresponding patient characteristic. The bias is then driven by an interplay of the relative center size, the overlap between covariate distributions, and the magnitude of the interaction effect. Interestingly, the bias on indirectly standardized risks is smaller than on directly standardized risks. We illustrate our findings by simulation and in an analysis of 30-day mortality on Riksstroke. © 2015 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd.
Gene X Environment Interactions in Autism Spectrum Disorders: Role of Epigenetic Mechanisms

Directory of Open Access Journals (Sweden)

Sylvie eTordjman

2014-08-01

Full Text Available Several studies support currently the hypothesis that autism etiology is based on a polygenic and epistatic model. However, despite advances in epidemiological, molecular and clinical genetics, the genetic risk factors remain difficult to identify, with the exception of a few chromosomal disorders and several single gene disorders associated with an increased risk for autism. Furthermore, several studies suggest a role of environmental factors in autism spectrum disorders (ASD. First, arguments for a genetic contribution to autism, based on updated family and twin studies, are examined. Second, a review of possible prenatal, perinatal and postnatal environmental risk factors for ASD are presented. Then, the hypotheses are discussed concerning the underlying mechanisms related to a role of environmental factors in the development of ASD in association with genetic factors. In particular, epigenetics as a candidate biological mechanism for gene X environment interactions is considered and the possible role of epigenetic mechanisms reported in genetic disorders associated with ASD is discussed. Furthermore, the example of in utero exposure to valproate provides a good illustration of epigenetic mechanisms involved in ASD and innovative therapeutic strategies. Epigenetic remodeling by environmental factors opens new perspectives for a better understanding, prevention and early therapeutic intervention of ASD.
RAD9, RAD17; RAD24, and RAD53 control one pathway of resistance to γ irradiation in Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Koltovaya, N.A.; Nikulushkina, Yu.V.; Roshina, M.P.; Devin, A.B.

2009-01-01

Mechanisms for the genetic control of the cell cycle transition (checkpoint control) have been studied in more detail in yeast Saccharomyces cerevisiae. To clarify tho role of the RAD9, RAD17, RAD24, and RAD53 checkpoint genes in cell radioresistance, diploid double mutants were analyzed for cell sensitivity to ionizing radiation. All mutations in combination with rad9Δ were shown to manifest the epistatic type of interaction. Our results suggest that the RAD9, RAD17, RAD24, and RAD53 checkpoint genes belong to a single epistasis group called the RAD9 group and participate in the same pathway. RAD9 and RAD53 have a positive effect on sensitivity to γ irradiation, whereas RAD17 and RAD24 have a negative effect. For haploid interactions between mutations may differ in the case of γ or UV irradiation, mutations - for example, rad9Δ and rad24Δ - were shown to have an additive effect in the first case and epistatic - in the second. The analyzed genes can also participate in minor mechanisms of radioresistance that are relatively independent of the above major mechanism
C. elegans ring finger protein RNF-113 is involved in interstrand DNA crosslink repair and interacts with a RAD51C homolog.

Directory of Open Access Journals (Sweden)

Hyojin Lee

Full Text Available The Fanconi anemia (FA pathway recognizes interstrand DNA crosslinks (ICLs and contributes to their conversion into double-strand DNA breaks, which can be repaired by homologous recombination. Seven orthologs of the 15 proteins associated with Fanconi anemia are functionally conserved in the model organism C. elegans. Here we report that RNF-113, a ubiquitin ligase, is required for RAD-51 focus formation after inducing ICLs in C. elegans. However, the formation of foci of RPA-1 or FCD-2/FANCD2 in the FA pathway was not affected by depletion of RNF-113. Nevertheless, the RPA-1 foci formed did not disappear with time in the depleted worms, implying serious defects in ICL repair. As a result, RNF-113 depletion increased embryonic lethality after ICL treatment in wild-type worms, but it did not increase the ICL-induced lethality of rfs-1/rad51C mutants. In addition, the persistence of RPA-1 foci was suppressed in doubly-deficient rnf-113;rfs-1 worms, suggesting that there is an epistatic interaction between the two genes. These results lead us to suggest that RNF-113 and RFS-1 interact to promote the displacement of RPA-1 by RAD-51 on single-stranded DNA derived from ICLs.
A Bone-Implant Interaction Mouse Model for Evaluating Molecular Mechanism of Biomaterials/Bone Interaction.

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Liu, Wenlong; Dan, Xiuli; Wang, Ting; Lu, William W; Pan, Haobo

2016-11-01

The development of an optimal animal model that could provide fast assessments of the interaction between bone and orthopedic implants is essential for both preclinical and theoretical researches in the design of novel biomaterials. Compared with other animal models, mice have superiority in accessing the well-developed transgenic modification techniques (e.g., cell tracing, knockoff, knockin, and so on), which serve as powerful tools in studying molecular mechanisms. In this study, we introduced the establishment of a mouse model, which was specifically tailored for the assessment of bone-implant interaction in a load-bearing bone marrow microenvironment and could potentially allow the molecular mechanism study of biomaterials by using transgenic technologies. The detailed microsurgery procedures for developing a bone defect (Φ = 0.8 mm) at the metaphysis region of the mouse femur were recorded. According to our results, the osteoconductive and osseointegrative properties of a well-studied 45S5 bioactive glass were confirmed by utilizing our mouse model, verifying the reliability of this model. The feasibility and reliability of the present model were further checked by using other materials as objects of study. Furthermore, our results indicated that this animal model provided a more homogeneous tissue-implant interacting surface than the rat at the early stage of implantation and this is quite meaningful for conducting quantitative analysis. The availability of transgenic techniques to mechanism study of biomaterials was further testified by establishing our model on Nestin-GFP transgenic mice. Intriguingly, the distribution of Nestin + cells was demonstrated to be recruited to the surface of 45S5 glass as early as 3 days postsurgery, indicating that Nestin + lineage stem cells may participate in the subsequent regeneration process. In summary, the bone-implant interaction mouse model could serve as a potential candidate to evaluate the early stage tissue

Interaction between 5-HTTLPR and BDNF Val66Met polymorphisms on HPA axis reactivity in preschoolers.

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Dougherty, Lea R; Klein, Daniel N; Congdon, Eliza; Canli, Turhan; Hayden, Elizabeth P

2010-02-01

This study examined whether the interaction between the serotonin transporter promoter region (5-HTTLPR) and brain-derived neurotrophic factor (BDNF) Val66Met polymorphisms was associated with hypothalamic-pituitary-adrenal (HPA) axis reactivity to stress. A community sample of 144 preschool-aged children was genotyped and exposed to stress-inducing laboratory tasks. Salivary cortisol was obtained at four time points during a standardized laboratory assessment before and after stressors involving separation from a parent and frustrating tasks. Children homozygous for the short-5-HTTLPR allele and carrying the Met-BDNF allele evidenced a significantly lower initial level of cortisol, followed by a positive increase in cortisol in response to the laboratory stressors. In contrast, children who were homozygous for the short-5-HTTLPR and the Val-BDNF alleles evidenced a greater decline in cortisol in response to the laboratory stressors. Findings indicated that the BDNF gene moderated the association between 5-HTTLPR and children's biological stress responses, suggesting that epistatic effects play a role in individual differences in stress regulation, and possibly genetic vulnerability to stress-related disorders. Copyright 2009 Elsevier B.V. All rights reserved.
Gene × Environment Interactions in Autism Spectrum Disorders: Role of Epigenetic Mechanisms

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Tordjman, Sylvie; Somogyi, Eszter; Coulon, Nathalie; Kermarrec, Solenn; Cohen, David; Bronsard, Guillaume; Bonnot, Olivier; Weismann-Arcache, Catherine; Botbol, Michel; Lauth, Bertrand; Ginchat, Vincent; Roubertoux, Pierre; Barburoth, Marianne; Kovess, Viviane; Geoffray, Marie-Maude; Xavier, Jean

2014-01-01

Several studies support currently the hypothesis that autism etiology is based on a polygenic and epistatic model. However, despite advances in epidemiological, molecular and clinical genetics, the genetic risk factors remain difficult to identify, with the exception of a few chromosomal disorders and several single gene disorders associated with an increased risk for autism. Furthermore, several studies suggest a role of environmental factors in autism spectrum disorders (ASD). First, arguments for a genetic contribution to autism, based on updated family and twin studies, are examined. Second, a review of possible prenatal, perinatal, and postnatal environmental risk factors for ASD are presented. Then, the hypotheses are discussed concerning the underlying mechanisms related to a role of environmental factors in the development of ASD in association with genetic factors. In particular, epigenetics as a candidate biological mechanism for gene × environment interactions is considered and the possible role of epigenetic mechanisms reported in genetic disorders associated with ASD is discussed. Furthermore, the example of in utero exposure to valproate provides a good illustration of epigenetic mechanisms involved in ASD and innovative therapeutic strategies. Epigenetic remodeling by environmental factors opens new perspectives for a better understanding, prevention, and early therapeutic intervention of ASD. PMID:25136320
An Interactive Web-Based Program for Stepfamilies: Development and Evaluation of Efficacy

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Gelatt, Vicky A.; Adler-Baeder, Francesca; Seeley, John R.

2010-01-01

This study evaluated the efficacy of a family life education program for stepfamilies that is self-administered, interactive, and web-based. The program uses behavior-modeling videos to demonstrate effective couple, parenting, and stepparenting practices. A diverse sample of 300 parents/stepparents of a child aged 11-15 years were randomized into…
Intramolecular epistasis and the evolution of a new enzymatic function.

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Sajid Noor

Full Text Available Atrazine chlorohydrolase (AtzA and its close relative melamine deaminase (TriA differ by just nine amino acid substitutions but have distinct catalytic activities. Together, they offer an informative model system to study the molecular processes that underpin the emergence of new enzymatic function. Here we have constructed the potential evolutionary trajectories between AtzA and TriA, and characterized the catalytic activities and biophysical properties of the intermediates along those trajectories. The order in which the nine amino acid substitutions that separate the enzymes could be introduced to either enzyme, while maintaining significant catalytic activity, was dictated by epistatic interactions, principally between three amino acids within the active site: namely, S331C, N328D and F84L. The mechanistic basis for the epistatic relationships is consistent with a model for the catalytic mechanisms in which protonation is required for hydrolysis of melamine, but not atrazine.
A study of the use of simulated work task situations in interactive information retrieval evaluations

DEFF Research Database (Denmark)

Borlund, Pia

2016-01-01

Purpose – The purpose of this paper is to report a study of how the test instrument of a simulated work task situation is used in empirical evaluations of interactive information retrieval (IIR) and reported in the research literature. In particular, the author is interested to learn whether....... The paper addresses the need to carefully design and tailor simulated work task situations to suit the test participants in order to obtain the intended authentic and realistic IIR under study. Keywords Interactive information retrieval study, IIR study, Test design, Simulated work task situations, Meta-evaluation...... situations in IIR evaluations. In particular, with respect to the design and creation of realistic simulated work task situations. There is a lack of tailoring of the simulated work task situations to the test participants. Likewise, the requirement to include the test participants’ personal information...
Evaluation of the total gamma-ray production cross-sections for nonelastic interaction of fast neutrons with iron nuclei

International Nuclear Information System (INIS)

Savin, M.V.; Nefedov, Yu.Ya; Livke, A.V.; Zvenigorodskij, A.G.

2001-01-01

Experimental data on the total gamma-ray production cross-sections for inelastic interaction of fast neutrons with iron nuclei were analysed. The total gamma-ray production cross-sections, grouped according to E γ , were evaluated in the neutron energy range 0.5-19 MeV. The statistical spline approximation method was used to evaluate the experimental data. Evaluated data stored in the ENDF, JENDL, BROND, and other libraries on gamma-ray production spectra and cross-sections for inelastic interaction of fast neutrons with iron nuclei, were analysed. (author)
Evaluation of pedestrian safety at intersections: A theoretical framework based on pedestrian-vehicle interaction patterns.

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Ni, Ying; Wang, Menglong; Sun, Jian; Li, Keping

2016-11-01

Pedestrians are the most vulnerable road users, and pedestrian safety has become a major research focus in recent years. Regarding the quality and quantity issues with collision data, conflict analysis using surrogate safety measures has become a useful method to study pedestrian safety. However, given the inequality between pedestrians and vehicles in encounters and the multiple interactions between pedestrians and vehicles, it is insufficient to simply use the same indicator(s) or the same way to aggregate indicators for all conditions. In addition, behavioral factors cannot be neglected. To better use information extracted from trajectories for safety evaluation and pay more attention on effects of behavioral factors, this paper develops a more sophisticated framework for pedestrian conflict analysis that takes pedestrian-vehicle interactions into consideration. A concept of three interaction patterns has been proposed for the first time, namely "hard interaction," "no interaction," and "soft-interaction." Interactions have been categorized under one of these patterns by analyzing profiles of speed and conflict indicators during the whole interactive processes. In this paper, a support vector machine (SVM) approach has been adopted to classify severity levels for a dataset including 1144 events extracted from three intersections in Shanghai, China, followed by an analysis of variable importance. The results revealed that different conflict indicators have different contributions to indicating the severity level under various interaction patterns. Therefore, it is recommended either to use specific conflict indicators or to use weighted indicator aggregation for each interaction pattern when evaluating pedestrian safety. The implementation has been carried out at the fourth crosswalk, and the results indicate that the proposed method can achieve a higher accuracy and better robustness than conventional methods. Furthermore, the method is helpful for better
Evaluating interaction energies of weakly bonded systems using the Buckingham-Hirshfeld method

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Krishtal, A.; Van Alsenoy, C.; Geerlings, P.

2014-05-01

We present the finalized Buckingham-Hirshfeld method (BHD-DFT) for the evaluation of interaction energies of non-bonded dimers with Density Functional Theory (DFT). In the method, dispersion energies are evaluated from static multipole polarizabilities, obtained on-the-fly from Coupled Perturbed Kohn-Sham calculations and partitioned into diatomic contributions using the iterative Hirshfeld partitioning method. The dispersion energy expression is distributed over four atoms and has therefore a higher delocalized character compared to the standard pairwise expressions. Additionally, full multipolar polarizability tensors are used as opposed to effective polarizabilities, allowing to retain the anisotropic character at no additional computational cost. A density dependent damping function for the BLYP, PBE, BP86, B3LYP, and PBE0 functionals has been implemented, containing two global parameters which were fitted to interaction energies and geometries of a selected number of dimers using a bi-variate RMS fit. The method is benchmarked against the S22 and S66 data sets for equilibrium geometries and the S22x5 and S66x8 data sets for interaction energies around the equilibrium geometry. Best results are achieved using the B3LYP functional with mean average deviation values of 0.30 and 0.24 kcal/mol for the S22 and S66 data sets, respectively. This situates the BHD-DFT method among the best performing dispersion inclusive DFT methods. Effect of counterpoise correction on DFT energies is discussed.
MATERNAL DEPRESSION AND ATTACHMENT: THE EVALUATION OF MOTHER-CHILD INTERACTIONS DURING FEEDING PRACTICE

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Alessandra eSantona

2015-08-01

Full Text Available Internal working models of attachment (IWM can moderate the effect of maternal depression on mother-child interactions and child development. Clinical depression pre-dating birthgiving has been found to predict incoherent and less sensitive caregiving. Dysfunctional patterns observed, included interactive modes linked to feeding behaviors which may interfere with hunger-satiation biological rhythms and the establishment of children’s autonomy and individuation. Feeding interactions between depressed mothers and their children seem to be characterized by repetitive interactive failures: children refuse food through oppositional behavior or negativity. The aim of this study was to investigate parenting skills in the context of feeding in mothers with major depression from the point of view of attachment theory. This perspective emphasises parents’ emotion, relational and affective history and personal resources. The sample consisted of 60 mother-child dyads. Mothers were divided into two groups: 30 with Major Depression and 30 without disorders. Children’s age ranged between 12 and 36 months The measures employed were the Adult Attachment Interview and the Scale for the Evaluation of Alimentary Interactions between Mothers and Children. Insecure attachment prevailed in mothers with major depression,, with differences on the Subjective Experience and State of Mind Scales. Groups also differed in maternal sensitivity, degrees of interactive
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

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Inbar Yuval

2010-07-01

Full Text Available Abstract Background Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design. Results Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 Å for all residues and 0.73 Å for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site http://bioinfo.weizmann.ac.il/hunter/ was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions. Conclusions Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.
Epistatic participation of REV1 and REV3 in the formation of UV-induced frameshift mutations in cell cycle-arrested yeast cells

Energy Technology Data Exchange (ETDEWEB)

Heidenreich, Erich [Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna (Austria)]. E-mail: erich.heidenreich@meduniwien.ac.at; Eisler, Herfried [Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna (Austria); Steinboeck, Ferdinand [Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna (Austria)

2006-01-29

Mutations arising in times of cell cycle arrest may provide a selective advantage for unicellular organisms adapting to environmental changes. For multicellular organisms, however, they may pose a serious threat, in that such mutations in somatic cells contribute to carcinogenesis and ageing. The budding yeast Saccharomyces cerevisiae presents a convenient model system for studying the incidence and the mechanisms of stationary-phase mutation in a eukaryotic organism. Having studied the emergence of frameshift mutants after several days of starvation-induced cell cycle arrest, we previously reported that all (potentially error-prone) translesion synthesis (TLS) enzymes identified in S. cerevisiae did not contribute to the basal level of spontaneous stationary-phase mutations. However, we observed that an increased frequency of stationary-phase frameshift mutations, brought about by a defective nucleotide excision repair (NER) pathway or by UV irradiation, was dependent on Rev3p, the catalytic subunit of the TLS polymerase zeta (Pol {zeta}). Employing the same two conditions, we now examined the effect of deletions of the genes coding for polymerase eta (Pol {eta}) (RAD30) and Rev1p (REV1). In a NER-deficient strain background, the increased incidence of stationary-phase mutations was only moderately influenced by a lack of Pol {eta} but completely reduced to wild type level by a knockout of the REV1 gene. UV-induced stationary-phase mutations were abundant in wild type and rad30{delta} strains, but substantially reduced in a rev1{delta} as well as a rev3{delta} strain. The similarity of the rev1{delta} and the rev3{delta} phenotype and an epistatic relationship evident from experiments with a double-deficient strain suggests a participation of Rev1p and Rev3p in the same mutagenic pathway. Based on these results, we propose that the response of cell cycle-arrested cells to an excess of exo- or endogenously induced DNA damage includes a novel replication
Evaluation for the design of experience in virtual environments: modeling breakdown of interaction and illusion.

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Marsh, T; Wright, P; Smith, S

2001-04-01

New and emerging media technologies have the potential to induce a variety of experiences in users. In this paper, it is argued that the inducement of experience presupposes that users are absorbed in the illusion created by these media. Looking to another successful visual medium, film, this paper borrows from the techniques used in "shaping experience" to hold spectators' attention in the illusion of film, and identifies what breaks the illusion/experience for spectators. This paper focuses on one medium, virtual reality (VR), and advocates a transparent or "invisible style" of interaction. We argue that transparency keeps users in the "flow" of their activities and consequently enhances experience in users. Breakdown in activities breaks the experience and subsequently provides opportunities to identify and analyze potential causes of usability problems. Adopting activity theory, we devise a model of interaction with VR--through consciousness and activity--and introduce the concept of breakdown in illusion. From this, a model of effective interaction with VR is devised and the occurrence of breakdown in interaction and illusion is identified along a continuum of engagement. Evaluation guidelines for the design of experience are proposed and applied to usability problems detected in an empirical study of a head-mounted display (HMD) VR system. This study shows that the guidelines are effective in the evaluation of VR. Finally, we look at the potential experiences that may be induced in users and propose a way to evaluate user experience in virtual environments (VEs) and other new and emerging media.
An Interactive Website to Reduce Sexual Risk Behavior: Process Evaluation of TeensTalkHealth.

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Brady, Sonya S; Sieving, Renee E; Terveen, Loren G; Rosser, B R Simon; Kodet, Amy J; Rothberg, Vienna D

2015-09-02

Different theoretical frameworks support the use of interactive websites to promote sexual health. Although several Web-based interventions have been developed to address sexual risk taking among young people, no evaluated interventions have attempted to foster behavior change through moderated interaction among a virtual network of adolescents (who remain anonymous to one another) and health professionals. The objective was to conduct a summative process evaluation of TeensTalkHealth, an interactive sexual health website designed to promote condom use and other healthy decision making in the context of romantic and sexual relationships. Evaluation data were obtained from 147 adolescents who participated in a feasibility and acceptability study. Video vignettes, teen-friendly articles, and other content served as conversation catalysts between adolescents and health educators on message boards. Adolescents' perceptions that the website encouraged condom use across a variety of relationship situations were very high. Almost 60% (54/92, 59%) of intervention participants completed two-thirds or more of requested tasks across the 4-month intervention. Adolescents reported high levels of comfort, perceived privacy, ease of website access and use, and perceived credibility of health educators. Potential strategies to enhance engagement and completion of intervention tasks during future implementations of TeensTalkHealth are discussed, including tailoring of content, periodic website chats with health educators and anonymous peers, and greater incorporation of features from popular social networking websites. TeensTalkHealth is a feasible, acceptable, and promising approach to complement and enhance existing services for youth.
Polyploidy Enhances F1 Pollen Sterility Loci Interactions That Increase Meiosis Abnormalities and Pollen Sterility in Autotetraploid Rice1[OPEN

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Wu, Jinwen; Chen, Lin; Chen, Zhixiong; Wang, Lan; Lu, Yonggen

2015-01-01

Intersubspecific autotetraploid rice (Oryza sativa ssp. indica × japonica) hybrids have greater biological and yield potentials than diploid rice. However, the low fertility of intersubspecific autotetraploid hybrids, which is largely caused by high pollen abortion rates, limits their commercial utility. To decipher the cytological and molecular mechanisms underlying allelic interactions in autotetraploid rice, we developed an autotetraploid rice hybrid that was heterozygous (SiSj) at F1 pollen sterility loci (Sa, Sb, and Sc) using near-isogenic lines. Cytological studies showed that the autotetraploid had higher percentages (>30%) of abnormal chromosome behavior and aberrant meiocytes (>50%) during meiosis than did the diploid rice hybrid control. Analysis of gene expression profiles revealed 1,888 genes that were differentially expressed between the autotetraploid and diploid hybrid lines at the meiotic stage, among which 889 and 999 were up- and down-regulated, respectively. Of the 999 down-regulated genes, 940 were associated with the combined effect of polyploidy and pollen sterility loci interactions (IPE). Gene Ontology enrichment analysis identified a prominent functional gene class consisting of seven genes related to photosystem I (Gene Ontology 0009522). Moreover, 55 meiosis-related or meiosis stage-specific genes were associated with IPE in autotetraploid rice, including Os02g0497500, which encodes a DNA repair-recombination protein, and Os02g0490000, which encodes a component of the ubiquitin-proteasome pathway. These results suggest that polyploidy enhances epistatic interactions between alleles of pollen sterility loci, thereby altering the expression profiles of important meiosis-related or meiosis stage-specific genes and resulting in high pollen sterility. PMID:26511913
A GOAL QUESTION METRIC (GQM APPROACH FOR EVALUATING INTERACTION DESIGN PATTERNS IN DRAWING GAMES FOR PRESCHOOL CHILDREN

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Dana Sulistiyo Kusumo

2017-06-01

Full Text Available In recent years, there has been an increasing interest to use smart devices’ drawing games for educational benefit. In Indonesia, our government classifies children age four to six years old as preschool children. Not all preschool children can use drawing games easily. Further, drawing games may not fulfill all Indonesia's preschool children’s drawing competencies. This research proposes to use Goal-Question Metric (GQM to investigate and evaluate interaction design patterns of preschool children in order to achieve the drawing competencies for preschool children in two drawing Android-based games: Belajar Menggambar (in English: Learn to Draw and Coret: Belajar Menggambar (in English: Scratch: Learn to Draw. We collected data from nine students of a preschool children education in a user research. The results show that GQM can assist to evaluate interaction design patterns in achieving the drawing competencies. Our approach can also yield interaction design patterns by comparing interaction design patterns in two drawing games used.
A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

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Elisa Cirillo

2017-11-01

Full Text Available Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products. Current pathway analysis software often does not support data visualization of variants in pathways as an alternate method to interpret genetic association results, and specific statistical methods for pathway analysis of SNP data are not combined with these visualization features. In this review, we first describe the visualization options of the tools that were identified by a literature review, in order to provide insight for improvements in this developing field. Tool evaluation was performed using a computational epistatic dataset of gene–gene interactions for obesity risk. Next, we report the necessity to include in these tools statistical methods designed for the pathway-based analysis with SNP data, expressly aiming to define features for more comprehensive pathway-based analysis tools. We conclude by recognizing that pathway analysis of genetic variations data requires a sophisticated combination of the most useful and informative visual aspects of the various tools evaluated.
QTL analysis of citrus tristeza virus-citradia interaction.

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Asins, M J; Bernet, G P; Ruiz, C; Cambra, M; Guerri, J; Carbonell, E A

2004-02-01

Citrus tristeza virus (CTV) has caused the death of millions of trees grafted on sour orange ( Citrus aurantium). However, this rootstock is very well adapted to the Mediterranean, semi-arid conditions. The aim of the present research is to genetically analyze the accumulation of CTV in a progeny derived from the cross between C. aurantium and Poncirus trifoliata, both resistant to CTV isolate T-346. Graft propagation of 104 hybrids was done on healthy sweet orange as a rootstock. Three months later, each rootstock was graft inoculated with two patches of infected tissue (isolate T-346). One, 2, and sometimes, 3 and 4 years after inoculation, hybrids and infected patches were tested for CTV by tissue-blot immuno-assay. Additionally, CTV multiplication was evaluated every year as the optical density of double-antibody sandwich enzyme-linked immuno-sorbent assay reactions. Linkage maps for P. trifoliata based on 63 markers, and for C. aurantium based on 157 markers, were used. Most molecular markers were microsatellites and IRAP (inter-retrotransposon amplified polymorphisms). Some analogues of resistance and expressed sequences were also included for candidate gene analysis. Resistance against CTV was analyzed as a quantitative trait (CTV accumulation) by QTL (quantitative trait loci) analysis to avoid the assumption of monogenic control. Three major resistance QTLs were detected where the P. trifoliata resistance gene, Ctv-R, had been previously located in other progenies. Up to five minor QTLs were detected ( Ctv-A(1) to Ctv-A(5)). A significant epistatic interaction involving Ctv-R(1) and Ctv-A(1) was also found. An analogue of a resistance gene is a candidate for Ctv-A(3), and two expressed sequences are candidates for Ctv-A(1) and Ctv-A(5). Single-strand conformational polymorphism analysis of CTV genes QTL P20 and P25 (coat protein) in susceptible hybrids, was carried out to test whether or not any QTL accumulation was a defeated resistance gene. Since the
Incorporating stakeholders' preferences for ex ante evaluation of energy and climate policy interactions. Development of a Multi Criteria Analysis weighting methodology

International Nuclear Information System (INIS)

Grafakos, S.; Zevgolis, D.; Oikonomou, V.

2008-03-01

Evaluation of energy and climate policy interactions is a complex issue which has not been addressed systematically. Multi Criteria Decision Analysis (MCDA) evaluation processes have been applied widely to different policy and decision cases as they have the ability to cope with high complexity, by structuring and analyzing the policy problem in a transparent and systematic way. Criteria weights elicitation techniques are developed within the framework of MCDA to integrate stakeholders' preferential information in the decision making and evaluation process. There are variant methods to determine criteria weights which can be used in various ways for different policy evaluation purposes. During decision making, policy makers and relevant stakeholders implicitly or explicitly express their relative importance between the evaluation criteria by assigning weighting factors to them. More particular, climate change policy problems lack a simple, transparent and structured way to incorporate stakeholders' views and values. In order to incorporate stakeholders' weighting preferences into an ex ante evaluation of climate change and energy policy instruments interaction, an integrative constructive weighting methodology has been developed. This paper presents the main characteristics of evaluation of energy and climate policy interactions, the reasoning behind the development of the weighting tool, its main theoretical and functional characteristics and the results of its application to obtain and incorporate stakeholders' preferences on energy and climate change policy evaluation criteria. The weighting method that has been elaborated and applied to derive stakeholders' preferences for criteria weights is a combination of pair wise comparisons and ratio importance weighting methods. Initially introduces the stakeholders to the evaluation process through a warming up holistic approach for ranking the criteria and then requires them to express their ratio relative importance
Polyploidy Enhances F1 Pollen Sterility Loci Interactions That Increase Meiosis Abnormalities and Pollen Sterility in Autotetraploid Rice.

Science.gov (United States)

Wu, Jinwen; Shahid, Muhammad Qasim; Chen, Lin; Chen, Zhixiong; Wang, Lan; Liu, Xiangdong; Lu, Yonggen

2015-12-01

Intersubspecific autotetraploid rice (Oryza sativa ssp. indica × japonica) hybrids have greater biological and yield potentials than diploid rice. However, the low fertility of intersubspecific autotetraploid hybrids, which is largely caused by high pollen abortion rates, limits their commercial utility. To decipher the cytological and molecular mechanisms underlying allelic interactions in autotetraploid rice, we developed an autotetraploid rice hybrid that was heterozygous (S(i)S(j)) at F1 pollen sterility loci (Sa, Sb, and Sc) using near-isogenic lines. Cytological studies showed that the autotetraploid had higher percentages (>30%) of abnormal chromosome behavior and aberrant meiocytes (>50%) during meiosis than did the diploid rice hybrid control. Analysis of gene expression profiles revealed 1,888 genes that were differentially expressed between the autotetraploid and diploid hybrid lines at the meiotic stage, among which 889 and 999 were up- and down-regulated, respectively. Of the 999 down-regulated genes, 940 were associated with the combined effect of polyploidy and pollen sterility loci interactions (IPE). Gene Ontology enrichment analysis identified a prominent functional gene class consisting of seven genes related to photosystem I (Gene Ontology 0009522). Moreover, 55 meiosis-related or meiosis stage-specific genes were associated with IPE in autotetraploid rice, including Os02g0497500, which encodes a DNA repair-recombination protein, and Os02g0490000, which encodes a component of the ubiquitin-proteasome pathway. These results suggest that polyploidy enhances epistatic interactions between alleles of pollen sterility loci, thereby altering the expression profiles of important meiosis-related or meiosis stage-specific genes and resulting in high pollen sterility. © 2015 American Society of Plant Biologists. All Rights Reserved.
Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb.

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Neufeld, Stanley J; Wang, Fan; Cobb, John

2014-11-01

The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb. Copyright © 2014 by the Genetics Society of America.

An Interactive Website to Reduce Sexual Risk Behavior: Process Evaluation of TeensTalkHealth

Science.gov (United States)

Sieving, Renee E; Terveen, Loren G; Rosser, BR Simon; Kodet, Amy J; Rothberg, Vienna D

2015-01-01

Background Different theoretical frameworks support the use of interactive websites to promote sexual health. Although several Web-based interventions have been developed to address sexual risk taking among young people, no evaluated interventions have attempted to foster behavior change through moderated interaction among a virtual network of adolescents (who remain anonymous to one another) and health professionals. Objective The objective was to conduct a summative process evaluation of TeensTalkHealth, an interactive sexual health website designed to promote condom use and other healthy decision making in the context of romantic and sexual relationships. Methods Evaluation data were obtained from 147 adolescents who participated in a feasibility and acceptability study. Video vignettes, teen-friendly articles, and other content served as conversation catalysts between adolescents and health educators on message boards. Results Adolescents’ perceptions that the website encouraged condom use across a variety of relationship situations were very high. Almost 60% (54/92, 59%) of intervention participants completed two-thirds or more of requested tasks across the 4-month intervention. Adolescents reported high levels of comfort, perceived privacy, ease of website access and use, and perceived credibility of health educators. Potential strategies to enhance engagement and completion of intervention tasks during future implementations of TeensTalkHealth are discussed, including tailoring of content, periodic website chats with health educators and anonymous peers, and greater incorporation of features from popular social networking websites. Conclusions TeensTalkHealth is a feasible, acceptable, and promising approach to complement and enhance existing services for youth. PMID:26336157
Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

Directory of Open Access Journals (Sweden)

Mats Pettersson

2011-07-01

Full Text Available Dissection of the genetic architecture of complex traits persists as a major challenge in biology; despite considerable efforts, much remains unclear including the role and importance of genetic interactions. This study provides empirical evidence for a strong and persistent contribution of both second- and third-order epistatic interactions to long-term selection response for body weight in two divergently selected chicken lines. We earlier reported a network of interacting loci with large effects on body weight in an F(2 intercross between these high- and low-body weight lines. Here, most pair-wise interactions in the network are replicated in an independent eight-generation advanced intercross line (AIL. The original report showed an important contribution of capacitating epistasis to growth, meaning that the genotype at a hub in the network releases the effects of one or several peripheral loci. After fine-mapping of the loci in the AIL, we show that these interactions were persistent over time. The replication of five of six originally reported epistatic loci, as well as the capacitating epistasis, provides strong empirical evidence that the originally observed epistasis is of biological importance and is a contributor in the genetic architecture of this population. The stability of genetic interaction mechanisms over time indicates a non-transient role of epistasis on phenotypic change. Third-order epistasis was for the first time examined in this study and was shown to make an important contribution to growth, which suggests that the genetic architecture of growth is more complex than can be explained by two-locus interactions only. Our results illustrate the importance of designing studies that facilitate exploration of epistasis in populations for obtaining a comprehensive understanding of the genetics underlying a complex trait.
Interactive segmentation techniques algorithms and performance evaluation

CERN Document Server

He, Jia; Kuo, C-C Jay

2013-01-01

This book focuses on interactive segmentation techniques, which have been extensively studied in recent decades. Interactive segmentation emphasizes clear extraction of objects of interest, whose locations are roughly indicated by human interactions based on high level perception. This book will first introduce classic graph-cut segmentation algorithms and then discuss state-of-the-art techniques, including graph matching methods, region merging and label propagation, clustering methods, and segmentation methods based on edge detection. A comparative analysis of these methods will be provided
What?s Downstream? A Set of Classroom Exercises to Help Students Understand Recessive Epistasis ?

OpenAIRE

Knight, Jennifer K.; Wood, William B.; Smith, Michelle K.

2013-01-01

Undergraduate students in genetics and developmental biology courses often struggle with the concept of epistasis because they are unaware that the logic of gene interactions differs between enzymatic pathways and signaling pathways. If students try to develop and memorize a single simple rule for predicting epistatic relationships without taking into account the nature of the pathway under consideration, they can become confused by cases where the rule does not apply. To remedy this problem,...
The development and evaluation of an interactive videodisc system to train radiation therapy technology students on the use of the linear accelerator

International Nuclear Information System (INIS)

Russell, C.M.

1988-01-01

The purpose of this study was twofold. The first part was to describe the development and evaluation of an interactive videodisc system to train radiation therapy technology students how to treat malignancies using a Linear Accelerator. The second part of the study was to evaluate the effectiveness of the interactive videodisc system as a simulation. The Gagne-Briggs instructional model was adapted to develop the interactive videodisc system. A model emerged as part of the project to conduct the formative evaluation of the prototype. A quasiexperimental research design was used to conduct the summative evaluation with two groups of first-year Radiation Therapy Technology students who entered the program in consecutive years. All testing and evaluation instruments were developed for the study with the exception of the clinical evaluation form. This latter form was already being used at the clinical sites. T-tests were used to analyze all data. A significant difference in cognitive achievement was evidenced between students exposed to the interactive videodisc system and students who were not exposed to the system. There was no significant difference found in clinical performance achievement and in attitude toward the clinical experience between both sets of participants. Instructor time was reduced by 1 and 1/2 hours for students on the interactive videodisc system. In conclusion, the interactive videodisc system was found to be more effective as an instructional method for cognitive achievement and as equally an effective method preparing students for clinical performance
Event Generators for Simulating Heavy Ion Interactions of Interest in Evaluating Risks in Human Spaceflight

Science.gov (United States)

Wilson, Thomas L.; Pinsky, Lawrence; Andersen, Victor; Empl, Anton; Lee, Kerry; Smirmov, Georgi; Zapp, Neal; Ferrari, Alfredo; Tsoulou, Katerina; Roesler, Stefan;

2005-01-01

Simulating the Space Radiation environment with Monte Carlo Codes, such as FLUKA, requires the ability to model the interactions of heavy ions as they penetrate spacecraft and crew member's bodies. Monte-Carlo-type transport codes use total interaction cross sections to determine probabilistically when a particular type of interaction has occurred. Then, at that point, a distinct event generator is employed to determine separately the results of that interaction. The space radiation environment contains a full spectrum of radiation types, including relativistic nuclei, which are the most important component for the evaluation of crew doses. Interactions between incident protons with target nuclei in the spacecraft materials and crew member's bodies are well understood. However, the situation is substantially less comfortable for incident heavier nuclei (heavy ions). We have been engaged in developing several related heavy ion interaction models based on a Quantum Molecular Dynamics-type approach for energies up through about 5 GeV per nucleon (GeV/A) as part of a NASA Consortium that includes a parallel program of cross section measurements to guide and verify this code development.

AKTIP/Ft1, a New Shelterin-Interacting Factor Required for Telomere Maintenance.

KAUST Repository

Burla, Romina

2015-06-25

Telomeres are nucleoprotein complexes that protect the ends of linear chromosomes from incomplete replication, degradation and detection as DNA breaks. Mammalian telomeres are protected by shelterin, a multiprotein complex that binds the TTAGGG telomeric repeats and recruits a series of additional factors that are essential for telomere function. Although many shelterin-associated proteins have been so far identified, the inventory of shelterin-interacting factors required for telomere maintenance is still largely incomplete. Here, we characterize AKTIP/Ft1 (human AKTIP and mouse Ft1 are orthologous), a novel mammalian shelterin-bound factor identified on the basis of its homology with the Drosophila telomere protein Pendolino. AKTIP/Ft1 shares homology with the E2 variant ubiquitin-conjugating (UEV) enzymes and has been previously implicated in the control of apoptosis and in vesicle trafficking. RNAi-mediated depletion of AKTIP results in formation of telomere dysfunction foci (TIFs). Consistent with these results, AKTIP interacts with telomeric DNA and binds the shelterin components TRF1 and TRF2 both in vivo and in vitro. Analysis of AKTIP- depleted human primary fibroblasts showed that they are defective in PCNA recruiting and arrest in the S phase due to the activation of the intra S checkpoint. Accordingly, AKTIP physically interacts with PCNA and the RPA70 DNA replication factor. Ft1-depleted p53-/- MEFs did not arrest in the S phase but displayed significant increases in multiple telomeric signals (MTS) and sister telomere associations (STAs), two hallmarks of defective telomere replication. In addition, we found an epistatic relation for MST formation between Ft1 and TRF1, which has been previously shown to be required for replication fork progression through telomeric DNA. Ch-IP experiments further suggested that in AKTIP-depleted cells undergoing the S phase, TRF1 is less tightly bound to telomeric DNA than in controls. Thus, our results collectively
AKTIP/Ft1, a New Shelterin-Interacting Factor Required for Telomere Maintenance.

KAUST Repository

Burla, Romina; Carcuro, Mariateresa; Raffa, Grazia D; Galati, Alessandra; Raimondo, Domenico; Rizzo, Angela; La Torre, Mattia; Micheli, Emanuela; Ciapponi, Laura; Cenci, Giovanni; Cundari, Enrico; Musio, Antonio; Biroccio, Annamaria; Cacchione, Stefano; Gatti, Maurizio; Saggio, Isabella

2015-01-01

Telomeres are nucleoprotein complexes that protect the ends of linear chromosomes from incomplete replication, degradation and detection as DNA breaks. Mammalian telomeres are protected by shelterin, a multiprotein complex that binds the TTAGGG telomeric repeats and recruits a series of additional factors that are essential for telomere function. Although many shelterin-associated proteins have been so far identified, the inventory of shelterin-interacting factors required for telomere maintenance is still largely incomplete. Here, we characterize AKTIP/Ft1 (human AKTIP and mouse Ft1 are orthologous), a novel mammalian shelterin-bound factor identified on the basis of its homology with the Drosophila telomere protein Pendolino. AKTIP/Ft1 shares homology with the E2 variant ubiquitin-conjugating (UEV) enzymes and has been previously implicated in the control of apoptosis and in vesicle trafficking. RNAi-mediated depletion of AKTIP results in formation of telomere dysfunction foci (TIFs). Consistent with these results, AKTIP interacts with telomeric DNA and binds the shelterin components TRF1 and TRF2 both in vivo and in vitro. Analysis of AKTIP- depleted human primary fibroblasts showed that they are defective in PCNA recruiting and arrest in the S phase due to the activation of the intra S checkpoint. Accordingly, AKTIP physically interacts with PCNA and the RPA70 DNA replication factor. Ft1-depleted p53-/- MEFs did not arrest in the S phase but displayed significant increases in multiple telomeric signals (MTS) and sister telomere associations (STAs), two hallmarks of defective telomere replication. In addition, we found an epistatic relation for MST formation between Ft1 and TRF1, which has been previously shown to be required for replication fork progression through telomeric DNA. Ch-IP experiments further suggested that in AKTIP-depleted cells undergoing the S phase, TRF1 is less tightly bound to telomeric DNA than in controls. Thus, our results collectively
Interactive contour delineation of organs at risk in radiotherapy: Clinical evaluation on NSCLC patients

International Nuclear Information System (INIS)

Dolz, J.; Kirişli, H. A.; Massoptier, L.; Fechter, T.; Karnitzki, S.; Oehlke, O.; Nestle, U.; Vermandel, M.

2016-01-01

Purpose: Accurate delineation of organs at risk (OARs) on computed tomography (CT) image is required for radiation treatment planning (RTP). Manual delineation of OARs being time consuming and prone to high interobserver variability, many (semi-) automatic methods have been proposed. However, most of them are specific to a particular OAR. Here, an interactive computer-assisted system able to segment various OARs required for thoracic radiation therapy is introduced. Methods: Segmentation information (foreground and background seeds) is interactively added by the user in any of the three main orthogonal views of the CT volume and is subsequently propagated within the whole volume. The proposed method is based on the combination of watershed transformation and graph-cuts algorithm, which is used as a powerful optimization technique to minimize the energy function. The OARs considered for thoracic radiation therapy are the lungs, spinal cord, trachea, proximal bronchus tree, heart, and esophagus. The method was evaluated on multivendor CT datasets of 30 patients. Two radiation oncologists participated in the study and manual delineations from the original RTP were used as ground truth for evaluation. Results: Delineation of the OARs obtained with the minimally interactive approach was approved to be usable for RTP in nearly 90% of the cases, excluding the esophagus, which segmentation was mostly rejected, thus leading to a gain of time ranging from 50% to 80% in RTP. Considering exclusively accepted cases, overall OARs, a Dice similarity coefficient higher than 0.7 and a Hausdorff distance below 10 mm with respect to the ground truth were achieved. In addition, the interobserver analysis did not highlight any statistically significant difference, at the exception of the segmentation of the heart, in terms of Hausdorff distance and volume difference. Conclusions: An interactive, accurate, fast, and easy-to-use computer-assisted system able to segment various OARs
Interactive contour delineation of organs at risk in radiotherapy: Clinical evaluation on NSCLC patients.

Science.gov (United States)

Dolz, J; Kirişli, H A; Fechter, T; Karnitzki, S; Oehlke, O; Nestle, U; Vermandel, M; Massoptier, L

2016-05-01

Accurate delineation of organs at risk (OARs) on computed tomography (CT) image is required for radiation treatment planning (RTP). Manual delineation of OARs being time consuming and prone to high interobserver variability, many (semi-) automatic methods have been proposed. However, most of them are specific to a particular OAR. Here, an interactive computer-assisted system able to segment various OARs required for thoracic radiation therapy is introduced. Segmentation information (foreground and background seeds) is interactively added by the user in any of the three main orthogonal views of the CT volume and is subsequently propagated within the whole volume. The proposed method is based on the combination of watershed transformation and graph-cuts algorithm, which is used as a powerful optimization technique to minimize the energy function. The OARs considered for thoracic radiation therapy are the lungs, spinal cord, trachea, proximal bronchus tree, heart, and esophagus. The method was evaluated on multivendor CT datasets of 30 patients. Two radiation oncologists participated in the study and manual delineations from the original RTP were used as ground truth for evaluation. Delineation of the OARs obtained with the minimally interactive approach was approved to be usable for RTP in nearly 90% of the cases, excluding the esophagus, which segmentation was mostly rejected, thus leading to a gain of time ranging from 50% to 80% in RTP. Considering exclusively accepted cases, overall OARs, a Dice similarity coefficient higher than 0.7 and a Hausdorff distance below 10 mm with respect to the ground truth were achieved. In addition, the interobserver analysis did not highlight any statistically significant difference, at the exception of the segmentation of the heart, in terms of Hausdorff distance and volume difference. An interactive, accurate, fast, and easy-to-use computer-assisted system able to segment various OARs required for thoracic radiation therapy has
Interactive contour delineation of organs at risk in radiotherapy: Clinical evaluation on NSCLC patients

Energy Technology Data Exchange (ETDEWEB)

Dolz, J., E-mail: jose.dolz.upv@gmail.com [AQUILAB, Loos-les-Lille 59120, France and University Lille, Inserm, CHU Lille, U1189–ONCO-THAI–Image Assisted Laser Therapy for Oncology, Lille F-59000 (France); Kirişli, H. A.; Massoptier, L. [AQUILAB, Loos-les-Lille 59120 (France); Fechter, T.; Karnitzki, S.; Oehlke, O.; Nestle, U. [Department of Radiation Oncology, University Medical Center, Freiburg 79106 (Germany); Vermandel, M. [Inserm Onco Thai U1189, Université Lille 2, CHRU Lille, Lille 59037 (France)

2016-05-15

Purpose: Accurate delineation of organs at risk (OARs) on computed tomography (CT) image is required for radiation treatment planning (RTP). Manual delineation of OARs being time consuming and prone to high interobserver variability, many (semi-) automatic methods have been proposed. However, most of them are specific to a particular OAR. Here, an interactive computer-assisted system able to segment various OARs required for thoracic radiation therapy is introduced. Methods: Segmentation information (foreground and background seeds) is interactively added by the user in any of the three main orthogonal views of the CT volume and is subsequently propagated within the whole volume. The proposed method is based on the combination of watershed transformation and graph-cuts algorithm, which is used as a powerful optimization technique to minimize the energy function. The OARs considered for thoracic radiation therapy are the lungs, spinal cord, trachea, proximal bronchus tree, heart, and esophagus. The method was evaluated on multivendor CT datasets of 30 patients. Two radiation oncologists participated in the study and manual delineations from the original RTP were used as ground truth for evaluation. Results: Delineation of the OARs obtained with the minimally interactive approach was approved to be usable for RTP in nearly 90% of the cases, excluding the esophagus, which segmentation was mostly rejected, thus leading to a gain of time ranging from 50% to 80% in RTP. Considering exclusively accepted cases, overall OARs, a Dice similarity coefficient higher than 0.7 and a Hausdorff distance below 10 mm with respect to the ground truth were achieved. In addition, the interobserver analysis did not highlight any statistically significant difference, at the exception of the segmentation of the heart, in terms of Hausdorff distance and volume difference. Conclusions: An interactive, accurate, fast, and easy-to-use computer-assisted system able to segment various OARs
Epistasis between QTLs for bone density variation in Copenhagen × dark agouti F2 rats

Science.gov (United States)

Liu, Lixiang; Alam, Imranul; Sun, Qiwei; Econs, Michael J.; Foroud, Tatiana; Turner, Charles H.

2010-01-01

The variation in several of the risk factors for osteoporotic fracture, including bone mineral density (BMD), has been shown to be strongly influenced by genetic differences. However, the genetic architecture of BMD is complex in both humans and in model organisms. We previously reported quantitative trait locus (QTL) results for BMD from a genome screen of 828 F2 progeny of Copenhagen and dark agouti rats. These progeny also provide an excellent opportunity to search for epistatic effects, or interaction between genetic loci, that contribute to fracture risk. Microsatellite marker data from a 20-cM genome screen was analyzed along with weight-adjusted bone density (DXA and pQCT) phenotypic data using the R/qtl software package. Genotype and phenotype data were permuted to determine genome-wide significance thresholds for the full model and epistasis (interaction) LOD scores corresponding to an alpha level of 0.01. A novel locus on chromosome 15 and a previously reported chromosome 14 QTL demonstrated a strong epistatic effect on BMD at the femur by DXA (LOD = 5.4). Two novel QTLs on chromosomes 2 and 12 were found to interact to affect total BMD at the femur midshaft by pQCT (LOD = 5.0). These results provide new information regarding the mode of action of previously identified QTL in the rat, as well as identifying novel loci that act in combination with known QTL or with other novel loci to contribute to BMD variation. PMID:19153792
Epistasis between QTLs for bone density variation in Copenhagen x dark agouti F2 rats.

Science.gov (United States)

Koller, Daniel L; Liu, Lixiang; Alam, Imranul; Sun, Qiwei; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

2009-03-01

The variation in several of the risk factors for osteoporotic fracture, including bone mineral density (BMD), has been shown to be strongly influenced by genetic differences. However, the genetic architecture of BMD is complex in both humans and in model organisms. We previously reported quantitative trait locus (QTL) results for BMD from a genome screen of 828 F2 progeny of Copenhagen and dark agouti rats. These progeny also provide an excellent opportunity to search for epistatic effects, or interaction between genetic loci, that contribute to fracture risk. Microsatellite marker data from a 20-cM genome screen was analyzed along with weight-adjusted bone density (DXA and pQCT) phenotypic data using the R/qtl software package. Genotype and phenotype data were permuted to determine genome-wide significance thresholds for the full model and epistasis (interaction) LOD scores corresponding to an alpha level of 0.01. A novel locus on chromosome 15 and a previously reported chromosome 14 QTL demonstrated a strong epistatic effect on BMD at the femur by DXA (LOD = 5.4). Two novel QTLs on chromosomes 2 and 12 were found to interact to affect total BMD at the femur midshaft by pQCT (LOD = 5.0). These results provide new information regarding the mode of action of previously identified QTL in the rat, as well as identifying novel loci that act in combination with known QTL or with other novel loci to contribute to BMD variation.
The social-devaluation effect: Interactive evaluation deteriorates likeability of objects based on daily relationship

Directory of Open Access Journals (Sweden)

Atsunori eAriga

2015-01-01

Full Text Available Although previous research has explored the effects of discussion on optimal and collective group outcomes, it is unclear how an individual's preference for an object is modulated by discussion with others. This study investigated the determinants of likeability ratings under two conditions. In Experiment 1, pairs of participants consisting of friends evaluated various photographic images. Under the interactive condition, the participants discussed their impressions of each image for 30 seconds and then independently rated how much they liked it. Under the non-interactive condition, the participants did not interact with each other but instead only thought about their impressions of each image for 30 seconds before rating its likeability. The results indicate that the exchange of impressions between the participants affected the individual likeability ratings of objects. More specifically, the interactive participants generally rated the images as less likeable than did the non-interactive participants (social-devaluation effect. However, in Experiment 2, the effect was eliminated when the pairs consisted of strangers. These findings suggest that shared information modulates individual preferences but only when a daily relationship exists within a group.
The user in interactive information retrieval evaluation

DEFF Research Database (Denmark)

Ingwersen, Peter

2011-01-01

) Request types, test persons, task-based simulations of search situations and relevance or performance measures in IIR; 2) Ultra-Light Interactive IR experiments; 3) Interactive-Light IR studies; and 4) Naturalistic field investigations of IIR. The chapter concludes with a summary section, a reference list...
Relevant patient perceptions and experiences for evaluating quality of interaction with physiotherapists during outpatient rehabilitation: a qualitative study.

Science.gov (United States)

Del Baño-Aledo, M Elena; Medina-Mirapeix, Francesc; Escolar-Reina, Pilar; Montilla-Herrador, Joaquina; Collins, Sean M

2014-03-01

To identify elements of the physiotherapist-patient interaction considered by patients when they evaluate the quality of care in outpatient rehabilitation settings. A qualitative study with nine focus groups, Two researchers conducted the focus groups, and a topic guide with predetermined questions was used. Each group discussion was audiotaped,, transcribed verbatim and analyzed thematically according to a modified grounded theory approach. Three postacute ambulatory centers in Barcelona, Madrid and Seville (Spain). Fifty-seven adults undergoing outpatient rehabilitation for musculoskeletal conditions/injuries. Patients based their evaluations of quality of care on their assessment of physiotherapists' willingness to provide information and education, technical expertise and interpersonal manners (eg. respect, emotional support and sensitivity changes in the patient's status). Both positive and negative aspects of the physiotherapist-patient interaction emerged under all these themes, except for friendly and respectful communication. This study identified which elements of the physiotherapist-patient interaction are considered by patients when evaluating the quality of care in rehabilitation outpatient settings. Further research should work to develop self-report questionnaires about patients' experiences of the physiotherapist-patient interaction in rehabilitation services to provide empirical and quantitative evidence. Copyright © 2013 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.
Introduction to a Protein Interaction System Used for Quantitative Evaluation of Biomolecular Interactions

OpenAIRE

Yamniuk, Aaron

2013-01-01

A central goal of molecular biology is the determination of biomolecular function. This comes largely from a knowledge of the non-covalent interactions that biological small and macro-molecules experience. The fundamental mission of the Molecular Interactions Research Group (MIRG) of the ABRF is to show how solution biophysical tools are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core t...
SNP-SNP interactions of three new pri-miRNAs with the target gene PGC and multidimensional analysis of H. pylori in the gastric cancer/atrophic gastritis risk in a Chinese population.

Science.gov (United States)

Xu, Qian; Wu, Ye-Feng; Li, Ying; He, Cai-Yun; Sun, Li-Ping; Liu, Jing-Wei; Yuan, Yuan

2016-04-26

Gastric cancer (GC) is a multistep complex disease involving multiple genes, and gene-gene interactions have a greater effect than a single gene in determining cancer susceptibility. This study aimed to explore the interaction of the let-7e rs8111742, miR-365b rs121224, and miR-4795 rs1002765 single nucleotide polymorphisms (SNPs) with SNPs of the predicted target gene PGC and Helicobacter pylori status in GC and atrophic gastritis (AG) risk. Three miRNA SNPs and seven PGC SNPs were detected in 2448 cases using the Sequenom MassArray platform. Two pairwise combinations of miRNA and PGC SNPs were associated with increased AG risk (let-7e rs8111742 - PGC rs6458238 and miR-4795 rs1002765 - PGC rs9471643). Singly, miR-365b rs121224 and PGC rs6912200 had no effect individually but in combination they demonstrated an epistatic interaction associated with AG risk. Similarly, let-7e rs8111742 and miR-4795 rs1002765 SNPs interacted with H. pylori infection to increase GC risk (rs8111742: Pinteraction = 0.024; rs1002765: Pinteraction = 0.031, respectively). A three-dimensional interaction analysis found miR-4795 rs1002765, PGC rs9471643, and H. pylori infection positively interacted to increase AG risk (Pinteraction = 0.027). Also, let-7e rs8111742, PGC rs6458238, and H. pylori infection positively interacted to increase GC risk (Pinteraction = 0.036). Furthermore, both of these three-dimensional interactions had a dosage-effect correspondence (Ptrend < 0.001) and were verified by MDR. In conclusion, the miRNAs SNPs (let-7e rs8111742 and miR-4795 rs1002765) might have more superior efficiency when combined with PGC SNPs and/or H. pylori for GC or AG risk than a single SNP on its own.
Proposing an Evaluation Framework for Interventions: Focusing on Students' Behaviours in Interactive Science Exhibitions

Science.gov (United States)

Hauan, Nils Petter; DeWitt, Jennifer; Kolstø, Stein Dankert

2017-01-01

Materials designed for self-guided experiences such as worksheets and digital applications are widely used as tools to enable interactive science exhibitions to support students' progress towards conceptual understanding. However, there is a need to find expedient ways to evaluate the quality of educational experiences resulting from the use of…
An Evaluation-Driven Design Approach to Develop Learning Environments Based on Full-Body Interaction

Science.gov (United States)

Malinverni, Laura; Schaper, Marie-Monique; Pares, Narcís

2016-01-01

The development of learning environments based on full-body interaction has become an increasingly important field of research in recent years. However, the design and evaluation strategies currently used present some significant limitations. Two major shortcomings are: the inadequate involvement of children in the design process and a lack of…

SciSpark: Highly Interactive and Scalable Model Evaluation and Climate Metrics for Scientific Data and Analysis

Data.gov (United States)

National Aeronautics and Space Administration — We will construct SciSpark, a scalable system for interactive model evaluation and for the rapid development of climate metrics and analyses. SciSpark directly...
Replication Kits for the papers "Automated Usability Evaluation of Virtual Reality Applications" and "VR Interaction Modalities for the Evaluation of Technical Device Prototypes" submitted to the CHI 2018

OpenAIRE

Harms, Patrick; Holderied, Hanna

2017-01-01

This replication kit contains all necessary data to reproduce the setup and results of both papers 'Automated Usability Evaluation of Virtual Reality Applications' and 'VR Interaction Modalities for the Evaluation of Technical Device Prototypes' as submitted to the CHI 2018. It includes the Unity Projects that show a coffee machine and a copier scene (sometimes refered to as printer scene, as well, as it is an integrated device) that can be interacted with with the help of the four interactio...
Generation mean analysis for quantitative traits in sesame (Sesamum indicum L. crosses

Directory of Open Access Journals (Sweden)

Vijayarajan Sharmila

2007-01-01

Full Text Available To study the nature and magnitude of gene effects for yield and its components in sesame (Sesamum indicum L. we carried out generation mean analysis using the following four crosses of different sesame cultivars: VS 9510 x Co1; NIC 7907 x TMV 3; Cianno 13/10x VRI 1; and Si 1115/1 x TMV 3. The P1, P2, F1, F2, BC1 and BC2 of these generations were studied for seven quantitative traits. The analysis showed the presence of additive, dominance and epistatic gene interactions. The additive dominance model was adequate for plant height in the NIC 7907 x TMV3 and Si 1115/1x TMV 3 crosses and for capsule length in the VS 9510 x Co1, NIC 7907 x TMV 3 and Si 1115/1 x TMV 3 crosses. An epistatic digenic model was assumed for the remaining crosses. Duplicate-type epistasis played a greater role than complementary epistasis. The study revealed the importance of both additive and non-additive types of gene action for all the traits studied.
Genetic characterization and fine mapping of S25, a hybrid male sterility gene, on rice chromosome 12.

Science.gov (United States)

Kubo, Takahiko; Yoshimura, Atsushi; Kurata, Nori

2018-02-10

Hybrid male sterility genes are important factors in creating postzygotic reproductive isolation barriers in plants. One such gene, S25, is known to cause severe transmission ratio distortion in inter-subspecific progeny of cultivated rice Oryza sativa ssp. indica and japonica. To further characterize the S25 gene, we fine-mapped and genetically characterized the S25 gene using near-isogenic lines with reciprocal genetic backgrounds. We mapped the S25 locus within the 0.67-1.02 Mb region on rice chromosome 12. Further genetic analyses revealed that S25 substantially reduced male fertility in the japonica background, but not in the indica background. In first-generation hybrid progeny, S25 had a milder effect than it had in the japonica background. These results suggest that the expression of S25 is epistatically regulated by at least one partially dominant gene present in the indica genome. This finding supports our previous studies showing that hybrid male sterility due to pollen killer genes results from epistatic interaction with other genes that are hidden in the genetic background.
Learning objects and interactive whiteboards: a evaluation proposal of learning objects for mathematics teaching

Directory of Open Access Journals (Sweden)

Silvio Henrique Fiscarelli

2016-05-01

Full Text Available The current conditions of the classroom learning tend to be a one-way process based in teacher exposition, this make a negative impact on learning make it a mechanical and not meaningful activity. One possibility to improve the quality of teaching is to innovate methodologies and varying forms of presenting information to students, such as the use of technology in the teaching process. The Interactive Whiteboard (IBW is one of the technologies that are being implemented in Brazilian schools. One of the promising possibilities to add value to the use of LDI in classroom are "learning objects" (LO. However, one problem is that often the LO are not fully suited to the dynamics of IWB, whether functional or pedagogical point of view. The objective of this study is to analyze and propose a set of indicators that evaluate the learning objects for use in conjunction with Interactive Whiteboards. The selection and definition of evaluation indicators was carried from the literature review on the subject and based on LDI experiences of use in Municipal Elementary School. After defining the set of indicators was conducted a evaluation of a sample of 30 OA utilized to teaching mathematics in 3rd grade of elementary school. The results of the evaluation indicate that the proposed indicators are suitable for a pre-analysis of OA and assisting in the process of selection of these.
A multimedia interactive education system for prostate cancer patients: development and preliminary evaluation.

Science.gov (United States)

Diefenbach, Michael A; Butz, Brian P

2004-01-21

A cancer diagnosis is highly distressing. Yet, to make informed treatment choices patients have to learn complicated disease and treatment information that is often fraught with medical and statistical terminology. Thus, patients need accurate and easy-to-understand information. To introduce the development and preliminary evaluation through focus groups of a novel highly-interactive multimedia-education software program for patients diagnosed with localized prostate cancer. The prostate interactive education system uses the metaphor of rooms in a virtual health center (ie, reception area, a library, physician offices, group meeting room) to organize information. Text information contained in the library is tailored to a person's information-seeking preference (ie, high versus low information seeker). We conducted a preliminary evaluation through 5 separate focus groups with prostate cancer survivors (N = 18) and their spouses (N = 15). Focus group results point to the timeliness and high acceptability of the software among the target audience. Results also underscore the importance of a guide or tutor who assists in navigating the program and who responds to queries to facilitate information retrieval. Focus groups have established the validity of our approach and point to new directions to further enhance the user interface.
Structuring Design and Evaluation of an Interactive Installation Through Swarms of Light Rays with Human-Artifact Model

DEFF Research Database (Denmark)

Erkut, Cumhur; Fehr, Jonas

2016-01-01

We present the design and evaluation of an interactive installation to be explored by movement and sound under Human-Activity Model. In the installation, movement qualities that are extracted from the motion tracking data excite a dynamical system (a synthetic flock of agents), which responds...... out a questionnaire afterwards. In this paper, we report our preliminary work on the analysis of the tensions of interaction with the installation under the Human-Artifact Model. Our results indicate exploration and discovery as the main motives of the interaction. This is different than utilitarian...
Numerical evaluation of energy barriers and magnetic relaxation in interacting nanostructured magnetic systems

International Nuclear Information System (INIS)

Chubykalo-Fesenko, Oksana A.; Chantrell, Roy W.

2004-01-01

We discuss a model to quantify long-time thermally induced magnetization reversal in magnetic systems with distributed properties. Two algorithms, based on kinetic and Metropolis Monte Carlo are introduced. While the former requires the constant recalculation of all energy barriers and is useful when the interactions are weak, the latter uses the Metropolis Monte Carlo to estimate the magnetization trajectory and, consequently, only the most probable transition rates are evaluated. The ridge optimization method is used to evaluate the energy barriers in a multidimensional energy landscape. The algorithms are applied to a granular system modeled by means of Voronoi polyhedra and having random in-plane anisotropy
Robust ray-tracing algorithms for interactive dose rate evaluation

International Nuclear Information System (INIS)

Perrotte, L.

2011-01-01

More than ever, it is essential today to develop simulation tools to rapidly evaluate the dose rate received by operators working on nuclear sites. In order to easily study numerous different scenarios of intervention, computation times of available softwares have to be all lowered. This mainly implies to accelerate the geometrical computations needed for the dose rate evaluation. These computations consist in finding and sorting the whole list of intersections between a big 3D scene and multiple groups of 'radiative' rays meeting at the point where the dose has to be measured. In order to perform all these computations in less than a second, we first propose a GPU algorithm that enables the efficient management of one big group of coherent rays. Then we present a modification of this algorithm that guarantees the robustness of the ray-triangle intersection tests through the elimination of the precision issues due to floating-point arithmetic. This modification does not require the definition of scene-dependent coefficients ('epsilon' style) and only implies a small loss of performance (less than 10%). Finally we propose an efficient strategy to handle multiple ray groups (corresponding to multiple radiative objects) which use the previous results.Thanks to these improvements, we are able to perform an interactive and robust dose rate evaluation on big 3D scenes: all of the intersections (more than 13 million) between 700 000 triangles and 12 groups of 100 000 rays each are found, sorted along each ray and transferred to the CPU in 470 milliseconds. (author) [fr
Self-Consistent Criteria for Evaluation of Neutron Interaction

International Nuclear Information System (INIS)

Henry, H.F.; Newlon, C.E.; Knight, J.R.

2007-01-01

New safe interaction criteria for containers of fissionable materials handled at the Oak Ridge Gaseous Diffusion Plant have been developed on the basis of an interaction theory using the basic concepts of a safe solid angle subtended by interacting containers, and the multiplication factor as determined by two-group theory for an individually safe containers The calculated results agree satisfactorily with experimental data obtained with identical interacting units involving both cylinders and slabs containing highly enriched uranium, the core compositions of which were varied between H/U-235 atomic ratios of 44.3 and 337. The application of the derived interaction criteria to items containing material with low moderation or low U-235 assay, and to containers for which nuclear safety is dependent upon control of the U-235 mass or U-235 concentration is discussed.
Synthesis of dimeric arylβ-D-galactopyranosides for the evaluation of their interaction with the Erythrina cristagalli lectin

International Nuclear Information System (INIS)

Figueiredo, Rute Cunha; Meyer, Nadia Burkowski; Prado, Maria Auxiliadora Fontes; Alves, Ricardo Jose; Rojo, Javier

2009-01-01

The synthesis of two new D-galactose-based dimers having a 1,4-butanediamine spacer is reported aiming at the evaluation of their interaction with the Erythrina cristagalli lectin. The title compounds were prepared in four and five steps from 2,3,4,6-tetra-O-acetyl-β-D-galactopyranoside bromide, in 20 % and 15 % overall yield, respectively, using the Doebner modification of the Koenavenagel reaction as the key sep. The lectin-carbohydrate interaction could be evaluated for only one dimer, due to solubility problems. A twofold enhancement of affinity was observed, compared to the corresponding monovalent ligand. (author)
QTL Analysis of Kernel-Related Traits in Maize Using an Immortalized F2 Population

Science.gov (United States)

Hu, Yanmin; Li, Weihua; Fu, Zhiyuan; Ding, Dong; Li, Haochuan; Qiao, Mengmeng; Tang, Jihua

2014-01-01

Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04–6.06, 7.02–7.03, and 10.06–10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%). PMID:24586932
DRD2/AKT1 interaction on D2 c-AMP independent signaling, attentional processing, and response to olanzapine treatment in schizophrenia.

Science.gov (United States)

Blasi, Giuseppe; Napolitano, Francesco; Ursini, Gianluca; Taurisano, Paolo; Romano, Raffaella; Caforio, Grazia; Fazio, Leonardo; Gelao, Barbara; Di Giorgio, Annabella; Iacovelli, Luisa; Sinibaldi, Lorenzo; Popolizio, Teresa; Usiello, Alessandro; Bertolino, Alessandro

2011-01-18

The D2/AKT1/GSK-3β signaling pathway has been involved in the downstream intracellular effects of dopamine, in the pathophysiology of cognitive deficits and related brain activity in schizophrenia, as well as in response to treatment with antipsychotics. Polymorphisms in the D2 (DRD2 rs1076560) and AKT1 (AKT1 rs1130233) genes have been associated with their respective protein expression and with higher-order cognition and brain function, including attention. Given the strong potential for their relationship, we investigated the interaction of these polymorphisms on multiple molecular and in vivo phenotypes associated with this signaling pathway. We measured AKT1 and GSK-3β proteins and phosphorylation in human peripheral blood mononuclear cells, functional MRI cingulate response during attentional control, behavioral accuracy during sustained attention, and response to 8 wk of treatment with olanzapine in a total of 190 healthy subjects and 66 patients with schizophrenia. In healthy subjects, we found that the interaction between the T allele of DRD2 rs1076560 and the A allele of AKT1 rs1130233 was associated with reduced AKT1 protein levels and reduced phosphorylation of GSK-3β, as well as with altered cingulate response and reduced behavioral accuracy during attentional processing. On the other hand, interaction of these two alleles was associated with greater improvement of Positive and Negative Syndrome Scale scores in patients with schizophrenia after treatment with olanzapine. The present results indicate that these functional polymorphisms are epistatically associated with multiple phenotypes of relevance to schizophrenia. Our results also lend support to further investigation of this downstream molecular pathway in the etiology and treatment of this disorder.
Systematic research review of observational approaches used to evaluate mother-child mealtime interactions during preschool years.

Science.gov (United States)

Bergmeier, Heidi; Skouteris, Helen; Hetherington, Marion

2015-01-01

The family meal and social interactions during the meal are important events in a child's life. Specifically, mealtime interactions have been linked to child weight status, the development of children's eating patterns, and socialization. Mealtime interactions may be observed and evaluated to provide insights into this important event beyond self-reported measurements. We aimed to identify, review, and examine studies in which mother-child mealtime behaviors were measured through observation. MEDLINE Complete, PsycINFO, and PsycARTICLES were systematically searched by using sensitive search strategies. We included observational studies of mother-child eating and mealtimes and associations between mother-child interactions and preschool child eating or weight status published to March 2014. Thirteen articles were included in our review. All studies but one were cross-sectional, and none of the studies evaluated how mutual dimensions (e.g., parent responsiveness to the child and child responsiveness to the parent) of dyadic interactions between mothers and children influence maternal feeding practices, children's eating, and weight. The parenting style was associated with maternal feeding practices but not directly with children's eating. Parental discouragements to eat and negative statements about food were associated with higher child weight status. Parental encouragement to eat was associated with higher child weight status as well as maternal body mass index. No associations were shown between maternal reports of feeding practices and observed maternal feeding practices. Parents' overarching attitudes and approaches to parenting appear to be associated with their feeding practices or styles. Future studies should implement longitudinal observational methods with the capacity to measure levels of dimensions within bidirectional parent-child interactions and the extent to which these factors influence maternal practices, children's eating, and weight status. �
The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae.

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Francisco Salinas

Full Text Available Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.
Environmental stresses can alleviate the average deleterious effect of mutations

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Leibler Stanislas

2003-05-01

Full Text Available Abstract Background Fundamental questions in evolutionary genetics, including the possible advantage of sexual reproduction, depend critically on the effects of deleterious mutations on fitness. Limited existing experimental evidence suggests that, on average, such effects tend to be aggravated under environmental stresses, consistent with the perception that stress diminishes the organism's ability to tolerate deleterious mutations. Here, we ask whether there are also stresses with the opposite influence, under which the organism becomes more tolerant to mutations. Results We developed a technique, based on bioluminescence, which allows accurate automated measurements of bacterial growth rates at very low cell densities. Using this system, we measured growth rates of Escherichia coli mutants under a diverse set of environmental stresses. In contrast to the perception that stress always reduces the organism's ability to tolerate mutations, our measurements identified stresses that do the opposite – that is, despite decreasing wild-type growth, they alleviate, on average, the effect of deleterious mutations. Conclusions Our results show a qualitative difference between various environmental stresses ranging from alleviation to aggravation of the average effect of mutations. We further show how the existence of stresses that are biased towards alleviation of the effects of mutations may imply the existence of average epistatic interactions between mutations. The results thus offer a connection between the two main factors controlling the effects of deleterious mutations: environmental conditions and epistatic interactions.
Control of trichome branching by Chromatin Assembly Factor-1

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Hennig Lars

2008-05-01

Full Text Available Abstract Background Chromatin dynamics and stability are both required to control normal development of multicellular organisms. Chromatin assembly factor CAF-1 is a histone chaperone that facilitates chromatin formation and the maintenance of specific chromatin states. In plants and animals CAF-1 is essential for normal development, but it is poorly understood which developmental pathways require CAF-1 function. Results Mutations in all three CAF-1 subunits affect Arabidopsis trichome morphology and lack of CAF-1 function results in formation of trichomes with supernumerary branches. This phenotype can be partially alleviated by external sucrose. In contrast, other aspects of the CAF-1 mutant phenotype, such as defective meristem function and organ formation, are aggravated by external sucrose. Double mutant analyses revealed epistatic interactions between CAF-1 mutants and stichel, but non-epistatic interactions between CAF-1 mutants and glabra3 and kaktus. In addition, mutations in CAF-1 could partly suppress the strong overbranching and polyploidization phenotype of kaktus mutants. Conclusion CAF-1 is required for cell differentiation and regulates trichome development together with STICHEL in an endoreduplication-independent pathway. This function of CAF-1 can be partially substituted by application of exogenous sucrose. Finally, CAF-1 is also needed for the high degree of endoreduplication in kaktus mutants and thus for the realization of kaktus' extreme overbranching phenotype.
Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL.

Science.gov (United States)

Branham, Sandra E; Levi, Amnon; Katawczik, Melanie; Fei, Zhangjun; Wechter, W Patrick

2018-04-01

Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon. The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok'neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.
Evaluation of an Interactive Undergraduate Cosmology Curriculum

Science.gov (United States)

White, Aaron; Coble, Kimberly A.; Martin, Dominique; Hayes, Patrycia; Targett, Tom; Cominsky, Lynn R.

2018-06-01

The Big Ideas in Cosmology is an immersive set of web-based learning modules that integrates text, figures, and visualizations with short and long interactive tasks as well as labs that allow students to manipulate and analyze real cosmological data. This enables the transformation of general education astronomy and cosmology classes from primarily lecture and book-based courses to a format that builds important STEM skills, while engaging those outside the field with modern discoveries and a more realistic sense of practices and tools used by professional astronomers. Over two semesters, we field-tested the curriculum in general education cosmology classes at a state university in California [N ~ 80]. We administered pre- and post-instruction multiple-choice and open-ended content surveys as well as the CLASS, to gauge the effectiveness of the course and modules. Questions addressed included the structure, composition, and evolution of the universe, including students’ reasoning and “how we know.”Module development and evaluation was supported by NASA ROSES E/PO Grant #NNXl0AC89G, the Illinois Space Grant Consortium, the Fermi E/PO program, Sonoma State University’s Space Science Education and Public Outreach Group, and San Francisco State University. The modules are published by Great River Learning/Kendall-Hunt.
Some fundamental aspects of fault-tree and digraph-matrix relationships for a systems-interaction evaluation procedure

International Nuclear Information System (INIS)

Alesso, H.P.

1982-01-01

Recent events, such as Three Mile Island-2, Brown's Ferry-3, and Crystal River-3, have demonstrated that complex accidents can occur as a result of dependent (common-cause/mode) failures. These events are now being called Systems Interactions. A procedure for the identification and evaluation of Systems Interactions is being developed by the NRC. Several national laboratories and utilities have contributed preliminary procedures. As a result, there are several important views of the Systems Interaction problem. This report reviews some fundamental mathematical background of both fault-oriented and success-oriented risk analyses in order to bring out the advantages and disadvantages of each. In addition, it outlines several fault-oriented/dependency analysis approaches and several success-oriented/digraph-matrix approaches. The objective is to obtain a broad perspective of present options for solving the Systems Interaction problem

Participant Interaction in Asynchronous Learning Environments: Evaluating Interaction Analysis Methods

Science.gov (United States)

Blanchette, Judith

2012-01-01

The purpose of this empirical study was to determine the extent to which three different objective analytical methods--sequence analysis, surface cohesion analysis, and lexical cohesion analysis--can most accurately identify specific characteristics of online interaction. Statistically significant differences were found in all points of…
Interactive model evaluation tool based on IPython notebook

Science.gov (United States)

Balemans, Sophie; Van Hoey, Stijn; Nopens, Ingmar; Seuntjes, Piet

2015-04-01

In hydrological modelling, some kind of parameter optimization is mostly performed. This can be the selection of a single best parameter set, a split in behavioural and non-behavioural parameter sets based on a selected threshold or a posterior parameter distribution derived with a formal Bayesian approach. The selection of the criterion to measure the goodness of fit (likelihood or any objective function) is an essential step in all of these methodologies and will affect the final selected parameter subset. Moreover, the discriminative power of the objective function is also dependent from the time period used. In practice, the optimization process is an iterative procedure. As such, in the course of the modelling process, an increasing amount of simulations is performed. However, the information carried by these simulation outputs is not always fully exploited. In this respect, we developed and present an interactive environment that enables the user to intuitively evaluate the model performance. The aim is to explore the parameter space graphically and to visualize the impact of the selected objective function on model behaviour. First, a set of model simulation results is loaded along with the corresponding parameter sets and a data set of the same variable as the model outcome (mostly discharge). The ranges of the loaded parameter sets define the parameter space. A selection of the two parameters visualised can be made by the user. Furthermore, an objective function and a time period of interest need to be selected. Based on this information, a two-dimensional parameter response surface is created, which actually just shows a scatter plot of the parameter combinations and assigns a color scale corresponding with the goodness of fit of each parameter combination. Finally, a slider is available to change the color mapping of the points. Actually, the slider provides a threshold to exclude non behaviour parameter sets and the color scale is only attributed to the
Evaluation of a Panel of Single-Nucleotide Polymorphisms in miR-146a and miR-196a2 Genomic Regions in Patients with Chronic Periodontitis.

Science.gov (United States)

Venugopal, Priyanka; Lavu, Vamsi; RangaRao, Suresh; Venkatesan, Vettriselvi

2017-04-01

Periodontitis is an inflammatory disease caused by bacterial triggering of the host immune-inflammatory response, which in turn is regulated by microRNAs (miRNA). Polymorphisms in the miRNA pathways affect the expression of several target genes such as tumor necrosis factor-α and interleukins, which are associated with progression of disease. The objective of this study was to identify the association between the MiR-146a single nucleotide polymorphisms (SNPs) (rs2910164, rs57095329, and rs73318382), the MiR-196a2 (rs11614913) SNP and chronic periodontitis. Genotyping was performed for the MiR-146a (rs2910164, rs57095329, and rs73318382) and the MiR-196a2 (rs11614913) polymorphisms in 180 healthy controls and 190 cases of chronic periodontitis by the direct Sanger sequencing technique. The strength of the association between the polymorphisms and chronic periodontitis was evaluated using logistic regression analysis. Haplotype and linkage analyses among the polymorphisms was performed. Multifactorial dimensionality reduction was performed to determine epistatic interaction among the polymorphisms. The MiR-196a2 polymorphism revealed a significant inverse association with chronic periodontitis. Haplotype analysis of MiR-146a and MiR-196a2 polymorphisms revealed 13 different combinations, of which 5 were found to have an inverse association with chronic periodontitis. The present study has demonstrated a significant inverse association of MiR-196a2 polymorphism with chronic periodontitis.
Interaction debugging : an integral approach to analyze human-robot interaction

NARCIS (Netherlands)

Kooijmans, T.; Kanda, T.; Bartneck, C.; Ishiguro, H.; Hagita, N.

2006-01-01

Along with the development of interactive robots, controlled experiments and field trials are regularly conducted to stage human-robot interaction. Experience in this field has shown that analyzing human-robot interaction for evaluation purposes fosters the development of improved systems and the
Evaluation of Lagrangian, Eulerian, and arbitrary Lagrangian-Eulerian methods for fluid-structure interaction problems in HCDA analysis

International Nuclear Information System (INIS)

Chang, Y.W.; Chu, H.Y.; Gvildys, J.; Wang, C.Y.

1979-01-01

The analysis of fluid-structure interaction involves the calculation of both fluid transient and structure dynamics. In the structural analysis, Lagrangian meshes have been used exclusively, whereas for the fluid transient, Lagrangian, Eulerian, and arbitrary Lagrangian-Eulerian (quasi-Eulerian) meshes have been used. This paper performs an evaluation on these three types of meshes. The emphasis is placed on the applicability of the method in analyzing fluid-structure interaction problems in HCDA analysis
A communicational framework for evaluating interaction with IT by analyzing user-reception of electronic texts

DEFF Research Database (Denmark)

Wentzer, Helle

2006-01-01

Interpreting IT as a medium for continuous communication across time and place of the communicators offers a way of analyzing the effect of IT in concrete practices. The users’ readings determine the actual communication with IT. A poetics of how meaning is translated from one person to another...... through semiotic texts is presented, termed the poetics of the e-text. The poetics of the e-text offers a meta-communicational framework for identifying user constraints in the possibilities of interacting with the system. Identifying communicational problems with ICT-mediated interactions again offer...... grounds for redesigning and re-author the e-text. The poetics of the e-text are subsequently applied as a method of analyzing user-reception and evaluating the interaction with ICT. Examples are given from user-receptions of collaborating with ICT in home care, Denmark....
An evaluation framework for multimodal interaction determining quality aspects and modality choice

CERN Document Server

Wechsung, Ina

2014-01-01

This book presents (1) an exhaustive and empirically validated taxonomy of quality aspects of multimodal interaction as well as respective measurement methods, (2) a validated questionnaire specifically tailored to the evaluation of multimodal systems and covering most of the taxonomy‘s quality aspects, (3) insights on how the quality perceptions of multimodal systems relate to the quality perceptions of its individual components, (4) a set of empirically tested factors which influence modality choice, and (5) models regarding the relationship of the perceived quality of a modality and the actual usage of a modality.
Evaluation of Processes of Interaction between the Enterprise and Potential Contractors in the Context of Ensuring Economic Security of Foreign Economic Activity

Directory of Open Access Journals (Sweden)

Havlovska Nataliia I.

2016-08-01

Full Text Available The author’s approach to evaluating appropriateness of interaction of domestic enterprises-subjects of foreign economic activity with foreign partners taking into account balancing benefits and safety has been presented. To solve the problems set in the study, there were used means of economic and mathematical simulation, namely, conceptual provisions of the theory of games. Preconditions for simulating scenarios of interaction between contractors and evaluation of effects of this interaction have been determined. A dyadic game model, in which each player will only have two pure strategies, has been proposed, and possibility of using a three-player game with development of a corresponding matrix of wins of each player has been considered. On the basis of the calculation of possible options of interaction between the major players possible options for this interaction have been found and a questionnaire for expert evaluation of the matrix elements of each player’s decisions has been developed. There suggested solutions of the game by relevant matrices, where two Nash equilibrium situations and 10 Pareto efficient situations are defined. The optimal solution of the game for all participants in the interaction, which allows to achieve a sufficient level of efficiency and safety of each player has been found
An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

Science.gov (United States)

Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

2012-01-01

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059
A multiplexed microfluidic system for evaluation of dynamics of immune-tumor interactions.

Science.gov (United States)

Moore, N; Doty, D; Zielstorff, M; Kariv, I; Moy, L Y; Gimbel, A; Chevillet, J R; Lowry, N; Santos, J; Mott, V; Kratchman, L; Lau, T; Addona, G; Chen, H; Borenstein, J T

2018-05-25

Recapitulation of the tumor microenvironment is critical for probing mechanisms involved in cancer, and for evaluating the tumor-killing potential of chemotherapeutic agents, targeted therapies and immunotherapies. Microfluidic devices have emerged as valuable tools for both mechanistic studies and for preclinical evaluation of therapeutic agents, due to their ability to precisely control drug concentrations and gradients of oxygen and other species in a scalable and potentially high throughput manner. Most existing in vitro microfluidic cancer models are comprised of cultured cancer cells embedded in a physiologically relevant matrix, collocated with vascular-like structures. However, the recent emergence of immune checkpoint inhibitors (ICI) as a powerful therapeutic modality against many cancers has created a need for preclinical in vitro models that accommodate interactions between tumors and immune cells, particularly for assessment of unprocessed tumor fragments harvested directly from patient biopsies. Here we report on a microfluidic model, termed EVIDENT (ex vivo immuno-oncology dynamic environment for tumor biopsies), that accommodates up to 12 separate tumor biopsy fragments interacting with flowing tumor-infiltrating lymphocytes (TILs) in a dynamic microenvironment. Flow control is achieved with a single pump in a simple and scalable configuration, and the entire system is constructed using low-sorption materials, addressing two principal concerns with existing microfluidic cancer models. The system sustains tumor fragments for multiple days, and permits real-time, high-resolution imaging of the interaction between autologous TILs and tumor fragments, enabling mapping of TIL-mediated tumor killing and testing of various ICI treatments versus tumor response. Custom image analytic algorithms based on machine learning reported here provide automated and quantitative assessment of experimental results. Initial studies indicate that the system is capable of
Laboratory Evaluation of Interactions in the Degradation of a Polypropylene Geotextile in Marine Environments

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José Ricardo Carneiro

2018-01-01

Full Text Available The long-term behaviour of geosynthetics applied in coastal engineering structures can be adversely affected by many agents. This paper studies the resistance of a nonwoven polypropylene geotextile against some degradation agents present in marine environments and evaluates the existence of interactions between them. For that purpose, the geotextile was exposed to some laboratory degradation tests: immersion tests (in seawater, deionised water, and sodium chloride 35 g·L−1, thermooxidation, and artificial weathering. The geotextile was (1 exposed separately to each degradation test and (2 exposed successively to combinations of two or three degradation tests. The damage caused by the degradation tests was evaluated by monitoring the tensile properties of the geotextile. Based on the changes occurred in tensile strength, reduction factors were determined. The reduction factors obtained directly in the multiple exposures were compared with those obtained by the traditional methodology for the combined effect of the degradation agents. The results, among other findings, showed the existence of relevant interactions between the degradation agents and showed that the reduction factors obtained by the traditional methodology were unable to represent accurately (by underestimating the degradation occurred in the geotextile.
Evaluation on Impact Interaction between Abutment and Steel Girder Subjected to Nonuniform Seismic Excitation

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Yue Zheng

2015-01-01

Full Text Available This paper aims to evaluate the impact interaction between the abutment and the girder subjected to nonuniform seismic excitation. An impact model based on tests is presented by taking material properties of the backfill of the abutment into consideration. The conditional simulation is performed to investigate the spatial variation of earthquake ground motions. A two-span continuous steel box girder bridge is taken as the example to analyze and assess the pounding interaction between the abutment and the girder. The detailed nonlinear finite element (FE model is established and the steel girder and the reinforced concrete piers are modeled by nonlinear fiber elements. The pounding element of the abutment is simulated by using a trilinear compression gap element. The elastic-perfectly plastic element is used to model the nonlinear rubber bearings. The comparisons of the pounding forces, the shear forces of the nonlinear bearings, the moments of reinforced concrete piers, and the axial pounding stresses of the steel girder are studied. The made observations indicate that the nonuniform excitation for multisupport bridge is imperative in the analysis and evaluation of the pounding effects of the bridges.
Interactive Information Retrieval

DEFF Research Database (Denmark)

Borlund, Pia

2013-01-01

The paper introduces the research area of interactive information retrieval (IIR) from a historical point of view. Further, the focus here is on evaluation, because much research in IR deals with IR evaluation methodology due to the core research interest in IR performance, system interaction...... and satisfaction with retrieved information. In order to position IIR evaluation, the Cranfield model and the series of tests that led to the Cranfield model are outlined. Three iconic user-oriented studies and projects that all have contributed to how IIR is perceived and understood today are presented......: The MEDLARS test, the Book House fiction retrieval system, and the OKAPI project. On this basis the call for alternative IIR evaluation approaches motivated by the three revolutions (the cognitive, the relevance, and the interactive revolutions) put forward by Robertson & Hancock-Beaulieu (1992) is presented...
Computational psychotherapy research: scaling up the evaluation of patient-provider interactions.

Science.gov (United States)

Imel, Zac E; Steyvers, Mark; Atkins, David C

2015-03-01

In psychotherapy, the patient-provider interaction contains the treatment's active ingredients. However, the technology for analyzing the content of this interaction has not fundamentally changed in decades, limiting both the scale and specificity of psychotherapy research. New methods are required to "scale up" to larger evaluation tasks and "drill down" into the raw linguistic data of patient-therapist interactions. In the current article, we demonstrate the utility of statistical text analysis models called topic models for discovering the underlying linguistic structure in psychotherapy. Topic models identify semantic themes (or topics) in a collection of documents (here, transcripts). We used topic models to summarize and visualize 1,553 psychotherapy and drug therapy (i.e., medication management) transcripts. Results showed that topic models identified clinically relevant content, including affective, relational, and intervention related topics. In addition, topic models learned to identify specific types of therapist statements associated with treatment-related codes (e.g., different treatment approaches, patient-therapist discussions about the therapeutic relationship). Visualizations of semantic similarity across sessions indicate that topic models identify content that discriminates between broad classes of therapy (e.g., cognitive-behavioral therapy vs. psychodynamic therapy). Finally, predictive modeling demonstrated that topic model-derived features can classify therapy type with a high degree of accuracy. Computational psychotherapy research has the potential to scale up the study of psychotherapy to thousands of sessions at a time. We conclude by discussing the implications of computational methods such as topic models for the future of psychotherapy research and practice. (PsycINFO Database Record (c) 2015 APA, all rights reserved).
FENDL/E. Evaluated nuclear data library of neutron nuclear interaction cross-sections and photon production cross-sections and photon-atom interaction cross sections for fusion applications. Version 1.1 of November 1994

International Nuclear Information System (INIS)

Pashchenko, A.B.; Wienke, H.; Ganesan, S.; McLaughlin, P.K.

1996-01-01

This document presents the description of a physical tape containing the basic evaluated nuclear data library of neutron nuclear interaction cross-sections and photon production cross-sections and photon-atom interaction cross-sections for fusion applications. It is part of FENDL, the evaluated nuclear data library for fusion applications. The nuclear data are available cost-free for distribution to interested scientists upon request. The data can also be retrieved by the user via online access through international computer networks. (author). 11 refs, 1 tab
Measuring the Impact of a Moving Target: Towards a Dynamic Framework for Evaluating Collaborative Adaptive Interactive Technologies

OpenAIRE

O?Grady, Laura; Witteman, Holly; Bender, Jacqueline L; Urowitz, Sara; Wiljer, David; Jadad, Alejandro R

2009-01-01

Background Website evaluation is a key issue for researchers, organizations, and others responsible for designing, maintaining, endorsing, approving, and/or assessing the use and impact of interventions designed to influence health and health services. Traditionally, these evaluations have included elements such as content credibility, interface usability, and overall design aesthetics. With the emergence of collaborative, adaptive, and interactive ("Web 2.0") technologies such as wikis and o...
User-evaluated Gestures for Touchless Interactions from a Distance

NARCIS (Netherlands)

Fikkert, F.W.; van der Vet, P.E.; Nijholt, Antinus

2010-01-01

Very big displays are now commonplace but interactions with them are limited, even poorly understood. Recently, understanding touch-based interactions have received a great deal of attention due to the popularity and low costs of these displays. The direct extension of such interactions, touch less
Evaluation of bentonite alteration due to interactions with iron. Sensitivity analyses to identify the important factors for the bentonite alteration

International Nuclear Information System (INIS)

Sasamoto, Hiroshi; Wilson, James; Sato, Tsutomu

2013-01-01

Performance assessment of geological disposal systems for high-level radioactive waste requires a consideration of long-term systems behaviour. It is possible that the alteration of swelling clay present in bentonite buffers might have an impact on buffer functions. In the present study, iron (as a candidate overpack material)-bentonite (I-B) interactions were evaluated as the main buffer alteration scenario. Existing knowledge on alteration of bentonite during I-B interactions was first reviewed, then the evaluation methodology was developed considering modeling techniques previously used overseas. A conceptual model for smectite alteration during I-B interactions was produced. The following reactions and processes were selected: 1) release of Fe 2+ due to overpack corrosion; 2) diffusion of Fe 2+ in compacted bentonite; 3) sorption of Fe 2+ on smectite edge and ion exchange in interlayers; 4) dissolution of primary phases and formation of alteration products. Sensitivity analyses were performed to identify the most important factors for the alteration of bentonite by I-B interactions. (author)
Evaluations of antimony and strontium interaction in an Al–Si–Cu–Zn die cast alloy

Energy Technology Data Exchange (ETDEWEB)

Farahany, Saeed, E-mail: saeedfarahany@gmail.com; Idris, Mohd Hasbullah; Ourdjini, Ali

2014-05-01

Graphical abstract: - Highlights: • Probable interactions between Sb and Sr in a complex Al–Si alloy were evaluated. • Sequence of addition did not affect thermal and microscopical characteristics. • Threshold ratio for the Sb and Sr interaction is proposed. - Abstract: The interaction between antimony and strontium in an ADC12 die casting alloy is investigated comprehensively by using a computer aided cooling curve thermal analysis coupled with microstructure inspection. The results of the thermal analysis show significant changes in Al–Si eutectic reaction based on different concentrations of Sb and Sr. Sb reduces the efficiency of Sr in modifying the eutectic Si. Based upon the data obtained in this study, the threshold Sr/Sb ratio should exceed about 0.5 in order to obtain fully modified structure. Moreover, a pre-eutectic reaction of Al{sub 2}Si{sub 2}Sr intermetallic was detected for high concentrations of Sr.
Aging/Systems Interaction Study, Component Residual Lifetime Evaluation and Feasibility of Relicensing. Progress report, FY 1985

International Nuclear Information System (INIS)

Close, J.A.; Jacobs, P.T.; Korth, G.E.; Mudlin, J.M.; Server, W.L.; Spaletta, H.W.

1985-10-01

This report documents the work performed on four research tasks in Fiscal Year 1985 (FY-1985) which were part of the Aging/Systems Interaction Study, Component Residual Lifetime Evaluation and Feasibility of Relicensing Project. The technical and management/institutional objectives for the project are described, followed by a description of the results of each task. The work on Task 1 involved identifying and prioritizing new research activities for the Nuclear Regulatory Commission (NRC) Nuclear Plant Aging Research (NPAR) Program. A proposed methodology and plan for aging-system interaction studies was developed in Task 2. The description of Task 3 work comprises a summary of nuclear plant life extension activities in the US, the technical basis associated with the residual life of metallic materials and a proposed plan for research on residual life assessment. Task 4 describes the initial evaluation of selected Standard Review Plan (NUREG-0800) sections to investigate the feasibility of relicensing. 14 refs., 13 figs., 20 tabs

An evaluation of diverse methods of obtaining effective Schroedinger interaction potentials for elastic scattering

International Nuclear Information System (INIS)

Amos, K.; Allen, L.J.; Steward, C.; Hodgson, P.E.; Sofianos, S.A.

1995-01-01

Direct solution of the Schroedinger equation and inversion methods of analysis of elastic scattering data are considered to evaluate the information that they can provide about the physical interaction between colliding nuclear particles. It was found that both optical model and inversion methods based upon inverse scattering theories are subject to ambiguities. Therefore, it is essential that elastic scattering data analyses are consistent with microscopic calculations of the potential. 25 refs
An evaluation of diverse methods of obtaining effective Schroedinger interaction potentials for elastic scattering

Energy Technology Data Exchange (ETDEWEB)

Amos, K.; Allen, L.J.; Steward, C. [Melbourne Univ., Parkville, VIC (Australia). School of Physics; Hodgson, P.E. [Oxford Univ. (United Kingdom). Dept. of Physics; Sofianos, S.A. [University of South Africa (UNISA), Pretoria (South Africa). Dept. of Physics

1995-10-01

Direct solution of the Schroedinger equation and inversion methods of analysis of elastic scattering data are considered to evaluate the information that they can provide about the physical interaction between colliding nuclear particles. It was found that both optical model and inversion methods based upon inverse scattering theories are subject to ambiguities. Therefore, it is essential that elastic scattering data analyses are consistent with microscopic calculations of the potential. 25 refs.
The sex-specific associations of the aromatase gene with Alzheimer's disease and its interaction with IL10 in the Epistasis Project.

Science.gov (United States)

Medway, Christopher; Combarros, Onofre; Cortina-Borja, Mario; Butler, Helen T; Ibrahim-Verbaas, Carla A; de Bruijn, Renée F A G; Koudstaal, Peter J; van Duijn, Cornelia M; Ikram, M Arfan; Mateo, Ignacio; Sánchez-Juan, Pascual; Lehmann, Michael G; Heun, Reinhard; Kölsch, Heike; Deloukas, Panos; Hammond, Naomi; Coto, Eliecer; Alvarez, Victoria; Kehoe, Patrick G; Barber, Rachel; Wilcock, Gordon K; Brown, Kristelle; Belbin, Olivia; Warden, Donald R; Smith, A David; Morgan, Kevin; Lehmann, Donald J

2014-02-01

Epistasis between interleukin-10 (IL10) and aromatase gene polymorphisms has previously been reported to modify the risk of Alzheimer's disease (AD). However, although the main effects of aromatase variants suggest a sex-specific effect in AD, there has been insufficient power to detect sex-specific epistasis between these genes to date. Here we used the cohort of 1757 AD patients and 6294 controls in the Epistasis Project. We replicated the previously reported main effects of aromatase polymorphisms in AD risk in women, for example, adjusted odds ratio of disease for rs1065778 GG=1.22 (95% confidence interval: 1.01-1.48, P=0.03). We also confirmed a reported epistatic interaction between IL10 rs1800896 and aromatase (CYP19A1) rs1062033, again only in women: adjusted synergy factor=1.94 (1.16-3.25, 0.01). Aromatase, a rate-limiting enzyme in the synthesis of estrogens, is expressed in AD-relevant brain regions ,and is downregulated during the disease. IL-10 is an anti-inflammatory cytokine. Given that estrogens have neuroprotective and anti-inflammatory activities and regulate microglial cytokine production, epistasis is biologically plausible. Diminishing serum estrogen in postmenopausal women, coupled with suboptimal brain estrogen synthesis, may contribute to the inflammatory state, that is a pathological hallmark of AD.
FENDL/E-2.0. Evaluated nuclear data library of neutron-nucleus interaction cross sections and photon production cross sections and photon-atom interaction cross sections for fusion applications. Version 1, March 1997. Summary documentation

International Nuclear Information System (INIS)

Pashchenko, A.B.; Wienke, H.

1998-01-01

This document presents the description of a physical tape containing the basic evaluated nuclear data library of neutron-nucleus interaction cross sections, photon production cross sections and photon-atom interaction cross sections for fusion applications. It is part of the evaluated nuclear data library for fusion applications FENDL-2. The data are available cost-free from the Nuclear Data Section upon request. The data can also be retrieved by the user via online access through international computer networks. (author)
SLP-2 interacts with Parkin in mitochondria and prevents mitochondrial dysfunction in Parkin-deficient human iPSC-derived neurons and Drosophila.

Science.gov (United States)

Zanon, Alessandra; Kalvakuri, Sreehari; Rakovic, Aleksandar; Foco, Luisa; Guida, Marianna; Schwienbacher, Christine; Serafin, Alice; Rudolph, Franziska; Trilck, Michaela; Grünewald, Anne; Stanslowsky, Nancy; Wegner, Florian; Giorgio, Valentina; Lavdas, Alexandros A; Bodmer, Rolf; Pramstaller, Peter P; Klein, Christine; Hicks, Andrew A; Pichler, Irene; Seibler, Philip

2017-07-01

Mutations in the Parkin gene (PARK2) have been linked to a recessive form of Parkinson's disease (PD) characterized by the loss of dopaminergic neurons in the substantia nigra. Deficiencies of mitochondrial respiratory chain complex I activity have been observed in the substantia nigra of PD patients, and loss of Parkin results in the reduction of complex I activity shown in various cell and animal models. Using co-immunoprecipitation and proximity ligation assays on endogenous proteins, we demonstrate that Parkin interacts with mitochondrial Stomatin-like protein 2 (SLP-2), which also binds the mitochondrial lipid cardiolipin and functions in the assembly of respiratory chain proteins. SH-SY5Y cells with a stable knockdown of Parkin or SLP-2, as well as induced pluripotent stem cell-derived neurons from Parkin mutation carriers, showed decreased complex I activity and altered mitochondrial network morphology. Importantly, induced expression of SLP-2 corrected for these mitochondrial alterations caused by reduced Parkin function in these cells. In-vivo Drosophila studies showed a genetic interaction of Parkin and SLP-2, and further, tissue-specific or global overexpression of SLP-2 transgenes rescued parkin mutant phenotypes, in particular loss of dopaminergic neurons, mitochondrial network structure, reduced ATP production, and flight and motor dysfunction. The physical and genetic interaction between Parkin and SLP-2 and the compensatory potential of SLP-2 suggest a functional epistatic relationship to Parkin and a protective role of SLP-2 in neurons. This finding places further emphasis on the significance of Parkin for the maintenance of mitochondrial function in neurons and provides a novel target for therapeutic strategies. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Evaluating Treatments for Functionally Equivalent Problem Behavior Maintained by Adult Compliance with Mands during Interactive Play

Science.gov (United States)

Schmidt, Jonathan D.; Bednar, Mary K.; Willse, Lena V.; Goetzel, Amanda L.; Concepcion, Anthony; Pincus, Shari M.; Hardesty, Samantha L.; Bowman, Lynn G.

2017-01-01

A primary goal of behavioral interventions is to reduce dangerous or inappropriate behavior and to generalize treatment effects across various settings. However, there is a lack of research evaluating generalization of treatment effects while individuals with functionally equivalent problem behavior interact with each other. For the current study,…
Evaluating the usability of an interactive, bi-lingual, touchscreen-enabled breastfeeding educational programme: application of Nielson’s heuristics

OpenAIRE

Ashish Joshi; Douglas M Puricelli Perin; Chioma Amadi; Kate Trout

2015-01-01

Background: Usability challenges have to be met in an interactive computer program development and should meet all users’ needs. Objective: The study purpose was to conduct heuristic evaluation of an interactive, bilingual touch screen enabled breastfeeding educational program for Hispanic women living in rural settings.Methods: Two usability experts used Nielsen’s heuristics while reviewing the user interface in May 2013 using principles of Nielson’s Heuristics. Nielson’s heuristics are a se...
A/α-specific effect of the mms3 mutation on ultraviolet mutagenesis in Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Martin, P.; Prakash, L.; Prakash, S.

1981-01-01

A new gene involved in error-prone repair of ultraviolet (uv) damage has been identified in Saccharomyces cerevisiae by the mms3-1 mutation. Uv-induced reversion is reduced in diploids that are homozygous for mms3-1, only if they are also heterozygous (MATa/MATα) at the mating type locus. The mms3-1 mutation has no effect on uv-induced reversion either in haploids or MATa/MATα or MATα/MATα diploids. The mutation confers sensitivity to uv and methyl methane sulfonate in both haploids and diploids. Even though mutation induction by uv is restored to wild-type levels in MATa/MATa mms3-1/mms3-1 or MATα/MATα mms3-1/mms3-1 diploids, such strains still retain sensitivity to the lethal effects of uv. Survival after uv irradiation in mms3-1 rad double mutant combinations indicates that mms3-1 is epistatic to rad6-1 whereas non-epistatic interactions are observed with rad3 and rad52 mutants. When present in the homozygous state in MATa/MATα his1-1/his1-315 heteroallelic diploids, mms3-1 was found to lower uv-induced mitotic recombination
[Systematic evaluation of retention behavior of carbohydrates in hydrophilic interaction liquid chromatography].

Science.gov (United States)

Fu, Qing; Wang, Jun; Liang, Tu; Xu, Xiaoyong; Jin, Yu

2013-11-01

A systematic evaluation of retention behavior of carbohydrates in hydrophilic interaction liquid chromatography (HILIC) was performed. The influences of mobile phase, stationary phase and buffer salt on the retention of carbohydrates were investigated. According to the results, the retention time of carbohydrates decreased as the proportion of acetonitrile in mobile phase decreased. Increased time of carbohydrates was observed as the concentration of buffer salt in mobile phase increased. The retention behavior of carbohydrates was also affected by organic solvent and HILIC stationary phase. Furthermore, an appropriate retention equation was used in HILIC mode. The retention equation lnk = a + blnC(B) + cC(B) could quantitatively describe the retention factors of carbohydrates of plant origin with good accuracy: the relative error of the predicted time to actual time was less than 0.3%. The evaluation results could provide guidance for carbohydrates to optimize the experimental conditions in HILIC method development especially for carbohydrate separation
Evaluation of crack interaction effect for in-plane surface cracks using elastic finite element analyses

International Nuclear Information System (INIS)

Huh, Nam Su; Choi, Suhn; Park, Keun Bae; Kim, Jong Min; Choi, Jae Boong; Kim, Young Jin

2008-01-01

The crack-tip stress fields and fracture mechanics assessment parameters, such as the elastic stress intensity factor and the elastic-plastic J-integral, for a surface crack can be significantly affected by adjacent cracks. Such a crack interaction effect due to multiple cracks can magnify the fracture mechanics assessment parameters. There are many factors to be considered, for instance the relative distance between adjacent cracks, crack shape and loading condition, to quantify a crack interaction effect on the fracture mechanics assessment parameters. Thus, the current guidance on a crack interaction effect (crack combination rule), including ASME Sec. XI, BS7910, British Energy R6 and API RP579, provide different rules for combining multiple surface cracks into a single surface crack. The present paper investigates a crack interaction effect by evaluating the elastic stress intensity factor of adjacent surface cracks in a plate along the crack front through detailed 3-dimensional elastic finite element analyses. The effects of the geometric parameters, the relative distance between cracks and the crack shape, on the stress intensity factor are systematically investigated. As for the loading condition, only axial tension is considered. Based on the elastic finite element results, the acceptability of the crack combination rules provided in the existing guidance was investigated, and the relevant recommendations on a crack interaction for in-plane surface cracks in a plate were discussed
Evaluating the usability of an interactive, bi-lingual, touchscreen-enabled breastfeeding educational programme: application of Nielson’s heuristics

Directory of Open Access Journals (Sweden)

Ashish Joshi

2015-03-01

Full Text Available Background: Usability challenges have to be met in an interactive computer program development and should meet all users’ needs. Objective: The study purpose was to conduct heuristic evaluation of an interactive, bilingual touch screen enabled breastfeeding educational program for Hispanic women living in rural settings.Methods: Two usability experts used Nielsen’s heuristics while reviewing the user interface in May 2013 using principles of Nielson’s Heuristics. Nielson’s heuristics are a set of usability engineering principles developed to identify issues in user interface design and involves analysis of the interface. The heuristic evaluations were carried out in the interface, program sections, and interactive educational modules. A total of 271 screens were evaluated and included: interface (n=5, program sections (n=223 and educational content (n=43.Results: A total of 97 violations were identified and were mostly related to interface (8violations/5screens and program components (89violations/266screens. The most common violations reported were recognition rather than recall (62%, n=60, consistency and standards (14%, n=14, and match between the system and real world (9%, n= 9. Majority of the violations had minor usability issues (73%, n=71. The only catastrophic violation reported was due to the visibility of system status in the assessment modules.Conclusion: The results demonstrated that the system was more consistent with Nielsen’s usability heuristics.
Modelling the Interaction Levels in HCI Using an Intelligent Hybrid System with Interactive Agents: A Case Study of an Interactive Museum Exhibition Module in Mexico

Directory of Open Access Journals (Sweden)

Ricardo Rosales

2018-03-01

Full Text Available Technology has become a necessity in our everyday lives and essential for completing activities we typically take for granted; technologies can assist us by completing set tasks or achieving desired goals with optimal affect and in the most efficient way, thereby improving our interactive experiences. This paper presents research that explores the representation of user interaction levels using an intelligent hybrid system approach with agents. We evaluate interaction levels of Human-Computer Interaction (HCI with the aim of enhancing user experiences. We consider the description of interaction levels using an intelligent hybrid system to provide a decision-making system to an agent that evaluates interaction levels when using interactive modules of a museum exhibition. The agents represent a high-level abstraction of the system, where communication takes place between the user, the exhibition and the environment. In this paper, we provide a means to measure the interaction levels and natural behaviour of users, based on museum user-exhibition interaction. We consider that, by analysing user interaction in a museum, we can help to design better ways to interact with exhibition modules according to the properties and behaviour of the users. An interaction-evaluator agent is proposed to achieve the most suitable representation of the interaction levels with the aim of improving user interactions to offer the most appropriate directions, services, content and information, thereby improving the quality of interaction experienced between the user-agent and exhibition-agent.
Fixation Probability in a Two-Locus Model by the Ancestral Recombination–Selection Graph

Science.gov (United States)

Lessard, Sabin; Kermany, Amir R.

2012-01-01

We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial. This holds at least as long as the recombination fraction and the selection intensity are small enough and the population size is large enough. In particular this confirms the Hill–Robertson effect, which predicts that recombination renders more likely the ultimate fixation of beneficial mutants at different loci in a population in the presence of random genetic drift even in the absence of epistasis. More importantly, we show that this is true from weak negative epistasis to positive epistasis, at least under weak selection. In the case of deleterious mutants, the fixation probability decreases as the recombination rate increases. This supports Muller’s ratchet mechanism to explain the accumulation of deleterious mutants in a population lacking recombination. PMID:22095080
Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa.

Science.gov (United States)

Zhou, Daling; Du, Qingzhang; Chen, Jinhui; Wang, Qingshi; Zhang, Deqiang

2017-10-01

Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
Identification of metabolic QTLs and candidate genes for glucosinolate synthesis in Brassica oleracea leaves, seeds and flower buds.

Directory of Open Access Journals (Sweden)

Tamara Sotelo

Full Text Available Glucosinolates are major secondary metabolites found in the Brassicaceae family. These compounds play an essential role in plant defense against biotic and abiotic stresses, but more interestingly they have beneficial effects on human health. We performed a genetic analysis in order to identify the genome regions regulating glucosinolates biosynthesis in a DH mapping population of Brassica oleracea. In order to obtain a general overview of regulation in the whole plant, analyses were performed in the three major organs where glucosinolates are synthesized (leaves, seeds and flower buds. Eighty two significant QTLs were detected, which explained a broad range of variability in terms of individual and total glucosinolate (GSL content. A meta-analysis rendered eighteen consensus QTLs. Thirteen of them regulated more than one glucosinolate and its content. In spite of the considerable variability of glucosinolate content and profiles across the organ, some of these consensus QTLs were identified in more than one tissue. Consensus QTLs control the GSL content by interacting epistatically in complex networks. Based on in silico analysis within the B. oleracea genome along with synteny with Arabidopsis, we propose seven major candidate loci that regulate GSL biosynthesis in the Brassicaceae family. Three of these loci control the content of aliphatic GSL and four of them control the content of indolic glucosinolates. GSL-ALK plays a central role in determining aliphatic GSL variation directly and by interacting epistatically with other loci, thus suggesting its regulatory effect.
Evaluation of Two Methods for Modeling Measurement Errors When Testing Interaction Effects with Observed Composite Scores

Science.gov (United States)

Hsiao, Yu-Yu; Kwok, Oi-Man; Lai, Mark H. C.

2018-01-01

Path models with observed composites based on multiple items (e.g., mean or sum score of the items) are commonly used to test interaction effects. Under this practice, researchers generally assume that the observed composites are measured without errors. In this study, we reviewed and evaluated two alternative methods within the structural…
Development and evaluation of an interactive electronic laboratory manual for cooperative learning of medical histology.

Science.gov (United States)

Khalil, Mohammed K; Kirkley, Debbie L; Kibble, Jonathan D

2013-01-01

This article describes the development of an interactive computer-based laboratory manual, created to facilitate the teaching and learning of medical histology. The overarching goal of developing the manual is to facilitate self-directed group interactivities that actively engage students during laboratory sessions. The design of the manual includes guided instruction for students to navigate virtual slides, exercises for students to monitor learning, and cases to provide clinical relevance. At the end of the laboratory activities, student groups can generate a laboratory report that may be used to provide formative feedback. The instructional value of the manual was evaluated by a questionnaire containing both closed-ended and open-ended items. Closed-ended items using a five-point Likert-scale assessed the format and navigation, instructional contents, group process, and learning process. Open-ended items assessed student's perception on the effectiveness of the manual in facilitating their learning. After implementation for two consecutive years, student evaluation of the manual was highly positive and indicated that it facilitated their learning by reinforcing and clarifying classroom sessions, improved their understanding, facilitated active and cooperative learning, and supported self-monitoring of their learning. Copyright © 2013 American Association of Anatomists.
Comparative evaluation of the drug interaction screening programs MediQ and ID PHARMA CHECK in neurological inpatients.

Science.gov (United States)

Zorina, Olesya I; Haueis, Patrick; Semmler, Alexander; Marti, Isabelle; Gonzenbach, Roman R; Guzek, Markus; Kullak-Ublick, Gerd A; Weller, Michael; Russmann, Stefan

2012-08-01

The comparative evaluation of clinical decision support software (CDSS) programs regarding their sensitivity and positive predictive value for the identification of clinically relevant drug interactions. In this research, we used a cross-sectional study that identified potential drug interactions using the CDSS MediQ and the ID PHARMA CHECK in 484 neurological inpatients. Interactions were reclassified according to the Zurich Interaction System, a multidimensional classification that incorporates the Operational Classification of Drug Interactions. In 484 patients with 2812 prescriptions, MediQ and ID PHARMA CHECK generated a total of 1759 and 1082 alerts, respectively. MediQ identified 658 unique potentially interacting combinations, 8 classified as "high danger," 164 as "average danger," and 486 as "low danger." ID PHARMA CHECK detected 336 combinations assigned to one or several of 12 risk and management categories. Altogether, both CDSS issued alerts relating to 808 unique potentially interacting combinations. According to the Zurich Interaction System, 6 of these were contraindicated, 25 were provisionally contraindicated, 190 carried a conditional risk, and 587 had a minimal risk of adverse events. The positive predictive value for alerts having at least a conditional risk was 0.24 for MediQ and 0.48 for ID PHARMA CHECK. CDSS showed major differences in the identification and grading of interactions, and many interactions were only identified by one of the two CDSS. For both programs, only a small proportion of all identified interactions appeared clinically relevant, and the selected display of alerts that imply management changes is a key issue in the further development and local setup of such programs. Copyright © 2012 John Wiley & Sons, Ltd.
A discussion of techniques used in defining the Interactive Measurement Evaluation and Control System at Rocky Flats

International Nuclear Information System (INIS)

Greer, B.K.; Hunt, V.; Schweitzer, M.F.

1983-01-01

This paper describes both the general methodology used to study the current needs for a measurement control and evaluation system at Rocky Flats Plant and the recommendations for implementation into the Interactive Measurement Evaluation and Control System (IMECS). The study resulted in a clear assessment of the current system and recommendations for the system which will be its replacement. To arrive at the recommendations, the authors used a formal analysis approach that is based on an in-depth study of the measurement evaluation and control problems and user needs. The problems and needs were defined by interviews with present and potential users of this kind of system throughout the nuclear industry. Some of the recommendations are to provide: timely sample measurement feedback; representative measurement error estimates; a history data base of sample measurements To meet the user needs, the new system will: be interactive with user selection menus; use standards which cover the range of application; facilitate historical analysis of sample data and bookkeeping. The implementation of this program is projected to be more cost effective than the current program. Also included are the authors' recommendations to those involved in the design of a system of similar large magnitude
Using publicly available data to quantify plant–pollinator interactions and evaluate conservation seeding mixes in the Northern Great Plains

Science.gov (United States)

Otto, Clint R.; O'Dell, Samuel; Bryant, R. B.; Euliss, Ned H. Jr.; Bush, Rachel; Smart, Matthew

2017-01-01

Concern over declining pollinators has led to multiple conservation initiatives for improving forage for bees in agroecosystems. Using data available through the Pollinator Library (npwrc.usgs.gov/pollinator/), we summarize plant–pollinator interaction data collected from 2012–2015 on lands managed by the U.S. Fish and Wildlife Service and private lands enrolled in U.S. Department of Agriculture conservation programs in eastern North Dakota (ND). Furthermore, we demonstrate how plant–pollinator interaction data from the Pollinator Library and seed cost information can be used to evaluate hypothetical seeding mixes for pollinator habitat enhancements. We summarize records of 314 wild bee and 849 honey bee (Apis mellifera L.) interactions detected on 63 different plant species. The wild bee observations consisted of 46 species, 15 genera, and 5 families. Over 54% of all wild bee observations were represented by three genera―Bombus, Lassioglossum, and Melissodes. The most commonly visited forbs by wild bees were Monarda fistulosa, Sonchus arvensis, and Zizia aurea. The most commonly visited forbs by A. mellifera were Cirsium arvense, Melilotus officinalis, and Medicago sativa. Among all interactions, 13% of A. mellifera and 77% of wild bee observations were made on plants native to ND. Our seed mix evaluation shows that mixes may often need to be tailored to meet the unique needs of wild bees and managed honey bees in agricultural landscapes. Our evaluation also demonstrates the importance of incorporating both biologic and economic information when attempting to design cost-effective seeding mixes for supporting pollinators in a critically important part of the United States.

Relevance Epistasis Network of Gastritis for Intra-chromosomes in the Korea Associated Resource (KARE Cohort Study

Directory of Open Access Journals (Sweden)

Hyun-hwan Jeong

2014-12-01

Full Text Available Gastritis is a common but a serious disease with a potential risk of developing carcinoma. Helicobacter pylori infection is reported as the most common cause of gastritis, but other genetic and genomic factors exist, especially single-nucleotide polymorphisms (SNPs. Association studies between SNPs and gastritis disease are important, but results on epistatic interactions from multiple SNPs are rarely found in previous genome-wide association (GWA studies. In this study, we performed computational GWA case-control studies for gastritis in Korea Associated Resource (KARE data. By transforming the resulting SNP epistasis network into a gene-gene epistasis network, we also identified potential gene-gene interaction factors that affect the susceptibility to gastritis.
Evaluation of Early Ground Control Station Configurations for Interacting with a UAS Traffic Management (UTM) System

Science.gov (United States)

Dao, Arik-Quang V.; Martin, Lynne; Mohlenbrink, Christoph; Bienert, Nancy; Wolte, Cynthia; Gomez, Ashley; Claudatos, Lauren; Mercer, Joey

2017-01-01

The purpose of this paper is to report on a human factors evaluation of ground control station design concepts for interacting with an unmanned traffic management system. The data collected for this paper comes from recent field tests for NASA's Unmanned Traffic Management (UTM) project, and covers the following topics; workload, situation awareness, as well as flight crew communication, coordination, and procedures. The goal of this evaluation was to determine if the various software implementations for interacting with the UTM system can be described and classified into design concepts to provide guidance for the development of future UTM interfaces. We begin with a brief description of NASA's UTM project, followed by a description of the test range configuration related to a second development phase. We identified (post hoc) two classes in which the ground control stations could be grouped. This grouping was based on level of display integration. The analysis was exploratory and informal. It was conducted to compare ground stations across those two classes and against the aforementioned topics. Herein, we discuss the results.
Evaluation of an interactive, case-based review session in teaching medical microbiology.

Science.gov (United States)

Blewett, Earl L; Kisamore, Jennifer L

2009-08-27

Oklahoma State University-Center for Health Sciences (OSU-CHS) has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial. Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session. Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session. The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified.
Hydroxyurea-Lactose Interaction Study: In Silico and In Vitro Evaluation.

Science.gov (United States)

Bachchhao, Kunal B; Patil, R R; Patil, C R; Patil, Dipak D

2017-11-01

The Maillard reaction between hydroxyurea (a primary amine-containing drug) and lactose (used as an excipient) was explored. The adduct of these compounds was synthesized by heating hydroxyurea with lactose monohydrate at 60 °C in borate buffer (pH 9.2) for 12 h. Synthesis of the adduct was confirmed using UV-visible spectroscopy and Fourier transform infrared, differential scanning calorimetry, high-pressure liquid chromatography, and liquid chromatography-mass spectrometry studies. An in silico investigation of how the adduct formation affected the interactions of hydroxyurea with its biological target oxyhemoglobin, to which it binds to generate nitric oxide and regulates fetal hemoglobin synthesis, was carried out. The in silico evaluations were complemented by an in vitro assay of the anti-sickling activity. Co-incubation of hydroxyurea with deoxygenated blood samples reduced the percentage of sickled cells from 38% to 12 ± 1.6%, whereas the percentage of sickled cells in samples treated with the adduct was 17 ± 1.2%. This indicated loss of anti-sickling activity in the case of the adduct. This study confirmed that hydroxyurea can participate in a Maillard reaction if lactose is used as a diluent. Although an extended study at environmentally feasible temperatures was not carried out in the present investigation, the partial loss of the anti-sickling activity of hydroxyurea was investigated along with the in silico drug-target interactions. The results indicated that the use of lactose in hydroxyurea formulations needs urgent reconsideration and that lactose must be replaced by other diluents that do not form Maillard adducts.
Evaluation of Mobile Phones for Large Display Interaction

OpenAIRE

Bauer, Jens; Thelen, Sebastian; Ebert, Achim

2012-01-01

Large displays have become more and more common in the last few years. While interaction with these displays can be conducted using standard methods such as computer mouse and keyboard, this approach causes issues in multi-user environments, where the various conditions for providing multiple keyboards and mice, together with the facilities to employ them, cannot be met. To solve this problem, interaction using mobile phones was proposed by several authors. Previous solutions were specialized...
Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods.

Science.gov (United States)

Christensen, Anders S; Kromann, Jimmy C; Jensen, Jan H; Cui, Qiang

2017-10-28

To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy in solution is computed via a thermodynamic cycle that integrates dimer binding energy in the gas phase at the coupled cluster level and solute-solvent interaction with density functional theory; the estimated uncertainty of such calculated interaction energy is ±1.5 kcal/mol. The dataset is used to benchmark the performance of a set of semi-empirical quantum mechanical (SQM) methods that include DFTB3-D3, DFTB3/CPE-D3, OM2-D3, PM6-D3, PM6-D3H+, and PM7 as well as the HF-3c method. We find that while all tested SQM methods tend to underestimate binding energies in the gas phase with a root-mean-squared error (RMSE) of 2-5 kcal/mol, they overestimate binding energies in the solution phase with an RMSE of 3-4 kcal/mol, with the exception of DFTB3/CPE-D3 and OM2-D3, for which the systematic deviation is less pronounced. In addition, we find that HF-3c systematically overestimates binding energies in both gas and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need to be treated in a balanced fashion.
Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods

Science.gov (United States)

Christensen, Anders S.; Kromann, Jimmy C.; Jensen, Jan H.; Cui, Qiang

2017-10-01

To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy in solution is computed via a thermodynamic cycle that integrates dimer binding energy in the gas phase at the coupled cluster level and solute-solvent interaction with density functional theory; the estimated uncertainty of such calculated interaction energy is ±1.5 kcal/mol. The dataset is used to benchmark the performance of a set of semi-empirical quantum mechanical (SQM) methods that include DFTB3-D3, DFTB3/CPE-D3, OM2-D3, PM6-D3, PM6-D3H+, and PM7 as well as the HF-3c method. We find that while all tested SQM methods tend to underestimate binding energies in the gas phase with a root-mean-squared error (RMSE) of 2-5 kcal/mol, they overestimate binding energies in the solution phase with an RMSE of 3-4 kcal/mol, with the exception of DFTB3/CPE-D3 and OM2-D3, for which the systematic deviation is less pronounced. In addition, we find that HF-3c systematically overestimates binding energies in both gas and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need to be treated in a balanced fashion.
An Evaluation of the Interactive Query Expansion in an Online Library Catalogue with a Graphical User Interface.

Science.gov (United States)

Hancock-Beaulieu, Micheline; And Others

1995-01-01

An online library catalog was used to evaluate an interactive query expansion facility based on relevance feedback for the Okapi, probabilistic, term weighting, retrieval system. A graphical user interface allowed searchers to select candidate terms extracted from relevant retrieved items to reformulate queries. Results suggested that the…
Evaluation of documented drug interactions and contraindications associated with herbs and dietary supplements: a systematic literature review.

Science.gov (United States)

Tsai, H-H; Lin, H-W; Simon Pickard, A; Tsai, H-Y; Mahady, G B

2012-11-01

The use of herbs and dietary supplements (HDS) alone or concomitantly with medications can potentially increase the risk of adverse events experienced by the patients. This review aims to evaluate the documented HDS-drug interactions and contraindications. A structured literature review was conducted on PubMed, EMBASE, Cochrane Library, tertiary literature and Internet. While 85 primary literatures, six books and two web sites were reviewed for a total of 1,491 unique pairs of HDS-drug interactions, 213 HDS entities and 509 medications were involved. HDS products containing St. John's Wort, magnesium, calcium, iron, ginkgo had the greatest number of documented interactions with medications. Warfarin, insulin, aspirin, digoxin, and ticlopidine had the greatest number of reported interactions with HDS. Medications affecting the central nervous system or cardiovascular system had more documented interactions with HDS. Of the 882 HDS-drug interactions being described its mechanism and severity, 42.3% were due to altered pharmacokinetics and 240 were described as major interactions. Of the 152 identified HDS contraindications, the most frequent involved gastrointestinal (16.4%), neurological (14.5%), and renal/genitourinary diseases (12.5%). Flaxseed, echinacea, and yohimbe had the largest number of documented contraindications. Although HDS-drug interactions and contraindications primarily concerned a relatively small subset of commonly used medications and HDS entities, this review provides the summary to identify patients, HDS products, and medications that are more susceptible to HDS-drug interactions and contraindications. The findings would facilitate the health-care professionals to communicate these documented interactions and contraindications to their patients and/or caregivers thereby preventing serious adverse events and improving desired therapeutic outcomes. © 2012 Blackwell Publishing Ltd.
Evaluating Multiple Levels of an Interaction Fidelity Continuum on Performance and Learning in Near-Field Training Simulations.

Science.gov (United States)

Bhargava, Ayush; Bertrand, Jeffrey W; Gramopadhye, Anand K; Madathil, Kapil C; Babu, Sabarish V

2018-04-01

With costs of head-mounted displays (HMDs) and tracking technology decreasing rapidly, various virtual reality applications are being widely adopted for education and training. Hardware advancements have enabled replication of real-world interactions in virtual environments to a large extent, paving the way for commercial grade applications that provide a safe and risk-free training environment at a fraction of the cost. But this also mandates the need to develop more intrinsic interaction techniques and to empirically evaluate them in a more comprehensive manner. Although there exists a body of previous research that examines the benefits of selected levels of interaction fidelity on performance, few studies have investigated the constituent components of fidelity in a Interaction Fidelity Continuum (IFC) with several system instances and their respective effects on performance and learning in the context of a real-world skills training application. Our work describes a large between-subjects investigation conducted over several years that utilizes bimanual interaction metaphors at six discrete levels of interaction fidelity to teach basic precision metrology concepts in a near-field spatial interaction task in VR. A combined analysis performed on the data compares and contrasts the six different conditions and their overall effects on performance and learning outcomes, eliciting patterns in the results between the discrete application points on the IFC. With respect to some performance variables, results indicate that simpler restrictive interaction metaphors and highest fidelity metaphors perform better than medium fidelity interaction metaphors. In light of these results, a set of general guidelines are created for developers of spatial interaction metaphors in immersive virtual environments for precise fine-motor skills training simulations.
A life evaluation under creep-fatigue-environment interaction of Ni-base wrought alloys

International Nuclear Information System (INIS)

Hattori, Hiroshi; Kitagawa, Masaki; Ohtomo, Akira; Itoh, Mitsuyoshi

1986-01-01

In order to determine a failure criteria under cyclic loading and affective environment for HTGR systems, a series of strain controlled low-cycle fatigue tests were carried out at HTGR maximum gas temperatures in air, in vacuum and in HTGR helium environments on two nickel-base wrought alloys, namely Inconel 617 and Hastelloy XR. This paper first describes the creep-fatigue-environment properties of these alloys followed by a proposal of an evaluation method of creep-fatigue-environment interaction based on the experimental data to define the more reasonable design criteria, which is a modification of the linear damage summation rule. Second, the creep-fatigue properties of Hastelloy XR at 900 deg C and the result evaluated by this proposed method are shown. This criterion is successfully applied to the life prediction at 900 deg C. In addition, the creep-fatigue properties of Hastelloy XR-II are discussed. (author)
Interactive benchmarking

DEFF Research Database (Denmark)

Lawson, Lartey; Nielsen, Kurt

2005-01-01

We discuss individual learning by interactive benchmarking using stochastic frontier models. The interactions allow the user to tailor the performance evaluation to preferences and explore alternative improvement strategies by selecting and searching the different frontiers using directional...... in the suggested benchmarking tool. The study investigates how different characteristics on dairy farms influences the technical efficiency....
[Evaluate drug interaction of multi-components in Morus alba leaves based on α-glucosidase inhibitory activity].

Science.gov (United States)

Ji, Tao; Su, Shu-Lan; Guo, Sheng; Qian, Da-Wei; Ouyang, Zhen; Duan, Jin-Ao

2016-06-01

Column chromatography was used for enrichment and separation of flavonoids, alkaloids and polysaccharides from the extracts of Morus alba leaves; glucose oxidase method was used with sucrose as the substrate to evaluate the multi-components of M. alba leaves in α-glucosidase inhibitory models; isobole method, Chou-Talalay combination index analysis and isobolographic analysis were used to evaluate the interaction effects and dose-effect characteristics of two components, providing scientific basis for revealing the hpyerglycemic mechanism of M. alba leaves. The components analysis showed that flavonoid content was 5.3%; organic phenolic acids content was 10.8%; DNJ content was 39.4%; and polysaccharide content was 18.9%. Activity evaluation results demonstrated that flavonoids, alkaloids and polysaccharides of M. alba leaves had significant inhibitory effects on α-glucosidase, and the inhibitory rate was increased with the increasing concentration. Alkaloids showed most significant inhibitory effects among these three components. Both compatibility of alkaloids and flavonoids, and the compatibility of alkaloids and polysaccharides demonstrated synergistic effects, but the compatibility of flavonoids and polysaccharides showed no obvious synergistic effects. The results have confirmed the interaction of multi-components from M. alba leaves to regulate blood sugar, and provided scientific basis for revealing hpyerglycemic effectiveness and mechanism of the multi-components from M. alba leaves. Copyright© by the Chinese Pharmaceutical Association.
Evaluation of multiple intelligences in children aged 7 to 11 years through the implementation of an interactive software

OpenAIRE

Rebolledo Rodríguez, Rigel A.; Samaniego González, Euclides

2017-01-01

This document describes the evaluation project of multiple intelligences in children aged 7 to 11 years through the implementation of an interactive software, developed on Android for tablets, allowing parents, teachers, tutors, psy-chologists or other responsible adult, identifying the different types of intelligences that have children in order to know each other and develop their skills and their future potential. Similarly, research was developed to evaluate the effective-ness of the t...
Finite-field evaluation of the Lennard-Jones atom-wall interaction constant C3 for alkali-metal atoms

International Nuclear Information System (INIS)

Johnson, W.R.; Dzuba, V.A.; Safronova, U.I.; Safronova, M.S.

2004-01-01

A finite-field scaling method is applied to evaluate the Lennard-Jones interaction constant C 3 for alkali-metal atoms. The calculations are based on the relativistic single-double approximation in which single and double excitations of Dirac-Hartree-Fock wave functions are included to all orders in perturbation theory
Evaluating Otto the Auto: Does Engagement in an Interactive Website Improve Young Children's Transportation Safety?

Science.gov (United States)

Schwebel, David C; Johnston, Anna; Shen, Jiabin; Li, Peng

2017-07-19

Transportation-related injuries are a leading cause of pediatric death, and effective interventions are limited. Otto the Auto is a website offering engaging, interactive activities. We evaluated Otto among a sample of sixty-nine 4- and 5-year-old children, who participated in a randomized parallel group design study. Following baseline evaluation, children engaged with either Otto or a control website for 2 weeks and then were re-evaluated. Children who used Otto failed to show increases in transportation safety knowledge or behavior compared to the control group, although there was a dosage effect whereby children who engaged in the website more with parents gained safer behavior patterns. We conclude Otto may have some efficacy when engaged by children with their parents, but continued efforts to develop and refine engaging, effective, theory-driven strategies to teach children transportation safety, including via internet, should be pursued.
Evaluation of an interactive, case-based review session in teaching medical microbiology

Directory of Open Access Journals (Sweden)

Kisamore Jennifer L

2009-08-01

Full Text Available Abstract Background Oklahoma State University-Center for Health Sciences (OSU-CHS has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial. Methods Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session. Results Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session. Conclusion The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified.
Evaluation of an interactive, case-based review session in teaching medical microbiology

Science.gov (United States)

Blewett, Earl L; Kisamore, Jennifer L

2009-01-01

Background Oklahoma State University-Center for Health Sciences (OSU-CHS) has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial. Methods Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session. Results Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session. Conclusion The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified. PMID:19712473
Genetic Segregation Analysis of a Rapeseed Dwarf Mutant

International Nuclear Information System (INIS)

Xiang, G.; Yu, S.; Zhang, T.; Zhao, J.; Lei, S.; Du, C.

2016-01-01

Dwarf resources in Brassica napus are very important for developing high-yield cultivars through dwarf-type and lodging-resistant breeding. However, few dwarf varieties have been available for this species. Here, we reported a new rapeseed dwarf mutant GRC1157, which exhibits obvious phenotypic variations on dwarf. Six generations (P /sub 1/, P/sub 1/, F/sub 1/, F/sub 1/, B/sub 1/, and B/sub 1/) were produced from a cross between dwarf mutant GRC1157 and an elite tall-type line XR16 to analyze genetic inheritances of plant height (PH), numbers of the 1st valid branch (VBN), main inflorescence length (MIL), pod numbers per main inflorescence (MPN), pod length (PL) and seed numbers per pod (PSN) using the mixed major gene plus polygene inheritance model. The genetic analysis shows different traits were controlled by different inheritance models: PH and PL by two pairs of additive-dominant-epistatic major genes plus additive-dominant-epistatic polygenes, MPN and PSN by two-pair additive-dominant-epistatic major genes plus additive-dominant polygenes, MIL by two-pair additive-dominant-epistatic major genes and VBN by one-pair additive-dominant major genes plus additive-dominant-epistatic polygenes. Furthermore, positive correlations between PH and some other traits were observed, suggesting that some traits may be co-regulated by several linkage or same loci/genes. In addition, high heritability (40.35-93.7 percent) were found for five traits (except VBN) in different segregating generations, indicating these traits were mainly affected by hereditary factors and suitable for early artificial selection. In sum, the dwarf mutant GRC1157 can serve as a valuable resource for rapeseed dwarf breeding and the genetic analysis in this study provided a foundation for further mapping and cloning dwarf genes in mutant GRC1157. (author)
CountMeIn: Evaluating Social Presence in a Collaborative Pervasive Mobile Game Using NFC and Touchscreen Interaction

NARCIS (Netherlands)

Wolbert, M.; El Ali, A.; Nack, F.

2014-01-01

This paper presents the motivation, design and evaluation of CountMeIn, a mobile collaborative pervasive memory game to revive social interactions in public places (e.g. a train station or bus stop). Two versions of CountMeIn were tested; an NFC-based and a touchscreen version. In a 2×1

WIPP [Waste Isolation Pilot Plant] panel entryway seal: Numerical simulation of seal composite interaction for preliminary design evaluation

International Nuclear Information System (INIS)

Argueello, J.G.

1988-04-01

This report presents the results of a series of structural analyses performed to evaluate the structural interaction of the components of a potential two-component panel entryway seal configuration with each other and with the rock salt formation at the repository horizon of the Waste Isolation Pilot Plant. A two-dimensional axisymmetric geomechanical model is used to numerically simulate the interaction of the components of a 30.48 m (100 ft) long seal, consisting of concrete end caps and a crushed salt core, with each other and with the surrounding formation. Issues addressed in this report pertain to the consolidation of the crushed salt in terms of how much of the seal core reaches effective consolidation in the presence of the stiff concrete end caps since these could conceivably cause bridging (retardation of closure around the core) to occur. In addition, the stress field in the end caps is evaluated to determine if the concrete component maintains its integrity. The stresses induced in the surrounding formation are also evaluated to determine if the presence of the concrete component in the seal system results in a ''tightening'' of the formation around the seal. 20 refs., 43 figs., 2 tabs
Interaction of atmospheric pollutants

Energy Technology Data Exchange (ETDEWEB)

Bustueva, K A; Sanotsky, I V

1975-01-01

In evaluating the health effects of chemical and physical factors, it is of great importance to know the possible interactions between different pollutants. The biological effects of interactions, when present, may be synergistic, antagonistic or additive. Each type of interaction calls for a different evaluation and different practical measures. As yet the understanding of such effects is not clear, probably because of differing definitions of terminology. For example, the combined effect of sulfur dioxide and particulates is interpreted as a synergistic effect; in the author's opinion, this is an aggravating effect. The type of interaction depends on the levels of concentration observed, for example, the synergism shown at high levels of concentration is not always demonstrated for low levels of concentration. In fact there is little evidence of synergistic effects from ambient air pollutant; the more common type of interaction is additive in effect. 12 references.
Using Publicly Available Data to Quantify Plant-Pollinator Interactions and Evaluate Conservation Seeding Mixes in the Northern Great Plains.

Science.gov (United States)

Otto, C R V; O'Dell, S; Bryant, R B; Euliss, N H; Bush, R M; Smart, M D

2017-06-01

Concern over declining pollinators has led to multiple conservation initiatives for improving forage for bees in agroecosystems. Using data available through the Pollinator Library (npwrc.usgs.gov/pollinator/), we summarize plant-pollinator interaction data collected from 2012-2015 on lands managed by the U.S. Fish and Wildlife Service and private lands enrolled in U.S. Department of Agriculture conservation programs in eastern North Dakota (ND). Furthermore, we demonstrate how plant-pollinator interaction data from the Pollinator Library and seed cost information can be used to evaluate hypothetical seeding mixes for pollinator habitat enhancements. We summarize records of 314 wild bee and 849 honey bee (Apis mellifera L.) interactions detected on 63 different plant species. The wild bee observations consisted of 46 species, 15 genera, and 5 families. Over 54% of all wild bee observations were represented by three genera-Bombus, Lassioglossum, and Melissodes. The most commonly visited forbs by wild bees were Monarda fistulosa, Sonchus arvensis, and Zizia aurea. The most commonly visited forbs by A. mellifera were Cirsium arvense, Melilotus officinalis, and Medicago sativa. Among all interactions, 13% of A. mellifera and 77% of wild bee observations were made on plants native to ND. Our seed mix evaluation shows that mixes may often need to be tailored to meet the unique needs of wild bees and managed honey bees in agricultural landscapes. Our evaluation also demonstrates the importance of incorporating both biologic and economic information when attempting to design cost-effective seeding mixes for supporting pollinators in a critically important part of the United States. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.
Evaluation of Tissue Interactions with Mechanical Elements of a Transscleral Drug Delivery Device

Directory of Open Access Journals (Sweden)

Jeffrey T. Borenstein

2012-03-01

Full Text Available The goal of this work was to evaluate tissue-device interactions due to implantation of a mechanically operated drug delivery system onto the posterior sclera. Two test devices were designed and fabricated to model elements of the drug delivery device—one containing a free-spinning ball bearing and the other encasing two articulating gears. Openings in the base of test devices modeled ports for drug passage from device to sclera. Porous poly(tetrafluoroethylene (PTFE membranes were attached to half of the gear devices to minimize tissue ingrowth through these ports. Test devices were sutured onto rabbit eyes for 10 weeks. Tissue-device interactions were evaluated histologically and mechanically after removal to determine effects on device function and changes in surrounding tissue. Test devices were generally well-tolerated during residence in the animal. All devices encouraged fibrous tissue formation between the sclera and the device, fibrous tissue encapsulation and invasion around the device, and inflammation of the conjunctiva. Gear devices encouraged significantly greater inflammation in all cases and a larger rate of tissue ingrowth. PTFE membranes prevented tissue invasion through the covered drug ports, though tissue migrated in through other smaller openings. The torque required to turn the mechanical elements increased over 1000 times for gear devices, but only on the order of 100 times for membrane-covered gear devices and less than 100 times for ball bearing devices. Maintaining a lower device profile, minimizing microscale motion on the eye surface and covering drug ports with a porous membrane may minimize inflammation, decreasing the risk of damage to surrounding tissues and minimizing disruption of device operation.
Standard problems to evaluate soil structure interaction computer codes

International Nuclear Information System (INIS)

Miller, C.A.; Costantino, C.J.; Philippacopoulos, A.J.

1979-01-01

The seismic response of nuclear power plant structures is often calculated using lumped parameter methods. A finite element model of the structure is coupled to the soil with a spring-dashpot system used to represent the interaction process. The parameters of the interaction model are based on analytic solutions to simple problems which are idealizations of the actual problems of interest. The objective of the work reported in this paper is to compare predicted responses using the standard lumped parameter models with experimental data. These comparisons are shown to be good for a fairly uniform soil system and for loadings which do not result in nonlinear interaction effects such as liftoff. 7 references, 7 figures
Genetics of productive peduncles on main stem and branches in mungbean (vigna radiata (L.) wilczek)

International Nuclear Information System (INIS)

Khattak, G.S.

2010-01-01

Components of genetic variation for productive peduncles on main stem and branches in mungbean were estimated using triple test cross procedure. Treatments used for estimation of genetic variation for both traits exhibited highly significant differences which indicate the existence of considerable genetic variation among inbred lines, testers and developed recombinants. Epistatic effect showed significant role in the inheritance of both traits. Productive peduncles on main stem exhibited almost equal values for both i type, and j + l type non-allelic interaction whereas i type interactions value was more compared to j + l type interactions in productive peduncles on branches. This indicated that additive x additive type non-allelic interaction plays an important role in the inheritance of productive peduncles on branches. The complex inheritance of both traits can be exploited for improvement by delay in selection until the material is advanced through bulk procedure. (author)
Visualization of acoustic particle interaction and agglomeration: Theory evaluation

International Nuclear Information System (INIS)

Hoffmann, T.L.; Koopmann, G.H.

1997-01-01

In this paper experimentally observed trajectories of particles undergoing acoustically induced interaction and agglomeration processes are compared to and validated with numerically generated trajectories based on existing agglomeration theories. Models for orthokinetic, scattering, mutual radiation pressure, and hydrodynamic particle interaction are considered in the analysis. The characteristic features of the classical orthokinetic agglomeration hypothesis, such as collision processes and agglomerations due to the relative entrainment motion, are not observed in the digital images. The measured entrainment rates of the particles are found to be consistently lower than the theoretically predicted values. Some of the experiments reveal certain characteristics which may possibly be related to mutual scattering interaction. The study's most significant discovery is the so-called tuning fork agglomeration [T. L. Hoffmann and G. H. Koopmann, J. Acoust. Soc. Am. 99, 2130 endash 2141 (1996)]. It is shown that this phenomenon contradicts the theories for mutual scattering interaction and mutual radiation pressure interaction, but agrees with the acoustic wake effect model in its intrinsic feature of attraction between particles aligned along the acoustic axis. A model by Dianov et al. [Sov. Phys. Acoust. 13 (3), 314 endash 319 (1968)] is used to describe this effect based on asymmetric flow fields around particles under Oseen flow conditions. It is concluded that this model is consistent with the general characteristics of the tuning fork agglomerations, but lacks certain refinements with respect to accurate quantification of the effect. copyright 1997 Acoustical Society of America
First evaluations of ex-vessel fuel-coolant interaction with MC3D

International Nuclear Information System (INIS)

Meignen, R.; Dupas, J.; Chaumont, B.

2003-01-01

In the frame of severe accident nuclear safety studies, we evaluate for French PWR's the potential of Steam Explosion in the reactor pit, consecutively to a vessel failure and to the mixing of the corium with the water that might be present. The evaluations are made with MC3D. This thermalhydraulic multiphasic code has firstly been qualified and its main parameters chosen so that a sufficient validation is obtained with regards to reactor situations. The safety study for ex-vessel situations is a step-by-step procedure that leads to a progressive process of hypotheses relaxations. We find that it is important to adequately model the corium ejection from the RPV. The rapid transition of the flow at the breach towards 2-phase dispersed flow leads to an important mixing of corium and water. The vessel pressurization is a very important parameter and strong pressure cases lead to a fine fragmentation and thus a high voiding. The small pressure cases are more dangerous for two reasons: the corium is dispersed in larger drops, and some important interactions (in the premixing sense) are reported
Structure and interaction in dense colloidal systems: evaluation of scattering data by the generalized indirect Fourier transformation method

International Nuclear Information System (INIS)

Fritz, Gerhard; Glatter, Otto

2006-01-01

The generalized indirect Fourier transformation (GIFT) technique is a versatile tool for the evaluation of small angle scattering data. It does not depend on models for the size and shape of the particles and requires model assumptions only for the interaction effects that are typically not as sensitive to the details of the assumptions. We review here the development of the technique from its inception, focusing on the included interaction models for hard, charged and attractive spheres, and lamellae. A considerable number of applications has also been reported ranging from surfactants, emulsions, microemulsions, food science, and ceramics to melts and block-copolymers
Design, synthesis, and evaluation of an alpha-helix mimetic library targeting protein-protein interactions.

Science.gov (United States)

Shaginian, Alex; Whitby, Landon R; Hong, Sukwon; Hwang, Inkyu; Farooqi, Bilal; Searcey, Mark; Chen, Jiandong; Vogt, Peter K; Boger, Dale L

2009-04-22

The design and solution-phase synthesis of an alpha-helix mimetic library as an integral component of a small-molecule library targeting protein-protein interactions are described. The iterative design, synthesis, and evaluation of the candidate alpha-helix mimetic was initiated from a precedented triaryl template and refined by screening the designs for inhibition of MDM2/p53 binding. Upon identifying a chemically and biologically satisfactory design and consistent with the screening capabilities of academic collaborators, the corresponding complete library was assembled as 400 mixtures of 20 compounds (20 x 20 x 20-mix), where the added subunits are designed to mimic all possible permutations of the naturally occurring i, i + 4, i + 7 amino acid side chains of an alpha-helix. The library (8000 compounds) was prepared using a solution-phase synthetic protocol enlisting acid/base liquid-liquid extractions for purification on a scale that insures its long-term availability for screening campaigns. Screening of the library for inhibition of MDM2/p53 binding not only identified the lead alpha-helix mimetic upon which the library was based, but also suggests that a digestion of the initial screening results that accompany the use of such a comprehensive library can provide insights into the nature of the interaction (e.g., an alpha-helix mediated protein-protein interaction) and define the key residues and their characteristics responsible for recognition.
Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae

Science.gov (United States)

Bergman, Juraj; Mitrikeski, Petar T.

2015-01-01

Summary Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait. PMID:27904371
The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host

Directory of Open Access Journals (Sweden)

Abdussamad Juwaeriah

2011-01-01

Full Text Available Abstract Background The emergence of the 2009 H1N1 Influenza pandemic followed a multiple reassortment event from viruses originally circulating in swines and humans, but the adaptive nature of this emergence is poorly understood. Results Here we base our analysis on 1180 complete genomes of H1N1 viruses sampled in North America between 2000 and 2010 in swine and human hosts. We show that while transmission to a human host might require an adaptive phase in the HA and NA antigens, the emergence of the 2009 pandemic was essentially nonadaptive. A more detailed analysis of the NA protein shows that the 2009 pandemic sequence is characterized by novel epitopes and by a particular substitution in loop 150, which is responsible for a nonadaptive structural change tightly associated with the emergence of the pandemic. Conclusions Because this substitution was not present in the 1918 H1N1 pandemic virus, we posit that the emergence of pandemics is due to epistatic interactions between sites distributed over different segments. Altogether, our results are consistent with population dynamics models that highlight the epistatic and nonadaptive rise of novel epitopes in viral populations, followed by their demise when the resulting virus is too virulent.
The reality and importance of founder speciation in evolution.

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Templeton, Alan R

2008-05-01

A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone. (c) 2008 Wiley Periodicals, Inc.
Cation-π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation.

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Davis, Matthew R; Dougherty, Dennis A

2015-11-21

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4(+) and NMe4(+) to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the "fluorination strategy" to study cation-π interactions in vivo.
Epistasis can accelerate adaptive diversification in haploid asexual populations.

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Griswold, Cortland K

2015-03-07

A fundamental goal of the biological sciences is to determine processes that facilitate the evolution of diversity. These processes can be separated into ecological, physiological, developmental and genetic. An ecological process that facilitates diversification is frequency-dependent selection caused by competition. Models of frequency-dependent adaptive diversification have generally assumed a genetic basis of phenotype that is non-epistatic. Here, we present a model that indicates diversification is accelerated by an epistatic basis of phenotype in combination with a competition model that invokes frequency-dependent selection. Our model makes use of a genealogical model of epistasis and insights into the effects of balancing selection on the genealogical structure of a population to understand how epistasis can facilitate diversification. The finding that epistasis facilitates diversification may be informative with respect to empirical results that indicate an epistatic basis of phenotype in experimental bacterial populations that experienced adaptive diversification. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
An interactive FORTRAN program for the evaluation of structure factors and pair distribution functions from neutron diffraction experiments

International Nuclear Information System (INIS)

Abel, W.

1985-02-01

This report describes an interactive program to evaluate neutron diffraction data using the Graphic System (GS) under MVS (TSO). Different evaluation steps may be directed by a CLIST. The present program is limited to cylindrical sample geometry. From the fully corrected static structure factor the pair correlation function g(r) and the radial density function may be calculated from which the mean coordination number can be obtained by numerical integration over the main peak. Producing a hardcopy output on a mechanical plotter is provided. (orig.) [de
Quantifying Quality Aspects of Multimodal Interactive Systems

CERN Document Server

Kühnel, Christine

2012-01-01

This book systematically addresses the quantification of quality aspects of multimodal interactive systems. The conceptual structure is based on a schematic view on human-computer interaction where the user interacts with the system and perceives it via input and output interfaces. Thus, aspects of multimodal interaction are analyzed first, followed by a discussion of the evaluation of output and input and concluding with a view on the evaluation of a complete system.
Evaluation of the interaction of surfactants with stratum corneum model membrane from Bothrops jararaca by DSC.

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Baby, André Rolim; Lacerda, Aurea Cristina Lemos; Velasco, Maria Valéria Robles; Lopes, Patrícia Santos; Kawano, Yoshio; Kaneko, Telma Mary

2006-07-06

The interaction of surfactants sodium dodecyl sulfate (SDS), cetyl trimethyl ammonium chloride (CTAC) and lauryl alcohol ethoxylated (12 mol ethylene oxide) (LAE-12OE) was evaluated on the stratum corneum (SC) of shed snake skins from Bothrops jararaca, used as model membrane, and thermal characterized by differential scanning calorimetry (DSC). Surfactant solutions were employed above of the critical micellar concentration (CMC) with treatment time of 8h. The SDS interaction with the SC model membrane has increased the characteristic transition temperature of 130 degrees C in approximately 10 degrees C for the water loss and keratin denaturation, indicating an augmentation of the water content. Samples treated with CTAC have a decrease of the water loss temperature, while, for the LAE-12OE treated samples, changes on the transition temperature have not been observed.
New bases for the evaluation of interaction energies: An ab initio study of the CO-Ne van der Waals complex intermolecular potential and ro-vibrational spectrum

International Nuclear Information System (INIS)

Bouzon Capelo, Silvia; Baranowska-Laczkowska, Angelika; Fernandez, Berta

2011-01-01

Graphical abstract: CO-Ne IPES. Highlights: → From the LPol, MLPol, and aug-pc-2 bases we obtained new bases for the evaluation of CO-Ne interaction energies. → We checked the bases on the evaluation of the rovibrational spectrum. → The results were satisfactory, being the new bases more efficient than those previously available. - Abstract: Recently we have derived new efficient basis sets for the evaluation of interaction energies in the X-Y (X, Y = He, Ne, Ar) van der Waals complexes. Here we extend the study to the CO-Ne complex. For this, we start with a systematic basis set study, where the LPol, MLPol and Jensen's aug-pc-2 basis sets are considered as starting point (for the Ne atom LPol bases are developed). As reference we take interaction energy results obtained with Dunning's augmented correlation consistent polarized valence basis sets. In all cases we test extensions with different sets of midbond functions. With the selected bases we evaluate CCSD(T) interaction potentials, and to check the potentials further, we obtain the ro-vibrational spectrum of the complex. The results are compared to the available experimental data.
Empirical evaluation of neutral interactions in host-parasite networks.

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Canard, E F; Mouquet, N; Mouillot, D; Stanko, M; Miklisova, D; Gravel, D

2014-04-01

While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analyzed the concordance between neutral expectations and empirical observations at interaction, species, and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait matching would determine potential interactions between species, while abundance would determine their realization.

Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations.

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Cardinal, Andrea J; Whetten, Rebecca; Wang, Sanbao; Auclair, Jérôme; Hyten, David; Cregan, Perry; Bachlava, Eleni; Gillman, Jason; Ramirez, Martha; Dewey, Ralph; Upchurch, Greg; Miranda, Lilian; Burton, Joseph W

2014-01-01

fap 1 mutation is caused by a G174A change in GmKASIIIA that disrupts a donor splice site recognition and creates a GATCTG motif that enhanced its expression. Soybean oil with reduced palmitic acid content is desirable to reduce the health risks associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its molecular basis, estimate the amount of phenotypic variation in fatty acid composition explained by this locus, determine if there are epistatic interactions between the fap1 and fap nc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations. This study detected two major QTL for 16:0 content located in chromosome 5 (GmFATB1a, fap nc) and chromosome 9 near BARCSOYSSR_09_1707 that explained, with their interaction, 66-94 % of the variation in 16:0 content in the three populations. Sequencing results of a putative candidate gene, GmKASIIIA, revealed a single unique polymorphism in the germplasm line C1726, which was predicted to disrupt the donor splice site recognition between exon one and intron one and produce a truncated KASIIIA protein. This G to A change also created the GATCTG motif that enhanced gene expression of the mutated GmKASIIIA gene. Lines homozygous for the GmKASIIIA mutation (fap1) had a significant reduction in 16:0, 18:0, and oil content; and an increase in unsaturated fatty acids content. There were significant epistatic interactions between GmKASIIIA (fap1) and fap nc for 16:0 and oil contents, and seed yield in two populations. In conclusion, the fap1 phenotype is caused by a single unique SNP in the GmKASIIIA gene.
A novel apparatus for interocular interaction evaluation in children with and without anisometropic amblyopia.

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Lai, Xin Jie Angela; Alexander, Jack; He, Ming Guang; Yang, Zhi Kuan; Suttle, Catherine

2012-07-01

Dichoptic visual stimulation may be achieved using shutter goggles and mirror systems. These methods vary in their feasibility for use in children. This study aims to investigate the feasibility of use of a simple trial frame-based system to evaluate interactions in children. Low contrast acuity, contrast sensitivity and alignment sensitivity were measured in the non-dominant eye of 10 normally-sighted children, 14 anisometropic children without amblyopia and 14 anisometropic amblyopic children (aged 5-11 years) using goggles and a trial frame apparatus (TFA). The dominant eye was either fully or partially occluded. The difference in visual functions in the non-dominant eye between the full and partial occlusion conditions was termed the 'interaction index'. Agreement between the TFA and goggles in terms of visual functions and interactions was assessed in anisometropic children with and without amblyopia using the Bland-Altman method and t-test. Training sessions allowed subjects to become accustomed to the systems and tasks. The duration of training, the number of breaks requested by subjects and their willingness to attend further experiments were recorded in 10 subjects from each group and were compared between groups and between systems. Both Bland-Altman and t-test methods indicated acceptable agreement between the TFA and goggles in visual function and interaction measures (p > 0.05), except for contrast sensitivity measured in anisometropic children without amblyopia (p = 0.042). For all subject groups, contrast sensitivity training was significantly longer using goggles than using the TFA (p ≤ 0.001). Significantly more breaks were requested in acuity and contrast sensitivity testing, when goggles were used than when the TFA was used (p amblyopia showed a significantly greater willingness to attend more experiments using the TFA than using goggles (p = 0.025). The TFA may be a useful tool in studies of interactions in amblyopes, particularly in studies
Interactive Information Retrieval: An Introduction

Directory of Open Access Journals (Sweden)

Borlund, Pia

2013-09-01

Full Text Available The paper introduces the research area of interactive information retrieval (IIR from a historical point of view. Further, the focus here is on evaluation, because much research in IR deals with IR evaluation methodology due to the core research interest in IR performance, system interaction and satisfaction with retrieved information. In order to position IIR evaluation, the Cranfield model and the series of tests that led to the Cranfield model are outlined. Three iconic user-oriented studies and projects that all have contributed to how IIR is perceived and understood today are presented: The MEDLARS test, the Book House fiction retrieval system, and the OKAPI project. On this basis the call for alternative IIR evaluation approaches motivated by the three revolutions (the cognitive, the relevance, and the interactive revolutions put forward by Robertson & Hancock-Beaulieu (1992 is presented. As a response to this call the 'IIR evaluation model' by Borlund (e.g., 2003a is introduced. The objective of the IIR evaluation model is to facilitate IIR evaluation as close as possible to actual information searching and IR processes, though still in a relatively controlled evaluation environment, in which the test instrument of a simulated work task situation plays a central part.
Influence and interactions of cathepsin D, HLA-DRB1 and APOE on cognitive abilities in an older non-demented population.

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Payton, A; van den Boogerd, E; Davidson, Y; Gibbons, L; Ollier, W; Rabbitt, P; Worthington, J; Horan, M; Pendleton, N

2006-01-01

Cathepsin D (CTSD), human leukocyte antigen DRB1 (HLA-DRB1) and apolipoprotein E (APOE) have all been associated with cognitive ability in both demented and non-demented individuals. CTSD is a pleiotrophic protein whose functions include the processing of proteins prior to presentation by HLA. Several studies have also reported that a functional exon 2 polymorphism in the CTSD gene interacts with APOEepsilon4 resulting in an increased risk of developing Alzheimer's disease (AD). We have previously reported that the CTSD exon 2 polymorphism regulates fluid intelligence. In this study, we extend this finding to other cognitive domains and investigate interactions with APOE and HLA-DRB1. Using a cohort of 766 non-demented volunteers, we found that the CTSD exon 2 T allele was associated with a decrease in several cognitive domains that comprise processing speed [random letters (RLs) test, P = 0.012; alphabet-coding task (ACT), P = 0.001], spatial recall (SR) (P = 0.016) and an additional test of fluid intelligence (P = 0.010). We also observed that the HLA-DR1 was associated with enhanced cumulative recall ability (P = 0.006), and conversely HLA-DR5 was associated with diminished delayed verbal recall and SR abilities (P = 0.014 and P = 0.003, respectively). When analysed independently, APOEepsilon4 did not influence any cognitive domains. In contrast, CTSD T/APOEepsilon4-positive volunteers scored lower on tests of fluid intelligence (P = 0.015), processing speed (ACT, P = 0.001; RL, P = 0.013) and immediate recall (P = 0.029). Scores were lower for all these tests than when CTSD and APOE were analysed independently. This supports previous findings in AD that have also reported an epistatic interaction. In addition, we found that CTSD T/HLA-DR2-positive volunteers had reduced processing speed (ACT, P = 0.040; RL, P = 0.014) and had significantly lower cumulative and SR abilities (P = 0.003 and P = 0.001, respectively). Biological interaction between these two
Perturbative evaluation of the zero-point function for self-interacting scalar field on a manifold with boundary

International Nuclear Information System (INIS)

Tsoupros, George

2002-01-01

The character of quantum corrections to the gravitational action of a conformally invariant field theory for a self-interacting scalar field on a manifold with boundary is considered at third loop-order in the perturbative expansion of the zero-point function. Diagramatic evaluations and higher loop-order renormalization can be best accomplished on a Riemannian manifold of positive constant curvature accommodating a boundary of constant extrinsic curvature. The associated spherical formulation for diagramatic evaluations reveals a non-trivial effect which the topology of the manifold has on the vacuum processes and which ultimately dissociates the dynamical behaviour of the quantized field from its behaviour in the absence of a boundary. The first surface divergence is evaluated and the necessity for simultaneous renormalization of volume and surface divergences is shown
Evaluation of an Interactive Workshop Designed to Teach Practical Welfare Techniques to Beef Cattle Caretakers and Decision Makers

Science.gov (United States)

Dewell, Reneé; Hanthorn, Christy; Danielson, Jared; Burzette, Rebecca; Coetzee, Johann; Griffin, D. Dee; Ramirez, Alejandro; Dewell, Grant

2015-01-01

The purpose of the project was to evaluate the use of an interactive workshop designed to teach novel practical welfare techniques to beef cattle caretakers and decision makers. Following training, respondents reported being more likely to use or recommend use of local anesthesia for dehorning and castration and were more inclined to use meloxicam…
Seismic evaluation of a cooling water reservoir facility including fluid-structure and soil-structure interaction effects

International Nuclear Information System (INIS)

Kabir, A.F.; Maryak, M.E.

1991-01-01

Seismic analyses and structural evaluations were performed for a cooling water reservoir of a nuclear reactor facility. The horizontal input seismic motion was the NRC Reg. guide 1.60 spectrum shape anchored at 0.20g zero period acceleration. Vertical input was taken as two-thirds of the horizontal input. Soil structure interaction and hydrodynamic effects were addressed in the seismic analyses. Uncertainties in the soil properties were accounted for by considering three soil profiles. Two 2-dimensional SSI models and a 3-dimensional static model. Representing different areas of the reservoir structures were developed and analyzed to obtain seismic forces and moments, and accelerations at various locations. The results included in this paper indicated that both hydrodynamic and soil-structure interaction effects are significant contributors to the seismic responses of the water-retaining walls of the reservoir
Expanding Interaction Potentials within Virtual Environments: Investigating the Usability of Speech and Manual Input Modes for Decoupled Interaction

Directory of Open Access Journals (Sweden)

Alex Stedmon

2011-01-01

Full Text Available Distributed technologies and ubiquitous computing now support users who may be detached or decoupled from traditional interactions. In order to investigate the potential usability of speech and manual input devices, an evaluation of speech input across different user groups and a usability assessment of independent-user and collaborative-user interactions was conducted. Whilst the primary focus was on a formative usability evaluation, the user group evaluation provided a formal basis to underpin the academic rigor of the exercise. The results illustrate that using a speech interface is important in understanding user acceptance of such technologies. From the usability assessment it was possible to translate interactions and make them compatible with innovative input devices. This approach to interaction is still at an early stage of development, and the potential or validity of this interfacing concept is still under evaluation; however, as a concept demonstrator, the results of these initial evaluations demonstrate the potential usability issues of both input devices as well as highlighting their suitability for advanced virtual applications.
Performance evaluation of Maxwell and Cercignani-Lampis gas-wall interaction models in the modeling of thermally driven rarefied gas transport

KAUST Repository

Liang, Tengfei; Li, Qi; Ye, Wenjing

2013-01-01

A systematic study on the performance of two empirical gas-wall interaction models, the Maxwell model and the Cercignani-Lampis (CL) model, in the entire Knudsen range is conducted. The models are evaluated by examining the accuracy of key
Designing and Evaluating Tutoring Feedback Strategies for Digital Learning Environments on the Basis of the Interactive Tutoring Feedback Model

Science.gov (United States)

Narciss, Susanne

2013-01-01

This paper describes the interactive tutoring feedback model (ITF-model; Narciss, 2006; 2008), and how it can be applied to the design and evaluation of feedback strategies for digital learning environments. The ITF-model conceptualizes formative tutoring feedback as a multidimensional instructional activity that aims at contributing to the…
Food-drug interactions

DEFF Research Database (Denmark)

Schmidt, Lars E; Dalhoff, Kim

2002-01-01

Interactions between food and drugs may inadvertently reduce or increase the drug effect. The majority of clinically relevant food-drug interactions are caused by food-induced changes in the bioavailability of the drug. Since the bioavailability and clinical effect of most drugs are correlated......, the bioavailability is an important pharmacokinetic effect parameter. However, in order to evaluate the clinical relevance of a food-drug interaction, the impact of food intake on the clinical effect of the drug has to be quantified as well. As a result of quality review in healthcare systems, healthcare providers...... are increasingly required to develop methods for identifying and preventing adverse food-drug interactions. In this review of original literature, we have tried to provide both pharmacokinetic and clinical effect parameters of clinically relevant food-drug interactions. The most important interactions are those...
Functional regression method for whole genome eQTL epistasis analysis with sequencing data.

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Xu, Kelin; Jin, Li; Xiong, Momiao

2017-05-18

Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves. A single number for measuring gene expression which is widely used for microarray measured gene expression analysis is highly unlikely to sufficiently account for large expression variation across the gene. Simultaneously analyzing epistatic architecture using the RNA-seq and whole genome sequencing (WGS) data poses enormous challenges. We develop a nonlinear functional regression model (FRGM) with functional responses where the position-level read counts within a gene are taken as a function of genomic position, and functional predictors where genotype profiles are viewed as a function of genomic position, for epistasis analysis with RNA-seq data. Instead of testing the interaction of all possible pair-wises SNPs, the FRGM takes a gene as a basic unit for epistasis analysis, which tests for the interaction of all possible pairs of genes and use all the information that can be accessed to collectively test interaction between all possible pairs of SNPs within two genome regions. By large-scale simulations, we demonstrate that the proposed FRGM for epistasis analysis can achieve the correct type 1 error and has higher power to detect the interactions between genes than the existing methods. The proposed methods are applied to the RNA-seq and WGS data from the 1000 Genome Project. The numbers of pairs of significantly interacting genes after Bonferroni correction
Plasticity effect of rider-horse interaction on genetic evaluations for Show Jumping discipline in sport horses.

Science.gov (United States)

Bartolomé, E; Menéndez-Buxadera, A; Molina, A; Valera, M

2018-04-01

To obtain a sport horse that excels in the highest levels of competition, breeders must take into account certain genetic and environmental factors that could influence the sport horse's performance, such as the rider-horse interaction (RHI). The main aim of this study was to describe this interaction in a genetic model by modelling it in relation to the horse's age. A total of 31,129 sport results from Spanish Sport Horses were used from a total of 1,101 animals evaluated, and these were grouped in three age levels and had been ridden by 606 different riders. Only riders who had ridden more than one horse (and vice-versa) were considered for the analyses. Five linear models with different random effects were analysed according to the covariates, the homogeneity/heterogeneity of the RHI and the relevant residual random effects. The model of best fit was then selected for the genetic evaluation of the animal. In general, models including the RHI effect (M2, M4 and M5) fitted better than the other models, and the best fit was obtained for M4 (with heterogeneous residual variance). The genetic variance increased constantly with age, whereas heritability showed a response on three intervals. This study revealed the varied evolution of the RHI with age, showing the different "plastic abilities" of this relationship. © 2018 Blackwell Verlag GmbH.
Simulations and experimental evaluation of an active orthosis for interaction in virtual environments

Directory of Open Access Journals (Sweden)

Tsveov Mihail

2018-01-01

Full Text Available In this work, the development of a human arm active orthosis is presented. The orthosis is designed primarily for training and rehabilitation in virtual environments.The orthosis system is intended for embodiment in virtual reality where it is allowing human to perceive forces at different body parts or the weight of lifted objects. In the paper the choice of a mechanical structure is shown equivalent to the structure of the human arm. A mechanical model of the orthosis arm as haptic device is built, where kinematic and dynamic parameters are evaluated. Impedance control scheme is selected as the most suitable for force refection at the hand or arm. An open-loop impedance controller is presented in the paper. Computer experiments are carried out using the dimensions of a real arm orthosis. Computer experiments have been carried out to provide force reflection by VR, according to virtual scenario. The conducted simulations show the range of the forces on the operator hand, orthosis can provide. The results of additional measurements and experimental evaluations of physical quantities in the interaction in a virtual environment are revealed in the paper.
Procedures for Evaluation of Atomic, Molecular and Plasma-Material Interaction Data for Fusion. Summary Report of an IAEA Consultants' Meeting

International Nuclear Information System (INIS)

Chung, Hyun-Kyung

2012-05-01

This report summarizes the proceedings of the IAEA Consultants' Meeting on 'Procedures for Evaluation of Atomic, Molecular and Plasma-Material Interaction Data for Fusion' on 7-9 February 2012. Fourteen participants from 8 Institutes of 3 Member States attended the three-day meeting held at the National Institute for Fusion Science, Toki in Japan. The report includes discussions on data evaluation activities, meeting conclusions and recommendations and the abstracts of presentations presented in the meeting. (author)
Views from Within a Narrative: Evaluating Long-Term Human-Robot Interaction in a Naturalistic Environment Using Open-Ended Scenarios.

Science.gov (United States)

Syrdal, Dag Sverre; Dautenhahn, Kerstin; Koay, Kheng Lee; Ho, Wan Ching

2014-01-01

This article describes the prototyping of human-robot interactions in the University of Hertfordshire (UH) Robot House. Twelve participants took part in a long-term study in which they interacted with robots in the UH Robot House once a week for a period of 10 weeks. A prototyping method using the narrative framing technique allowed participants to engage with the robots in episodic interactions that were framed using narrative to convey the impression of a continuous long-term interaction. The goal was to examine how participants responded to the scenarios and the robots as well as specific robot behaviours, such as agent migration and expressive behaviours. Evaluation of the robots and the scenarios were elicited using several measures, including the standardised System Usability Scale, an ad hoc Scenario Acceptance Scale, as well as single-item Likert scales, open-ended questionnaire items and a debriefing interview. Results suggest that participants felt that the use of this prototyping technique allowed them insight into the use of the robot, and that they accepted the use of the robot within the scenario.
Competency-Based Teaching in Radiology - Implementation and Evaluation of Interactive Workstation-Based Learning to Apply NKLM-Based Content.

Science.gov (United States)

Koestner, Wolfgang; Otten, Wiebke; Kaireit, Till; Wacker, Frank K; Dettmer, Sabine

2017-11-01

Purpose New teaching formats are required to implement competency-based teaching in radiology teaching. Therefore, we have established and evaluated two practical competency-based radiological courses. Materials and Methods The courses were held in a multimedia room with 25 computers and a professional DICOM viewer. Students were taught basic image analysis and presented clinical cases with a DICOM viewer under supervision of an instructor using desktop monitoring software. Two courses (elective course and obligatory course) were evaluated by the students (n = 160 and n = 100) and instructors (n = 9) using an anonymized online survey. Results Courses were evaluated positively by the students and instructors. From the perspective of the students, the courses increased understanding of cross-sectional anatomy (elective/obligatory course: 97 %/95 %) and radiologic findings (97 %/99 %). Furthermore, the course increased the students' interest in radiology (61 %/65 %). The students considered this way of teaching to be relevant to their future occupation (92 % of students in the obligatory course). The higher incidence of teacher-student interaction and the possibility of independent image analysis were rated positively. The majority of instructors did not observe increased distractibility due to the computers (67 %) or notice worse preparation for MC tests (56 %). However, 56 % of instructors reported greater preparation effort. Conclusion Practical competency-based radiological teaching using a DICOM viewer is a feasible innovative approach with high acceptance among students and instructors. It fosters competency-based learning as proposed by the model curriculum of the German Radiological Society (DRG) and the National Competency-based Catalogue of Learning Objectives for Undergraduate Medical Education (NKLM). Key Points · Practical competency-based radiological teaching is highly accepted by students and instructors
Heuristics to Evaluate Interactive Systems for Children with Autism Spectrum Disorder (ASD).

Science.gov (United States)

Khowaja, Kamran; Salim, Siti Salwah; Asemi, Adeleh

2015-01-01

In this paper, we adapted and expanded a set of guidelines, also known as heuristics, to evaluate the usability of software to now be appropriate for software aimed at children with autism spectrum disorder (ASD). We started from the heuristics developed by Nielsen in 1990 and developed a modified set of 15 heuristics. The first 5 heuristics of this set are the same as those of the original Nielsen set, the next 5 heuristics are improved versions of Nielsen's, whereas the last 5 heuristics are new. We present two evaluation studies of our new heuristics. In the first, two groups compared Nielsen's set with the modified set of heuristics, with each group evaluating two interactive systems. The Nielsen's heuristics were assigned to the control group while the experimental group was given the modified set of heuristics, and a statistical analysis was conducted to determine the effectiveness of the modified set, the contribution of 5 new heuristics and the impact of 5 improved heuristics. The results show that the modified set is significantly more effective than the original, and we found a significant difference between the five improved heuristics and their corresponding heuristics in the original set. The five new heuristics are effective in problem identification using the modified set. The second study was conducted using a system which was developed to ascertain if the modified set was effective at identifying usability problems that could be fixed before the release of software. The post-study analysis revealed that the majority of the usability problems identified by the experts were fixed in the updated version of the system.
Heuristics to Evaluate Interactive Systems for Children with Autism Spectrum Disorder (ASD.

Directory of Open Access Journals (Sweden)

Kamran Khowaja

Full Text Available In this paper, we adapted and expanded a set of guidelines, also known as heuristics, to evaluate the usability of software to now be appropriate for software aimed at children with autism spectrum disorder (ASD. We started from the heuristics developed by Nielsen in 1990 and developed a modified set of 15 heuristics. The first 5 heuristics of this set are the same as those of the original Nielsen set, the next 5 heuristics are improved versions of Nielsen's, whereas the last 5 heuristics are new. We present two evaluation studies of our new heuristics. In the first, two groups compared Nielsen's set with the modified set of heuristics, with each group evaluating two interactive systems. The Nielsen's heuristics were assigned to the control group while the experimental group was given the modified set of heuristics, and a statistical analysis was conducted to determine the effectiveness of the modified set, the contribution of 5 new heuristics and the impact of 5 improved heuristics. The results show that the modified set is significantly more effective than the original, and we found a significant difference between the five improved heuristics and their corresponding heuristics in the original set. The five new heuristics are effective in problem identification using the modified set. The second study was conducted using a system which was developed to ascertain if the modified set was effective at identifying usability problems that could be fixed before the release of software. The post-study analysis revealed that the majority of the usability problems identified by the experts were fixed in the updated version of the system.
Evaluating Interactions of Forest Conservation Policies on Avoided Deforestation

Science.gov (United States)

Robalino, Juan; Sandoval, Catalina; Barton, David N.; Chacon, Adriana; Pfaff, Alexander

2015-01-01

We estimate the effects on deforestation that have resulted from policy interactions between parks and payments and between park buffers and payments in Costa Rica between 2000 and 2005. We show that the characteristics of the areas where protected and unprotected lands are located differ significantly. Additionally, we find that land characteristics of each of the policies and of the places where they interact also differ significantly. To adequately estimate the effects of the policies and their interactions, we use matching methods. Matching is implemented not only to define adequate control groups, as in previous research, but also to define those groups of locations under the influence of policies that are comparable to each other. We find that it is more effective to locate parks and payments away from each other, rather than in the same location or near each other. The high levels of enforcement inside both parks and lands with payments, and the presence of conservation spillovers that reduce deforestation near parks, significantly reduce the potential impact of combining these two policies. PMID:25909323

Evaluating interactions of forest conservation policies on avoided deforestation.

Directory of Open Access Journals (Sweden)

Juan Robalino

Full Text Available We estimate the effects on deforestation that have resulted from policy interactions between parks and payments and between park buffers and payments in Costa Rica between 2000 and 2005. We show that the characteristics of the areas where protected and unprotected lands are located differ significantly. Additionally, we find that land characteristics of each of the policies and of the places where they interact also differ significantly. To adequately estimate the effects of the policies and their interactions, we use matching methods. Matching is implemented not only to define adequate control groups, as in previous research, but also to define those groups of locations under the influence of policies that are comparable to each other. We find that it is more effective to locate parks and payments away from each other, rather than in the same location or near each other. The high levels of enforcement inside both parks and lands with payments, and the presence of conservation spillovers that reduce deforestation near parks, significantly reduce the potential impact of combining these two policies.
Evaluating interactions of forest conservation policies on avoided deforestation.

Science.gov (United States)

Robalino, Juan; Sandoval, Catalina; Barton, David N; Chacon, Adriana; Pfaff, Alexander

2015-01-01

We estimate the effects on deforestation that have resulted from policy interactions between parks and payments and between park buffers and payments in Costa Rica between 2000 and 2005. We show that the characteristics of the areas where protected and unprotected lands are located differ significantly. Additionally, we find that land characteristics of each of the policies and of the places where they interact also differ significantly. To adequately estimate the effects of the policies and their interactions, we use matching methods. Matching is implemented not only to define adequate control groups, as in previous research, but also to define those groups of locations under the influence of policies that are comparable to each other. We find that it is more effective to locate parks and payments away from each other, rather than in the same location or near each other. The high levels of enforcement inside both parks and lands with payments, and the presence of conservation spillovers that reduce deforestation near parks, significantly reduce the potential impact of combining these two policies.
Students' Evaluation of Classroom Interactions of Their Biology ...

African Journals Online (AJOL)

Nekky Umera

teacher classroom interactions were positively correlated and uncertainty, ... implementation is that, if biology teachers were to display more leadership, helpful and ... Accepted methods to overcome poor academic achievement in science have ... activities and experiences through which teachers; curriculum, materials, and.
Understanding the Effect of Response Rate and Class Size Interaction on Students Evaluation of Teaching in a Higher Education

Science.gov (United States)

Al Kuwaiti, Ahmed; AlQuraan, Mahmoud; Subbarayalu, Arun Vijay

2016-01-01

Objective: This study aims to investigate the interaction between response rate and class size and its effects on students' evaluation of instructors and the courses offered at a higher education Institution in Saudi Arabia. Study Design: A retrospective study design was chosen. Methods: One thousand four hundred and forty four different courses…
Thermal Interaction of Closely Spaced Persons

DEFF Research Database (Denmark)

Brohus, Henrik; Nielsen, Peter V.; Tøgersen, Michael

2011-01-01

This paper presents results from a pilot study on the thermal interaction of closely spaced persons in a large enclosure. The surface temperature at different densities of persons is evaluated using a high resolution thermo vision camera in a controlled thermal environment. The corresponding ther...... thermal sensation is evaluated using questionnaires for the various densities. The results indicate that it may be acceptable to consider persons standalone, in a thermal sense, disregarding thermal interaction at usual densities in the design of large enclosures.......This paper presents results from a pilot study on the thermal interaction of closely spaced persons in a large enclosure. The surface temperature at different densities of persons is evaluated using a high resolution thermo vision camera in a controlled thermal environment. The corresponding...
The lesson learnt during interact - I and INTERACT - II actris measurement campaigns

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Rosoldi Marco

2018-01-01

Full Text Available The INTERACT-II (INTERcomparison of Aerosol and Cloud Tracking campaign, performed at the CNR-IMAA Atmospheric Observatory (760 m a.s.l., 40.60° N, 15.72° E, aims to evaluate the performances of commercial automatic lidars and ceilometers for atmospheric aerosol profiling, through the comparison with Potenza EARLINET (European Aerosol Research Lidar NETwork lidars. The results of the campaign and the overall lesson learnt within INTERACT-I and INTERACT-II ACTRIS campaigns will be presented.
EVALUATING AUSTRALIAN FOOTBALL LEAGUE PLAYER CONTRIBUTIONS USING INTERACTIVE NETWORK SIMULATION

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Jonathan Sargent

2013-03-01

Full Text Available This paper focuses on the contribution of Australian Football League (AFL players to their team's on-field network by simulating player interactions within a chosen team list and estimating the net effect on final score margin. A Visual Basic computer program was written, firstly, to isolate the effective interactions between players from a particular team in all 2011 season matches and, secondly, to generate a symmetric interaction matrix for each match. Negative binomial distributions were fitted to each player pairing in the Geelong Football Club for the 2011 season, enabling an interactive match simulation model given the 22 chosen players. Dynamic player ratings were calculated from the simulated network using eigenvector centrality, a method that recognises and rewards interactions with more prominent players in the team network. The centrality ratings were recorded after every network simulation and then applied in final score margin predictions so that each player's match contribution-and, hence, an optimal team-could be estimated. The paper ultimately demonstrates that the presence of highly rated players, such as Geelong's Jimmy Bartel, provides the most utility within a simulated team network. It is anticipated that these findings will facilitate optimal AFL team selection and player substitutions, which are key areas of interest to coaches. Network simulations are also attractive for use within betting markets, specifically to provide information on the likelihood of a chosen AFL team list "covering the line".
Research on Credit Evaluation of Mobile Medical APP Interactive Online Consultation Service-Take Haodaifu APP Online Payment Service as an Example

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Xiong, Dandan; Zhao, Lei

2017-10-01

Mobile medical industry is developing rapidly, but the relevant credit evaluation system is still in the exploratory stage. Haodaifu in the interactive online consulting services more representatives and has a credit evaluation system, but the system is not perfect. There are many problems in the system, such as credits indicators cannot better reflect the results of user’s evaluation, the lack of user qualification supervision, evaluation index system and assessment channels are not perfect. On the basis of drawing on the advantages of E-commerce evaluation system and combining with the characteristics of mobile medical itself, two suggestions are put forward: Improve the credit evaluation model (Generate physician static credit index, Change the doctor 's dynamic credit index algorithm, Update the dynamic credit index), Improve the basic mechanism of credit evaluation.
Evaluation of kriging based surrogate models constructed from mesoscale computations of shock interaction with particles

Energy Technology Data Exchange (ETDEWEB)

Sen, Oishik, E-mail: oishik-sen@uiowa.edu [Mechanical and Industrial Engineering, The University of Iowa, Iowa City, IA 52242 (United States); Gaul, Nicholas J., E-mail: nicholas-gaul@ramdosolutions.com [RAMDO Solutions, LLC, Iowa City, IA 52240 (United States); Choi, K.K., E-mail: kyung-choi@uiowa.edu [Mechanical and Industrial Engineering, The University of Iowa, Iowa City, IA 52242 (United States); Jacobs, Gustaaf, E-mail: gjacobs@sdsu.edu [Aerospace Engineering, San Diego State University, San Diego, CA 92115 (United States); Udaykumar, H.S., E-mail: hs-kumar@uiowa.edu [Mechanical and Industrial Engineering, The University of Iowa, Iowa City, IA 52242 (United States)

2017-05-01

Macro-scale computations of shocked particulate flows require closure laws that model the exchange of momentum/energy between the fluid and particle phases. Closure laws are constructed in this work in the form of surrogate models derived from highly resolved mesoscale computations of shock-particle interactions. The mesoscale computations are performed to calculate the drag force on a cluster of particles for different values of Mach Number and particle volume fraction. Two Kriging-based methods, viz. the Dynamic Kriging Method (DKG) and the Modified Bayesian Kriging Method (MBKG) are evaluated for their ability to construct surrogate models with sparse data; i.e. using the least number of mesoscale simulations. It is shown that if the input data is noise-free, the DKG method converges monotonically; convergence is less robust in the presence of noise. The MBKG method converges monotonically even with noisy input data and is therefore more suitable for surrogate model construction from numerical experiments. This work is the first step towards a full multiscale modeling of interaction of shocked particle laden flows.
The genetics of tolerance to tristeza disease in citrus rootstocks

Directory of Open Access Journals (Sweden)

Rita Bordignon

2004-01-01

Full Text Available Controlled pollinations between four elite citrus rootstocks, Citrus limonia - 'Limeira' rangpur lime (Cravo, C. sunki - 'Sunki' mandarin (Sunki, C. aurantium - 'São Paulo' sour orange (Azeda and Poncirus trifoliata - 'Davis A' trifoliate orange (Trifoliata, resulted in 1614 nucelar and 1938 hybrid plants identified by the isozyme loci Pgi-1, Pgm-1, Got-1, Got-2, Aps-1, Me-1, Prxa-1 and or by the morphological markers broadness of leaf petiole wing or trifoliolate leaves. Tolerance to the citrus tristeza virus (CTV was evaluated under nursery and field conditions for several years by the reaction of Valencia orange infected with a severe strain of CTV and grafted onto the hybrids and nucellar clones. Genetic analyses indicated that tolerance was controlled by at least two loci designated here as Az and t interacting in dominant-recessive epistasis. Genotypes Az__ __ __ and __ __ tt were tolerant while azaz T__ was intolerant. The intolerant Azeda was azaz TT, the tolerant rootstocks Sunki and Cravo were Azaz tt and the Trifoliata was Azaz TT. The different degrees of intolerance seen in some hybrids may reflect the inability of segregating modifiers from parental clones to overcome the epistatic interaction that controls the major tolerance reaction.
In-site interaction evaluation of Tn density by inhibition/competition assays

Energy Technology Data Exchange (ETDEWEB)

Robles, Ana [Radiopharmacy Department, Nuclear Research Center, Faculty of Sciences, University of the Republic, Montevideo (Uruguay)], E-mail: anamar@cin.edu.uy; Medeiros, Andrea [Biochemistry Department, Faculty of Medicine, University of the Republic, Montevideo (Uruguay); Berois, Nora [Laboratory of Glycobiology and Tumor Immunology, Pasteur Institute of Montevideo (Uruguay); Balter, Henia S. [Radiopharmacy Department, Nuclear Research Center, Faculty of Sciences, University of the Republic, Montevideo (Uruguay); Pauwels, Ernest K. [University Medical Center Leiden, Department of Radiology, Leiden (Netherlands); Osinaga, Eduardo [Laboratory of Glycobiology and Tumor Immunology, Pasteur Institute of Montevideo (Uruguay); Department of Immunobiology, Faculty of Medicine, University of the Republic, Montevideo (Uruguay)

2010-05-15

The tumor-associated structure N-acetyl-galactosamine-O-Ser/Thr (Tn antigen), which is overexpressed in various tumor cell types, notably of the breast, ovary and colon, is an interesting determinant that is useful for cancer diagnosis and follow-up. The aim of this research was to study different assay strategies in order to determine the most sensitive system for further application in epitope characterization and binding assessment. The tetrameric isolectin obtained from Vicia villosa seeds (VVLB{sub 4}) shows high affinity for the tumor-associated structure. A monoclonal antibody against VVLB{sub 4}, MabVV{sub 34}, was generated, and the interaction between MabVV{sub 34} and VVLB{sub 4} was studied by means of binding and inhibition assays. Several synthetic peptides (10 amino acid sequences) designed from the amino acid sequence of VVLB{sub 4} and obtained from trypsin digestion were tested to determine which amino acids were involved in the interaction between MabVV{sub 34} and VVLB{sub 4}. The further unraveling of this epitope was investigated by inhibition using designed synthetic peptides as well as mixtures mimicking variable density effect. Under the experimental circumstances, MabVV{sub 34} was able to inhibit the binding of VVLB{sub 4} to Tn. Two of the four peptide sequences assayed showed better inhibition properties. Finally, mixtures containing these selected sequences allowed the evaluation of binding and inhibition as a function of Tn density. We conclude that the present study facilitates the further development of a specific Tn marker and may contribute to the development of Tn-like radiolabelled peptides or Tn-specific radiolabelled fragments providing a highly selective tool for cancer diagnosis and treatment. This strategy may contribute to characterize the new generation of radiopharmaceuticals for diagnosis and therapy based on biomolecules like antibodies, fragments or peptides, whose application is directly guided by their specific
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis.

Science.gov (United States)

Colak, Recep; Kim, TaeHyung; Kazan, Hilal; Oh, Yoomi; Cruz, Miguel; Valladares-Salgado, Adan; Peralta, Jesus; Escobedo, Jorge; Parra, Esteban J; Kim, Philip M; Goldenberg, Anna

2016-01-15

Rapid advances in genotyping and genome-wide association studies have enabled the discovery of many new genotype-phenotype associations at the resolution of individual markers. However, these associations explain only a small proportion of theoretically estimated heritability of most diseases. In this work, we propose an integrative mixture model called JBASE: joint Bayesian analysis of subphenotypes and epistasis. JBASE explores two major reasons of missing heritability: interactions between genetic variants, a phenomenon known as epistasis and phenotypic heterogeneity, addressed via subphenotyping. Our extensive simulations in a wide range of scenarios repeatedly demonstrate that JBASE can identify true underlying subphenotypes, including their associated variants and their interactions, with high precision. In the presence of phenotypic heterogeneity, JBASE has higher Power and lower Type 1 Error than five state-of-the-art approaches. We applied our method to a sample of individuals from Mexico with Type 2 diabetes and discovered two novel epistatic modules, including two loci each, that define two subphenotypes characterized by differences in body mass index and waist-to-hip ratio. We successfully replicated these subphenotypes and epistatic modules in an independent dataset from Mexico genotyped with a different platform. JBASE is implemented in C++, supported on Linux and is available at http://www.cs.toronto.edu/∼goldenberg/JBASE/jbase.tar.gz. The genotype data underlying this study are available upon approval by the ethics review board of the Medical Centre Siglo XXI. Please contact Dr Miguel Cruz at mcruzl@yahoo.com for assistance with the application. anna.goldenberg@utoronto.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.
Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents.

Science.gov (United States)

Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

2013-02-01

Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.
Designing and Evaluating Tutoring Feedback Strategies for digital learning environments on the basis of the Interactive Tutoring Feedback Model

Directory of Open Access Journals (Sweden)

Susanne Narciss

2013-06-01

Full Text Available This paper describes the interactive tutoring feedback model (ITF-model; Narciss, 2006; 2008, and how it can be applied to the design and evaluation of feedback strategies for digital learning environments. The ITF-model conceptualizes formative tutoring feedback as a multidimensional instructional activity that aims at contributing to the regulation of a learning process in order to help learners acquire or improve the competencies needed to master learning tasks. It integrates findings from systems theory with recommendations of prior research on interactive instruction and elaborated feedback, on task analyses, on error analyses, and on tutoring techniques. Based on this multi-dimensional view of formative tutoring feedback methodological implications for designing and investigating multiple effects of feedback under multiple individual and situational conditions are described. Furthermore, the paper outlines how the implications of the ITF-model have been applied in several studies to the design and evaluation of tutoring feedback strategies for digital learning environments (e.g., Narciss, 2004; Narciss & Huth, 2006; Narciss, Schnaubert, Andres, Eichelmann, Goguadze, & Sosnovsky, 2013.
Interaction of core self-evaluations and perceived organizational support on work-to-family enrichment.

Science.gov (United States)

McNall, Laurel A; Masuda, Aline D; Shanock, Linda Rhoades; Nicklin, Jessica M

2011-01-01

The purpose of this article was to offer an empirical test of J. H. Greenhaus and G. N. Powell's (2006) model of work-family enrichment by examining dispositional (i.e., core self-evaluations; CSEs) and situational (i.e., perceived organizational support; POS) factors associated with work-to-family enrichment (WFE) and whether these variables interact in predicting WFE. In a survey of 220 employed adults, our hierarchical regression analysis revealed that in highly supportive work environments, individuals reported high WFE regardless of CSE. However, when POS was low, individuals high in CSEs reported higher WFE than those low in CSEs, in support of conservation of resources theory (S. E. Hobfoll, 2002). Implications for research and practice are discussed.
The IIR evaluation model

DEFF Research Database (Denmark)

Borlund, Pia

2003-01-01

An alternative approach to evaluation of interactive information retrieval (IIR) systems, referred to as the IIR evaluation model, is proposed. The model provides a framework for the collection and analysis of IR interaction data. The aim of the model is two-fold: 1) to facilitate the evaluation ...
Evaluating interactive computer-based scenarios designed for learning medical technology.

Science.gov (United States)

Persson, Johanna; Dalholm, Elisabeth Hornyánszky; Wallergård, Mattias; Johansson, Gerd

2014-11-01

The use of medical equipment is growing in healthcare, resulting in an increased need for resources to educate users in how to manage the various devices. Learning the practical operation of a device is one thing, but learning how to work with the device in the actual clinical context is more challenging. This paper presents a computer-based simulation prototype for learning medical technology in the context of critical care. Properties from simulation and computer games have been adopted to create a visualization-based, interactive and contextually bound tool for learning. A participatory design process, including three researchers and three practitioners from a clinic for infectious diseases, was adopted to adjust the form and content of the prototype to the needs of the clinical practice and to create a situated learning experience. An evaluation with 18 practitioners showed that practitioners were positive to this type of tool for learning and that it served as a good platform for eliciting and sharing knowledge. Our conclusion is that this type of tools can be a complement to traditional learning resources to situate the learning in a context without requiring advanced technology or being resource-demanding. Copyright © 2014 Elsevier Ltd. All rights reserved.
A general method, a la Transport, for evaluation of the perturbing effects of solenoidal inserts in storage ring interaction regions

International Nuclear Information System (INIS)

Murray, J.J.

1976-07-01

It may be expected that solenoid magnets will be used in many storage ring experiments. Typically an insert would consist of a main solenoid at the interaction point with a symmetrical pair of compensating solenoids located somewhere between the main solenoid and the ends of the interaction region. The magnetic fields of such an insert may significantly affect storage ring performance. We suggest here a simple, systematic method for evaluation of the effects, which together with adequate design supervision and field measurements will help to prevent any serious operational problems that might result if significant perturbations went unnoticed. 5 refs
Evaluation of Restoration and Flow Interactions on River Structure and Function: Channel Widening of the Thur River, Switzerland

Directory of Open Access Journals (Sweden)

Eduardo J. Martín

2018-04-01

Full Text Available Removal of lateral constraints to restore rivers has become increasingly common in river resource management, but little is known how the interaction of de-channelization with flow influences ecosystem structure and function. We evaluated the ecosystem effects of river widening to improve sediment relations in the Thur River, Switzerland, 12 years after implementation. We tested if restored and non-restored reaches differed in water physico-chemistry, hyporheic function, primary production, and macroinvertebrate density and composition in relation to the flow regime. Our results showed that (i spatio-temporal variation in sediment respiration and macroinvertebrate taxonomic richness were driven by interactions between restoration and flow; (ii riverbed conditions including substrate size, organic matter content, and groundwater–surface water exchange changed due to restoration, but (iii physico-chemistry, hydraulic conditions, and primary production were not altered by restoration. Importantly, our study revealed that abiotic conditions, except channel morphology, changed only marginally, whereas other ecosystem attributes responded markedly to changes in flow-restoration interactions. These results highlight integrating a more holistic ecosystem perspective in the design and monitoring of restoration projects such as river widening in resource management, preferably in relation to flow-sediment regimes and interactions with the biotic components of the ecosystem.
Consensus-based evaluation of clinical significance and management of anticancer drug interactions

NARCIS (Netherlands)

Jansman, F.G.A.; Reyners, A.K.L.; van Roon, E.N.; Smorenburg, C.H.; Helgason, H.H.; le Comte, M.; Wensveen, B.M.; van den Tweel, A.M.A.; de Blois, M.; Kwee, W.; Kerremans, A.L.; Brouwers, J.R.B.J.

Background: Anticancer drug interactions can affect the efficacy and toxicity of anticancer treatment and that of the interacting drugs. However, information on the significance, prevention, and management of these interactions is currently lacking. Objective: The purpose of this study was to assess

Use of live interactive webcasting for an international postgraduate module in ehealth: case study evaluation.

Science.gov (United States)

Jones, Ray B; Maramba, Inocencio; Boulos, Maged N Kamel; Alexander, Tara

2009-11-13

Producing "traditional" e-learning can be time consuming, and in a topic such as eHealth, it may have a short shelf-life. Students sometimes report feeling isolated and lacking in motivation. Synchronous methods can play an important part in any blended approach to learning. The aim was to develop, deliver, and evaluate an international postgraduate module in eHealth using live interactive webcasting. We developed a hybrid solution for live interactive webcasting using a scan converter, mixer, and digitizer, and video server to embed a presenter-controlled talking head or copy of the presenter's computer screen (normally a PowerPoint slide) in a student chat room. We recruited 16 students from six countries and ran weekly 2.5-hour live sessions for 10 weeks. The content included the use of computers by patients, patient access to records, different forms of e-learning for patients and professionals, research methods in eHealth, geographic information systems, and telehealth. All sessions were recorded-presentations as video files and the student interaction as text files. Students were sent an email questionnaire of mostly open questions seeking their views of this form of learning. Responses were collated and anonymized by a colleague who was not part of the teaching team. Sessions were generally very interactive, with most students participating actively in breakout or full-class discussions. In a typical 2.5-hour session, students posted about 50 messages each. Two students did not complete all sessions; one withdrew from the pressure of work after session 6, and one from illness after session 7. Fourteen of the 16 responded to the feedback questionnaire. Most students (12/14) found the module useful or very useful, and all would recommend the module to others. All liked the method of delivery, in particular the interactivity, the variety of students, and the "closeness" of the group. Most (11/14) felt "connected" with the other students on the course. Many
Identifying User Interaction Patterns in E-Textbooks.

Science.gov (United States)

Saarinen, Santeri; Heimonen, Tomi; Turunen, Markku; Mikkilä-Erdmann, Mirjamaija; Raisamo, Roope; Erdmann, Norbert; Yrjänäinen, Sari; Keskinen, Tuuli

2015-01-01

We introduce a new architecture for e-textbooks which contains two navigational aids: an index and a concept map. We report results from an evaluation in a university setting with 99 students. The interaction sequences of the users were captured during the user study. We found several clusters of user interaction types in our data. Three separate user types were identified based on the interaction sequences: passive user, term clicker, and concept map user. We also discovered that with the concept map interface users started to interact with the application significantly sooner than with the index interface. Overall, our findings suggest that analysis of interaction patterns allows deeper insights into the use of e-textbooks than is afforded by summative evaluation.
Team interaction skills evaluation criteria for nuclear power plant control room operators

International Nuclear Information System (INIS)

Montgomery, J.C.; Toquam, J.; Gaddy, C.

1991-09-01

Previous research has shown the value of good team interaction skills to group performance, yet little progress has been made on in terms of how such skills can be measured. In this study rating scales developed previously (Montgomery, et al., 1990) were extensively revised and cast into a Behaviorally Anchored Rating Scale (BARS) and a Behavioral Frequency format. Rating data were collected using 13 training instructors at the Diablo Canyon Nuclear Plant, who rated three videotapes of simulator scenario performance during a day-long training session and later evaluated control room crews during requalification training. High levels of interrater agreement on both rating scales were found. However, the factor structure of the ratings was generally inconsistent with that hypothesized. Analysis of training ratings using Cronbach's components of accuracy (Cronbach, 1955) indicated that BARS ratings generally exhibited less error than did the Behavioral Frequency ratings. The results are discussed in terms of both field and research implications
Evaluating a staff training program on the interaction between staff and people with intellectual disability and challenging behaviour : An observational study

NARCIS (Netherlands)

Embregts, P.J.C.M.; Zijlmans, L.; Gerits, L.; Bosman, A.M.T.

2018-01-01

Background: The aim of this study was to evaluate the effects of a training program focusing on improvement of emotional intelligence (EI) and support staffs’ awareness of their behaviour towards people with an intellectual disability based on interactional patterns. The support provided regarding
Evaluation of different delivery modes of an interactive e-learning programme for teaching cultural diversity.

Science.gov (United States)

Hawthorne, Kamila; Prout, Hayley; Kinnersley, Paul; Houston, Helen

2009-01-01

UK medical schools find it challenging to provide standardised teaching to expanding year intakes. In addition, developing and implementing diversity training can cause difficulties. This paper describes the evaluation of an interactive e-learning programme to raise awareness and understanding of communication difficulties in diversity consultations. The programme was part of an undergraduate portfolio-based community module. Three hundred and two students were assigned to one of three delivery methods--a large group setting, small groups with a facilitator, and as part of distance learning while on community placement. The evaluation included analysis of their coursework marks, a self-completed evaluation questionnaire, and small group discussions. Two hundred and twenty-three students took part in the evaluation. They were able to apply the concepts they learnt to clinical examples from their own experiences. Type of delivery did not affect coursework marks, but students tended to prefer the e-learning as part of a distance learning package. They offered helpful suggestions to improve its complexity and range. The acceptability and utility of this e-learning module both in face to face teaching and remote placement has been demonstrated, and evaluation by the students has provided valuable information for its further development. All medical schools should include some diversity training, and further research should concentrate on the effects of this type of learning on longer term outcomes such as attitude and performance tests. Such tools could reduce demands on staff time in facilitation of small groupwork, and their cost effectiveness could be increased by making them available to other medical schools.
Evaluation of Algorithms for Photon Depth of Interaction Estimation for the TRIMAGE PET Component

Science.gov (United States)

Camarlinghi, Niccolò; Belcari, Nicola; Cerello, Piergiorgio; Pennazio, Francesco; Sportelli, Giancarlo; Zaccaro, Emanuele; Del Guerra, Alberto

2016-02-01

The TRIMAGE consortium aims to develop a multimodal PET/MR/EEG brain scanner dedicated to the early diagnosis of schizophrenia and other mental health disorders. The TRIMAGE PET component features a full ring made of 18 detectors, each one consisting of twelve 8 ×8 Silicon PhotoMultipliers (SiPMs) tiles coupled to two segmented LYSO crystal matrices with staggered layers. The identification of the pixel where a photon interacted is performed on-line at the front-end level, thus allowing the FPGA board to emit fully digital event packets. This allows to increase the effective bandwidth, but imposes restrictions on the complexity of the algorithms to be implemented. In this work, two algorithms, whose implementation is feasible directly on an FPGA, are presented and evaluated. The first algorithm is driven by physical considerations, while the other consists in a two-class linear Support Vector Machine (SVM). The validation of the algorithm performance is carried out by using simulated data generated with the GAMOS Monte Carlo. The obtained results show that the achieved accuracy in layer identification is above 90% for both the proposed approaches. The feasibility of tagging and rejecting events that underwent multiple interactions within the detector is also discussed.
Evaluating Types of Students' Interactions in a Wiki-Based Collaborative Learning Project

Science.gov (United States)

Prokofieva, Maria

2013-01-01

Wiki technology has been promoted as a collaborative software platform. This study investigates interactions that occur in a wiki-based collaborative learning project. The study draws on interaction literature and investigates the types of interactions with which students are engaged in wiki-based group projects, clusters that reflect online…
Evaluation of genotype x environment interactions in maize hybrids using GGE biplot analysis

Directory of Open Access Journals (Sweden)

Fatma Aykut Tonk

2011-01-01

Full Text Available Seventeen hybrid maize genotypes were evaluated at four different locations in 2005 and 2006 cropping seasonsunder irrigated conditions in Turkey. The analysis of variance showed that mean squares of environments (E, genotypes (G andGE interactions (GEI were highly significant and accounted for 74, 7 and 19 % of treatment combination sum squares, respectively.To determine the effects of GEI on grain yield, the data were subjected to the GGE biplot analysis. Maize hybrid G16 can be proposedas reliably growing in test locations for high grain yield. Also, only the Yenisehir location could be best representative of overalllocations for deciding about which experimental hybrids can be recommended for grain yield in this study. Consequently, using ofgrain yield per plant instead of grain yield per plot in hybrid maize breeding programs could be preferred by private companies dueto some advantages.
Evaluation of potential interactions between forest biomass production and Canadian wildlife. Final report

Energy Technology Data Exchange (ETDEWEB)

Coulombe, R.; Lemay, A.B.

1983-06-01

Forest management for biomass production can be undertaken in all provinces of Canada. Raw material can be extracted either from sawmills, logged areas, silvicultural treatments or short-rotation intensive culture. All forests are suitable habitats for wildlife. However, some species (e.g. woodland caribou, lynx, marten, owl) are extremely dependant on mature forests. Logging these forests generally contributes to reduction of habitats and thus populations. Management of second growth forests should take into consideration these species by extending rotations so part of the forests will serve the species. Removal of snags and downed logs to increase amount of raw material will contribute to reduced habitats of, for instance, tree-nesting birds. As these aspects have not been intensively studied within the Canadian forest regions, interactions can hardly be specified. Studies are recommended to analyse the overall problems and define measures to prevent detrimental effects. Other species (rare, threatened or endangered) will need specific attention and precaution while managing forests. Some are highly sensitive to noise and human disturbance (e.g. whooping crane, white pelican, peregrine falcon), others are very sensitive to harassment. Increased human presence within managed forests will necessitate more educational programs to prevent detrimental effects. Some species of reptiles, amphibians and fish are so poorly documented that only basic studies of the biology, ecology and distribution will permit to identify and evaluate interactions with these new forestry concepts. 289 refs., 19 figs., 36 tabs.
Pharmacokinetic Evaluation of the Interactions of Amenamevir (ASP2151) with Ketoconazole, Rifampicin, Midazolam, and Warfarin in Healthy Adults.

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Kusawake, Tomohiro; den Adel, Martin; Groenendaal-van de Meent, Dorien; Garcia-Hernandez, Alberto; Takada, Akitsugu; Kato, Kota; Ohtsu, Yoshiaki; Katashima, Masataka

2017-11-01

Amenamevir is a nonnucleoside antiherpes virus compound available for treating herpes zoster infections. Four studies aimed to determine any potential interactions between amenamevir and ketoconazole, rifampicin, midazolam, or warfarin in healthy male participants. Two studies were open-label studies that evaluated the effects of multiple doses of ketoconazole (400 mg) and rifampicin (600 mg) on the pharmacokinetics of a single oral dose of amenamevir. The other two studies were randomized, double-blind, parallel-group studies that evaluated the effects of multiple doses of amenamevir on the pharmacokinetics of a single dose of midazolam (7.5 mg) and warfarin (25 mg). A drug interaction was considered to occur if the 90% confidence interval (CI) of the least squares geometric mean ratio (GMR) of amenamevir to the comparator was outside the prespecified interval of 0.80-1.25. Interactions were observed between amenamevir and ketoconazole, rifampicin, and midazolam, but not between amenamevir and warfarin. After a single 400-mg dose of amenamevir, the GMRs of amenamevir plus ketoconazole or rifampicin versus amenamevir alone for C max and the area under the plasma concentration-time curve from time zero to infinity (AUC inf ) were 1.30 (90% CI 1.17-1.45) and 2.58 (90% CI 2.32-2.87), respectively, for ketoconazole and 0.42 (90% CI 0.37-0.49) and 0.17 (90% CI 0.15-0.19), respectively, for rifampicin. Following multiple doses of amenamevir (400 mg), the GMRs of midazolam plus amenamevir versus midazolam alone for AUC inf and C max were 0.53 (90% CI 0.47-0.61) and 0.63 (90% CI 0.50-0.80), respectively. After a single dose of warfarin, the (S)-warfarin and (R)-warfarin mean C max increased and mean AUC inf decreased in the presence of amenamevir; however, the 90% CIs of the GMRs for these parameters remained within the predefined limits. These findings confirm that amenamevir (as a cytochrome P450 3A4 substrate) can interact with ketoconazole or rifampicin, and (as a
No praise, please: Depressive symptoms, reactivity to positive social interaction, and fear of positive evaluation.

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Reichenberger, Julia; Wiggert, Nicole; Agroskin, Dmitrij; Wilhelm, Frank H; Blechert, Jens

2017-03-01

Depression is characterized by depressed mood and loss of interest or pleasure. Resulting alterations in emotional reactivity have been explained by three different accounts: 'positive attenuation', 'negative potentiation', and 'emotion context insensitivity'. Despite the importance of depression-related emotional alteration in social interactions, research with naturalistic interpersonal stimuli is scarce and underlying mechanisms largely unknown. Hence, the present study examined subjective emotional reactivity to brief negative, positive, and neutral social-evaluative videos as a function of depressive symptoms in an adult sample (N = 84). Fear of positive evaluation (FPE) and fear of negative evaluation (FNE), often conceptualized as cognitive components of social anxiety, were examined as possible mediators. Results revealed that more depression symptoms were related to diminished pleasantness responses to both positive and neutral videos. When considering all three video conditions simultaneously, only responses to positive videos remained significantly related to depression scores, supporting the 'positive attenuation' account. Moreover, FPE was found to uniquely mediate the relationship between depressive symptoms and pleasantness responses to positive videos. Results indicate that emotional reactivity to positive interpersonal stimuli is relevant for theoretical and clinical considerations of depression. This research underlines the importance of FPE not only for understanding social anxiety but also depression. Copyright © 2016 Elsevier Ltd. All rights reserved.
Application of Differential Colorimetry To Evaluate Anthocyanin-Flavonol-Flavanol Ternary Copigmentation Interactions in Model Solutions.

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Gordillo, Belén; Rodríguez-Pulido, Francisco J; González-Miret, M Lourdes; Quijada-Morín, Natalia; Rivas-Gonzalo, Julián C; García-Estévez, Ignacio; Heredia, Francisco J; Escribano-Bailón, M Teresa

2015-09-09

The combined effect of anthocyanin-flavanol-flavonol ternary interactions on the colorimetric and chemical stability of malvidin-3-glucoside has been studied. Model solutions with fixed malvidin-3-glucoside/(+)-catechin ratio (MC) and variable quercetin-3-β-d-glucoside concentration (MC+Q) and solutions with fixed malvidin-3-glucoside/quercetin-3-β-d-glucoside ratio (MQ) and variable (+)-catechin concentration (MQ+C) were tested at levels closer to those existing in wines. Color variations during storage were evaluated by differential colorimetry. Changes in the anthocyanin concentration were monitored by HPLC-DAD. CIELAB color-difference formulas were demonstrated to be of practical interest to assess the stronger and more stable interaction of quercetin-3-β-d-glucoside with MC binary mixture than (+)-catechin with MQ mixture. The results imply that MC+Q ternary solutions kept their intensity and bluish tonalities for a longer time in comparison to MQ+C solutions. The stability of malvidin-3-glucoside improves when the concentration of quercetin-3-β-d-glucoside increases in MC+Q mixtures, whereas the addition of (+)-catechin in MQ+C mixtures resulted in an opposite effect.
Evaluation of intensity and energy interaction parameters for the complexation of Pr(III) with selected nucleoside and nucleotide through absorption spectral studies

Science.gov (United States)

Bendangsenla, N.; Moaienla, T.; David Singh, Th.; Sumitra, Ch.; Rajmuhon Singh, N.; Indira Devi, M.

2013-02-01

The interactions of Pr(III) with nucleosides and nucleotides have been studied in different organic solvents employing absorption difference and comparative absorption spectrophotometry. The magnitudes of the variations in both energy and intensity interaction parameters were used to explore the degree of outer and inner sphere co-ordination, incidence of covalency and the extent of metal 4f-orbital involvement in chemical bonding. Various electronic spectral parameters like Slater-Condon (Fk), Racah (Ek), Lande parameter (ξ4f), Nephelauxatic ratio (β), bonding (b1/2), percentage covalency (δ) and intensity parameters like oscillator strength (P) and Judd Ofelt electronic dipole intensity parameter (Tλ, λ = 2, 4, 6) have been evaluated. The variation of these evaluated parameters were employed to interpret the nature of binding of Pr(III) with different ligands i.e. Adenosine/ATP in presence and absence of Ca2+.
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening.

Science.gov (United States)

Jasper, Julia B; Humbeck, Lina; Brinkjost, Tobias; Koch, Oliver

2018-03-16

Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerprint approach (PADIF, protein per atom score contributions derived interaction fingerprint) is presented which was specifically designed for utilising the GOLD scoring functions' atom contributions together with a specific scoring scheme. This allows the incorporation of known protein-ligand complex structures for a target-specific scoring. Unlike many other methods, this approach uses weighting factors reflecting the relative frequency of a specific interaction in the references and penalizes destabilizing interactions. In addition, and for the first time, an exhaustive validation study was performed that assesses the performance of PADIF and two other interaction fingerprints in virtual screening. Here, PADIF shows superior results, and some rules of thumb for a successful use of interaction fingerprints could be identified.
Systems interaction and single failure criterion

International Nuclear Information System (INIS)

1983-10-01

This study is a continued assessment of US research. All three of the systems interaction review methodologies which NRC's Systems Interaction Section (SIS) is studying are recommended. They are the Digraph-Matrix Analysis and Interactive Fault Tree/Failure Modes and Effects Analysis methodologies. A third methodology was developed for the Indian Point 3 system interaction review. It is recommended to developing the capability to perform and evaluate systems interaction reviews at Swedish nuclear plants. The Swedish demonstration studies should be performed on BWR's. (G.B.)
Evaluating the Intraspecific Interactions of Indian Rosewood (Dalbergia sissoo Roxb. Trees in Indian Rosewood Reserveof Khuzestan Province

Directory of Open Access Journals (Sweden)

Y. Erfanifard

2016-05-01

Full Text Available Positive and negative (facilitative and competitive interactions of plants are important issues in autecology and can be evaluated by the spatial pattern analysis in plant ecosystems. This study investigates the intraspecific interactions of Indian rosewood (Dalbergia sissoo Roxb. trees in Indian rosewood Reserve of Khuzestan province. Three 150 m × 200 m plots were selected and the spatial locations of all Indian rosewoods (239 trees were specified. Structurally different summary statistics (nearest neighbour distribution function D(r, K2-index K2(r, pair correlation function g(r, and O-ring O(r were also implemented to analyze the spatial pattern of the trees. The distribution of Indian rosewood trees significantly followed inhomogeneous Poisson process (α=0.05. The results of D(r and K2(r showed that the maximum distance to nearest tree was 12 m and density was decreased to this scale. The results of g(r and O(r also revealed the significant aggregation of Indian rosewood trees at scales of 1.5 to 4 m (α=0.05. In general, it was concluded that Indian rosewood trees had positive intraspecific interactions in Indian rosewood Reserve of Khuzestan province and their aggregation showed their facilitative effects on one another.
[Framework on drug interactions between herbal medicine and western medicine: building Ⅰ/Ⅱ/Ⅲ class pathways of interactions].

Science.gov (United States)

Jin, Rui; Huang, Jian-Mei; Wang, Yu-Guang; Zhang, Bing

2016-02-01

Combined use of Chinese medicine and western medicine is one of the hot spots in the domestic medical and academic fields for many years. There are lots of involved reports and studies on interaction problems due to combined used of Chinese medicine and western medicine, however, framework understanding is still rarely seen, affecting the clinical rationality of drug combinations. Actually, the inference ideas of drug interactions in clinical practice are more extensive and practical, and the overall viewpoint and pragmatic idea are the important factors in evaluating the rationality of clinical drug combinations. Based on above points, this paper systemically analyzed the existing information and examples, deeply discuss the embryology background (environment and action mechanism of interactions), and principally divided the interactions into three important and independent categories. Among the three categories, the first category (Ⅰapproach) was defined as the physical/chemical reactions after direct contact in vivo or in vitro, such as the combination of Chinese medicine injections and western medicine injections (in vitro), combination of bromide and Chinese medicines containing cinnabar (in vivo). The evaluation method for such interactions may be generalized theory of Acid-Base reaction. The second category (Ⅱ approach) was defined as the interactions through the pharmacokinetic process including absorption (such as the combination of aspirin and Huowei capsule), distribution (such as the combination of artosin and medicinal herbs containing coumarin), metabolism (such as the combination of phenobarbital and glycyrrhiza) and excretion (such as the combination of furadantin and Crataegi Fructus). The existing pharmacokinetic theory can act as the evaluation method for this type of interaction. The third category (Ⅲ approach) was defined as the synergy/antagonism interactions by pharmacological effects or biological pathways. The combination of warfarin
[Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

Science.gov (United States)

Gao, Yong-Ming; Wan, Ping

2002-06-01

Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x
Evaluating the Sharing Stories youth theatre program: an interactive theatre and drama-based strategy for sexual health promotion among multicultural youth.

Science.gov (United States)

Roberts, Meagan; Lobo, Roanna; Sorenson, Anne

2017-03-01

Issue addressed Rates of sexually transmissible infections among young people are high, and there is a need for innovative, youth-focused sexual health promotion programs. This study evaluated the effectiveness of the Sharing Stories youth theatre program, which uses interactive theatre and drama-based strategies to engage and educate multicultural youth on sexual health issues. The effectiveness of using drama-based evaluation methods is also discussed. Methods The youth theatre program participants were 18 multicultural youth from South East Asian, African and Middle Eastern backgrounds aged between 14 and 21 years. Four sexual health drama scenarios and a sexual health questionnaire were used to measure changes in knowledge and attitudes. Results Participants reported being confident talking to and supporting their friends with regards to safe sex messages, improved their sexual health knowledge and demonstrated a positive shift in their attitudes towards sexual health. Drama-based evaluation methods were effective in engaging multicultural youth and worked well across the cultures and age groups. Conclusions Theatre and drama-based sexual health promotion strategies are an effective method for up-skilling young people from multicultural backgrounds to be peer educators and good communicators of sexual health information. Drama-based evaluation methods are engaging for young people and an effective way of collecting data from culturally diverse youth. So what? This study recommends incorporating interactive and arts-based strategies into sexual health promotion programs for multicultural youth. It also provides guidance for health promotion practitioners evaluating an arts-based health promotion program using arts-based data collection methods.
Diachronic Perspective and Interaction

DEFF Research Database (Denmark)

Marchetti, Emanuela; Valente, Andrea

. An ongoing participatory inquiry is being conducted, to explore deeper forms of learning and communication for historical museums. Our hypothesis is that the diachronic perspective on historical processes, defined as social interaction within the environment through time, is a key missing element....... Although this interaction style may appeal to teachers, as it reminds of school teaching, it has several disadvantages: a dialogue never occurs between adults and children, who listen in silence, hence it becomes hard to evaluate what has being learnt and how deeply, and finally it is not very engaging....... Explorations of more interactive representations of the diachronic perspective, through play and tangible interaction, may foster a dialogue with young visitors. Therefore, a new interactive installation is being designed, intended as a tool to enrich learning, allowing children to experience historical...

Evaluating public education messages aimed at monitoring and responding to social interactive technology on smartphones among young drivers.

Science.gov (United States)

Gauld, Cassandra S; Lewis, Ioni; White, Katherine M; Fleiter, Judy J; Watson, Barry

2017-07-01

Young drivers are more likely than any other age group to access social interactive technology (e.g., Facebook, E-mail) on a smartphone while driving. The current study formed part of a larger investigation and was guided by The Step Approach to Message Design and Testing (SatMDT) to evaluate the relative effectiveness of three different public education messages aimed at reducing smartphone use among young drivers. The messages were each adapted to the specific behaviours of monitoring/reading and responding to social interactive technology on smartphones. Participants (n=288; 199F, 89M) were drivers aged 17-25 years who resided in the Australian state of Queensland. Message acceptance (i.e., intention and effectiveness) and message rejection were both assessed using a self-report survey. Multivariate analyses found that, overall, the messages targeting monitoring/reading behaviour were considered more effective than those targeting responding behaviour. The message that challenged the underlying motivation that believing you are a good driver makes it easier to monitor/read social interactive technology while driving was considered particularly effective by young male drivers. Copyright © 2017 Elsevier Ltd. All rights reserved.
Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals.

Science.gov (United States)

Morgante, Fabio; Huang, Wen; Maltecca, Christian; Mackay, Trudy F C

2018-06-01

Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.
Systems interaction and single failure criterion

International Nuclear Information System (INIS)

1981-01-01

This report documents the results of a six-month study to evaluate the ongoing research programs of the U.S. Nuclear Regulatory Commission (NRC) and U.S. commercial nuclear station owners which address the safety significance of systems interaction and the regulatory adequacy of the single failure criterion. The evaluation of system interactions provided is the initial phase of a more detailed study leading to the development and application of methodology for quantifying the relative safety of operating nuclear plants. (Auth.)
Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry.

Science.gov (United States)

DeBlasio, Stacy L; Bereman, Michael S; Mahoney, Jaclyn; Thannhauser, Theodore W; Gray, Stewart M; MacCoss, Michael J; Cilia Heck, Michelle

2017-09-01

Protein interactions between virus and host are essential for viral propagation and movement, as viruses lack most of the proteins required to thrive on their own. Precision methods aimed at disrupting virus-host interactions represent new approaches to disease management but require in-depth knowledge of the identity and binding specificity of host proteins within these interaction networks. Protein coimmunoprecipitation (co-IP) coupled with mass spectrometry (MS) provides a high-throughput way to characterize virus-host interactomes in a single experiment. Common co-IP methods use antibodies immobilized on agarose or magnetic beads to isolate virus-host complexes in solutions of host tissue homogenate. Although these workflows are well established, they can be fairly laborious and expensive. Therefore, we evaluated the feasibility of using antibody-coated microtiter plates coupled with MS analysis as an easy, less expensive way to identify host proteins that interact with Potato leafroll virus (PLRV), an insect-borne RNA virus that infects potatoes. With the use of the bead-free platform, we were able to detect 36 plant and 1 nonstructural viral protein significantly coimmunoprecipitating with PLRV. Two of these proteins, a 14-3-3 signal transduction protein and malate dehydrogenase 2 (mMDH2), were detected as having a weakened or lost association with a structural mutant of the virus, demonstrating that the bead-free method is sensitive enough to detect quantitative differences that can be used to pin-point domains of interaction. Collectively, our analysis shows that the bead-free platform is a low-cost alternative that can be used by core facilities and other investigators to identify plant and viral proteins interacting with virions and/or the viral structural proteins.
Staging Urban Interactions with Media Facades

DEFF Research Database (Denmark)

Brynskov, Martin; Dalsgaard, Peter; Ebsen, Tobias

2009-01-01

Using media façades as a subcategory of urban computing, this paper contributes to the understanding of spatial interaction, sense-making, and social mediation as part of identifying key characteristics of interaction with media façades. Our research addresses in particular the open......-ended but framed nature of interaction, which in conjunction with varying interpretations enables individual sense-making. Moreover, we contribute to the understanding of flexible social interaction by addressing urban interaction in relation to distributed attention, shared focus, dialogue and collective action......, and reflective evaluation of a 180 m2(1937 square feet) interactive media façade in operation 24/7 for more than 50 days....
Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions.

Directory of Open Access Journals (Sweden)

David J Hauber

Full Text Available Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1 selection is weak; and 2 similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent sites in the highly expressed Escherichia coli ribosomal protein gene rplQ from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAG mutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s| > 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele.
Yakima River Species Interactions Studies; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2004-2005 Annual Report.

Energy Technology Data Exchange (ETDEWEB)

Pearsons, Todd N.; Temple, Gabriel M.; Fritts, Anthony L. (Washington Department of Fish and Wildlife, Olympia, WA)

2005-05-01

This report is intended to satisfy two concurrent needs: (1) provide a contract deliverable from the Washington Department of Fish and Wildlife (WDFW) to the Bonneville Power Administration (BPA), with emphasis on identification of salient results of value to ongoing Yakima/Klickitat Fisheries Project (YKFP) planning, and (2) summarize results of research that have broader scientific relevance. This is the thirteenth of a series of progress reports that address species interactions research and supplementation monitoring of fishes in response to supplementation of salmon and steelhead in the upper Yakima River basin (Hindman et al. 1991; McMichael et al. 1992; Pearsons et al. 1993; Pearsons et al. 1994; Pearsons et al. 1996; Pearsons et al. 1998, Pearsons et al. 1999, Pearsons et al. 2001a, Pearsons et al. 2001b, Pearsons et al. 2002, Pearsons et al. 2003, Pearsons et al. 2004). Journal articles and book chapters have also been published from our work (McMichael 1993; Martin et al. 1995; McMichael et al. 1997; McMichael and Pearsons 1998; McMichael et al. 1998; Pearsons and Fritts 1999; McMichael et al. 1999; McMichael et al. 1999; Pearsons and Hopley 1999; Ham and Pearsons 2000; Ham and Pearsons 2001; Amaral et al. 2001; McMichael and Pearsons 2001; Pearsons 2002, Fritts and Pearsons 2004, Pearsons et al. in press, Major et al. in press). This progress report summarizes data collected between January 1, 2004 and December 31, 2004. These data were compared to findings from previous years to identify general trends and make preliminary comparisons. Interactions between fish produced as part of the YKFP, termed target species or stocks, and other species or stocks (non-target taxa) may alter the population status of non-target species or stocks. This may occur through a variety of mechanisms, such as competition, predation, and interbreeding (Pearsons et al. 1994; Busack et al. 1997; Pearsons and Hopley 1999). Furthermore, the success of a supplementation program may
In vitro evaluation of the interactions between human corneal endothelial cells and extracellular matrix proteins

International Nuclear Information System (INIS)

Choi, Jin San; Kim, Eun Young; Kim, Min Jeong; Giegengack, Matthew; Khan, Faraaz A; Soker, Shay; Khang, Gilson

2013-01-01

The corneal endothelium is the innermost cell layer of the cornea and rests on Descemet's membrane consisting of various extracellular matrix (ECM) proteins which can directly affect the cellular behaviors such as cell adhesion, proliferation, polarity, morphogenesis and function. The objective of this study was to investigate the interactions between the ECM environment and human corneal endothelial cells (HCECs), with the ultimate goal to improve cell proliferation and function in vitro. To evaluate the interaction of HCECs with ECM proteins, cells were seeded on ECM-coated tissue culture dishes, including collagen type I (COL I), collagen type IV (COL IV), fibronectin (FN), FNC coating mix (FNC) and laminin (LM). Cell adhesion and proliferation of HCECs on each substratum and expression of CEC markers were studied. The results showed that HCECs plated on the COL I, COL IV, FN and FNC-coated plates had enhanced cell adhesion initially; the number for COL I, COL IV, FN and FNC was significantly higher than the control (P < 0.05). In addition, cells grown on ECM protein-coated dishes showed more compact cellular morphology and CEC marker expression compared to cells seeded on uncoated dishes. Collectively, our results suggest that an adequate ECM protein combination can provide a long-term culture environment for HCECs for corneal endothelium transplantation. (paper)
The Calcium-Sensing Receptor Gene Polymorphism rs1801725 and Calcium-Related Phenotypes in Hemodialysis Patients

Directory of Open Access Journals (Sweden)

Alicja E. Grzegorzewska

2018-05-01

Full Text Available Background/Aims: The calcium-sensing receptor gene (CASR rs1801725 variant is responsible for a non-conservative amino-acid change (A986S in the calcium-sensing receptor cytoplasmic tail. We hypothesized that rs1801725 polymorphism might be helpful in understanding Ca-related abnormalities in HD patients. Methods: In 1215 subjects (245 on cinacalcet, we determined the associations of rs1801725 with secondary hyperparathyroidism (sHPT-related laboratory parameters, PTH-decreasing effect of cinacalcet hydrochloride, coronary artery disease (CAD, myocardial infarction (MI, nephrolithiasis-related ESRD, and mortality. CASR rs7652589(AT haplotypes and rs1801725 epistatic interactions with vitamin D signaling pathway genes were examined for associations with selected phenotypes. Results: The rs1801725 variant allele showed an increasing independent effect on plasma PTH (Pcorrected = 0.009. CASR rs7652589_rs1801725 AT haplotype was associated with 1.7-fold higher frequency of PTH levels over 437 pg/mL than the reference haplotype GG (P = 0.001. CASR rs7652589_rs1801725 AG haplotype was 1.5-fold more frequent in nephrolithiasis-related ESRD than the GG haplotype (P = 0.004. There were no significant associations between rs1801725, CAD, MI, and response to cinacalcet. Variant homozygosity of rs1801725 correlated independently with higher infection-related mortality compared with heterozygosity (HR 7.95, 95%CI 2.15 – 29.37, P = 0.003 and major homozygosity (HR 5.89, 95%CI 1.69 – 20.55, P = 0.040. CASR rs1801725 did not show epistatic interactions with vitamin D signaling pathway genes concerning tested associations. Conclusion: The variant allele of CASR rs1801725 solely and together with the variant allele of rs7652589 increases risk of more advanced sHPT. Homozygosity of the rs1801725 variant allele contributes to infection-related mortality in HD patients.
Mood swings: design and evaluation of affective interactive art

NARCIS (Netherlands)

Bialoskorski, Leticia S.S.; Westerink, Joyce H.D.M.; van den Broek, Egon

2009-01-01

The field of affective computing is concerned with developing emphatic products, such as affective consumer products, affective games, and affective art. This paper describes Mood Swings, an affective interactive art system, which interprets and visualizes affect expressed by a person. Mood Swings
Towards a standard on evaluation of tactile/haptic interactions

NARCIS (Netherlands)

Sinclair, I.; Carter, J.; Kassner, S.; Erp, J.B.F. van; Weber, G.; Elliott, L.; Andrew, I.

2012-01-01

Tactile and haptic interaction is becoming increasingly important; ergonomic standards can ensure that systems are designed with sufficient concern for ergonomics and interoperability. ISO (through working group TC159/SC4/WG9) is developing international standards in this subject area, dual-tracked
Magnetic moments and the Skyrme interaction

Energy Technology Data Exchange (ETDEWEB)

Lipparini, E; Stringari, S; Traini, M [Trento Univ. (Italy). Dipartmento di Matematica e Fisica

1977-12-12

The magnetic properties of the Skyrme interaction have been studied by performing a restricted Hartree-Fock calculation in order to evaluate the magnetic polarizability and the corrections to the Schmidt moments in nuclei with closed jj shells plus or minus one nucleon. Different corrections to the Schmidt values have been evaluated and discussed: the M1 core polarization and the renormalization of the gyromagnetic factors due to exchange and spin-orbit forces. Several variants of the Skyrme interaction have been studied and discussed in detail.
Soil-structure interaction effects on the reliability evaluation of reactor containments

International Nuclear Information System (INIS)

Pires, J.; Hwang, H.; Reich, M.

1986-01-01

The probability-based method for the seismic reliability assessment of nuclear structures, which has been developed at Brookhaven National Laboratory (BNL), is extended to include the effects of soil-structure interaction. A reinforced concrete containment building is analyzed in order to examine soil-structure interaction effects on: (1) structural fragilities; (2) floor response spectra statistics; and (3) correlation coefficients for total acceleration responses at specified structural locations
Research on interactive genetic-geological models to evaluate favourability for undiscovered uranium resources

International Nuclear Information System (INIS)

Finch, W.I.; Granger, H.C.; Lupe, R.; McCammon, R.B.

1980-01-01

Current methods of evaluating favourability for undiscovered uranium resources are unduly subjective, quite possibly inconsistent and, as a consequence, of questionable reliability. This research is aimed at reducing the subjectivity and increasing the reliability by designing an improved method that depends largely on geological data and their statistical frequency of occurrence. This progress report outlines a genetic approach to modelling the geological factors that controlled uranium mineralization in order to evaluate the favourability for the occurrence of undiscovered uranium deposits of the type modelled. A genetic model is constructed from all the factors that describe the processes, in chronological sequence, that formed uranium deposits thought to have a common origin. The field and laboratory evidence for the processes constitute a geologic-occurrence base that parallels the chronological sequence of events. The genetic model and the geologic-occurrence base are portrayed as two columns of an interactive matrix called the ''genetic-geologic model''. For each column, eight chronological stages are used to describe the overall formation of the uranium deposits. These stages consist of (1) precursor processes; (2) host-rock formation; (3) preparation of host-rock; (4) uranium-source development; (5) transport of uranium; (6) primary uranium deposition; (7) post-deposition modification; and (8) preservation. To apply the genetic-geological model to evaluate favourability, a question is posed that determines the presence or absence of each attribute listed under the geologic-occurrence base. By building a logic circuit of the attributes according to either their essential or non-essential nature, the resultant match between a well-documented control area and the test area may be determined. The degree of match is a measure of favourability for uranium occurrence as hypothesized in the genetic model
Electrochemical evaluation of avidin-biotin interaction on self-assembled gold electrodes

International Nuclear Information System (INIS)

Ding, S.-J.; Chang, B.-W.; Wu, C.-C.; Lai, M.-F.; Chang, H.-C.

2005-01-01

The avidin-biotin interaction on 11-mercaptoundecanoic acid self-assembled gold electrodes was investigated by means of cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The interfacial properties of the modified electrodes were evaluated in the presence of the Fe(China) 6 3-/4- couple redox as a probe. A simple equivalent circuit model with a constant phase element was used to interpret the obtained impedance spectra. The results of cyclic voltammetry showed that the voltammetric behavior of the redox probe was influenced by the electrode surface modification. It is evident that the accumulation of treated substances and the binding of biotin to avidin on the electrode surface resulted in the increasing electron-transfer resistance and the decreasing capacitance. The changes in the electron-transfer resistance on the avidin-modified electrodes were more sensitive than that in the capacitance while detecting biotin over the 2-10 μg/mL concentration. The detection amount can be as low as 20 ng/mL based on the electron-transfer resistance that presented the change of 4.3 kΩ without the use of labels. The development of a rapid, facile, and sensitive method for the quantitation of nanogram quantities of biomolecules utilizing EIS may be achieved
The interactive effects of affect and shopping goal on information search and product evaluations.

Science.gov (United States)

Chen, Fangyuan; Wyer, Robert S; Shen, Hao

2015-12-01

Although shoppers often want to evaluate products to make a purchase decision, they can also shop for enjoyment. In each case, the amount of time they spend on shopping and the number of options they consider can depend on the mood they happen to be in. We predicted that mood can signal whether the goal has been attained and when people should stop processing information. When people are primarily motivated to purchase a particular type of product, positive mood signals that they have done enough. Thus, they consider less information if they are happy than if they are unhappy. When people shop for enjoyment, however, positive mood signals that they are still having fun. Thus, they consider more information when they are happy than when they are not. Four experiments among university students (N = 827) examined these possibilities. Experiment 1 provided initial evidence for the interactive effects of mood and goals on search behavior and product evaluation. Other studies examined the implications of this conceptualization for different domains: (a) the relative impact of brand and attribute information on judgments (Experiment 2), (b) gender differences in shopping behavior (Experiment 3), and (c) the number of options that people review in an actual online shopping website (Experiment 4). (c) 2015 APA, all rights reserved).
Interactive segmentation: a scalable superpixel-based method

Science.gov (United States)

Mathieu, Bérengère; Crouzil, Alain; Puel, Jean-Baptiste

2017-11-01

This paper addresses the problem of interactive multiclass segmentation of images. We propose a fast and efficient new interactive segmentation method called superpixel α fusion (SαF). From a few strokes drawn by a user over an image, this method extracts relevant semantic objects. To get a fast calculation and an accurate segmentation, SαF uses superpixel oversegmentation and support vector machine classification. We compare SαF with competing algorithms by evaluating its performances on reference benchmarks. We also suggest four new datasets to evaluate the scalability of interactive segmentation methods, using images from some thousand to several million pixels. We conclude with two applications of SαF.
Evaluating interactive technology for an evolving case study on learning and satisfaction of graduate nursing students.

Science.gov (United States)

Vogt, Marjorie A; Schaffner, Barbara H

2016-07-01

Nursing education is challenged to prepare students for complex healthcare needs through the integration of teamwork and informatics. Technology has become an important teaching tool in the blended classroom to enhance group based learning experiences. Faculty evaluation of classroom technologies is imperative prior to adoption. Few studies have directly compared various technologies and their impact on student satisfaction and learning. The purpose of this study was to evaluate technology enhanced teaching methods on the learning and satisfaction of graduate students in an advanced pharmacology class using an unfolding case study. After IRB approval, students were randomly assigned to one of three groups: blogging group, wiki group or webinar group. Students completed the evolving case study using the assigned interactive technology. Student names were removed from the case studies. Faculty evaluated the case study using a rubric, while blinded to the assigned technology method used. No significant difference was found on case study grades, the range of grades on the assignment demonstrated little differences between the methods used. Students indicated an overall positive impact related to networking and collaboration on a satisfaction survey. Impact of technology methods needs to be explored in other areas of graduate nursing education. Copyright © 2016 Elsevier Ltd. All rights reserved.
Evaluation of inelastic constitutive models under plasticity-creep interaction for 2 1/4 Cr-1 Mo steel: Results of joint work (A)

International Nuclear Information System (INIS)

Inoue, T.; Ohno, N.; Suzuki, A.; Igari, T.

1987-01-01

The authorization of constitutive models under plasticity-creep condition and life estimation methods in fatigue-creep regime is expected to be achieved from the viewpoint of design purposes of high temperature components of reactor structures. The present Subcommittee has performed the cooperative project consisting of the following two parts: (A) To review and evaluate inelastic constitutive models relevant to the material response under plasticity-creep interaction and (B) to recommend some adequate methods to estimate material life under fatigue-creep interaction by taking account of the effect of plasticity-creep interaction on the stress-strain hysteresis loops. The material treated is normalized and tempered 2 1/4 Cr-1Mo steel at 600 0 C. The part (A) plays a preliminary role for the part (B), since the constitutive models examined in the part (A) were used to describe the stress-strain hysteresis loops necessary to predict analytically the lives under fatigue-creep interaction. In the part (A), thererfore, it is important to check how accurately the constitutive models simulate the stress-strain hysteresis loops especially by taking account of the effect of plasticity-creep interaction. (orig./GL)
Nonunion of acetabular fractures: evaluation with interactive multiplanar CT

International Nuclear Information System (INIS)

Kuhlman, J.E.; Fishman, E.K.; Ney, D.R.; Brooker, A.F. Jr.; Magid, D.

1989-01-01

Nonunions involving fractures of the acetabulum are reportedly rare, with few citings and little discussion in the literature. It is possible that acetabular nonunions go undetected because imaging of the acetabulum is difficult by conventional radiography. We report two cases of fracture nonunion involving the weight-bearing surface of the acetabulum diagnosed with the aid of computed tomography (CT) and a newly developed interactive 2D/3D orthotool that uniquely processes and reformats routine CT data. The interactive 2D/3D orthotool is a sophisticated computer program that allows dynamic viewing of standard multiplanar reconstructions in the axial, coronal, and sagittal planes as well as multiple oblique projections. The 2D/3D orthotool provides on screen correlation of two-dimensional multiplanar images with three-dimensional reconstructions of the pelvis. The authors found this capability ideally suited for studying fractures with off-axis orientation such as those through the acetabular dome, greatly facilitating the diagnosis of nonunion

A microscopic evaluation of collagen-bilirubin interactions: in vitro surface phenomenon.

Science.gov (United States)

Usharani, N; Jayakumar, G C; Rao, J R; Chandrasekaran, B; Nair, B U

2014-02-01

This study is carried out to understand the morphology variations of collagen I matrices influenced by bilirubin. The characteristics of bilirubin interaction with collagen ascertained using various techniques like XRD, CLSM, fluorescence, SEM and AFM. These techniques are used to understand the distribution, expression and colocalization patterns of collagen-bilirubin complexes. The present investigation mimic the in vivo mechanisms created during the disorder condition like jaundice. Fluorescence technique elucidates the crucial role played by bilirubin deposition and interaction during collagen organization. Influence of bilirubin during collagen fibrillogenesis and banding patterns are clearly visualize using SEM. As a result, collagen-bilirubin complex provides different reconstructed patterns because of the influence of bilirubin concentration. Selectivity, specificity and spatial organization of collagen-bilirubin are determined through AFM imaging. Consequently, it is observed that the morphology and quantity of the bilirubin binding to collagen varied by the concentrations and the adsorption rate in protein solutions. Microscopic studies of collagen-bilirubin interaction confirms that bilirubin influence the fibrillogenesis and alter the rate of collagen organization depending on the bilirubin concentration. This knowledge helps to develop a novel drug to inhibit the interface point of interaction between collagen and bilirubin. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.
Brain Interaction during Cooperation: Evaluating Local Properties of Multiple-Brain Network.

Science.gov (United States)

Sciaraffa, Nicolina; Borghini, Gianluca; Aricò, Pietro; Di Flumeri, Gianluca; Colosimo, Alfredo; Bezerianos, Anastasios; Thakor, Nitish V; Babiloni, Fabio

2017-07-21

Subjects' interaction is the core of most human activities. This is the reason why a lack of coordination is often the cause of missing goals, more than individual failure. While there are different subjective and objective measures to assess the level of mental effort required by subjects while facing a situation that is getting harder, that is, mental workload, to define an objective measure based on how and if team members are interacting is not so straightforward. In this study, behavioral, subjective and synchronized electroencephalographic data were collected from couples involved in a cooperative task to describe the relationship between task difficulty and team coordination, in the sense of interaction aimed at cooperatively performing the assignment. Multiple-brain connectivity analysis provided information about the whole interacting system. The results showed that averaged local properties of a brain network were affected by task difficulty. In particular, strength changed significantly with task difficulty and clustering coefficients strongly correlated with the workload itself. In particular, a higher workload corresponded to lower clustering values over the central and parietal brain areas. Such results has been interpreted as less efficient organization of the network when the subjects' activities, due to high workload tendencies, were less coordinated.
Evaluation of the effect of prepulses on HF laser-target interactions

International Nuclear Information System (INIS)

Matzen, M.K.

1979-06-01

We have assessed the effect of multinanosecond, low-power-density prepulses on the interaction of multinanosecond, 10 14 W/cm 2 , approx. 3 -μm HF laser pulses with slab targets. The emphasis is on analyzing absorption and x-ray conversion efficiency. A survey of previous experiments gives no evidence that these prepulses will affect the total absorption. However, prepulses have been observed to cause qualitative changes in both the x-ray spectrum and conversion efficiency. Numerical simulations indicate that the laser-target interaction is effectively insensitive to low-power-density prepulses. These studies imply that basic laser-target experiments with multiplexed, HF laser pulses will provide an important characterization of the interaction of long pulse, multi-line, approx. 3 μm radiation with targets. Future wavelength comparison experiments will require prepulse suppression or target isolation
Ethological Evaluation of the Effects of Social Defeat Stress in Mice: Beyond the Social Interaction Ratio

Science.gov (United States)

Henriques-Alves, Aron M.; Queiroz, Claudio M.

2016-01-01

In rodents, repeated exposure to unavoidable aggression followed by sustained sensory treat can lead to prolonged social aversion. The chronic social defeat stress model explores that phenomenon and it has been used as an animal model for human depression. However, some authors have questioned whether confounding effects may arise as the model also boosts anxiety-related behaviors. Despite its wide acceptance, most studies extract limited information from the behavior of the defeated animal. Often, the normalized occupancy around the social stimulus, the interaction zone, is taken as an index of depression. We hypothesized that this parameter is insufficient to fully characterize the behavioral consequences of this form of stress. Using an ethological approach, we showed that repeated social defeat delayed the expression of social investigation in long (10 min) sessions of social interaction. Also, the incidence of defensive behaviors, including stretched-attend posture and high speed retreats, was significantly higher in defeated mice in comparison to controls. Interestingly, a subpopulation of defeated mice showed recurrent and non-habituating stretched-attend posture and persistent flights during the entire session. Two indexes were created based on defensive behaviors to show that only recurrent flights correlates with sucrose intake. Together, the present study corroborates the idea that this model of social stress can precipitate a myriad of behaviors not readily disentangled. We propose that long sessions (>150 s) and detailed ethological evaluation during social interaction tests are necessary to provide enough information to correctly classify defeated animals in terms of resilience and susceptibility to social defeat stress. PMID:26869895
Ethological Evaluation of the Effects of Social Defeat Stress in Mice: Beyond the Social Interaction Ratio.

Science.gov (United States)

Henriques-Alves, Aron M; Queiroz, Claudio M

2015-01-01

In rodents, repeated exposure to unavoidable aggression followed by sustained sensory treat can lead to prolonged social aversion. The chronic social defeat stress model explores that phenomenon and it has been used as an animal model for human depression. However, some authors have questioned whether confounding effects may arise as the model also boosts anxiety-related behaviors. Despite its wide acceptance, most studies extract limited information from the behavior of the defeated animal. Often, the normalized occupancy around the social stimulus, the interaction zone, is taken as an index of depression. We hypothesized that this parameter is insufficient to fully characterize the behavioral consequences of this form of stress. Using an ethological approach, we showed that repeated social defeat delayed the expression of social investigation in long (10 min) sessions of social interaction. Also, the incidence of defensive behaviors, including stretched-attend posture and high speed retreats, was significantly higher in defeated mice in comparison to controls. Interestingly, a subpopulation of defeated mice showed recurrent and non-habituating stretched-attend posture and persistent flights during the entire session. Two indexes were created based on defensive behaviors to show that only recurrent flights correlates with sucrose intake. Together, the present study corroborates the idea that this model of social stress can precipitate a myriad of behaviors not readily disentangled. We propose that long sessions (>150 s) and detailed ethological evaluation during social interaction tests are necessary to provide enough information to correctly classify defeated animals in terms of resilience and susceptibility to social defeat stress.
Ethological evaluation of the effects of social defeat stress in mice: beyond the social interaction ratio

Directory of Open Access Journals (Sweden)

Aron Miranda Henriques-Alves

2016-02-01

Full Text Available In rodents, repeated exposure to unavoidable aggression followed by sustained sensory treat can lead to prolonged social aversion. The chronic social defeat stress model explores that phenomenon and it has been used as an animal model for human depression. However, some authors have questioned whether confounding effects may arise as the model also boosts anxiety-related behaviors. Despite its wide acceptance, most studies extract limited information from the behavior of the defeated animal. Often, the normalized occupancy around the social stimulus, the interaction zone, is taken as an index of depression. We hypothesized that this parameter is insufficient to fully characterize the behavioral consequences of this form of stress. Using an ethological approach, we showed that repeated social defeat delayed the expression of social investigation in long (10 min sessions of social interaction. Also, the incidence of defensive behaviors, including stretched-attend posture and high speed retreats, was significantly higher in defeated mice in comparison to controls. Interestingly, a subpopulation of defeated mice showed recurrent and non-habituating stretched-attend posture and persistent flights during the entire session. Two indexes were created based on defensive behaviors to show that only recurrent flights correlates with sucrose intake. Together, the present study corroborates the idea that this model of social stress can precipitate a myriad of behaviors not readily disentangled. We propose that long sessions (> 150 s and detailed ethological evaluation during social interaction tests are necessary to provide enough information to correctly classify defeated animals in terms of resilience and susceptibility to social defeat stress.
"Help Me Pull That Cursor" A Collaborative Interactive Floor Enhancing Community Interaction

Directory of Open Access Journals (Sweden)

Peter Krogh

2004-05-01

Full Text Available In this paper we describe the development, experiments and evaluation of the iFloor, an interactive floor prototype installed at the local central municipality library. The primary purpose of the iFloor prototype is to support and stimulate community interaction between collocated people. The context of the library demands that any user can walk up and use the prototype without any devices or prior introduction. To achieve this, the iFloor proposes innovative interaction (modes/paradigms/patterns for floor surfaces through the means of video tracking. Browsing and selecting content is done in a collaborative process and mobile phones are used for posting messages onto the floor. The iFloor highlights topics on social issues of ubiquitous computing environments in public spaces, and provides an example of how to exploit human spatial movements, positions and arrangements in interaction with computers.
Transgressive Hybrids as Hopeful Monsters.

Science.gov (United States)

Dittrich-Reed, Dylan R; Fitzpatrick, Benjamin M

2013-06-01

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt's infamous "hopeful monster". Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, "monstrous" phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts "hopeless" monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts "hopeful" monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant "hopeful monsters" will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.
POEM: Identifying joint additive effects on regulatory circuits

Directory of Open Access Journals (Sweden)

Maya eBotzman

2016-04-01

Full Text Available Motivation: Expression Quantitative Trait Locus (eQTL mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress towards a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such ‘modularization’ approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic effects.Results: Here we present POEM (Pairwise effect On Expression Modules, a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs.Availability: The software described in this article is available at csgi.tau.ac.il/POEM/.
Orthodontic brackets in high field MR imaging: experimental evaluation of magnetic field interactions at 3.0 tesla

International Nuclear Information System (INIS)

Kemper, J.; Adam, G.; Klocke, A.; Kahl-Nieke, B.

2005-01-01

Purpose: To evaluate static magnetic field interactions for 32 commonly used orthodontic brackets in a 3.0 T magnetic resonance imaging (MRI) system. Materials and methods: 32 orthodontic brackets consisting of a steel alloy (n=27), a cobalt-chromium alloy (n=2), ceramic (n=1), ceramic with a steel slot (n=1), and titanium (n=1) from 13 different manufacturers were tested for magnetic field interactions in a static magnetic field at 3.0 T (Gyroscan Intera 3.0 T, Philips Medical Systems, Best, Netherlands). The magnetic deflection force F Z [mN] was evaluated by determining the deflection angle β[ ] using the established deflection angle test according to the ASTM guidelines. The magnetic-field-induced rotational force F rot or torque was qualitatively determined using a 5-point grading scale (0: no torque; +4: very strong torque). Results: In 18 of the 32 brackets, the deflection angle β was found to be > 45 and the translational force exceeded the gravitational force F G on the particular bracket (F Z : 1.2-45.7 mN). The translational force F Z was found to be up to 68.5 times greater than the gravitational force F G (F Z /F G : 1.4-68.5). The rotational force F rot was correspondingly high (+3/+4) for those brackets. For the remaining 14 objects, the deflection angles were < 45 and the torque measurements ranged from 0 to +2. The static magnetic field did not affect the titanium bracket and the ceramic bracket. No measurable translational and rotational forces were found. (orig.)
A test to evaluation non-linear soil structure interaction

International Nuclear Information System (INIS)

Hagiwara, T.; Kitada, Y.

2005-01-01

JNES is planning a new project to study non-linear soil-structure interaction (SSI) effect under large earthquake ground motions equivalent to and/or over a design earthquake ground motion of S2. Concerning the SSI test, it is pointed out that handling of the scale effect of the specimen taking into account the surrounding soil on the earthquake response evaluation to the actual structure is essential issue for the scaled model test. Thus, for the test, the largest specimen possible and the biggest input motion possible are necessary. Taking into account the above issues, new test methodology, which utilizes artificial earthquake ground motion, is considered desirable if it can be performed at a realistic cost. With this motivation, we have studied the test methodology which applying blasting power as for a big earthquake ground motion. The information from a coalmine company in the U.S.A. indicates that the works performed in the surface coalmine to blast a rock covering a coal layer generates a big artificial ground motion, which is similar to earthquake ground motion. Application of this artificial earthquake ground motion for the SSI test is considered very promising because the blasting work is carried out periodically for mining coal so that we can apply artificial motions generated by the work if we construct a building model at a closed point to the blasting work area. The major purposes of the test are to understand (a) basic earthquake response characteristics of a Nuclear Power Plant (NPP) reactor building when a large earthquake strikes the NPP site and (b) nonlinear characteristics of SSI phenomenon during a big earthquake. In the paper of ICONE-13, we will introduce the test method and basic characteristics of measured artificial ground motions generated by the blasting works on an actual site. (authors)
Extending NGOMSL Model for Human-Humanoid Robot Interaction in the Soccer Robotics Domain

Directory of Open Access Journals (Sweden)

Rajesh Elara Mohan

2008-01-01

Full Text Available In the field of human-computer interaction, the Natural Goals, Operators, Methods, and Selection rules Language (NGOMSL model is one of the most popular methods for modelling knowledge and cognitive processes for rapid usability evaluation. The NGOMSL model is a description of the knowledge that a user must possess to operate the system represented as elementary actions for effective usability evaluations. In the last few years, mobile robots have been exhibiting a stronger presence in commercial markets and very little work has been done with NGOMSL modelling for usability evaluations in the human-robot interaction discipline. This paper focuses on extending the NGOMSL model for usability evaluation of human-humanoid robot interaction in the soccer robotics domain. The NGOMSL modelled human-humanoid interaction design of Robo-Erectus Junior was evaluated and the results of the experiments showed that the interaction design was able to find faults in an average time of 23.84 s. Also, the interaction design was able to detect the fault within the 60 s in 100% of the cases. The Evaluated Interaction design was adopted by our Robo-Erectus Junior version of humanoid robots in the RoboCup 2007 humanoid soccer league.
Evaluation of social interaction, task management, and trust among dental hygiene students in a collaborative learning environment.

Science.gov (United States)

Saylor, Catherine D; Keselyak, Nancy T; Simmer-Beck, Melanie; Tira, Daniel

2011-02-01

The purpose of this study was to evaluate the impact of collaborative learning on the development of social interaction, task management, and trust in dental hygiene students. These three traits were assessed with the Teamwork Assessment Scale in two different learning environments (traditional lecture/lab and collaborative learning environment). A convenience sample of fifty-six entry-level dental hygiene students taking an introductory/preclinic course at two metropolitan area dental hygiene programs provided comparable experimental and control groups. Factor scores were computed for the three traits, and comparisons were conducted using the Ryan-Einot-Gabriel-Welsh multiple comparison procedure among specific cell comparisons generated from a two-factor repeated measures ANOVA. The results indicate that the collaborative learning environment influenced dental hygiene students positively regarding the traits of social interaction, task management, and trust. However, comparing dental hygiene students to undergraduate students overall indicates that dental hygiene students already possess somewhat higher levels of these traits. Future studies on active learning strategies should examine factors such as student achievement and explore other possible active learning methodologies.
Evaluating the usability of an interactive, bi-lingual, touchscreen-enabled breastfeeding educational programme: application of Nielson's heuristics.

Science.gov (United States)

Joshi, Ashish; Perin, Douglas M Puricelli; Amadi, Chioma; Trout, Kate

2015-03-05

The study purpose was to conduct heuristic evaluation of an interactive, bilingual touchscreen-enabled breastfeeding educational programme for Hispanic women living in rural settings in Nebraska. Three raters conducted the evaluation during May 2013 using principles of Nielson's heuristics. A total of 271 screens were evaluated and included: interface (n = 5), programme sections (n = 223) and educational content (n = 43). A total of 97 heuristic violations were identified and were mostly related to interface (8 violations/5 screens) and programme components (89 violations/266 screens). The most common heuristic violations reported were recognition rather than recall (62%, n = 60), consistency and standards (14%, n = 14) and match between the system and real world (9%, n = 9). Majority of the heuristic violations had minor usability issues (73%, n = 71). The only grade 4 heuristic violation reported was due to the visibility of system status in the assessment modules. The results demonstrated that the system was more consistent with Nielsen's usability heuristics. With Nielsen's usability heuristics, it is possible to identify problems in a timely manner, and help facilitate the identification and prioritisation of problems needing urgent attention at an earlier stage before the final deployment of the system.
Environmental interactions and the SP-100 power system

International Nuclear Information System (INIS)

Ferguson, D.C.

1993-01-01

The Civil Space Technology Initiative High-Capacity-Power Environmental Interactions Program has made great progress in defining and evaluating the interactions of the SP-100 power system with its expected ambient environments. The NASCAP/LEO and POLAR computer codes demonstrated that local electric fields at the user interface module are high. Therefore, particular attention must be paid to geometries and materials in this region to prevent arcing at conductor-insulator junctions in low Earth orbit. NASCAP/LEO and EPSAT computer models revealed that SP-100 payloads float about 100 V negative of the LEO plasma. In addition, ground tests and modeling done for the Space Station Freedom Electrical Grounding Tiger Team found that dielectric coatings often break down at such voltages in a plasma. Thus, surface coatings for SP-100 payloads should be carefully selected. Sputtering may also be a concern for long-duration missions in LEO at these voltages. Much work has been done on a sputtering model to evaluate surface material loss rates on SP-100 payloads. In ground plasma chamber tests of cables and cable insulators at SP-100 voltages, parasitic power losses due to the plasma current collected from possible pinholes or coating defects were quantified and shown to be small. Modeling revealed that the power loss from currents to other surfaces is also small. The atomic oxygen durability of SP-100 materials and coatings continues to be investigated in ground tests. In the upcoming Evaluation of Oxygen Interaction with Materials (EOIM-3) Shuttle flight experiment, a host of SP-100 materials will be evaluated for atomic oxygen durability in LEO. Finally, an evaluation of the interactions of the SP-100 power system with lunar and planetary environments has started. At a workshop on chemical and electrical interactions on Mars recently held at the NASA Lewis Research Center, many of primary interactions were identified
Interactive Foresight Simulation

DEFF Research Database (Denmark)

Hansen, Mette Sanne; Rasmussen, Lauge Baungaard; Jacobsen, Peter

2016-01-01

The Combined Simulation Approach (CSA) is a way to evaluate risks and address potential unforeseen problems in a more interactive way than what is often observed in practice in companies or sectors. The approach is based on a combination of scenario analysis and discrete-event computer simulation...
Evaluating the Quality of the Interaction between Persons with Profound Intellectual and Multiple Disabilities and Direct Support Staff: A Preliminary Application of Three Observation Scales from Parent-Infant Research

Science.gov (United States)

Hostyn, Ine; Petry, Katja; Lambrechts, Greet; Maes, Bea

2011-01-01

Background: Affective and reciprocal interactions with others are essential for persons with profound intellectual and multiple disabilities (PIMD), but it is a challenge to assess their quality. This study aimed to investigate the usefulness of instruments from parent-infant research to evaluate these interactions. Method: Eighteen videotaped…
Major histocompatibility complex harbors widespread genotypic variability of non-additive risk of rheumatoid arthritis including epistasis.

Science.gov (United States)

Wei, Wen-Hua; Bowes, John; Plant, Darren; Viatte, Sebastien; Yarwood, Annie; Massey, Jonathan; Worthington, Jane; Eyre, Stephen

2016-04-25

Genotypic variability based genome-wide association studies (vGWASs) can identify potentially interacting loci without prior knowledge of the interacting factors. We report a two-stage approach to make vGWAS applicable to diseases: firstly using a mixed model approach to partition dichotomous phenotypes into additive risk and non-additive environmental residuals on the liability scale and secondly using the Levene's (Brown-Forsythe) test to assess equality of the residual variances across genotype groups per marker. We found widespread significant (P 5e-05) vGWAS signals within the major histocompatibility complex (MHC) across all three study cohorts of rheumatoid arthritis. We further identified 10 epistatic interactions between the vGWAS signals independent of the MHC additive effects, each with a weak effect but jointly explained 1.9% of phenotypic variance. PTPN22 was also identified in the discovery cohort but replicated in only one independent cohort. Combining the three cohorts boosted power of vGWAS and additionally identified TYK2 and ANKRD55. Both PTPN22 and TYK2 had evidence of interactions reported elsewhere. We conclude that vGWAS can help discover interacting loci for complex diseases but require large samples to find additional signals.
Game Mechanics and Bodily Interactions: Designing Interactive Technologies for Sports Training

DEFF Research Database (Denmark)

Jensen, Mads Møller

and enjoyment. Thus, despite being two coexisting research areas, they do not extend or contribute to one another per se. However, bridging this gap by combining skill acquisition knowledge from sports training technologies with motivational game mechanics from bodily games holds great potential for designing...... and developing relevant and engaging training experiences. I term this combination interactive sports training games. This dissertation bridges this gap by exploring how to design and develop bodily interactions that leverage the quality and engagement of sports training by using game mechanics, but also how...... to identify and avoid the pitfalls and challenges that emerge in the process. It further explores how competition can be facilitated in bodily games and how it affects players. These explorations are done by designing, developing and evaluating innovative interactive sports training games. The results...
Modelling operator cognitive interactions in nuclear power plant safety evaluation

International Nuclear Information System (INIS)

Senders, J.W.; Moray, N.; Smiley, A.; Sellen, A.

1985-08-01

The overall objectives of the study were to review methods which are applicable to the analysis of control room operator cognitive interactions in nuclear plant safety evaluations and to indicate where future research effort in this area should be directed. This report is based on an exhaustive search and review of the literature on NPP (Nuclear Power Plant) operator error, human error, human cognitive function, and on human performance. A number of methods which have been proposed for the estimation of data for probabilistic risk analysis have been examined and have been found wanting. None addresses the problem of diagnosis error per se. Virtually all are concerned with the more easily detected and identified errors of action. None addresses underlying cause and mechanism. It is these mechanisms which must be understood if diagnosis errors and other cognitive errors are to be controlled and predicted. We have attempted to overcome the deficiencies of earlier work and have constructed a model/taxonomy, EXHUME, which we consider to be exhaustive. This construct has proved to be fruitful in organizing our thinking about the kinds of error that can occur and the nature of self-correcting mechanisms, and has guided our thinking in suggesting a research program which can provide the data needed for quantification of cognitive error rates and of the effects of mitigating efforts. In addition a preliminary outline of EMBED, a causal model of error, is given based on general behavioural research into perception, attention, memory, and decision making. 184 refs

Evaluation of Drug-Drug Interaction Potential Between Sacubitril/Valsartan (LCZ696) and Statins Using a Physiologically Based Pharmacokinetic Model.

Science.gov (United States)

Lin, Wen; Ji, Tao; Einolf, Heidi; Ayalasomayajula, Surya; Lin, Tsu-Han; Hanna, Imad; Heimbach, Tycho; Breen, Christopher; Jarugula, Venkateswar; He, Handan

2017-05-01

Sacubitril/valsartan (LCZ696) has been approved for the treatment of heart failure. Sacubitril is an in vitro inhibitor of organic anion-transporting polypeptides (OATPs). In clinical studies, LCZ696 increased atorvastatin C max by 1.7-fold and area under the plasma concentration-time curve by 1.3-fold, but had little or no effect on simvastatin or simvastatin acid exposure. A physiologically based pharmacokinetics modeling approach was applied to explore the underlying mechanisms behind the statin-specific LCZ696 drug interaction observations. The model incorporated OATP-mediated clearance (CL int,T ) for simvastatin and simvastatin acid to successfully describe the pharmacokinetic profiles of either analyte in the absence or presence of LCZ696. Moreover, the model successfully described the clinically observed drug effect with atorvastatin. The simulations clarified the critical parameters responsible for the observation of a low, yet clinically relevant, drug-drug interaction DDI between sacubitril and atorvastatin and the lack of effect with simvastatin acid. Atorvastatin is administered in its active form and rapidly achieves C max that coincide with the low C max of sacubitril. In contrast, simvastatin requires a hydrolysis step to the acid form and therefore is not present at the site of interactions at sacubitril concentrations that are inhibitory. Similar models were used to evaluate the drug-drug interaction risk for additional OATP-transported statins which predicted to maximally result in a 1.5-fold exposure increase. Copyright © 2017. Published by Elsevier Inc.
Finite element calculation of the interaction energy of shape memory alloy

International Nuclear Information System (INIS)

Yang, Seung Yong

2004-01-01

Strain energy due to the mechanical interaction between self-accommodation groups of martensitic phase transformation is called interaction energy. Evaluation of the interaction energy should be accurate since the energy appears in constitutive models for predicting the mechanical behavior of shape memory alloy. In this paper, the interaction energy is evaluated in terms of theoretical formulation and explicit finite element calculation. A simple example with two habit plane variants was considered. It was shown that the theoretical formulation assuming elastic interaction between the self-accommodation group and matrix gives larger interaction energy than explicit finite element calculation in which transformation softening is accounted for
Cannabidiol exhibits anxiolytic but not antipsychotic property evaluated in the social interaction test.

Science.gov (United States)

Almeida, Valéria; Levin, Raquel; Peres, Fernanda Fiel; Niigaki, Suzy T; Calzavara, Mariana B; Zuardi, Antônio W; Hallak, Jaime E; Crippa, José A; Abílio, Vanessa C

2013-03-05

Cannabidiol (CBD), a non-psychotomimetic compound of the Cannabis sativa, has been reported to have central therapeutic actions, such as antipsychotic and anxiolytic effects. We have recently reported that Spontaneously Hypertensive Rats (SHRs) present a deficit in social interaction that is ameliorated by atypical antipsychotics. In addition, SHRs present a hyperlocomotion that is reverted by typical and atypical antipsychotics, suggesting that this strain could be useful to study negative symptoms (modeled by a decrease in social interaction) and positive symptoms (modeled by hyperlocomotion) of schizophrenia as well as the effects of potential antipsychotics drugs. At the same time, an increase in social interaction in control animals similar to that induced by benzodiazepines is used to screen potential anxiolytic drugs. The aim of this study was to investigate the effects of CBD on social interaction presented by control animals (Wistar) and SHRs. The lowest dose of CBD (1mg/kg) increased passive and total social interaction of Wistar rats. However, the hyperlocomotion and the deficit in social interaction displayed by SHRs were not altered by any dose of CBD. Our results do not support an antipsychotic property of cannabidiol on symptoms-like behaviors in SHRs but reinforce the anxiolytic profile of this compound in control rats. Copyright © 2012 Elsevier Inc. All rights reserved.
Training of goal directed arm movements with motion interactive video games in children with cerebral palsy - a kinematic evaluation.

Science.gov (United States)

Sandlund, Marlene; Domellöf, Erik; Grip, Helena; Rönnqvist, Louise; Häger, Charlotte K

2014-10-01

The main aim of this study was to evaluate the quality of goal-directed arm movements in 15 children with cerebral palsy (CP) following four weeks of home-based training with motion interactive video games. A further aim was to investigate the applicability and characteristics of kinematic parameters in a virtual context in comparison to a physical context. Kinematics and kinetics were captured while the children performed arm movements directed towards both virtual and physical targets. The children's movement precision improved, their centre of pressure paths decreased, as did the variability in maximal shoulder angles when reaching for virtual objects. Transfer to a situation with physical targets was mainly indicated by increased movement smoothness. Training with motion interactive games seems to improve arm motor control in children with CP. The results highlight the importance of considering both the context and the task itself when investigating kinematic parameters.
IDRC and BetterEvaluation launch an interactive guide to manage ...

International Development Research Centre (IDRC) Digital Library (Canada)

2016-10-21

Oct 21, 2016 ... ... evaluations, this guide is intended for program and project managers. ... used to hire evaluators, and guide the management of the evaluation. ... Strategic Evaluation on Communicating Research for Influence: Part I.
Influence of the soil/solution ratio, interaction time, and extractant on the evaluation of iron chelate sorption/desorption by soils.

Science.gov (United States)

Hernández-Apaolaza, Lourdes; Lucena, Juan J

2011-03-23

Synthetic Fe chelates are the most efficient agricultural practice to control Fe deficiency in crops, EDTA/Fe3+ and o,o-EDDHA/Fe3+ being the most commonly used. Their efficacy as Fe sources and carriers in soils can be severely limited by their retention on it. The aim of this work is to evaluate the possible bias introduced in the studies of the iron chelate retention by soils. For that purpose, results obtained for EDTA and EDDHA iron chelates from two batch studies with different soil/solution ratios were compared with data obtained for a leaching column experiment. Moreover, different extractants were tested to study the o,o-EDDHA/Fe3+ and o,p-EDDHA/Fe3+ desorption from a calcareous soil, and also the effect of the interaction time in their retention process has been evaluated. In summary, the mobility through a calcareous soil of the studied iron chelates differs greatly depending on the type of iron chelate and also on the procedure used to evaluate the retention and the soil/solution ratio used. In general, the leaching column method is preferred because the achieved conclusions are more representative of the natural conditions, but batch methods are very useful as a preliminary experiment, especially one with a high soil/solution ratio. The iron chelate desorption could be quantified by using a sequential extraction with water, sodium sulfate, and DTPA as extractants. Under the experimental conditions used in this study, o,o-EDDHA/Fe3+ retention increased with interaction time.
Evaluation of algorithms for photon depth of interaction estimation for the TRIMAGE PET component

Energy Technology Data Exchange (ETDEWEB)

Camarlinghi, Niccolo; Belcari, Nicola [University of Pisa (Italy); Cerello, Piergiorgio [University of Torino (Italy); Sportelli, Giancarlo [University of Pisa (Italy); Pennazio, Francesco [University of Torino (Italy); Zaccario, Emanuele; Del Guerra, Alberto [University of Pisa (Italy)

2015-05-18

The TRIMAGE consortium aims to develop a multimodal PET/MR/EEG brain scanner dedicated to the early diagnosis of schizophrenia and other mental health disorders. The PET component features a full ring made of 18 detectors, each one consisting of twelve 8x8 Silicon PhotoMultipliers (SiPMs) tiles coupled to two segmented LYSO crystal matrices with staggered layers. In each module, the crystals belonging to the bottom layer are coupled one to one to the SiPMs, while each crystal of the top layer is coupled to four crystals of the bottom layer. This configuration allows to increase the crystal thickness while reducing the depth of interaction uncertainty, as photons interacting in different layers are expected to produce different light patterns on the SiPMs. The PET scanner will implement the pixel/layer identification on a front-end FPGA. This will allow increasing the effective bandwidth, setting at the same time restrictions on the complexity of the algorithms to be implemented. In this work two algorithms whose implementation is feasible directly on an FPGA are presented and evaluated. The first algorithm implements a method based on adaptive thresholding, while the other uses a linear Support Vector Machine (SVM) trained to distinguish the light pattern coming from two different layers. The validation of the algorithm performance is carried out by using simulated data generated with the GAMOS Monte Carlo. The obtained results show that the achieved accuracy in layer and pixel identification is above the 90% for both the proposed approaches.
On-orbit evaluation of the control system/structural mode interactions on OSO-8

Science.gov (United States)

Slafer, L. I.

1980-01-01

The Orbiting Solar Observatory-8 experienced severe structural mode/control loop interaction problems during the spacecraft development. Extensive analytical studies, using the hybrid coordinate modeling approach, and comprehensive ground testing were carried out in order to achieve the system's precision pointing performance requirements. A recent series of flight tests were conducted with the spacecraft in which a wide bandwidth, high resolution telemetry system was utilized to evaluate the on-orbit flexible dynamics characteristics of the vehicle along with the control system performance. This paper describes the results of these tests, reviewing the basic design problem, analytical approach taken, ground test philosophy, and on-orbit testing. Data from the tests was used to determine the primary mode frequency, damping, and servo coupling dynamics for the on-orbit condition. Additionally, the test results have verified analytically predicted differences between the on-orbit and ground test environments. The test results have led to a validation of both the analytical modeling and servo design techniques used during the development of the control system, and also verified the approach taken to vehicle and servo ground testing.
Experimental evaluation of the interaction effect between plastic and creep deformation

International Nuclear Information System (INIS)

Ikegami, K.; Niitsu, Y.

1985-01-01

An experimental study of plasticity-creep interaction effects is reported. The combined stress tests are performed on thin wall tubular specimens of SUS 304 stainless steel at room temperature and high temperature (600 0 C). The plastic behaviors subsequent to creep pre-strain and creep behaviors subsequent to plastic pre-strain are obtained for loading along straight stress paths with a corner. The inelastic behaviors including both plastic and creep deformations are experimentally investigated. The interaction effects between plastic and creep deformations are quantitatively estimated with the equi-plastic strain surface. (author)
Evaluating the Impact of the "Teaching as a Chemistry Laboratory Graduate Teaching Assistant" Program on Cognitive and Psychomotor Verbal Interactions in the Laboratory

Science.gov (United States)

Flaherty, A.; O'Dwyer, A.; Mannix-McNamara, P.; Leahy, J. J.

2017-01-01

Designing and evaluating teacher development programs for graduate teaching assistants (GTAs) who teach in the laboratory is a prominent feature of chemistry education research. However, few studies have investigated the impact of a GTA teacher development program on the verbal interactions between participating GTAs and students in the…
Cation-π interactions in structural biology

OpenAIRE

Gallivan, Justin P.; Dougherty, Dennis A.

1999-01-01

Cation-pi interactions in protein structures are identified and evaluated by using an energy-based criterion for selecting significant sidechain pairs. Cation-pi interactions are found to be common among structures in the Protein Data Bank, and it is clearly demonstrated that, when a cationic sidechain (Lys or Arg) is near an aromatic sidechain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-pi interaction. The sidechain of Arg is more likely tha...
Herb-drug interactions: challenges and opportunities for improved predictions.

Science.gov (United States)

Brantley, Scott J; Argikar, Aneesh A; Lin, Yvonne S; Nagar, Swati; Paine, Mary F

2014-03-01

Supported by a usage history that predates written records and the perception that "natural" ensures safety, herbal products have increasingly been incorporated into Western health care. Consumers often self-administer these products concomitantly with conventional medications without informing their health care provider(s). Such herb-drug combinations can produce untoward effects when the herbal product perturbs the activity of drug metabolizing enzymes and/or transporters. Despite increasing recognition of these types of herb-drug interactions, a standard system for interaction prediction and evaluation is nonexistent. Consequently, the mechanisms underlying herb-drug interactions remain an understudied area of pharmacotherapy. Evaluation of herbal product interaction liability is challenging due to variability in herbal product composition, uncertainty of the causative constituents, and often scant knowledge of causative constituent pharmacokinetics. These limitations are confounded further by the varying perspectives concerning herbal product regulation. Systematic evaluation of herbal product drug interaction liability, as is routine for new drugs under development, necessitates identifying individual constituents from herbal products and characterizing the interaction potential of such constituents. Integration of this information into in silico models that estimate the pharmacokinetics of individual constituents should facilitate prospective identification of herb-drug interactions. These concepts are highlighted with the exemplar herbal products milk thistle and resveratrol. Implementation of this methodology should help provide definitive information to both consumers and clinicians about the risk of adding herbal products to conventional pharmacotherapeutic regimens.
SEEPAGE/INVERT INTERACTIONS

International Nuclear Information System (INIS)

P.S. Domski

2000-01-01

As directed by a written development plan (CRWMS M andO 1999a), a conceptual model for water entering the drift and reacting with the invert materials is to be developed. The purpose of this conceptual model is to assist Performance Assessment Operations (PAO) and its Engineered Barrier Performance Department in modeling the geochemical environment within a repository drift, thus allowing PAO to provide a more detailed and complete in-drift geochemical model abstraction, and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near-Field Environment (NFE), Revision 2 (NRC 1999). This AMR also seeks to: (1) Develop a logical conceptual model for physical/chemical interactions between seepage and the invert materials; (2) screen potential processes and reactions that may occur between seepage and invert to evaluate the potential consequences of the interactions; and (3) outline how seepage/invert processes may be quantified. This document provides the conceptual framework for screening out insignificant processes and for identifying and evaluating those seepage/invert interactions that have the potential to be important to subsequent PAO analyses including the Engineered Barrier System (EBS) physical and chemical model abstraction effort. This model has been developed to serve as a basis for the in-drift geochemical analyses performed by PAO. Additionally, the concepts discussed within this report may also apply to certain near and far-field geochemical processes and may have conceptual application within the unsaturated zone (UZ) and saturated zone (SZ) transport modeling efforts. The seepage/invert interactions will not directly affect any principal factors
Interaction region

International Nuclear Information System (INIS)

Anon.

1982-01-01

The Interaction Region Group addressed the basic questions of how to collide the SLC beams, how to maximize and monitor the luminosity, and how to minimize the detector backgrounds at the interaction region. In practice, five subgroups evolved to study these questions. The final focus group provided three alternative designs to acheive the 1 to 2 micron beam spot size required by the SLC, as well as studying other problems including: eta, eta' matching from the collider arcs, the implementation of soft bends near the interaction region, beam emittance growth, and magnet tolerances in the final focus. The beam position monitor group proposed two devices, a strip line monitor, and a beamstrahlung monitor, to bring the beams into collision. The luminosity monitor group reviewed the possible QED processes that would be insensitive to weak interaction (Z 0 ) effects. The beam dumping group proposed locations for kicker and septum magnets in the final focus that would achieve a high dumping efficiency and would meet the desired beam tolerances at the Moller scattering target in the beam dump line. Working with the Polarization Group, the Moller experiment was designed into the beam dump beam line. A beam dump was proposed that would maintain radiation backgrounds (penetrating muons) at acceptible levels. The detector backgrounds group proposed soft-bend and masking configurations to shield the detector from synchrotron radiation from the hard/soft bends and from the final focus quadrupoles and evaluated the effectiveness of these designs for the three final focus optics designs. Backgrounds were also estimated from: large angle synchrotron radiation, local and distant beam-gas interactions, 2-photon interactions, and from neutrons and backscattered photons from the beamstrahlung dump
Narrow Escape of Interacting Diffusing Particles

Science.gov (United States)

Agranov, Tal; Meerson, Baruch

2018-03-01

The narrow escape problem deals with the calculation of the mean escape time (MET) of a Brownian particle from a bounded domain through a small hole on the domain's boundary. Here we develop a formalism which allows us to evaluate the nonescape probability of a gas of diffusing particles that may interact with each other. In some cases the nonescape probability allows us to evaluate the MET of the first particle. The formalism is based on the fluctuating hydrodynamics and the recently developed macroscopic fluctuation theory. We also uncover an unexpected connection between the narrow escape of interacting particles and thermal runaway in chemical reactors.
40 CFR 610.23 - Operator interaction effects.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 29 2010-07-01 2010-07-01 false Operator interaction effects. 610.23 Section 610.23 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) ENERGY POLICY FUEL... Analysis § 610.23 Operator interaction effects. The device will also be evaluated with respect to: (a) The...
Interaction Effects of Students, Drugs and Alienation

Science.gov (United States)

Jones, Woodrow, Jr.

1977-01-01

This study examined the interaction effect of students, drugs, and alienation in a large university, i.e., the linkages of both social and political alienation with drug behavior. The interaction terms which composed these forms of alienation were evaluated as to their comparative ability to produce drug behavior. (Author)
Evaluation of an interactive case simulation system in dermatology and venereology for medical students

Directory of Open Access Journals (Sweden)

Hindbeck Hans

2006-08-01

Full Text Available Abstract Background Most of the many computer resources used in clinical teaching of dermatology and venereology for medical undergraduates are information-oriented and focus mostly on finding a "correct" multiple-choice alternative or free-text answer. We wanted to create an interactive computer program, which facilitates not only factual recall but also clinical reasoning. Methods Through continuous interaction with students, a new computerised interactive case simulation system, NUDOV, was developed. It is based on authentic cases and contains images of real patients, actors and healthcare providers. The student selects a patient and proposes questions for medical history, examines the skin, and suggests investigations, diagnosis, differential diagnoses and further management. Feedback is given by comparing the user's own suggestions with those of a specialist. In addition, a log file of the student's actions is recorded. The program includes a large number of images, video clips and Internet links. It was evaluated with a student questionnaire and by randomising medical students to conventional teaching (n = 85 or conventional teaching plus NUDOV (n = 31 and comparing the results of the two groups in a final written examination. Results The questionnaire showed that 90% of the NUDOV students stated that the program facilitated their learning to a large/very large extent, and 71% reported that extensive working with authentic computerised cases made it easier to understand and learn about diseases and their management. The layout, user-friendliness and feedback concept were judged as good/very good by 87%, 97%, and 100%, respectively. Log files revealed that the students, in general, worked with each case for 60–90 min. However, the intervention group did not score significantly better than the control group in the written examination. Conclusion We created a computerised case simulation program allowing students to manage patients in a non
Importance of Sodium Fuel Interaction in Fast Reactor Safety Evaluation - CEA Point of View

International Nuclear Information System (INIS)

Tanguy, P.

1976-01-01

The consequences of interactions between molten metal (aluminium-uranium alloy) and water have long been a subject of concern for those in charge of reactor safety, following accidents observed or induced in certain reactors (BORAX, SL1, SPERT 1 D). In such accidents, as in similar cases occurring in traditional industries (aluminium foundries, steel works, paper mills...) the contact between the hot liquid product and the coolant entails rapid vaporization of the latter with effects identical to that of an explosive. Although chemical reactions of water decomposition occur in some cases, the main phenomenon is the conversion of the thermal energy stored in the hot substance into mechanical energy. Despite the fact that a molten oxide fuel differs from an aluminium-uranium alloy, as does sodium from water, the consequences of possible contact between the molten mixed uranium and plutonium oxide and sodium must be carefully studied since such a contact may occur in accident conditions in sodium-cooled fast neutron reactors. The essential purpose of an evaluation of reactor safety in accident conditions is in fact to ensure the containment of dangerous products Consequently, any phenomenon likely to endanger containment barriers must be carefully examined. In conclusion: Whereas an accident within an assembly seems to show little likelihood of creating conditions seriously endangering fuel containment, the gravity of problems associated with an overall accident on the core is worthy of thorough and attentive study. In the case of an overall accident on the core of a fast reactor, the interaction between the molten fuel and the sodium is of consequence at two levels. The first is the retention of mechanical energy which may be considerable. The second is the recovery of fuel fragments in an overall cooled configuration but where local cooling problems may give rise to interaction. A greater effort is required in performing tests and mastering their results to
Genotype by environment interaction effects in genetic evaluation of preweaning gain for Line 1 Hereford cattle from Miles City, Montana.

Science.gov (United States)

MacNeil, M D; Cardoso, F F; Hay, E

2017-09-01

It has long been recognized that genotype × environment interaction potentially influences genetic evaluation of beef cattle. However, this recognition has largely been ignored in systems for national cattle evaluation. The objective of this investigation was to determine if direct and maternal genetic effects on preweaning gain would be reranked depending on an environmental gradient as determined by year effects. Data used were from the 76-yr selection experiment with the Line 1 Hereford cattle raised at Miles City, MT. The data comprised recorded phenotypes from 7,566 animals and an additional 1,862 ancestral records included in the pedigree. The presence of genotype × environment interaction was examined using reaction norms wherein year effects on preweaning gain were hypothesized to linearly influence the EBV. Estimates of heritability for direct and maternal effects, given the average environment, were 10 ± 2 and 26 ± 3%, respectively. In an environment that is characterized by the 5th (95th) percentile of the distribution of year effects, the corresponding estimates of heritability were 18 ± 3 (22 ± 3%) and 30 ± 3% (30 ± 3%), respectively. Rank correlations of direct and maternal EBV appropriate to the 5th and 95th percentiles of the year effects were 0.67 and 0.92, respectively. In the average environment, the genetic trends were 255 ± 1 g/yr for direct effects and 557 ± 3 g/yr for maternal effects. In the fifth percentile environment, the corresponding estimates of genetic trend were 271 ± 1 and 540 ± 3 g/yr, respectively, and in the 95th percentile environment, they were 236 ± 1 and 578 ± 3 g/yr, respectively. Linear genetic trends in environmental sensitivity were observed for both the direct (-8.06 × 10 ± 0.49 × 10) and maternal (8.72 × 10 ± 0.43 × 10) effects. Therefore, changing systems of national cattle evaluation to more fully account for potential genotype × environment interaction would improve the assessment of breeding

A competing risks approach to "biologic" interaction

DEFF Research Database (Denmark)

Andersen, Per Kragh; Skrondal, Anders

2015-01-01

framework using competing risks and argue that sufficient cause interaction between two factors can be evaluated via the parameters in a particular statistical model, the additive hazard rate model. We present empirical conditions for presence of sufficient cause interaction and an example based on data......In epidemiology, the concepts of "biologic" and "statistical" interactions have been the subject of extensive debate. We present a new approach to biologic interaction based on Rothman's original (Am J Epidemiol, 104:587-592, 1976) discussion of sufficient causes. We do this in a probabilistic...
Comparative Human and Automatic Evaluation of Glass-Box and Black-Box Approaches to Interactive Translation Prediction

Directory of Open Access Journals (Sweden)

Torregrosa Daniel

2017-06-01

Full Text Available Interactive translation prediction (ITP is a modality of computer-aided translation that assists professional translators by offering context-based computer-generated continuation suggestions as they type. While most state-of-the-art ITP systems follow a glass-box approach, meaning that they are tightly coupled to an adapted machine translation system, a black-box approach which does not need access to the inner workings of the bilingual resources used to generate the suggestions has been recently proposed in the literature: this new approach allows new sources of bilingual information to be included almost seamlessly. In this paper, we compare for the first time the glass-box and the black-box approaches by means of an automatic evaluation of translation tasks between related languages such as English–Spanish and unrelated ones such as Arabic–English and English–Chinese, showing that, with our setup, 20%–50% of keystrokes could be saved using either method and that the black-box approach outperformed the glass-box one in five out of six scenarios operating under similar conditions. We also performed a preliminary human evaluation of English to Spanish translation for both approaches. On average, the evaluators saved 10% keystrokes and were 4% faster with the black-box approach, and saved 15% keystrokes and were 12% slower with the glass-box one; but they could have saved 51% and 69% keystrokes respectively if they had used all the compatible suggestions. Users felt the suggestions helped them to translate faster and easier. All the tools used to perform the evaluation are available as free/open–source software.
DISTANCE LEARNING STUDENTS’ NEED: Evaluating Interactions from Moore’s Theory of Transactional Distance

Directory of Open Access Journals (Sweden)

Rusmanizah USTATI

2013-04-01

Full Text Available This study draws on the experience from a focus group interviews under the distance learning programme known as Program Pensiswazahan Guru (PPG organized by the Malaysian Ministry of Education in collaboration with local universities and institutes of education. Its purpose is to uncover students’ perception about the platform used by International Islamic University Malaysia (IIUM which is the Learning Management System (LMS. LMS is a vital instructional medium especially for the varsity distant learners. Michael Moore’s Theory of Transactional Distance is used as the guiding framework to gain insights on learning and interactions in this e-learning setting. Teacher-student interactions are analyzed for better understanding of the phenomena under study. The findings indicate that in terms of usability LMS is perceived as a good platform to acquire information on content and to receive feedback from instructors. However, IIUM learners hope for more interactivity where learners can communicate amongst themselves beside engaging with the instructor-learner- content interactions that they currently experience via the system. This study aspires to provide insights on the significance of interactions from distance learners’ perception.
Emotional intelligence and social interaction.

Science.gov (United States)

Lopes, Paulo N; Brackett, Marc A; Nezlek, John B; Schütz, Astrid; Sellin, Ina; Salovey, Peter

2004-08-01

Two studies found positive relationships between the ability to manage emotions and the quality of social interactions, supporting the predictive and incremental validity of an ability measure of emotional intelligence, the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT). In a sample of 118 American college students (Study 1), higher scores on the managing emotions subscale of the MSCEIT were positively related to the quality of interactions with friends, evaluated separately by participants and two friends. In a diary study of social interaction with 103 German college students (Study 2), managing emotions scores were positively related to the perceived quality of interactions with opposite sex individuals. Scores on this subscale were also positively related to perceived success in impression management in social interactions with individuals of the opposite sex. In both studies, the main findings remained statistically significant after controlling for Big Five personality traits.
Botanical-drug interactions: a scientific perspective.

Science.gov (United States)

de Lima Toccafondo Vieira, Manuela; Huang, Shiew-Mei

2012-09-01

There is a continued predisposition of concurrent use of drugs and botanical products. A general lack of knowledge of the interaction potential together with an under-reporting of botanical use poses a challenge for the health care providers and a safety concern for patients. Botanical-drug interactions increase the patient risk, especially with regard to drugs with a narrow therapeutic index (e.g., warfarin, cyclosporine, and digoxin). Examples of case reports and clinical studies evaluating botanical-drug interactions of commonly used botanicals in the US are presented. The potential pharmacokinetic and pharmacodynamic bases of such interactions are discussed, as well as the challenges associated with the interpretation of the available data and prediction of botanical-drug interactions. Recent FDA experiences with botanical products and interactions including labeling implications as a risk management strategy are highlighted. Georg Thieme Verlag KG Stuttgart · New York.
Data Evaluation and the Establishment of a Standard Library of Atomic, Molecular and Plasma-Material Interaction Data for Fusion. Summary Report of an IAEA Consultants' Meeting

International Nuclear Information System (INIS)

Braams, B.J.

2012-08-01

Seven experts in the field of atomic, molecular and plasma-material interaction (A+M+PMI) data and data evaluation for fusion plasma physics met with IAEA A+M Data Unit staff at IAEA Headquarters to provide advice towards the establishment of an evaluated and recommended library of A+M+PMI data for fusion. The proceedings and conclusions of the meeting are summarized here. (author)
Evaluating DEM results with FEM perspectives of load : soil interaction

NARCIS (Netherlands)

Tadesse, D.

2004-01-01

Keywords: Load - soil interaction, soil structure, soil mechanical properties, FEM (Finite Element Method), Plaxis (Finite Element Code), granular particles, shear stress, DEM (Distinct Element Method),
Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method

NARCIS (Netherlands)

Stjernschantz, E.M.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N.P.E.; Oostenbrink, C.

2006-01-01

An extensive evaluation of the linear interaction energy (LIE) method for the prediction of binding affinity of docked compounds has been performed, with an emphasis on its applicability in lead optimization. An automated setup is presented, which allows for the use of the method in an industrial
Evaluation of Synergistic Interactions Between Cell-Free Supernatant of Lactobacillus Strains and Amikacin and Genetamicin Against Pseudomonas aeruginosa.

Science.gov (United States)

Aminnezhad, Sargol; Kermanshahi, Rouha Kasra; Ranjbar, Reza

2015-04-01

The indiscriminate use of antibiotics in the treatment of infectious diseases can increase the development of antibiotic resistance. Therefore, there is a big demand for new sources of antimicrobial agents and alternative treatments for reduction of antibiotic dosage required to decrease the associated side effects. In this study, the synergistic action of aminoglycoside antibiotics and cell-free supernatant (CFS) of probiotic (Lactobacillus rahmnosus and L. casei) against Pseudomonas aeruginosa PTCC 1430 was evaluated. A growth medium for culturing of probiotic bacteria was separated by centrifugation. The antimicrobial effects of CFS of probiotic bacteria were evaluated using the agar well diffusion assay. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were evaluated using the micro dilution method. Finally, an interaction between CFS and amikacin or gentamicin against P. aeruginosa PTCC 1430 was examined through the checkerboard method and fractional inhibitory concentration (FIC). Furthermore, CFSs from Lactobacillus strains were analyzed by reversed phase HPLC (RP-HPLC) for antimicrobial compounds. The results showed a significant effect of CFS on the growth of P. aeruginosa. The MIC and MBC of CFS from L. casei were 62.5 µL⁄mL while the MIC and MBC of CFS from L. rhamnosus were 62.5 μL⁄mL and 125 μL⁄mL, respectively. Using the FIC indices, synergistic interactions were observed in combination of CFS and antibiotics. Fractional Inhibitory Concentration indices of CFS from L. casei and aminoglycoside antibiotics were 0.124 and 0.312 while FIC indices of CFS from L. rhamnosus and aminoglycoside antibiotics were 0.124 and 0.56, respectively showing a synergism effect. The results of RP-HPLC showed that CFS of Lactobacillus strains contained acetic acid, lactic acid and hydrogen peroxide (H2O2). Our findings indicate that probiotic bacterial strains of Lactobacillus have a significant inhibitory effect on the
Long-range interactions among three alkali-metal atoms

International Nuclear Information System (INIS)

Marinescu, M.; Starace, A.F.

1996-01-01

The long-range asymptotic form of the interaction potential surface for three neutral alkali-metal atoms in their ground states may be expressed as an expansion in inverse powers of inter-nuclear distances. The first leading powers are proportional to the dispersion coefficients for pairwise atomic interactions. They are followed by a term responsible for a three body dipole interaction. The authors results consist in evaluation of the three body dipole interaction coefficient between three alkali-metal atoms. The generalization to long-range n atom interaction terms will be discussed qualitatively
Herb–Drug Interactions: Challenges and Opportunities for Improved Predictions

Science.gov (United States)

Brantley, Scott J.; Argikar, Aneesh A.; Lin, Yvonne S.; Nagar, Swati

2014-01-01

Supported by a usage history that predates written records and the perception that “natural” ensures safety, herbal products have increasingly been incorporated into Western health care. Consumers often self-administer these products concomitantly with conventional medications without informing their health care provider(s). Such herb–drug combinations can produce untoward effects when the herbal product perturbs the activity of drug metabolizing enzymes and/or transporters. Despite increasing recognition of these types of herb–drug interactions, a standard system for interaction prediction and evaluation is nonexistent. Consequently, the mechanisms underlying herb–drug interactions remain an understudied area of pharmacotherapy. Evaluation of herbal product interaction liability is challenging due to variability in herbal product composition, uncertainty of the causative constituents, and often scant knowledge of causative constituent pharmacokinetics. These limitations are confounded further by the varying perspectives concerning herbal product regulation. Systematic evaluation of herbal product drug interaction liability, as is routine for new drugs under development, necessitates identifying individual constituents from herbal products and characterizing the interaction potential of such constituents. Integration of this information into in silico models that estimate the pharmacokinetics of individual constituents should facilitate prospective identification of herb–drug interactions. These concepts are highlighted with the exemplar herbal products milk thistle and resveratrol. Implementation of this methodology should help provide definitive information to both consumers and clinicians about the risk of adding herbal products to conventional pharmacotherapeutic regimens. PMID:24335390
Quality evaluation and in vitro interaction studies between levofloxacin 250mg and diclofenac sodium 50mg tablets.

Science.gov (United States)

Fayyaz, Muhammad; Yousuf, Rabia Ismail; Shoaib, Muhammad Harris; Ali, Tariq; Nasiri, Iqbal; Ashraf, Nida

2015-01-01

Fluoroquinolones are broad-spectrum antibiotics, work against Gram-positive and Gram-negative bacteria and are a clinically proven option for many resistant infections. Among fluoroquinolones Levofloxacin works best against acute sinusitis, inflammation of the lower airways, acute exacerbation of chronic bronchitis, community acquired pneumonia, complicated urinary tract infection including Pyelonephritis, chronic bacterial prostatitis and skin and soft tissue infection. Levofloxacin is a frequently prescribed antibacterial agent with Diclofenac Sodium for pain management in infectious conditions. The objective of the present work is to evaluate the level of interaction between Levofloxacin and Diclofenac Sodium. In this work market available brands of both drugs were also evaluated for quality.The physiochemical parameters like weight variation, thickness variation, and mechanical strength were determined. Similarly the percentage drug release and content uniformity test were also analyzed; the tested quality attributes were found within the recommended pharmacopeia ranges except brand L(6) that had high drug content 124.629±3.614 while brand L(4) and L(5) were not found similar in pH 1.2. When subjected to model dependent analysis Levofloxacin showed compliance with (first order, Higuchi, Hixson Crowell and Weibull) at pH (1.2, 4.5 and 6.8). However Diclofenac Sodium showed adherence with (first order, Hixson Crowell and Weibull) at pH (1.2, 4.5 and 6.8) but following Higuchi at pH 1.2 and 4.5 only. The interaction studies were also performed spectrophotometrically and simultaneous equation was used to estimate the percentage availability of both the drugs at pH 4.5, 6.8, FaSSGF and FaSSIF. The studies showed that the percent availability of Levofloxacin was increased significantly in FaSSIF i.e. 129.173±0.323 at 45 minutes in the presence of Diclofenac Sodium.
Toward an Ontology of Simulated Social Interaction

DEFF Research Database (Denmark)

Seibt, Johanna

2017-01-01

and asymmetric modes of realizing Á, called the ‘simulatory expansion’ of interaction type Á. Simulatory expansions of social interactions can be used to map out different kinds and degrees of sociality in human-human and human-robot interaction, relative to current notions of sociality in philosophy......, anthropology, and linguistics. The classificatory framework developed (SISI) thus represents the field of possible simulated social interactions. SISI can be used to clarify which conceptual and empirical grounds we can draw on to evaluate capacities and affordances of robots for social interaction......The paper develops a general conceptual framework for the ontological classification of human-robot interaction. After arguing against fictionalist interpretations of human-robot interactions, I present five notions of simulation or partial realization, formally defined in terms of relationships...
Nanoparticle-assay marker interaction: effects on nanotoxicity assessment

International Nuclear Information System (INIS)

Zhao, Xinxin; Xiong, Sijing; Huang, Liwen Charlotte; Ng, Kee Woei; Loo, Say Chye Joachim

2015-01-01

Protein-based cytotoxicity assays such as lactate dehydrogenase (LDH) and tumor necrosis factor-alpha (TNF-α) are commonly used in cytotoxic evaluation of nanoparticles (NPs) despite numerous reports on possible interactions with protein markers in these assays that can confound the results obtained. In this study, conventional cytotoxicity assays where assay markers may (LDH and TNF- α) or may not (PicoGreen and WST-8) come into contact with NPs were used to evaluate the cytotoxicity of NPs. The findings revealed selective interactions between negatively charged protein assay markers (LDH and TNF- α) and positively charged ZnO NPs under abiotic conditions. The adsorption and interaction with these protein assay markers were strongly influenced by surface charge, concentration, and specific surface area of the NPs, thereby resulting in less than accurate cytotoxic measurements, as observed from actual cell viability measurements. An improved protocol for LDH assay was, therefore, proposed and validated by eliminating any effects associated with protein–particle interactions. In view of this, additional measures and precautions should be taken when evaluating cytotoxicity of NPs with standard protein-based assays, particularly when they are of opposite charges
Nanoparticle-assay marker interaction: effects on nanotoxicity assessment

Energy Technology Data Exchange (ETDEWEB)

Zhao, Xinxin; Xiong, Sijing; Huang, Liwen Charlotte; Ng, Kee Woei, E-mail: kwng@ntu.edu.sg; Loo, Say Chye Joachim, E-mail: joachimloo@ntu.edu.sg [Nanyang Technological University, School of Materials Science and Engineering (Singapore)

2015-01-15

Protein-based cytotoxicity assays such as lactate dehydrogenase (LDH) and tumor necrosis factor-alpha (TNF-α) are commonly used in cytotoxic evaluation of nanoparticles (NPs) despite numerous reports on possible interactions with protein markers in these assays that can confound the results obtained. In this study, conventional cytotoxicity assays where assay markers may (LDH and TNF- α) or may not (PicoGreen and WST-8) come into contact with NPs were used to evaluate the cytotoxicity of NPs. The findings revealed selective interactions between negatively charged protein assay markers (LDH and TNF- α) and positively charged ZnO NPs under abiotic conditions. The adsorption and interaction with these protein assay markers were strongly influenced by surface charge, concentration, and specific surface area of the NPs, thereby resulting in less than accurate cytotoxic measurements, as observed from actual cell viability measurements. An improved protocol for LDH assay was, therefore, proposed and validated by eliminating any effects associated with protein–particle interactions. In view of this, additional measures and precautions should be taken when evaluating cytotoxicity of NPs with standard protein-based assays, particularly when they are of opposite charges.
Nanoparticle-assay marker interaction: effects on nanotoxicity assessment

Science.gov (United States)

Zhao, Xinxin; Xiong, Sijing; Huang, Liwen Charlotte; Ng, Kee Woei; Loo, Say Chye Joachim

2015-01-01

Protein-based cytotoxicity assays such as lactate dehydrogenase (LDH) and tumor necrosis factor-alpha (TNF-α) are commonly used in cytotoxic evaluation of nanoparticles (NPs) despite numerous reports on possible interactions with protein markers in these assays that can confound the results obtained. In this study, conventional cytotoxicity assays where assay markers may (LDH and TNF- α) or may not (PicoGreen and WST-8) come into contact with NPs were used to evaluate the cytotoxicity of NPs. The findings revealed selective interactions between negatively charged protein assay markers (LDH and TNF- α) and positively charged ZnO NPs under abiotic conditions. The adsorption and interaction with these protein assay markers were strongly influenced by surface charge, concentration, and specific surface area of the NPs, thereby resulting in less than accurate cytotoxic measurements, as observed from actual cell viability measurements. An improved protocol for LDH assay was, therefore, proposed and validated by eliminating any effects associated with protein-particle interactions. In view of this, additional measures and precautions should be taken when evaluating cytotoxicity of NPs with standard protein-based assays, particularly when they are of opposite charges.
Evaluation of toxic and interactive toxic effects of three agrochemicals and copper using a battery of microbiotests.

Science.gov (United States)

Kungolos, A; Emmanouil, C; Tsiridis, V; Tsiropoulos, N

2009-08-01

Three commonly used test organisms of different trophic levels (Vibrio fischeri, Pseudokirchneriella subcapitata and Daphnia magna) were exposed to selected agrochemicals (fosthiazate, metalaxyl-M, imidacloprid) and copper, in single doses or in binary mixtures. The toxicity of each single compound varied up to two orders of magnitude, depending on the test species examined. V. fischeri was the most sensitive test organism regarding fosthiazate and metalaxyl-M, indicating an IC(50) value of 0.20 mg/L (0.17-0.25 mg/L) and 0.88 mg/L (0.35-1.57 mg/L), respectively. Imidacloprid was the least toxic compound, indicating an EC(50) value on D. magna of 64.6 mg/L (43.3-122.5 mg/L) and an IC(50) value on V. fischeri of 226 mg/L (159-322 mg/L), while for imidacloprid at a concentration of 1000 mg/L the effect on P. subcapitata was lower than 50%. Copper was the most toxic compound towards all test organisms exhibiting the highest toxic effect on P. subcapitata, with an IC(50) value of 0.05 mg/L (0.003-0.008 mg/L). The toxic effects of the binary mixtures have been compared to the theoretically expected effect, resulting from a simple mathematical model based on the theory of probabilities. The independent action model was used in order to predict the theoretically expected effect. The interactive effects were mostly antagonistic or additive, while in few cases (interactive effects of metalaxyl-M and copper on V. fischeri) a synergistic mode of action was observed for some concentration combinations. Experiments showed that interactive effects of chemicals may vary depending on the test species used as well as on the chemicals and their respective concentrations. Although most of the concentrations of chemicals tested in this study are higher than the ones usually found in natural environment, the evaluation of their interactive toxic effects using a battery of bioassays may comprise a useful tool for the estimation of the environmental hazard of chemicals.
The Contribution of the Dyadic Parent-Child Interaction Coding System (DPICS) Warm-Up Segments in Assessing Parent-Child Interactions

Science.gov (United States)

Shanley, Jenelle R.; Niec, Larissa N.

2011-01-01

This study evaluated the inclusion of uncoded segments in the Dyadic Parent-Child Interaction Coding System, an analogue observation of parent-child interactions. The relationships between warm-up and coded segments were assessed, as well as the segments' associations with parent ratings of parent and child behaviors. Sixty-nine non-referred…
Using Mobile Phones to Increase Classroom Interaction

Science.gov (United States)

Cobb, Stephanie; Heaney, Rose; Corcoran, Olivia; Henderson-Begg, Stephanie

2010-01-01

This study examines the possible benefits of using mobile phones to increase interaction and promote active learning in large classroom settings. First year undergraduate students studying Cellular Processes at the University of East London took part in a trial of a new text-based classroom interaction system and evaluated their experience by…
Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches.

Science.gov (United States)

Li, Amanda; Muddana, Hari S; Gilson, Michael K

2014-04-08

Quantum mechanical (QM) calculations of noncovalent interactions are uniquely useful as tools to test and improve molecular mechanics force fields and to model the forces involved in biomolecular binding and folding. Because the more computationally tractable QM methods necessarily include approximations, which risk degrading accuracy, it is essential to evaluate such methods by comparison with high-level reference calculations. Here, we use the extensive Benchmark Energy and Geometry Database (BEGDB) of CCSD(T)/CBS reference results to evaluate the accuracy and speed of widely used QM methods for over 1200 chemically varied gas-phase dimers. In particular, we study the semiempirical PM6 and PM7 methods; density functional theory (DFT) approaches B3LYP, B97-D, M062X, and ωB97X-D; and symmetry-adapted perturbation theory (SAPT) approach. For the PM6 and DFT methods, we also examine the effects of post hoc corrections for hydrogen bonding (PM6-DH+, PM6-DH2), halogen atoms (PM6-DH2X), and dispersion (DFT-D3 with zero and Becke-Johnson damping). Several orders of the SAPT expansion are also compared, ranging from SAPT0 up to SAPT2+3, where computationally feasible. We find that all DFT methods with dispersion corrections, as well as SAPT at orders above SAPT2, consistently provide dimer interaction energies within 1.0 kcal/mol RMSE across all systems. We also show that a linear scaling of the perturbative energy terms provided by the fast SAPT0 method yields similar high accuracy, at particularly low computational cost. The energies of all the dimer systems from the various QM approaches are included in the Supporting Information, as are the full SAPT2+(3) energy decomposition for a subset of over 1000 systems. The latter can be used to guide the parametrization of molecular mechanics force fields on a term-by-term basis.

Separation and characterization of resins and asphaltenes coming from Castilla crude Evaluation of their molecular interaction

International Nuclear Information System (INIS)

Navarro, Lina; Alvarez, Mario; Grosso, Jorge Luis; Navarro, Uriel

2004-01-01

The study of resins and asphaltenes, the heaviest fractions of oil, has become an area of interest due to the abundance of heavy crude oils in Colombia and Latin America. We studied the chemical composition of the heavy fractions of Castilla crude oil, evaluated some of its molecular parameters and found evidence of the interaction between the resins extracted from the crude with the asphaltenes of the original crude. With this objective, we carried out at the pilot plant level precipitation of the resin-asphaltene (R-A) aggregate by adding and mixing under controlled conditions, a paraffin solvent, from the Apiay refinery, called Apiasol. By extracting Soxhlet with the same solvent, resin 1 of aggregate R-A was separated. Resin ll defined as the soluble fraction that is part of the maltenes, was separated from the deasphalted crude by open column chromatography, using alumina as support, according to the SAR method (Saturated, Aromatics, Resins). The fractions of resins and the asphaltenes obtained, were characterized by: Nuclear Magnetic Resonance (NMR), FT-lR, DRX, elementary analysis (C, H, N, S), metal content (Ni and V), distribution of molecular weight by GPC, and average molecular weight by VPO. The results obtained show evidence that resin l which is part of the aggregate has less average molecular weight than resin ll which is present in the fraction of maltenes. In addition, some changes were found in the elementary analysis of among the resins. On the one hand, and taking into account the existing theories of molecular interactions among these fractions, it was found that the resins l separated from the R-A aggregate, when added to the crude, they stabilize their asphaltenes. This evaluation was carried out by analyzing the flocculation point of the crude and its mixtures with 1,9% and 3,8% of resin l, when they are titrated with a precipitating agent in an NIR cell that works with high pressure and temperature
Experimental and analytical studies for a BWR nuclear reactor building. Evaluation of soil-structure interaction behaviour

International Nuclear Information System (INIS)

Mizuno, N.; Tsushima, Y.

1975-01-01

This paper evaluates the spatial characteristics of dynamic properties, especially soil-structure interaction behaviour, of the BWR nuclear building by experimental and analytical studies. It is well known that the damping effects in soil-structure interaction are remarkable on the building with short periods by the dissipation of vibrational energy to the soil. The authors have previously reported an analytical method for estimating the damping effects the properties of which are characterized as follows: 1) The complex damping is used, because the so-called structural damping may be more suitable for estimating the damping effects of an elastic structure. 2) H. Tajimi's theory is used for estimating the dynamical soil-foundation stiffness with the dissipation of vibrational energy on the elastic half-space soil. In this paper, an approximate explanation is presented in regard to the more developmental mathematical method for estimating the damping effects than the above-mentioned previous method, which is 'Modes Superposition Method for Multi-Degrees of Freedom System' with the constant complex stiffness showing the structural damping effects and the dynamical soil-foundation stiffness approximated by the linear or quadratic functions of the eigenvalues. An approximate explanation is presented in regard to the experimental results of the No. 1 reactor building (BWR) of Hamaoka Nuclear Power Station, The Chubu Electric Power Co., Ltd. (Auth.)
Multimodal interaction design in collocated mobile phone use

NARCIS (Netherlands)

El-Ali, A.; Lucero, A.; Aaltonen, V.

2011-01-01

In the context of the Social and Spatial Interactions (SSI) platform, we explore how multimodal interaction design (input and output) can augment and improve the experience of collocated, collaborative activities using mobile phones. Based largely on our prototype evaluations, we reflect on and
Experiences with Interactive Multi-touch Tables

Science.gov (United States)

Fikkert, Wim; Hakvoort, Michiel; van der Vet, Paul; Nijholt, Anton

Interactive multi-touch tables can be a powerful means of communication for collaborative work as well as an engaging environment for competition. Through enticing gameplay we have evaluated user experience on competitive gameplay, collaborative work and musical expression. In addition, we report on our extensive experiences with two types of interactive multi-touch tables and we introduce a software framework that abstracts from their technical differences.
Maternal-Zygotic Epistasis and the Evolution of Genetic Diseases

Directory of Open Access Journals (Sweden)

Nicholas K. Priest

2010-01-01

Full Text Available Many birth defects and genetic diseases are expressed in individuals that do not carry the disease causing alleles. Genetic diseases observed in offspring can be caused by gene expression in mothers and by interactions between gene expression in mothers and offspring. It is not clear whether the underlying pattern of gene expression (maternal versus offspring affects the incidence of genetic disease. Here we develop a 2-locus population genetic model with epistatic interactions between a maternal gene and a zygotic gene to address this question. We show that maternal effect genes that affect disease susceptibility in offspring persist longer and at higher frequencies in a population than offspring genes with the same effects. We find that specific forms of maternal-zygotic epistasis can maintain disease causing alleles at high frequencies over a range of plausible values. Our findings suggest that the strength and form of epistasis and the underlying pattern of gene expression may greatly influence the prevalence of human genetic diseases.
A survey about methods dedicated to epistasis detection

Directory of Open Access Journals (Sweden)

Clément eNiel

2015-09-01

Full Text Available During the past decade, findings of genome-wide association studies (GWAS improved our knowledge and understanding of disease genetics. To date, thousands of SNPs have been associated to diseases and other complex traits. Statistical analysis typically looks for association between a phenotype and a SNP taken individually via single-locus tests. However, geneticists admit this is an oversimplified approach to tackle the complexity of underlying biological mechanisms. Interaction between SNPs, namely epistasis, must be considered. Unfortunately, epistasis detection gives rise to analytic challenges since analyzing every SNP combination is at present impractical at a genome-wide scale. In this review, we will present the main strategies recently proposed to detect epistatic interactions, along with their operating principle. Some of these methods are exhaustive, such as multifactor dimensionality reduction, likelihood ratio-based tests or receiver operating characteristic curve analysis; some are non-exhaustive, such as machine learning techniques (random forests, Bayesian networks or combinatorial optimization approaches (ant colony optimization, computational evolution system.
A Zeno-like paradox in linear interaction

International Nuclear Information System (INIS)

Weiss, J.

1998-01-01

The so-called Zeno-like paradox of infinite regressions and progressions connected by light cones, typical to particle dynamics of direct-interaction (ADD) theory, is examined for linear AAD interaction. It is shown that the paradox is resolved via convenient evaluating integral expressions which determine conserved quantities of Lorentz group to exhibit integral-free forms. As a result the formalism is also permitted to emerge the field confinement as one of substantial properties of linear interaction. (author)
Virtual Reality Interaction Using Mobile Devices

KAUST Repository

Aseeri, Sahar A.

2013-07-01

With the use of an immersive display system such as CAVE system, the user is able to realize a 3D immersive virtual environment realistically. However, interacting with virtual worlds in CAVE systems using traditional input devices to perform easy operations such as manipulation, object selection, and navigation is often difficult. This difficulty could diminish the immersion and sense of presence when it comes to 3D virtual environment tasks. Our research aims to implement and evaluate alternative approaches of interaction with immersive virtual environments on mobile devices for manipulation and object selection tasks. As many researchers have noted, using a mobile device as an interaction device has a number of advantages, including built-in display, built-in control, and touch screen facility. These advantages facilitate simple tasks within immersive virtual environments. This research proposes new methods using mobile devices like Smart-phones to perform di↵erent kinds of interactions both as an input device, (e.g. performing selection and manipulation of objects) and as an output device (e.g. utilizing the screen as an extra view for a virtual camera or information display). Moreover, we developed a prototype system to demonstrate and informally evaluate these methods. The research conclusion suggests using mobile devices as a 3D-controller. This will be a more intuitive approach to interact within the virtual environment.
Realistic effective interactions for nuclear systems

International Nuclear Information System (INIS)

Hjort-Jensen, M.; Osnes, E.; Kuo, T.T.S.

1994-09-01

A review of perturbative many-body descriptions of several nuclear systems is presented. Symmetric and asymmetric nuclear matter and finite nuclei with few valence particles are examples of systems considered. The many-body description starts with the most recent meson-exchange potential models for the nucleon-nucleon interaction, an interaction which in turn is used in perturbative schemes to evaluate the effective interaction for finite nuclei and infinite nuclear matter. A unified perturbative approach based on time-dependent perturbation theory is elaborated. For finite nuclei new results are presented for the effective interaction and the energy spectra in the mass areas of oxygen, calcium and tin. 166 refs., 83 refs., 21 tabs
Evaluation of Pseudo-Haptic Interactions with Soft Objects in Virtual Environments.

Directory of Open Access Journals (Sweden)

Min Li

Full Text Available This paper proposes a pseudo-haptic feedback method conveying simulated soft surface stiffness information through a visual interface. The method exploits a combination of two feedback techniques, namely visual feedback of soft surface deformation and control of the indenter avatar speed, to convey stiffness information of a simulated surface of a soft object in virtual environments. The proposed method was effective in distinguishing different sizes of virtual hard nodules integrated into the simulated soft bodies. To further improve the interactive experience, the approach was extended creating a multi-point pseudo-haptic feedback system. A comparison with regards to (a nodule detection sensitivity and (b elapsed time as performance indicators in hard nodule detection experiments to a tablet computer incorporating vibration feedback was conducted. The multi-point pseudo-haptic interaction is shown to be more time-efficient than the single-point pseudo-haptic interaction. It is noted that multi-point pseudo-haptic feedback performs similarly well when compared to a vibration-based feedback method based on both performance measures elapsed time and nodule detection sensitivity. This proves that the proposed method can be used to convey detailed haptic information for virtual environmental tasks, even subtle ones, using either a computer mouse or a pressure sensitive device as an input device. This pseudo-haptic feedback method provides an opportunity for low-cost simulation of objects with soft surfaces and hard inclusions, as, for example, occurring in ever more realistic video games with increasing emphasis on interaction with the physical environment and minimally invasive surgery in the form of soft tissue organs with embedded cancer nodules. Hence, the method can be used in many low-budget applications where haptic sensation is required, such as surgeon training or video games, either using desktop computers or portable devices, showing
Evaluating Pharmacokinetic and Pharmacodynamic Interactions with Computational Models in Supporting Cumulative Risk Assessment

Science.gov (United States)

Tan, Yu-Mei; Clewell, Harvey; Campbell, Jerry; Andersen, Melvin

2011-01-01

Simultaneous or sequential exposure to multiple chemicals may cause interactions in the pharmacokinetics (PK) and/or pharmacodynamics (PD) of the individual chemicals. Such interactions can cause modification of the internal or target dose/response of one chemical in the mixture by other chemical(s), resulting in a change in the toxicity from that predicted from the summation of the effects of the single chemicals using dose additivity. In such cases, conducting quantitative cumulative risk assessment for chemicals present as a mixture is difficult. The uncertainties that arise from PK interactions can be addressed by developing physiologically based pharmacokinetic (PBPK) models to describe the disposition of chemical mixtures. Further, PK models can be developed to describe mechanisms of action and tissue responses. In this article, PBPK/PD modeling efforts conducted to investigate chemical interactions at the PK and PD levels are reviewed to demonstrate the use of this predictive modeling framework in assessing health risks associated with exposures to complex chemical mixtures. PMID:21655141
Evaluating web-based static, animated and interactive maps for injury prevention

Directory of Open Access Journals (Sweden)

Jonathan Cinnamon

2009-11-01

Full Text Available Public health planning can benefit from visual exploration and analysis of geospatial data. Maps and geovisualization tools must be developed with the user-group in mind. User-needs assessment and usability testing are crucial elements in the iterative process of map design and implementation. This study presents the results of a usability test of static, animated and interactive maps of injury rates and socio-demographic determinants of injury by a sample of potential end-users in Toronto, Canada. The results of the user-testing suggest that different map types are useful for different purposes and for satisfying the varying skill level of the individual user. The static maps were deemed to be easy to use and versatile, while the animated maps could be made more useful if animation controls were provided. The split-screen concept of the interactive maps was highlighted as particularly effective for map comparison. Overall, interactive maps were identified as the preferred map type for comparing patterns of injury and related socio-demographic risk factors. Information collected from the user-tests is being used to expand and refine the injury web maps for Toronto, and could inform other public health-related geo-visualization projects.
A conceptual framework to evaluate human-wildlife interactions within coupled human and natural systems

Directory of Open Access Journals (Sweden)

Anita T. Morzillo

2014-09-01

Full Text Available Landscape characteristics affect human-wildlife interactions. However, there is a need to better understand mechanisms that drive those interactions, particularly feedbacks that exist between wildlife-related impacts, human reaction to and behavior as a result of those impacts, and how land use and landscape characteristics may influence those components within coupled human and natural systems. Current conceptual models of human-wildlife interactions often focus on species population size as the independent variable driving those interactions. Such an approach potentially overlooks important feedbacks among and drivers of human-wildlife interactions that result from mere wildlife presence versus absence. We describe an emerging conceptual framework that focuses on wildlife as a driver of human behavior and allows us to better understand linkages between humans, wildlife, and the broader landscape. We also present results of a pilot analysis related to our own ongoing study of urban rodent control behavior to illustrate one application of this framework within a study of urban landscapes.
Predicting drug?drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge

OpenAIRE

Takeda, Takako; Hao, Ming; Cheng, Tiejun; Bryant, Stephen H.; Wang, Yanli

2017-01-01

Drug?drug interactions (DDIs) may lead to adverse effects and potentially result in drug withdrawal from the market. Predicting DDIs during drug development would help reduce development costs and time by rigorous evaluation of drug candidates. The primary mechanisms of DDIs are based on pharmacokinetics (PK) and pharmacodynamics (PD). This study examines the effects of 2D structural similarities of drugs on DDI prediction through interaction networks including both PD and PK knowledge. Our a...
Interaction between liquid droplets and heated surface

Energy Technology Data Exchange (ETDEWEB)

Nigmatulin, B I [Research and Engineering Centre, LWR Nuclear Plants Safety, Elektrogorsk (Russian Federation); Vasiliev, N I [Research and Engineering Centre, LWR Nuclear Plants Safety, Elektrogorsk (Russian Federation); Guguchkin, V V [Research and Engineering Centre, LWR Nuclear Plants Safety, Elektrogorsk (Russian Federation)

1993-06-01

In this paper, experimental methods and investigation results of interaction between droplets of different liquids and a heated surface are presented. Wetted area, contact time period and transition boundary from wetted to non-wetted interaction regimes are experimentally evaluated. A simple connection of the wetted area value and contact time period with the heat removal efficiency is shown. (orig.)
Energy analysis of crack-damage interaction

Science.gov (United States)

Chudnovsky, A.; Wu, Shaofu

1989-01-01

The energy release rates associated with a main crack propagating into a surrounding damage zone, and a damage zone translation relative to the main crack, as well as an energy of interaction between the two are analyzed. The displacement and stress fields for the crack-damage interaction problem are reconstructed employing a semi-empirical stress analysis and experimental evaluation of the average craze density in the crazed zone.
Limbic-Auditory Interactions of Tinnitus: An Evaluation Using Diffusion Tensor Imaging.

Science.gov (United States)

Gunbey, H P; Gunbey, E; Aslan, K; Bulut, T; Unal, A; Incesu, L

2017-06-01

Tinnitus is defined as an imaginary subjective perception in the absence of an external sound. Convergent evidence proposes that tinnitus perception includes auditory, attentional and emotional components. The aim of this study was to investigate the thalamic, auditory and limbic interactions associated with tinnitus-related distress by Diffusion Tensor Imaging (DTI). A total of 36 tinnitus patients, 20 healthy controls underwent an audiological examination, as well as a magnetic resonance imaging protocol including structural and DTI sequences. All participants completed the Tinnitus Handicap Inventory (THI) and Visual Analog Scales (VAS) related with tinnitus. The fractional anisotropy (FA) and apparent diffusion coefficient (ADC) values were obtained for the auditory cortex (AC), inferior colliculus (IC), lateral lemniscus (LL), medial geniculate body (MGB), thalamic reticular nucleus (TRN), amygdala (AMG), hippocampus (HIP), parahippocampus (PHIP) and prefrontal cortex (PFC). In tinnitus patients the FA values of IC, MGB, TRN, AMG, HIP decreased and the ADC values of IC, MGB, TRN, AMG, PHIP increased significantly. The contralateral IC-LL and bilateral MGB FA values correlated negatively with hearing loss. A negative relation was found between the AMG-HIP FA values and THI and VAS scores. Bilateral ADC values of PHIP and PFC significantly correlated with the attention deficiency-VAS scores. In conclusion, this is the first DTI study to investigate the grey matter structures related to tinnitus perception and the significant correlation of FA and ADC with clinical parameters suggests that DTI can provide helpful information for tinnitus. Magnifying the microstructures in DTI can help evaluate the three faces of tinnitus nature: hearing, emotion and attention.
Filling potholes on the implementation highway: Evaluating the implementation of Parent-Child Interaction Therapy in Los Angeles County.

Science.gov (United States)

Timmer, Susan G; Urquiza, Anthony J; Boys, Deanna K; Forte, Lindsay A; Quick-Abdullah, Daphne; Chan, Sam; Gould, William

2016-03-01

In October 2012, first 5 LA funded a unique collaboration between Los Angeles County Department of Mental Health (DMH) and UC Davis PCIT Training Center (UCD PCIT) to train county-contracted agencies to provide Parent-Child Interaction Therapy (PCIT). This $20 million dollar, 5-year grant represented the largest implementation effort of an empirically based treatment to date. The purpose of this paper was to describe the first 2 years of the implementation process of this project, beginning with project start up and pre-implementation phases, and to present agency training and client performance outcomes from our first year of training. Results presented in this evaluation suggest that it is possible to train LA County providers in PCIT, and that PCIT is an effective intervention for DMH-contracted providers in LA County. This evaluation also discusses challenges to successful implementation. Barriers to progress included unanticipated delays building county infrastructure, trainee attrition, and insufficient client referrals. We discuss the results of the current implementation with respect to theory, research, and others' training models, with the aim of evaluating and prioritizing different implementation drivers, noting the ongoing competition between knowing what to do and the need for action. Copyright © 2015 Elsevier Ltd. All rights reserved.
[Drug interactions in chronic prescription].

Science.gov (United States)

Comet, D; Casajuana, J; Bordas, J M; Fuentes, M A; Arnáiz, J A; Núñez, B; Pou, R

1997-06-30

Application of computerized program for detection of potential drug interactions (PDI) in chronic prescriptions in four primary care centers. To evaluate the clinical significance of PDI identified according to clinical criterions. An observational crossover study. Clutat Vella health district (City of Barcelona). Using information of Consejo General de Colegios Oficiales de Farmaceuticos databases and the chronic prescriptions database of the primary care centers, computerized drug-interaction system have been developed for detection of PDI in patients. A panel of primary care physicians and clinical pharmacists developed criteria that were used to evaluate the clinical significance of PDI. 9840 Cards of Authorized Prescription (CAP) were analyzed, 36108 medicaments and 42877 drugs. A total of 2140 patients were involved for a total of 3406 PDI, 21.75% of patients with CAP. Clinical signification for the panel was found in 40.07% of these 3406 PIF; 3.78% were suggest to avoid the association drugs. The incidence of PDI with clinical signification are lower than other studies of the literature; it suggest a appropriate knowledge of drug prescription. The application of computerized program make much more easy the detection of adverse drug interactions in chronic prescription.
Work-domain knowledge in usability evaluation

DEFF Research Database (Denmark)

Følstad, Asbjørn; Hornbæk, Kasper

2010-01-01

Usability evaluation helps to determine whether interactive systems support users in their work tasks. However, knowledge about those tasks and, more generally, about the work-domain is difficult to bring to bear on the processes and outcome of usability evaluation. One way to include such work......-domain knowledge might be Cooperative Usability Testing, an evaluation method that consists of (a) interaction phases, similar to classic usability testing, and (b) interpretation phases, where the test participant and the moderator discuss incidents and experiences from the interaction phases. We have studied...... whether such interpretation phases improve the relevance of usability evaluations in the development of work-domain specific systems. The study included two development cases. We conclude that the interpretation phases generate additional insight and redesign suggestions related to observed usability...

Evaluation of Drug Interactions and Prescription Errors of Poultry Veterinarians in North of Iran

Directory of Open Access Journals (Sweden)

Madadi MS

2014-03-01

Full Text Available Drug prescription errors are a common cause of adverse incidents and may lead to adverse outcomes, sometimes in subtle ways, being compounded by circumstances or further errors. Therefore, it is important that veterinarians issue the correct drug at the correct dose. Using two or more prescribed drugs may lead to drug interactions. Some drug interactions are very harmful and may have potential threats to the patient's health that is called antagonism. In a survey study, medication errors of 750 prescriptions, including dosage errors and drug interactions were studied. The results indicated that 20.8% of prescriptions had at least one drug interaction. The most interactions were related to antibiotics (69.1%, Sulfonamides (46.7%, Methenamine (46.7% and Florfenicol (20.2%. Analysis of dosage errors indicated that total drugs consumed by broilers in the summer are more than winter seasons. Based on these results, avoiding medication errors are important in the balanced prescribing of drugs and regular education of veterinary practitioners in a certain interval is needed.
In-orbit evaluation of the control system/structural mode interactions of the OSO-8 spacecraft

Science.gov (United States)

Slafer, L. I.

1979-01-01

The Orbiting Solar Observatory-8 experienced severe structural mode/control loop interaction problems during the spacecraft development. Extensive analytical studies, using the hybrid coordinate modeling approach, and comprehensive ground testing were carried out in order to achieve the system's precision pointing performance requirements. A recent series of flight tests were conducted with the spacecraft in which a wide bandwidth, high resolution telemetry system was utilized to evaluate the on-orbit flexible dynamics characteristics of the vehicle along with the control system performance. The paper describes the results of these tests, reviewing the basic design problem, analytical approach taken, ground test philosophy, and on-orbit testing. Data from the tests was used to determine the primary mode frequency, damping, and servo coupling dynamics for the on-orbit condition. Additionally, the test results have verified analytically predicted differences between the on-orbit and ground test environments, and have led to a validation of both the analytical modeling and servo design techniques used during the development of the control system.
Evaluation of the Humanity Research Paradigms based on Analysis of Human – Environment Interaction

Directory of Open Access Journals (Sweden)

Reza Sameh

2015-09-01

Full Text Available As claimed by many behavioral scientists, designing should be based on the knowledge of interaction between human and environment. Environmental quality is also created in the context in which humans interact with their environment. To achieve such quality, designers should develop appropriate models for explaining this relationship, and this requires an understanding of human nature and the environment. Criticisms on the Modern Movement have shown that architects have often used incomplete and simplistic models in this regard, while most of design ideas are based on the definitions of human and environment and the interaction between them. However, the most important question that is raised is that how understanding of human nature and the environment and their interaction, which depends on foundations of different views, can affect the pursuit of quality in designing? Therefore, the present paper, in addition to introduction and comparison of common paradigms in humanities as the and methodological foundation of human sciences, aims to deal with the relationship of human and the environment from the perspective of objectivist, relativist, and critical paradigms in order to identify the characteristics and differences in their views on the analysis of the quality of this interaction. This is the most important step that paves the way for understanding the qualitative foundations of the environment and human life quality and also the quality of interaction between them.
Evaluation of Selected CYP51A1 Polymorphisms in View of Interactions with Substrate and Redox Partner

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Tadeja Režen

2017-06-01

Full Text Available Cholesterol is essential for development, growth, and maintenance of organisms. Mutations in cholesterol biosynthetic genes are embryonic lethal and few polymorphisms have been so far associated with pathologies in humans. Previous analyses show that lanosterol 14α-demethylase (CYP51A1 from the late part of cholesterol biosynthesis has only a few missense mutations with low minor allele frequencies and low association with pathologies in humans. The aim of this study is to evaluate the role of amino acid changes in the natural missense mutations of the hCYP51A1 protein. We searched SNP databases for existing polymorphisms of CYP51A1 and evaluated their effect on protein function. We found rare variants causing detrimental missense mutations of CYP51A1. Some missense variants were also associated with a phenotype in humans. Two missense variants have been prepared for testing enzymatic activity in vitro but failed to produce a P450 spectrum. We performed molecular modeling of three selected missense variants to evaluate the effect of the amino acid substitution on potential interaction with its substrate and the obligatory redox partner POR. We show that two of the variants, R277L and especially D152G, have possibly lower binding potential toward obligatory redox partner POR. D152G and R431H have also potentially lower affinity toward the substrate lanosterol. We evaluated the potential effect of damaging variants also using data from other in vitro CYP51A1 mutants. In conclusion, we propose to include damaging CYP51A1 variants into personalized diagnostics to improve genetic counseling for certain rare disease phenotypes.
Evaluation of the Interaction between the Poincianella pyramidalis (Tul. LP Queiroz Extract and Antimicrobials Using Biological and Analytical Models.

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Thiago P Chaves

Full Text Available Poincianella pyramidalis (Tul. LP Queiroz (Fabaceae is an endemic tree of northeastern Brazil, occurring mainly in the Caatinga. Its medicinal use is widespread and is an important therapeutic option against diarrhea, dysentery, and respiratory and urinary infections, among other diseases. In this study we determined the chemical marker and evaluated the interaction between P. pyramidalis extract and a commercial antimicrobial through the use of biological and analytical models. To obtain the extract, an ethanol-water mixture (50:50 v/v was used as solvent. It was nebulized in a spray dryer using colloidal silicon dioxide as a drying adjuvant. The extract (ENPp was subjected to HPLC analysis to verify the presence of certain secondary metabolites. The Minimum Inhibitory Concentration (MIC of the extract against Gram-negative bacteria was determined by broth microdilution and the MIC of synthetic antimicrobial drugs in the presence and absence of the extract. The antioxidant activity of ENPp was evaluated by the DPPH method. The compatibility between the antimicrobial and the extract was evaluated by thermal analysis (TG/DTA. The acute toxicity of the extract was evaluated in vivo in rodents. The results indicate significant additive action of the extract on synthetic antibiotics, considerable antioxidant activity and absence of toxicity. This extract shows high potential for the development of formulations for antimicrobial therapy when used with a vegetable-active ingredient.
Evaluation, Language, and Untranslatables

Science.gov (United States)

Dahler-Larsen, Peter; Abma, Tineke; Bustelo, María; Irimia, Roxana; Kosunen, Sonja; Kravchuk, Iryna; Minina, Elena; Segerholm, Christina; Shiroma, Eneida; Stame, Nicoletta; Tshali, Charlie Kabanga

2017-01-01

The issue of translatability is pressing in international evaluation, in global transfer of evaluative instruments, in comparative performance management, and in culturally responsive evaluation. Terms that are never fully understood, digested, or accepted may continue to influence issues, problems, and social interactions in and around and after…
Evaluation of conservatism in analysis of fuel-coolant interaction

International Nuclear Information System (INIS)

Reynolds, A.B.; Erdman, C.A.; Garner, P.L.; Haas, P.M.; Allen, C.L.

Using the ANL parametric model developed by Cho e.a. the following mechanisms and parameters involved in fuel-coolant interaction were examined: coherence of fuel-sodium mixing; two-phase heat transfer; sodium-to-fuel mass ratio; fuel particle size; heat transfer to plenum and core cladding; constraint geometry. Both overpower and loss-of-flow transients were studied. Main attention is given to the maximum mechanical work to be expected. As a general conclusion, it can be stated that more realistic models will result in a reduction of the estimated mechanical work
The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide.

Science.gov (United States)

Abramov, Y A; Volkov, A; Wu, G; Coppens, P

2000-11-01

A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods.
Evaluation of limited sampling models for prediction of oral midazolam AUC for CYP3A phenotyping and drug interaction studies.

Science.gov (United States)

Mueller, Silke C; Drewelow, Bernd

2013-05-01

The area under the concentration-time curve (AUC) after oral midazolam administration is commonly used for cytochrome P450 (CYP) 3A phenotyping studies. The aim of this investigation was to evaluate a limited sampling strategy for the prediction of AUC with oral midazolam. A total of 288 concentration-time profiles from 123 healthy volunteers who participated in four previously performed drug interaction studies with intense sampling after a single oral dose of 7.5 mg midazolam were available for evaluation. Of these, 45 profiles served for model building, which was performed by stepwise multiple linear regression, and the remaining 243 datasets served for validation. Mean prediction error (MPE), mean absolute error (MAE) and root mean squared error (RMSE) were calculated to determine bias and precision The one- to four-sampling point models with the best coefficient of correlation were the one-sampling point model (8 h; r (2) = 0.84), the two-sampling point model (0.5 and 8 h; r (2) = 0.93), the three-sampling point model (0.5, 2, and 8 h; r (2) = 0.96), and the four-sampling point model (0.5,1, 2, and 8 h; r (2) = 0.97). However, the one- and two-sampling point models were unable to predict the midazolam AUC due to unacceptable bias and precision. Only the four-sampling point model predicted the very low and very high midazolam AUC of the validation dataset with acceptable precision and bias. The four-sampling point model was also able to predict the geometric mean ratio of the treatment phase over the baseline (with 90 % confidence interval) results of three drug interaction studies in the categories of strong, moderate, and mild induction, as well as no interaction. A four-sampling point limited sampling strategy to predict the oral midazolam AUC for CYP3A phenotyping is proposed. The one-, two- and three-sampling point models were not able to predict midazolam AUC accurately.
From chatterbots to natural interaction

DEFF Research Database (Denmark)

Rehm, Matthias; André, Elisabeth

2005-01-01

In this paper, we present a game of dice that combines multi-party communication with a tangible interface. The game has been used as a testbed to study typical conversational behavior patterns in interactions between human users and synthetic agents. In particular, we were interested in the ques...... in the question to what extent the interaction with the agent can be considered as natural. As an evaluation criterion, we propose to investigate whether the communicative behaviors of humans differ when conversing with an agent as opposed to conversing with other humans...
Wrist-worn pervasive gaze interaction

DEFF Research Database (Denmark)

Hansen, John Paulin; Lund, Haakon; Biermann, Florian

2016-01-01

This paper addresses gaze interaction for smart home control, conducted from a wrist-worn unit. First we asked ten people to enact the gaze movements they would propose for e.g. opening a door or adjusting the room temperature. On basis of their suggestions we built and tested different versions...... selection. Their subjective evaluations were positive with regard to the speed of the interaction. We conclude that gaze gesture input seems feasible for fast and brief remote control of smart home technology provided that robustness of tracking is improved....
Interaction Modes for Emergency Mobile Apps

Directory of Open Access Journals (Sweden)

Claudia Nass

2018-01-01

Full Text Available While seemingly irrational behaviors such as panicking or displaying antisocial behavior are the responses to emergency situations the media and movies lead us to believe, several studies show that people rather react based on decision-making such as acting altruistically and protectively. However, what can we really expect from people in a crowd in terms of participation in an emergency response system? In this paper, we present a mobile application called the RESCUER App, which allows civilians to participate in the emergency response process by providing information about the emergency to a command center and to receive instructions from this command center. We developed a human reaction model for emergencies to better understand the human–computer interaction capabilities of people in an emergency situation. Based on this model, we defined three different interaction modes: one-click interaction, guided interaction, and chat interaction. These interaction modes were implemented in an interactive prototype and evaluated in an experiment in which high cognitive load was induced to simulate a stress situation, similar to the stress experienced in an emergency. The experiment results showed that the three predefined interaction modes enabled people to interact with the RESCUER App even though they were in a stress situation.
Methods used in evaluating data for the interaction of neutrons with light elements (A < 19)

International Nuclear Information System (INIS)

Stewart, L.

1980-01-01

In the interaction of neutrons with light nuclei, many anomalies are observed. In particular, the probability for gamma-ray production is generally small over most of the neutron energy range. On the other hand, 6 Li, 3 He, 10 B, and 7 Be have thermal absorption cross sections which range from 940 to 48,000 barns. 10 B is the only isotope that has a positive Q for a 3-body reaction, the (n,t2α). As the neutron energy increases, however, 3- and 4-particle direct breakup and sequential formation cross sections dominate the nonelastic for D, T, 6 Li, 7 Be, 10 B, and 12 C above a few MeV. For higher-mass isotopes, particle emission (protons and α's) are often the preferred mode for deexcitation of levels excited via (n,n') reactions, where energetically possible. Very few of these partial cross sections have been measured with the necessary precision. Problems are particularly inherent in experiments on negative-Q reactions near the 3-body threshold. The many-body problem must be treated as several two-body sequential steps in a theoretical analysis; the emitted particle angular distribution is required as input, but is rarely known. Precise knowledge about individual partial cross sections is often important, especially when neutron multiplication, breeding of fusion fuel, radioactive contamination, depletion or buildup of the target, energy transfer, or time-dependent parameters are required. Specific examples are described for the evaluation of neutron interactions with light elements which employ isotopic spin, inverse reactions, charge-conjugate reactions, and the elastic scattering of charged particles (with Wick's Limit). 18 figures, 1 table
Predictability of Genetic Interactions from Functional Gene Modules

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Jonathan H. Young

2017-02-01

Full Text Available Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal.
Game user experience evaluation

CERN Document Server

Bernhaupt, Regina

2015-01-01

Evaluating interactive systems for their user experience (UX) is a standard approach in industry and research today. This book explores the areas of game design and development and Human Computer Interaction (HCI) as ways to understand the various contributing aspects of the overall gaming experience. Fully updated, extended and revised this book is based upon the original publication Evaluating User Experience in Games, and provides updated methods and approaches ranging from user- orientated methods to game specific approaches. New and emerging methods and areas explored include physiologi
Reflections on the pathogenesis of Down syndrome.

Science.gov (United States)

Opitz, J M; Gilbert-Barness, E F

1990-01-01

what extent the Down syndrome phenotype can be resolved into the additive effect of several pleiotropic oligogenes with epistatic interaction or the indirect secondary "mass" effect of a specific segment of 21q with epistatic interaction involving multiple loci on 21q and other chromosomes.
Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

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Huang Yung-Fen

2012-02-01

Full Text Available Abstract Background Proanthocyanidins (PAs, or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1 showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA
QTLs for tolerance of drought and breeding for tolerance of abiotic and biotic stress: an integrated approach.

Directory of Open Access Journals (Sweden)

Shalabh Dixit

Full Text Available BACKGROUND: The coupling of biotic and abiotic stresses leads to high yield losses in rainfed rice (Oryza sativa L. growing areas. While several studies target these stresses independently, breeding strategies to combat multiple stresses seldom exist. This study reports an integrated strategy that combines QTL mapping and phenotypic selection to develop rice lines with high grain yield (GY under drought stress and non-stress conditions, and tolerance of rice blast. METHODOLOGY: A blast-tolerant BC2F3-derived population was developed from the cross of tropical japonica cultivar Moroberekan (blast- and drought-tolerant and high-yielding indica variety Swarna (blast- and drought-susceptible through phenotypic selection for blast tolerance at the BC2F2 generation. The population was studied for segregation distortion patterns and QTLs for GY under drought were identified along with study of epistatic interactions for the trait. RESULTS: Segregation distortion, in favour of Moroberekan, was observed at 50 of the 59 loci. Majority of these marker loci co-localized with known QTLs for blast tolerance or NBS-LRR disease resistance genes. Despite the presence of segregation distortion, high variation for DTF, PH and GY was observed and several QTLs were identified under drought stress and non-stress conditions for the three traits. Epistatic interactions were also detected for GY which explained a large proportion of phenotypic variance observed in the population. CONCLUSIONS: This strategy allowed us to identify QTLs for GY along with rapid development of high-yielding purelines tolerant to blast and drought with considerably reduced efforts. Apart from this, it also allowed us to study the effects of the selection cycle for blast tolerance. The developed lines were screened at IRRI and in the target environment, and drought and blast tolerant lines with high yield were identified. With tolerance to two major stresses and high yield potential, these
Irinotecan and Δ9-Tetrahydrocannabinol Interactions in Rat Liver: A Preliminary Evaluation Using Biochemical and Genotoxicity Markers

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Ana Lucić Vrdoljak

2018-06-01

Full Text Available There is growing interest regarding the use of herbal preparations based on Cannabis sativa for medicinal purposes, despite the poorly understood interactions of their main constituent Δ9-tetrahydrocannabinol (THC with conventional drugs, especially cytostatics. The objective of this pilot study was to prove whether the concomitant intake of THC impaired liver function in male Wistar rats treated with the anticancer drug irinotecan (IRI, and evaluate the toxic effects associated with this exposure. IRI was administered once intraperitoneally (at 100 mg/kg of the body weight (b.w., while THC was administered per os repeatedly for 1, 3, and 7 days (at 7 mg/kg b.w.. Functional liver impairments were studied using biochemical markers of liver function (aspartate aminotransferase—AST, alanine aminotransferase—ALP, alkaline phosphatase—AP, and bilirubin in rats given a combined treatment, single IRI, single THC, and control groups. Using common oxidative stress biomarkers, along with measurement of primary DNA damage in hepatocytes, the degree of impairments caused at the cellular level was also evaluated. THC caused a time-dependent enhancement of acute toxicity in IRI-treated rats, which was confirmed by body and liver weight reduction. Although single THC affected ALP and AP levels more than single IRI, the levels of liver function markers measured after the administration of a combined treatment mostly did not significantly differ from control. Combined exposure led to increased oxidative stress responses in 3- and 7-day treatments, compared to single IRI. Single IRI caused the highest DNA damage at all timepoints. Continuous 7-day oral exposure to single THC caused an increased mean value of comet tail length compared to its shorter treatments. Concomitant intake of THC slightly affected the levels of IRI genotoxicity at all timepoints, but not in a consistent manner. Further studies are needed to prove our preliminary observations
Theoretical Framework for Interaction Game Design

Science.gov (United States)

2016-05-19

evaluation of a virtual basketball game, investigation of the effect of back imitation, a method for inducing intentional stance in HAI (Human-Agent...Interaction), using physiological indices for discriminating intrinsic and extrinsic stress, and SES (Synthetic Evidential Study). Project had to be...evaluation of a virtual basketball game, investigation of the effect of back imitation, a method for inducing intentional stance in HAI (Human-Agent

Antimicrobial peptides interact with peptidoglycan

Science.gov (United States)

Neelay, Om P.; Peterson, Christian A.; Snavely, Mary E.; Brown, Taylor C.; TecleMariam, Ariam F.; Campbell, Jennifer A.; Blake, Allison M.; Schneider, Sydney C.; Cremeens, Matthew E.

2017-10-01

Traditional therapeutics are losing effectiveness as bacterial resistance increases, and antimicrobial peptides (AMPs) can serve as an alternative source for antimicrobial agents. Their mode of action is commonly hypothesized to involve pore formation in the lipid membrane, thereby leading to cell death. However, bacterial cell walls are much more complex than just the lipid membrane. A large portion of the wall is comprised of peptidoglycan, yet we did not find any report of AMP-peptidoglycan interactions. Consequently, this work evaluated AMP-peptidoglycan and AMP-phospholipid (multilamellar vesicles) interactions through tryptophan fluorescence. Given that peptidoglycan is insoluble and vesicles are large particles, we took advantage of the unique properties of Trp-fluorescence to use one technique for two very different systems. Interestingly, melittin and cecropin A interacted with peptidoglycan to a degree similar to vancomycin, a positive control. Whether these AMP-peptidoglycan interactions relate to a killing mode of action requires further study.
Drug interactions between common illicit drugs and prescription therapies.

Science.gov (United States)

Lindsey, Wesley T; Stewart, David; Childress, Darrell

2012-07-01

The aim was to summarize the clinical literature on interactions between common illicit drugs and prescription therapies. Medline, Iowa Drug Information Service, International Pharmaceutical Abstracts, EBSCO Academic Search Premier, and Google Scholar were searched from date of origin of database to March 2011. Search terms were cocaine, marijuana, cannabis, methamphetamine, amphetamine, ecstasy, N-methyl-3,4-methylenedioxymethamphetamine, methylenedioxymethamphetamine, heroin, gamma-hydroxybutyrate, sodium oxybate, and combined with interactions, drug interactions, and drug-drug interactions. This review focuses on established clinical evidence. All applicable full-text English language articles and abstracts found were evaluated and included in the review as appropriate. The interactions of illicit drugs with prescription therapies have the ability to potentiate or attenuate the effects of both the illicit agent and/or the prescription therapeutic agent, which can lead to toxic effects or a reduction in the prescription agent's therapeutic activity. Most texts and databases focus on theoretical or probable interactions due to the kinetic properties of the drugs and do not fully explore the pharmacodynamic and clinical implications of these interactions. Clinical trials with coadministration of illicit drugs and prescription drugs are discussed along with case reports that demonstrate a potential interaction between agents. The illicit drugs discussed are cocaine, marijuana, amphetamines, methylenedioxymethamphetamine, heroin, and sodium oxybate. Although the use of illicit drugs is widespread, there are little experimental or clinical data regarding the effects of these agents on common prescription therapies. Potential drug interactions between illicit drugs and prescription drugs are described and evaluated on the Drug Interaction Probability Scale by Horn and Hansten.
Genomewide mapping reveals a combination of different genetic ...

Indian Academy of Sciences (India)

could not investigate all kinds of genetic effects, especially epistatic effects, simultaneously on the whole genome. ... consistent with different loci affecting heterosis for different ...... Jones D. F. 1917 Dominance of linked factors as a means of.
On the role of temporary storage in interactive evolution

DEFF Research Database (Denmark)

Dahlstedt, Palle

2009-01-01

In typical implementations of interactive evolution of aesthetic material, population size and generation count are limited due to the time-consuming manual evaluation process. We show how a simple device can help to compensate for this, and help to enhance the functionality of interactive...
The n→π* Interaction.

Science.gov (United States)

Newberry, Robert W; Raines, Ronald T

2017-08-15

groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation. Although individual n→π* interactions are relatively weak (∼0.3-0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affected by the n→π* interaction and will clarify their specific contributions to the structures of biomacromolecules.
Three additional genes involved in pyrimidine dimer removal in Saccharomyces cerevisiae: RAD7, RAD14, and MMS19

Energy Technology Data Exchange (ETDEWEB)

Prakash, L; Prakash, S

1979-01-01

The ability to remove ultraviolet (uv)-induced pyrimidine dimers from the nuclear DNA of yeast was examined in two radiation-sensitive (rad) mutants and one methyl methanesulfonate-sensitive (mms) mutant of the yeast Saccharomyces cerevisiae. The susceptibility of DNA from irradiated cells to nicking by an endonuclease activity prepared from crude extracts of Micrococcus luteus was used to measure the presence of dimers in DNA. The rad7, rad14, and mms19 mutants were found to be defective in their ability to remove uv-induced dimers from nuclear DNA. All three mutants belong to the same episatic group as the other mutants involved in excision-repair. All three mutants show enhanced uv-induced mutations. The rad 14 mutant also shows epistatic interactions with genes in the other two uv repair pathways.
[Patient-doctor interaction in rehabilitation: is there a relationship between perceived interaction quality and long term treatment results?].

Science.gov (United States)

Dibbelt, S; Schaidhammer, M; Fleischer, C; Greitemann, B

2010-10-01

A body of evidence suggests that good interaction is crucial for high-quality medical practice and that it has a considerable impact on treatment outcomes. Less is known about the role and significance of doctor-patient interaction in rehabilitation. The study's aim was to capture perceived quality of doctor-patient interaction in rehabilitation by a rating instrument (P.A.INT-Questionnaire) and to examine the relationship between perceived quality of interaction and long-term treatment outcomes. Referring to the approach of Bensing (1990) and Rogers (1972) we defined "quality of interaction" in terms of 3 dimensions: (1) affective behaviour, i. e., empathy, positive regard and coherence; (2) instrumental behaviour: providing and collecting information, structuring and reinforcement; (3) participation and involvement of patients. 2 parallel versions of the Questionnaire were developed for patients and physicians. 7 rehabilitation clinics in north-western Germany participated in the multi-centre study. 61 doctors and their 470 patients evaluated both their shared dialogues upon admission, discharge and at least one ward round. Furthermore, patients rated their health status on admission (t0), discharge (t1) and 6 months after discharge (t2) using the IRES-3 (Indicators of Rehabilitation Status Questionnaire Version 3). (1) Comparisons of patient and physician evaluations on admission revealed the following: Affective quality of contact (empathy and coherence) was rated positively and without discrepancies by both patients and physicians. On the other hand, instrumental behaviour (information and structuring) was rated less positively by patients than by physicians. (2) Patients who rated the dialogue on admission more positively showed stronger treatment effects with respect to pain, to anxiety and depression 6 months after discharge. Also disability days decreased about 40% stronger in the group of positive raters. (3) Patient ratings of quality of interaction
A Hybrid Recommender System Based on User-Recommender Interaction

OpenAIRE

Zhang, Heng-Ru; Min, Fan; He, Xu; Xu, Yuan-Yuan

2015-01-01

Recommender systems are used to make recommendations about products, information, or services for users. Most existing recommender systems implicitly assume one particular type of user behavior. However, they seldom consider user-recommender interactive scenarios in real-world environments. In this paper, we propose a hybrid recommender system based on user-recommender interaction and evaluate its performance with recall and diversity metrics. First, we define the user-recommender interaction...
An Evaluation of Multimodal Interactions with Technology while Learning Science Concepts

Science.gov (United States)

Anastopoulou, Stamatina; Sharples, Mike; Baber, Chris

2011-01-01

This paper explores the value of employing multiple modalities to facilitate science learning with technology. In particular, it is argued that when multiple modalities are employed, learners construct strong relations between physical movement and visual representations of motion. Body interactions with visual representations, enabled by…
Analysis of the dynamic interaction between SVOCs and airborne particles

DEFF Research Database (Denmark)

Liu, Cong; Shi, Shanshan; Weschler, Charles J.

2013-01-01

A proper quantitative understanding of the dynamic interaction between gas-phase semivolatile organic compounds (SVOCs) and airborne particles is important for human exposure assessment and risk evaluation. Questions regarding how to properly address gas/particle interactions have introduced...
Sensory impacts of food-packaging interactions.

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Duncan, Susan E; Webster, Janet B

2009-01-01

Sensory changes in food products result from intentional or unintentional interactions with packaging materials and from failure of materials to protect product integrity or quality. Resolving sensory issues related to plastic food packaging involves knowledge provided by sensory scientists, materials scientists, packaging manufacturers, food processors, and consumers. Effective communication among scientists and engineers from different disciplines and industries can help scientists understand package-product interactions. Very limited published literature describes sensory perceptions associated with food-package interactions. This article discusses sensory impacts, with emphasis on oxidation reactions, associated with the interaction of food and materials, including taints, scalping, changes in food quality as a function of packaging, and examples of material innovations for smart packaging that can improve sensory quality of foods and beverages. Sensory evaluation is an important tool for improved package selection and development of new materials.
Interaction between holo transferrin and HSA-PPIX complex in the presence of lomefloxacin: An evaluation of PPIX aggregation in protein-protein interactions

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Sattar, Zohreh; Iranfar, Hediye; Asoodeh, Ahmad; Saberi, Mohammad Reza; Mazhari, Mahboobeh; Chamani, Jamshidkhan

2012-11-01

Human serum albumin (HSA) and holo transferrin (TF) are two serum carrier proteins that are able to interact with each other, thereby altering their binding behavior toward their ligands. During the course of this study, the interaction between HSA-PPIX and TF, in the presence and absence of lomefloxacin (LMF), was for the first time investigated using different spectroscopic and molecular modeling techniques. Fluorescence spectroscopy experiments were performed in order to study conformational changes of proteins. The RLS technique was utilized to investigate the effect of LMF on J-aggregation of PPIX, which is the first report of its kind. Our findings present clear-cut evidence for the alteration of interactions between HSA and TF in the presence of PPIX and changes in drug-binding to HSA and HSA-PPIX complex upon interaction with TF. Moreover, molecular modeling studies suggested that the binding site for LMF became switched in the presence of PPIX, and that LMF bound to the site IIA of HSA. The obtained results should give new insight into research in this field and may cast some light on the dynamics of drugs in biological systems.
A Deported View Concept for Touch Interaction

DEFF Research Database (Denmark)

Alapetite, Alexandre; Andersen, Henning Boje; Fogh, Rune

2013-01-01

Following the paradigm shift where physical controls are replaced by touch-enabled surfaces, we report on an experimental evaluation of a user interface concept that allows touchscreen-based panels to be manipulated partially blindly (aircrafts, cars). The proposed multi-touch interaction strategy...... – involving visual front-view feedback to the user from a copy of the peripheral panel being manipulated – compares favourably against trackballs or head-down interactions....
Detection of Social Interaction in Smart Spaces.

Science.gov (United States)

Cook, Diane J; Crandall, Aaron; Singla, Geetika; Thomas, Brian

2010-02-01

The pervasive sensing technologies found in smart environments offer unprecedented opportunities for monitoring and assisting the individuals who live and work in these spaces. An aspect of daily life that is important for one's emotional and physical health is social interaction. In this paper we investigate the use of smart environment technologies to detect and analyze interactions in smart spaces. We introduce techniques for collect and analyzing sensor information in smart environments to help in interpreting resident behavior patterns and determining when multiple residents are interacting. The effectiveness of our techniques is evaluated using two physical smart environment testbeds.
Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects

Directory of Open Access Journals (Sweden)

Omnia Gamal El-Dien

2016-03-01

Full Text Available The open-pollinated (OP family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.
Selenistasis: Epistatic Effects of Selenium on Cardiovascular Phenotype

Directory of Open Access Journals (Sweden)

Joseph Loscalzo

2013-01-01

Full Text Available Although selenium metabolism is intricately linked to cardiovascular biology and function, and deficiency of selenium is associated with cardiac pathology, utilization of selenium in the prevention and treatment of cardiovascular disease remains an elusive goal. From a reductionist standpoint, the major function of selenium in vivo is antioxidant defense via its incorporation as selenocysteine into enzyme families such as glutathione peroxidases and thioredoxin reductases. In addition, selenium compounds are heterogeneous and have complex metabolic fates resulting in effects that are not entirely dependent on selenoprotein expression. This complex biology of selenium in vivo may underlie the fact that beneficial effects of selenium supplementation demonstrated in preclinical studies using models of oxidant stress-induced cardiovascular dysfunction, such as ischemia-reperfusion injury and myocardial infarction, have not been consistently observed in clinical trials. In fact, recent studies have yielded data that suggest that unselective supplementation of selenium may, indeed, be harmful. Interesting biologic actions of selenium are its simultaneous effects on redox balance and methylation status, a combination that may influence gene expression. These combined actions may explain some of the biphasic effects seen with low and high doses of selenium, the potentially harmful effects seen in normal individuals, and the beneficial effects noted in preclinical studies of disease. Given the complexity of selenium biology, systems biology approaches may be necessary to reach the goal of optimization of selenium status to promote health and prevent disease.
Initial evaluation of an interactive test of sentence gist recognition.

Science.gov (United States)

Tye-Murray, N; Witt, S; Castelloe, J

1996-12-01

The laser videodisc-based Sentence Gist Recognition (SGR) test consists of sets of topically related sentences that are cued by short film clips. Clients respond to test items by selecting picture illustrations and may interact with the talker by using repair strategies when they do not recognize a test item. The two experiments, involving 40 and 35 adult subjects, respectively, indicated that the SGR may better predict subjective measures of speechreading and listening performance than more traditional audiologic sentence and nonsense syllable tests. Data from cochlear implant users indicated that the SGR accounted for a greater percentage of the variance for selected items of the Communication Profile for the Hearing-Impaired and the Speechreading Questionnaire for Cochlear-Implant Users than two other audiologic tests. As in previous work, subjects were most apt to ask the talker to repeat an utterance that they did not recognize than to ask the talker to restructure it. It is suggested that the SGR may reflect the interactive nature of conversation and provide a simulated real-world listening and/or speechreading task. The principles underlaying this test are consistent with the development of other computer technologies and concepts, such as compact discinteractive and virtual reality.
Sound Synthesis and Evaluation of Interactive Footsteps for Virtual Reality Applications

DEFF Research Database (Denmark)

Nordahl, Rolf; Serafin, Stefania; Turchet, Luca

2010-01-01

A system to synthesize in real-time the sound of footsteps on different materials is presented. The system is based on microphones which allow the user to interact with his own footwear. This solution distinguishes our system from previous efforts that require specific shoes enhanced with sensors...
[Drug-Drug Interactions with Consideration of Pharmacogenetics].

Science.gov (United States)

Ozawa, Shogo

2018-01-01

　Elderly patients often suffer from a variety of diseases and therefore may be prescribed several kinds of drugs. Interactions between these drugs may cause problems in some patients. Guidelines for drug interactions were released on July 8, 2014 "Drug Interaction Guideline for Drug Development and Labeling Recommendations (Final Draft)". These guidelines include the theoretical basis for evaluating the mechanisms of drug interaction, the possible extent of drug interactions, and take into consideration special populations (e.g., infants, children, elderly patients, patients with hepatic or renal dysfunction, and subjects with minor deficient alleles for drug metabolizing enzymes and drug transporters). In this symposium article, I discuss this last special population: altered drug metabolism and drug interactions in subjects with minor alleles of genes encoding deficient drug metabolizing enzymes. I further discuss a drug label for eliglustat (Cerdelga) with instructions for patients with ultra-rapid, extensive, intermediate, and poor metabolizer phenotypes that arise from different CYP2D6 gene alleles.
Interactive Graph Layout of a Million Nodes

Directory of Open Access Journals (Sweden)

Peng Mi

2016-12-01

Full Text Available Sensemaking of large graphs, specifically those with millions of nodes, is a crucial task in many fields. Automatic graph layout algorithms, augmented with real-time human-in-the-loop interaction, can potentially support sensemaking of large graphs. However, designing interactive algorithms to achieve this is challenging. In this paper, we tackle the scalability problem of interactive layout of large graphs, and contribute a new GPU-based force-directed layout algorithm that exploits graph topology. This algorithm can interactively layout graphs with millions of nodes, and support real-time interaction to explore alternative graph layouts. Users can directly manipulate the layout of vertices in a force-directed fashion. The complexity of traditional repulsive force computation is reduced by approximating calculations based on the hierarchical structure of multi-level clustered graphs. We evaluate the algorithm performance, and demonstrate human-in-the-loop layout in two sensemaking case studies. Moreover, we summarize lessons learned for designing interactive large graph layout algorithms on the GPU.

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