WorldWideScience

Sample records for based gene-gene interactions

  1. Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies

    Directory of Open Access Journals (Sweden)

    Lehr Thorsten

    2011-03-01

    Full Text Available Abstract Background Several methods have been presented for the analysis of complex interactions between genetic polymorphisms and/or environmental factors. Despite the available methods, there is still a need for alternative methods, because no single method will perform well in all scenarios. The aim of this work was to evaluate the performance of three selected rule based classifier algorithms, RIPPER, RIDOR and PART, for the analysis of genetic association studies. Methods Overall, 42 datasets were simulated with three different case-control models, a varying number of subjects (300, 600, SNPs (500, 1500, 3000 and noise (5%, 10%, 20%. The algorithms were applied to each of the datasets with a set of algorithm-specific settings. Results were further investigated with respect to a the Model, b the Rules, and c the Attribute level. Data analysis was performed using WEKA, SAS and PERL. Results The RIPPER algorithm discovered the true case-control model at least once in >33% of the datasets. The RIDOR and PART algorithm performed poorly for model detection. The RIPPER, RIDOR and PART algorithm discovered the true case-control rules in more than 83%, 83% and 44% of the datasets, respectively. All three algorithms were able to detect the attributes utilized in the respective case-control models in most datasets. Conclusions The current analyses substantiate the utility of rule based classifiers such as RIPPER, RIDOR and PART for the detection of gene-gene/gene-environment interactions in genetic association studies. These classifiers could provide a valuable new method, complementing existing approaches, in the analysis of genetic association studies. The methods provide an advantage in being able to handle both categorical and continuous variable types. Further, because the outputs of the analyses are easy to interpret, the rule based classifier approach could quickly generate testable hypotheses for additional evaluation. Since the algorithms are

  2. HSD3B and gene-gene interactions in a pathway-based analysis of genetic susceptibility to bladder cancer.

    Directory of Open Access Journals (Sweden)

    Angeline S Andrew

    Full Text Available Bladder cancer is the 4(th most common cancer among men in the U.S. We analyzed variant genotypes hypothesized to modify major biological processes involved in bladder carcinogenesis, including hormone regulation, apoptosis, DNA repair, immune surveillance, metabolism, proliferation, and telomere maintenance. Logistic regression was used to assess the relationship between genetic variation affecting these processes and susceptibility in 563 genotyped urothelial cell carcinoma cases and 863 controls enrolled in a case-control study of incident bladder cancer conducted in New Hampshire, U.S. We evaluated gene-gene interactions using Multifactor Dimensionality Reduction (MDR and Statistical Epistasis Network analysis. The 3'UTR flanking variant form of the hormone regulation gene HSD3B2 was associated with increased bladder cancer risk in the New Hampshire population (adjusted OR 1.85 95%CI 1.31-2.62. This finding was successfully replicated in the Texas Bladder Cancer Study with 957 controls, 497 cases (adjusted OR 3.66 95%CI 1.06-12.63. The effect of this prevalent SNP was stronger among males (OR 2.13 95%CI 1.40-3.25 than females (OR 1.56 95%CI 0.83-2.95, (SNP-gender interaction P = 0.048. We also identified a SNP-SNP interaction between T-cell activation related genes GATA3 and CD81 (interaction P = 0.0003. The fact that bladder cancer incidence is 3-4 times higher in males suggests the involvement of hormone levels. This biologic process-based analysis suggests candidate susceptibility markers and supports the theory that disrupted hormone regulation plays a role in bladder carcinogenesis.

  3. GEGEINTOOL: A Computer-Based Tool for Automated Analysis of Gene-Gene Interactions in Large Epidemiological Studies in Cardiovascular Genomics

    OpenAIRE

    Oscar Coltell; José M. Ordovás; Carmen Saiz; Manuel Forner; Francisco Gabriel; Dolores Corella

    2013-01-01

    Current methods of data analysis of gene-gene interactions in complex diseases, after taking into account environmental factors using traditional approaches, are inefficient. High-throughput methods of analysis in large scale studies including thousands of subjects and hundreds of SNPs should be implemented. We developed an integrative computer tool, GEGEINTOOL (GEne- GEne INTeraction tOOL), for large-scale analysis of gene-gene interactions, in human studies of complex diseases including a l...

  4. A novel method to identify high order gene-gene interactions in genome-wide association studies: Gene-based MDR

    OpenAIRE

    Oh Sohee; Lee Jaehoon; Kwon Min-Seok; Weir Bruce; Ha Kyooseob; Park Taesung

    2012-01-01

    Abstract Background Because common complex diseases are affected by multiple genes and environmental factors, it is essential to investigate gene-gene and/or gene-environment interactions to understand genetic architecture of complex diseases. After the great success of large scale genome-wide association (GWA) studies using the high density single nucleotide polymorphism (SNP) chips, the study of gene-gene interaction becomes a next challenge. Multifactor dimensionality reduction (MDR) analy...

  5. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions

    OpenAIRE

    Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

    2015-01-01

    Background Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. Methods In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using IN...

  6. Extracting gene-gene interactions through curve fitting.

    Science.gov (United States)

    Das, Ranajit; Mitra, Sushmita; Murthy, C A

    2012-12-01

    This paper presents a simple and novel curve fitting approach for generating simple gene regulatory subnetworks from time series gene expression data. Microarray experiments simultaneously generate massive data sets and help immensely in the large-scale study of gene expression patterns. Initial biclustering reduces the search space in the high-dimensional microarray data. The least-squares error between fitting of gene pairs is minimized to extract a set of gene-gene interactions, involving transcriptional regulation of genes. The higher error values are eliminated to retain only the strong interacting gene pairs in the resultant gene regulatory subnetwork. Next the algorithm is extended to a generalized framework to enhance its capability. The methodology takes care of the higher-order dependencies involving multiple genes co-regulating a single gene, while eliminating the need for user-defined parameters. It has been applied to the time-series Yeast data, and the experimental results biologically validated using standard databases and literature. PMID:22997274

  7. Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines

    Science.gov (United States)

    Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

    2015-01-01

    Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM. PMID:25987962

  8. Effects related to gene-gene interactions of peroxisome proliferator-activated receptor on essential hypertension

    Institute of Scientific and Technical Information of China (English)

    俞浩

    2013-01-01

    Objective To explore the impact of the gene-gene interaction among the single nucleotide polymorphisms(SNPs) of peroxisome proliferator-activated receptorα/δ/γ on essential hypertension(EH).Methods

  9. A review for detecting gene-gene interactions using machine learning methods in genetic epidemiology.

    Science.gov (United States)

    Koo, Ching Lee; Liew, Mei Jing; Mohamad, Mohd Saberi; Salleh, Abdul Hakim Mohamed

    2013-01-01

    Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs), support vector machine (SVM), and random forests (RFs) in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease. PMID:24228248

  10. A Combinatorial Approach to Detecting Gene-Gene and Gene-Environment Interactions in Family Studies

    OpenAIRE

    Lou, Xiang-Yang; Chen, Guo-Bo; Yan, Lei; Ma, Jennie Z.; Mangold, Jamie E.; Zhu, Jun; Elston, Robert C.; Li, Ming D.

    2008-01-01

    Widespread multifactor interactions present a significant challenge in determining risk factors of complex diseases. Several combinatorial approaches, such as the multifactor dimensionality reduction (MDR) method, have emerged as a promising tool for better detecting gene-gene (G × G) and gene-environment (G × E) interactions. We recently developed a general combinatorial approach, namely the generalized multifactor dimensionality reduction (GMDR) method, which can entertain both qualitative ...

  11. A Review for Detecting Gene-Gene Interactions Using Machine Learning Methods in Genetic Epidemiology

    OpenAIRE

    Ching Lee Koo; Mei Jing Liew; Mohd Saberi Mohamad; Abdul Hakim Mohamed Salleh

    2013-01-01

    Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learn...

  12. Gene-Gene and Gene-Environment Interactions in Ulcerative Colitis

    OpenAIRE

    Wang, Ming-Hsi; FIOCCHI, CLAUDIO; Zhu, Xiaofeng; Ripke, Stephan; Kamboh, M. Ilyas; Rebert, Nancy; Duerr, Richard H.; Achkar, Jean-Paul

    2013-01-01

    Genome-wide association studies (GWAS) have identified at least 133 ulcerative colitis (UC) associated loci. The role of genetic factors in clinical practice is not clearly defined. The relevance of genetic variants to disease pathogenesis is still uncertain because of not characterized gene-gene and gene-environment interactions. We examined the predictive value of combining the 133 UC risk loci with genetic interactions in an ongoing inflammatory bowel disease (IBD) GWAS. The Wellcome Trust...

  13. Confronting the missing epistasis problem: on the reproducibility of gene-gene interactions.

    Science.gov (United States)

    Murk, William; Bracken, Michael B; DeWan, Andrew T

    2015-08-01

    Epistasis (gene-gene interaction) is thought to play an integral role in the genetic basis of complex traits, and a significant amount of research has been invested into identifying this phenomenon in human disease. However, the overall success of empirical studies of epistasis in humans is unclear, as such studies are rarely systematically evaluated. Here, we have selected asthma as an example of a well-studied, complex human disease, and provide a critical analysis and replication attempt of nearly all prior reports of epistasis for this disease. Of 191 previously reported interactions, we find that 39.8% were not originally identified using an explicit test for interaction and thus may not have been true epistatic effects to begin with. Moreover, directions of effect were not described for 46.1% of the interactions, which prevents their rigorous replication. In the original studies, attempts at replication were made for 15.2% of the interactions, and 7.3% were actually replicated. In the current study, we were able to evaluate 85.9% of the interactions using a large asthma dataset from the GABRIEL Consortium. None of these interactions could be replicated based on strict criteria. However, we found nominally significant (p < 0.05) evidence in support of 23.8% of the evaluated interactions. Although many reports of epistasis are not robustly supported in the published literature, our results suggest that at least some of these reports may have been true-positive examples of epistasis. In general, improvements in empirical studies of epistasis are called for, in order to better understand the importance of this phenomenon in human disease. PMID:25998948

  14. Maternal-fetal metabolic gene-gene interactions and risk of neural tube defects.

    Science.gov (United States)

    Lupo, Philip J; Mitchell, Laura E; Canfield, Mark A; Shaw, Gary M; Olshan, Andrew F; Finnell, Richard H; Zhu, Huiping

    2014-01-01

    Single-gene analyses indicate that maternal genes associated with metabolic conditions (e.g., obesity) may influence the risk of neural tube defects (NTDs). However, to our knowledge, there have been no assessments of maternal-fetal metabolic gene-gene interactions and NTDs. We investigated 23 single nucleotide polymorphisms among 7 maternal metabolic genes (ADRB3, ENPP1, FTO, LEP, PPARG, PPARGC1A, and TCF7L2) and 2 fetal metabolic genes (SLC2A2 and UCP2). Samples were obtained from 737 NTD case-parent triads included in the National Birth Defects Prevention Study for birth years 1999-2007. We used a 2-step approach to evaluate maternal-fetal gene-gene interactions. First, a case-only approach was applied to screen all potential maternal and fetal interactions (n = 76), as this design provides greater power in the assessment of gene-gene interactions compared to other approaches. Specifically, ordinal logistic regression was used to calculate the odds ratio (OR) and 95% confidence interval (CI) for each maternal-fetal gene-gene interaction, assuming a log-additive model of inheritance. Due to the number of comparisons, we calculated a corrected p-value (q-value) using the false discovery rate. Second, we confirmed all statistically significant interactions (q < 0.05) using a log-linear approach among case-parent triads. In step 1, there were 5 maternal-fetal gene-gene interactions with q < 0.05. The "top hit" was an interaction between maternal ENPP1 rs1044498 and fetal SLC2A2 rs6785233 (interaction OR = 3.65, 95% CI: 2.32-5.74, p = 2.09×10(-8), q=0.001), which was confirmed in step 2 (p = 0.00004). Our findings suggest that maternal metabolic genes associated with hyperglycemia and insulin resistance and fetal metabolic genes involved in glucose homeostasis may interact to increase the risk of NTDs. PMID:24332798

  15. Identification of Significant Association and Gene-Gene Interaction of GABA Receptor Subunit Genes in Autism

    OpenAIRE

    Ma, D Q; Whitehead, P. L.; Menold, M M; Martin, E. R.; Ashley-Koch, A. E.; Mei, H; Ritchie, M. D.; Delong, G R; Abramson, R.K.; Wright, H. H.; Cuccaro, M. L.; Hussman, J. P.; Gilbert, J.R.; Pericak-Vance, M A

    2005-01-01

    Autism is a common neurodevelopmental disorder with a significant genetic component. Existing research suggests that multiple genes contribute to autism and that epigenetic effects or gene-gene interactions are likely contributors to autism risk. However, these effects have not yet been identified. Gamma-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the adult brain, has been implicated in autism etiology. Fourteen known autosomal GABA receptor subunit genes were studied...

  16. Powerful tests for detecting a gene effect in the presence of possible gene-gene interactions using garrote kernel machines

    OpenAIRE

    Maity, Arnab; Lin, Xihong

    2011-01-01

    We propose in this paper a powerful testing procedure for detecting a gene effect on a continuous outcome in the presence of possible gene-gene interactions (epistasis) in a gene set, e.g. a genetic pathway or network. Traditional tests for this purpose require a large number of degrees of freedom by testing the main effect and all the corresponding interactions under a parametric assumption, and hence suffer from low power. In this paper, we propose a powerful kernel machine based test. Spec...

  17. Genome-wide search identifies a gene-gene interaction between 20p13 and 2q14 in asthma

    OpenAIRE

    Murk, William; DeWan, Andrew T.

    2016-01-01

    Background Many studies have attempted to identify gene-gene interactions affecting asthma susceptibility. However, these studies have typically used candidate gene approaches in limiting the genetic search space, and there have been few searches for gene-gene interactions on a genome-wide scale. We aimed to conduct a genome-wide gene-gene interaction study for asthma, using data from the GABRIEL Consortium. Results A two-stage study design was used, including a screening analysis (N = 1625 s...

  18. Molecular Basis of Gene-Gene Interaction: Cyclic Cross-Regulation of Gene Expression and Post-GWAS Gene-Gene Interaction Involved in Atrial Fibrillation

    Science.gov (United States)

    Xu, Chengqi; Zhang, Hongfu; Lu, Qiulun; Chang, Le; Wang, Fan; Wang, Pengxia; Zhang, Rongfeng; Hu, Zhenkun; Song, Qixue; Yang, Xiaowei; Li, Cong; Li, Sisi; Zhao, Yuanyuan; Yang, Qin; Yin, Dan; Wang, Xiaojing; Si, Wenxia; Li, Xiuchun; Xiong, Xin; Wang, Dan; Huang, Yuan; Luo, Chunyan; Li, Jia; Wang, Jingjing; Chen, Jing; Wang, Longfei; Wang, Li; Han, Meng; Ye, Jian; Chen, Feifei; Liu, Jingqiu; Liu, Ying; Wu, Gang; Yang, Bo; Cheng, Xiang; Liao, Yuhua; Wu, Yanxia; Ke, Tie; Chen, Qiuyun; Tu, Xin; Elston, Robert; Rao, Shaoqi; Yang, Yanzong; Xia, Yunlong; Wang, Qing K.

    2015-01-01

    Atrial fibrillation (AF) is the most common cardiac arrhythmia at the clinic. Recent GWAS identified several variants associated with AF, but they account for <10% of heritability. Gene-gene interaction is assumed to account for a significant portion of missing heritability. Among GWAS loci for AF, only three were replicated in the Chinese Han population, including SNP rs2106261 (G/A substitution) in ZFHX3, rs2200733 (C/T substitution) near PITX2c, and rs3807989 (A/G substitution) in CAV1. Thus, we analyzed the interaction among these three AF loci. We demonstrated significant interaction between rs2106261 and rs2200733 in three independent populations and combined population with 2,020 cases/5,315 controls. Compared to non-risk genotype GGCC, two-locus risk genotype AATT showed the highest odds ratio in three independent populations and the combined population (OR=5.36 (95% CI 3.87-7.43), P=8.00×10-24). The OR of 5.36 for AATT was significantly higher than the combined OR of 3.31 for both GGTT and AACC, suggesting a synergistic interaction between rs2106261 and rs2200733. Relative excess risk due to interaction (RERI) analysis also revealed significant interaction between rs2106261 and rs2200733 when exposed two copies of risk alleles (RERI=2.87, P<1.00×10-4) or exposed to one additional copy of risk allele (RERI=1.29, P<1.00×10-4). The INTERSNP program identified significant genotypic interaction between rs2106261 and rs2200733 under an additive by additive model (OR=0.85, 95% CI: 0.74-0.97, P=0.02). Mechanistically, PITX2c negatively regulates expression of miR-1, which negatively regulates expression of ZFHX3, resulting in a positive regulation of ZFHX3 by PITX2c; ZFHX3 positively regulates expression of PITX2C, resulting in a cyclic loop of cross-regulation between ZFHX3 and PITX2c. Both ZFHX3 and PITX2c regulate expression of NPPA, TBX5 and NKX2.5. These results suggest that cyclic cross-regulation of gene expression is a molecular basis for gene-gene

  19. Using Linkage Analysis to Detect Gene-Gene Interactions. 2. Improved Reliability and Extension to More-Complex Models.

    Directory of Open Access Journals (Sweden)

    Susan E Hodge

    Full Text Available Detecting gene-gene interaction in complex diseases has become an important priority for common disease genetics, but most current approaches to detecting interaction start with disease-marker associations. These approaches are based on population allele frequency correlations, not genetic inheritance, and therefore cannot exploit the rich information about inheritance contained within families. They are also hampered by issues of rigorous phenotype definition, multiple test correction, and allelic and locus heterogeneity. We recently developed, tested, and published a powerful gene-gene interaction detection strategy based on conditioning family data on a known disease-causing allele or a disease-associated marker allele4. We successfully applied the method to disease data and used computer simulation to exhaustively test the method for some epistatic models. We knew that the statistic we developed to indicate interaction was less reliable when applied to more-complex interaction models. Here, we improve the statistic and expand the testing procedure. We computer-simulated multipoint linkage data for a disease caused by two interacting loci. We examined epistatic as well as additive models and compared them with heterogeneity models. In all our models, the at-risk genotypes are "major" in the sense that among affected individuals, a substantial proportion has a disease-related genotype. One of the loci (A has a known disease-related allele (as would have been determined from a previous analysis. We removed (pruned family members who did not carry this allele; the resultant dataset is referred to as "stratified." This elimination step has the effect of raising the "penetrance" and detectability at the second locus (B. We used the lod scores for the stratified and unstratified data sets to calculate a statistic that either indicated the presence of interaction or indicated that no interaction was detectable. We show that the new method is robust

  20. Using Linkage Analysis to Detect Gene-Gene Interactions. 2. Improved Reliability and Extension to More-Complex Models.

    Science.gov (United States)

    Hodge, Susan E; Hager, Valerie R; Greenberg, David A

    2016-01-01

    Detecting gene-gene interaction in complex diseases has become an important priority for common disease genetics, but most current approaches to detecting interaction start with disease-marker associations. These approaches are based on population allele frequency correlations, not genetic inheritance, and therefore cannot exploit the rich information about inheritance contained within families. They are also hampered by issues of rigorous phenotype definition, multiple test correction, and allelic and locus heterogeneity. We recently developed, tested, and published a powerful gene-gene interaction detection strategy based on conditioning family data on a known disease-causing allele or a disease-associated marker allele4. We successfully applied the method to disease data and used computer simulation to exhaustively test the method for some epistatic models. We knew that the statistic we developed to indicate interaction was less reliable when applied to more-complex interaction models. Here, we improve the statistic and expand the testing procedure. We computer-simulated multipoint linkage data for a disease caused by two interacting loci. We examined epistatic as well as additive models and compared them with heterogeneity models. In all our models, the at-risk genotypes are "major" in the sense that among affected individuals, a substantial proportion has a disease-related genotype. One of the loci (A) has a known disease-related allele (as would have been determined from a previous analysis). We removed (pruned) family members who did not carry this allele; the resultant dataset is referred to as "stratified." This elimination step has the effect of raising the "penetrance" and detectability at the second locus (B). We used the lod scores for the stratified and unstratified data sets to calculate a statistic that either indicated the presence of interaction or indicated that no interaction was detectable. We show that the new method is robust and reliable for

  1. Maternal-Fetal Metabolic Gene-Gene Interactions and Risk of Neural Tube Defects

    OpenAIRE

    Lupo, Philip J.; Mitchell, Laura E; Canfield, Mark A.; Shaw, Gary M.; Olshan, Andrew F.; Finnell, Richard H.; Zhu, Huiping

    2013-01-01

    Single-gene analyses indicate that maternal genes associated with metabolic conditions (e.g., obesity) may influence the risk of neural tube defects (NTDs). However, to our knowledge, there have been no assessments of maternal-fetal metabolic gene-gene interactions and NTDs. We investigated 23 single nucleotide polymorphisms among 7 maternal metabolic genes (ADRB3, ENPP1, FTO, LEP, PPARG, PPARGC1A, and TCF7L2) and 2 fetal metabolic genes (SLC2A2 and UCP2). Samples were obtained from 737 NTD c...

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

    Directory of Open Access Journals (Sweden)

    Yeonok eLee

    2013-11-01

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

  3. Spatially Uniform ReliefF (SURF for computationally-efficient filtering of gene-gene interactions

    Directory of Open Access Journals (Sweden)

    Greene Casey S

    2009-09-01

    Full Text Available Abstract Background Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be the result of single points of failure but instead likely arise from the joint failure of two or more interacting components. The hope in genome-wide screens is that these points of failure can be linked to single nucleotide polymorphisms (SNPs which confer disease susceptibility. Detecting interacting variants that lead to disease in the absence of single-gene effects is difficult however, and methods to exhaustively analyze sets of these variants for interactions are combinatorial in nature thus making them computationally infeasible. Efficient algorithms which can detect interacting SNPs are needed. ReliefF is one such promising algorithm, although it has low success rate for noisy datasets when the interaction effect is small. ReliefF has been paired with an iterative approach, Tuned ReliefF (TuRF, which improves the estimation of weights in noisy data but does not fundamentally change the underlying ReliefF algorithm. To improve the sensitivity of studies using these methods to detect small effects we introduce Spatially Uniform ReliefF (SURF. Results SURF's ability to detect interactions in this domain is significantly greater than that of ReliefF. Similarly SURF, in combination with the TuRF strategy significantly outperforms TuRF alone for SNP selection under an epistasis model. It is important to note that this success rate increase does not require an increase in algorithmic complexity and allows for increased success rate, even with the removal of a nuisance parameter from the algorithm. Conclusion Researchers performing genetic association studies and aiming to discover gene-gene interactions associated with increased disease susceptibility should use SURF in place of ReliefF. For instance, SURF should be

  4. A Pilot Study of Gene/Gene and Gene/Environment Interactions in Alzheimer Disease

    OpenAIRE

    Ghebranious, Nader; Mukesh, Bickol; Giampietro, Philip F.; Glurich, Ingrid; Mickel, Susan F.; Waring, Stephen C.; Catherine A McCarty

    2011-01-01

    Background: Although some genes associated with increased risk of Alzheimer Disease (AD) have been identified, few data exist related to gene/gene and gene/environment risk of AD. The purpose of this pilot study was to explore gene/gene and gene/environment associations in AD and to obtain data for sample size estimates for larger, more definitive studies of AD.

  5. Genome-wide search for gene-gene interactions in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Shuo Jiao

    Full Text Available Genome-wide association studies (GWAS have successfully identified a number of single-nucleotide polymorphisms (SNPs associated with colorectal cancer (CRC risk. However, these susceptibility loci known today explain only a small fraction of the genetic risk. Gene-gene interaction (GxG is considered to be one source of the missing heritability. To address this, we performed a genome-wide search for pair-wise GxG associated with CRC risk using 8,380 cases and 10,558 controls in the discovery phase and 2,527 cases and 2,658 controls in the replication phase. We developed a simple, but powerful method for testing interaction, which we term the Average Risk Due to Interaction (ARDI. With this method, we conducted a genome-wide search to identify SNPs showing evidence for GxG with previously identified CRC susceptibility loci from 14 independent regions. We also conducted a genome-wide search for GxG using the marginal association screening and examining interaction among SNPs that pass the screening threshold (p<10(-4. For the known locus rs10795668 (10p14, we found an interacting SNP rs367615 (5q21 with replication p = 0.01 and combined p = 4.19×10(-8. Among the top marginal SNPs after LD pruning (n = 163, we identified an interaction between rs1571218 (20p12.3 and rs10879357 (12q21.1 (nominal combined p = 2.51×10(-6; Bonferroni adjusted p = 0.03. Our study represents the first comprehensive search for GxG in CRC, and our results may provide new insight into the genetic etiology of CRC.

  6. Gene-gene interaction of erythropoietin gene polymorphisms and diabetic retinopathy in Chinese Han.

    Science.gov (United States)

    Fan, YanFei; Fu, Yin-Yu; Chen, Zhi; Hu, Yuan-Yuan; Shen, Jie

    2016-08-01

    The aim of this study was to investigate the association of three single nucleotide polymorphisms in the erythropoietin gene polymorphisms with diabetic retinopathy and additional role of gene-gene interaction on diabetic retinopathy risk. A total of 1193 patients (579 men, 614 women) with type 2 diabetes mellitus were selected, including 397 diabetic retinopathy patients and 796 controls (type 2 diabetes mellitus patients without diabetic retinopathy); the mean age of all participants was 56.7 ± 13.9 years. Three single nucleotide polymorphisms were selected: rs507392, rs1617640, and rs551238. The t-test was used for comparison of erythropoietin protein level erythropoietin levels in patients having different erythropoietin genotypes. Logistic regression model was used to examine the association between three single nucleotide polymorphisms and diabetic retinopathy. Odds ratio (OR) and 95% confident interval (95% CI) were calculated. Generalized multifactor dimensionality reduction was employed to analyze the impact of interaction among three single nucleotide polymorphisms on CVD risk. After covariates adjustment, the carriers of homozygous mutant of three single nucleotide polymorphisms have higher diabetic retinopathy risk than those with wild-type homozygotes, OR (95% CI) were 2.04 (1.12-2.35), 1.87 (1.10-2.41) and 1.15 (1.06-1.76), respectively. Generalized multifactor dimensionality reduction model indicated a significant three-locus model (p = 0.0010) involving rs507392, rs1617640, and rs551238. Overall, the three-locus models had a cross-validation consistency of 10 of 10, and had the testing accuracy of 60.72%. Subjects with TC or CC-TG or GG-AC or CC genotype have the highest diabetic retinopathy risk. In conclusion, our results support an important association of rs507392, rs1617640 and rs551238 minor allele of erythropoietin with increased diabetic retinopathy risk, and additional interaction among three single nucleotide polymorphisms. PMID

  7. Powerful tests for detecting a gene effect in the presence of possible gene-gene interactions using garrote kernel machines.

    Science.gov (United States)

    Maity, Arnab; Lin, Xihong

    2011-12-01

    We propose in this article a powerful testing procedure for detecting a gene effect on a continuous outcome in the presence of possible gene-gene interactions (epistasis) in a gene set, e.g., a genetic pathway or network. Traditional tests for this purpose require a large number of degrees of freedom by testing the main effect and all the corresponding interactions under a parametric assumption, and hence suffer from low power. In this article, we propose a powerful kernel machine based test. Specifically, our test is based on a garrote kernel method and is constructed as a score test. Here, the term garrote refers to an extra nonnegative parameter that is multiplied to the covariate of interest so that our score test can be formulated in terms of this nonnegative parameter. A key feature of the proposed test is that it is flexible and developed for both parametric and nonparametric models within a unified framework, and is more powerful than the standard test by accounting for the correlation among genes and hence often uses a much smaller degrees of freedom. We investigate the theoretical properties of the proposed test. We evaluate its finite sample performance using simulation studies, and apply the method to the Michigan prostate cancer gene expression data. PMID:21504419

  8. Association and gene-gene interactions study of reelin signaling pathway related genes with autism in the Han Chinese population.

    Science.gov (United States)

    Shen, Yidong; Xun, Guanglei; Guo, Hui; He, Yiqun; Ou, Jianjun; Dong, Huixi; Xia, Kun; Zhao, Jingping

    2016-04-01

    Autism is a neurodevelopmental disorder with unclear etiology. Reelin had been proposed to participate in the etiology of autism due to its important role in brain development. The goal of this study was to explore the association and gene-gene interactions of reelin signaling pathway related genes (RELN, VLDLR, LRP8, DAB1, FYN, and CDK5) with autism in Han Chinese population. Genotyping data of the six genes were obtained from a recent genome-wide association study performed in 430 autistic children who fulfilled the DSM-IV-TR criteria for autistic disorder, and 1,074 healthy controls. Single marker case-control association analysis and haplotype case-control association analysis were conducted after the data was screened. Multifactor dimensionality reduction (MDR) was applied to further test gene-gene interactions. Neither the single marker nor the haplotype association tests found any significant difference between the autistic group and the control group after permutation test of 1,000 rounds. The 4-locus MDR model (comprising rs6143734, rs1858782, rs634500, and rs1924267 which belong to RELN and DAB1) was determined to be the model with the highest cross-validation consistency (CVC) and testing balanced accuracy. The results indicate that an interaction between RELN and DAB1 may increase the risk of autism in the Han Chinese population. Furthermore, it can also be inferred that the involvement of RELN in the etiology of autism would occur through interaction with DAB1. Autism Res 2016, 9: 436-442. © 2015 International Society for Autism Research, Wiley Periodicals, Inc. PMID:26285919

  9. Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene Interaction in a case-control study

    Directory of Open Access Journals (Sweden)

    Brott Marcia J

    2009-12-01

    Full Text Available Abstract Background There is a growing awareness that interaction between multiple genes play an important role in the risk of common, complex multi-factorial diseases. Many common diseases are affected by certain genotype combinations (associated with some genes and their interactions. The identification and characterization of these susceptibility genes and gene-gene interaction have been limited by small sample size and large number of potential interactions between genes. Several methods have been proposed to detect gene-gene interaction in a case control study. The penalized logistic regression (PLR, a variant of logistic regression with L2 regularization, is a parametric approach to detect gene-gene interaction. On the other hand, the Multifactor Dimensionality Reduction (MDR is a nonparametric and genetic model-free approach to detect genotype combinations associated with disease risk. Methods We compared the power of MDR and PLR for detecting two-way and three-way interactions in a case-control study through extensive simulations. We generated several interaction models with different magnitudes of interaction effect. For each model, we simulated 100 datasets, each with 200 cases and 200 controls and 20 SNPs. We considered a wide variety of models such as models with just main effects, models with only interaction effects or models with both main and interaction effects. We also compared the performance of MDR and PLR to detect gene-gene interaction associated with acute rejection(AR in kidney transplant patients. Results In this paper, we have studied the power of MDR and PLR for detecting gene-gene interaction in a case-control study through extensive simulation. We have compared their performances for different two-way and three-way interaction models. We have studied the effect of different allele frequencies on these methods. We have also implemented their performance on a real dataset. As expected, none of these methods were

  10. A model of gene-gene and gene-environment interactions and its implications for targeting environmental interventions by genotype

    Directory of Open Access Journals (Sweden)

    Wallace Helen M

    2006-10-01

    Full Text Available Abstract Background The potential public health benefits of targeting environmental interventions by genotype depend on the environmental and genetic contributions to the variance of common diseases, and the magnitude of any gene-environment interaction. In the absence of prior knowledge of all risk factors, twin, family and environmental data may help to define the potential limits of these benefits in a given population. However, a general methodology to analyze twin data is required because of the potential importance of gene-gene interactions (epistasis, gene-environment interactions, and conditions that break the 'equal environments' assumption for monozygotic and dizygotic twins. Method A new model for gene-gene and gene-environment interactions is developed that abandons the assumptions of the classical twin study, including Fisher's (1918 assumption that genes act as risk factors for common traits in a manner necessarily dominated by an additive polygenic term. Provided there are no confounders, the model can be used to implement a top-down approach to quantifying the potential utility of genetic prediction and prevention, using twin, family and environmental data. The results describe a solution space for each disease or trait, which may or may not include the classical twin study result. Each point in the solution space corresponds to a different model of genotypic risk and gene-environment interaction. Conclusion The results show that the potential for reducing the incidence of common diseases using environmental interventions targeted by genotype may be limited, except in special cases. The model also confirms that the importance of an individual's genotype in determining their risk of complex diseases tends to be exaggerated by the classical twin studies method, owing to the 'equal environments' assumption and the assumption of no gene-environment interaction. In addition, if phenotypes are genetically robust, because of epistasis

  11. Genome-wide gene-gene interaction analysis for next-generation sequencing.

    Science.gov (United States)

    Zhao, Jinying; Zhu, Yun; Xiong, Momiao

    2016-03-01

    The critical barrier in interaction analysis for next-generation sequencing (NGS) data is that the traditional pairwise interaction analysis that is suitable for common variants is difficult to apply to rare variants because of their prohibitive computational time, large number of tests and low power. The great challenges for successful detection of interactions with NGS data are (1) the demands in the paradigm of changes in interaction analysis; (2) severe multiple testing; and (3) heavy computations. To meet these challenges, we shift the paradigm of interaction analysis between two SNPs to interaction analysis between two genomic regions. In other words, we take a gene as a unit of analysis and use functional data analysis techniques as dimensional reduction tools to develop a novel statistic to collectively test interaction between all possible pairs of SNPs within two genome regions. By intensive simulations, we demonstrate that the functional logistic regression for interaction analysis has the correct type 1 error rates and higher power to detect interaction than the currently used methods. The proposed method was applied to a coronary artery disease dataset from the Wellcome Trust Case Control Consortium (WTCCC) study and the Framingham Heart Study (FHS) dataset, and the early-onset myocardial infarction (EOMI) exome sequence datasets with European origin from the NHLBI's Exome Sequencing Project. We discovered that 6 of 27 pairs of significantly interacted genes in the FHS were replicated in the independent WTCCC study and 24 pairs of significantly interacted genes after applying Bonferroni correction in the EOMI study. PMID:26173972

  12. Quantitative Multifactor Dimensionality Reduction Method for Detecting Gene-Gene Interaction

    OpenAIRE

    Gilbert-Diamond, Diane; Andrews, Peter; Moore, Jason H.; Gui, Jiang

    2013-01-01

    Background and Objective: The problem of identifying SNP-SNP interactions in case-control studies has been studied extensively and a number of new techniques have been developed. Little progress has been made, however in the analysis of SNP-SNP interactions in relation to continuous data. Methods: 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 Quantita...

  13. GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

    Directory of Open Access Journals (Sweden)

    Wang Kai

    2011-05-01

    Full Text Available Abstract Background Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs have multiple cores, whereas Graphics Processing Units (GPUs also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Findings Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1 the interaction of SNPs within it in parallel, and 2 the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. Conclusions GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.

  14. GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

    Science.gov (United States)

    2011-01-01

    Background Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Findings Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. Conclusions GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/. PMID:21615923

  15. Dominance from the perspective of gene-gene and gene-chemical interactions.

    Science.gov (United States)

    Gladki, Arkadiusz; Zielenkiewicz, Piotr; Kaczanowski, Szymon

    2016-02-01

    In this study, we used genetic interaction (GI) and gene-chemical interaction (GCI) data to compare mutations with different dominance phenotypes. Our analysis focused primarily on Saccharomyces cerevisiae, where haploinsufficient genes (HI; genes with dominant loss-of-function mutations) were found to be participating in gene expression processes, namely, the translation and regulation of gene transcription. Non-ribosomal HI genes (mainly regulators of gene transcription) were found to have more GIs and GCIs than haplosufficient (HS) genes. Several properties seem to lead to the enrichment of interactions, most notably, the following: importance, pleiotropy, gene expression level and gene expression variation. Importantly, after these properties were appropriately considered in the analysis, the correlation between dominance and GI/GCI degrees was still observed. Strikingly, for the GCIs of heterozygous strains, haploinsufficiency was the only property significantly correlated with the number of GCIs. We found ribosomal HI genes to be depleted in GIs/GCIs. This finding can be explained by their high variation in gene expression under different genetic backgrounds and environmental conditions. We observed the same distributions of GIs among non-ribosomal HI, ribosomal HI and HS genes in three other species: Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens. One potentially interesting exception was the lack of significant differences in the degree of GIs between non-ribosomal HI and HS genes in Schizosaccharomyces pombe. PMID:26613610

  16. Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks.

    Directory of Open Access Journals (Sweden)

    Stephen D Turner

    Full Text Available Genome-wide association studies (GWAS are routinely being used to examine the genetic contribution to complex human traits, such as high-density lipoprotein cholesterol (HDL-C. Although HDL-C levels are highly heritable (h(2∼0.7, the genetic determinants identified through GWAS contribute to a small fraction of the variance in this trait. Reasons for this discrepancy may include rare variants, structural variants, gene-environment (GxE interactions, and gene-gene (GxG interactions. Clinical practice-based biobanks now allow investigators to address these challenges by conducting GWAS in the context of comprehensive electronic medical records (EMRs. Here we apply an EMR-based phenotyping approach, within the context of routine care, to replicate several known associations between HDL-C and previously characterized genetic variants: CETP (rs3764261, p = 1.22e-25, LIPC (rs11855284, p = 3.92e-14, LPL (rs12678919, p = 1.99e-7, and the APOA1/C3/A4/A5 locus (rs964184, p = 1.06e-5, all adjusted for age, gender, body mass index (BMI, and smoking status. By using a novel approach which censors data based on relevant co-morbidities and lipid modifying medications to construct a more rigorous HDL-C phenotype, we identified an association between HDL-C and TRIB1, a gene which previously resisted identification in studies with larger sample sizes. Through the application of additional analytical strategies incorporating biological knowledge, we further identified 11 significant GxG interaction models in our discovery cohort, 8 of which show evidence of replication in a second biobank cohort. The strongest predictive model included a pairwise interaction between LPL (which modulates the incorporation of triglyceride into HDL and ABCA1 (which modulates the incorporation of free cholesterol into HDL. These results demonstrate that gene-gene interactions modulate complex human traits, including HDL cholesterol.

  17. Evidence of gene-gene interaction and age-at-diagnosis effects in type 1 diabetes

    DEFF Research Database (Denmark)

    Howson, Joanna M M; Cooper, Jason D; Smyth, Deborah J; Walker, Neil M; Stevens, Helen; She, Jin-Xiong; Eisenbarth, George S; Rewers, Marian; Todd, John A; Akolkar, Beena; Concannon, Patrick; Erlich, Henry A; Julier, Cécile; Morahan, Grant; Nerup, Jørn; Nierras, Concepcion; Pociot, Flemming; Rich, Stephen S

    2012-01-01

    The common genetic loci that independently influence the risk of type 1 diabetes have largely been determined. Their interactions with age-at-diagnosis of type 1 diabetes, sex, or the major susceptibility locus, HLA class II, remain mostly unexplored. A large collection of more than 14,866 type 1...... diabetes samples (6,750 British diabetic individuals and 8,116 affected family samples of European descent) were genotyped at 38 confirmed type 1 diabetes-associated non-HLA regions and used to test for interaction of association with age-at-diagnosis, sex, and HLA class II genotypes using regression...... models. The alleles that confer susceptibility to type 1 diabetes at interleukin-2 (IL-2), IL2/4q27 (rs2069763) and renalase, FAD-dependent amine oxidase (RNLS)/10q23.31 (rs10509540), were associated with a lower age-at-diagnosis (P = 4.6 × 10⁻⁶ and 2.5 × 10⁻⁵, respectively). For both loci, individuals...

  18. High Order Gene-Gene Interactions in Eight Single Nucleotide Polymorphisms of Renin-Angiotensin System Genes for Hypertension Association Study

    Directory of Open Access Journals (Sweden)

    Cheng-Hong Yang

    2015-01-01

    Full Text Available Several single nucleotide polymorphisms (SNPs of renin-angiotensin system (RAS genes are associated with hypertension (HT but most of them are focusing on single locus effects. Here, we introduce an unbalanced function based on multifactor dimensionality reduction (MDR for multiloci genotypes to detect high order gene-gene (SNP-SNP interaction in unbalanced cases and controls of HT data. Eight SNPs of three RAS genes (angiotensinogen, AGT; angiotensin-converting enzyme, ACE; angiotensin II type 1 receptor, AT1R in HT and non-HT subjects were included that showed no significant genotype differences. In 2- to 6-locus models of the SNP-SNP interaction, the SNPs of AGT and ACE genes were associated with hypertension (bootstrapping odds ratio [Boot-OR] = 1.972~3.785; 95%, confidence interval (CI 1.26~6.21; P<0.005. In 7- and 8-locus model, SNP A1166C of AT1R gene is joined to improve the maximum Boot-OR values of 4.050 to 4.483; CI = 2.49 to 7.29; P<1.63E−08. In conclusion, the epistasis networks are identified by eight SNP-SNP interaction models. AGT, ACE, and AT1R genes have overall effects with susceptibility to hypertension, where the SNPs of ACE have a mainly hypertension-associated effect and show an interacting effect to SNPs of AGT and AT1R genes.

  19. Neural networks for modeling gene-gene interactions in association studies

    Directory of Open Access Journals (Sweden)

    Bammann Karin

    2009-12-01

    Full Text Available Abstract Background Our aim is to investigate the ability of neural networks to model different two-locus disease models. We conduct a simulation study to compare neural networks with two standard methods, namely logistic regression models and multifactor dimensionality reduction. One hundred data sets are generated for each of six two-locus disease models, which are considered in a low and in a high risk scenario. Two models represent independence, one is a multiplicative model, and three models are epistatic. For each data set, six neural networks (with up to five hidden neurons and five logistic regression models (the null model, three main effect models, and the full model with two different codings for the genotype information are fitted. Additionally, the multifactor dimensionality reduction approach is applied. Results The results show that neural networks are more successful in modeling the structure of the underlying disease model than logistic regression models in most of the investigated situations. In our simulation study, neither logistic regression nor multifactor dimensionality reduction are able to correctly identify biological interaction. Conclusions Neural networks are a promising tool to handle complex data situations. However, further research is necessary concerning the interpretation of their parameters.

  20. Discovery of gene-gene interactions across multiple independent data sets of late onset Alzheimer disease from the Alzheimer Disease Genetics Consortium.

    Science.gov (United States)

    Hohman, Timothy J; Bush, William S; Jiang, Lan; Brown-Gentry, Kristin D; Torstenson, Eric S; Dudek, Scott M; Mukherjee, Shubhabrata; Naj, Adam; Kunkle, Brian W; Ritchie, Marylyn D; Martin, Eden R; Schellenberg, Gerard D; Mayeux, Richard; Farrer, Lindsay A; Pericak-Vance, Margaret A; Haines, Jonathan L; Thornton-Wells, Tricia A

    2016-02-01

    Late-onset Alzheimer disease (AD) has a complex genetic etiology, involving locus heterogeneity, polygenic inheritance, and gene-gene interactions; however, the investigation of interactions in recent genome-wide association studies has been limited. We used a biological knowledge-driven approach to evaluate gene-gene interactions for consistency across 13 data sets from the Alzheimer Disease Genetics Consortium. Fifteen single nucleotide polymorphism (SNP)-SNP pairs within 3 gene-gene combinations were identified: SIRT1 × ABCB1, PSAP × PEBP4, and GRIN2B × ADRA1A. In addition, we extend a previously identified interaction from an endophenotype analysis between RYR3 × CACNA1C. Finally, post hoc gene expression analyses of the implicated SNPs further implicate SIRT1 and ABCB1, and implicate CDH23 which was most recently identified as an AD risk locus in an epigenetic analysis of AD. The observed interactions in this article highlight ways in which genotypic variation related to disease may depend on the genetic context in which it occurs. Further, our results highlight the utility of evaluating genetic interactions to explain additional variance in AD risk and identify novel molecular mechanisms of AD pathogenesis. PMID:26827652

  1. MDM2 SNP309, gene-gene interaction, and tumor susceptibility: an updated meta-analysis

    Directory of Open Access Journals (Sweden)

    Wu Wei

    2011-05-01

    Full Text Available Abstract Background The tumor suppressor gene p53 is involved in multiple cellular pathways including apoptosis, transcriptional control, and cell cycle regulation. In the last decade it has been demonstrated that the single nucleotide polymorphism (SNP at codon 72 of the p53 gene is associated with the risk for development of various neoplasms. MDM2 SNP309 is a single nucleotide T to G polymorphism located in the MDM2 gene promoter. From the time that this well-characterized functional polymorphism was identified, a variety of case-control studies have been published that investigate the possible association between MDM2 SNP309 and cancer risk. However, the results of the published studies, as well as the subsequent meta-analyses, remain contradictory. Methods To investigate whether currently published epidemiological studies can clarify the potential interaction between MDM2 SNP309 and the functional genetic variant in p53 codon72 (Arg72Pro and p53 mutation status, we performed a meta-analysis of the risk estimate on 27,813 cases with various tumor types and 30,295 controls. Results The data we reviewed indicated that variant homozygote 309GG and heterozygote 309TG were associated with a significant increased risk of all tumor types (homozygote comparison: odds ratio (OR = 1.25, 95% confidence interval (CI = 1.13-1.37; heterozygote comparison: OR = 1.10, 95% CI = 1.03-1.17. We also found that the combination of GG and Pro/Pro, TG and Pro/Pro, GG and Arg/Arg significantly increased the risk of cancer (OR = 3.38, 95% CI = 1.77-6.47; OR = 1.88, 95% CI = 1.26-2.81; OR = 1.96, 95% CI = 1.01-3.78, respectively. In a stratified analysis by tumor location, we also found a significant increased risk in brain, liver, stomach and uterus cancer (OR = 1.47, 95% CI = 1.06-2.03; OR = 2.24, 95%CI = 1.57-3.18; OR = 1.54, 95%CI = 1.04-2.29; OR = 1.34, 95%CI = 1.07-1.29, respectively. However, no association was seen between MDM2 SNP309 and tumor susceptibility

  2. MDM2 SNP309, gene-gene interaction, and tumor susceptibility: an updated meta-analysis

    International Nuclear Information System (INIS)

    The tumor suppressor gene p53 is involved in multiple cellular pathways including apoptosis, transcriptional control, and cell cycle regulation. In the last decade it has been demonstrated that the single nucleotide polymorphism (SNP) at codon 72 of the p53 gene is associated with the risk for development of various neoplasms. MDM2 SNP309 is a single nucleotide T to G polymorphism located in the MDM2 gene promoter. From the time that this well-characterized functional polymorphism was identified, a variety of case-control studies have been published that investigate the possible association between MDM2 SNP309 and cancer risk. However, the results of the published studies, as well as the subsequent meta-analyses, remain contradictory. To investigate whether currently published epidemiological studies can clarify the potential interaction between MDM2 SNP309 and the functional genetic variant in p53 codon72 (Arg72Pro) and p53 mutation status, we performed a meta-analysis of the risk estimate on 27,813 cases with various tumor types and 30,295 controls. The data we reviewed indicated that variant homozygote 309GG and heterozygote 309TG were associated with a significant increased risk of all tumor types (homozygote comparison: odds ratio (OR) = 1.25, 95% confidence interval (CI) = 1.13-1.37; heterozygote comparison: OR = 1.10, 95% CI = 1.03-1.17). We also found that the combination of GG and Pro/Pro, TG and Pro/Pro, GG and Arg/Arg significantly increased the risk of cancer (OR = 3.38, 95% CI = 1.77-6.47; OR = 1.88, 95% CI = 1.26-2.81; OR = 1.96, 95% CI = 1.01-3.78, respectively). In a stratified analysis by tumor location, we also found a significant increased risk in brain, liver, stomach and uterus cancer (OR = 1.47, 95% CI = 1.06-2.03; OR = 2.24, 95%CI = 1.57-3.18; OR = 1.54, 95%CI = 1.04-2.29; OR = 1.34, 95%CI = 1.07-1.29, respectively). However, no association was seen between MDM2 SNP309 and tumor susceptibility in the stratified analysis by p53 mutation status

  3. Using the Generalized Index of Dissimilarity to Detect Gene-Gene Interactions in Multi-Class Phenotypes.

    Science.gov (United States)

    Yee, Jaeyong; Kim, Yongkang; Park, Taesung; Park, Mira

    2016-01-01

    To find genetic association between complex diseases and phenotypic traits, one important procedure is conducting a joint analysis. Multifactor dimensionality reduction (MDR) is an efficient method of examining the interactions between genes in genetic association studies. It commonly assumes a dichotomous classification of the binary phenotypes. Its usual approach to determining the genomic association is to construct a confusion matrix to estimate a classification error, where a binary risk status is determined and assigned to each genotypic multifactor class. While multi-class phenotypes are commonly observed, the current MDR approach does not handle these phenotypes appropriately because the thresholds for the risk statuses may not be clear. In this study, we suggest a new method for estimating gene-gene interactions for multi-class phenotypes. Our approach adopts the index of dissimilarity (IDS) as an evaluation measure. This is analytically equivalent to the common association measure of balanced accuracy (BA) for the binary traits, while it is not required to determine the risk status for the estimation. Moreover, it is easily expandable to the generalized index of dissimilarity (GIDS), which has an explicit form that can handle any number of categories. The performance of the proposed method was compared with those of other approaches via simulation studies in which fifteen genetic models were generated with three class outcomes. A consistently better performance was observed using the proposed method. The effect of a varying number of categories was examined. The proposed method was also illustrated using real genome-wide association studies (GWAS) data from the Korean Association Resource (KARE) project. PMID:27556585

  4. Gene-gene-environment interactions between drugs, transporters, receptors, and metabolizing enzymes: Statins, SLCO1B1, and CYP3A4 as an example.

    Science.gov (United States)

    Sadee, Wolfgang

    2013-09-01

    Pharmacogenetic biomarker tests include mostly specific single gene-drug pairs, capable of accounting for a portion of interindividual variability in drug response and toxicity. However, multiple genes are likely to contribute, either acting independently or epistatically, with the CYP2C9-VKORC1-warfarin test panel, an example of a clinically used gene-gene-dug interaction. I discuss here further instances of gene-gene-drug interactions, including a proposed dynamic effect on statin therapy by genetic variants in both a transporter (SLCO1B1) and a metabolizing enzyme (CYP3A4) in liver cells, the main target site where statins block cholesterol synthesis. These examples set a conceptual framework for developing diagnostic panels involving multiple gene-drug combinations. PMID:23436703

  5. A gene-gene interaction between polymorphisms in the OCT2 and MATE1 genes influences the renal clearance of metformin

    DEFF Research Database (Denmark)

    Hougaard Christensen, Mette Marie; Pedersen, Rasmus Steen; Stage, Tore Bjerregaard;

    2013-01-01

    The aim of this study was to determine the association between the renal clearance (CL(renal)) of metformin in healthy Caucasian volunteers and the single-nucleotide polymorphism (SNP) c.808G>T (rs316019) in OCT2 as well as the relevance of the gene-gene interactions between this SNP and (a) the...... promoter SNP g.-66T>C (rs2252281) in MATE1 and (b) the OCT1 reduced-function diplotypes....

  6. Glutathione S-transferase P1, gene-gene interaction, and lung cancer susceptibility in the Chinese population: An updated meta-analysis and review

    Directory of Open Access Journals (Sweden)

    Xue-Ming Li

    2015-01-01

    Full Text Available Aim of Study: To assess the impact of glutathione S-transferase P1 (GSTP1 Ile105Val polymorphism on the risk of lung cancer in the Chinese population, an updated meta-analysis and review was performed. Materials and Methods: Relevant studies were identified from PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure, and Chinese Biology Medicine published through January 22, 2015. The odds ratios (ORs and 95% confidence intervals (CIs were calculated to estimate the strength of the associations. Results: A total of 13 case-control studies, including 2026 lung cancer cases and 2451 controls, were included in this meta-analysis. Overall, significantly increased lung cancer risk was associated with the variant genotypes of GSTP1 polymorphism in the Chinese population (GG vs. AA: OR = 1.36, 95% CI = 1.01-1.84. In subgroup analyses stratified by geographic area and source of controls, the significant results were found in population-based studies (GG vs. AA: OR = 1.62, 95% CI: 1.13-2.31; GG vs. AG: OR = 1.49, 95% CI: 1.03-2.16; GG vs. AA + AG: OR = 1.55, 95% CI: 1.12-2.26. A gene-gene interaction analysis showed that there was an interaction for individuals with combination of GSTM1 (or GSTT1 null genotype and GSTP1 (AG + GG mutant genotype for lung cancer risk in Chinese. Conclusion: This meta-analysis suggests that GSTP1 Ile105Val polymorphism may increase the risk of lung cancer in the Chinese population.

  7. GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease

    Directory of Open Access Journals (Sweden)

    Mellick George

    2006-01-01

    Full Text Available Abstract Background The identification and characterization of genes that influence the risk of common, complex multifactorial disease primarily through interactions with other genes and environmental factors remains a statistical and computational challenge in genetic epidemiology. We have previously introduced a genetic programming optimized neural network (GPNN as a method for optimizing the architecture of a neural network to improve the identification of gene combinations associated with disease risk. The goal of this study was to evaluate the power of GPNN for identifying high-order gene-gene interactions. We were also interested in applying GPNN to a real data analysis in Parkinson's disease. Results We show that GPNN has high power to detect even relatively small genetic effects (2–3% heritability in simulated data models involving two and three locus interactions. The limits of detection were reached under conditions with very small heritability (DLST gene and sex. Conclusion These results indicate that GPNN may be a useful pattern recognition approach for detecting gene-gene and gene-environment interactions.

  8. Association of peroxisome proliferator-activated receptor single-nucleotide polymorphisms and gene-gene interactions with the lipoprotein(a)

    Institute of Scientific and Technical Information of China (English)

    解惠坚

    2014-01-01

    Objective To examine the associations of 10 singlenucleotide polymorphisms(SNPs)in peroxisome proliferator-activated receptor(PPARs)gene with lipoprotein(a)level,and to investigate if there is gene-gene interaction among the SNPs on lipoprotein(a)level.Methods Totally 644 subjects(234 men and 410 women)were enrolled from Prevention of Multiple Metabolic Disorders and Metabolic Syndrome Study Cohort,which was an urban community survey study conducted in Jiangsu province.Ten SNPs in PPARα(rs135539,rs4253778,

  9. The Association of Peroxisome Proliferator-Activated Receptor δ and Additional Gene-Gene Interaction with C-Reactive Protein in Chinese Population

    Directory of Open Access Journals (Sweden)

    Xiao-Ying Ding

    2016-01-01

    Full Text Available Aims. To examine the association between 4 single nucleotide polymorphisms (SNPs of peroxisome proliferator-activated receptors δ (PPARδ polymorphisms and C-reactive protein (CRP level and additional gene-gene interaction. Methods. Line regression analysis was performed to verify polymorphism association between SNP and CRP levels. Generalized multifactor dimensionality reduction (GMDR was employed to analyze the interaction. Results. A total of 1028 subjects (538 men, 490 women were selected. The carriers of the C allele (TC or CC of rs2016520 were associated with a significant decreased level of CRP, regression coefficients was −0.338, and standard error was 0.104 (p=0.001. The carriers of the G allele (CG or GG of rs9794 were also significantly associated with decreased level of CRP, regression coefficients was −0.219, and standard error was 0.114 (p=0.012. We also found a potential gene-gene interaction between rs2016520 and rs9794. Subjects with rs2016520-TC or CC, rs9794-CG or GG genotypes have lowest CRP level, difference (95% CI = −0.50 (−0.69 to −0.21 (p<0.001, compared to subjects with rs2016520-TT and rs9794-CC genotypes. Conclusions. rs2016520 and rs9794 minor allele of PPARδ and combined effect between the two SNP were associated with decreased CRP level.

  10. Genetic Association and Gene-gene interaction of HAS2, HABP1 and HYAL3 Implicate Hyaluronan Metabolic Genes in Glaucomatous Neurodegeneration

    Directory of Open Access Journals (Sweden)

    Kaustuv Basu

    2012-01-01

    Full Text Available Hyaluronan (HA plays a significant role in maintaining aqueous humor outflow in trabecular meshwork, the primary ocular tissue involved in glaucoma. We examined potential association of the single nucleotide polymorphisms (SNPs of the HA synthesizing gene – hyaluronan synthase 2 (HAS2, hyaluronan binding protein 1 (HABP1 and HA catabolic gene hyaluronidase 3 (HYAL3 in the primary open angle glaucoma (POAG patients in the Indian population. Thirteen tagged SNPs (6 for HAS2, 3 for HABP1 and 4 for HYAL3 were genotyped in 116 high tension (HTG, 321 non-high tension glaucoma (NHTG samples and 96 unrelated, age-matched, glaucoma-negative, control samples. Allelic and genotypic association were analyzed by PLINK v1.04; haplotypes were identified using PHASE v2.1 and gene-gene interaction was analyzed using multifactor dimensionality reduction (MDR v2.0. An allelic association (rs6651224; p = 0.03; OR: 0.49; 95% CI: 0.25–0.94 was observed at the second intron (C>G of HAS2 both for NHTG and HTG. rs1057308 revealed a genotypic association (p = 0.03 at the 5’ UTR of HAS2 with only HTG. TCT haplotype (rs1805429 – rs2472614 – rs8072363 in HABP1 and TTAG and TTGA (rs2285044 – rs3774753 – rs1310073 – rs1076872 in HYAL3 were found to be significantly high (p < 0.05 both for HTG and NHTG compared to controls. Gene-gene interaction revealed HABP1 predominantly interacts with HAS2 in HTG while it associates with both HYAL3 and HAS2 in NHTG. This is the first genetic evidence, albeit from a smaller study, that the natural polymorphisms in the genes involved in hyaluronan metabolism are potentially involved in glaucomatous neurodegeneration.

  11. Ant colony optimisation of decision tree and contingency table models for the discovery of gene-gene interactions.

    Science.gov (United States)

    Sapin, Emmanuel; Keedwell, Ed; Frayling, Tim

    2015-12-01

    In this study, ant colony optimisation (ACO) algorithm is used to derive near-optimal interactions between a number of single nucleotide polymorphisms (SNPs). This approach is used to discover small numbers of SNPs that are combined into a decision tree or contingency table model. The ACO algorithm is shown to be very robust as it is proven to be able to find results that are discriminatory from a statistical perspective with logical interactions, decision tree and contingency table models for various numbers of SNPs considered in the interaction. A large number of the SNPs discovered here have been already identified in large genome-wide association studies to be related to type II diabetes in the literature, lending additional confidence to the results. PMID:26577156

  12. Gene-Gene Interaction between PPARδ and PPARγ Is Associated with Abdominal Obesity in a Chinese Population

    Institute of Scientific and Technical Information of China (English)

    Yi Ding; Zhi-Rong Guo; Ming Wu; Qiu Chen; Hao Yu; Wen-Shu Luo

    2012-01-01

    The peroxisome proliferator-activated receptors (PPARs) -α,-δ/β and -γ are the ligand-activated transcription factors that function as the master regulators of glucose,fatty acid and lipoprotein metabolism,energy balance,cell proliferation and differentiation,inflammation,and atherosclerosis.The objective of the current study was to examine the main and interactive effect of seven single nucleotide polymorphisms (SNPs) of PPARδ/γ in contribution to abdominal obesity.A total of 820 subjects were randomly selected and no individuals were related.The selected SNPs in PPARδ (rs2016520 and rs9794) and PPARγ (rs10865710,rs1805192,rs709158,rs3856806,and rs4684847) were genotyped.Mean difference and 95% confident interval were calculated.Interactions were explored by the method of generalized multifactor dimensionality reduction.After adjustment for gender,age,and smoking status,it was found that the carriers of the C allele (TC + CC) of rs2016520 were associated with a decreased risk of abdominal obesity compared to the carriers of the TT genotype (mean difference =-2.63,95% CI =-3.61--1.64,P < 0.0001).A significant two-locus model (P =0.0107) involving rs2016520 and rs10865710 and a significant three-locus model (P =0.0107) involving rs2016520,rs9794,and rs1805192 were observed.Overall,the three-locus model had the highest level of testing accuracy (59.85%) and showed a better cross-validation consistency (9/10) than two-locus model.Therefore,for abdominal obesity defined by waist circumference,we chose the three-locus model as the best interaction model.In conclusion,the C allele in rs2016520 was significantly associated with a lower abdominal obesity.Moreover,an interaction among rs2016520,rs1805192,and rs9794 on incident abdominal obesity could be demonstrated.

  13. Rapid Testing of Gene-Gene Interactions in Genome-Wide Association Studies of Binary and Quantitative Phenotypes

    OpenAIRE

    Bhattacharya, Kanishka; McCarthy, Mark I; Morris, Andrew P

    2011-01-01

    Genome-wide association (GWA) studies have been extremely successful in identifying novel loci contributing effects to a wide range of complex human traits. However, despite this success, the joint marginal effects of these loci account for only a small proportion of the heritability of these traits. Interactions between variants in different loci are not typically modelled in traditional GWA analysis, but may account for some of the missing heritability in humans, as they do in other model o...

  14. Influences of XDH genotype by gene-gene interactions with SUCLA2 for thiopurine-induced leukopenia in Korean patients with Crohn's disease.

    Science.gov (United States)

    Park, Soo-Kyung; Hong, Myunghee; Ye, Byong Duk; Kim, Kyung-Jo; Park, Sang Hyoung; Yang, Dong-Hoon; Hwang, Sung-Wook; Kwak, Min Seob; Lee, Ho-Su; Song, Kyuyoung; Yang, Suk-Kyun

    2016-06-01

    Background The impact of genetic variation in the thiopurine S-methyltransferase (TPMT) gene on thiopurine-induced leukopenia has been well demonstrated. Although xanthine dehydrogenase (XDH) is the second major contributor to azathioprine breakdown, polymorphisms in XDH have rarely been studied in IBD patients. We aim to access association between XDH variants and thiopurine-induced leukopenia by gene-gene interaction in a Crohn's disease (CD) population. Study A total of 964 CD patients treated with thiopurines were recruited from a tertiary referral center. The association between four XDH variants (p.Gly172Arg, p.Asn1109Thr, p.Arg149Cys, and p.Thr910Lys) and thiopurine-induced leukopenia was analyzed in cases with early leukopenia (n = 66), late leukopenia (n = 264), and in controls without leukopenia (n = 632). Three non-synonymous SNPs, which we previously reported association with thiopurine-induced leukopenia, NUDT15 (p.Arg139Cys), SUCLA2 (p.Ser199Thr), and TPMT *3C were selected for epistasis analysis with the XDH variants. Results There was no significant association for two variants of XDH and thiopurine-induced leukopenia. In the epistasis analysis, only XDH (p.Asn1109Thr) * SUCLA2 (p.Ser199Thr) showed a statistically significant association with early leukopenia [odds ratio (OR) = 0.16; p = 0.03]. After genotype stratification, a positive association on the background of SUCLA2 wild-type (199Ser) between the XDH (p.Asn1109Thr) and early leukopenia (OR = 4.39; p = 0.01) was detected. Conclusion Genes associated with thiopurine-induced leukopenia can act in a complex interactive manner. Further studies are warranted to explore the mechanisms underlying the effects of the combination of XDH (p.Asn1109Thr) and SUCLA2 (199Ser) on thiopurine-induced leukopenia. PMID:26863601

  15. Gene Network Biological Validity Based on Gene-Gene Interaction Relevance

    OpenAIRE

    Francisco Gómez-Vela; Norberto Díaz-Díaz

    2014-01-01

    In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in...

  16. ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.

    Directory of Open Access Journals (Sweden)

    Brett A McKinney

    Full Text Available Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k for each gene to optimize the Relief-F test statistics (importance scores for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to

  17. Detection for gene-gene co-association via kernel canonical correlation analysis

    Directory of Open Access Journals (Sweden)

    Yuan Zhongshang

    2012-10-01

    Full Text Available Abstract Background Currently, most methods for detecting gene-gene interaction (GGI in genomewide association studies (GWASs are limited in their use of single nucleotide polymorphism (SNP as the unit of association. One way to address this drawback is to consider higher level units such as genes or regions in the analysis. Earlier we proposed a statistic based on canonical correlations (CCU as a gene-based method for detecting gene-gene co-association. However, it can only capture linear relationship and not nonlinear correlation between genes. We therefore proposed a counterpart (KCCU based on kernel canonical correlation analysis (KCCA. Results Through simulation the KCCU statistic was shown to be a valid test and more powerful than CCU statistic with respect to sample size and interaction odds ratio. Analysis of data from regions involving three genes on rheumatoid arthritis (RA from Genetic Analysis Workshop 16 (GAW16 indicated that only KCCU statistic was able to identify interactions reported earlier. Conclusions KCCU statistic is a valid and powerful gene-based method for detecting gene-gene co-association.

  18. 年龄相关性白内障人群DNA损伤修复基因与环境因素的交互作用%Study on gene-gene, gene-environmental interactions of DNA repair genes related with age-related cataract

    Institute of Scientific and Technical Information of China (English)

    杨梅; 苏舒; 周婧; 朱蓉嵘; 秦柏; 杨铃; 张俊芳; 施健; 梁从凯

    2014-01-01

    Objective To investigate the interaction between polymorphisms and environment factors in age related cataract (ARC).Methods Population-based case-control study.All of 448 cataract cases were selected from cataract eye database and 248 controls were recruited from Funing county.All 18 single nucleotide polymorphism (SNPs) of WRN,OGG1,BLM and ERCC6 genes were genotyped using realtime fluorescent quantitative PCR.The possible risk of ARC was estimated by unconditional Logistic regression.The interaction effects between gene-gene and gene-environment were evaluated by use of multifactor dimensionality reduction (MDR).Results Risk of ARC in illiterate group was significantly increased (OR =1.53,P < 0.05),compared to noilliterate group.The risk of cataract in farmers was significantly high with ORs of 3.75.Long exposure to sunlight may increase cataract risk.Factors such as smoking,drinking,hypertension had no relationship with ARC (P > 0.05).WRN-rs11574311 was still associated with ARC with statistical significance after Bonferroni correction (OR =1.98,Pa < 0.018).There was no evidence for any association at a significance level of P < 0.05 for the remaining alleles.MDR analysis showed a significant interaction model among the six factors:education,solar radiation,WRNrs11574311,WRN-rs1801195,WRN-rs4733220 and BLM-rs17273206 (consistency inspection accuracy of 0.683 on average,cross validation at 10/10,P =0.005).Logistic regression model showed that the "highrisk" individuals had a significantly increased risk of ARC,compared to those " low-risk" individual classified by the MDR mode mentioned above(OR =5.51,P <0.05).Conclusion WRN-rs11574311 allele was the risk factor for ARC,and individuals who carried WRN-rs1801195,WRN-rs4733220 and BLMrs17273206 allele and low level of education,long sunlight time significantly increased the risk of the ARC.%目的 探讨基因-基因、基因-环境交互作用在年龄相关性白内障(ARC)发生中的作用.方法 采

  19. Gene-gene, gene-environment, gene-nutrient interactionsand single nucleotide polymorphisms of inflammatorycytokines

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    Inflammation plays a significant role in the etiologyof type 2 diabetes mellitus (T2DM). The rise in thepro-inflammatory cytokines is the essential step inglucotoxicity and lipotoxicity induced mitochondrialinjury, oxidative stress and beta cell apoptosis inT2DM. Among the recognized markers are interleukin(IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha(TNF-α), C-reactive protein, resistin, adiponectin, tissueplasminogen activator, fibrinogen and heptoglobins.Diabetes mellitus has firm genetic and very strongenvironmental influence; exhibiting a polygenic modeof inheritance. Many single nucleotide polymorphisms(SNPs) in various genes including those of pro and antiinflammatorycytokines have been reported as a riskfor T2DM. Not all the SNPs have been confirmed byunifying results in different studies and wide variationshave been reported in various ethnic groups. Theinter-ethnic variations can be explained by the factthat gene expression may be regulated by gene-gene,gene-environment and gene-nutrient interactions. Thisreview highlights the impact of these interactions ondetermining the role of single nucleotide polymorphismof IL-6, TNF-α, resistin and adiponectin in pathogenesisof T2DM.

  20. Common variants on 17q25 and gene-gene interactions conferring risk of schizophrenia in Han Chinese population and regulating gene expressions in human brain.

    Science.gov (United States)

    Guan, L; Wang, Q; Wang, L; Wu, B; Chen, Y; Liu, F; Ye, F; Zhang, T; Li, K; Yan, B; Lu, C; Su, L; Jin, G; Wang, H; Tian, H; Wang, L; Chen, Z; Wang, Y; Chen, J; Yuan, Y; Cong, W; Zheng, J; Wang, J; Xu, X; Liu, H; Xiao, W; Han, C; Zhang, Y; Jia, F; Qiao, X; Zhang, D; Zhang, M; Ma, H

    2016-09-01

    Recently, two genome-wide association studies (GWASs) of schizophrenia (SCZ) in Han Chinese identified several susceptibility loci. Replication efforts aiming to validate the GWAS findings were made and focused on the top hits. We conducted a more extensive follow-up study in an independent sample of 1471 cases and 1528 matched controls to verify 26 genetic variants by including nine top single-nucleotide polymorphisms (SNPs) that reached genome-wide significance and 17 promising SNPs nominated in the initial discovery phase. rs8073471 in an intron of tubulin-folding cofactor D (TBCD) obtained nominal significance (Phuman central nervous system. We observed that rs3744165 × rs8073471 interaction modulated the expression profile of TEAD3 (P=1.87 × 10(-8)), SH3TC2 (P=2.00 × 10(-8)), KCNK9 (P=5.20 × 10(-7)) and PPDPF (P=1.13 × 10(-6)) in postmortem cortex tissue; EFNA1 (P=7.26 × 10(-9)), RNU4ATAC (P=2.32 × 10(-8)) and NUPL2 (P=6.79 × 10(-8)) in cerebellum tissue. To the best of our knowledge, our study is the first one that links TBCD and ZNF750 mutations to SCZ susceptibility and to the transcript levels in human brain tissues. Further efforts are needed to understand the role of those variants in the pathogenesis of SCZ. PMID:26728569

  1. Vision-based interaction

    CERN Document Server

    Turk, Matthew

    2013-01-01

    In its early years, the field of computer vision was largely motivated by researchers seeking computational models of biological vision and solutions to practical problems in manufacturing, defense, and medicine. For the past two decades or so, there has been an increasing interest in computer vision as an input modality in the context of human-computer interaction. Such vision-based interaction can endow interactive systems with visual capabilities similar to those important to human-human interaction, in order to perceive non-verbal cues and incorporate this information in applications such

  2. Interactive example-based hatching

    NARCIS (Netherlands)

    Gerl, Moritz; Isenberg, Tobias

    2013-01-01

    We present an approach for interactively generating pen-and-ink hatching renderings based on hand-drawn examples. We aim to overcome the regular and synthetic appearance of the results of existing methods by incorporating human virtuosity and illustration skills in the computer generation of such im

  3. Results-Based Interaction Design

    Science.gov (United States)

    Weiss, Meredith

    2008-01-01

    Interaction design is a user-centered approach to development in which users and their goals are the driving force behind a project's design. Interaction design principles are fundamental to the design and implementation of effective websites, but they are not sufficient. This article argues that, to reach its full potential, a website should also…

  4. Variance-based interaction index measuring heteroscedasticity

    Science.gov (United States)

    Ito, Keiichi; Couckuyt, Ivo; Poles, Silvia; Dhaene, Tom

    2016-06-01

    This work is motivated by the need to deal with models with high-dimensional input spaces of real variables. One way to tackle high-dimensional problems is to identify interaction or non-interaction among input parameters. We propose a new variance-based sensitivity interaction index that can detect and quantify interactions among the input variables of mathematical functions and computer simulations. The computation is very similar to first-order sensitivity indices by Sobol'. The proposed interaction index can quantify the relative importance of input variables in interaction. Furthermore, detection of non-interaction for screening can be done with as low as 4 n + 2 function evaluations, where n is the number of input variables. Using the interaction indices based on heteroscedasticity, the original function may be decomposed into a set of lower dimensional functions which may then be analyzed separately.

  5. Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines

    OpenAIRE

    Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

    2015-01-01

    Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellit...

  6. Interactive Reliability-Based Optimal Design

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Thoft-Christensen, Palle; Siemaszko, A.;

    1994-01-01

    Interactive design/optimization of large, complex structural systems is considered. The objective function is assumed to model the expected costs. The constraints are reliability-based and/or related to deterministic code requirements. Solution of this optimization problem is divided in four main...... used in interactive optimization....

  7. Spatial interactions in agent-based modeling

    CERN Document Server

    Ausloos, Marcel; Merlone, Ugo

    2014-01-01

    Agent Based Modeling (ABM) has become a widespread approach to model complex interactions. In this chapter after briefly summarizing some features of ABM the different approaches in modeling spatial interactions are discussed. It is stressed that agents can interact either indirectly through a shared environment and/or directly with each other. In such an approach, higher-order variables such as commodity prices, population dynamics or even institutions, are not exogenously specified but instead are seen as the results of interactions. It is highlighted in the chapter that the understanding of patterns emerging from such spatial interaction between agents is a key problem as much as their description through analytical or simulation means. The chapter reviews different approaches for modeling agents' behavior, taking into account either explicit spatial (lattice based) structures or networks. Some emphasis is placed on recent ABM as applied to the description of the dynamics of the geographical distribution o...

  8. Gene-gene interactions among the peroxisome proliferator-activated receptor polymorphisms for hypertriglyceridemia%过氧化物酶体增殖物激活受体的基因-基因交互作用对高甘油三酯血症的影响

    Institute of Scientific and Technical Information of China (English)

    顾淑君; 刘萌萌; 郭志荣; 武鸣; 陈秋; 周正元; 俞浩; 张丽君; 骆文书

    2012-01-01

    三酯血症组分别为314(66.2%)、137(28.9%)、23 (4.9%)(x2=50.92,P<0.01),A等位基因频数在高甘油三酯血症组和非高甘油三酯血症组分别为244(35.2%)和183( 19.3%)(x2=52.89,P<0.01).调整年龄、性别、吸烟、饮酒、高脂、低纤饮食和职业体力因素后,rs 1800206、rs2016520、rs3856806和rs1805192位点与高甘油三酯血症有关联,OR(95% CI)值分别为3.88(2.69 ~5.60)、0.71(0.52 ~ 0.96)、1.40( 1.03 ~ 1.90)、2.56(1.88~3.49).GMDR模型分析显示,以质量性状的TG为结局,二阶模型(rs1800206和rs1805192)为最佳模型(P<0.01).以数量性状的TG为结局,三阶模型(rs 1800206、rs1805192和rs2016520)为最佳模型(P<0.01).结论 rs1800206、rs2016520、rs3856806和rs1805192位点与高甘油三酯血症有关联,多个SNP之间存在基因-基因的交互作用.%Objective To investigate the association of ten SNP at peroxisome proliferator-activated receptors (PPARα,δ,γ) with hypertriglyceridemia and the gene-gene interaction.Methods Participants were recruited from the Prevention of MetS and Multi-metabolic Disorders in Jiangsu province of China Study (PMMJS).A total of 820 subjects were selected from the 4083 participants who had received follow-up examination,by using simple random sampling.Participants in baseline and follow-up study surveys were both collected blood samples 11 ml in the morning after at least 8 hours of fasting.Blood samples which collected at the baseline were subjected to PPARα,PPARδ and PPARγ genotype analyses.Blood samples which collected at the follow-up were used to measure serum triglyceride levels.The logistic regression model was used to analyze the association between different SNP and hypertriglyceridemia,and the generalized multifactor dimensionality reduction (GMDR) was applied to explore the gene-gene interaction.Results The samples included 474 in the non-hypertriglyceridemia group and 346 in the hypertriglyceridemia group.The genotype frequencies of rs1800206 in

  9. Tagging of blast resistance gene(s) to DNA markers and marker-assisted selection (MAS) in rice improvement

    International Nuclear Information System (INIS)

    This paper reports progress made on the tagging of blast resistance gene(s) to DNA markers and on the initiation of marker-assisted selection (MAS) for blast resistance in rice improvement. A pair of near isogenic lines, K8OR and K79S, were developed using a Chinese landrace Hong-jiao-zhan as the resistance donor. Ten putatively positive markers were identified by screening 177 mapped DNA markers. Using the F2 population of 143 plants and the derived F3 lines, three Restriction Fragment Length Polymorphism (RFLP) markers (RG81, RG869 and RZ397) on chromosome 12 of rice were identified to be closely linked to the blast resistance gene Pi-12(t). The genetic distance between Pi-12(t) and the closest marker RG869 was 5.1 cM. By employing the bulk segregant analysis (BSA) procedure, six of 199 arbitrary primers were found to produce positive Randomly Amplified Polymorphic DNA (RAPD) bands. Tight linkage between Pi-12(t) and three RAPD bands, each from a different primer, was confirmed after amplification of DNA of all F2 individuals. Two fragments were cloned and sequenced, and two sequence characterised amplified re-ion (SCAR) markers were established. In two other F3 populations, Xian-feng I/Tetep and Xian-feng, 1/Hong-jiao-zhan, the blast resistance was found to be controlled by interactions of two or more genes. One resistance gene was located in the vicinity of RG81 in both populations. Work to identify other gene(s) is currently under way. Marker assisted selection for blast resistance was initiated. Crosses were made between elite varieties and blast resistance donors to develop populations for DNA marker-assisted selection of blast resistance. In addition, 48 varieties widely used in current rice breeding programs were provided by rice breeders. DNA marker-based polymorphism among, these varieties and resistance donors were analysed to produce a database for future MAS program. (author)

  10. Movement-based Interaction in Camera Spaces

    DEFF Research Database (Denmark)

    Eriksson, Eva; Riisgaard Hansen, Thomas; Lykke-Olesen, Andreas

    2006-01-01

    In this paper we present three concepts that address movement-based interaction using camera tracking. Based on our work with several movement-based projects we present four selected applications, and use these applications to leverage our discussion, and to describe our three main concepts space......, relations, and feedback. We see these as central for describing and analysing movement-based systems using camera tracking and we show how these three concepts can be used to analyse other camera tracking applications....

  11. Evidence-Based Interactive Management of Change

    Directory of Open Access Journals (Sweden)

    Albert Fleischmann

    2011-06-01

    Full Text Available Evidence-based interactive management of change means hands-on experience of modified work processes, given evidence of change. For this kind of pro-active organizational development support we use an organisational process memory and a communication-based representation technique for role-specific and task-oriented process execution. Both are effective means for organizations becoming agile through interactively modelling the business at the process level and re-constructing or re-arranging process representations according to various needs. The tool allows experiencing role-specific workflows, as the communication-based refinement of work models allows for executable process specifications. When presenting the interactive processes to individuals involved in the business processes, changes can be explored interactively in a context-sensitive way before re-implementing business processes and information systems. The tool is based on a service-oriented architecture and a flexible representation scheme comprising the exchange of message between actors, business objects and actors (roles. The interactive execution of workflows does not only enable the individual reorganization of work but also changes at the level of the entire organization due to the represented interactions.

  12. An interactive segmentation method based on superpixel

    DEFF Research Database (Denmark)

    Yang, Shu; Zhu, Yaping; Wu, Xiaoyu

    2015-01-01

    This paper proposes an interactive image-segmentation method which is based on superpixel. To achieve fast segmentation, the method is used to establish a Graphcut model using superpixels as nodes, and a new energy function is proposed. Experimental results demonstrate that the authors' method has...... excellent performance in terms of segmentation accuracy and computation efficiency compared with other segmentation algorithm based on pixels....

  13. Evolutionary algorithm based configuration interaction approach

    CERN Document Server

    Chakraborty, Rahul

    2016-01-01

    A stochastic configuration interaction method based on evolutionary algorithm is designed as an affordable approximation to full configuration interaction (FCI). The algorithm comprises of initiation, propagation and termination steps, where the propagation step is performed with cloning, mutation and cross-over, taking inspiration from genetic algorithm. We have tested its accuracy in 1D Hubbard problem and a molecular system (symmetric bond breaking of water molecule). We have tested two different fitness functions based on energy of the determinants and the CI coefficients of determinants. We find that the absolute value of CI coefficients is a more suitable fitness function when combined with a fixed selection scheme.

  14. A Somatosensory Interaction System based on Kinect

    Directory of Open Access Journals (Sweden)

    Liang Xiu Bo

    2016-01-01

    Full Text Available The somatosensory interaction technique is one form of the perceptual user interface which is used in video game and virtual reality more and more widly. In this paper, a somatosensory interaction system based on Kinect is presented. Firstly, the user performances his action in front of a kinect, the sensing data from kinect is preprocessed and the main features of the action are extracted. Secondly, the performaced action is recognized by the matching algorithm based on Dynamic Time Warping Hidden Markov Model. Finally, the recognized motion is employed to interact with the virtual human and virtual environment. A series of experiments have been done to test the availablity of our system. Results show that the recognition rate is high enough to be used in virtual reality applications.

  15. Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases.

    Science.gov (United States)

    Lin, Peng-Lin; Yu, Ya-Wen; Chung, Ren-Hua

    2016-01-01

    Pathway analysis has become popular as a secondary analysis strategy for genome-wide association studies (GWAS). Most of the current pathway analysis methods aggregate signals from the main effects of single nucleotide polymorphisms (SNPs) in genes within a pathway without considering the effects of gene-gene interactions. However, gene-gene interactions can also have critical effects on complex diseases. Protein-protein interaction (PPI) networks have been used to define gene pairs for the gene-gene interaction tests. Incorporating the PPI information to define gene pairs for interaction tests within pathways can increase the power for pathway-based association tests. We propose a pathway association test, which aggregates the interaction signals in PPI networks within a pathway, for GWAS with case-control samples. Gene size is properly considered in the test so that genes do not contribute more to the test statistic simply due to their size. Simulation studies were performed to verify that the method is a valid test and can have more power than other pathway association tests in the presence of gene-gene interactions within a pathway under different scenarios. We applied the test to the Wellcome Trust Case Control Consortium GWAS datasets for seven common diseases. The most significant pathway is the chaperones modulate interferon signaling pathway for Crohn's disease (p-value = 0.0003). The pathway modulates interferon gamma, which induces the JAK/STAT pathway that is involved in Crohn's disease. Several other pathways that have functional implications for the seven diseases were also identified. The proposed test based on gene-gene interaction signals in PPI networks can be used as a complementary tool to the current existing pathway analysis methods focusing on main effects of genes. An efficient software implementing the method is freely available at http://puppi.sourceforge.net. PMID:27622767

  16. Interactive analysis of geodata based intelligence

    Science.gov (United States)

    Wagner, Boris; Eck, Ralf; Unmüessig, Gabriel; Peinsipp-Byma, Elisabeth

    2016-05-01

    When a spatiotemporal events happens, multi-source intelligence data is gathered to understand the problem, and strategies for solving the problem are investigated. The difficulties arising from handling spatial and temporal intelligence data represent the main problem. The map might be the bridge to visualize the data and to get the most understand model for all stakeholders. For the analysis of geodata based intelligence data, a software was developed as a working environment that combines geodata with optimized ergonomics. The interaction with the common operational picture (COP) is so essentially facilitated. The composition of the COP is based on geodata services, which are normalized by international standards of the Open Geospatial Consortium (OGC). The basic geodata are combined with intelligence data from images (IMINT) and humans (HUMINT), stored in a NATO Coalition Shared Data Server (CSD). These intelligence data can be combined with further information sources, i.e., live sensors. As a result a COP is generated and an interaction suitable for the specific workspace is added. This allows the users to work interactively with the COP, i.e., searching with an on board CSD client for suitable intelligence data and integrate them into the COP. Furthermore, users can enrich the scenario with findings out of the data of interactive live sensors and add data from other sources. This allows intelligence services to contribute effectively to the process by what military and disaster management are organized.

  17. Interactive Knowledge Acquisition in Case Based Reasoning

    OpenAIRE

    Cordier, Amélie; Fuchs, Béatrice; Lieber, Jean; Mille, Alain

    2007-01-01

    International audience In Case Based Reasoning (CBR), knowledge acquisition plays an important role as it allows to progressively improve the system's competencies. One of the approaches of knowledge acquisition consists in performing it while the system is used to solve a problem. An advantage of this strategy is that it is not to constraining for the expert: the system exploits its interactions to acquire pieces of knowledge it needs to solve the current problem and takes the opportunity...

  18. Interactive early warning technique based on SVDD

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    After reviewing current researches on early warning,it is found that"bad" data of some systems is not easy to obtain,which makes methods proposed by these researches unsuitable for monitored systems.An interactive early warning technique based on SVDD(support vector data description)is proposed to adopt"good" data as samples to overcome the difficulty in obtaining the"bad"data.The process consists of two parts:(1)A hypersphere is fitted on"good"data using SVDD.If the data object are outside the hypersphere,it would be taken as"suspicious";(2)A group of experts would decide whether the suspicious data is"bad"or"good",early warning messages would be issued according to the decisions.And the detailed process of implementation is proposed.At last,an experiment based on data of a macroeconomic system is conducted to verify the proposed technique.

  19. Learning through Interaction: Improving Practice with Design-Based Research

    Science.gov (United States)

    Voigt, Christian; Swatman, Paula M. C.

    2006-01-01

    This article presents the first stage of a design-based research project to introduce case-based learning using existing interactive technologies in a major Australian university. The paper initially outlines the relationship between case-based learning, student interaction and the study of interactions--and includes a review of research into…

  20. Machine Learning Based on Attribute Interactions

    OpenAIRE

    Jakulin, Aleks

    2005-01-01

    Two attributes $A$ and $B$ are said to interact when it helps to observe the attribute values of both attributes together. This is an example of a $2$-way interaction. In general, a group of attributes ${\\cal X}$ is involved in a $k$-way interaction when we cannot reconstruct their relationship merely with $\\ell$-way interactions, $\\ell < k$. These two definitions formalize the notion of an interaction in a nutshell. An additional notion is the one of context. We interpret context as just...

  1. Interacting with Stroke-Based Rendering on a Wall Display

    NARCIS (Netherlands)

    Grubert, Jens; Hanckock, Mark; Carpendale, Sheelagh; Tse, Edward; Isenberg, Tobias

    2007-01-01

    We introduce two new interaction techniques for creating and interacting with non-photorealistic images using stroke-based rendering. We provide bimanual control of a large interactive canvas through both remote pointing and direct touch. Remote pointing allows people to sit and interact at a distan

  2. laser interaction and plasma based accelerator

    International Nuclear Information System (INIS)

    Plasma is an attractive medium for particle acceleration because of the high electric field can be sustained by Plasma. Our objective in this thesis concentrate mainly to study the physics of particle acceleration by different methods like microwave radiation propagates in the waveguides and also like beating two intense lasers in plasma based accelerators. So, it has been of great interest to consider the following subjects:1-The dynamics of an electron in the fields associated with transverse magnetic (TM) wave propagating inside rectangular waveguide is studied analytically. We have solved exactly the relativistic momentum and energy equations of a single electron which injected initially along the propagation of microwave. Expressions for the acceleration gradient and deflection angle are obtained.2-The dynamics of an electron in the fields associated with TE-electromagnetic wave propagating inside a circular waveguide is analytically studied. The motion of this electron along the axis of the waveguide is investigated in the existence of a helical magnet (in which the field is perpendicular to the axis of waveguide and rotating as a function of position along the magnet).3-The study of the beat wave plasma accelerator due to the interaction of two linearly polarized Bessel laser beams is investigated. The electron acceleration which driven by the generated longitudinal plasma waves with phase velocities near the speed of the light is studied. The wave equation descried the fields of this beat wave is obtained.

  3. Mining Tree Based Frequent Pattern from Human Interaction in Meeting

    Directory of Open Access Journals (Sweden)

    Puja R. Kose*1

    2014-01-01

    Full Text Available In modern life, interactions between human beings are frequently occurring in meetings, where topics are discussed and new decisions are made. To understand and interpret how people interact in a meeting discussion study of semantic knowledge is important. It becomes possible to extract frequent patterns of human interaction based on the captured content of face-to-face meetings by using mining method. Human interactions are categorized as proposing an idea, giving comments, expressing a positive opinion, acknowledgement; indicate the intention of user towards a topic or role in a discussion.Tree is used for representing a human interaction flow in a discussion session. Tree-based interaction mining algorithms are studied to analyze the structures of the trees and to extract interaction flow patterns. It can successfully extract several interesting patterns which is useful for the interpretation of human behavior in meeting discussions, such as determining frequent interactions, typical interaction flows, and relationships between different types of interactions.

  4. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    OpenAIRE

    Peng Liu; Lei Yang; Daming Shi; Xianglong Tang

    2015-01-01

    A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction net...

  5. Reality-based brain-computer interaction

    OpenAIRE

    Sjölie, Daniel

    2011-01-01

    Recent developments within human-computer interaction (HCI) and cognitive neuroscience have come together to motivate and enable a framework for HCI with a solid basis in brain function and human reality. Human cognition is increasingly considered to be critically related to the development of human capabilities in the everyday environment (reality). At the same time, increasingly powerful computers continuously make the development of complex applications with realistic interaction easier. A...

  6. An Interactive Tool for Creating Multi-Agent Systems and Interactive Agent-based Games

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Pagliarini, Luigi

    2011-01-01

    Utilizing principles from parallel and distributed processing combined with inspiration from modular robotics, we developed the modular interactive tiles. As an educational tool, the modular interactive tiles facilitate the learning of multi-agent systems and interactive agent-based games. The...

  7. AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects

    OpenAIRE

    Zhang, Qingrun; Long, Quan; Ott, Jurg

    2014-01-01

    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 wh...

  8. Entrez Gene: gene-centered information at NCBI.

    Science.gov (United States)

    Maglott, Donna; Ostell, Jim; Pruitt, Kim D; Tatusova, Tatiana

    2007-01-01

    Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. Entrez Gene includes records from genomes that have been completely sequenced, that have an active research community to contribute gene-specific information or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases and from other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is provided via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programing utilities (E-Utilities), and for bulk transfer by ftp. PMID:17148475

  9. Group Interaction Method Based on Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Wu Qun

    2013-06-01

    Full Text Available This paper presents a group interaction method based on Wireless Sensor Network which supplies new attempts and ideas for human-computer interaction. Firstly, analyze group interaction framework that is different from the monomer interaction, then integrate data language of group interaction based on user’s purpose so that the Wireless Sensor Network technology and methods are applied to the system of group interaction. Finally, group interaction toys based on Wireless Sensor Network are developed. Each of toy monomers is compactly filled with sensors, wireless communication devices, LED lights. The Wireless Sensor Network which is composed of many monomers makes interface function come true in virtual. The users not only act on the physical object but also act directly on the "data" when they use the device. Currently the functions including light transmission and light color blending have been accomplished and developing.

  10. Designing Software-Based Interactive Installations

    DEFF Research Database (Denmark)

    Andreasen, Troels; Juul, Niels Christian; Rosendahl, Mads

    2014-01-01

    installations and support the description of the approach with a single case- a bumper car competition. Why. To some extent, standard techniques for software development can be adapted for interactive installations. However, there is a need to emphasize the unique aspects of installations, bringing tangible...

  11. Adaptive Game Level Creation through Rank-based Interactive Evolution

    DEFF Research Database (Denmark)

    Liapis, Antonios; Martínez, Héctor Pérez; Togelius, Julian;

    2013-01-01

    This paper introduces Rank-based Interactive Evolution (RIE) which is an alternative to interactive evolution driven by computational models of user preferences to generate personalized content. In RIE, the computational models are adapted to the preferences of users which, in turn, are used...... artificial agents. Results suggest that RIE is both faster and more robust than standard interactive evolution and outperforms other state-of-the-art interactive evolution approaches....

  12. A Measure of Segregation Based on Social Interactions

    OpenAIRE

    Echenique, Federico; Fryer, Roland

    2007-01-01

    We develop an index of segregation based on two premises: (1) a measure of segregation should disaggregate to the level of individuals, and (2) an individual is more segregated the more segregated are the agents with whom she interacts. We present an index that satisfies (1) and (2) and that is based on agents' social interactions: the extent to which blacks interact with blacks, whites with whites, etc. We use the index to measure school and residential segregation. Using detailed data on fr...

  13. Mind Machine Interaction Based Robot for Disables

    OpenAIRE

    Priya Bag*; Rakesh Patel

    2014-01-01

    This paper elucidates the research and implementation of brain-actuated disability robot. The idea of controlling robot not by manual control, but by mere “thinking” (i.e., the brain activity of human) has fascinated humankind since ever. The robot is controlled through human Brain signal. BCI is a natural way to augment human capabilities by providing a new interaction link with the outside world and is particularly relevant as an aid for paralyzed humans, although it also op...

  14. Repetition-based Interactive Facade Modeling

    KAUST Repository

    AlHalawani, Sawsan

    2012-07-01

    Modeling and reconstruction of urban environments has gained researchers attention throughout the past few years. It spreads in a variety of directions across multiple disciplines such as image processing, computer graphics and computer vision as well as in architecture, geoscience and remote sensing. Having a virtual world of our real cities is very attractive in various directions such as entertainment, engineering, governments among many others. In this thesis, we address the problem of processing a single fa cade image to acquire useful information that can be utilized to manipulate the fa cade and generate variations of fa cade images which can be later used for buildings\\' texturing. Typical fa cade structures exhibit a rectilinear distribution where in windows and other elements are organized in a grid of horizontal and vertical repetitions of similar patterns. In the firt part of this thesis, we propose an efficient algorithm that exploits information obtained from a single image to identify the distribution grid of the dominant elements i.e. windows. This detection method is initially assisted with the user marking the dominant window followed by an automatic process for identifying its repeated instances which are used to define the structure grid. Given the distribution grid, we allow the user to interactively manipulate the fa cade by adding, deleting, resizing or repositioning the windows in order to generate new fa cade structures. Having the utility for the interactive fa cade is very valuable to create fa cade variations and generate new textures for building models. Ultimately, there is a wide range of interesting possibilities of interactions to be explored.

  15. Physically-based interactive Schlieren flow visualization

    Energy Technology Data Exchange (ETDEWEB)

    Mccormick, Patrick S [Los Alamos National Laboratory; Brownlee, Carson S [Los Alamos National Laboratory; Pegoraro, Vincent [UNIV OF UTAH; Shankar, Siddharth [UNIV OF UTAH; Hansen, Charles D [UNIV OF UTAH

    2009-01-01

    Understanding fluid flow is a difficult problem and of increasing importance as computational fluid dynamics produces an abundance of simulation data. Experimental flow analysis has employed techniques such as shadowgraph and schlieren imaging for centuries which allow empirical observation of inhomogeneous flows. Shadowgraphs provide an intuitive way of looking at small changes in flow dynamics through caustic effects while schlieren cutoffs introduce an intensity gradation for observing large scale directional changes in the flow. The combination of these shading effects provides an informative global analysis of overall fluid flow. Computational solutions for these methods have proven too complex until recently due to the fundamental physical interaction of light refracting through the flow field. In this paper, we introduce a novel method to simulate the refraction of light to generate synthetic shadowgraphs and schlieren images of time-varying scalar fields derived from computational fluid dynamics (CFD) data. Our method computes physically accurate schlieren and shadowgraph images at interactive rates by utilizing a combination of GPGPU programming, acceleration methods, and data-dependent probabilistic schlieren cutoffs. Results comparing this method to previous schlieren approximations are presented.

  16. Interactive Sonification of Grid-based Games

    OpenAIRE

    Nickerson, Louise Valgerður; Hermann, Thomas

    2008-01-01

    This paper presents novel designs for the sonification (auditory representation) of data from grid-based games such as Connect Four, Sudoku and others, motivated by the search for effective auditory representations that are useful for visually-impaired users as well as to support overviews in case that the visual sense is already otherwise allocated. Grid-based games are ideal to develop sonification strategies since they offer the advantage of providing an excellent test environment to evalu...

  17. Gene-gene and gene-environment interactions in prostate, breast and colorectal cancer

    DEFF Research Database (Denmark)

    Kopp, Tine Iskov

    The incidence of cancer in the western world has increased steeply during the last 50 years. For three of the most prevalent cancer types in Denmark, prostate, breast and colorectal cancer (PC, BC and CRC, respectively), only a small fraction (1-15%) of the incidences are caused by highly penetrant...... as having strong influence on carcinogenesis. Therefore, very frequent, low effect polymorphisms may have a greater contribution on a population level in combination with environmental factors. Indeed, several dietary and life style factors are now well-established risk factors for different cancer types...... and lifestyle factors may provide information about the underlying mechanisms and reveal new biological pathways. The aim of this PhD thesis was to investigate relevant risk factors in relation to the three major cancer types in Denmark: PC, BC and CRC, respectively. The two major risk factors examined...

  18. Effects of dopamine-related gene-gene interactions on working memory component processes

    NARCIS (Netherlands)

    Stelzel, C.; Basten, U.; Montag, C.; Reuter, M.; Fiebach, C.J.

    2009-01-01

    Dopamine modulates complex cognitive functions like working memory and cognitive control. It is widely accepted that an optimal level of prefrontal dopamine supports working memory performance. In the present study we used a molecular genetic approach to test whether the optimal activity of the dopa

  19. Unified parity-conserving interactions based on SU4

    International Nuclear Information System (INIS)

    A unified parity-conserving theory of strong and electromagnetic interactions is proposed based on SU(4). The correct electric charge quantization is obtained and an equal number of quarks of charge -1/3 and of leptons of charge +1 is predicted. When weak interactions are introduced, two alternative choices for the gauge group are possible: SU(5) or SO(9). (author)

  20. A Usability Study of Interactive Web-Based Modules

    Science.gov (United States)

    Girard, Tulay; Pinar, Musa

    2011-01-01

    This research advances the understanding of the usability of marketing case study modules in the area of interactive web-based technologies through the assignment of seven interactive case modules in a Principles of Marketing course. The case modules were provided for marketing students by the publisher, McGraw Hill Irwin, of the "Marketing"…

  1. Internet-based Interactive Construction Management Learning System.

    Science.gov (United States)

    Sawhney, Anil; Mund, Andre; Koczenasz, Jeremy

    2001-01-01

    Describes a way to incorporate practical content into the construction engineering and management curricula: the Internet-based Interactive Construction Management Learning System, which uses interactive and adaptive learning environments to train students in the areas of construction methods, equipment and processes using multimedia, databases,…

  2. Helium-3 Microscopic Optical Model Potential Based on Skyrme Interaction

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>The helium-3 microscopic optical potential is obtained by Green function method through nuclear matter approximation and local density approximation based on the effective Skyrme interaction. The reaction cross

  3. EyeScreen: A Vision-Based Gesture Interaction System

    Institute of Scientific and Technical Information of China (English)

    LI Shan-qing; XU Yi-hua; JIA Yun-de

    2007-01-01

    EyeScreen is a vision-based interaction system which provides a natural gesture interface for human-computer interaction (HCI) by tracking human fingers and recognizing gestures. Multi-view video images are captured by two cameras facing a computer screen, which can be used to detect clicking actions of a fingertip and improve the recognition rate. The system enables users to directly interact with rendered objects on the screen. Robustness of the system has been verified by extensive experiments with different user scenarios. EyeScreen can be used in many applications such as intelligent interaction and digital entertainment.

  4. Expectation-Based Loss Aversion and Strategic Interaction

    OpenAIRE

    Simon Dato; Andreas Grunewald; Daniel Müller

    2015-01-01

    This paper provides a comprehensive analysis regarding strategic interaction under expectation-based loss-aversion. First, we develop a coherent framework for the analysis by extending the equilibrium concepts of Koszegi and Rabin (2006, 2007) to strategic interaction and demonstrate how to derive equilibria. Second, we delineate how expectation-based loss-averse players differ in their strategic behavior from their counterparts with standard expected-utility preferences. Third, we analyze eq...

  5. Theoretical analysis of noncanonical base pairing interactions in RNA molecules

    Indian Academy of Sciences (India)

    Dhananjay Bhattacharyya; Siv Chand Koripella; Abhijit Mitra; Vijay Babu Rajendran; Bhabdyuti Sinha

    2007-08-01

    Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their ‘away from equilibrium’ geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H…O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H…O/N and/or one C-H…O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.

  6. Interactive Coherence-Based Façade Modeling

    KAUST Repository

    Musialski, Przemyslaw

    2012-05-01

    We propose a novel interactive framework for modeling building facades from images. Our method is based on the notion of coherence-based editing which allows exploiting partial symmetries across the facade at any level of detail. The proposed workflow mixes manual interaction with automatic splitting and grouping operations based on unsupervised cluster analysis. In contrast to previous work, our approach leads to detailed 3d geometric models with up to several thousand regions per facade. We compare our modeling scheme to others and evaluate our approach in a user study with an experienced user and several novice users.

  7. An Interactive Tool for Creating Multi-Agent Systems and Interactive Agent-based Games

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Pagliarini, Luigi

    2011-01-01

    Utilizing principles from parallel and distributed processing combined with inspiration from modular robotics, we developed the modular interactive tiles. As an educational tool, the modular interactive tiles facilitate the learning of multi-agent systems and interactive agent-based games. The...... modular and physical property of the tiles provides students with hands-on experience in exploring the theoretical aspects underlying multi-agent systems which often appear as challenging to students. By changing the representation of the cognitive challenging aspects of multi-agent systems education to a...

  8. RNA-RNA interaction prediction based on multiple sequence alignments

    CERN Document Server

    Li, Andrew X; Qin, Jing; Reidys, Christian M

    2010-01-01

    Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes for pairs of RNA sequences. These algorithms and the biological requirement of more reliable interactions motivate to utilize the additional information contained in multiple sequence alignments and to generalize the above framework to the partition function and base pairing probabilities for multiple sequence alignments.

  9. Tablet-Based Interaction for Immersive 3D Data Exploration

    OpenAIRE

    Lopez, David; Oehlberg, Lora; Doger, Candemir; Isenberg, Tobias

    2014-01-01

    Our overall vision is to enable researchers to explore 3D datasets with as much immersion as possible, arising both from visuals as well as from interaction . We therefore explore ways to combine an immersive large view of the 3D data with means to intuitively control this view with touch input on a separate mobile monoscopic tablet. This combination has the potential to increase people's acceptance of stereoscopic environments for 3D data visualization since--through touch-based interaction-...

  10. ACID-BASE INTERACTIONS BETWEEN POLYMERS AND FILLERS

    Institute of Scientific and Technical Information of China (English)

    WANG Qingguo; CHEN Fute; HUANG Yuanfu; ZHOU Qingli

    1987-01-01

    Inverse gas chromatography(IGC) and Fourier-transform infrared (FT-IR) techniques were applied to determining the relative acid-base strength of polymers and coupling agents. The acid-base characteristics of fillers such as CaCO3 could be altered by treatment with different coupling agents. It was shown that some mechanical properties of filled polymers were obviously associated with acid-base interactions between polymers and fillers.

  11. Movement-based interaction in camera spaces: a conceptual framework

    DEFF Research Database (Denmark)

    Eriksson, Eva; Hansen, Thomas Riisgaard; Lykke-Olesen, Andreas

    2007-01-01

    In this paper we present three concepts that address movement-based interaction using camera tracking. Based on our work with several movementbased projects we present four selected applications, and use these applications to leverage our discussion, and to describe our three main concepts space......, relations, and feedback. We see these as central for describing and analysing movement-based systems using camera tracking and we show how these three concepts can be used to analyse other camera tracking applications....

  12. Computer-Based Interaction Analysis with DEGREE Revisited

    Science.gov (United States)

    Barros, B.; Verdejo, M. F.

    2016-01-01

    We review our research with "DEGREE" and analyse how our work has impacted the collaborative learning community since 2000. Our research is framed within the context of computer-based interaction analysis and the development of computer-supported collaborative learning (CSCL) tools. We identify some aspects of our work which have been…

  13. Design of Experience and Flow in Movement-based Interaction

    NARCIS (Netherlands)

    Nijholt, Anton; Dijk, van Betsy; Reidsma, Dennis; Egges, A.; Kamphuis, A.; Overmars, M.

    2008-01-01

    Movement-based and exertion interfaces assume that their users move. Users have to perform exercises, they have to dance, they have to golf or football, or they want to train particular bodily skills. Many examples of those interfaces exist, sometimes asking for subtle interaction between user and i

  14. Observations on Experience and Flow in Movement-Based Interaction

    NARCIS (Netherlands)

    Nijholt, Anton; Pasch, Marco; Dijk, van Betsy; Reidsma, Dennis; Heylen, Dirk; England, David

    2011-01-01

    Movement-based interfaces assume that their users move. Users have to perform exercises, they have to dance, they have to golf or football, or they want to train particular bodily skills. Many examples of those interfaces exist, sometimes asking for subtle interaction between user and interface and

  15. Sensing Landscape History with an Interactive Location Based Service

    NARCIS (Netherlands)

    Lammeren, van R.J.A.; Roncken, P.A.; Goossen, C.M.

    2009-01-01

    This paper introduces the STEAD approach for interpreting data acquired by a "human sensor", who uses an informal interactive location-based service (iLBS) to sense cultural-historic facts and anecdotes of, and in the landscape. This user-generated data is collected outdoors and in situ. The approac

  16. AUTHENTICITY IN TASK-BASED INTERACTION: A CONVERSATION ANALYSIS PERSPECTIVE

    OpenAIRE

    HANAN WAER

    2009-01-01

    In recent years, there has been an increasing interest in task-based learning. Authenticity has been characterized as a main aspect in defining a task (Long 1985; Skehan 1996; Ellis 2003). However, far too little attention has been paid to investigating authenticity in task-based interaction (TBI). To the best knowledge of the researcher, no research has been done using conversation analysis (CA) to investigate authenticity in TBI. Therefore, the present paper focuses on the issue of authent...

  17. Conceptual misfits in email-based current awareness interaction

    OpenAIRE

    Attfield, Simon; Blandford, Ann

    2010-01-01

    Purpose - This research aims to identify some requirements for supporting user interactions with electronic current-awareness alert systems based on data from a professional work environment. Design/methodology/approach - Qualitative data was gathered using contextual inquiry observations with twenty-one workers at the London office of an international law firm. The analysis uses CASSM (‘Concept-based Analysis of Surface and Structural Misfits’), a usability evaluation method structured ...

  18. An Interactive Multimedia Based Instruction in Experimental Modelling

    DEFF Research Database (Denmark)

    Knudsen, Morten; Nielsen, J.N.; Østergaard, J.;

    1997-01-01

    A CD-ROM based interactive multimedia instruction in experimental modelling for Danish Engineering School teachers is described. The content is based on a new sensitivity approach for direct estimation of physical parameters in linear and nonlinear dynamic systems. The presentation is inspired of...... Solomans=s inventory of learning styles. To enhance active learning and motivation by real life problems, the simulation tool Matlab is integrated in the authoring program Medi8or....

  19. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    Zaki Nazar

    2009-05-01

    Full Text Available Abstract Background Protein-protein interaction (PPI is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. Results To assess the ability of the proposed method to recognize the difference between "interacted" and "non-interacted" proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction. Conclusion Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.

  20. Detection of Gene Interactions Based on Syntactic Relations

    Directory of Open Access Journals (Sweden)

    Mi-Young Kim

    2008-01-01

    Full Text Available Interactions between proteins and genes are considered essential in the description of biomolecular phenomena, and networks of interactions are applied in a system's biology approach. Recently, many studies have sought to extract information from biomolecular text using natural language processing technology. Previous studies have asserted that linguistic information is useful for improving the detection of gene interactions. In particular, syntactic relations among linguistic information are good for detecting gene interactions. However, previous systems give a reasonably good precision but poor recall. To improve recall without sacrificing precision, this paper proposes a three-phase method for detecting gene interactions based on syntactic relations. In the first phase, we retrieve syntactic encapsulation categories for each candidate agent and target. In the second phase, we construct a verb list that indicates the nature of the interaction between pairs of genes. In the last phase, we determine direction rules to detect which of two genes is the agent or target. Even without biomolecular knowledge, our method performs reasonably well using a small training dataset. While the first phase contributes to improve recall, the second and third phases contribute to improve precision. In the experimental results using ICML 05 Workshop on Learning Language in Logic (LLL05 data, our proposed method gave an F-measure of 67.2% for the test data, significantly outperforming previous methods. We also describe the contribution of each phase to the performance.

  1. Interaction profile-based protein classification of death domain

    Directory of Open Access Journals (Sweden)

    Pio Frederic

    2004-06-01

    Full Text Available Abstract Background The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experimental and computational efforts on the creation and analysis of information derived from 3D structure. In particular, the high-throughput generation of protein-protein interaction data from a few organisms makes such an approach very important towards understanding the molecular recognition that make-up the entire protein-protein interaction network. Since the generation of sequences, and experimental protein-protein interactions increases faster than the 3D structure determination of protein complexes, there is tremendous interest in developing in silico methods that generate such structure for prediction and classification purposes. In this study we focused on classifying protein family members based on their protein-protein interaction distinctiveness. Structure-based classification of protein-protein interfaces has been described initially by Ponstingl et al. 1 and more recently by Valdar et al. 2 and Mintseris et al. 3, from complex structures that have been solved experimentally. However, little has been done on protein classification based on the prediction of protein-protein complexes obtained from homology modeling and docking simulation. Results We have developed an in silico classification system entitled HODOCO (Homology modeling, Docking and Classification Oracle, in which protein Residue Potential Interaction Profiles (RPIPS are used to summarize protein-protein interaction characteristics. This system applied to a dataset of 64 proteins of the death domain superfamily was used to classify each member into its proper subfamily. Two classification methods were attempted, heuristic and support vector machine learning. Both methods were tested with a 5-fold cross-validation. The heuristic approach yielded a 61% average accuracy, while the machine

  2. Traffic and Driving Simulator Based on Architecture of Interactive Motion

    Directory of Open Access Journals (Sweden)

    Alexander Paz

    2015-01-01

    Full Text Available This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i motion-based driving simulation, (ii pedestrian simulation, (iii motorcycling and bicycling simulation, and (iv traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination.

  3. Traffic and Driving Simulator Based on Architecture of Interactive Motion

    Science.gov (United States)

    Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

    2015-01-01

    This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination. PMID:26491711

  4. Web-based Interactive Landform Simulation Model - Grand Canyon

    Science.gov (United States)

    Luo, W.; Pelletier, J. D.; Duffin, K.; Ormand, C. J.; Hung, W.; Iverson, E. A.; Shernoff, D.; Zhai, X.; Chowdary, A.

    2013-12-01

    Earth science educators need interactive tools to engage and enable students to better understand how Earth systems work over geologic time scales. The evolution of landforms is ripe for interactive, inquiry-based learning exercises because landforms exist all around us. The Web-based Interactive Landform Simulation Model - Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is a continuation and upgrade of the simple cellular automata (CA) rule-based model (WILSIM-CA, http://www.niu.edu/landform/) that can be accessed from anywhere with an Internet connection. Major improvements in WILSIM-GC include adopting a physically based model and the latest Java technology. The physically based model is incorporated to illustrate the fluvial processes involved in land-sculpting pertaining to the development and evolution of one of the most famous landforms on Earth: the Grand Canyon. It is hoped that this focus on a famous and specific landscape will attract greater student interest and provide opportunities for students to learn not only how different processes interact to form the landform we observe today, but also how models and data are used together to enhance our understanding of the processes involved. The latest development in Java technology (such as Java OpenGL for access to ubiquitous fast graphics hardware, Trusted Applet for file input and output, and multithreaded ability to take advantage of modern multi-core CPUs) are incorporated into building WILSIM-GC and active, standards-aligned curricula materials guided by educational psychology theory on science learning will be developed to accompany the model. This project is funded NSF-TUES program.

  5. Towards accurate porosity descriptors based on guest-host interactions.

    Science.gov (United States)

    Paik, Dooam; Haranczyk, Maciej; Kim, Jihan

    2016-05-01

    For nanoporous materials at the characterization level, geometry-based approaches have become the methods of choice to provide information, often encoded in numerical descriptors, about the pores and the channels of a porous material. Examples of most common descriptors of the latter are pore limiting diameters, accessible surface area and accessible volume. The geometry-based methods exploit hard-sphere approximation for atoms, which (1) reduces costly computations of the interatomic interactions between the probe guest molecule and the porous material framework atoms, (2) effectively exploit applied mathematics methods such as Voronoi decomposition to represent and characterize porosity. In this work, we revisit and quantify the shortcoming of the geometry-based approaches. To do so, we have developed a series of algorithms to calculate pore descriptors such as void fraction, accessible surface area, pore limiting diameters (largest included sphere, and largest free sphere) based on a classical force field model of interactions between the guest and the framework atoms. Our resulting energy-based methods are tested on diverse sets of metal-organic frameworks and zeolite structures and comparisons against results obtained from geometric-based method indicate deviations in the cases for structures with small pore sizes. The method provides both high accuracy and performance making it suitable when screening a large database of materials. PMID:27054971

  6. Using Agent Based Modeling (ABM) to Develop Cultural Interaction Simulations

    Science.gov (United States)

    Drucker, Nick; Jones, Phillip N.

    2012-01-01

    Today, most cultural training is based on or built around "cultural engagements" or discrete interactions between the individual learner and one or more cultural "others". Often, success in the engagement is the end or the objective. In reality, these interactions usually involve secondary and tertiary effects with potentially wide ranging consequences. The concern is that learning culture within a strict engagement context might lead to "checklist" cultural thinking that will not empower learners to understand the full consequence of their actions. We propose the use of agent based modeling (ABM) to collect, store, and, simulating the effects of social networks, promulgate engagement effects over time, distance, and consequence. The ABM development allows for rapid modification to re-create any number of population types, extending the applicability of the model to any requirement for social modeling.

  7. Interactive Learning Based Realizability and 1-Backtracking Games

    OpenAIRE

    Federico Aschieri

    2011-01-01

    We prove that interactive learning based classical realizability (introduced by Aschieri and Berardi for first order arithmetic) is sound with respect to Coquand game semantics. In particular, any realizer of an implication-and-negation-free arithmetical formula embodies a winning recursive strategy for the 1-Backtracking version of Tarski games. We also give examples of realizer and winning strategy extraction for some classical proofs. We also sketch some ongoing work about how to extend ou...

  8. Multiple input support in a model-based interaction framework

    OpenAIRE

    Chatty, Stéphane; Lemort, Alexandre; Valès, Stéphane

    2007-01-01

    Developing for tabletops puts special requirements on interface programming frameworks: managing parallel input, device discovery, device equivalence, and describing combined interactions. We analyse these issues and describe the solutions that were used in IntuiKit, a model- based framework aimed at making the design and development of post-WIMP user interfaces more accessible. Some solutions are simple consequences of the support of multi- modality, while others are more specific to multipl...

  9. Competence–Based Support of Interaction between Business Network Members

    OpenAIRE

    Smirnov, Alexander; Kashevnik, Alexey; Shilov, Nikolay

    2008-01-01

    In a complicated business network finding a supplier can be a very time consuming task. The technology of competence management is aimed to support such kind of tasks. The paper presents an approach to support interaction between business network members based on such technologies as competence management and knowledge management. The conceptual models of the context-driven competence management system and production network member competence profile are described. The usage of th...

  10. Quadrupole Beam-Based Alignment in the RHIC Interaction Regions

    International Nuclear Information System (INIS)

    Continued beam-based alignment (BBA) efforts have provided significant benefit to both heavy ion and polarized proton operations at RHIC. Recent studies demonstrated previously unknown systematic beam position monitor (BPM) offset errors and produced accurate measurements of individual BPM offsets in the experiment interaction regions. Here we describe the algorithm used to collect and analyze data during the 2010 and early 2011 RHIC runs and the results of these measurements.

  11. INTERACTIVE IMAGE SEGMENTATION BASED ON HARMONIC FUNCTIONS & RECONSTRUCTIONS

    OpenAIRE

    Alisha Abraham

    2013-01-01

    This paper gives idea GRF functions instead of a graph-based algorithm for interactive imagesegmentation. Specifically, given a 3 X 3 local window, the colour of each pixel in it will be linearlyreconstructed with those of the remaining eight pixels. The optimal weights will be transferred to linearlyreconstruct its class label. This treatment is largely motivated from the manifold learning algorithm of locallylinear embedding. But beyond LLE where only one data point is reconstructed in each...

  12. Evaluating heuristics for tabletop user segmentation based on simultaneous interaction

    OpenAIRE

    García Sanjuan, Fernando; Jaén Martínez, Francisco Javier; Catalá Bolós, Alejandro

    2013-01-01

    Differentiating between users that interact on a tabletop could be beneficial for collaborative tasks to support territoriality-oriented features such as a more efficient space management or a better presentation of the contents. In this paper, we design a novel algorithm for the user differentiation or segmentation based on the simultaneous manipulation of the controls. This is a potential differentiating factor that has remained unexplored so far, and in combination with other factors may b...

  13. Defect Interaction in Iron and Iron-based Alloys

    Science.gov (United States)

    Xu, Haixuan; Stocks, G. Malcolm; Stoller, Roger

    2014-03-01

    Magnetism has a profound influence on the defect properties in iron and iron-based alloys. For instance, it has been shown from first principles calculations that the helium interstitial occupies the tetrahedral site instead of octahedral site in contrast to all previous work that neglected the magnetic effects. In this study, we explore the effects of magnetism on the defect interaction, primarily interstitial-type defects, in bcc iron and Fe-Cr systems. The magnetic moment change during the interaction of two 1/2 interstitial loops in bcc iron was calculated using the ab initio locally self-consistent multiple-scattering (LSMS) method and a significant fluctuation was observed. Adding Cr significantly modifies the magnetic structure of the defects and defect interactions. In addition, the effects of magnetism on the defect energetics are evaluated. This study provides useful insights on whether magnetism can be used as a effective means to manipulate the defect evolution in iron-based structural alloys. This material is based upon work supported as part of the Center for Defect Physics, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.

  14. [Interaction of Ag+ ions with ribonucleotides of canonical bases].

    Science.gov (United States)

    Sorokin, V A; Valeev, V A; Gladchenko, G O; Sysa, I V; Degtiar, M V; Volchok, I V; Blagoĭ, Iu P

    1999-01-01

    The interaction of Ag+ ions with ribonucleotides of canonical bases in aqueous solution was studied by differential UV spectroscopy. Atoms coordinating silver ions (N7, O6 of guanosine 5'-monophosphate, N3, O2 of cytidine 5'-monophosphate, N7, N1, N3 of adenosine 5'-monophosphate and N3 of uridine 5'-monophosphate) and the binding constants characterizing the formation of appropriate complexes were determined. The differences in the relative affinity of Ag+ ions for the atoms of nucleotide bases correlate with the potential on them. PMID:10418671

  15. Dynamic obstacles avoidance based on image-based dynamic window approach for human-vehicle interaction

    OpenAIRE

    Kang, Yue; Alves De Lima, Danilo; Corrêa Victorino, Alessandro

    2015-01-01

    — This paper presents an approach for the development of Advanced Driving Assistance System (ADAS) based on the human-vehicle interaction using Image-based Dynamic Window Approach (IDWA). The IDWA is associated to a method for dynamic obstacles avoidance in order to prevent human driving errors, in the context of intelligent robotic vehicles. The human-vehicle interaction is presented by the correction of the Human Driving Behavior (HDB) controller for driving defaults of human drivers, with ...

  16. The Design of Tools for Sketching Sensor-Based Interaction

    DEFF Research Database (Denmark)

    Brynskov, Martin; Lunding, Rasmus; Vestergaard, Lasse Steenbock

    2012-01-01

    In this paper we motivate, present, and give an initial evaluation of DUL Radio, a small wireless toolkit for sketching sensor-based interaction. In the motivation, we discuss the purpose of this specific platform, which aims to balance ease-of-use (learning, setup, initialization), size, speed, ...... users include designers, students, artists etc. with minimal programming and hardware skills, but this paper adresses the issues with designing the tools, which includes technical details......., flexibility and cost, aimed at wearable and ultra-mobile prototyping where fast reaction is needed (e.g. in controlling sound), and we discuss the general issues facing this category of embodied interaction design tools. We then present the platform in more detail, both regarding hard- ware and software....... In the brief evaluation, we present our initial experiences with the platform both in design projects and in teaching. We conclude that DUL Radio does seem to be a relatively easy-to-use tool for sketching sensor-based interaction compared to other solutions, but that there are many ways to improve it. Target...

  17. The "Wedding-Ring": An agent-based marriage model based on social interaction

    Directory of Open Access Journals (Sweden)

    Alexia Prskawetz

    2007-08-01

    Full Text Available In this paper we develop an agent-based marriage model based on social interaction. We build an population of interacting agents whose chances of marrying depend on the availability of partners, and whose willingness to marry depends on the share of relevant others in their social network who are already married. We then let the typical aggregate age pattern of marriage emerge from the bottom-up. The results of our simulation show that micro-level hypotheses founded on existing theory and evidence on social interaction can reproduce age-at-marriage patterns with both realistic shape and realistic micro-level dynamics.

  18. Gesture Interaction Browser-Based 3D Molecular Viewer.

    Science.gov (United States)

    Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

    2016-01-01

    The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education. PMID:27350455

  19. ANNIE - INTERACTIVE PROCESSING OF DATA BASES FOR HYDROLOGIC MODELS.

    Science.gov (United States)

    Lumb, Alan M.; Kittle, John L.

    1985-01-01

    ANNIE is a data storage and retrieval system that was developed to reduce the time and effort required to calibrate, verify, and apply watershed models that continuously simulate water quantity and quality. Watershed models have three categories of input: parameters to describe segments of a drainage area, linkage of the segments, and time-series data. Additional goals for ANNIE include the development of software that is easily implemented on minicomputers and some microcomputers and software that has no special requirements for interactive display terminals. Another goal is for the user interaction to be based on the experience of the user so that ANNIE is helpful to the inexperienced user and yet efficient and brief for the experienced user. Finally, the code should be designed so that additional hydrologic models can easily be added to ANNIE.

  20. Interactive Learning Based Realizability and 1-Backtracking Games

    Directory of Open Access Journals (Sweden)

    Federico Aschieri

    2011-01-01

    Full Text Available We prove that interactive learning based classical realizability (introduced by Aschieri and Berardi for first order arithmetic is sound with respect to Coquand game semantics. In particular, any realizer of an implication-and-negation-free arithmetical formula embodies a winning recursive strategy for the 1-Backtracking version of Tarski games. We also give examples of realizer and winning strategy extraction for some classical proofs. We also sketch some ongoing work about how to extend our notion of realizability in order to obtain completeness with respect to Coquand semantics, when it is restricted to 1-Backtracking games.

  1. Interactive Learning Based Realizability and 1-Backtracking Games

    CERN Document Server

    Aschieri, Federico

    2011-01-01

    We prove that interactive learning based classical realizability (introduced by Aschieri and Berardi for first order arithmetic) is sound with respect to Coquand game semantics. In particular, any realizer of an implication-and-negation-free arithmetical formula embodies a winning recursive strategy for the 1-Backtracking version of Tarski games. We also give examples of realizer and winning strategy extraction for some classical proofs. We also sketch some ongoing work about how to extend our notion of realizability in order to obtain completeness with respect to Coquand semantics, when it is restricted to 1-Backtracking games.

  2. POKEHEAD: An Open Source Interactive Headphone Based HCI Platform

    DEFF Research Database (Denmark)

    Højlund, Marie; Trento, Stefano; Goudarzi, Visda;

    2012-01-01

    desire to take advantage of the ubiquitous nature of headphone users in a social and private setting along with networked mobile devices such as smart phones and/or portable media player devices. Our goals were to design an intuitive autonomous, versatile, and practical interface context using a simple......This paper introduces a novel interactive, human-computer interface and remote social communication system based on an augmented, hi-fidelity audio headphone platform. Specifically, this system- named Pokehead, currently utilizes the DUL embedded open-source accelerometer platform to gather 3-axis...

  3. Tunable Stable Levitation Based on Casimir Interaction between Nanostructures

    Science.gov (United States)

    Liu, Xianglei; Zhang, Zhuomin M.

    2016-03-01

    Quantum levitation enabled by repulsive Casimir force has been desirable due to the potential exciting applications in passive-suspension devices and frictionless bearings. In this paper, dynamically tunable stable levitation is theoretically demonstrated based on the configuration of dissimilar gratings separated by an intervening fluid using exact scattering theory. The levitation position is insensitive to temperature variations and can be actively tuned by adjusting the lateral displacement between the two gratings. This work investigates the possibility of applying quantum Casimir interactions into macroscopic mechanical devices working in a noncontact and low-friction environment for controlling the position or transducing lateral movement into vertical displacement at the nanoscale.

  4. Sensing Landscape History with an Interactive Location Based Service

    OpenAIRE

    Paul Roncken; Martin Goossen; Ron van Lammeren

    2009-01-01

    This paper introduces the STEAD approach for interpreting data acquired by a “human sensor”, who uses an informal interactive location-based service (iLBS) to sense cultural-historic facts and anecdotes of, and in the landscape. This user-generated data is collected outdoors and in situ. The approach consists of four related facets (who, what, where, when). Three of the four facets are discussed and illustrated by user generated data collected during a Dutch survey in 2008. These data represe...

  5. A prototype system based on visual interactive SDM called VGC

    Science.gov (United States)

    Jia, Zelu; Liu, Yaolin; Liu, Yanfang

    2009-10-01

    In many application domains, data is collected and referenced by its geo-spatial location. Spatial data mining, or the discovery of interesting patterns in such databases, is an important capability in the development of database systems. Spatial data mining recently emerges from a number of real applications, such as real-estate marketing, urban planning, weather forecasting, medical image analysis, road traffic accident analysis, etc. It demands for efficient solutions for many new, expensive, and complicated problems. For spatial data mining of large data sets to be effective, it is also important to include humans in the data exploration process and combine their flexibility, creativity, and general knowledge with the enormous storage capacity and computational power of today's computers. Visual spatial data mining applies human visual perception to the exploration of large data sets. Presenting data in an interactive, graphical form often fosters new insights, encouraging the information and validation of new hypotheses to the end of better problem-solving and gaining deeper domain knowledge. In this paper a visual interactive spatial data mining prototype system (visual geo-classify) based on VC++6.0 and MapObject2.0 are designed and developed, the basic algorithms of the spatial data mining is used decision tree and Bayesian networks, and data classify are used training and learning and the integration of the two to realize. The result indicates it's a practical and extensible visual interactive spatial data mining tool.

  6. INTERACTING MULTIPLE MODEL ALGORITHM BASED ON JOINT LIKELIHOOD ESTIMATION

    Institute of Scientific and Technical Information of China (English)

    Sun Jie; Jiang Chaoshu; Chen Zhuming; Zhang Wei

    2011-01-01

    A novel approach is proposed for the estimation of likelihood on Interacting Multiple-Model (IMM) filter.In this approach,the actual innovation,based on a mismatched model,can be formulated as sum of the theoretical innovation based on a matched model and the distance between matched and mismatched models,whose probability distributions are known.The joint likelihood of innovation sequence can be estimated by convolution of the two known probability density functions.The likelihood of tracking models can be calculated by conditional probability formula.Compared with the conventional likelihood estimation method,the proposed method improves the estimation accuracy of likelihood and robustness of IMM,especially when maneuver occurs.

  7. Interactive Webmap-Based Science Planning for BepiColombo

    Science.gov (United States)

    McAuliffe, J.; Martinez, S.; Ortiz de Landaluce, I.; de la Fuente, S.

    2015-10-01

    For BepiColombo, ESA's Mission to Mercury, we will build a web-based, map-based interface to the Science Planning System. This interface will allow the mission's science teams to visually define targets for observations and interactively specify what operations will make up the given observation. This will be a radical departure from previous ESA mission planning methods. Such an interface will rely heavily on GIS technologies. This interface will provide footprint coverage of all existing archived data for Mercury, including a set of built-in basemaps. This will allow the science teams to analyse their planned observations and operational constraints with relevant contextual information from their own instrument, other BepiColombo instruments or from previous missions. The interface will allow users to import and export data in commonly used GIS formats, such that it can be visualised together with the latest planning information (e.g. import custom basemaps) or analysed in other GIS software. The interface will work with an object-oriented concept of an observation that will be a key characteristic of the overall BepiColombo scienceplanning concept. Observation templates or classes will be tracked right through the planning-executionprocessing- archiving cycle to the final archived science products. By using an interface that synthesises all relevant available information, the science teams will have a better understanding of the operational environment; it will enhance their ability to plan efficiently minimising or removing manual planning. Interactive 3D visualisation of the planned, scheduled and executed observations, simulation of the viewing conditions and interactive modification of the observation parameters are also being considered.

  8. Versatile Supramolecular Gene Vector Based on Host-Guest Interaction.

    Science.gov (United States)

    Liu, Jia; Hennink, Wim E; van Steenbergen, Mies J; Zhuo, Renxi; Jiang, Xulin

    2016-04-20

    It is a great challenge to arrange multiple functional components into one gene vector system to overcome the extra- and intracellular obstacles for gene therapy. In this study, we developed a supramolecular approach for constructing a versatile gene delivery system composed of adamantyl-terminated functional polymers and a β-cyclodextrin based polymer. Adamantyl-functionalized low molecular weight PEIs (PEI-Ad) and PEG (Ad-PEG) as well as poly(β-cyclodextrin) (PCD) were synthesized by one-step chemical reactions. The supramolecular inclusion complex formed from PCD to assemble LMW PEI-Ad4 via host-guest interactions can condense plasmid DNA to form nanopolyplexes by electrostatic interactions. The supramolecular polyplexes can be further PEGylated with Ad-PEG to form inclusion complexes, which showed increased salt and serum stability. In vitro experiments revealed that these supramolecular assembly polyplexes had good cytocompatibility and showed high transfection activity close to that of the commercial ExGen 500 at high dose of DNA. Also, the supramolecular vector system exhibited about 60% silencing efficiency as a siRNA vector. Thus, a versatile effective supramolecular gene vector based on host-guest complexes was fabricated with good cytocompatbility and transfection activity. PMID:27019340

  9. Hamiltonian multiplex interaction based on excitons effect in semiconductor QCs

    Directory of Open Access Journals (Sweden)

    Arezu Jahanshir

    2014-11-01

    Full Text Available The subject of modern technology has been the focus of extensive theoretical investigations in semiconducting nanostructures which we know as quantum dots (QCs. The possibility of monitoring and controlling the properties of QCs attracted considerable attention to these objects, as an important basic system in future technology. So, the quantum-mechanical effects play a significant role in the description of the formation mechanism QCs, determination of mass spectrum, binding energy and other characteristics. Based on QFT and by using oscillator representation method (ORM and operator product expansion technique developed in QFT, we study the properties of electron-hole QDs, determine mass spectrum and peruse spin-spin interactions in exciton system and its multiple pair systems. This method has applications to calculate the binding energy of exciton system in ground and excited states with semi-nuclear structure in semiconductor QCs or cold atomic few-body systems and develop the general calculation’s theory of few-body systems based on the Coulomb interaction between particles by forming excitonic pairs in semiconductor QCs. We investigate the binding energy of exciton bound states. It is shown that fermion particles have a very small mass, and after bonding together by dynamically force, constituent particles become massive, which is analogous to what happens in QCD.

  10. Analyzing Interaction of μ-, δ- and κ-opioid Receptor Gene Variants on Alcohol or Drug Dependence Using a Pattern Discovery-based Method

    OpenAIRE

    Li, Zhong; Zhang, Huiping

    2013-01-01

    Background Polymorphisms in the μ-, δ- and κ-opioid receptor genes (OPRM1, OPRD1 and OPRK1) have been reported to be associated with substance (alcohol or drug) dependence. The influence of an individual gene on a disease trait should be more evident when analyzed in the context of gene-gene interactions. Thus, we assessed the joint effect of variants in these three opioid receptor genes on alcohol, cocaine, or opioid dependence. Methods Genotype data for 13 OPRM1 Single Nucleotide Polymorphi...

  11. The Use of a Web-Based Classroom Interaction System in Introductory Physics Classes

    Science.gov (United States)

    Corpuz, Edgar D.; Corpuz, Ma. Aileen A.; Rosalez, Rolando

    2010-10-01

    A web-based interaction system was used in algebra-based and calculus-based physics classes to enhance students' classroom interaction. The interactive teaching approach primarily incorporated elements of Mazur's Peer Instruction and Interactive Lecture Demonstration. In our implementation, students used personal digital assistants (PDAs) to interact with their instructor during lecture and classroom demonstration. In this paper, we document the perceptions and attitudes of algebra-based and calculus-based physics students towards the interactive teaching approach and likewise present data on how this approach affected students' performance on the Force Concept Inventory (FCI).

  12. Graphics processing unit-based alignment of protein interaction networks.

    Science.gov (United States)

    Xie, Jiang; Zhou, Zhonghua; Ma, Jin; Xiang, Chaojuan; Nie, Qing; Zhang, Wu

    2015-08-01

    Network alignment is an important bridge to understanding human protein-protein interactions (PPIs) and functions through model organisms. However, the underlying subgraph isomorphism problem complicates and increases the time required to align protein interaction networks (PINs). Parallel computing technology is an effective solution to the challenge of aligning large-scale networks via sequential computing. In this study, the typical Hungarian-Greedy Algorithm (HGA) is used as an example for PIN alignment. The authors propose a HGA with 2-nearest neighbours (HGA-2N) and implement its graphics processing unit (GPU) acceleration. Numerical experiments demonstrate that HGA-2N can find alignments that are close to those found by HGA while dramatically reducing computing time. The GPU implementation of HGA-2N optimises the parallel pattern, computing mode and storage mode and it improves the computing time ratio between the CPU and GPU compared with HGA when large-scale networks are considered. By using HGA-2N in GPUs, conserved PPIs can be observed, and potential PPIs can be predicted. Among the predictions based on 25 common Gene Ontology terms, 42.8% can be found in the Human Protein Reference Database. Furthermore, a new method of reconstructing phylogenetic trees is introduced, which shows the same relationships among five herpes viruses that are obtained using other methods. PMID:26243827

  13. Ultrasonic power measurement system based on acousto-optic interaction

    Science.gov (United States)

    He, Liping; Zhu, Fulong; Chen, Yanming; Duan, Ke; Lin, Xinxin; Pan, Yongjun; Tao, Jiaquan

    2016-05-01

    Ultrasonic waves are widely used, with applications including the medical, military, and chemical fields. However, there are currently no effective methods for ultrasonic power measurement. Previously, ultrasonic power measurement has been reliant on mechanical methods such as hydrophones and radiation force balances. This paper deals with ultrasonic power measurement based on an unconventional method: acousto-optic interaction. Compared with mechanical methods, the optical method has a greater ability to resist interference and also has reduced environmental requirements. Therefore, this paper begins with an experimental determination of the acoustic power in water contained in a glass tank using a set of optical devices. Because the light intensity of the diffraction image generated by acousto-optic interaction contains the required ultrasonic power information, specific software was written to extract the light intensity information from the image through a combination of filtering, binarization, contour extraction, and other image processing operations. The power value can then be obtained rapidly by processing the diffraction image using a computer. The results of this work show that the optical method offers advantages that include accuracy, speed, and a noncontact measurement method.

  14. A Comparison of Interaction in AV-based and Internet-based Distance Courses

    Directory of Open Access Journals (Sweden)

    Melodee Landis

    2001-04-01

    Full Text Available At the center of the debate over the viability of distance education is whether the newer electronic technologies can offer enough interaction to maintain quality learner outcomes and critical mass. Two of the most commonly used forms of distance education are 1 two-way, fully interactive audio-video classrooms and 2 on-line instruction through the Internet or Worldwide Web. This study used qualitative methods to compare and contrast the interaction that occurred in distance learning courses offered via each medium. The research process confirmed findings that there were fundamental differences in the interaction that occurred in the two environments. On-line interaction is so profoundly different than interaction in the traditional and AV-based class room that it appears instructors and students will need a substantial period of adjustment to feel comfortable with it and to fully appreciate its value. It appears that, as distance teaching and learning moves to a “mixed media” approach to teaching and learning, how interaction is handled with each of the media may be important to the success of a distance program.

  15. Mixed Reality-based Interactive Technology for Aircraft Cabin Assembly

    Institute of Scientific and Technical Information of China (English)

    LI Shiqi; PENG Tao; WANG Junfeng; XU Chi

    2009-01-01

    Due to the narrowness of space and the complexity of structure, the assembly of aircraft cabin has become one of the major bottlenecks in the whole manufacturing process. To solve the problem, at the beginning of aircraft design, the different stages of the lifecycle of aircraft must be thought about, which include the trial manufacture, assembly, maintenance, recycling and destruction of the product. Recently, thanks to the development of the virtual reality and augmented reality, some low-cost and fast solutions are found for the product assembly. This paper presents a mixed reality-based interactive technology for the aircraft cabin assembly, which can enhance the efficiency of the assemblage in a virtual environment in terms of vision, information and operation. In the mixed reality-based assembly environment, the physical scene can be obtained by a camera and then generated by a computer. The virtual parts, the features of visual assembly, the navigation information, the physical parts and the physical assembly environment will be mixed and presented in the same assembly scene. The mixed or the augmented information will provide some assembling information as a detailed assembly instruction in the mixed reality-based assembly environment. Constraint proxy and its match rules help to reconstruct and visualize the restriction relationship among different parts, and to avoid the complex calculation of constraint's match. Finally, a desktop prototype system of virtual assembly has been built to assist the assembly verification and training with the virtual hand.

  16. Microscopic positive-energy potential based on Gogny interaction

    CERN Document Server

    Blanchon, G; Arellano, H F; Mau, N Vinh

    2014-01-01

    We present nucleon elastic scattering calculation based on Green's function formalism in the Random-Phase Approximation. For the first time, the Gogny effective interaction is used consistently throughout the whole calculation to account for the complex, non-local and energy-dependent optical potential. Effects of intermediate single-particle resonances are included and found to play a crucial role in the account for measured reaction cross section. Double counting of the particle-hole second-order contribution is carefully addressed. The resulting integro-differential Schr\\"odinger equation for the scattering process is solved without localization procedures. The method is applied to neutron and proton elastic scattering from $^{40}$Ca. A successful account for differential and integral cross sections, including analyzing powers, is obtained for incident energies up to 30 MeV. Discrepancies at higher energies are related to much too high volume integral of the real potential for large partial waves. Moreover...

  17. Interactive brain shift compensation using GPU based programming

    Science.gov (United States)

    van der Steen, Sander; Noordmans, Herke Jan; Verdaasdonk, Rudolf

    2009-02-01

    Processing large images files or real-time video streams requires intense computational power. Driven by the gaming industry, the processing power of graphic process units (GPUs) has increased significantly. With the pixel shader model 4.0 the GPU can be used for image processing 10x faster than the CPU. Dedicated software was developed to deform 3D MR and CT image sets for real-time brain shift correction during navigated neurosurgery using landmarks or cortical surface traces defined by the navigation pointer. Feedback was given using orthogonal slices and an interactively raytraced 3D brain image. GPU based programming enables real-time processing of high definition image datasets and various applications can be developed in medicine, optics and image sciences.

  18. Vision Based Game Development Using Human Computer Interaction

    CERN Document Server

    Sumathi, S; Maheswari, M Uma

    2010-01-01

    A Human Computer Interface (HCI) System for playing games is designed here for more natural communication with the machines. The system presented here is a vision-based system for detection of long voluntary eye blinks and interpretation of blink patterns for communication between man and machine. This system replaces the mouse with the human face as a new way to interact with the computer. Facial features (nose tip and eyes) are detected and tracked in realtime to use their actions as mouse events. The coordinates and movement of the nose tip in the live video feed are translated to become the coordinates and movement of the mouse pointer on the application. The left or right eye blinks fire left or right mouse click events. The system works with inexpensive USB cameras and runs at a frame rate of 30 frames per second.

  19. Chemical interaction matrix between reagents in a Purex based process

    International Nuclear Information System (INIS)

    The United States Department of Energy (DOE) is the responsible entity for the disposal of the United States excess weapons grade plutonium. DOE selected a PUREX-based process to convert plutonium to low-enriched mixed oxide fuel for use in commercial nuclear power plants. To initiate this process in the United States, a Mixed Oxide (MOX) Fuel Fabrication Facility (MFFF) is under construction and will be operated by Shaw AREVA MOX Services at the Savannah River Site. This facility will be licensed and regulated by the U.S. Nuclear Regulatory Commission (NRC). A PUREX process, similar to the one used at La Hague, France, will purify plutonium feedstock through solvent extraction. MFFF employs two major process operations to manufacture MOX fuel assemblies: (1) the Aqueous Polishing (AP) process to remove gallium and other impurities from plutonium feedstock and (2) the MOX fuel fabrication process (MP), which processes the oxides into pellets and manufactures the MOX fuel assemblies. The AP process consists of three major steps, dissolution, purification, and conversion, and is the center of the primary chemical processing. A study of process hazards controls has been initiated that will provide knowledge and protection against the chemical risks associated from mixing of reagents over the life time of the process. This paper presents a comprehensive chemical interaction matrix evaluation for the reagents used in the PUREX-based process. Chemical interaction matrix supplements the process conditions by providing a checklist of any potential inadvertent chemical reactions that may take place. It also identifies the chemical compatibility/incompatibility of the reagents if mixed by failure of operations or equipment within the process itself or mixed inadvertently by a technician in the laboratories. (authors)

  20. Real-time retrieval for case-based reasoning in interactive multiagent-based simulations

    CERN Document Server

    De Loor, Pierre; Pierre, Chevaillier; 10.1016/j.eswa.2010.10.048

    2011-01-01

    The aim of this paper is to present the principles and results about case-based reasoning adapted to real- time interactive simulations, more precisely concerning retrieval mechanisms. The article begins by introducing the constraints involved in interactive multiagent-based simulations. The second section pre- sents a framework stemming from case-based reasoning by autonomous agents. Each agent uses a case base of local situations and, from this base, it can choose an action in order to interact with other auton- omous agents or users' avatars. We illustrate this framework with an example dedicated to the study of dynamic situations in football. We then go on to address the difficulties of conducting such simulations in real-time and propose a model for case and for case base. Using generic agents and adequate case base structure associated with a dedicated recall algorithm, we improve retrieval performance under time pressure compared to classic CBR techniques. We present some results relating to the perfor...

  1. Enhancing food engineering education with interactive web-based simulations

    Directory of Open Access Journals (Sweden)

    Alexandros Koulouris

    2015-04-01

    Full Text Available In the traditional deductive approach in teaching any engineering topic, teachers would first expose students to the derivation of the equations that govern the behavior of a physical system and then demonstrate the use of equations through a limited number of textbook examples. This methodology, however, is rarely adequate to unmask the cause-effect and quantitative relationships between the system variables that the equations embody. Web-based simulation, which is the integration of simulation and internet technologies, has the potential to enhance the learning experience by offering an interactive and easily accessible platform for quick and effortless experimentation with physical phenomena.This paper presents the design and development of a web-based platform for teaching basic food engineering phenomena to food technology students. The platform contains a variety of modules (“virtual experiments” covering the topics of mass and energy balances, fluid mechanics and heat transfer. In this paper, the design and development of three modules for mass balances and heat transfer is presented. Each webpage representing an educational module has the following features: visualization of the studied phenomenon through graphs, charts or videos, computation through a mathematical model and experimentation.  The student is allowed to edit key parameters of the phenomenon and observe the effect of these changes on the outputs. Experimentation can be done in a free or guided fashion with a set of prefabricated examples that students can run and self-test their knowledge by answering multiple-choice questions.

  2. An object-oriented feature-based design system face-based detection of feature interactions

    International Nuclear Information System (INIS)

    This paper presents an object-oriented, feature-based design system which supports the integration of design and manufacture by ensuring that part descriptions fully account for any feature interactions. Manufacturing information is extracted from the feature descriptions in the form of volumes and Tool Access Directions, TADs. When features interact, both volumes and TADs are updated. This methodology has been demonstrated by developing a prototype system in which ACIS attributes are used to record feature information within the data structure of the solid model. The system implemented in the C++ programming language and embedded in a menu-driven X-windows user interface to the ACIS 3D Toolkit. (author)

  3. Magnetic interactions in martensitic Ni-Mn based Heusler systems

    Energy Technology Data Exchange (ETDEWEB)

    Aksoy, Seda

    2010-04-22

    In this work, magnetic, magnetocaloric and structural properties are investigated in Ni-Mn-based martensitic Heusler alloys with the aim to tailor these properties as well as to understand in detail the magnetic interactions in the various crystallographic states of these alloys. We choose Ni{sub 50}Mn{sub 34}In{sub 16} as a prototype which undergoes a martensitic transformation and exhibits field-induced strain and the inverse magnetocaloric effect. Using the structural phase diagram of martensitic Ni-Mn-based Heusler alloys, we substitute gallium and tin for indium to carry these effects systematically closer to room temperature by shifting the martensitic transformation. A magneto-calorimeter is designed and built to measure adiabatically the magnetocaloric effect in these alloys. The temperature dependence of strain under an external magnetic field is studied in Ni{sub 50}Mn{sub 50-x}Z{sub x} (Z: Ga, Sn, In and Sb) and Ni{sub 50}Mn{sub 34}In{sub 16-x}Z{sub x} (Z: Ga and Sn). An argument based on the effect of the applied magnetic field on martensite nucleation is adopted to extract information on the direction of the magnetization easy axis in the martensitic unit cell in Heusler alloys. Parallel to these studies, the structure in the presence of an external field is also studied by powder neutron diffraction. It is demonstrated that martensite nucleation is influenced by cooling the sample under a magnetic field such that the austenite phase is arrested within the martensitic state. The magnetic interactions in Ni{sub 50}Mn{sub 37}Sn{sub 13} and Ni{sub 50}Mn{sub 40}Sb{sub 10} are characterized by using neutron polarization analysis. Below the martensitic transformation temperature, M{sub s}, an antiferromagnetically correlated state is found. Ferromagnetic resonance experiments are carried out on Ni{sub 50}Mn{sub 37}Sn{sub 13} and Ni{sub 50}Mn{sub 34}In{sub 16} to gain more detailed information on the nature of the magnetic interactions. The experimental

  4. Study on the Strategies of Distance Learning Support Services Based on Effective Interaction

    Institute of Scientific and Technical Information of China (English)

    王文琳; 靳桂阳

    2014-01-01

    The paper firstly analyzes the problems of distance learning interaction in order to clarify the significance of implement-ing effective interaction. Then it puts forward the learning support services strategies based on effective interaction, which means to design strategies from the perspective of effective interaction to improve the effect of distance learning.

  5. Photon-Electron Interactions in Graphene-Based Heterojunctions

    Science.gov (United States)

    Liu, Fangze

    Graphene, a single layer of carbon atoms arranged in honeycomb lattice, has been one of the most attractive materials for fundamental and applied research in the past decade. Its unique electronic, optical, thermal, chemical and mechanical properties have lead to the discovery of new physics and many promising applications. In particular, research on photon-electron interaction in graphene-based heterojunctions has revealed a new route to design photoactive devices. In this thesis, I present our work on the synthesis of graphene by chemical vapor deposition (CVD) and the study of graphene-based optoelectronic devices. In addition to the conventional synthesis of graphene on copper (Cu) foils, we also present the CVD synthesis of graphene on a new substrate: palladium (Pd). Especially, we performed detailed study of the nucleation, evolution and morphology of graphene growth on Pd substrate. It helps us to understand the growth reaction mechanism and achieve controllable synthesis of graphene from single layer to multiple layers with different morphologies. We then studied the broadband and ultrasensitive photocurrent and photovoltage response of graphene/silicon (Si) Schottky diodes. For the same architecture, we identified a new photoconductive mode with ultra high photoconductive gain, namely "quantum carrier reinvestment (QCR)". A gain exceeding 107 A/W was demonstrated. The underlying physics of photon-electron interactions in these junctions were studied by a combination of optical characterization tools including Raman spectroscopy, UV-Vis spectroscopy and scanning optical microscopy. The results obtained have been discussed in the framework of the unique electronic band structure, density states, and mobility of graphene, along with the manner in witch photoexcited carrier behave under various externally tuned parameters. We also systematically studied the optimization of performance of graphene/Si and thin transparent graphite/Si junction solar cells and

  6. ON MODELING CONTROLLER-SWITCH INTERACTION IN OPENFLOW BASED SDNS

    Directory of Open Access Journals (Sweden)

    Ameen Chilwan1

    2014-12-01

    Full Text Available With an increase in number of software defined network (SDN deployments, and OpenFlow consolidating as the protocol of choice for controller-switch interactions, a need to analytically model the system for performance analysis is increasing. An attempt has previously been made in [1] to model the system considering both a controller and a switch as an M/M/1 queue. The method, although useful, lacks accuracy for higher probabilities of new flows entering the network. The approach is also deficient of details on how it can be extended to more than one node in the data plane . These two short-comings are addressed in this paper where the controller and switch are modeled collectively as Jackson’s network, with essential tuning to suit OpenFlow-based SDN. The consequent analysis shows the resilience of the model even for higher number of new flow entries. An example is also used to illustrate the case of multiple nodes in the data plane

  7. Sensing Landscape History with an Interactive Location Based Service

    Science.gov (United States)

    van Lammeren, Ron; Goossen, Martin; Roncken, Paul

    2009-01-01

    This paper introduces the STEAD approach for interpreting data acquired by a “human sensor”, who uses an informal interactive location-based service (iLBS) to sense cultural-historic facts and anecdotes of, and in the landscape. This user-generated data is collected outdoors and in situ. The approach consists of four related facets (who, what, where, when). Three of the four facets are discussed and illustrated by user generated data collected during a Dutch survey in 2008. These data represent the personal cultural-historic knowledge and anecdotes of 150 people using a customized iLBS for experiencing the cultural history of a landscape. The “who” facet shows three dominant mentality groups (cosmopolitans, modern materialists and post modern hedonists) that generated user content. The “what” facet focuses on three subject types of pictures and four picture framing classes. Pictures of the place type showed to be dominant and foreground framing class was slightly favourite. The “where” facet is explored via density, distribution, and distance of the pictures made. The illustrations of the facets indirectly show the role of the “human sensor” with respect to the domain of interest. The STEAD approach needs further development of the when-facet and of the relations between the four facets. Finally the results of the approach may support data archives of iLBS applications. PMID:22399994

  8. Magnetostatic interactions in artificial ferrimagnet based magnetic tunnel junctions

    Energy Technology Data Exchange (ETDEWEB)

    Tiusan, C.; Dimopoulos, T.; Buda, L.; Da Costa, V.; Ounadjela, K.; Hehn, M.; van den Berg, H.

    2001-06-01

    Magnetostatic interactions between the soft and the hard magnetic electrodes in magnetic tunnel junctions (MTJs) using artificial ferrimagnets (AFis) are analyzed. We attribute these interactions to the dispersion fields associated to magnetic inhomogeneities arising from domain walls due to local anisotropic ordering. These magnetostatic interactions can be controlled by adjusting the net magnetic moment of the AFi to optimize the magnetotransport response of the MTJ devices.{copyright} 2001 American Institute of Physics.

  9. Interactive Packaging Solutions Based on RFIDTechnology and Controlled Delamination Material

    OpenAIRE

    Gao, Jie; Pang, Zhibo; Chen, Qiang; Zheng, Li-Rong

    2010-01-01

    Interactive packaging is an emerging research area in recent years. It brings people convenient and smart lives, reduces consumption of traditional packaging materials and direct or indirect labor costs as well. Being integrated in interactive packaging, Radio Frequency Identification (RFID) technology becomes one of the most proactive development enablers. In this paper, an interactive and intelligent packaging solution integrating passive RFID system and Controlled Delamination Material (CD...

  10. Intelligent and Interactive Package Based on RFID and WSN

    OpenAIRE

    Gao, Jie

    2011-01-01

       An intelligent and interactive package can interact with people smartly, safely and friendly. It involves many technologies such as electronics, optics, biologic, magnetics and electro-mechanics. By combined with Radio Frequency Identification (RFID) and Wireless Sensor Network (WSN), intelligent and interactive packaging technology has been an emerging and global research topic over the years.    In this thesis, a new technology, named Controlled Delamination Material (CDM), is introduced...

  11. Social Network Extraction and Analysis Based on Multimodal Dyadic Interaction

    OpenAIRE

    Bogdan Raducanu; Sergio Escalera; Xavier Baró; Petia Radeva; Jordi Vitrià

    2012-01-01

    Social interactions are a very important component in people’s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times’ Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose ...

  12. Eye-based head gestures for interaction in the car

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Witzner Hansen, Dan

    2013-01-01

    that can be used as an alternative input in the multimodal interaction context. Two approaches are described for using this method for interaction with objects inside or outside the car. Some application examples are described where the discrete or continuous head movements in combination with the driver......’s visual attention can be used for controlling the objects inside the car....

  13. Formalizing argument-based agent interaction in electronic institutions

    OpenAIRE

    Chesñevar, Carlos Iván

    2001-01-01

    During the last decade the notion of agent has gained acceptance within the AI community, mainly due to its adequacy to formalize complex environments. Agents can be thought as active software objects, which may be autonomous and able to perceive, reason, act, and interact with other agents. When agents interact with each other, a multi-agent system (MAS) arises.

  14. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data

    OpenAIRE

    Rao Kanury; Shapiro Alex; Kumar Dhiraj; Pache Lars; Jäger Stefanie; Mahon Cathal; Bennett Melanie J; Fahey Marie E; Chanda Sumit K; Craik Charles S; Frankel Alan D; Krogan Nevan J

    2011-01-01

    Abstract Background The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data. Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to generate integrated HIV-human interaction networks. Results We have developed a web-based platform, termed GPS-Prot http://www.gpspro...

  15. Study on Distance Learning Support Services Strategy Based on Effective Interaction

    Institute of Scientific and Technical Information of China (English)

    王文琳; 靳桂阳

    2014-01-01

    Achieving effective interaction can the students get good learning results, and enhance the quality of distance learning. The paper firstly analyzes the research on distance learning support services and the problems of distance learning interaction in or-der to clarify the significance of implementing effective interaction. Then it puts forward the learning support services strategies based on effective interaction, which means to promote distance learning interaction and enhance the students' self-learning abili-ty.

  16. Illuminating Spatial and Temporal Organization of Protein Interaction Networks by Mass Spectrometry-Based Proteomics

    OpenAIRE

    Yang, Jiwen; Wagner, Sebastian A; Beli, Petra

    2015-01-01

    Protein–protein interactions are at the core of all cellular functions and dynamic alterations in protein interactions regulate cellular signaling. In the last decade, mass spectrometry (MS)-based proteomics has delivered unprecedented insights into human protein interaction networks. Affinity purification-MS (AP-MS) has been extensively employed for focused and high-throughput studies of steady state protein–protein interactions. Future challenges remain in mapping transient protein interact...

  17. Preprint Touch-less Interactive Augmented Reality Game on Vision Based Wearable Device

    OpenAIRE

    Lv, Zhihan; Halawani, Alaa; Feng, Shengzhong; Rehman, Shafiq Ur; Li, Haibo

    2015-01-01

    This is the preprint version of our paper on Personal and Ubiquitous Computing. There is an increasing interest in creating pervasive games based on emerging interaction technologies. In order to develop touch-less, interactive and augmented reality games on vision-based wearable device, a touch-less motion interaction technology is designed and evaluated in this work. Users interact with the augmented reality games with dynamic hands/feet gestures in front of the camera, which triggers the i...

  18. Expectation-driven interaction: a model based on Luhmann's contingency approach

    CERN Document Server

    Barber, M J; Buchinger, E; Cessac, B; Streit, L; Blanchard, Ph.

    2006-01-01

    We introduce an agent-based model of interaction, drawing on the contingency approach from Luhmann's theory of social systems. The agent interactions are defined by the exchange of distinct messages. Message selection is based on the history of the interaction and developed within the confines of the problem of double contingency. We examine interaction strategies in the light of the message-exchange description using analytical and computational methods.

  19. An association study of NRAMP1, VDR, MBL and their interaction with the susceptibility to tuberculosis in a Chinese population

    Directory of Open Access Journals (Sweden)

    Linlin Wu

    2015-09-01

    Conclusions: Our study suggests that genotypes of many polymorphic genes are associated with TB, it is necessary to further explore the mechanism of genotypes and gene-gene interaction in susceptibility to tuberculosis.

  20. The competitive facility location based on the spatial interaction model

    Directory of Open Access Journals (Sweden)

    naeme zarrinpoor

    2012-03-01

    Full Text Available In this paper, a nonlinear model for locating service facilities is introduced in a competitive ‎ region. In the proposed model the factors of travel time, quality of service facilities and price ‎ are considered that are the most important effective factors in attracting and maintaining the ‎ customers in the competitive environments. For identifying the customers’ probabilistic ‎ behavior in selecting the competitor’s and entering firm’s facilities, the spatial interaction ‎ model and Logit function are used. Since the decision making for locating is not only based on ‎ the sale quantity and market demand captured and ignoring other important organizational ‎ goals such as minimizing the cost may provide problems in long term for firms, therefore in ‎ addition to the capturing demand, the fixed cost of locating is considered in the model that ‎ will provide better results in the real world problems. Due to the computational complexity, a ‎ genetic algorithm is developed for solving the model. The numerical results verify the ‎ performance of the proposed model and effectiveness of ‏ ‏ ‎ the genetic algorithm in solving it ‏ ‏ and show that the study of costumers’ ‎ ‏ ‏ probabilistic demand considering the factors of price, ‎ travel time and quality of service facilities has the major role in the increasing of sale and profit ‎ of the entering firm so that, in spite of selecting the most appropriate locations by the ‎ competitor, the ‏ ‏ sale and profit quantities of entering firm are more than the competitor’s, in the ‎ equal situation of price, quality and number of facilities. ‎

  1. Interactive computer-based training program for radiological workers

    International Nuclear Information System (INIS)

    Lawrence Livermore National Laboratory is redesigning its existing Computer-Based Training (CBT) programs for radiological workers. The redesign represents a major effort that is aimed at producing a single highly interactive and flexible CBT program. The new CBT program is designed to address a variety of radiological workers, including researchers, x-ray operators, and individuals working in tritium, uranium, plutonium, and accelerator facilities. The program addresses the diversity of backgrounds found at a national laboratory. The CBT program includes photographs, line drawings and illustrations, sound, video, and simulations, and it allows for easy insertion and replacement of text, graphics, sound, and video. The new design supports timely updates and customization for use at other University of California sites. The CBT program is divided into ten basic modules. Introduction and Lessons Learned, History and Uses, Fundamentals, Background Radiation, Biological Effects of Radiation, Characteristics of Radionuclides, Radiological Controls, Monitoring, Emergency Response, Responsibilities. Some of the main modules features as many as seven or eight submodules. For example, the module on Characteristics of Radionuclides features submodules on common radionuclides, tritium uranium, plutonium, x-ray machines, E-beam devices, radiographic devices, and accelerators. Required submodules are tailored to an individual's type of work and facility, and they are determined by the answers to an onscreen questionnaire given at the outset of training. Individuals can challenge most individual modules, but certain submodules will be mandatory based on the initial survey. For example, individuals working in the uranium facility will be required to complete the submodule on 'History and Uses of Uranium'. However, all other submodules under the main module, 'History and Uses', will be available if selected for preview. For each module, an opportunity is provided for further

  2. Interactive, Computer-Based Training Program for Radiological Workers

    International Nuclear Information System (INIS)

    Lawrence Livermore National Laboratory (LLNL) is redesigning its Computer-Based Training (CBT) program for radiological workers. The redesign represents a major effort to produce a single, highly interactive and flexible CBT program that will meet the training needs of a wide range of radiological workers--from researchers and x-ray operators to individuals working in tritium, uranium, plutonium, and accelerator facilities. The new CBT program addresses the broad diversity of backgrounds found at a national laboratory. When a training audience is homogeneous in terms of education level and type of work performed, it is difficult to duplicate the effectiveness of a flexible, technically competent instructor who can tailor a course to the express needs and concerns of a course's participants. Unfortunately, such homogeneity is rare. At LLNL, they have a diverse workforce engaged in a wide range of radiological activities, from the fairly common to the quite exotic. As a result, the Laboratory must offer a wide variety of radiological worker courses. These include a general contamination-control course in addition to radioactive-material-handling courses for both low-level laboratory (i.e., bench-top) activities as well as high-level work in tritium, uranium, and plutonium facilities. They also offer training courses for employees who work with radiation-generating devices--x-ray, accelerator, and E-beam operators, for instance. However, even with the number and variety of courses the Laboratory offers, they are constrained by the diversity of backgrounds (i.e., knowledge and experience) of those to be trained. Moreover, time constraints often preclude in-depth coverage of site- and/or task-specific details. In response to this situation, several years ago LLNL began moving toward computer-based training for radiological workers. Today, that CBT effort includes a general radiological safety course developed by the Department of Energy's Hanford facility and a

  3. Pendaphonics: A Tangible Pendulum-based Sonic Interaction Experience

    DEFF Research Database (Denmark)

    Overholt, Daniel; Hansen, Anne-Marie S.; Burleson, Winslow;

    2009-01-01

    , presents a strategy for the design and evaluation of a low-cost, flexible, distributed system for public interaction and performance in a large scale tangible system. Pendaphonics has been installed in a public new media arts space, where over 200 people experienced the initial opening of the environment......, and is now active within five different research university interaction laboratories. This paper presents the development process and findings from observations and evaluation of Pendaphonics’ users and the social interaction patterns among performers and members of the public. In particular, the...

  4. Interaction Junk: User Interaction-Based Evaluation of Visual Analytic Systems

    Energy Technology Data Exchange (ETDEWEB)

    Endert, Alexander; North, Chris

    2012-10-14

    With the growing need for visualization to aid users in understanding large, complex datasets, the ability for users to interact and explore these datasets is critical. As visual analytic systems have advanced to leverage powerful computational models and data analytics capabilities, the modes by which users engage and interact with the information are limited. Often, users are taxed with directly manipulating parameters of these models through traditional GUIs (e.g., using sliders to directly manipulate the value of a parameter). However, the purpose of user interaction in visual analytic systems is to enable visual data exploration – where users can focus on their task, as opposed to the tool or system. As a result, users can engage freely in data exploration and decision-making, for the purpose of gaining insight. In this position paper, we discuss how evaluating visual analytic systems can be approached through user interaction analysis, where the goal is to minimize the cognitive translation between the visual metaphor and the mode of interaction (i.e., reducing the “Interactionjunk”). We motivate this concept through a discussion of traditional GUIs used in visual analytics for direct manipulation of model parameters, and the importance of designing interactions the support visual data exploration.

  5. Gene-gene interaction in regulatory T-cell function in atopy and asthma development in childhood

    NARCIS (Netherlands)

    Bottema, R.W.B.; Kerkhof, M.; Reijmerink, N.E.; Thijs, C.; Smit, H.A.; Schayck, C.P. van; Brunekreef, B.; Oosterhout, A.J.; Postma, D.S.; Koppelman, G.H.

    2010-01-01

    BACKGROUND: Regulatory T-cell dysfunction is associated with development of the complex genetic conditions atopy and asthma. Therefore, we hypothesized that single nucleotide polymorphisms in genes involved in the development and function of regulatory T cells are associated with atopy and asthma de

  6. Gene-gene interaction in regulatory T-cell function in atopy and asthma development in childhood

    NARCIS (Netherlands)

    Bottema, Renske W. B.; Kerkhof, Marjan; Reijmerink, Naomi E.; Thijs, Carel; Smit, Henriette A.; van Schayck, Constant P.; Brunekreef, Bert; van Oosterhout, Antoon J.; Postma, Dirkje S.; Koppelman, Gerard H.

    2010-01-01

    Background: Regulatory T-cell dysfunction is associated with development of the complex genetic conditions atopy and asthma. Therefore, we hypothesized that single nucleotide polymorphisms in genes involved in the development and function of regulatory T cells are associated with atopy and asthma de

  7. Genetic polymorphisms and possible gene-gene interactions in metabolic and DNA repair genes: Effects on DNA damage

    Czech Academy of Sciences Publication Activity Database

    Naccarati, Alessio; Souček, P.; Štětina, R.; Haufroid, V.; Kumar, R.; Vodičková, Ludmila; Trtková, K.; Dušinská, M.; Hemminki, K.; Vodička, Pavel

    2006-01-01

    Roč. 593, 1-2 (2006), s. 22-31. ISSN 0027-5107 R&D Projects: GA ČR GA310/03/0437 Institutional research plan: CEZ:AV0Z5039906 Keywords : Single-strand breaks * Genetic polymorphisms * Metabolism Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.111, year: 2006

  8. Support for Dynamic Service Composition with Role-Based Interaction Model

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    This paper aims to present a role-based interaction model for dynamic service composition in Grid environments. Assigning roles to a service means to associate with it capabilities that describes all the operations the service intends to perform. When all of the services can be recognized by their roles, the appropriate services can be selected. Based on the interaction policy, a role-based interaction model not only facilitates access control, but also offers flexible interaction mechanism for adapting service-oriented applications. This interaction model adopts programmable reactive tuple space to facilitate context-dependent coordination.

  9. Mobile gaze-based screen interaction in 3D environments

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Witzner Hansen, Dan

    2011-01-01

    Head-mounted eye trackers can be used for mobile interaction as well as gaze estimation purposes. This paper presents a method that enables the user to interact with any planar digital display in a 3D environment using a head-mounted eye tracker. An effective method for identifying the screens in...... the field of view of the user is also presented which can be applied in a general scenario in which multiple users can interact with multiple screens. A particular application of using this technique is implemented in a home environment with two big screens and a mobile phone. In this application a...... user was able to interact with these screens using a wireless head-mounted eye tracker....

  10. A Framework for music-based interactive sonification

    OpenAIRE

    Correia Da Silva Diniz, Nuno; Deweppe, Alexander; Demey, Michiel; Leman, Marc

    2010-01-01

    In this paper, a framework for interactive sonification is introduced. It is argued that electroacoustic composition techniques can provide a methodology for structuring and presenting multivariable data through sound. Furthermore, an embodied music cognition driven interface is applied to provide an interactive exploration of the generated output. The motivation and theoretical foundation for this work are presented as well as the framework’s implementation and an exploratory use case.

  11. Web user interaction : a declarative approach based on XForms

    OpenAIRE

    Honkala, Mikko

    2007-01-01

    This thesis studies next-generation web user interaction definition languages, as well as browser software architectures. The motivation comes from new end-user requirements for web applications: demand for higher interaction, adaptation for mobile and multimodal usage, and rich multimedia content. At the same time, there is a requirement for non-programmers to be able to author, customize, and maintain web user interfaces. Current user interface tools do not support well these new kinds ...

  12. Finding interaction partners using cognition-based decision strategies

    OpenAIRE

    Dutta, Partha S.; Moreau, Luc; Jennings, N. R.

    2003-01-01

    In this paper, we develop decision making heuristics for rational agents using artefacts of cognition such as observation, learning and memory. Specifically, we extend previous research in this area by incorporating essential aspects of multi-agent interactions such as building behavioural models via observation, selectively choosing interaction partners and forming cooperating groups by identifying mutual capabilities. In particular, we demonstrate that cognitive capabilities enable agents t...

  13. Creep-plasticity interaction model based on internal time concept

    International Nuclear Information System (INIS)

    The present paper describes the general framework for creep-plasticity interaction model by introducing a new intrinsic time measure derived from the fundamental integral stress-strain relation itself. By combining creep model of Norton type, the present interaction model is almost identical with the recent unified model of ONERA. Also, the obtained numerical example is shown to improve the stress-strain response compared to the previous internal time theory. (author)

  14. Acid-base interactions in microbial adhesion to hexadecane and chloroform

    NARCIS (Netherlands)

    Bos, R; Busscher, HJ; Geertsema-Doornbusch, GI; Van Der Mei, HC; Mittal, KL

    2000-01-01

    Acid-base interactions play an important role in adhesion, including microbial adhesion to surfaces. Qualitatively acid-base interactions in microbial adhesion can be demonstrated by comparing adhesion to hexadecane (a negatively charged interface in aqueous solutions, unable to exert acid-base inte

  15. The in Silico Insight into Carbon Nanotube and Nucleic Acid Bases Interaction

    Science.gov (United States)

    Karimi, Ali Asghar; Ghalandari, Behafarid; Tabatabaie, Seyed Saleh; Farhadi, Mohammad

    2016-01-01

    Background To explore practical applications of carbon nanotubes (CNTs) in biomedical fields the properties of their interaction with biomolecules must be revealed. Recent years, the interaction of CNTs with biomolecules is a subject of research interest for practical applications so that previous research explored that CNTs have complementary structure properties with single strand DNA (ssDNA). Objectives Hence, the quantum mechanics (QM) method based on ab initio was used for this purpose. Therefore values of binding energy, charge distribution, electronic energy and other physical properties of interaction were studied for interaction of nucleic acid bases and SCNT. Materials and Methods In this study, the interaction between nucleic acid bases and a (4, 4) single-walled carbon nanotube (SCNT) were investigated through calculations within quantum mechanics (QM) method at theoretical level of Hartree-Fock (HF) method using 6-31G basis set. Hence, the physical properties such as electronic energy, total dipole moment, charge distributions and binding energy of nucleic acid bases interaction with SCNT were investigated based on HF method. Results It has been found that the guanine base adsorption is bound stronger to the outer surface of nanotube in comparison to the other bases, consistent with the recent theoretical studies. In the other words, the results explored that guanine interaction with SCNT has optimum level of electronic energy so that their interaction is stable. Also, the calculations illustrated that SCNT interact to nucleic acid bases by noncovalent interaction because of charge distribution an electrostatic area is created in place of interaction. Conclusions Consequently, small diameter SCNT interaction with nucleic acid bases is noncovalent. Also, the results revealed that small diameter SCNT interaction especially SCNT (4, 4) with nucleic acid bases can be useful in practical application area of biomedical fields such detection and drug delivery.

  16. Social Network Extraction and Analysis Based on Multimodal Dyadic Interaction

    Directory of Open Access Journals (Sweden)

    Bogdan Raducanu

    2012-02-01

    Full Text Available Social interactions are a very important component in people’s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times’ Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links’ weights are a measure of the “influence” a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

  17. Situated dialog in speech-based human-computer interaction

    CERN Document Server

    Raux, Antoine; Lane, Ian; Misu, Teruhisa

    2016-01-01

    This book provides a survey of the state-of-the-art in the practical implementation of Spoken Dialog Systems for applications in everyday settings. It includes contributions on key topics in situated dialog interaction from a number of leading researchers and offers a broad spectrum of perspectives on research and development in the area. In particular, it presents applications in robotics, knowledge access and communication and covers the following topics: dialog for interacting with robots; language understanding and generation; dialog architectures and modeling; core technologies; and the analysis of human discourse and interaction. The contributions are adapted and expanded contributions from the 2014 International Workshop on Spoken Dialog Systems (IWSDS 2014), where researchers and developers from industry and academia alike met to discuss and compare their implementation experiences, analyses and empirical findings.

  18. Interactive Multimedia-Based E-Learning: A Study of Effectiveness

    Science.gov (United States)

    Zhang, Dongsong

    2005-01-01

    The author conducted two experiments to assess effectiveness of interactive e-learning. Students in a fully interactive multimedia-based e-learning environment achieved better performance and higher levels of satisfaction than those in a traditional classroom and those in a less interactive e-learning environment.

  19. Magnet-based Around Device Interaction for Playful Music Composition and Gaming

    NARCIS (Netherlands)

    A. El Ali; H. Ketabdar

    2013-01-01

    Around Device Interaction (ADI) has expanded the interaction space on mobile devices to allow 3D gesture interaction around the device. In this paper, the authors look specifically at magnet-based ADI and its applied use in a playful, music-related context. Using three musical applications developed

  20. A Qualitative Examination of Two Year-Olds Interaction with Tablet Based Interactive Technology

    Science.gov (United States)

    Geist, Eugene A.

    2012-01-01

    The purpose of this study was to observe children naturally interacting with these touch screen devices. Little direct instruction was given to the children on the use of the devices however an adult did assist when needed. The device was introduced to the children as would be any other educational material such as play-dough, new items in the…

  1. Web-Based Interactive Visualization in an Information Retrieval Course.

    Science.gov (United States)

    Brusilovsky, Peter

    Interactive visualization is a powerful educational tool. It has been used to enhance the teaching of various subjects from computer science to chemistry to engineering. In computer science education, this powerful tool is used almost exclusively in programming and data structure courses. This paper suggests that visualization could be very…

  2. Component Based System Framework for Dynamic B2B Interaction

    NARCIS (Netherlands)

    Hu jinmin, H.J.; Grefen, P.W.P.J.

    2002-01-01

    Business-to-business (B2B) collaboration is becoming a pivotal way to bring today's enterprises to success in the dynamically changing, e-business environment. Though many business-to-business protocols are developed to support B2B interaction, none are generally accepted. A B2B system should suppor

  3. Map-based mobile services design, interaction and usability

    CERN Document Server

    Meng, Liqui; Winter, Stephan; Popovich, Vasily

    2008-01-01

    Reports the research and technical achievements on the following theme blocks: Design of mobile map services and its constraints; Typology and usability of mobile map services; Visualization solutions on small displays for time-critical tasks; Mobile map users; Interaction and adaptation in mobile environments; and more.

  4. Interaction force microscopy based on quartz tuning fork force sensor

    Science.gov (United States)

    Qin, Yexian

    The ability to sense small changes in the interaction force between a scanning probe microscope (SPM) tip and a substrate requires cantilevers with a sharp mechanical resonance. A typical commercially available cantilever in air is characterized by a resonance with a Q factor of 100 ˜ 300. The low Q factor can be attributed to imperfections in the cantilever itself as well as damping effects of the surrounding air. To substantially increase the Q factor, novel concepts are required. For this reason, we have performed a systematic study of quartz tuning fork resonators for possible use with SPMs. We find that tuning fork resonators operating in air are characterized by Q factors in the order of 104, thereby greatly improving the SPM's ability to measure small shifts in the interaction force. By carefully attaching commercially available SPM tips to the tuning fork, it is possible to obtain SPM images using non-contact imaging techniques and analyze the tip-sample interactions. The assembly of uniform molecular monolayers on atomically flat substrates for molecular electronics applications has received widespread attention during the past ten years. Scanning probe techniques are often used to assess substrate topography, molecular ordering and electronic properties, yet little is known about the fundamental tip-molecule interaction. To address this issue we have built an Interaction Force Microscope using a quartz tuning fork to probe tip-molecular monolayer interactions using scanning probe microscopy. The high quality factor and stable resonant frequency of a quartz tuning fork allows accurate measurement of small shifts in the resonant frequency as the tip interacts with the substrate. To permit an accurate measure of surface interaction forces, the electrical and piezomechanical properties of a tuning fork have been calibrated using a fiber optical interferometer. In prior work [1], we have studied molecular layers formed from either 4-Trifluoro

  5. Illuminating spatial and temporal organization of protein interaction networks by mass spectrometry-based proteomics

    OpenAIRE

    Jiwen eYang; Sebastian Alexander Wagner; Petra eBeli

    2015-01-01

    Protein-protein interactions are at the core of all cellular functions and dynamic alterations in protein interactions regulate cellular signaling. In the last decade, mass spectrometry-based proteomics has delivered unprecedented insights into human protein interaction networks. Affinity purification-mass spectrometry has been extensively employed for focused and high-throughput studies of steady state protein-protein interactions. Future challenges remain in mapping transient protein intera...

  6. A secure mobile phone-based interactive logon in Windows

    OpenAIRE

    Bodriagov, Oleksandr

    2010-01-01

    Password-based logon schemes have many security weaknesses. Smart card and biometric based authentication solutions are available as a replacement for standard password-based schemes for security sensitive environments. However, the cost of deployment and maintenance of these systems is quite high. On the other hand, mobile network operators have a huge base of deployed smart cards that can be reused to provide authentication in other areas significantly reducing costs. This master s thesis ...

  7. Interaction Protocols in Multi-Agent Systems based on Agent Petri Nets Model

    Directory of Open Access Journals (Sweden)

    Kamel Barkaoui

    2013-08-01

    Full Text Available This paper deals with the modeling of interaction between agents in Multi Agents System (MAS based on Agent Petri Nets (APN. Our models are created based on communicating agents. Indeed, an agent initiating a conversation with other can specify the interaction protocol wishes to follow. The combination of APN and FIPA Protocols schemes leads to a set of deployment formal rules for points where model interaction can be successfully implemented. We introduce some models FIPA standard protocols.

  8. Preprint Extending Touch-less Interaction on Vision Based Wearable Device

    OpenAIRE

    Lv, Zhihan; Feng, Liangbing; Feng, Shengzhong; Li, Haibo

    2015-01-01

    This is the preprint version of our paper on IEEE Virtual Reality Conference 2015. A touch-less interaction technology on vision based wearable device is designed and evaluated. Users interact with the application with dynamic hands/feet gestures in front of the camera. Several proof-of-concept prototypes with eleven dynamic gestures are developed based on the touch-less interaction. At last, a comparing user study evaluation is proposed to demonstrate the usability of the touch-less approach...

  9. HEMORHEOLOGICAL IMPLICATIONS OF PERFLUOROCARBON BASED OXYGEN CARRIER INTERACTION WITH COLLOID PLASMA EXPANDERS AND BLOOD

    OpenAIRE

    Vásquez, Diana M.; Ortiz, Daniel; Alvarez, Oscar A.; Briceño, Juan C.; Cabrales, Pedro

    2013-01-01

    Perfluorocarbon (PFC) emulsion based oxygen carriers lack colloid osmotic pressure (COP) and must be administered with colloid-based plasma expanders (PEs). Although PFC emulsions have been widely studied, there is limited information about PFC emulsion interaction with PEs and blood. Their interaction forms aggregates due to electrostatic and rheological phenomena, and change blood rheology and blood flow. This study analyzes the effects of the interaction between PFC emulsions with blood in...

  10. Workstation-based interactive accident simulator for the MHTGR

    International Nuclear Information System (INIS)

    This paper summarizes research performed at Oak Ridge National Laboratory (ORNL) to assist the Nuclear Regulatory Commission (NRC) in preliminary determinations of licensability of the US Department of Energy (DOE) reference design of a standard modular high- temperature gas-cooled reactor (MHTGR). Accidents transients in MHTGRs are characterized by very long heatup times due to the large core heat capacity. This paper describes the development and use of an interactive simulation tool for performing independent analyses of MHTGR postulated core heatup accidents

  11. The competitive facility location based on the spatial interaction model

    OpenAIRE

    naeme zarrinpoor; maryam esmaeeli

    2012-01-01

    In this paper, a nonlinear model for locating service facilities is introduced in a competitive ‎ region. In the proposed model the factors of travel time, quality of service facilities and price ‎ are considered that are the most important effective factors in attracting and maintaining the ‎ customers in the competitive environments. For identifying the customers’ probabilistic ‎ behavior in selecting the competitor’s and entering firm’s facilities, the spatial interaction ‎ model and Logit...

  12. Structuring Task-based Interaction through Collaborative Learning Techniques (2)

    Institute of Scientific and Technical Information of China (English)

    William Littlewood

    2004-01-01

    @@ Techniques for collaborative learning In this section the focus will move from broad strategies to specific techniques (often also called "structures") through which the strategies can be realized. It gives a selection of techniques which have proved (in my own experience as well as that of others) particularly useful in pro-viding contexts for practice, exploration and /or interaction in the second language classroom.

  13. Intentions: a confident-based interaction design for smart spaces

    OpenAIRE

    Vega Barbas, Mario; Valero Duboy, Miguel Ángel

    2013-01-01

    The paradigm of ubiquitous computing has become a reference for the design of Smart Spaces. Current trends in Ambient Intelligence are increasingly related to the scope of Internet of Things. This paradigm has the potential to support cost-effective solutions in the fields of telecare, e-health and Ambient Assisted Living. Nevertheless, ubiquitous computing does not provide end users with a role for proactive interactions with the environment. Thus, the deployment of smart health care service...

  14. New Understandings of Quantum Mechanics Based on Interaction

    OpenAIRE

    Zeng, Tian-Hai

    2010-01-01

    The interaction between two parts in a compound quantum system may be reconsidered more completely than before and some new understandings and conclusions different from current quantum mechanics are obtained, including the conservation law in the evolution in an isolated quantum system, new understandings of duality of particle and wave and the superposition principle of states, three laws corresponding to Newton's laws, new understandings of measurement and the uncertainty relation, argumen...

  15. Model-based description of environment interaction for mobile robots

    Science.gov (United States)

    Borghi, Giuseppe; Ferrari, Carlo; Pagello, Enrico; Vianello, Marco

    1999-01-01

    We consider a mobile robot that attempts to accomplish a task by reaching a given goal, and interacts with its environment through a finite set of actions and observations. The interaction between robot and environment is modeled by Partially Observable Markov Decision Processes (POMDP). The robot takes its decisions in presence of uncertainty about the current state, by maximizing its reward gained during interactions with the environment. It is able to self-locate into the environment by collecting actions and perception histories during the navigation. To make the state estimation more reliable, we introduce an additional information in the model without adding new states and without discretizing the considered measures. Thus, we associate to the state transition probabilities also a continuous metric given through the mean and the variance of some significant sensor measurements suitable to be kept under continuous form, such as odometric measurements, showing that also such unreliable data can supply a great deal of information to the robot. The overall control system of the robot is structured as a two-levels layered architecture, where the low level implements several collision avoidance algorithms, while the upper level takes care of the navigation problem. In this paper, we concentrate on how to use POMDP models at the upper level.

  16. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    , and demonstrated in public settings. We then describe INTERACT, a proposed research project that stages the robotic marionettes in a live performance. The interdisciplinary project brings humanities research to bear on scientific and technological inquiry, and culminates in the development a live......This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...

  17. Interactions

    DEFF Research Database (Denmark)

    The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists such as...

  18. Aerosol-cirrus interactions: a number based phenomenon at all?

    Directory of Open Access Journals (Sweden)

    M. Seifert

    2004-01-01

    Full Text Available In situ measurements of the partitioning of aerosol particles within cirrus clouds were used to investigate aerosol-cloud interactions in ice clouds. The number density of interstitial aerosol particles (non-activated particles in between the cirrus crystals was compared to the number density of cirrus crystal residuals. The data was obtained during the two INCA (Interhemispheric Differences in Cirrus Properties from Anthropogenic Emissions campaigns, performed in the Southern Hemisphere (SH and Northern Hemisphere (NH midlatitudes. Different aerosol-cirrus interactions can be linked to the different stages of the cirrus lifecycle. Cloud formation is linked to positive correlations between the number density of interstitial aerosol (Nint and crystal residuals (Ncvi, whereas the correlations are smaller or even negative in a dissolving cloud. Unlike warm clouds, where the number density of cloud droplets is positively related to the aerosol number density, we observed a rather complex relationship when expressing Ncvi as a function of Nint for forming clouds. The data sets are similar in that they both show local maxima in the Nint range 100 to 200cm, where the SH- maximum is shifted towards the higher value. For lower number densities Nint and Ncvi are positively related. The slopes emerging from the data suggest that a tenfold increase in the aerosol number density corresponds to a 3 to 4 times increase in the crystal number density. As Nint increases beyond the ca. 100 to 200cm, the mean crystal number density decreases at about the same rate for both data sets. For much higher aerosol number densities, only present in the NH data set, the mean Ncvi remains low. The situation for dissolving clouds allows us to offer two possible, but at this point only speculative, alternative interactions between aerosols and cirrus: evaporating clouds might be associated with a source of aerosol particles, or air pollution (high aerosol number density might

  19. Testing gene-environment interactions in family-based association studies using trait-based ascertained samples

    OpenAIRE

    Zhang, Weiming; Langefeld, Carl D.; Grunwald, Gary K; Fingerlin, Tasha E

    2013-01-01

    The study of gene-environment interactions is an increasingly important aspect of genetic epidemiological investigation. Historically, it has been difficult to study gene-environment interactions using a family-based design for quantitative traits or when parent-offspring trios were incomplete. The QBAT-I[1] provides researchers a tool to estimate and test for a gene-environment interaction in families of arbitrary structure that are sampled without regard to the phenotype of interest, but is...

  20. Comprehensive characterization of molecular interactions based on nanomechanics.

    Directory of Open Access Journals (Sweden)

    Murali Krishna Ghatkesar

    Full Text Available Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6 Da adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions.

  1. Inferring microbial interaction networks based on consensus similarity network fusion.

    Science.gov (United States)

    Jiang, XingPeng; Hu, XiaoHua

    2014-11-01

    With the rapid accumulation of high-throughput metagenomic sequencing data, it is possible to infer microbial species relations in a microbial community systematically. In recent years, some approaches have been proposed for identifying microbial interaction network. These methods often focus on one dataset without considering the advantage of data integration. In this study, we propose to use a similarity network fusion (SNF) method to infer microbial relations. The SNF efficiently integrates the similarities of species derived from different datasets by a cross-network diffusion process. We also introduce consensus k-nearest neighborhood (Ck-NN) method instead of k-NN in the original SNF (we call the approach CSNF). The final network represents the augmented species relationships with aggregated evidence from various datasets, taking advantage of complementarity in the data. We apply the method on genus profiles derived from three microbiome datasets and we find that CSNF can discover the modular structure of microbial interaction network which cannot be identified by analyzing a single dataset. PMID:25326827

  2. Effects of van der Waals interaction for first-principles calculations on iron-based superconductors

    International Nuclear Information System (INIS)

    Highlights: •van der Waals density functional calculations for iron-based superconductors. •Optimized structures are evaluated. •van der Waals density functional reproduce lattice constants of FeSe. •Except for FeSe, van der Waals interaction hardly affects crystal structures. -- Abstract: We investigate effects of van der Waals (vdW) interaction on various iron-based superconductors by first-principles calculations based on the van der Waals density functional (vdW-DF) taking account of non-local and long range interaction. vdW-DF reproduces well the lattice constants of FeSe, while the crystal structure of other iron-based superconductors are not so sensitive to vdW interaction. These results suggest that the effects of vdW interaction on layered superconductors are often essential although they depend on the characters of the interlayer couplings

  3. Genetic control of eosinophilia in mice: gene(s) expressed in bone marrow-derived cells control high responsiveness

    International Nuclear Information System (INIS)

    A heterogeneity in the capacity of strains of mice to mount eosinophilia is described. BALB/c and C3H are eosinophil high responder strains (EO-HR) and CBA and A/J are eosinophil low responder strains (EO-LR), judged by the response of blood eosinophils to Ascaris suum, and the response of blood, bone marrow, and spleen eosinophils to keyhole limpet hemocyanin given 2 days after 150 mg/kg cyclophosphamide. Some of the gene(s) for high responsiveness appear to be dominant because (EO-HR x EO-LR)F1 mice were intermediate to high responders. This gene is expressed in bone marrow-derived cells because radiation chimeras of the type EO-HR→F1 were high responders and EO-LR→F1 were low responders. This description of a genetic control of eosinophilia in mice may be useful in understanding the role of this cell in parasite immunity and allergy

  4. Gold nanoparticle based colorimetric probe for dopamine detection based on the interaction between dopamine and melamine

    International Nuclear Information System (INIS)

    We report on a probe for the colorimetric and bare-eye detection of dopamine (DA). The optical effect is based on the finding that DA inhibits the melamine-induced aggregation of red gold nanoparticles (AuNPs) to form blue AuNP clusters. We presume that the aggregation induced by melamine is due to its strong hydrogen-bonding interactions with DA. The color changes can be monitored by spectrophotometry or the bare eye. The probes works over the 33 nM to 3.33 mM DA concentration range, and levels down to 33 nM can be quantified. The nanoprobe was successfully applied to the determination of DA in spiked serum. (author)

  5. Template-based structure modeling of protein-protein interactions

    OpenAIRE

    Szilagyi, Andras; Zhang, Yang

    2013-01-01

    The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been wit...

  6. Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

    OpenAIRE

    Lei Yang; Xianglong Tang

    2014-01-01

    Cliques (maximal complete subnets) in protein-protein interaction (PPI) network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based m...

  7. EWS based visual and interactive simulator for plant engineering

    International Nuclear Information System (INIS)

    The 'Plant Engineering Visual and Interactive Simulator (PLEVIS)' is a realtime plant engineering simulator and runs on a general-purpose desk-top engineering workstation with a high-resolution bit-mapped display. PLEVIS is unique in that simulation models are integrated with a control/interlock model editor. PLEVIS can be used in a wide variety of applications, some of which are: (1) Design and modification studies of a control and interlock system, (2) Plant response evaluation for plant start-up testing and troubleshooting, (3) Transient recognition and mitigation studies, and (4) Familiarization with the plant process and control/ interlock system concept. The basic features of PLEVIS in order to realize the above applications are described in the presentation. (1 ref., 6 figs.)

  8. Self-Healing Supramolecular Hydrogels Based on Reversible Physical Interactions

    Directory of Open Access Journals (Sweden)

    Satu Strandman

    2016-04-01

    Full Text Available Dynamic and reversible polymer networks capable of self-healing, i.e., restoring their mechanical properties after deformation and failure, are gaining increasing research interest, as there is a continuous need towards extending the lifetime and improving the safety and performance of materials particularly in biomedical applications. Hydrogels are versatile materials that may allow self-healing through a variety of covalent and non-covalent bonding strategies. The structural recovery of physical gels has long been a topic of interest in soft materials physics and various supramolecular interactions can induce this kind of recovery. This review highlights the non-covalent strategies of building self-repairing hydrogels and the characterization of their mechanical properties. Potential applications and future prospects of these materials are also discussed.

  9. Configuration based Collisional-Radiative Model including configuration interaction

    Science.gov (United States)

    Busquet, Michel

    2007-11-01

    Atomic levels mixing through Configuration Interaction (CI) yields important effects. It transfers oscillator strengthes from allowed lines to forbidden lines, and produces strong shift and broadening of line arrays, although the total emissivity is almost insensitive to CI, being proportional to the average wave number. However for hi Z material, like Xe or Sn (potential xuv-ray source for micro-lithography), a non-LTE calculation accounting for all relevant levels wiill be untractable with billions of states. The model we constructed, CAVCRM (caf'e-crème), is a non-LTE C.R.M. where states are configurations but it includes C.I. to give full richness of spectral quantities, using the latest version of the HULLAC-v9 suite of codes and our newly developped algorithm for large set of states with as many as 50,000 states [1]. [1] M.Klapisch et al, this conference

  10. Nonreciprocity and magnetic-free isolation based on optomechanical interactions

    CERN Document Server

    Ruesink, Freek; Alù, Andrea; Verhagen, Ewold

    2016-01-01

    Photonic nonreciprocal components, such as isolators and circulators, provide highly desirable functionalities for optical circuitry. This motivates the active investigation of mechanisms that break reciprocity, and pose alternatives to magneto-optic effects in on-chip systems. In this work, we use optomechanical interactions to strongly break reciprocity in a compact system. We derive minimal requirements to create nonreciprocity in a wide class of systems that couple two optical modes to a mechanical mode, highlighting the importance of optically biasing the modes at a controlled phase difference. We realize these principles in a silica microtoroid optomechanical resonator and use quantitative heterodyne spectroscopy to demonstrate up to 10 dB optical isolation at telecom wavelengths. We show that nonreciprocal transmission is preserved for nondegenerate modes, and demonstrate nonreciprocal parametric amplification. These results open a route to exploiting various nonreciprocal effects in optomechanical sys...

  11. Hydrogen-plasticity interactions in nickel and nickel base alloys

    International Nuclear Information System (INIS)

    We evaluate the different contributions of the hydrogen-dislocation interactions to the plasticity of fcc materials in order to feed predictive models of stress corrosion cracking. Static strain ageing experiments are used to quantify the hardening contribution of solute drag by dislocations to the flow stress. We demonstrate the role of hydrogen transport by dislocations on the fracture mechanism. We model the influence of the screening of the elastic field of dislocations by hydrogen on elementary plasticity mechanisms and we conclude that the decrease of the cross slip ability arises from the combined action of elastic and core effects. The testing of single crystals shows that the major effect is on the cross slip mechanism. Tensile tests on polycrystals enlighten the diversity of macroscopic responses observed in alloys. (author)

  12. Fingerstroke time estimates for touchscreen-based mobile gaming interaction.

    Science.gov (United States)

    Lee, Ahreum; Song, Kiburm; Ryu, Hokyoung Blake; Kim, Jieun; Kwon, Gyuhyun

    2015-12-01

    The growing popularity of gaming applications and ever-faster mobile carrier networks have called attention to an intriguing issue that is closely related to command input performance. A challenging mirroring game service, which simultaneously provides game service to both PC and mobile phone users, allows them to play games against each other with very different control interfaces. Thus, for efficient mobile game design, it is essential to apply a new predictive model for measuring how potential touch input compares to the PC interfaces. The present study empirically tests the keystroke-level model (KLM) for predicting the time performance of basic interaction controls on the touch-sensitive smartphone interface (i.e., tapping, pointing, dragging, and flicking). A modified KLM, tentatively called the fingerstroke-level model (FLM), is proposed using time estimates on regression models. PMID:26401615

  13. The interaction triangle as a tool for understanding stakeholder interactions in marine ecosystem based management

    NARCIS (Netherlands)

    Rockmann, C.; Leeuwen, van J.; Goldsborough, D.G.; Kraan, M.L.; Piet, G.J.

    2015-01-01

    Expectations about ecosystem based management (EBM) differ due to diverging perspectives about what EBM should be and how it should work. While EBM by its nature requires trade-offs to be made between ecological, economic and social sustainability criteria, the diversity of cross-sectoral perspectiv

  14. Inquiry and groups: student interactions in cooperative inquiry-based science

    Science.gov (United States)

    Woods-McConney, Amanda; Wosnitza, Marold; Sturrock, Keryn L.

    2016-03-01

    Science education research has recommended cooperative inquiry based science in the primary science context for more than two decades but after more than 20 years, student achievement in science has not substantially improved. This study, through direct observation and analysis, investigated content-related student interactions in an authentic inquiry based primary science class setting. Thirty-one upper primary students were videotaped working in cooperative inquiry based science activities. Cooperative talk and negotiation of the science content was analysed to identify any high-level group interactions. The data show that while all groups have incidences of high-level content-related group interactions, the frequency and duration of these interactions were limited. No specific pattern of preceding events was identified and no episodes of high-level content-related group interactions were immediately preceded by the teacher's interactions with the groups. This in situ study demonstrated that even without any kind of scaffolding, specific skills in knowing how to implement cooperative inquiry based science, high-level content-related group interactions did occur very briefly. Support for teachers to develop their knowledge and skills in facilitating cooperative inquiry based science learning is warranted to ensure that high-level content-related group interactions and the associated conceptual learning are not left to chance in science classrooms.

  15. Interactive Reliability-Based Optimization of Structural Systems

    DEFF Research Database (Denmark)

    Pedersen, Claus

    In order to introduce the basic concepts within the field of reliability-based structural optimization problems, this chapter is devoted to a brief outline of the basic theories. Therefore, this chapter is of a more formal nature and used as a basis for the remaining parts of the thesis. In section...... 2.2 a general non-linear optimization problem and corresponding terminology are presented whereupon optimality conditions and the standard form of an iterative optimization algorithm are outlined. Subsequently, the special properties and characteristics concerning structural optimization problems...... reliability-based structural optimization (RBSO) problem is formulated and described....

  16. Ligand-target interaction-based weighting of substructures for virtual screening.

    Science.gov (United States)

    Crisman, Thomas J; Sisay, Mihiret T; Bajorath, Jürgen

    2008-10-01

    A methodology is introduced to assign energy-based scores to two-dimensional (2D) structural features based on three-dimensional (3D) ligand-target interaction information and utilize interaction-annotated features in virtual screening. Database molecules containing such fragments are assigned cumulative scores that serve as a measure of similarity to active reference compounds. The Interaction Annotated Structural Features (IASF) method is applied to mine five high-throughput screening (HTS) data sets and often identifies more hits than conventional fragment-based similarity searching or ligand-protein docking. PMID:18821751

  17. User interaction with legal knowledge-based systems

    NARCIS (Netherlands)

    Dijkstra, Jacob; Breuker, J.; Leenes, R.; Winkels, R.

    2000-01-01

    This paper gives an overview of my PhD study into the persuasiveness of (legal) knowledge-based systems'. The results of three experiments show the possible problems that may arise when computerised legal decision aids are put into practice. The users in the experiments had great difficulties with j

  18. An interactive Web-based radiation protection course in fluoroscopy

    International Nuclear Information System (INIS)

    The teaching of radiation protection to a large group of physicians, who are separated geographically and have complicated schedules, is a formidable problem. Therefore a Web-based solution is attractive, allowing access to the material at any time and place. In this implementation the didactic material is presented in a Web-based format. Subsequently, students attend a practical demonstration in one of the departments' fluoroscopy rooms. Because of local experience with distance education, WebCT was chosen to present the material. WebCT (Web Course Tools) was developed by the University of British Columbia (UBC) to allow educators, with or without technical expertise, to create a sophisticated Web-base. Authors use a standard Web browser to create courses, and students use their browsers to access course material. WebCT provides a wide variety of tools and features that can be added to a course. Among the most useful tools used in this fluoroscopy course are the glossary, multiple-choice questions for each section, and a final test which is scored by the computer. As with all Web-based material the courses can be viewed in the traditional linear fashion or in any random way through the use of linkages. (author)

  19. Guidelines for Interactive Reliability-Based Structural Optimization using Quasi-Newton Algorithms

    DEFF Research Database (Denmark)

    Pedersen, C.; Thoft-Christensen, Palle

    Guidelines for interactive reliability-based structural optimization problems are outlined in terms of modifications of standard quasi-Newton algorithms. The proposed modifications minimize the condition number of the approximate Hessian matrix in each iteration, restrict the relative and absolute...... increase of the condition number and preserve positive definiteness without discarding previously obtained information. All proposed modifications are also valid for non-interactive optimization problems. Heuristic rules from various optimization problems concerning when and how to impose interactions such...

  20. The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods

    OpenAIRE

    Panstruga Ralph; Lahaye Thomas; Bhat Riyaz A

    2006-01-01

    Abstract Non-invasive fluorophore-based protein interaction assays like fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC, also referred to as "split YFP") have been proven invaluable tools to study protein-protein interactions in living cells. Both methods are now frequently used in the plant sciences and are likely to develop into standard techniques for the identification, verification and in-depth analysis of polypeptide interactions. In this...

  1. Aggregator-Based Interactive Charging Management System for Electric Vehicle Charging

    OpenAIRE

    Mingchao Xia; Qingying Lai; Yajiao Zhong; Canbing Li; Hsiao-Dong Chiang

    2016-01-01

    With the ongoing large-scale implementation of electric vehicles (EVs), the exploration of a more flexible approach to maintain fair interaction between EVs and the power grid is urgently required. This paper presents an aggregator-based interactive charging management scheme adopting interruptible load (IL) pricing, in which the EV aggregator will respond to the load control command of the grid in an EV interactive mode. Charging managements are carried out according to battery state-of-char...

  2. A Cell-Based Protein-Protein Interaction Method Using a Permuted Luciferase Reporter

    OpenAIRE

    Eishingdrelo, Haifeng; Cai, Jidong; Weissensee, Paul; Sharma, Praveen; Tocci, Michael J; Wright, Paul S

    2011-01-01

    We have developed a novel cell-based protein-protein interaction assay method. The method relies on conversion of an inactive permuted luciferase containing a Tobacco Etch Virus protease (TEV) cleavage sequence fused onto protein (A) to an active luciferase upon interaction and cleavage by another protein (B) fused with the TEV protease. We demonstrate assay applicability for ligand-induced protein-protein interactions including G-protein coupled receptors, receptor tyrosine kinases and nucle...

  3. Vehicle-based interactive management with multi-agent approach

    Directory of Open Access Journals (Sweden)

    Yee Ming Chen

    2009-09-01

    Full Text Available Under the energy crisis and global warming, mass transportation becomes more important than before. The disadvantages of mass transportation, plus the high flexibility and efficiency of taxi and with the revolution of technology, electric-taxi is the better transportation choice for metropolis. On the other hand, among the many taxi service types, dial-a-ride (DAR service system is the better way for passenger and taxi. However the electricity replenishing of electric-taxi is the biggest shortage and constraint for DAR operation system. In order to more effectively manage the electric-taxi DAR operation system and the lots of disadvantages of physical system and observe the behaviors and interactions of simulation system, multi-agent simulation technique is the most suitable simulation technique. Finally, we use virtual data as the input of simulation system and analyze the simulation result. We successfully obtain two performance measures: average waiting time and service rate. Result shows the average waiting time is only 3.93 seconds and the service rate (total transport passenger number / total passenger number is 37.073%. So these two performance measures can support us to make management decisions. The multiagent oriented model put forward in this article is the subject of an application intended in the long term to supervise the user information system of an urban transport network.

  4. A Fast Goal Recognition Technique Based on Interaction Estimates

    Science.gov (United States)

    E-Martin, Yolanda; R-Moreno, Maria D.; Smith, David E.

    2015-01-01

    Goal Recognition is the task of inferring an actor's goals given some or all of the actor's observed actions. There is considerable interest in Goal Recognition for use in intelligent personal assistants, smart environments, intelligent tutoring systems, and monitoring user's needs. In much of this work, the actor's observed actions are compared against a generated library of plans. Recent work by Ramirez and Geffner makes use of AI planning to determine how closely a sequence of observed actions matches plans for each possible goal. For each goal, this is done by comparing the cost of a plan for that goal with the cost of a plan for that goal that includes the observed actions. This approach yields useful rankings, but is impractical for real-time goal recognition in large domains because of the computational expense of constructing plans for each possible goal. In this paper, we introduce an approach that propagates cost and interaction information in a plan graph, and uses this information to estimate goal probabilities. We show that this approach is much faster, but still yields high quality results.

  5. Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

    Indian Academy of Sciences (India)

    Purshotam Sharma; Abhijit Mitra; Sitansh Sharma; Harjinder Singh

    2007-09-01

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

  6. A Knowledge Based Interactive System for Complex Product Design

    Science.gov (United States)

    Gayretli, Ahmet

    This research presents a new Artificial Intelligence (AI) based product development approach for integrating mechanical design with electronic design to improve design and manufacture of electromechanical products by avoiding design conflicts in the early stages of the design process. The proposed approach has been implemented in a Delphi based environment integrated with a CAD system. The system assists designers from different disciplines in evaluating complex systems as far as parts relation, potential effects on each other, conflict management, costs, weight and physical constraints are concerned in the early design stages. This helps the designers to avoid design iterations leading to longer lead-time, hence increased cost. The developed system enables to rapidly develop and evaluate new complex products and add new functions to the existing products within given constraints.

  7. Mass spectrometry-based footprinting of protein–protein interactions

    OpenAIRE

    McKee, Christopher J.; Kessl, Jacques J; Norris, Jocelyn O.; Shkriabai, Nikolozi; Kvaratskhelia, Mamuka

    2008-01-01

    We present a high-resolution mass spectrometric (MS) footprinting method enabling identification of contact amino acids in protein–protein complexes. The method is based on comparing surface topologies of a free protein versus its complex with the binding partner using differential accessibility of small chemical group selective modifying reagents. Subsequent MS analysis reveals the individual amino acids selectively shielded from modification in the protein–protein complex. The current repor...

  8. Synergy Effects in Natural Language-Based Multimodal Interaction

    OpenAIRE

    Bretan, Ivan; Karlgren, Jussi

    1993-01-01

    We discuss the synergetic effects that can be obtained in an integrated multimodal interface framework comprising on one hand a visual language-based modality and on the other natural language analysis and generation components. Besides a visual language with high expressive power, the framework includes a cross-modal translation mechanism which enables mutual illumination of interface language syntax and semantics. Special attention has been payed to how to address pro...

  9. A novel interacting multiple model based network intrusion detection scheme

    Science.gov (United States)

    Xin, Ruichi; Venkatasubramanian, Vijay; Leung, Henry

    2006-04-01

    In today's information age, information and network security are of primary importance to any organization. Network intrusion is a serious threat to security of computers and data networks. In internet protocol (IP) based network, intrusions originate in different kinds of packets/messages contained in the open system interconnection (OSI) layer 3 or higher layers. Network intrusion detection and prevention systems observe the layer 3 packets (or layer 4 to 7 messages) to screen for intrusions and security threats. Signature based methods use a pre-existing database that document intrusion patterns as perceived in the layer 3 to 7 protocol traffics and match the incoming traffic for potential intrusion attacks. Alternately, network traffic data can be modeled and any huge anomaly from the established traffic pattern can be detected as network intrusion. The latter method, also known as anomaly based detection is gaining popularity for its versatility in learning new patterns and discovering new attacks. It is apparent that for a reliable performance, an accurate model of the network data needs to be established. In this paper, we illustrate using collected data that network traffic is seldom stationary. We propose the use of multiple models to accurately represent the traffic data. The improvement in reliability of the proposed model is verified by measuring the detection and false alarm rates on several datasets.

  10. Unified parity-conserving interactions based on SU/sub 4/

    Energy Technology Data Exchange (ETDEWEB)

    Abud, M.; Ruegg, H.; Savoy, C.A.; Buccella, F. (Geneva Univ. (Switzerland). Inst. de Physique Theorique)

    1977-07-30

    A unified parity-conserving theory of strong and electromagnetic interactions is proposed based on SU(4). The correct electric charge quantization is obtained and an equal number of quarks of charge -1/3 and of leptons of charge +1 is predicted. When weak interactions are introduced, two alternative choices for the gauge group are possible: SU(5) or SO(9).

  11. Virtual-Reality-Based Social Interaction Training for Children with High-Functioning Autism

    Science.gov (United States)

    Ke, Fengfeng; Im, Tami

    2013-01-01

    Employing the multiple-baseline across-subjects design, the authors examined the implementation and potential effect of a virtual-reality-based social interaction program on the interaction and communication performance of children with high functioning autism. The data were collected via behavior observation and analysis, questionnaires, and…

  12. iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

    Directory of Open Access Journals (Sweden)

    Jittrawan Thaiprasit

    2016-03-01

    Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of i

  13. Visible and ultraviolet light sources based nonlinear interaction of lasers

    DEFF Research Database (Denmark)

    Andersen, Martin Thalbitzer; Tidemand-Lichtenberg, Peter; Jain, Mayank; Pedersen, Christian

    narrow spectrum, high intensities and fast pulsing characteristics. Apart from potential significant reduction in filtration requirements as compared to the LED’s, these characreistics help in accurate examination of different trap parameters. In this poster recent work on a general approach for......Different light sources can be used for optically stimulated luminescence measurements and usually a halogen lamp in combination with filters or light emitting diodes (LED’s) are used to provide the desired stimulation wavelength. However lasers can provide a much more well-defined beam, very...... synthesizing any wavelength in the visible and ultraviolet light based sum frequency generation between two lasers is presented....

  14. Interactions between DNA purinic bases and amodiaquine: A theoretical approach

    OpenAIRE

    Valdemar Lacerda Júnior; José Maria Pires; Adilson Beatriz; Maria Lara Palmeira de Macedo Arguelho

    2010-01-01

    We study theoretically the amodiaquine-adenine and amodiaquine-guanine adducts formation using Density Functional Theory (B3LYP) and the 6-31G(d) basis set for the geometry optimizations and 6-31+G(d,p) for the analysis of the global indexes: electrophilicity (w), electronic chemical potential (m), hardness (h) and softness (S), based in the Frontier Molecular Orbital Theory – FMO. Local softness for nucleophilic reaction (sk+) sites over guanine was evaluated using Fukui function (f k)...

  15. A toy model for weak interaction based on condensed gauge bosons

    CERN Document Server

    Kohyama, Hiroaki

    2016-01-01

    We construct a toy model for weak interaction based on the assumption that gauge bosons form condensates. We then discuss the model predictions calculated from the effective Feynman rules which are derived through computing the effective action.

  16. A computer based, interactive, multimedia training module for self-paced learning

    International Nuclear Information System (INIS)

    Disadvantages of traditional safeguards inspectors training methods are outlined. A computer based, interactive, multimedia, self-paced training programme, called the CANDU power reactor training module (CPRTM) is described. 1 ref., 2 figs

  17. Structure and simulation of interactive computer systems based on multibasises switching processors

    OpenAIRE

    Tsanko, R.; Volynskyy, O.; Puyul, V.; Pituh, I.

    2012-01-01

    Submitted the architecture of computer systems based on multibasises switching processor, attributes, and interactive topology matrix patterns of movement data management interface frames actuators, block diagram of a multibasises specialized processor.

  18. Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Cindy

    2015-07-17

    The interactions among different microbial populations in a community could play more important roles in determining ecosystem functioning than species numbers and their abundances, but very little is known about such network interactions at a community level. The goal of this project is to develop novel framework approaches and associated software tools to characterize the network interactions in microbial communities based on high throughput, large scale high-throughput metagenomics data and apply these approaches to understand the impacts of environmental changes (e.g., climate change, contamination) on network interactions among different nitrifying populations and associated microbial communities.

  19. An attitude-based reasoning strategy to enhance interaction with augmented objects

    OpenAIRE

    Iglesias Alvarez, Josué; Gómez Cordero, David; Bernardos Barbolla, Ana M.; Casar Corredera, Jose Ramon

    2012-01-01

    This paper describes a mobile-based system to interact with objects in smart spaces, where the offer of resources may be extensive. The underlying idea is to use the augmentation capabilities of the mobile device to enable it as user-object mediator. In particular, the paper details how to build an attitude-based reasoning strategy that facilitates user-object interaction and resource filtering. The strategy prioritizes the available resources depending on the spatial history of the user, his...

  20. Checking Interaction-Based Declassification Policies for Android Using Symbolic Execution

    OpenAIRE

    Micinski, Kristopher; Fetter-Degges, Jonathan; Jeon, Jinseong; Foster, Jeffrey S.; Clarkson, Michael R.

    2015-01-01

    Mobile apps can access a wide variety of secure information, such as contacts and location. However, current mobile platforms include only coarse access control mechanisms to protect such data. In this paper, we introduce interaction-based declassification policies, in which the user's interactions with the app constrain the release of sensitive information. Our policies are defined extensionally, so as to be independent of the app's implementation, based on sequences of security-relevant eve...

  1. Single-photon absorber based on strongly interacting Rydberg atoms

    CERN Document Server

    Tresp, Christoph; Mirgorodskiy, Ivan; Gorniaczyk, Hannes; Paris-Mandoki, Asaf; Hofferberth, Sebastian

    2016-01-01

    Removing exactly one photon from an arbitrary input pulse is an elementary operation in quantum optics and enables applications in quantum information processing and quantum simulation. Here we demonstrate a deterministic single-photon absorber based on the saturation of an optically thick free-space medium by a single photon due to Rydberg blockade. Single-photon subtraction adds a new component to the Rydberg quantum optics toolbox, which already contains photonic logic building-blocks such as single-photon sources, switches, transistors, and conditional $\\pi$-phase shifts. Our approach is scalable to multiple cascaded absorbers, essential for preparation of non-classical light states for quantum information and metrology applications, and, in combination with the single-photon transistor, high-fidelity number-resolved photon detection.

  2. Interactions between DNA purinic bases and amodiaquine: A theoretical approach

    Directory of Open Access Journals (Sweden)

    Valdemar Lacerda Júnior

    2010-06-01

    Full Text Available We study theoretically the amodiaquine-adenine and amodiaquine-guanine adducts formation using Density Functional Theory (B3LYP and the 6-31G(d basis set for the geometry optimizations and 6-31+G(d,p for the analysis of the global indexes: electrophilicity (w, electronic chemical potential (m, hardness (h and softness (S, based in the Frontier Molecular Orbital Theory – FMO. Local softness for nucleophilic reaction (sk+ sites over guanine was evaluated using Fukui function (f k. We also evaluated the guanine Electrostatic Potential (EP values using the (MSK charge scheme. The theoretical calculations had demonstrated that the amodiaquine has greater electronic affinity for the guanine, with irreversible formation of the amodiaquine-guanine adduct, as reported before on a previous experimental work.

  3. Do interactions speak louder than words? Dialogic reading of an interactive tablet-based e-book with children between 16 months and three years of age

    DEFF Research Database (Denmark)

    Knoche, Hendrik; Rasmussen, Niklas Ammitzbøl; Boldreel, Kasper;

    2014-01-01

    the effect of interactive elements on speech production of 12 children between the ages of 16 and 33 months when engaged in individual dialogic reading sessions with a tablet-based e-book. Interaction with interactive elements did not reduce the children’s responses to dialogic reading prompts...

  4. SMP-Based Approach for Intelligent Service Interaction

    Directory of Open Access Journals (Sweden)

    Hosam AlHakami

    2014-11-01

    Full Text Available Service-oriented computing is establishing itself as a new computing paradigm in which services advertise their capabilities within a network, and then are used, composed and orchestrated by other services and end-users. Whilst many approaches to matching service providers with consumers of their services have been developed in the past, the proposed approach in this paper takes a different view of the problem in that it does not look for the fittest individual utility, but views it as a constrained optimisation problem that matches between a set of services and a set of service requests. Our approach addresses this problem using an adaptation of the well known stable-marriage problem and demonstrates how matching between services and requests to a certain threshold can be expressed. This will contribute a fair assignment between services and requests based on their preferences. As the current state of the service selection process considers only the view of requests, the proposed approach can ensure several features to the services such as service protection and service quality, e.g. it can ensure the preservation of service availability by redirecting a coming request to a similar service if the current service is busy.

  5. CaseWorld™: Interactive, media rich, multidisciplinary case based learning.

    Science.gov (United States)

    Gillham, David; Tucker, Katie; Parker, Steve; Wright, Victoria; Kargillis, Christina

    2015-11-01

    Nurse educators are challenged to keep up with highly specialised clinical practice, emerging research evidence, regulation requirements and rapidly changing information technology while teaching very large numbers of diverse students in a resource constrained environment. This complex setting provides the context for the CaseWorld project, which aims to simulate those aspects of clinical practice that can be represented by e-learning. This paper describes the development, implementation and evaluation of CaseWorld, a simulated learning environment that supports case based learning. CaseWorld provides nursing students with the opportunity to view unfolding authentic cases presented in a rich multimedia context. The first round of comprehensive summative evaluation of CaseWorld is discussed in the context of earlier formative evaluation, reference group input and strategies for integration of CaseWorld with subject content. This discussion highlights the unique approach taken in this project that involved simultaneous prototype development and large scale implementation, thereby necessitating strong emphasis on staff development, uptake and engagement. The lessons learned provide an interesting basis for further discussion of broad content sharing across disciplines and universities, and the contribution that local innovations can make to global education advancement. PMID:26522447

  6. 4.1 Web-based interactive learning programmes.

    Science.gov (United States)

    Nattestad, Anders; Attstrom, Rolf; Mattheos, Nikos; Ramseier, Christoph; Canegallo, Lorenza; Eaton, Ken; Feeney, Luke; Goffin, Guy; Markovska, Neda; Maixner, William; Persson, Rutger; Reynolds, Patricia; Ruotoistenmaki, Juha; Schittek, Martin; Spohn, Eric; Sudzina, Mike

    2002-01-01

    In the future, the training of competent dentists will need to take advantage of up-to-date digital technologies and learning practices. In order to accomplish this, the following goals should be considered: i) the design of 'customizable' web-based curriculum matrices that accommodate the training philosophies and resources of individual dental schools; ii) the development of digital instructional modules that can be incorporated or downloaded into specific parts of a curriculum; iii) the establishment of an e-consortium, which provides peer view and guidance in the design of teaching modules, and which is responsible for the storage, maintenance, and distribution of teaching modules within the consortium; iv) the development of central human and physical resources at each dental school to enable the seamless delivery of instructional modules in a variety of learning environments; and v) the assessment and provision of ICT training to students and faculty with respect to the use of computers and related digital technologies and educational software programmes. These goals should lead to the creation of a 'virtual dental school'. Within this project summative and formative evaluations should be performed during both the production and development of teaching material (e-learning material) and the learning process. During the learning process the following aspects should be measured and evaluated: i) students' behaviour; and ii) effectiveness, retention and the transfer of e-learned material into the clinical situation. To obtain evidence of the efficacy of e-learning material a certain amount of research has to be done in the near future. It is suggested that all parameters currently known have to be implemented during the development of a learning programme. Previous workers have evaluated the following elements with e-learning: i) planning, ii) programming and technical development, iii) learning behaviours, iv) learning outcomes of both the programme and the

  7. Method of predicting Splice Sites based on signal interactions

    Directory of Open Access Journals (Sweden)

    Deogun Jitender S

    2006-04-01

    Full Text Available Abstract Background Predicting and proper ranking of canonical splice sites (SSs is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE and Intronic (ISE Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

  8. A point-based rendering approach for real-time interaction on mobile devices

    Institute of Scientific and Technical Information of China (English)

    LIANG XiaoHui; ZHAO QinPing; HE ZhiYing; XIE Ke; LIU YuBo

    2009-01-01

    Mobile device is an Important interactive platform. Due to the limitation of computation, memory, display area and energy, how to realize the efficient and real-time interaction of 3D models based on mobile devices is an important research topic. Considering features of mobile devices, this paper adopts remote rendering mode and point models, and then, proposes a transmission and rendering approach that could interact in real time. First, improved simplification algorithm based on MLS and display resolution of mobile devices is proposed. Then, a hierarchy selection of point models and a QoS transmission control strategy are given based on interest area of operator, interest degree of object in the virtual environment and rendering error. They can save the energy consumption. Finally, the rendering and interaction of point models are completed on mobile devices. The experiments show that our method is efficient.

  9. An interactive game-based shoulder wheel system for rehabilitation

    Directory of Open Access Journals (Sweden)

    Chou LW

    2012-11-01

    Full Text Available Chun-Ming Chang,1,* Yen-Ching Chang,2,3 Hsiao-Yun Chang,4 Li-Wei Chou5,6,* 1Department of Applied Informatics and Multimedia, Asia University, Taichung, Taiwan; 2Department of Medical Informatics, Chung Shan Medical University, Taichung, Taiwan; 3Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan; 4Department of Biotechnology, Asia University, Taichung, Taiwan; 5Department of Physical Medicine and Rehabilitation, China Medical University Hospital, Taichung, Taiwan; 6School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan*These authors contributed equally to this workBackground: Increases in the aging population and in the number of accidents have resulted in more people suffering from physical impairments or disabilities. Rehabilitation therapy thus attracts greater attention as a means of helping patients recover and return to a normal life. With the extremely long and tedious nature of traditional rehabilitation, patients are reluctant to continue the entire process, thus the expected effects of the therapy cannot be obtained. Games are well known to help patients improve their concentration and shift their attention away from the discomfort of their injuries during rehabilitation. Thus, incorporating game technology into a rehabilitation program may be a promising approach.Methods: In this study, a gaming system used for shoulder rehabilitation was developed. The mechanical parts and electric circuits were integrated to mimic the functionalities of a shoulder wheel. Several games were also designed to suit the rehabilitation needs of the patients based on the age and gender differences among the individual users, enabling individuals to undergo the rehabilitation process by playing games. Two surveys were conducted to evaluate the satisfaction of the participants regarding the gaming system.Results: The results of the online survey among a larger population

  10. PPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology

    KAUST Repository

    Li, Chuanxi

    2014-01-01

    Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifi es and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At fi rst, IRO is applied in a binary classifi er to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the signifi cant performance of IRO on relation sentences classifi cation and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and Bioinfer, respectively, which are superior to most existing extraction methods. Copyright © 2014 Inderscience Enterprises Ltd.

  11. Tax competition with formula apportionment: the interaction between tax base and sharing mechanism

    OpenAIRE

    Kolmar, Martin; Wagener, Andreas

    2007-01-01

    The EU Commission is advocating a common consolidated tax base for the corporate income tax, accompanied by a revenue sharing mechanism based on formula apportionment. We analyse tax competition in such a regime, focussing on the interaction between the definition of the tax base and the apportionment method. Tax competition leads to suboptimally low tax rates if and only if the investment elasticity of the tax base is lower than the investment elasticity of the apportionment factor. For any ...

  12. GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data

    Directory of Open Access Journals (Sweden)

    Rao Kanury

    2011-07-01

    Full Text Available Abstract Background The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data. Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to generate integrated HIV-human interaction networks. Results We have developed a web-based platform, termed GPS-Prot http://www.gpsprot.org, that allows for facile integration of different HIV interaction data types as well as inclusion of interactions between human proteins derived from publicly-available databases, including MINT, BioGRID and HPRD. The software has the ability to group proteins into functional modules or protein complexes, generating more intuitive network representations and also allows for the uploading of user-generated data. Conclusions GPS-Prot is a software tool that allows users to easily create comprehensive and integrated HIV-host networks. A major advantage of this platform compared to other visualization tools is its web-based format, which requires no software installation or data downloads. GPS-Prot allows novice users to quickly generate networks that combine both genetic and protein-protein interactions between HIV and its human host into a single representation. Ultimately, the platform is extendable to other host-pathogen systems.

  13. Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering.

    Science.gov (United States)

    Yang, Lei; Tang, Xianglong

    2014-01-01

    Cliques (maximal complete subnets) in protein-protein interaction (PPI) network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO) annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP) and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning. PMID:24578640

  14. Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

    Directory of Open Access Journals (Sweden)

    Lei Yang

    2014-01-01

    Full Text Available Cliques (maximal complete subnets in protein-protein interaction (PPI network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning.

  15. Simplified method to predict mutual interactions of human transcription factors based on their primary structure

    KAUST Repository

    Schmeier, Sebastian

    2011-07-05

    Background: Physical interactions between transcription factors (TFs) are necessary for forming regulatory protein complexes and thus play a crucial role in gene regulation. Currently, knowledge about the mechanisms of these TF interactions is incomplete and the number of known TF interactions is limited. Computational prediction of such interactions can help identify potential new TF interactions as well as contribute to better understanding the complex machinery involved in gene regulation. Methodology: We propose here such a method for the prediction of TF interactions. The method uses only the primary sequence information of the interacting TFs, resulting in a much greater simplicity of the prediction algorithm. Through an advanced feature selection process, we determined a subset of 97 model features that constitute the optimized model in the subset we considered. The model, based on quadratic discriminant analysis, achieves a prediction accuracy of 85.39% on a blind set of interactions. This result is achieved despite the selection for the negative data set of only those TF from the same type of proteins, i.e. TFs that function in the same cellular compartment (nucleus) and in the same type of molecular process (transcription initiation). Such selection poses significant challenges for developing models with high specificity, but at the same time better reflects real-world problems. Conclusions: The performance of our predictor compares well to those of much more complex approaches for predicting TF and general protein-protein interactions, particularly when taking the reduced complexity of model utilisation into account. © 2011 Schmeier et al.

  16. A Multiple-Sessions Interactive Computer-Based Learning Tool for Ability Cultivation in Circuit Simulation

    Science.gov (United States)

    Xu, Q.; Lai, L. L.; Tse, N. C. F.; Ichiyanagi, K.

    2011-01-01

    An interactive computer-based learning tool with multiple sessions is proposed in this paper, which teaches students to think and helps them recognize the merits and limitations of simulation tools so as to improve their practical abilities in electrical circuit simulation based on the case of a power converter with progressive problems. The…

  17. Young Foreign Language Learners' Interactions during Task-Based Paired Assessments

    Science.gov (United States)

    Butler, Yuko Goto; Zeng, Wei

    2014-01-01

    Despite the popularity of task-based language teaching (TBLT) in foreign language (FL) education at elementary school, it remains unclear how young learners' FL abilities can best be evaluated with tasks. The present study seeks to understand developmental differences in interactions among elementary-school students during task-based language…

  18. Radio-induced apoptosis is impaired in individuals homozygous and heterozygous for the ataxia-telangiectasia gene(s)

    International Nuclear Information System (INIS)

    Ataxia-telangiectasia is a progressive recessive disease featuring neuro degeneration, immunodeficiency, chromosomal instability, radiation hypersensitivity and increased predisposition to cancer. Impaired induction of the tumor suppressor protein p53 after γ-irradiation was recently reported. All together these characteristics may be compatible with an inability to correctly regulate the apoptotic pathway of cell death in this syndrome. We show here that lymphocyte cultures from AT patients are characterized by a 3 times more elevated spontaneous level of apoptotic cells compared to normal ones. In spite of this, 24 h after exposure to γ-irradiation (5 to 10 Gy), AT lymphocytes show a dramatically reduced capacity to undergo apoptosis compared to normal cells. We obtained similar results on EBV-transformed lymphoblasts. Interestingly, lymphoblasts from obligate heterozygous for the AT mutation(s) show the same features as AT lymphoblasts, i.e. an elevated frequency of spontaneous and a reduced level of radio-induced apoptotic figures in comparison to normal cultured cells. In conclusion, we show here, for the first time, that mutation(s) in AT gene(s) results in an impaired ability to correctly regulate the apoptotic pathway of cell death. (author). 26 refs., 4 figs., 2 tabs

  19. Genetic control of eosinophilia in mice: gene(s) expressed in bone marrow-derived cells control high responsiveness

    Energy Technology Data Exchange (ETDEWEB)

    Vadas, M.A.

    1982-02-01

    A heterogeneity in the capacity of strains of mice to mount eosinophilia is described. BALB/c and C3H are eosinophil high responder strains (EO-HR) and CBA and A/J are eosinophil low responder strains (EO-LR), judged by the response of blood eosinophils to Ascaris suum, and the response of blood, bone marrow, and spleen eosinophils to keyhole limpet hemocyanin given 2 days after 150 mg/kg cyclophosphamide. Some of the gene(s) for high responsiveness appear to be dominant because (EO-HR x EO-LR)F/sub 1/ mice were intermediate to high responders. This gene is expressed in bone marrow-derived cells because radiation chimeras of the type EO-HR..-->..F/sub 1/ were high responders and EO-LR..-->..F/sub 1/ were low responders. This description of a genetic control of eosinophilia in mice may be useful in understanding the role of this cell in parasite immunity and allergy.

  20. A Study of User's Performance and Satisfaction on the Web Based Photo Annotation with Speech Interaction

    CERN Document Server

    Ramlan, Siti Azura

    2010-01-01

    This paper reports on empirical evaluation study of users' performance and satisfaction with prototype of Web Based speech photo annotation with speech interaction. Participants involved consist of Johor Bahru citizens from various background. They have completed two parts of annotation task; part A involving PhotoASys; photo annotation system with proposed speech interaction and part B involving Microsoft Microsoft Vista Speech Interaction style. They have completed eight tasks for each part including system login and selection of album and photos. Users' performance was recorded using computer screen recording software. Data were captured on the task completion time and subjective satisfaction. Participants need to complete a questionnaire on the subjective satisfaction when the task was completed. The performance data show the comparison between proposed speech interaction and Microsoft Vista Speech interaction applied in photo annotation system, PhotoASys. On average, the reduction in annotation performan...

  1. Signalling pathway impact analysis based on the strength of interaction between genes.

    Science.gov (United States)

    Bao, Zhenshen; Li, Xianbin; Zan, Xiangzhen; Shen, Liangzhong; Ma, Runnian; Liu, Wenbin

    2016-08-01

    Signalling pathway analysis is a popular approach that is used to identify significant cancer-related pathways based on differentially expressed genes (DEGs) from biological experiments. The main advantage of signalling pathway analysis lies in the fact that it assesses both the number of DEGs and the propagation of signal perturbation in signalling pathways. However, this method simplifies the interactions between genes by categorising them only as activation (+1) and suppression (-1), which does not encompass the range of interactions in real pathways, where interaction strength between genes may vary. In this study, the authors used newly developed signalling pathway impact analysis (SPIA) methods, SPIA based on Pearson correlation coefficient (PSPIA), and mutual information (MSPIA), to measure the interaction strength between pairs of genes. In analyses of a colorectal cancer dataset, a lung cancer dataset, and a pancreatic cancer dataset, PSPIA and MSPIA identified more candidate cancer-related pathways than were identified by SPIA. Generally, MSPIA performed better than PSPIA. PMID:27444024

  2. Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis

    OpenAIRE

    Batenchuk Cory; Tepliakova Lioudmila; Kærn Mads

    2010-01-01

    Abstract Background High-throughput genomics has enabled the global mapping of genetic interactions based on the phenotypic impact of combinatorial genetic perturbations. An important next step is to understand how these networks are dynamically remodelled in response to environmental stimuli. Here, we report on the development and testing of a method to identify such interactions. The method was developed from first principles by treating the impact on cellular growth of environmental pertur...

  3. Design of an Effective WSN-Based Interactive u-Learning Model

    OpenAIRE

    Hye-jin Kim; Caytiles, Ronnie D.; Tai-hoon Kim

    2012-01-01

    Wireless sensor networks include a wide range of potential applications to improve the quality of teaching and learning in a ubiquitous environment. WSNs become an evolving technology that acts as the ultimate interface between the learners and the context, enhancing the interactivity and improving the acquisition or collection of learner's contextual information in ubiquitous learning. This paper presents a model of an effective and interactive ubiquitous learning environment system based on...

  4. Genisa: A web-based interactive learning environment for teaching simulation modelling

    OpenAIRE

    Atolagbe, TA; Hlupic, V.; Taylor, SJE

    2001-01-01

    Intelligent Tutoring Systems (ITS) provide students with adaptive instruction and can facilitate the acquisition of problem solving skills in an interactive environment. This paper discusses the role of pedagogical strategies that have been implemented to facilitate the development of simulation modelling knowledge. The learning environment integrates case-based reasoning with interactive tools to guide tutorial remediation. The evaluation of the system shows that the model for pedagogical ac...

  5. Study of high-speed interaction processes between fluoropolymer projectiles and aluminum-based targets

    Institute of Scientific and Technical Information of China (English)

    Evgeny A. KHMELNIKOV; Alexey V. STYROV; Konstantin V. SMAGIN; Natalia S. KRAVCHENKO; Valery L. RUDENKO; Vladimir I. FALALEEV; Sergey S. SOKOLOV; Artem V. SVIDINSKY; Natalia F. SVIDINSKAYA

    2015-01-01

    The experimental results and numerical modeling of penetration process of fluoropolymer projectiles in aluminum-based targets are pre-sented. Analysis of mathematical models for interaction of elastoplastic projectile and target without taking additional energy released during interaction of fluoropolymer and aluminum into consideration is carried out. Energy fraction which is spent effectively on the increase in cavity volume is determined. The experimental and calculated results of penetration by combined and inert projectiles are compared.

  6. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining

    OpenAIRE

    Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

    2012-01-01

    Background Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genome-wide, Centrality and Ontology-based Network Discovery using Literature data (CONDL) approach to analyse the genes and gene interaction networks associated with fever or vaccine-related fever responses. Results Over 170,000 fever-related articles from PubMed abstracts and tit...

  7. An evaluation technique for content interaction in web-based teaching and learning environments

    OpenAIRE

    Lei, Xu; Pahl, Claus; Donnellan, David

    2003-01-01

    Interactivity is a central element in teaching and learning. The Web as a new educational platform enables new forms of teaching and learning. The consequence for the Web – a constantly evolving environment that provides less direct feedback – is the importance of evaluation. In particular the learners’ interaction with the Web-based multimedia features is central. We propose Web usage mining, a technology that has already been used to analyse e-commerce Web sites, in conjunction with a...

  8. Prediction of Substrate-Enzyme-Product Interaction Based on Molecular Descriptors and Physicochemical Properties

    OpenAIRE

    Bing Niu; Guohua Huang; Linfeng Zheng; Xueyuan Wang; Fuxue Chen; Yuhui Zhang; Tao Huang

    2013-01-01

    It is important to correctly and efficiently predict the interaction of substrate-enzyme and to predict their product in metabolic pathway. In this work, a novel approach was introduced to encode substrate/product and enzyme molecules with molecular descriptors and physicochemical properties, respectively. Based on this encoding method, KNN was adopted to build the substrate-enzyme-product interaction network. After selecting the optimal features that are able to represent the main factors of...

  9. A Q-based integrating interaction framework system for multi-agent coordination

    Institute of Scientific and Technical Information of China (English)

    WANG Zhen-jie; SHENG Huan-ye; XIAO Zheng-guang

    2005-01-01

    Interaction is one of the crucial features of multi-agent systems, in which there are two kinds of interaction: agent-to-agent and human-to-agent. In order to unify the two kinds of interaction while designing multiagent systems, this paper introduces Q language-a scenario description language for designing interaction among agents and humans. Based on Q, we propose an integrating interaction framework system for multi-agent coordination, in which Q scenarios are used to uniformly describe both kinds of interactions. Being in accordance to the characteristics of Q language, the Q-based framework makes the interaction process open and easily understood by the users. Additionally, it makes specific applications of multi-agent systems easy to be established by application designers. By applying agent negotiation in agent-mediated e-commerce and agent cooperation in interoperable information query on the Semantic Web, we illustrate how the presented framework for multi-agent coordination is implemented in concrete applications. At the same time, these two different applications also demonstrate usability of the presented framework and verify validity of Q language.

  10. Interaction of single walled carbon nanotubes with starch-based systems

    Science.gov (United States)

    Casey, A.; Farrell, G. F.; McNamara, M.; Byrne, H. J.; Chambers, G.

    2005-06-01

    The interaction of carbon nanotubes with soft organic molecules such as cyclodextrins and other saccharides has recently been shown to produce water-soluble composites. Such systems offer considerable advantages over polymer based composites due to their biocompatibility and non-covalent coupling which can potentially preserve the unique properties of the tubes. The mechanism of interaction of such systems has been proposed to be dominated by hydrophobic and hydrophilic interactions along the surface of the tube. In this study a number of composite systems have been formed with HiPco carbon nanotubes using starch.

  11. The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods

    Directory of Open Access Journals (Sweden)

    Panstruga Ralph

    2006-06-01

    Full Text Available Abstract Non-invasive fluorophore-based protein interaction assays like fluorescence resonance energy transfer (FRET and bimolecular fluorescence complementation (BiFC, also referred to as "split YFP" have been proven invaluable tools to study protein-protein interactions in living cells. Both methods are now frequently used in the plant sciences and are likely to develop into standard techniques for the identification, verification and in-depth analysis of polypeptide interactions. In this review, we address the individual strengths and weaknesses of both approaches and provide an outlook about new directions and possible future developments for both techniques.

  12. Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

    Science.gov (United States)

    Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

    2012-01-01

    Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging. PMID:22942008

  13. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

    Directory of Open Access Journals (Sweden)

    Richard R Stein

    2015-07-01

    Full Text Available Maximum entropy-based inference methods have been successfully used to infer direct interactions from biological datasets such as gene expression data or sequence ensembles. Here, we review undirected pairwise maximum-entropy probability models in two categories of data types, those with continuous and categorical random variables. As a concrete example, we present recently developed inference methods from the field of protein contact prediction and show that a basic set of assumptions leads to similar solution strategies for inferring the model parameters in both variable types. These parameters reflect interactive couplings between observables, which can be used to predict global properties of the biological system. Such methods are applicable to the important problems of protein 3-D structure prediction and association of gene-gene networks, and they enable potential applications to the analysis of gene alteration patterns and to protein design.

  14. Tele-Immersive Interaction with Intelligent Virtual Agents Based on Real-Time 3D Modeling

    Directory of Open Access Journals (Sweden)

    Shujun Zhang

    2012-02-01

    Full Text Available To enable intelligent agents interacting smoothly with human users, researchers have been deploying novel interaction modalities (e.g. non-verbal cue, vision and touch in addition to agents’ conversational skills. Models of multi-modality interaction can enhance agents’ real-time perception, cognition and reaction towards the user. In this paper we report a novel tele-immersive interaction system developed using real-time 3D modelling techniques. In such system user’s full body is reconstructed using multi-view cameras and CUDA based visual hull reconstruction algorithm. User’s mesh model is then loaded into a virtual environment for interacting with an autonomous agent. Technical details and initial results of the system are illustrated in this paper. Following that a novel interaction scenario is proposed which links the virtual agent with a remote physical robot who takes the role of mediating interactions between two geographically separated users. Finally we discuss in depth the implications of such human-agent interaction and possible future improvements and directions.

  15. Fluid, solid and fluid-structure interaction simulations on patient-based abdominal aortic aneurysm models.

    Science.gov (United States)

    Kelly, Sinead; O'Rourke, Malachy

    2012-04-01

    This article describes the use of fluid, solid and fluid-structure interaction simulations on three patient-based abdominal aortic aneurysm geometries. All simulations were carried out using OpenFOAM, which uses the finite volume method to solve both fluid and solid equations. Initially a fluid-only simulation was carried out on a single patient-based geometry and results from this simulation were compared with experimental results. There was good qualitative and quantitative agreement between the experimental and numerical results, suggesting that OpenFOAM is capable of predicting the main features of unsteady flow through a complex patient-based abdominal aortic aneurysm geometry. The intraluminal thrombus and arterial wall were then included, and solid stress and fluid-structure interaction simulations were performed on this, and two other patient-based abdominal aortic aneurysm geometries. It was found that the solid stress simulations resulted in an under-estimation of the maximum stress by up to 5.9% when compared with the fluid-structure interaction simulations. In the fluid-structure interaction simulations, flow induced pressure within the aneurysm was found to be up to 4.8% higher than the value of peak systolic pressure imposed in the solid stress simulations, which is likely to be the cause of the variation in the stress results. In comparing the results from the initial fluid-only simulation with results from the fluid-structure interaction simulation on the same patient, it was found that wall shear stress values varied by up to 35% between the two simulation methods. It was concluded that solid stress simulations are adequate to predict the maximum stress in an aneurysm wall, while fluid-structure interaction simulations should be performed if accurate prediction of the fluid wall shear stress is necessary. Therefore, the decision to perform fluid-structure interaction simulations should be based on the particular variables of interest in a given

  16. Decoherence under many-body system-environment interactions: a stroboscopic representation based on a fictitiously homogenized interaction rate

    OpenAIRE

    Alvarez, Gonzalo A.; Danieli, Ernesto P.; Levstein, Patricia R.; Pastawski, Horacio M.

    2007-01-01

    An environment interacting with portions of a system leads to multiexponential interaction rates. Within the Keldysh formalism, we fictitiously homogenize the system-environment interaction yielding a uniform decay rate facilitating the evaluation of the propagators. Through an injection procedure we neutralize the fictitious interactions. This technique justifies a stroboscopic representation of the system-environment interaction which is useful for numerical implementation and converges to ...

  17. Interaction Design of National Dance Based on Realistic 3D Character

    Directory of Open Access Journals (Sweden)

    Guoxin Tan

    2013-08-01

    Full Text Available Great improvement has been achieved in the protection of national dance through multimedia technology. An interactive design approach for national dance based on realistic 3D character is proposed in this paper. This approach comes with three sub steps: Firstly, the realistic face was reconstructed based on a front photo, in this step, the facial feature points of photo are selected interactively; and then, the realistic face was built through texture mapping and fusion based on the standardized face model database. Secondly, the construction of realistic body is realized through introducing the stretching model and the vector differential adjuster. Finally, the interactive display of national dance is realized by virtual reality engine. The experimental results show that this approach is user-friendly, and can generate a high-quality realistic 3D character in real time while protects the worthy cultural heritage effectively at the same time.

  18. Poultry production: a model for developing interactive Internet-based distance education.

    Science.gov (United States)

    Emmert, J L; Shortridge, A M; Sexton, S L

    2003-05-01

    Over the last several decades, many poultry science programs have merged with other departments, but the poultry industry has undergone tremendous expansion worldwide, leading to a growing instructional void with regard to poultry production information. The objective of this project was to address the demand for information by developing two Web-based poultry production courses that cover management of broilers, turkeys, breeders, and layers. The Internet was chosen as the platform because it is asynchronous and may be accessed from any connected site around the world. To be effective, web-based courseware must be theoretically grounded and interactive, but university-level web-based distance education courses often fail to meet these standards. During courseware development, the impact of instructional techniques and technologies on interactivity and learning outcomes was explored. A content expert, an instructional designer, and a graphic artist carefully reviewed a variety of instructional techniques to increase interactivity. Concept mapping was chosen because it has been shown to be a superior learning tool for enhancing the exchange of ideas and knowledge between instructors, students, and content. A unique instructional interface was established that includes threaded e-mail discussion, thought questions, animation, hypertext, rollover interactions, video clips, and concept mapping exercises. Results indicate that the integration of concept mapping into web-based learning environments successfully increased interactivity and learning outcomes. PMID:12762393

  19. Event-driven interactivity in application-based TV-programs

    OpenAIRE

    Moberg, Per

    2013-01-01

    In recent years TVs and set-top boxes has been featured with built-in internet connectivity which open up doors to new innovations and technologies. This research has particularly investigated the possibility of adding event-based interactivity into application based TV-programs and has focused on the hybrid standard HbbTV. A design suggestion of a framework to make use of eventdriven interactivity has been created and a proof-of-concept prototype  has been implemented. The study has demonstr...

  20. A hybrid configuration interaction treatment based on seniority number and excitation schemes

    Energy Technology Data Exchange (ETDEWEB)

    Alcoba, Diego R.; Capuzzi, Pablo [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Torre, Alicia; Lain, Luis, E-mail: qfplapel@lg.ehu.es [Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644 E-48080 Bilbao (Spain); Oña, Ofelia B. [Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de La Plata, CCT La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (S/N), Sucursal 4, CC 16, 1900 La Plata (Argentina); Van Raemdonck, Mario; Bultinck, Patrick [Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent (Belgium); Van Neck, Dimitri [Center for Molecular Modelling, Ghent University, Technologiepark 903, 9052 Zwijnaarde (Belgium)

    2014-12-28

    We present a configuration interaction method in which the Hamiltonian of an N-electron system is projected on Slater determinants selected according to the seniority-number criterion along with the traditional excitation-based procedure. This proposed method is especially useful to describe systems which exhibit dynamic (weak) correlation at determined geometric arrangements (where the excitation-based procedure is more suitable) but show static (strong) correlation at other arrangements (where the seniority-number technique is preferred). The hybrid method amends the shortcomings of both individual determinant selection procedures, yielding correct shapes of potential energy curves with results closer to those provided by the full configuration interaction method.

  1. Asymmetric nuclear matter based on chiral two- and three-nucleon interactions

    Science.gov (United States)

    Drischler, C.; Hebeler, K.; Schwenk, A.

    2016-05-01

    We calculate the properties of isospin-asymmetric nuclear matter based on chiral nucleon-nucleon (NN) and three-nucleon (3N) interactions. To this end, we develop an improved normal-ordering framework that allows us to include general 3N interactions starting from a plane-wave partial-wave-decomposed form. We present results for the energy per particle for general isospin asymmetries based on a set of different Hamiltonians, study their saturation properties, the incompressibility, symmetry energy, and also provide an analytic parametrization for the energy per particle as a function of density and isospin asymmetry.

  2. A hybrid configuration interaction treatment based on seniority number and excitation schemes

    International Nuclear Information System (INIS)

    We present a configuration interaction method in which the Hamiltonian of an N-electron system is projected on Slater determinants selected according to the seniority-number criterion along with the traditional excitation-based procedure. This proposed method is especially useful to describe systems which exhibit dynamic (weak) correlation at determined geometric arrangements (where the excitation-based procedure is more suitable) but show static (strong) correlation at other arrangements (where the seniority-number technique is preferred). The hybrid method amends the shortcomings of both individual determinant selection procedures, yielding correct shapes of potential energy curves with results closer to those provided by the full configuration interaction method

  3. Asymmetric nuclear matter based on chiral two- and three-nucleon interactions

    CERN Document Server

    Drischler, Christian; Schwenk, Achim

    2015-01-01

    We calculate the properties of isospin-asymmetric nuclear matter based on chiral nucleon-nucleon (NN) and three-nucleon (3N) interactions. To this end, we develop an improved normal-ordering framework that allows to include general 3N interactions starting from a plane-wave partial-wave-decomposed form. We present results for the energy per particle for general isospin asymmetries based on a set of different Hamiltonians, study their saturation properties, the incompressibility, symmetry energy, and also provide an analytic parametrization for the energy per particle as a function of density and isospin asymmetry.

  4. Prediction of oncogenic interactions and cancer-related signaling networks based on network topology.

    Directory of Open Access Journals (Sweden)

    Marcio Luis Acencio

    Full Text Available Cancer has been increasingly recognized as a systems biology disease since many investigators have demonstrated that this malignant phenotype emerges from abnormal protein-protein, regulatory and metabolic interactions induced by simultaneous structural and regulatory changes in multiple genes and pathways. Therefore, the identification of oncogenic interactions and cancer-related signaling networks is crucial for better understanding cancer. As experimental techniques for determining such interactions and signaling networks are labor-intensive and time-consuming, the development of a computational approach capable to accomplish this task would be of great value. For this purpose, we present here a novel computational approach based on network topology and machine learning capable to predict oncogenic interactions and extract relevant cancer-related signaling subnetworks from an integrated network of human genes interactions (INHGI. This approach, called graph2sig, is twofold: first, it assigns oncogenic scores to all interactions in the INHGI and then these oncogenic scores are used as edge weights to extract oncogenic signaling subnetworks from INHGI. Regarding the prediction of oncogenic interactions, we showed that graph2sig is able to recover 89% of known oncogenic interactions with a precision of 77%. Moreover, the interactions that received high oncogenic scores are enriched in genes for which mutations have been causally implicated in cancer. We also demonstrated that graph2sig is potentially useful in extracting oncogenic signaling subnetworks: more than 80% of constructed subnetworks contain more than 50% of original interactions in their corresponding oncogenic linear pathways present in the KEGG PATHWAY database. In addition, the potential oncogenic signaling subnetworks discovered by graph2sig are supported by experimental evidence. Taken together, these results suggest that graph2sig can be a useful tool for investigators involved

  5. Sequence-based prediction of protein-protein interaction sites with L1-logreg classifier.

    Science.gov (United States)

    Dhole, Kaustubh; Singh, Gurdeep; Pai, Priyadarshini P; Mondal, Sukanta

    2014-05-01

    Protein-protein interactions are of central importance for virtually every process in a living cell. Information about the interaction sites in proteins improves our understanding of disease mechanisms and can provide the basis for new therapeutic approaches. Since a multitude of unique residue-residue contacts facilitate the interactions, protein-protein interaction sites prediction has become one of the most important and challenging problems of computational biology. Although much progress in this field has been reported, this problem is yet to be satisfactorily solved. Here, a novel method (LORIS: L1-regularized LOgistic Regression based protein-protein Interaction Sites predictor) is proposed, that identifies interaction residues, using sequence features and is implemented via the L1-logreg classifier. Results show that LORIS is not only quite effective, but also, performs better than existing state-of-the art methods. LORIS, available as standalone package, can be useful for facilitating drug-design and targeted mutation related studies, which require a deeper knowledge of protein interactions sites. PMID:24486250

  6. Tangible Interaction in Learning Astronomy through Augmented Reality Book-Based Educational Tool

    Science.gov (United States)

    Sin, Aw Kien; Badioze Zaman, Halimah

    Live Solar System (LSS) is an Augmented Reality book-based educational tool. Augmented Reality (AR) has its own potential in the education field, because it can provide a seamless interaction between real and virtual objects. LSS applied the Tangible Augmented Reality approach in designing its user interface and interaction. Tangible Augmented Reality is an interface which combines the Tangible User Interface and Augmented Reality Interface. They are naturally complement each other. This paper highlights the tangible interaction in LSS. LSS adopts the 'cube' as the common physical object input device. Thus, LSS does not use the traditional computer input devices such as the mouse or keyboard. To give users a better exploration experience, Visual Information Seeking Mantra principle was applied in the design of LSS. Hence, LSS gives users an effective interactive-intuitive horizontal surface learning environment.

  7. A Framework for Building an Interactive Satellite TV Based M-Learning Environment

    Directory of Open Access Journals (Sweden)

    Ghassan Issa

    2010-07-01

    Full Text Available This paper presents a description of an interactive satellite TV based mobile learning (STV-ML framework, in which a satellite TV station is used as an integral part of a comprehensive interactive mobile learning (M-Learning environment. The proposed framework assists in building a reliable, efficient, and cost-effective environment to meet the growing demands of M-Learning all over the world, especially in developing countries. It utilizes recent advances in satellite reception, broadcasting technologies, and interactive TV to facilitate the delivery of gigantic learning materials. This paper also proposed a simple and flexible three-phase implementation methodology which includes construction of earth station, expansion of broadcasting channels, and developing true user interactivity. The proposed framework and implementation methodology ensure the construction of a true, reliable, and cost effective M-Learning system that can be used efficiently and effectively by a wide range of users and educational institutions to deliver ubiquitous learning.

  8. DEVELOPMENT OF INTERACTIVE E-BOOK BASED ON CHEMICAL REPRESENTATION REFER TO CURRICULUM 2013

    Directory of Open Access Journals (Sweden)

    L. Tania

    2015-11-01

    Full Text Available This research aimed to develop an interactive e-book based representations of chemistry; describes the characteristics of the interactive e-book developed; the teachers responses in content suitability with curriculum and graphics aspects; and student responses in readibility aspects. The method used was research and development. The characteristics of interactive e-book: it was developed referring to the core competencies (KI and basic competence (KD in the curriculum 2013, allowed active interaction between students and e-book, completed with pictures, animations or videos in three levels of the chemical representation. Teachers’ responses to the content suitability and graphic aspects were very good with the percentage of each 98.46% and 97.5%. The students’ responses in readibility aspects was very good with percentage of 88.5%.

  9. Plume Interaction and Base Flow Analysis of a Twin Engine Flight Vehicle

    Science.gov (United States)

    Chandra Murty, Mamidi Sri Rama; Chakraborty, Debasis

    2016-06-01

    3D RANS simulations are performed to study the multi jet interactions of a twin engine gimbal configuration of an aerospace vehicle at different time instants. Simulations captured all the essential features of the flow field and interaction between the neighboring jets did not occur because of low altitudes and moderate under-expansion of the jets considered in the simulations. For higher gimbal angle, two jets were the closest but still did not interact. Detail exploration of the downstream flow field revealed that the distinct features of the jets are retained at the farthest downstream locations; although the pressure field reached the uniformity. Average base pressure ratios for the three different time instances are 0.91, 0.547 and 0.522 and maximum base temperature is of the order 800 K.

  10. Study on Agent-based Intelligent Feedback System in Online Teaching and Interactive Learning

    Directory of Open Access Journals (Sweden)

    Ning Chen

    2013-01-01

    Full Text Available As a new education pattern, online teaching and interactive learning teaching breaks the constraints of time and space of the traditional teaching mode, but it has an obvious deficiency in personalized teaching which advocates teaching students in according to their aptitude. In order to solve this problem, on the base of the traditional network teaching system, it is necessary to increase an intelligence feedback system which is responsible for the task of such as adaptively pushing and updating the learning content, presenting the personalized home page, intelligently answering questions from the learner and so on. In online teaching and interactive learning practice, using this agent-based intelligent feedback system greatly enhanced the effect of personalized teaching and also promoted the development of the online teaching and interactive learning system.

  11. Using a dual safeguard web-based interactive teaching approach in an introductory physics class

    Science.gov (United States)

    Li, Lie-Ming; Li, Bin; Luo, Ying

    2015-06-01

    We modified the Just-in-Time Teaching approach and developed a dual safeguard web-based interactive (DGWI) teaching system for an introductory physics course. The system consists of four instructional components that improve student learning by including warm-up assignments and online homework. Student and instructor activities involve activities both in the classroom and on a designated web site. An experimental study with control groups evaluated the effectiveness of the DGWI teaching method. The results indicate that the DGWI method is an effective way to improve students' understanding of physics concepts, develop students' problem-solving abilities through instructor-student interactions, and identify students' misconceptions through a safeguard framework based on questions that satisfy teaching requirements and cover all of the course material. The empirical study and a follow-up survey found that the DGWI method increased student-teacher interaction and improved student learning outcomes.

  12. Interactions between base paper and coating color in metered size press coating

    OpenAIRE

    Forsström, Ulla

    2003-01-01

    The purpose of the thesis was to gain a greater understanding of the interactions between the base paper and coating color in the metered size press (MSP) nip. The effect of base paper in precoating with an MSP was investigated using mill woodfree base papers, laboratory sheets, pilot base papers and non-porous materials. The coating color formulations consisted of commercial raw materials, in most cases latex-CMC colors with a pigment mixture of CaCO3 and kaolin. Coating studies were carried...

  13. Perceptions of the Effectiveness of System Dynamics-Based Interactive Learning Environments: An Empirical Study

    Science.gov (United States)

    Qudrat-Ullah, Hassan

    2010-01-01

    The use of simulations in general and of system dynamics simulation based interactive learning environments (SDILEs) in particular is well recognized as an effective way of improving users' decision making and learning in complex, dynamic tasks. However, the effectiveness of SDILEs in classrooms has rarely been evaluated. This article describes…

  14. Ground-based remote sensing scheme for monitoring aerosol–cloud interactions (discussion)

    NARCIS (Netherlands)

    Sarna, K.; Russchenberg, H.W.J.

    2015-01-01

    A method for continuous observation of aerosol–cloud interactions with ground-based remote sensing instruments is presented. The main goal of this method is to enable the monitoring of cloud microphysical changes due to the changing aerosol concentration. We use high resolution measurements from lid

  15. Study of Personalized Network Tutoring System Based on Emotional-cognitive Interaction

    Science.gov (United States)

    Qi, Manfei; Ma, Ding; Wang, Wansen

    Aiming at emotion deficiency in present Network tutoring system, a lot of negative effects is analyzed and corresponding countermeasures are proposed. The model of Personalized Network tutoring system based on Emotional-cognitive interaction is constructed in the paper. The key techniques of realizing the system such as constructing emotional model and adjusting teaching strategies are also introduced.

  16. Ground-based remote sensing scheme for monitoring aerosol-cloud interactions

    NARCIS (Netherlands)

    Sarna, K.; Russchenberg, H.W.J.

    2016-01-01

    A new method for continuous observation of aerosol–cloud interactions with ground-based remote sensing instruments is presented. The main goal of this method is to enable the monitoring of the change of the cloud droplet size due to the change in the aerosol concentration. We use high-resolution mea

  17. Personality Types and Learners' Interaction in Web-Based Threaded Discussion

    Science.gov (United States)

    Lee, JeongMin; Lee, Youngmin

    2006-01-01

    This study examined the effects of group composition based on the learners' personality types as measured by the Myers-Briggs type indicator as they interacted in threaded discussions. Three groups comprised introverts, extroverts, and mixed introvert-extrovert classifications. Ninety-six participants were divided into 24 groups of 4 participants…

  18. An Electron Bunch Compressor Based on an FEL Interaction in the Far Infra Red

    CERN Document Server

    Gaupp, Andreas

    2013-01-01

    In this note an electron bunch compressor is proposed based on FEL type interaction of the electron bunch with far infrared (FIR) radiation. This mechanism maintains phase space density and thus requires a high quality electron beam to produce bunches of the length of a few ten micrometer.

  19. Elucidating Host-Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches

    DEFF Research Database (Denmark)

    Ravikumar, Vaishnavi; Jers, Carsten; Mijakovic, Ivan

    2015-01-01

    display host specificity through a complex network of molecular interactions that aid their survival and propagation. Co-infection states further lead to complications by increasing the microbial burden and risk factors. Quantitative proteomics based approaches and post-translational modification analysis...

  20. Interactive Computer Based Assessment Tasks: How Problem-Solving Process Data Can Inform Instruction

    Science.gov (United States)

    Zoanetti, Nathan

    2010-01-01

    This article presents key steps in the design and analysis of a computer based problem-solving assessment featuring interactive tasks. The purpose of the assessment is to support targeted instruction for students by diagnosing strengths and weaknesses at different stages of problem-solving. The first focus of this article is the task piloting…

  1. Rationale, Design and Implementation of a Computer Vision-Based Interactive E-Learning System

    Science.gov (United States)

    Xu, Richard Y. D.; Jin, Jesse S.

    2007-01-01

    This article presents a schematic application of computer vision technologies to e-learning that is synchronous, peer-to-peer-based, and supports an instructor's interaction with non-computer teaching equipments. The article first discusses the importance of these focused e-learning areas, where the properties include accurate bidirectional…

  2. The TEACH Method: An Interactive Approach for Teaching the Needs-Based Theories Of Motivation

    Science.gov (United States)

    Moorer, Cleamon, Jr.

    2014-01-01

    This paper describes an interactive approach for explaining and teaching the Needs-Based Theories of Motivation. The acronym TEACH stands for Theory, Example, Application, Collaboration, and Having Discussion. This method can help business students to better understand and distinguish the implications of Maslow's Hierarchy of Needs,…

  3. Inquiry and Groups: Student Interactions in Cooperative Inquiry-Based Science

    Science.gov (United States)

    Woods-McConney, Amanda; Wosnitza, Marold; Sturrock, Keryn L.

    2016-01-01

    Science education research has recommended cooperative inquiry based science in the primary science context for more than two decades but after more than 20 years, student achievement in science has not substantially improved. This study, through direct observation and analysis, investigated content-related student interactions in an authentic…

  4. Learning through Interaction in Children with Autism: Preliminary Data from a Social-Communication-Based Intervention

    Science.gov (United States)

    Casenhiser, Devin M.; Shanker, Stuart G.; Stieben, Jim

    2013-01-01

    The study evaluates a social-communication-based approach to autism intervention aimed at improving the social interaction skills of children with autism spectrum disorder. We report preliminary results from an ongoing randomized controlled trial of 51 children aged 2 years 0 months to 4 years 11 months. Participants were assigned to either a…

  5. A Perylene-Based Microporous Coordination Polymer Interacts Selectively with Electron-Poor Aromatics.

    Science.gov (United States)

    Tran, Ly D; Ma, Jialiu; Wong-Foy, Antek G; Matzger, Adam J

    2016-04-11

    The design, synthesis, and properties of the new microporous coordination polymer UMCM-310 are described. The unique electronic character of the perylene-based linker enables selective interaction with electron-poor aromatics leading to efficient separation of nitroaromatics. UMCM-310 possesses high surface area and large pore size and thus permits the separation of large organic molecules based on adsorption rather than size exclusion. PMID:26868729

  6. Family-based Gene-by-Environment Interaction Studies: Revelations and Remedies

    OpenAIRE

    Shi, Min; Umbach, David M; Weinberg, Clarice R

    2011-01-01

    Bias can arise in case-control studies of genotype effects if the underlying population is structured (genetically stratified or admixed). Nuclear-family-based studies enjoy robustness against such bias, provided that inference conditions properly on the parents. Investigators have extended family-based methods to study gene-by-environment interactions, regarding such extensions as retaining robustness. We demonstrate via simulations that, if population structure involves the exposure, nuclea...

  7. Web-Based 3D and Haptic Interactive Environments for e-Learning, Simulation, and Training

    Science.gov (United States)

    Hamza-Lup, Felix G.; Sopin, Ivan

    Knowledge creation occurs in the process of social interaction. As our service-based society is evolving into a knowledge-based society, there is an acute need for more effective collaboration and knowledge-sharing systems to be used by geographically scattered people. We present the use of 3D components and standards, such as Web3D, in combination with the haptic paradigm, for e-Learning and simulation.

  8. Area of interest based interaction and GeoVisualization with WebGL

    OpenAIRE

    Bektas, Kenan; Coltekin, Arzu

    2012-01-01

    In this paper we present an experimental approach and a prototype implementation to manage level of detail in geovisualizations. The approach is based on identifying the area of interest of the user (mouse location or gaze point) and removing perceptually irrelevant detail in the visual field. Prototype implementation achieves this in real time using WebGL. By utilizing this test environment we want to systematically reveal the potential of integrating gaze based interaction modalities to the...

  9. Virtual temporal bone: an interactive 3-dimensional learning aid for cranial base surgery

    OpenAIRE

    Kockro, R A; Hwang, P Y

    2009-01-01

    OBJECTIVE: We have developed an interactive virtual model of the temporal bone for the training and teaching of cranial base surgery. METHODS: The virtual model was based on the tomographic data of the Visible Human Project. The male Visible Human's computed tomographic data were volumetrically reconstructed as virtual bone tissue, and the individual photographic slices provided the basis for segmentation of the middle and inner ear structures, cranial nerves, vessels, and brainstem. These st...

  10. Decoherence under many-body system-environment interactions: A stroboscopic representation based on a fictitiously homogenized interaction rate

    International Nuclear Information System (INIS)

    An environment interacting with portions of a system leads to multiexponential interaction rates. Within the Keldysh formalism, we fictitiously homogenize the system-environment interaction yielding a uniform decay rate facilitating the evaluation of the propagators. Through an injection procedure we neutralize the fictitious interactions. This technique justifies a stroboscopic representation of the system-environment interaction which is useful for numerical implementation and converges to the natural continuous process. We apply this procedure to a fermionic two-level system and use the Jordan-Wigner transformation to solve a two-spin swapping gate in the presence of a spin environment

  11. Decoherence under many-body system-environment interactions: A stroboscopic representation based on a fictitiously homogenized interaction rate

    Science.gov (United States)

    Álvarez, Gonzalo A.; Danieli, Ernesto P.; Levstein, Patricia R.; Pastawski, Horacio M.

    2007-06-01

    An environment interacting with portions of a system leads to multiexponential interaction rates. Within the Keldysh formalism, we fictitiously homogenize the system-environment interaction yielding a uniform decay rate facilitating the evaluation of the propagators. Through an injection procedure we neutralize the fictitious interactions. This technique justifies a stroboscopic representation of the system-environment interaction which is useful for numerical implementation and converges to the natural continuous process. We apply this procedure to a fermionic two-level system and use the Jordan-Wigner transformation to solve a two-spin swapping gate in the presence of a spin environment.

  12. Exposure to superfluous information reduces cooperation and increases antisocial punishment in reputation-based interactions

    Directory of Open Access Journals (Sweden)

    ClausWedekind

    2014-08-01

    Full Text Available Human cooperation is often based on reputation gained from previous interactions with third parties. Such reputation can be built on generous or punitive actions, and both, one’s own reputation and the reputation of others have been shown to influence decision making in experimental games that control for confounding variables. Here we test how reputation-based cooperation and punishment react to disruption of the cognitive processing in different kinds of helping games with observers. Saying a few superfluous words before each interaction was used to possibly interfere with working memory. In a first set of experiments, where reputation could only be based on generosity, the disruption reduced the frequency of cooperation and lowered mean final payoffs. In a second set of experiments where reputation could only be based on punishment, the disruption increased the frequency of antisocial punishment (i.e. of punishing those who helped and reduced the frequency of punishing defectors. Our findings suggest that working memory can easily be constraining in reputation-based interactions within experimental games, even if these games are based on a few simple rules with a visual display that provides all the information the subjects need to play the strategies predicted from current theory. Our findings also highlight a weakness of experimental games, namely that they can be very sensitive to environmental variation and that quantitative conclusions about antisocial punishment or other behavioral strategies can easily be misleading.

  13. A feature-based approach to modeling protein-protein interaction hot spots.

    Science.gov (United States)

    Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

    2009-05-01

    Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions. PMID:19273533

  14. Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

    Science.gov (United States)

    Zhang, Shu-Bo; Tang, Qiang-Rong

    2016-07-21

    Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most powerful indicators for protein interaction. However, conventional methods based on GO similarity fail to take advantage of the specificity of GO terms in the ontology graph. We proposed a GO-based method to predict protein-protein interaction by integrating different kinds of similarity measures derived from the intrinsic structure of GO graph. We extended five existing methods to derive the semantic similarity measures from the descending part of two GO terms in the GO graph, then adopted a feature integration strategy to combines both the ascending and the descending similarity scores derived from the three sub-ontologies to construct various kinds of features to characterize each protein pair. Support vector machines (SVM) were employed as discriminate classifiers, and five-fold cross validation experiments were conducted on both human and yeast protein-protein interaction datasets to evaluate the performance of different kinds of integrated features, the experimental results suggest the best performance of the feature that combines information from both the ascending and the descending parts of the three ontologies. Our method is appealing for effective prediction of protein-protein interaction. PMID:27117309

  15. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Yitan; Xu, Yanxun; Helseth, Donald L.; Gulukota, Kamalakar; Yang, Shengjie; Pesce, Lorenzo L.; Mitra, Riten; Muller, Peter; Sengupta, Subhajit; Guo, Wentian; Foster, Ian; Bullock, JaQuel A.

    2015-08-01

    Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.

  16. Interactive Cosmetic Makeup of a 3D Point-Based Face Model

    Science.gov (United States)

    Kim, Jeong-Sik; Choi, Soo-Mi

    We present an interactive system for cosmetic makeup of a point-based face model acquired by 3D scanners. We first enhance the texture of a face model in 3D space using low-pass Gaussian filtering, median filtering, and histogram equalization. The user is provided with a stereoscopic display and haptic feedback, and can perform simulated makeup tasks including the application of foundation, color makeup, and lip gloss. Fast rendering is achieved by processing surfels using the GPU, and we use a BSP tree data structure and a dynamic local refinement of the facial surface to provide interactive haptics. We have implemented a prototype system and evaluated its performance.

  17. Novel Technology for Protein-Protein Interaction-based Targeted Drug Discovery

    Directory of Open Access Journals (Sweden)

    Jung Me Hwang

    2011-12-01

    Full Text Available We have developed a simple but highly efficient in-cell protein-protein interaction (PPI discovery system based on the translocation properties of protein kinase C- and its C1a domain in live cells. This system allows the visual detection of trimeric and dimeric protein interactions including cytosolic, nuclear, and/or membrane proteins with their cognate ligands. In addition, this system can be used to identify pharmacological small compounds that inhibit specific PPIs. These properties make this PPI system an attractive tool for screening drug candidates and mapping the protein interactome.

  18. Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes.

    Directory of Open Access Journals (Sweden)

    Jiawei Luo

    Full Text Available Computational approaches aided by computer science have been used to predict essential proteins and are faster than expensive, time-consuming, laborious experimental approaches. However, the performance of such approaches is still poor, making practical applications of computational approaches difficult in some fields. Hence, the development of more suitable and efficient computing methods is necessary for identification of essential proteins.In this paper, we propose a new method for predicting essential proteins in a protein interaction network, local interaction density combined with protein complexes (LIDC, based on statistical analyses of essential proteins and protein complexes. First, we introduce a new local topological centrality, local interaction density (LID, of the yeast PPI network; second, we discuss a new integration strategy for multiple bioinformatics. The LIDC method was then developed through a combination of LID and protein complex information based on our new integration strategy. The purpose of LIDC is discovery of important features of essential proteins with their neighbors in real protein complexes, thereby improving the efficiency of identification.Experimental results based on three different PPI(protein-protein interaction networks of Saccharomyces cerevisiae and Escherichia coli showed that LIDC outperformed classical topological centrality measures and some recent combinational methods. Moreover, when predicting MIPS datasets, the better improvement of performance obtained by LIDC is over all nine reference methods (i.e., DC, BC, NC, LID, PeC, CoEWC, WDC, ION, and UC.LIDC is more effective for the prediction of essential proteins than other recently developed methods.

  19. Investigation of hyperfine interactions in DNA nitrogenous bases using perturbed angular correlation spectroscopy

    International Nuclear Information System (INIS)

    Perturbed γγ angular correlations (PAC) spectroscopy has been used to study the DNA nitrogenous bases (adenine, cytosine, guanine, thymine), using 111In→111Cd and 111mCd→111Cd probe nuclei. One of the advantages of applying PAC technique to biological molecules is that the experiments can be carried out on molecules in aqueous solution [1], approaching the function of molecules under conditions that are close to in vivo conditions. The measurements were carried out for DNA nitrogenous bases molecules at 295 K and 77 K in order to investigate dynamic and static hyperfine interactions, respectively. The interpretation of the results was based on the measurements of dynamic interaction characterized by the decay constant from which valuable information on the macroscopic behavior of the molecules was obtained [2; 3]. On the other hand, PAC measurements at low temperature showed interaction frequency (νQ), asymmetry parameter (η) and the distribution of the quadrupole frequency (δ). These parameters provide a local microscopic description of the chemical environment in the neighborhood of the probe nuclei. Results showed differences in the hyperfine interactions of probe nuclei bound to the studied biomolecules. Such differences were observed by variations in the hyperfine parameters, which depended on the type of biomolecule and the results also showed that the probe nuclei bounded at the molecules in some cases and at others did not. (author)

  20. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.

    Directory of Open Access Journals (Sweden)

    Chris A Kieslich

    Full Text Available HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.

  1. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

    Science.gov (United States)

    Kieslich, Chris A.; Tamamis, Phanourios; Guzman, Yannis A.; Onel, Melis; Floudas, Christodoulos A.

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389

  2. Investigation of hyperfine interactions in DNA nitrogenous bases using perturbed angular correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Andreia dos Santos; Carbonari, Artur Wilson; Lapolli, Andre Luis; Saxena, Rajendra Narain [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Saitovitch, Henrique, E-mail: asilva@usp.br [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

    2013-07-01

    Perturbed γγ angular correlations (PAC) spectroscopy has been used to study the DNA nitrogenous bases (adenine, cytosine, guanine, thymine), using {sup 111}In→{sup 111}Cd and {sup 111m}Cd→{sup 111}Cd probe nuclei. One of the advantages of applying PAC technique to biological molecules is that the experiments can be carried out on molecules in aqueous solution [1], approaching the function of molecules under conditions that are close to in vivo conditions. The measurements were carried out for DNA nitrogenous bases molecules at 295 K and 77 K in order to investigate dynamic and static hyperfine interactions, respectively. The interpretation of the results was based on the measurements of dynamic interaction characterized by the decay constant from which valuable information on the macroscopic behavior of the molecules was obtained [2; 3]. On the other hand, PAC measurements at low temperature showed interaction frequency (ν{sub Q}), asymmetry parameter (η) and the distribution of the quadrupole frequency (δ). These parameters provide a local microscopic description of the chemical environment in the neighborhood of the probe nuclei. Results showed differences in the hyperfine interactions of probe nuclei bound to the studied biomolecules. Such differences were observed by variations in the hyperfine parameters, which depended on the type of biomolecule and the results also showed that the probe nuclei bounded at the molecules in some cases and at others did not. (author)

  3. Interactive Learning Environment: Web-based Virtual Hydrological Simulation System using Augmented and Immersive Reality

    Science.gov (United States)

    Demir, I.

    2014-12-01

    Recent developments in internet technologies make it possible to manage and visualize large data on the web. Novel visualization techniques and interactive user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The hydrological simulation system is a web-based 3D interactive learning environment for teaching hydrological processes and concepts. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create or load predefined scenarios, control environmental parameters, and evaluate environmental mitigation alternatives. The web-based simulation system provides an environment for students to learn about the hydrological processes (e.g. flooding and flood damage), and effects of development and human activity in the floodplain. The system utilizes latest web technologies and graphics processing unit (GPU) for water simulation and object collisions on the terrain. Users can access the system in three visualization modes including virtual reality, augmented reality, and immersive reality using heads-up display. The system provides various scenarios customized to fit the age and education level of various users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various visualization and interaction modes.

  4. Design and Implementation of an Interactive Web-Based Near Real-Time Forest Monitoring System.

    Directory of Open Access Journals (Sweden)

    Arun Kumar Pratihast

    Full Text Available This paper describes an interactive web-based near real-time (NRT forest monitoring system using four levels of geographic information services: 1 the acquisition of continuous data streams from satellite and community-based monitoring using mobile devices, 2 NRT forest disturbance detection based on satellite time-series, 3 presentation of forest disturbance data through a web-based application and social media and 4 interaction of the satellite based disturbance alerts with the end-user communities to enhance the collection of ground data. The system is developed using open source technologies and has been implemented together with local experts in the UNESCO Kafa Biosphere Reserve, Ethiopia. The results show that the system is able to provide easy access to information on forest change and considerably improves the collection and storage of ground observation by local experts. Social media leads to higher levels of user interaction and noticeably improves communication among stakeholders. Finally, an evaluation of the system confirms the usability of the system in Ethiopia. The implemented system can provide a foundation for an operational forest monitoring system at the national level for REDD+ MRV applications.

  5. Design and Implementation of an Interactive Web-Based Near Real-Time Forest Monitoring System.

    Science.gov (United States)

    Pratihast, Arun Kumar; DeVries, Ben; Avitabile, Valerio; de Bruin, Sytze; Herold, Martin; Bergsma, Aldo

    2016-01-01

    This paper describes an interactive web-based near real-time (NRT) forest monitoring system using four levels of geographic information services: 1) the acquisition of continuous data streams from satellite and community-based monitoring using mobile devices, 2) NRT forest disturbance detection based on satellite time-series, 3) presentation of forest disturbance data through a web-based application and social media and 4) interaction of the satellite based disturbance alerts with the end-user communities to enhance the collection of ground data. The system is developed using open source technologies and has been implemented together with local experts in the UNESCO Kafa Biosphere Reserve, Ethiopia. The results show that the system is able to provide easy access to information on forest change and considerably improves the collection and storage of ground observation by local experts. Social media leads to higher levels of user interaction and noticeably improves communication among stakeholders. Finally, an evaluation of the system confirms the usability of the system in Ethiopia. The implemented system can provide a foundation for an operational forest monitoring system at the national level for REDD+ MRV applications. PMID:27031694

  6. Physically-Based Interactive Flow Visualization Based on Schlieren and Interferometry Experimental Techniques

    KAUST Repository

    Brownlee, C.

    2011-11-01

    Understanding fluid flow is a difficult problem and of increasing importance as computational fluid dynamics (CFD) produces an abundance of simulation data. Experimental flow analysis has employed techniques such as shadowgraph, interferometry, and schlieren imaging for centuries, which allow empirical observation of inhomogeneous flows. Shadowgraphs provide an intuitive way of looking at small changes in flow dynamics through caustic effects while schlieren cutoffs introduce an intensity gradation for observing large scale directional changes in the flow. Interferometry tracks changes in phase-shift resulting in bands appearing. The combination of these shading effects provides an informative global analysis of overall fluid flow. Computational solutions for these methods have proven too complex until recently due to the fundamental physical interaction of light refracting through the flow field. In this paper, we introduce a novel method to simulate the refraction of light to generate synthetic shadowgraph, schlieren and interferometry images of time-varying scalar fields derived from computational fluid dynamics data. Our method computes physically accurate schlieren and shadowgraph images at interactive rates by utilizing a combination of GPGPU programming, acceleration methods, and data-dependent probabilistic schlieren cutoffs. Applications of our method to multifield data and custom application-dependent color filter creation are explored. Results comparing this method to previous schlieren approximations are finally presented. © 2011 IEEE.

  7. Literature based drug interaction prediction with clinical assessment using electronic medical records: novel myopathy associated drug interactions.

    Directory of Open Access Journals (Sweden)

    Jon D Duke

    Full Text Available Drug-drug interactions (DDIs are a common cause of adverse drug events. In this paper, we combined a literature discovery approach with analysis of a large electronic medical record database method to predict and evaluate novel DDIs. We predicted an initial set of 13197 potential DDIs based on substrates and inhibitors of cytochrome P450 (CYP metabolism enzymes identified from published in vitro pharmacology experiments. Using a clinical repository of over 800,000 patients, we narrowed this theoretical set of DDIs to 3670 drug pairs actually taken by patients. Finally, we sought to identify novel combinations that synergistically increased the risk of myopathy. Five pairs were identified with their p-values less than 1E-06: loratadine and simvastatin (relative risk or RR = 1.69; loratadine and alprazolam (RR = 1.86; loratadine and duloxetine (RR = 1.94; loratadine and ropinirole (RR = 3.21; and promethazine and tegaserod (RR = 3.00. When taken together, each drug pair showed a significantly increased risk of myopathy when compared to the expected additive myopathy risk from taking either of the drugs alone. Based on additional literature data on in vitro drug metabolism and inhibition potency, loratadine and simvastatin and tegaserod and promethazine were predicted to have a strong DDI through the CYP3A4 and CYP2D6 enzymes, respectively. This new translational biomedical informatics approach supports not only detection of new clinically significant DDI signals, but also evaluation of their potential molecular mechanisms.

  8. Quantifying molecule-surface interactions using AFM-based single-molecule manipulation

    Science.gov (United States)

    Tautz, F. S.; Wagner, C.; Temirov, R.; Fournier, N.; Green, M.; Esat, T.; Leinen, P.; Groetsch, A.; Ruiz, V. G.; Tkatchenko, A.; Li, C.; Muellen, K.; Rohlfing, M.

    2015-03-01

    Scanning probe microscopy plays an important role in the investigation of molecular adsorption. Promising, is the possibility to probe the molecule-surface interaction while tuning its strength through AFM tip-induced single-molecule manipulation. Here, we outline a strategy to achieve quantitative understanding of such manipulation experiments. The example of qPlus sensor based PTCDA molecule lifting experiments is used to demonstrate how different aspects of the molecule-surface interaction, namely the short-range adsorption potential, the asymptotic van der Waals potential, local chemical bonds which are the source of the surface corrugation, and molecule-molecule interactions can be measured with SPM and interpreted by the help of force-field simulations.

  9. Towards for Analyzing Alternatives of Interaction Design Based on Verbal Decision Analysis of User Experience

    Directory of Open Access Journals (Sweden)

    Marília Soares Mendes

    2010-04-01

    Full Text Available In domains (as digital TV, smart home, and tangible interfaces that represent a new paradigm of interactivity, the decision of the most appropriate interaction design solution is a challenge. HCI researchers have promoted in their works the validation of design alternative solutions with users before producing the final solution. User experience with technology is a subject that has also gained ground in these works in order to analyze the appropriate solution(s. Following this concept, a study was accomplished under the objective of finding a better interaction solution for an application of mobile TV. Three executable applications of mobile TV prototypes were built. A Verbal Decision Analysis model was applied on the investigations for the favorite characteristics in each prototype based on the user’s experience and their intentions of use. This model led a performance of a qualitative analysis which objectified the design of a new prototype.

  10. Spatial multi-level interacting particle simulations and information theory-based error quantification

    CERN Document Server

    Kalligiannaki, Evangelia; Plechac, Petr

    2012-01-01

    We propose a hierarchy of multi-level kinetic Monte Carlo methods for sampling high-dimensional, stochastic lattice particle dynamics with complex interactions. The method is based on the efficient coupling of different spatial resolution levels, taking advantage of the low sampling cost in a coarse space and by developing local reconstruction strategies from coarse-grained dynamics. Microscopic reconstruction corrects possibly significant errors introduced through coarse-graining, leading to the controlled-error approximation of the sampled stochastic process. In this manner, the proposed multi-level algorithm overcomes known shortcomings of coarse-graining of particle systems with complex interactions such as combined long and short-range particle interactions and/or complex lattice geometries. Specifically, we provide error analysis for the approximation of long-time stationary dynamics in terms of relative entropy and prove that information loss in the multi-level methods is growing linearly in time, whic...

  11. Prediction of Substrate-Enzyme-Product Interaction Based on Molecular Descriptors and Physicochemical Properties

    Directory of Open Access Journals (Sweden)

    Bing Niu

    2013-01-01

    Full Text Available It is important to correctly and efficiently predict the interaction of substrate-enzyme and to predict their product in metabolic pathway. In this work, a novel approach was introduced to encode substrate/product and enzyme molecules with molecular descriptors and physicochemical properties, respectively. Based on this encoding method, KNN was adopted to build the substrate-enzyme-product interaction network. After selecting the optimal features that are able to represent the main factors of substrate-enzyme-product interaction in our prediction, totally 160 features out of 290 features were attained which can be clustered into ten categories: elemental analysis, geometry, chemistry, amino acid composition, predicted secondary structure, hydrophobicity, polarizability, solvent accessibility, normalized van der Waals volume, and polarity. As a result, our predicting model achieved an MCC of 0.423 and an overall prediction accuracy of 89.1% for 10-fold cross-validation test.

  12. Prediction of substrate-enzyme-product interaction based on molecular descriptors and physicochemical properties.

    Science.gov (United States)

    Niu, Bing; Huang, Guohua; Zheng, Linfeng; Wang, Xueyuan; Chen, Fuxue; Zhang, Yuhui; Huang, Tao

    2013-01-01

    It is important to correctly and efficiently predict the interaction of substrate-enzyme and to predict their product in metabolic pathway. In this work, a novel approach was introduced to encode substrate/product and enzyme molecules with molecular descriptors and physicochemical properties, respectively. Based on this encoding method, KNN was adopted to build the substrate-enzyme-product interaction network. After selecting the optimal features that are able to represent the main factors of substrate-enzyme-product interaction in our prediction, totally 160 features out of 290 features were attained which can be clustered into ten categories: elemental analysis, geometry, chemistry, amino acid composition, predicted secondary structure, hydrophobicity, polarizability, solvent accessibility, normalized van der Waals volume, and polarity. As a result, our predicting model achieved an MCC of 0.423 and an overall prediction accuracy of 89.1% for 10-fold cross-validation test. PMID:24455714

  13. A domain-based approach to predict protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Resat Haluk

    2007-06-01

    Full Text Available Abstract Background Knowing which proteins exist in a certain organism or cell type and how these proteins interact with each other are necessary for the understanding of biological processes at the whole cell level. The determination of the protein-protein interaction (PPI networks has been the subject of extensive research. Despite the development of reasonably successful methods, serious technical difficulties still exist. In this paper we present DomainGA, a quantitative computational approach that uses the information about the domain-domain interactions to predict the interactions between proteins. Results DomainGA is a multi-parameter optimization method in which the available PPI information is used to derive a quantitative scoring scheme for the domain-domain pairs. Obtained domain interaction scores are then used to predict whether a pair of proteins interacts. Using the yeast PPI data and a series of tests, we show the robustness and insensitivity of the DomainGA method to the selection of the parameter sets, score ranges, and detection rules. Our DomainGA method achieves very high explanation ratios for the positive and negative PPIs in yeast. Based on our cross-verification tests on human PPIs, comparison of the optimized scores with the structurally observed domain interactions obtained from the iPFAM database, and sensitivity and specificity analysis; we conclude that our DomainGA method shows great promise to be applicable across multiple organisms. Conclusion We envision the DomainGA as a first step of a multiple tier approach to constructing organism specific PPIs. As it is based on fundamental structural information, the DomainGA approach can be used to create potential PPIs and the accuracy of the constructed interaction template can be further improved using complementary methods. Explanation ratios obtained in the reported test case studies clearly show that the false prediction rates of the template networks constructed

  14. Wearable Computing System with Input-Output Devices Based on Eye-Based Human Computer Interaction Allowing Location Based Web Services

    OpenAIRE

    Kohei Arai

    2013-01-01

    Wearable computing with Input-Output devices Base on Eye-Based Human Computer Interaction: EBHCI which allows location based web services including navigation, location/attitude/health condition monitoring is proposed. Through implementation of the proposed wearable computing system, all the functionality is confirmed. It is also found that the system does work well. It can be used easily and also is not expensive. Experimental results for EBHCI show excellent performance in terms of key-in a...

  15. Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins

    Science.gov (United States)

    Ielasi, Francesco S.; Alioscha-Perez, Mitchel; Donohue, Dagmara; Claes, Sandra; Sahli, Hichem; Schols, Dominique

    2016-01-01

    ABSTRACT The first step in the infection of humans by microbial pathogens is their adherence to host tissue cells, which is frequently based on the binding of carbohydrate-binding proteins (lectin-like adhesins) to human cell receptors that expose glycans. In only a few cases have the human receptors of pathogenic adhesins been described. A novel strategy—based on the construction of a lectin-glycan interaction (LGI) network—to identify the potential human binding receptors for pathogenic adhesins with lectin activity was developed. The new approach is based on linking glycan array screening results of these adhesins to a human glycoprotein database via the construction of an LGI network. This strategy was used to detect human receptors for virulent Escherichia coli (FimH adhesin), and the fungal pathogens Candida albicans (Als1p and Als3p adhesins) and C. glabrata (Epa1, Epa6, and Epa7 adhesins), which cause candidiasis. This LGI network strategy allows the profiling of potential adhesin binding receptors in the host with prioritization, based on experimental binding data, of the most relevant interactions. New potential targets for the selected adhesins were predicted and experimentally confirmed. This methodology was also used to predict lectin interactions with envelope glycoproteins of human-pathogenic viruses. It was shown that this strategy was successful in revealing that the FimH adhesin has anti-HIV activity. PMID:27406561

  16. Teacher-student interaction: The overlooked dimension of inquiry-based professional development

    Science.gov (United States)

    de Oliveira, Alandeom Wanderlei

    This study explores the teacher-student interactional dimension of inquiry-based science instruction. In it, microethnographic and grounded theory analyses are conducted in order to assess the impact of a professional development program designed to enhance in-service elementary teachers' interactional views (i.e., their understandings of inquiry-based social roles and relationships) and discursive practices (i.e., teachers' abilities to interact with student engaged in classroom inquiries) through a combination of expert instruction, immersion in scientific inquiry, and collaborative analysis of video-recorded classroom discourse. A sociolinguistic theoretical perspective on language use is adopted, viewing classroom discourse as comprising multiple linguistic signs (questions, responses, personal pronouns, hedges, backchannels, reactive tokens, directives, figures of speech, parallel repetitions) that convey not only semantic meanings (the literal information being exchanged) but also pragmatic meanings (information about teachers and students' social roles and relationships). A grounded theory analysis of the professional development activities uncovered a gradual shift in teachers' interactional views from a cognitive, monofunctional and decontextualized perspective to a social, multifunctional and contextualized conception of inquiry-based discourse. Furthermore, teachers developed increased levels of pragmatic awareness, being able to recognize the authoritative interactional functions served by discursive moves such as display questions, cued elicitation, convergent questioning, verbal cloze, affirmation, explicit evaluations of students' responses, verbatim repetitions, IRE triplets, IR couplets, second-person pronouns, "I/you" contrastive pairs, and direct or impolite directives. A comparative microethnographic analysis of teachers' classroom practices revealed that after participating in the program teachers demonstrated an improved ability to share

  17. Effects of Coulomb interactions on the superconducting gaps in iron-based superconductors

    Science.gov (United States)

    Leong, Zhidong; Phillips, Philip

    2016-04-01

    Recent angle-resolved photoemission spectroscopy measurements of Co-doped LiFeAs report a large and robust superconducting gap on the Γ -centered hole band that lies 8 meV below the Fermi level. We show that, unlike a conventional superconductor described by BCS theory, a multiband system with strong interband Coulomb interactions can explain these observations. We model LiFeAs with a five-band model in which the shallow hole band is coupled with the other bands by only Coulomb interactions. Using Eliashberg theory, we find reasonable interaction parameters that reproduce the Tc and all five gaps of LiFeAs. The energy independence of the Coulomb interactions then ensures the robustness of the gap induced on the shallow band. Furthermore, due to the repulsive nature of the Coulomb interactions, the gap changes sign between the shallow band and the other hole pockets, corresponding to an unconventional s± gap symmetry. Unlike other families of iron-based superconductors, the gap symmetry of LiFeAs has not been ascertained experimentally. The experimental implications of this sign-changing state are discussed.

  18. Probability-based model of protein-protein interactions on biological timescales

    Directory of Open Access Journals (Sweden)

    Bates Paul A

    2006-12-01

    Full Text Available Abstract Background Simulation methods can assist in describing and understanding complex networks of interacting proteins, providing fresh insights into the function and regulation of biological systems. Recent studies have investigated such processes by explicitly modelling the diffusion and interactions of individual molecules. In these approaches, two entities are considered to have interacted if they come within a set cutoff distance of each other. Results In this study, a new model of bimolecular interactions is presented that uses a simple, probability-based description of the reaction process. This description is well-suited to simulations on timescales relevant to biological systems (from seconds to hours, and provides an alternative to the previous description given by Smoluchowski. In the present approach (TFB the diffusion process is explicitly taken into account in generating the probability that two freely diffusing chemical entities will interact within a given time interval. It is compared to the Smoluchowski method, as modified by Andrews and Bray (AB. Conclusion When implemented, the AB & TFB methods give equivalent results in a variety of situations relevant to biology. Overall, the Smoluchowski method as modified by Andrews and Bray emerges as the most simple, robust and efficient method for simulating biological diffusion-reaction processes currently available.

  19. Commercial Motion Sensor Based Low-Cost and Convenient Interactive Treadmill

    Directory of Open Access Journals (Sweden)

    Jonghyun Kim

    2015-09-01

    Full Text Available Interactive treadmills were developed to improve the simulation of overground walking when compared to conventional treadmills. However, currently available interactive treadmills are expensive and inconvenient, which limits their use. We propose a low-cost and convenient version of the interactive treadmill that does not require expensive equipment and a complicated setup. As a substitute for high-cost sensors, such as motion capture systems, a low-cost motion sensor was used to recognize the subject’s intention for speed changing. Moreover, the sensor enables the subject to make a convenient and safe stop using gesture recognition. For further cost reduction, the novel interactive treadmill was based on an inexpensive treadmill platform and a novel high-level speed control scheme was applied to maximize performance for simulating overground walking. Pilot tests with ten healthy subjects were conducted and results demonstrated that the proposed treadmill achieves similar performance to a typical, costly, interactive treadmill that contains a motion capture system and an instrumented treadmill, while providing a convenient and safe method for stopping.

  20. Toward the design of a low cost vision-based gaze tracker for interaction skill acquisition

    Directory of Open Access Journals (Sweden)

    Martinez Francis

    2011-12-01

    Full Text Available The human gaze is a basic mean for non verbal interaction between humans; however, in several situations, especially in the context of upper limb motor impairments, the gaze constitutes also an alternative mean for human’s interactions with the environment (real or virtual. Mastering these interactions through specific tools, requires frequently the acquisition of new skills and understanding of mechanisms which allow to acquire the necessary skills. Therefore the technological tool is a key for new interaction skills’ acquisition. This paper presents a tool for interaction skill acquisition via a gaze. The proposed gaze tracker is a low cost head mounted system based on vision technology “only”. The system hardware specifications and the status of the gaze tracker design are presented; the dedicated algorithm for eye detection and tracking, and an improvement of G. Zelinsky model for eye movement predication during the search of a predefined object in an image are outlined. Results of the software preliminary evaluation are presented.

  1. Regulation of catalytic behaviour of hydrolases through interactions with functionalized carbon-based nanomaterials

    International Nuclear Information System (INIS)

    The interaction of enzymes with carbon-based nanomaterials (CBNs) is crucial for the function of biomolecules and therefore for the design and development of effective nanobiocatalytic systems. In this study, the effect of functionalized CBNs, such as graphene oxide (GO) and multi-wall carbon nanotubes (CNTs), on the catalytic behaviour of various hydrolases of biotechnological interest was monitored and the interactions between CBNs and proteins were investigated. The enzyme–nanomaterial interactions significantly affect the catalytic behaviour of enzymes, resulting in an increase up to 60 % of the catalytic efficiency of lipases and a decrease up to 30 % of the esterase. Moreover, the use of CNTs and GO derivatives, especially those that are amine-functionalized, led to increased thermal stability of most the hydrolases tested. Fluorescence and circular dichroism studies indicated that the altered catalytic behaviour of enzymes in the presence of CBNs arises from specific enzyme–nanomaterial interactions, which can lead to significant conformational changes. In the case of lipases, the conformational changes led to a more active and rigid structure, while in the case of esterases this led to destabilization and unfolding. Kinetic and spectroscopic studies indicated that the extent of the interactions between CBNs and hydrolases can be mainly controlled by the functionalization of nanomaterials than by their geometry.

  2. Interactive Application Development Policy Object 3D Virtual Tour History Pacitan District based Multimedia

    Directory of Open Access Journals (Sweden)

    Bambang Eka Purnama

    2013-04-01

    Full Text Available Pacitan has a wide range of tourism activity. One of the tourism district is Pacitan historical attractions. These objects have a history tour of the educational values, history and culture, which must be maintained and preserved as one tourism asset Kabupeten Pacitan. But the history of the current tour the rarely visited and some of the students also do not understand the history of each of these historical attractions. Hence made a information media of 3D virtual interactive applications Pacitan tour history in the form of interactive CD applications. The purpose of the creation of interactive applications is to introduce Pacitan history tours to students and the community. Creating interactive information media that can provide an overview of the history of the existing tourist sites in Pacitan The benefits of this research is the students and the public will get to know the history of historical attractions Pacitan. As a media introduction of historical attractions and as a medium of information to preserve the historical sights. Band is used in the manufacturing methods Applications 3D Virtual Interactive Attractions: History-Based Multimedia Pacitan authors used the method library, observation and interviews. Design using 3ds Max 2010, Adobe Director 11.5, Adobe Photoshop CS3 and Corel Draw. The results of this research is the creation of media interakif information that can provide knowledge about the history of Pacitan.

  3. Photo-physical and structural interactions between viologen phosphorus-based dendrimers and human serum albumin

    International Nuclear Information System (INIS)

    This work deals with photo-physical and structural interactions between viologen phosphorus dendrimers and human serum albumin (HSA). Viologens are derivatives of 4,4′-bipyridinium salts. Aiming to rationalize the parameters governing such interactions eight types of these polycationic dendrimers in which the generation, the number of charges, the nature of the core and of the terminal groups vary from one to another, were designed and used. The influence of viologen-based dendrimers' on human serum albumin has been investigated. The photo-physical interactions of the two systems have been monitored by fluorescence quenching of free L-tryptophan and of HSA tryptophan residue. Additionally, using circular dichroism (CD) the effect of dendrimers on the secondary structure of albumin was measured. The obtained results show that viologen dendrimers interact with human serum albumin quenching its fluorescence either by collisional (dynamic) way or by forming complexes in a ground state (static quenching). In some cases the quenching is accompanied by changes of the secondary structure of HSA. - Highlights: ► Photo-physical interactions between viologen phosphorus dendrimers and human serum albumin (HSA) were investigated. ► The viologen dendrimers can quench the fluorescence of tryptophan in HSA. ► CD spectra to explain the changes in secondary structure of albumin after exposition of dendrimers.

  4. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

    Directory of Open Access Journals (Sweden)

    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.

  5. Platoon Interactions and Real-World Traffic Simulation and Validation Based on the LWR-IM.

    Science.gov (United States)

    Ng, Kok Mun; Reaz, Mamun Bin Ibne

    2016-01-01

    Platoon based traffic flow models form the underlying theoretical framework in traffic simulation tools. They are essentially important in facilitating efficient performance calculation and evaluation in urban traffic networks. For this purpose, a new platoon-based macroscopic model called the LWR-IM has been developed in [1]. Preliminary analytical validation conducted previously has proven the feasibility of the model. In this paper, the LWR-IM is further enhanced with algorithms that describe platoon interactions in urban arterials. The LWR-IM and the proposed platoon interaction algorithms are implemented in the real-world class I and class II urban arterials. Another purpose of the work is to perform quantitative validation to investigate the validity and ability of the LWR-IM and its underlying algorithms to describe platoon interactions and simulate performance indices that closely resemble the real traffic situations. The quantitative validation of the LWR-IM is achieved by performing a two-sampled t-test on queues simulated by the LWR-IM and real queues observed at these real-world locations. The results reveal insignificant differences of simulated queues with real queues where the p-values produced concluded that the null hypothesis cannot be rejected. Thus, the quantitative validation further proved the validity of the LWR-IM and the embedded platoon interactions algorithm for the intended purpose. PMID:26731745

  6. Speech Based Question Recognition of Interactive Ubiquitous Teaching Robot using Supervised Classifier

    Directory of Open Access Journals (Sweden)

    Umarani S D#

    2011-06-01

    Full Text Available This paper presents the research work that aims at designing a speech based interactive ubiquitous teaching robot for quality enhancement of Higher Education ensuring better performance by making possibility of interaction between the Robot Teacher and Student/ Learner. Students/ Learner can ask technical questions for which the robot replies. Here the reply by the Robot is limited by the answers available in the database. The proposed speech based interactive teaching system has two phases; they are training and testing. A feed forward neural network is used as a supervised classifier after it istrained by means of a back propagation (BP algorithm using the features of sound signal from the Student/ Learner. The number of queries present in the database and non database queries recognized ispresented by Receiver Operating Characteristics curve (ROC. The ROC curve lies above the diagonal of the ROC plot. This indicates that the proposed method of interaction of Robot with the learners isacceptable. The percentage of question recognition resulted in 74%.

  7. Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

    Science.gov (United States)

    Liu, Shuang

    Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural

  8. Synthesis of bio-based aldehyde from seaweed polysaccharide and its interaction with bovine serum albumin.

    Science.gov (United States)

    Kholiya, Faisal; Chaudhary, Jai Prakash; Vadodariya, Nilesh; Meena, Ramavatar

    2016-10-01

    Here, we demonstrate a successful synthesis of bio-based aldehyde namely dialdehyde-carboxymethylagarose (DCMA) using carboxymethyagarose (CMA). Further reaction parameters (i.e. reaction temperature, pH and periodate concentration) were optimized to achieve maximum aldehyde content and product yield. The synthesis of DCMA was confirmed by employing FTIR, (1)H NMR, XRD, SEM, AFM, TGA, DSC, EA and GPC techniques. To investigate the aldehyde functionality, DCMA was allowed to interact with BSA and obtained results were found to be comparable with that of synthetic aldehyde (Formaldehyde). Further interaction of DCMA with BSA was confirmed by using UV-vis, FTIR, fluorescent spectroscopy, CD and DLS analysis. Results of this study revealed that bio-based aldehyde behaves like formaldehyde. This study adds value to abundant marine biopolymers and opens the new research area for polymer researchers. PMID:27312639

  9. Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease

    DEFF Research Database (Denmark)

    Jensen, Majken Karoline; Pers, Tune Hannes; Dworzynski, Piotr;

    2011-01-01

    Background-Network-based approaches may leverage genome-wide association (GWA) analysis by testing for the aggregate association across several pathway members. We aimed to examine if networks of genes that represent experimentally determined protein-protein interactions (PPIs) are enriched in...... number of complexes tested, 1 gene set was overrepresented in CHD-associated genes (P = 0.002). Centered on the beta 1-adrenergic receptor gene (ADRB1), this complex included 18 protein interaction partners that have not been identified as candidate loci for CHD. Of the 19 genes in the top complex, 5 are...... involved in abnormal cardiovascular system physiological features based on knockout mice (4-fold enrichment; Fisher exact test, P = 0.006). Ingenuity pathway analysis revealed that canonical pathways, especially related to blood pressure regulation, were significantly enriched in the genes from the top...

  10. Development of interactive patient-based multimedia computer programs in veterinary orthopedic radiology

    International Nuclear Information System (INIS)

    Three computerized multimedia programs on large and small animal veterinary orthopedic radiology were developed and implemented for the radiology curriculum as an alternative to traditional film-based laboratory learning. Programs utilized ''hot words'' (colored text words that displayed an overlaid image label that highlighted lesions) and interactive quizzes which responded appropriately to selected answers. ''Hot words'' helped students develop confidence in accurate lesion detection and the interactive quizzes transformed learning from a passive to an active process. Multiple examples were provided for reinforcement and concepts were incorporated from other clinical disciplines for curriculum integration. Programs were written using a presentation software program, Toolbook for DOS based platform, and contained radiographic images made by laser-scanning digitization. Multiple students could simultaneously access the programs through a network server. These pilot programs were implemented successfully and computerized multimedia presentation proved to be well suited to teaching radiology. Development of the programs required attention to a number of hardware, software, time and cost factors

  11. Petri Nets Based Modelling of Control Flow for Memory-Aid Interactive Programs in Telemedicine

    CERN Document Server

    Khoromskaia, V K

    2004-01-01

    Petri Nets (PN) based modelling of the control flow for the interactive memory assistance programs designed for personal pocket computers and having special requirements for robustness is considered. The proposed concept allows one to elaborate the programs which can give users a variety of possibilities for a day-time planning in the presence of environmental and time restrictions. First, a PN model for a known simple algorithm is constructed and analyzed using the corresponding state equations and incidence matrix. Then a PN graph for a complicated algorithm with overlapping actions and choice possibilities is designed, supplemented by an example of its analysis. Dynamic behaviour of this graph is tested by tracing of all possible paths of the flow of control using the PN simulator. It is shown that PN based modelling provides reliably predictable performance of interactive algorithms with branched structures and concurrency requirements.

  12. Optimization Method for Indoor Thermal Comfort Based on Interactive Numerical Calculation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In order to implement the optimal design of the indoor thermal comfort based on the numerical modeling method, the numerical calculation platform is combined seamlessly with the data-processing platform, and an interactive numerical calculation platform which includes the functions of numerical simulation and optimization is established. The artificial neural network (ANN) and the greedy strategy are introduced into the hill-climbing pattern heuristic search process, and the optimizing search direction can be predicted by using small samples; when searching along the direction using the greedy strategy, the optimal values can be quickly approached. Therefore, excessive external calling of the numerical modeling process can be avoided,and the optimization time is decreased obviously. The experimental results indicate that the satisfied output parameters of air conditioning can be quickly given out based on the interactive numerical calculation platform and the improved search method, and the optimization for indoor thermal comfort can be completed.

  13. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Energy Technology Data Exchange (ETDEWEB)

    Hamdani, Hazrina Yusof, E-mail: hazrina@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia); Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas (Malaysia); Artymiuk, Peter J., E-mail: p.artymiuk@sheffield.ac.uk [Dept. of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 T2N Sheffield (United Kingdom); Firdaus-Raih, Mohd, E-mail: firdaus@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia)

    2015-09-25

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  14. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Science.gov (United States)

    Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2015-09-01

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  15. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    International Nuclear Information System (INIS)

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods

  16. Implications for Utilizing YouTube based Community Interactions for Destination Marketing

    OpenAIRE

    Sambhanthan, Arunasalam; Thelijjagoda, Samantha; TAN, Joseph

    2013-01-01

    In recent time, YouTube has evolved into a powerful medium for social interaction. Utilizing YouTube for enhancing marketing endeavors is a strategy practiced by marketing professionals across several industries. This paper rationalizes on the different ways and means of leveraging YouTube-based platforms for effective destination marketing by the hospitality industry (hotels). More specifically, the typology of virtual communities is adapted to evaluate the YouTube platform for effective des...

  17. Exploring virus relationships based on virus-host protein-protein interaction network

    OpenAIRE

    Xu Feng; Zhao Chen; Li Yuhua; Li Jiang; Deng Youping; Shi Tieliu

    2011-01-01

    Abstract Background Currently, several systems have been proposed to classify viruses and indicate the relationships between different ones, though each system has its limitations because of the complexity of viral origins and their rapid evolution rate. We hereby propose a new method to explore the relationships between different viruses. Method A new method, which is based on the virus-host protein-protein interaction network, is proposed in this paper to categorize viruses. The distances b...

  18. Face to Face: Anthropometry-Based Interactive Face Shape Modeling Using Model Priors

    OpenAIRE

    Yu Zhang; Edmond C. Prakash

    2009-01-01

    This paper presents a new anthropometrics-based method for generating realistic, controllable face models. Our method establishes an intuitive and efficient interface to facilitate procedures for interactive 3D face modeling and editing. It takes 3D face scans as examples in order to exploit the variations presented in the real faces of individuals. The system automatically learns a model prior from the data-sets of example meshes of facial features using principal component analysis (PCA) an...

  19. APPLICATION OF THE HARD AND SOFT, ACIDS AND BASES (HSAB) THEORY TO TOXICANT-TARGET INTERACTIONS

    OpenAIRE

    LoPachin, Richard M.; Gavin, Terrence; DeCaprio, Anthony; David S Barber

    2011-01-01

    Many chemical toxicants and/or their active metabolites are electrophiles that cause cell injury by forming covalent bonds with nucleophilic targets on biological macromolecules. Covalent reactions between nucleophilic and electrophilic reagents are however discriminatory, since there is a significant degree of selectivity associated with these interactions. Over the course of the past few decades, the theory of Hard and Soft, Acid and Bases (HSAB) has proven to be a useful tool in predicting...

  20. A Descriptive Assessment of Instruction-Based Interactions in the Preschool Classroom

    OpenAIRE

    Ndoro, Virginia W; Hanley, Gregory P; Tiger, Jeffrey H; Heal, Nicole A

    2006-01-01

    The current study describes preschool teacher–child interactions during several commonly scheduled classroom activities in which teachers deliver instructions. An observation system was developed that incorporated measurement of evidence-based compliance strategies and included the types of instructions delivered (e.g., integral or deficient directives, embedded directives, “do” or “don't” commands), the children's behavior with respect to the instructions (e.g., compliance, noncompliance, ac...

  1. RecoMap : an interactive and adaptive map-based recommender

    OpenAIRE

    Ballatore, Andrea; McArdle, Gavin; Kelly, Caitriona; Bertolotto, Michela

    2010-01-01

    With the growing availability of geo-referenced information on the Web, the problem of spatial information overload has attracted interest both in the commercial and academic world. In order to tackle this issue, personalisation techniques can be used to tailor spatial contents based upon user interests. RecoMap, the system described in this paper, deducts user interests by monitoring user interaction and context to provide personalised spatial recommendations. After an overview of existing r...

  2. A bluetooth-based Interactive system to improve relationships between actors in educational environments

    OpenAIRE

    Ribeiro, F. Reinaldo; Metrôlho, J.C.M.M.; Costa, Mónica

    2010-01-01

    Nowadays there are a vast number of devices and technologies available for the common citizen to improve their communication with others. This fosters the design and implementation of systems that explore the available features of these devices. In this paper, we propose a Bluetooth-based interactive system for delivering personalized information in high education institutions. The system allows informing, on a personalized way, the actors of an education institution on a free way using popul...

  3. Interaction between Artemether-Lumefantrine and Nevirapine-Based Antiretroviral Therapy in HIV-1-Infected Patients▿

    OpenAIRE

    Kredo, T.; Mauff, K.; Van der Walt, J. S.; Wiesner, L.; G. Maartens; Cohen, K.; Smith, P.; Barnes, K. I.

    2011-01-01

    Artemether-lumefantrine and nevirapine-based antiretroviral therapy (ART) are the most commonly recommended first-line treatments for malaria and HIV, respectively, in Africa. Artemether, lumefantrine, and nevirapine are metabolized by the cytochrome P450 3A4 enzyme system, which nevirapine induces, creating potential for important drug interactions. In a parallel-design pharmacokinetic study, concentration-time profiles were obtained in two groups of HIV-infected patients: ART-naïve patients...

  4. Model-based video segmentation for vision-augmented interactive games

    Science.gov (United States)

    Liu, Lurng-Kuo

    2000-04-01

    This paper presents an architecture and algorithms for model based video object segmentation and its applications to vision augmented interactive game. We are especially interested in real time low cost vision based applications that can be implemented in software in a PC. We use different models for background and a player object. The object segmentation algorithm is performed in two different levels: pixel level and object level. At pixel level, the segmentation algorithm is formulated as a maximizing a posteriori probability (MAP) problem. The statistical likelihood of each pixel is calculated and used in the MAP problem. Object level segmentation is used to improve segmentation quality by utilizing the information about the spatial and temporal extent of the object. The concept of an active region, which is defined based on motion histogram and trajectory prediction, is introduced to indicate the possibility of a video object region for both background and foreground modeling. It also reduces the overall computation complexity. In contrast with other applications, the proposed video object segmentation system is able to create background and foreground models on the fly even without introductory background frames. Furthermore, we apply different rate of self-tuning on the scene model so that the system can adapt to the environment when there is a scene change. We applied the proposed video object segmentation algorithms to several prototype virtual interactive games. In our prototype vision augmented interactive games, a player can immerse himself/herself inside a game and can virtually interact with other animated characters in a real time manner without being constrained by helmets, gloves, special sensing devices, or background environment. The potential applications of the proposed algorithms including human computer gesture interface and object based video coding such as MPEG-4 video coding.

  5. Interacting Coastal Based Ecosystem Services: Recreation and Water Quality in Puget Sound, WA

    OpenAIRE

    Kreitler, Jason; Papenfus, Michael; Byrd, Kristin; Labiosa, William

    2013-01-01

    Coastal recreation and water quality are major contributors to human well-being in coastal regions. They can also interact, creating opportunities for ecosystem based management, ecological restoration, and water quality improvement that can positively affect people and the environment. Yet the effect of environmental quality on human behavior is often poorly quantified, but commonly assumed in coastal ecosystem service studies. To clarify this effect we investigate a water quality dataset fo...

  6. Volume-Rendering-Based Interactive 3D Measurement for Quantitative Analysis of 3D Medical Images

    OpenAIRE

    Yakang Dai; Jian Zheng; Yuetao Yang; Duojie Kuai; Xiaodong Yang

    2013-01-01

    3D medical images are widely used to assist diagnosis and surgical planning in clinical applications, where quantitative measurement of interesting objects in the image is of great importance. Volume rendering is widely used for qualitative visualization of 3D medical images. In this paper, we introduce a volume-rendering-based interactive 3D measurement framework for quantitative analysis of 3D medical images. In the framework, 3D widgets and volume clipping are integrated with volume render...

  7. Social-aware Opportunistic Routing Protocol based on User's Interactions and Interests

    OpenAIRE

    Moreira, Waldir; Mendes, Paulo; Sargento, Susana

    2014-01-01

    Nowadays, routing proposals must deal with a panoply of heterogeneous devices, intermittent connectivity, and the users' constant need for communication, even in rather challenging networking scenarios. Thus, we propose a Social-aware Content-based Opportunistic Routing Protocol, SCORP, that considers the users' social interaction and their interests to improve data delivery in urban, dense scenarios. Through simulations, using synthetic mobility and human traces scenarios, we compare the per...

  8. 3D MODELLING AND INTERACTIVE WEB-BASED VISUALIZATION OF CULTURAL HERITAGE OBJECTS

    OpenAIRE

    Koeva, M. N.

    2016-01-01

    Nowadays, there are rapid developments in the fields of photogrammetry, laser scanning, computer vision and robotics, together aiming to provide highly accurate 3D data that is useful for various applications. In recent years, various LiDAR and image-based techniques have been investigated for 3D modelling because of their opportunities for fast and accurate model generation. For cultural heritage preservation and the representation of objects that are important for tourism and their interact...

  9. Nano-scale displacement sensing based on Van der Waals interaction

    OpenAIRE

    Hu, Lin; Zhao, Jin; Yang, Jinlong

    2014-01-01

    We propose the nano-scale displacement sensor with high resolution for weak-force systems could be realized based on vertical stacked two-dimensional (2D) atomic corrugated layer materials bound through Van der Waals (VdW) interaction. Using first-principles calculations, we found the electronic structure of bi-layer blue phosphorus (BLBP) varies appreciably to both the lateral and vertical interlayer displacement. The variation of electronic structure due to the lateral displacement is attri...

  10. Driving behavior correction in human-vehicle interaction based on Dynamic Window Approach

    OpenAIRE

    Kang, Yue; Alves De Lima, Danilo; Corrêa Victorino, Alessandro

    2014-01-01

    This paper presents the approach of an applicable safety driving methodology for human drivers with focus on human-vehicle interaction. The approach is based on Dynamic Window Approach (DWA) in cooperation with perception of the obstacles. The human driving behaviors are modelled for the design of controller, refined by referential paths using evasive trajectory model, where linear and angular velocities are limited and corrected by DWA which performed as an obstacle avoidance strategy. Resul...

  11. Powerful Set-Based Gene-Environment Interaction Testing Framework for Complex Diseases.

    Science.gov (United States)

    Jiao, Shuo; Peters, Ulrike; Berndt, Sonja; Bézieau, Stéphane; Brenner, Hermann; Campbell, Peter T; Chan, Andrew T; Chang-Claude, Jenny; Lemire, Mathieu; Newcomb, Polly A; Potter, John D; Slattery, Martha L; Woods, Michael O; Hsu, Li

    2015-12-01

    Identification of gene-environment interaction (G × E) is important in understanding the etiology of complex diseases. Based on our previously developed Set Based gene EnviRonment InterAction test (SBERIA), in this paper we propose a powerful framework for enhanced set-based G × E testing (eSBERIA). The major challenge of signal aggregation within a set is how to tell signals from noise. eSBERIA tackles this challenge by adaptively aggregating the interaction signals within a set weighted by the strength of the marginal and correlation screening signals. eSBERIA then combines the screening-informed aggregate test with a variance component test to account for the residual signals. Additionally, we develop a case-only extension for eSBERIA (coSBERIA) and an existing set-based method, which boosts the power not only by exploiting the G-E independence assumption but also by avoiding the need to specify main effects for a large number of variants in the set. Through extensive simulation, we show that coSBERIA and eSBERIA are considerably more powerful than existing methods within the case-only and the case-control method categories across a wide range of scenarios. We conduct a genome-wide G × E search by applying our methods to Illumina HumanExome Beadchip data of 10,446 colorectal cancer cases and 10,191 controls and identify two novel interactions between nonsteroidal anti-inflammatory drugs (NSAIDs) and MINK1 and PTCHD3. PMID:26095235

  12. Soil-Pile Interaction in the Pile Vertical Vibration Based on Fictitious Soil-Pile Model

    OpenAIRE

    Guodong Deng; Jiasheng Zhang; Wenbing Wu; Xiong Shi; Fei Meng

    2014-01-01

    By introducing the fictitious soil-pile model, the soil-pile interaction in the pile vertical vibration is investigated. Firstly, assuming the surrounding soil of pile to be viscoelastic material and considering its vertical wave effect, the governing equations of soil-pile system subjected to arbitrary harmonic dynamic force are founded based on the Euler-Bernoulli rod theory. Secondly, the analytical solution of velocity response in frequency domain and its corresponding semianalytical solu...

  13. SIP-based resource allocation for interactive multimedia applications over DVB-S/RCS satellite system

    OpenAIRE

    Gineste, Mathieu; Nivor, Frédéric; Berthou, Pascal; Gayraud, Thierry

    2008-01-01

    This paper introduces a SIP-based approach to offer QoS guaranties to interactive multimedia applications over an efficient DVB-S2/RCS satellite access assignment scheme (on- demand). It focuses both on the communication opening which represents the weakness of on-demand capacity allocation and optimizes the remaining communication in the satellite context (due to important delays). It finally presents analytical and experimental results of the various proposed enhancements.

  14. AN INTERACTIVE WEB-BASED ANALYSIS FRAMEWORK FOR REMOTE SENSING CLOUD COMPUTING

    OpenAIRE

    Wang, X Z; Zhang, H. M.; Zhao, J. H.; Lin, Q. H.; Zhou, Y. C.; Li, J. H.

    2015-01-01

    Spatiotemporal data, especially remote sensing data, are widely used in ecological, geographical, agriculture, and military research and applications. With the development of remote sensing technology, more and more remote sensing data are accumulated and stored in the cloud. An effective way for cloud users to access and analyse these massive spatiotemporal data in the web clients becomes an urgent issue. In this paper, we proposed a new scalable, interactive and web-based cloud computing so...

  15. EXPLORING THE SELF-ENHANCED MECHANISM OF INTERACTIVE ADVERTISING PHENOMENON--BASED ON THE RESEARCH OF THREE CASES

    Directory of Open Access Journals (Sweden)

    Ren jian

    2015-04-01

    Full Text Available Under the background of the new media era with the rapid development of interactive advertising, this paper used case study method based on the summary of the research of the communication effect of interactive advertising from both domestic and foreign academia. This paper divided interactive advertising into three types to examine ---- interactive ads on official website, interactive ads based on SNS and interactive ads based on mobile media. Furthermore, this paper induced and summarized a selfenhanced dissemination mechanism of the interactive advertising, including three parts which are micro level, meso level and macro level mechanism, micro level embodies core interaction, inner interaction and outer interaction which reveal the whole process of interact with contents, with people and with computer, and the communication approach and spread speed shown in meso level which is self-fission-type spread, finally in macro level the communication effect of IA achieved the spiral increasing. In a word, this article enriches research procedure of the interactive advertising communication effects.

  16. iHand: an interactive bare-hand-based augmented reality interface on commercial mobile phones

    Science.gov (United States)

    Choi, Junyeong; Park, Jungsik; Park, Hanhoon; Park, Jong-Il

    2013-02-01

    The performance of mobile phones has rapidly improved, and they are emerging as a powerful platform. In many vision-based applications, human hands play a key role in natural interaction. However, relatively little attention has been paid to the interaction between human hands and the mobile phone. Thus, we propose a vision- and hand gesture-based interface in which the user holds a mobile phone in one hand but sees the other hand's palm through a built-in camera. The virtual contents are faithfully rendered on the user's palm through palm pose estimation, and reaction with hand and finger movements is achieved that is recognized by hand shape recognition. Since the proposed interface is based on hand gestures familiar to humans and does not require any additional sensors or markers, the user can freely interact with virtual contents anytime and anywhere without any training. We demonstrate that the proposed interface works at over 15 fps on a commercial mobile phone with a 1.2-GHz dual core processor and 1 GB RAM.

  17. Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interac-tion data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automati-cally selects the most appropriate functional classes as specific as possible during the learning proc-ess, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to “biology process” by three measures particularly designed for functional classes organ-ized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.

  18. Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

    Institute of Scientific and Technical Information of China (English)

    GAO Lei; LI Xia; GUO Zheng; ZHU MingZhu; LI YanHui; RAO ShaoQi

    2007-01-01

    GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interaction data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automatically selects the most appropriate functional classes as specific as possible during the learning process, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to "biology process" by three measures particularly designed for functional classes organized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.

  19. Genetic programming-based approach to elucidate biochemical interaction networks from data.

    Science.gov (United States)

    Kandpal, Manoj; Kalyan, Chakravarthy Mynampati; Samavedham, Lakshminarayanan

    2013-02-01

    Biochemical systems are characterised by cyclic/reversible reciprocal actions, non-linear interactions and a mixed relationship structures (linear and non-linear; static and dynamic). Deciphering the architecture of such systems using measured data to provide quantitative information regarding the nature of relationships that exist between the measured variables is a challenging proposition. Causality detection is one of the methodologies that are applied to elucidate biochemical networks from such data. Autoregressive-based modelling approach such as granger causality, partial directed coherence, directed transfer function and canonical variate analysis have been applied on different systems for deciphering such interactions, but with limited success. In this study, the authors propose a genetic programming-based causality detection (GPCD) methodology which blends evolutionary computation-based procedures along with parameter estimation methods to derive a mathematical model of the system. Application of the GPCD methodology on five data sets that contained the different challenges mentioned above indicated that GPCD performs better than the other methods in uncovering the exact structure with less false positives. On a glycolysis data set, GPCD was able to fill the 'interaction gaps' which were missed by other methods. PMID:23848052

  20. GIS-based interactive tool to map the advent of world conquerors

    Science.gov (United States)

    Lakkaraju, Mahesh

    The objective of this thesis is to show the scale and extent of some of the greatest empires the world has ever seen. This is a hybrid project between the GIS based interactive tool and the web-based JavaScript tool. This approach lets the students learn effectively about the emperors themselves while understanding how long and far their empires spread. In the GIS based tool, a map is displayed with various points on it, and when a user clicks on one point, the relevant information of what happened at that particular place is displayed. Apart from this information, users can also select the interactive animation button and can walk through a set of battles in chronological order. As mentioned, this uses Java as the main programming language, and MOJO (Map Objects Java Objects) provided by ESRI. MOJO is very effective as its GIS related features can be included in the application itself. This app. is a simple tool and has been developed for university or high school level students. D3.js is an interactive animation and visualization platform built on the Javascript framework. Though HTML5, CSS3, Javascript and SVG animations can be used to derive custom animations, this tool can help bring out results with less effort and more ease of use. Hence, it has become the most sought after visualization tool for multiple applications. D3.js has provided a map-based visualization feature so that we can easily display text-based data in a map-based interface. To draw the map and the points on it, D3.js uses data rendered in TOPO JSON format. The latitudes and longitudes can be provided, which are interpolated into the Map svg. One of the main advantages of doing it this way is that more information is retained when we use a visual medium.

  1. The Pathway Active Learning Environment: An interactive web-based tool for physics education

    Science.gov (United States)

    Nakamura, Christopher Matthew

    The work described here represents an effort to design, construct, and test an interactive online multimedia learning environment that can provide physics instruction to students in their homes. The system was designed with one-on-one human tutoring in mind as the mode of instruction. The system uses an original combination of a video-based tutor that incorporates natural language processing video-centered lessons and additional illustrative multimedia. Our Synthetic Interview (SI) tutor provides pre-recorded video answers from expert physics instructors in response to students' typed natural language questions. Our lessons cover Newton's laws and provide a context for the tutoring interaction to occur, connect physics ideas to real-world behavior of mechanical systems, and allow for quantitative testing of physics. Additional multimedia can be used to supplement the SI tutors' explanations and illustrate the physics of interest. The system is targeted at students of algebra-based and concept-based physics at the college and high school level. The system logs queries to the SI tutor, responses to lesson questions and several other interactions with the system, tagging those interactions with a username and timestamp. We have provided several groups of students with access to our system under several different conditions ranging from the controlled conditions of our interview facility to the naturalistic conditions of use at home. In total nearly two-hundred students have accessed the system. To gain insight into the ways students might use the system and understand the utility of its various components we analyzed qualitative interview data collected with 22 algebra-based physics students who worked with our system in our interview facility. We also performed a descriptive analysis of data from the system's log of user interactions. Finally we explored the use of machine learning to explore the possibility of using automated assessment to augment the interactive

  2. Web-based Interactive Document Editor System for Academic Knowledge Management

    OpenAIRE

    Muhammad Nasir, Muhammad Dzulqarnain; Matsuo, Tokuro; Fujimoto, Takayuki

    2007-01-01

    Computer-based knowledge management systems have become a major part of today’s communication system and with the Internet as a medium; distance is no longer the barrier. In line with this development, we propose an interactive web-based multi-user document editing system in which users can cooperatively create and edit documents. The goal of this study is not only to develop the system, but also to create an environment in which scholars can cooperatively write research/report papers even if...

  3. A energy-based interaction model for population opinion dynamics with topic coupling

    CERN Document Server

    Noorazar, Hossein; Vixie, Kevin R

    2016-01-01

    This article studies the opinion game dynamic from mathematical ground, the way people learn and consequently change their opinion towards or against a cause. The evolution of opinions are modeled by single interaction between two individuals and is determined by potential functions. Moreover, we model the case in which there are several topics being discussed in the system where topics are related and the opinion about one topic can change in response to change of that of another topic. Building the evolution based on mathematical ground gives the advantage of robust analysis of dynamics, getting connection between model structure and statistical properties, rather than statistical simulation based investigations.

  4. Synthesis of Novel Metal Ion Sensors Based on DNA-Metal Interactions

    Institute of Scientific and Technical Information of China (English)

    Akira Ono; Shiqi Cao; Humika Togashi; Yoko Miyake

    2005-01-01

    @@ 1Introduction The interactions of metal ions with nucleic acids, nucleosides, and nucleo-bases have been extensively investigated[1,2]. We have reported that thymine-thymine (T-T) and cytosine-cytosine (C- C) miss base pairs in DNA duplexes highly selectively capture HgⅡ ion and Ag Ⅰ ion, which result in formations of metal-mediated base pairs, T-HgⅡ -T and C-AgⅠ -C, in duplexes[3]. The phenomenon is expected to be useful for a variety of studies such as synthesis of nano-wires containing metal ions, developing metal-ion sensing methods, etc.Here, we report novel oligodeoxyribonucleotide (ODN)-based sensors that detect HgⅡ ions and AgⅠ ions in aqueous solutions.

  5. CLIMLAB: a Python-based software toolkit for interactive, process-oriented climate modeling

    Science.gov (United States)

    Rose, B. E. J.

    2015-12-01

    Global climate is a complex emergent property of the rich interactions between simpler components of the climate system. We build scientific understanding of this system by breaking it down into component process models (e.g. radiation, large-scale dynamics, boundary layer turbulence), understanding each components, and putting them back together. Hands-on experience and freedom to tinker with climate models (whether simple or complex) is invaluable for building physical understanding. CLIMLAB is an open-ended software engine for interactive, process-oriented climate modeling. With CLIMLAB you can interactively mix and match model components, or combine simpler process models together into a more comprehensive model. It was created primarily to support classroom activities, using hands-on modeling to teach fundamentals of climate science at both undergraduate and graduate levels. CLIMLAB is written in Python and ties in with the rich ecosystem of open-source scientific Python tools for numerics and graphics. The IPython notebook format provides an elegant medium for distributing interactive example code. I will give an overview of the current capabilities of CLIMLAB, the curriculum we have developed thus far, and plans for the future. Using CLIMLAB requires some basic Python coding skills. We consider this an educational asset, as we are targeting upper-level undergraduates and Python is an increasingly important language in STEM fields. However CLIMLAB is well suited to be deployed as a computational back-end for a graphical gaming environment based on earth-system modeling.

  6. Improving scientists' interaction with complex computational-visualization environments based on a distributed grid infrastructure.

    Science.gov (United States)

    Kalawsky, R S; O'Brien, J; Coveney, P V

    2005-08-15

    The grid has the potential to transform collaborative scientific investigations through the use of closely coupled computational and visualization resources, which may be geographically distributed, in order to harness greater power than is available at a single site. Scientific applications to benefit from the grid include visualization, computational science, environmental modelling and medical imaging. Unfortunately, the diversity, scale and location of the required resources can present a dilemma for the scientific worker because of the complexity of the underlying technology. As the scale of the scientific problem under investigation increases so does the nature of the scientist's interaction with the supporting infrastructure. The increased distribution of people and resources within a grid-based environment can make resource sharing and collaborative interaction a critical factor to their success. Unless the technological barriers affecting user accessibility are reduced, there is a danger that the only scientists to benefit will be those with reasonably high levels of computer literacy. This paper examines a number of important human factors of user interaction with the grid and expresses this in the context of the science undertaken by RealityGrid, a project funded by the UK e-Science programme. Critical user interaction issues will also be highlighted by comparing grid computational steering with supervisory control systems for local and remote access to the scientific environment. Finally, implications for future grid developers will be discussed with a particular emphasis on how to improve the scientists' access to what will be an increasingly important resource. PMID:16099754

  7. A force-based, parallel assay for the quantification of protein-DNA interactions.

    Directory of Open Access Journals (Sweden)

    Katja Limmer

    Full Text Available Analysis of transcription factor binding to DNA sequences is of utmost importance to understand the intricate regulatory mechanisms that underlie gene expression. Several techniques exist that quantify DNA-protein affinity, but they are either very time-consuming or suffer from possible misinterpretation due to complicated algorithms or approximations like many high-throughput techniques. We present a more direct method to quantify DNA-protein interaction in a force-based assay. In contrast to single-molecule force spectroscopy, our technique, the Molecular Force Assay (MFA, parallelizes force measurements so that it can test one or multiple proteins against several DNA sequences in a single experiment. The interaction strength is quantified by comparison to the well-defined rupture stability of different DNA duplexes. As a proof-of-principle, we measured the interaction of the zinc finger construct Zif268/NRE against six different DNA constructs. We could show the specificity of our approach and quantify the strength of the protein-DNA interaction.

  8. Ground-based remote sensing scheme for monitoring aerosol-cloud interactions

    Science.gov (United States)

    Sarna, K.; Russchenberg, H. W. J.

    2015-11-01

    A method for continuous observation of aerosol-cloud interactions with ground-based remote sensing instruments is presented. The main goal of this method is to enable the monitoring of cloud microphysical changes due to the changing aerosol concentration. We use high resolution measurements from lidar, radar and radiometer which allow to collect and compare data continuously. This method is based on a standardised data format from Cloudnet and can be implemented at any observatory where the Cloudnet data set is available. Two example study cases were chosen from the Atmospheric Radiation Measurement (ARM) Program deployment at Graciosa Island, Azores, Portugal in 2009 to present the method. We show the Pearson Product-Moment Correlation Coefficient, r, and the Coefficient of Determination, r2 for data divided into bins of LWP, each of 10 g m-2. We explain why the commonly used way of quantity aerosol cloud interactions by use of an ACI index (ACIr,τ = dln re,τ/dlnα) is not the best way of quantifying aerosol-cloud interactions.

  9. Providing Access to Census-based Interaction Data in the UK: That's WICID!

    Directory of Open Access Journals (Sweden)

    John Stillwell

    2006-08-01

    Full Text Available The Census Interaction Data Service (CIDS is funded by the Economic and Social Research Council in the UK to provide access for social science researchers and students to the detailed migration and journey-to-work statistics that are collected by the national statistical agencies. These interaction data sets are known collectively as the Special Migration Statistics (SMS and the Special Workplace Statistics (SWS. This paper outlines how problems of user access to these data have been tackled through the development of a web-based system known as WICID (Web-based Interface to Census Interaction Data. The paper illustrates various interface features including some of the query building facilities that enable users to extract counts of flows of particular groups of individuals between selected origin and destination areas. New tools are outlined for assisting area selection using digital maps of census geographies, for planning output and for adding value to the data through analysis. Mapping of flows of migrants between London boroughs and the rest of the UK demonstrates the value of the data. The paper begins with a summary of the data sets that are contained within the system and an outline of the system architecture.

  10. Ground-based remote sensing scheme for monitoring aerosol–cloud interactions

    Directory of Open Access Journals (Sweden)

    K. Sarna

    2015-11-01

    Full Text Available A method for continuous observation of aerosol–cloud interactions with ground-based remote sensing instruments is presented. The main goal of this method is to enable the monitoring of cloud microphysical changes due to the changing aerosol concentration. We use high resolution measurements from lidar, radar and radiometer which allow to collect and compare data continuously. This method is based on a standardised data format from Cloudnet and can be implemented at any observatory where the Cloudnet data set is available. Two example study cases were chosen from the Atmospheric Radiation Measurement (ARM Program deployment at Graciosa Island, Azores, Portugal in 2009 to present the method. We show the Pearson Product–Moment Correlation Coefficient, r, and the Coefficient of Determination, r2 for data divided into bins of LWP, each of 10 g m−2. We explain why the commonly used way of quantity aerosol cloud interactions by use of an ACI index (ACIr,τ = dln re,τ/dlnα is not the best way of quantifying aerosol–cloud interactions.

  11. Role of induced vortex interaction in a semi-active flapping foil based energy harvester

    Science.gov (United States)

    Wu, J.; Chen, Y. L.; Zhao, N.

    2015-09-01

    The role of induced vortex interaction in a semi-active flapping foil based energy harvester is numerically examined in this work. A NACA0015 airfoil, which acts as an energy harvester, is placed in a two-dimensional laminar flow. It performs an imposed pitching motion that subsequently leads to a plunging motion. Two auxiliary smaller foils, which rotate about their centers, are arranged above and below the flapping foil, respectively. As a consequence, the vortex interaction between the flapping foil and the rotating foil is induced. At a Reynolds number of 1100 and the position of the pitching axis at one-third chord, the effects of the distance between two auxiliary foils, the phase difference between the rotating motion and the pitching motion as well as the frequency of pitching motion on the power extraction performance are systematically investigated. It is found that compared to the single flapping foil, the efficiency improvement of overall power extraction for the flapping foil with two auxiliary foils can be achieved. Based on the numerical analysis, it is indicated that the enhanced power extraction, which is caused by the increased lift force, thanks to the induced vortex interaction, directly benefits the efficiency enhancement.

  12. Interaction-Aware Video Community-Based Content Delivery in Wireless Mobile Networks

    Directory of Open Access Journals (Sweden)

    Lujie Zhong

    2016-01-01

    Full Text Available The increase in the demand of content quality and the number of mobile users brings new challenges for the multimedia streaming services in wireless mobile networks. The virtual community technologies are promising by grouping the users with common characteristics to get the gains in the performance of resource lookup and system scalability. In this paper, we propose a novel interaction-aware video community-based content delivery (IVCCD in wireless mobile networks. IVCCD collects and analyzes the interaction information between users to construct user interaction model and further capture the common characteristics in the request and delivery of video content. IVCCD employs a partition-based community discovery scheme to group the mobile users in terms of the common characteristics and uses a community member management mechanism and a resource sharing scheme to achieve low-cost community maintenance and high searching performance. Extensive tests show how IVCCD achieves much better performance results in comparison with other state-of-the-art solutions.

  13. Development of Multilayer Microcapsules by a Phase Coacervation Method Based on Ionic Interactions for Textile Applications

    Directory of Open Access Journals (Sweden)

    Sudipta Chatterjee

    2014-06-01

    Full Text Available The present study describes the development of multilayer microcapsules by 11 alternate additions of chitosan (Chi and sodium dodecyl sulfate (SDS in a combined emulsification and phase coacervation method based on ionic interactions. After an alkali treatment, microcapsules are applied on polyester (PET fabric by a padding process to investigate their wash-durability on fabric. Air atmospheric plasma treatment is performed on PET fabric to modify the surface properties of the textiles. Zeta potential, X-ray photoelectron spectroscopy (XPS, wetting measurements, scanning electron microscopy (SEM, and atomic force microscopy (AFM with surface roughness measurements are realized to characterize and determine wash durability of microcapsule samples onto PET. After alkali treatment, the microcapsules are selected for textile application because they are submicron sized with the desired morphology. The results obtained from various characterization techniques indicate that microcapsules are wash-durable on PET fabric pre activated by air plasma atmospheric as Chi based microcapsules can interact directly with PET by ionic interactions.

  14. Determination of half-maximal inhibitory concentration using biosensor-based protein interaction analysis.

    Science.gov (United States)

    Aykul, Senem; Martinez-Hackert, Erik

    2016-09-01

    Half-maximal inhibitory concentration (IC50) is the most widely used and informative measure of a drug's efficacy. It indicates how much drug is needed to inhibit a biological process by half, thus providing a measure of potency of an antagonist drug in pharmacological research. Most approaches to determine IC50 of a pharmacological compound are based on assays that utilize whole cell systems. While they generally provide outstanding potency information, results can depend on the experimental cell line used and may not differentiate a compound's ability to inhibit specific interactions. Here we show using the secreted Transforming Growth Factor-β (TGF-β) family ligand BMP-4 and its receptors as example that surface plasmon resonance can be used to accurately determine IC50 values of individual ligand-receptor pairings. The molecular resolution achievable wih this approach can help distinguish inhibitors that specifically target individual complexes, or that can inhibit multiple functional interactions at the same time. PMID:27365221

  15. Vorticity-based correction for modelling of free-surface wave interacting with turbulent current

    Science.gov (United States)

    Zhang, Wei

    2014-11-01

    This paper describes a new vorticity-based correction model for studying the interaction between free-surface wave and turbulent current. To track free-surface movements, the volume of fluid (VOF) method is employed. The momentum equations are rewritten to avoid the numerically generated vorticity effects along the air-water interface. Simultaneously unsteady RANS equations are used, while standard k-epsilon model is adapted with modification to the production term by introducing the vorticity to limit the production of turbulent kinematic energy at free surface. To validate the numerical model used here, standalone wave and current cases are studied to ensure the accuracy of each component of the numerical model. The model is then used to simulate the interaction between the second-order stokes wave and turbulent current for both wave following and countering in a setting of shallow water wave flume. The results are compared with experimental measurement available in the literature.

  16. Viscoelastic model based force control for soft tissue interaction and its application in physiological motion compensation.

    Science.gov (United States)

    Moreira, Pedro; Zemiti, Nabil; Liu, Chao; Poignet, Philippe

    2014-09-01

    Controlling the interaction between robots and living soft tissues has become an important issue as the number of robotic systems inside the operating room increases. Many researches have been done on force control to help surgeons during medical procedures, such as physiological motion compensation and tele-operation systems with haptic feedback. In order to increase the performance of such controllers, this work presents a novel force control scheme using Active Observer (AOB) based on a viscoelastic interaction model. The control scheme has shown to be stable through theoretical analysis and its performance was evaluated by in vitro experiments. In order to evaluate how the force control scheme behaves under the presence of physiological motion, experiments considering breathing and beating heart disturbances are presented. The proposed control scheme presented a stable behavior in both static and moving environment. The viscoelastic AOB presented a compensation ratio of 87% for the breathing motion and 79% for the beating heart motion. PMID:24612709

  17. Di-nucleon structures in homogeneous nuclear matter based on two- and three-nucleon interactions

    CERN Document Server

    Arellano, H F; Rios, Arnau

    2016-01-01

    We investigate homogeneous nuclear matter within the Brueckner-Hartree-Fock (BHF) approach in the limits of isospin-symmetric nuclear matter (SNM) as well as pure neutron matter at zero temperature. The study is based on realistic representations of the internucleon interaction as given by Argonne v18, Paris, Nijmegen I and II potentials, in addition to chiral N$^{3}$LO interactions, including three-nucleon forces up to N$^{2}$LO. Particular attention is paid to the presence of di-nucleon bound states structures in $^1\\textrm{S}_0$ and $^3\\textrm{SD}_1$ channels, whose explicit account becomes crucial for the stability of self-consistent solutions at low densities. A characterization of these solutions and associated bound states is discussed. We confirm that coexisting BHF single-particle solutions in SNM, at Fermi momenta in the range $0.13-0.3$~fm$^{-1}$, is a robust feature under the choice of realistic internucleon potentials.

  18. Fast interactive segmentation algorithm of image sequences based on relative fuzzy connectedness

    Institute of Scientific and Technical Information of China (English)

    Tian Chunna; Gao Xinbo

    2005-01-01

    A fast interactive segmentation algorithm of image-sequences based on relative fuzzy connectedness is presented. In comparison with the original algorithm, the proposed one, with the same accuracy, accelerates the segmentation speed by three times for single image. Meanwhile, this fast segmentation algorithm is extended from single object to multiple objects and from single-image to image-sequences. Thus the segmentation of multiple objects from complex background and batch segmentation of image-sequences can be achieved. In addition, a post-processing scheme is incorporated in this algorithm, which extracts smooth edge with one-pixel-width for each segmented object. The experimental results illustrate that the proposed algorithm can obtain the object regions of interest from medical image or image-sequences as well as man-made images quickly and reliably with only a little interaction.

  19. Intra-Inter Triplet Object Interaction Mechanism in Triplet-Based Hierarchical Interconnection Network

    Directory of Open Access Journals (Sweden)

    Shahnawaz Talpur

    2013-07-01

    Full Text Available Object oriented languages usually avoid direct message passing, due to its complicated implementation, though that is the promising way to communicate in concurrently inherited objects. With the advancement in the high performance computing system, interaction between parallel application objects onto physical cores becomes one of the significant issues, which is not fully explored yet. In object oriented programming attribute data is included in objects and their state can be changed using the methods. Objects enable massage passing to other objects interacting with each other. Comprehensive problems can be molded by object-oriented methodology, and solves difficult program running object-oriented programs.Cores communicate with each other through communicator and groups in MPI, but in our reference architecture TBHIN (Triplet Based Hierarchical Interconnection Network, the cores are already faction in Triplets. We propose IITOIM Model to improve the performance with efficient intra-inter triplet cores communication mechanism between the objects in TBHIN

  20. String Theory Based Predictions for Novel Collective Modes in Strongly Interacting Fermi Gases

    CERN Document Server

    Bantilan, H; Ishii, T; Lewis, W E; Romatschke, P

    2016-01-01

    Very different strongly interacting quantum systems such as Fermi gases, quark-gluon plasmas formed in high energy ion collisions and black holes studied theoretically in string theory are known to exhibit quantitatively similar damping of hydrodynamic modes. It is not known if such similarities extend beyond the hydrodynamic limit. Do non-hydrodynamic collective modes in Fermi gases with strong interactions also match those from string theory calculations? In order to answer this question, we use calculations based on string theory to make predictions for novel types of modes outside the hydrodynamic regime in trapped Fermi gases. These predictions are amenable to direct testing with current state-of-the-art cold atom experiments.

  1. Interaction of biocompatible natural rosin-based surfactants with human serum albumin: A biophysical study

    International Nuclear Information System (INIS)

    Biophysical insight into interaction of biocompatible rosin-based surfactants with human serum albumin (HSA) was studied at physiological conditions using various spectroscopic, calorimetric and molecular docking approaches. The binding constant (Kb), enthalpy (ΔH0), entropy (ΔS0) and Gibbs free energy change (ΔG0) were calculated by spectroscopic and calorimetric method. We have also calculated the probability of energy transfer by FRET analysis. The circular dichroism study showed that the cationic surfactant QRMAE significantly altered the secondary structure of HSA as compared to the nonionic rosin surfactants. The thermodynamic study was performed by ITC to determine binding constant as well as change in enthalpy of HSA in presence of rosin surfactants. It clearly showed that hydrogen binding and hydrophobic interaction play an important role in the binding of HSA to rosin surfactants. We have also performed molecular docking studies to locate the binding site on HSA and to visualize the mode of interaction. The present study provides a significant insight into HSA–rosin surfactants interaction, which also improves our understanding of the possible effect of rosin surfactants on human health. - Highlights: • RMPEG 750 has the highest Kb, Kq and Ksv value as compared to other rosin surfactants. • The probability of energy transfer from HSA to rosin surfactants was maximum in the case of RMPEG 750. • Cationic surfactant QRMAE significantly altered the secondary structure of the HSA as compared to other rosin surfactants. • Molecular docking and ITC experiment studies, to locate the binding site on HSA and to investigate the mode of interaction

  2. Interaction of biocompatible natural rosin-based surfactants with human serum albumin: A biophysical study

    Energy Technology Data Exchange (ETDEWEB)

    Ishtikhar, Mohd [Protein Biophysics Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002 (India); Ali, Mohd Sajid [Surfactant Research Chair, Department of Chemistry, King Saud University, P.O. Box-2455, Riyadh 11451 (Saudi Arabia); Atta, Ayman M. [Surfactant Research Chair, Department of Chemistry, King Saud University, P.O. Box-2455, Riyadh 11451 (Saudi Arabia); Petroleum Application department, Egyptian Petroleum Research Institute, Ahmad Elzomor St., Nasr city, Cairo-11727 (Egypt); Al-Lohedan, H.A. [Surfactant Research Chair, Department of Chemistry, King Saud University, P.O. Box-2455, Riyadh 11451 (Saudi Arabia); Nigam, Lokesh; Subbarao, Naidu [Centre for Computational Biology and Bioinformatics, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067 (India); Hasan Khan, Rizwan, E-mail: rizwanhkhan@hotmail.com [Protein Biophysics Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002 (India)

    2015-11-15

    Biophysical insight into interaction of biocompatible rosin-based surfactants with human serum albumin (HSA) was studied at physiological conditions using various spectroscopic, calorimetric and molecular docking approaches. The binding constant (K{sub b}), enthalpy (ΔH{sup 0}), entropy (ΔS{sup 0}) and Gibbs free energy change (ΔG{sup 0}) were calculated by spectroscopic and calorimetric method. We have also calculated the probability of energy transfer by FRET analysis. The circular dichroism study showed that the cationic surfactant QRMAE significantly altered the secondary structure of HSA as compared to the nonionic rosin surfactants. The thermodynamic study was performed by ITC to determine binding constant as well as change in enthalpy of HSA in presence of rosin surfactants. It clearly showed that hydrogen binding and hydrophobic interaction play an important role in the binding of HSA to rosin surfactants. We have also performed molecular docking studies to locate the binding site on HSA and to visualize the mode of interaction. The present study provides a significant insight into HSA–rosin surfactants interaction, which also improves our understanding of the possible effect of rosin surfactants on human health. - Highlights: • RMPEG 750 has the highest Kb, Kq and Ksv value as compared to other rosin surfactants. • The probability of energy transfer from HSA to rosin surfactants was maximum in the case of RMPEG 750. • Cationic surfactant QRMAE significantly altered the secondary structure of the HSA as compared to other rosin surfactants. • Molecular docking and ITC experiment studies, to locate the binding site on HSA and to investigate the mode of interaction.

  3. Hydrogen internal friction and interaction of solute atoms in niobium- and vanadium-based alloys

    International Nuclear Information System (INIS)

    A computer model has been proposed to be used to calculate the internal friction spectrum, caused by the ''diffusion under stress'' of hydrogen atoms in a solid solution with a b.c.c. lattice containing substitutional atoms. The model takes into account the long-range pair interaction of dissolved atoms. It is suggested that such interaction acts on diffusion by producing short-range order of mobile hydrogen atoms and by changing their energy. These changes occur in the tetrahedral (before the jump) as well as in the octahedral (at the saddle point of the diffusion barrier) interstitial sites and, therefore, produce local changes of the hydrogen diffusion activation energy (the activation energy of internal friction). The relaxation strength is calculated from the local fields of atomic displacements around every atom that participates in diffusion. The model has been used to study the nature of hydrogen relaxation in Ti- and Zr-containing Nb- and V-based alloys and to calculate the ''chemical'' interaction energy of the H(D)-Ti(Zr) pairs. It was shown that the hydrogen relaxation mechanism in Nb(V)-Ti(Zr)-H(D) alloys consists in diffusion under stress of hydrogen or deuterium atoms in the vicinity of single substitutional atoms at low concentration of substitutional atoms and high hydrogen or deuterium concentration, and in the vicinity of substitutional pairs - at high concentration of substitutional atoms and low hydrogen or deuterium concentration. The ''chemical'' interaction H(D)-Ti(Zr) in niobium and vanadium is stronger or is of the same order, as the strain-induced (elastic) interaction. (orig.)

  4. D Modelling and Interactive Web-Based Visualization of Cultural Heritage Objects

    Science.gov (United States)

    Koeva, M. N.

    2016-06-01

    Nowadays, there are rapid developments in the fields of photogrammetry, laser scanning, computer vision and robotics, together aiming to provide highly accurate 3D data that is useful for various applications. In recent years, various LiDAR and image-based techniques have been investigated for 3D modelling because of their opportunities for fast and accurate model generation. For cultural heritage preservation and the representation of objects that are important for tourism and their interactive visualization, 3D models are highly effective and intuitive for present-day users who have stringent requirements and high expectations. Depending on the complexity of the objects for the specific case, various technological methods can be applied. The selected objects in this particular research are located in Bulgaria - a country with thousands of years of history and cultural heritage dating back to ancient civilizations. This motivates the preservation, visualisation and recreation of undoubtedly valuable historical and architectural objects and places, which has always been a serious challenge for specialists in the field of cultural heritage. In the present research, comparative analyses regarding principles and technological processes needed for 3D modelling and visualization are presented. The recent problems, efforts and developments in interactive representation of precious objects and places in Bulgaria are presented. Three technologies based on real projects are described: (1) image-based modelling using a non-metric hand-held camera; (2) 3D visualization based on spherical panoramic images; (3) and 3D geometric and photorealistic modelling based on architectural CAD drawings. Their suitability for web-based visualization are demonstrated and compared. Moreover the possibilities for integration with additional information such as interactive maps, satellite imagery, sound, video and specific information for the objects are described. This comparative study

  5. VR-based interactive CFD data comparison of flow fields in a human nasal cavity

    Science.gov (United States)

    Gerndt, Andreas; Kuhlen, Torsten; van Reimersdahl, Thomas; Haack, Matthias; Bischof, Christian

    2004-05-01

    The Virtual Reality Center Aachen is developing a Virtual Reality based operation planning system in cooperation with aerodynamics scientists and physicians of several clinical centers. This system is meant to help the preparation of nose surgeries aimed at the elimination of respiratory diseases. A core part is the interactive comparison of experimental data and simulation data in the area of fluid dynamics. In a first step, data comparison is to depict the differences between healthy noses and diseased noses. Later on, data comparison should supply evidence for successful virtual surgeries, which finally results in guidance on the real operation. During virtual surgery sessions, scientists can interactively explore, analyze, annotate, and compare various medical and aerodynamics data sets. Image-based methods are used to extract several features in one image and between compared data sets. The determination of linked features between different data sets is a particular challenge because of their different time frames, scales, and distortions. An optimized human computer interface enables the user to interact intuitively within a virtual environment in order to select and deal with these data sets. Additionally to this interactive exploration, the system also allows automatic searches for cut plane and key frame candidates corresponding to given feature patterns. The comparison system makes use of an already implemented parallelized Computational Fluid Dynamics (CFD) postprocessing, which also extracts enhanced flow features that allow automatic detection of relevant flow regions. Beside vortex detection, the computation of critical points including flow field segmentation is a current research activity. These flow features are favored characteristics for the comparison and help considerably to classify different nose geometries and operation recommendations.

  6. Network theory-based analysis of risk interactions in large engineering projects

    International Nuclear Information System (INIS)

    This paper presents an approach based on network theory to deal with risk interactions in large engineering projects. Indeed, such projects are exposed to numerous and interdependent risks of various nature, which makes their management more difficult. In this paper, a topological analysis based on network theory is presented, which aims at identifying key elements in the structure of interrelated risks potentially affecting a large engineering project. This analysis serves as a powerful complement to classical project risk analysis. Its originality lies in the application of some network theory indicators to the project risk management field. The construction of the risk network requires the involvement of the project manager and other team members assigned to the risk management process. Its interpretation improves their understanding of risks and their potential interactions. The outcomes of the analysis provide a support for decision-making regarding project risk management. An example of application to a real large engineering project is presented. The conclusion is that some new insights can be found about risks, about their interactions and about the global potential behavior of the project. - Highlights: ► The method addresses the modeling of complexity in project risk analysis. ► Network theory indicators enable other risks than classical criticality analysis to be highlighted. ► This topological analysis improves project manager's understanding of risks and risk interactions. ► This helps project manager to make decisions considering the position in the risk network. ► An application to a real tramway implementation project in a city is provided.

  7. Mass-based hygroscopicity parameter interaction model and measurement of atmospheric aerosol water uptake

    Directory of Open Access Journals (Sweden)

    E. Mikhailov

    2013-01-01

    Full Text Available In this study we derive and apply a mass-based hygroscopicity parameter interaction model for efficient description of concentration-dependent water uptake by atmospheric aerosol particles with complex chemical composition. The model approach builds on the single hygroscopicity parameter model of Petters and Kreidenweis (2007. We introduce an observable mass-based hygroscopicity parameter κm which can be deconvoluted into a dilute hygroscopicity parameter (κm0 and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems.

    For reference aerosol samples of sodium chloride and ammonium sulfate, the κm-interaction model (KIM captures the experimentally observed concentration and humidity dependence of the hygroscopicity parameter and is in good agreement with an accurate reference model based on the Pitzer ion-interaction approach (Aerosol Inorganic Model, AIM. Experimental results for pure organic particles (malonic acid, levoglucosan and for mixed organic-inorganic particles (malonic acid – ammonium sulfate are also well reproduced by KIM, taking into account apparent or equilibrium solubilities for stepwise or gradual deliquescence and efflorescence transitions.

    The mixed organic-inorganic particles as well as atmospheric aerosol samples exhibit three distinctly different regimes of hygroscopicity: (I a quasi-eutonic deliquescence & efflorescence regime at low-humidity where substances are just partly dissolved and exist also in a non-dissolved phase, (II a gradual deliquescence & efflorescence regime at intermediate humidity where different solutes undergo gradual dissolution or solidification in the aqueous phase; and (III a dilute regime at high humidity where the solutes are fully dissolved approaching their dilute hygroscopicity.

    For atmospheric aerosol samples

  8. Mass-based hygroscopicity parameter interaction model and measurement of atmospheric aerosol water uptake

    Directory of Open Access Journals (Sweden)

    E. Mikhailov

    2011-11-01

    Full Text Available In this study we derive and apply a mass-based hygroscopicity parameter interaction model for efficient description of concentration-dependent water uptake by atmospheric aerosol particles. The model approach builds on the single hygroscopicity parameter model of Petters and Kreidenweis (2007. We introduce an observable mass-based hygroscopicity parameter κm, which can be deconvoluted into a dilute intrinsic hygroscopicity parameter (κm,∞ and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems.

    For sodium chloride, the κm-interaction model (KIM captures the observed concentration and humidity dependence of the hygroscopicity parameter and is in good agreement with an accurate reference model based on the Pitzer ion-interaction approach (Aerosol Inorganic Model, AIM. For atmospheric aerosol samples collected from boreal rural air and from pristine tropical rainforest air (secondary organic aerosol we present first mass-based measurements of water uptake over a wide range of relative humidity (1–99% obtained with a new filter-based differential hygroscopicity analyzer (FDHA technique. By application of KIM to the measurement data we can distinguish three different regimes of hygroscopicity in the investigated aerosol samples: (I A quasi-eutonic regime at low relative humidity (~60% RH where the solutes co-exist in an aqueous and non-aqueous phase; (II a gradually deliquescent regime at intermediate humidity (~60%–90% RH where different solutes undergo gradual dissolution in the aqueous phase; and (III a dilute regime at high humidity (≳90% RH where the solutes are fully dissolved approaching their dilute intrinsic hygroscopicity. The characteristic features of the three hygroscopicity regimes are similar for both samples, while the RH threshold values vary as expected

  9. The weak π − π interaction originated resonant tunneling and fast switching in the carbon based electronic devices

    Directory of Open Access Journals (Sweden)

    Jun He

    2012-03-01

    Full Text Available By means of the nonequilibrium Green's functions and the density functional theory, we have investigated the electronic transport properties of C60 based electronic device with different intermolecular interactions. It is found that the electronic transport properties vary with the types of the interaction between two C60 molecules. A fast electrical switching behavior based on negative differential resistance has been found when two molecules are coupled by the weak π − π interaction. Compared to the solid bonding, the weak interaction is found to induce resonant tunneling, which is responsible for the fast response to the applied electric field and hence the velocity of switching.

  10. GestUI: A Model-driven Method and Tool for Including Gesture-based Interaction in User Interfaces

    Directory of Open Access Journals (Sweden)

    Otto Parra

    2016-04-01

    Full Text Available Among the technological advances in touch-based devices, gesture-based interaction have become a prevalent feature in many application domains. Information systems are starting to explore this type of interaction. As a result, gesture specifications are now being hard-coded by developers at the source code level that hinders their reusability and portability. Similarly, defining new gestures that reflect user requirements is a complex process. This paper describes a model-driven approach to include gesture-based interaction in desktop information systems. It incorporates a tool prototype that captures user-sketched multi-stroke gestures and transforms them into a model by automatically generating the gesture catalogue for gesture-based interaction technologies and gesture-based user interface source codes. We demonstrated our approach in several applications ranging from case tools to form-based information systems.

  11. Twenty weeks of home-based interactive training of children with cerebral palsy improves functional abilities

    DEFF Research Database (Denmark)

    Lorentzen, Jakob; Greve, Line Z; Kliim-Due, Mette;

    2015-01-01

    with 20 weeks interval without any intervening training. Daily activities, functional abilities of upper- and lower limbs, and balance were evaluated before, immediately after training and 12 weeks after training. The training consisted of 30 min daily home-based training for 20 weeks delivered through......BACKGROUND: Home-based training is becoming ever more important with increasing demands on the public health systems. We investigated whether individualized and supervised interactive home-based training delivered through the internet improves functional abilities in children with cerebral palsy...... (CP). METHODS: Thirty four children with CP (aged 9-16; mean age 10.9 ± 2.4 years) (GMFCS I-II; MACS I-II) were included in this non-randomized controlled clinical training study. 12 children (aged 7-16; mean age: 11.3+/-0.9 years) were allocated to a control group in which measurements were performed...

  12. An interactive Tool for Writer Identification based on Offline Text Dependent Approach

    Directory of Open Access Journals (Sweden)

    Saranya K

    2013-01-01

    Full Text Available Writer identification is the process of identifying the writer of the document based on their handwriting. The growth of computational engineering, artificial intelligence and pattern recognition fields owes greatly to one of the highly challenged problem of handwriting identification. This paper proposes the computational intelligence technique to develop discriminative model for writer identification based on handwritten documents. Scanned images of handwritten documents are segmented into words and these words are further segmented into characters for word level and character level writer identification. A set of features are extracted from the segmented words and characters. Feature vectors are trained using support vector machine and obtained 94.27% accuracy for word level, 90.10% for character level. An interactive tool has been developed based on the word level writer identification model.

  13. Decision-Theoretic Bidding Based on Learned Density Models in Simultaneous, Interacting Auctions

    CERN Document Server

    Csirik, J A; McAllester, D; Schapire, R E; Stone, P; 10.1613/jair.1200

    2011-01-01

    Auctions are becoming an increasingly popular method for transacting business, especially over the Internet. This article presents a general approach to building autonomous bidding agents to bid in multiple simultaneous auctions for interacting goods. A core component of our approach learns a model of the empirical price dynamics based on past data and uses the model to analytically calculate, to the greatest extent possible, optimal bids. We introduce a new and general boosting-based algorithm for conditional density estimation problems of this kind, i.e., supervised learning problems in which the goal is to estimate the entire conditional distribution of the real-valued label. This approach is fully implemented as ATTac-2001, a top-scoring agent in the second Trading Agent Competition (TAC-01). We present experiments demonstrating the effectiveness of our boosting-based price predictor relative to several reasonable alternatives.

  14. The mechanism of hetero-synaptic interaction based on spatiotemporal intracellular calcium dynamics.

    Directory of Open Access Journals (Sweden)

    Daiki Futagi

    2014-03-01

    Full Text Available In recent physiological experiments focusing on synaptic plasticity, it is shown that synaptic modifications induced at one synapse are accompanied by hetero-synaptic changes at neighbor sites (Bi, 2002. These evidences imply that the hetero-synaptic interaction plays an important role in reconfiguration of synaptic connections to form and maintain functional neural circuits (Takahashi et al., 2012. Although the mechanism of the interaction is still unclear, some physiological studies suggest that the hetero-synaptic interaction could be caused by propagation of intracellular calcium signals (Nishiyama et al., 2000. Concretely, a spike-triggered calcium increase initiates calcium ion propagation along a dendrite through activation of molecular processes at neighboring sites. Here we hypothesized that the mechanism of the hetero-synaptic interaction was based on the intracellular calcium signaling, which is regulated by interactions between NMDA receptors (NMDARs, voltage-dependent calcium channels (VDCCs and Ryanodine receptors (RyRs on endoplasmic reticulum (ER. To assess realizability of the hypothesized interaction mechanism, we simulated intracellular calcium dynamics at a cellular level, using the computational model that integrated the model of intracellular calcium dynamics (Keizer and Levine, 1996 and the multi-compartment neuron model (Poirazi et al., 2003. Using the proposed computational model, we induced calcium influxes at a local site in postsynaptic dendrite by controlling the spike timings of pre- and postsynaptic neurons. As a result, synchronized calcium influxes through NMDARs and VDCCs caused calcium release from ER. According to the phase plane analysis, RyR-mediated calcium release occurred when the calcium concentration in cytoplasm sufficiently increased under the condition of a high calcium concentration in ER. An NMDAR-mediated calcium influx was slow and persistent, consequently responsible for maintaining a high

  15. Interaction of Chloroprene and Nitrile- Butadiene Rubber with Lubricating Greases and Base Oils

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The present communication addresses compatibility of two synthetic rubber types, chloroprene and nitrilebutadiene ones, with a number of base oils of petroleum origin and lubricating greases produced thereof. Four base oils,including three naphthenic products with varying degrees of refining and one paraffinic product,were compared with each other in terms of their effect on the rubbers. Degenerative changes occurring in the rubbers on contact with the oils and greases were studied using accelerated ageing tests. Alterations in rubber parameters, such as hardness, weight and glass transition temperature, caused by interaction with oil were monitored. The main physicochemical mechanisms standing behind the changes observed in the rubber properties were found to be (i) migration of plasticizer from rubber into the oil phase, (ii) absorption of oil by rubber,and (iii) oxidation of rubber. An increase in glass transition temperature (Tg) of rubber aged in a base oil or grease was considered as an indirect indication that the plasticizer had migrated out of rubber;the plasticizer accumulation in the oil phase being directly confirmed by gas chromatography. In order to suppress the plasticizer migration, oil additivation with dioctyl adipate (DOA), a common plasticizer used in rubber formulations, was attempted. However, the BOA-additivated oils, while reducing plasticizer migration, were found to cause more swelling than the original oils in the case of chloroprene rubber. As an alternative, replacement of BOA by an alkylated aryl phosphate in nitrile- butadiene rubber formulations was considered, but it did not solve the problem either.The results of this study suggest conclusively that the type of rubber, the plasticizer, and the base oil are all the crucial parameters that should be considered when matching rubber with oil in real- life applications. Interaction of rubber with base oils and with greases produced thereof is largely controlled by (i) solvency of the

  16. AN INDUCTIVE, INTERACTIVE AND ADAPTIVE HYBRID PROBLEM-BASED LEARNING METHODOLOGY: APPLICATION TO STATISTICS

    Directory of Open Access Journals (Sweden)

    ADA ZHENG

    2011-10-01

    Full Text Available We have developed an innovative hybrid problem-based learning (PBL methodology. The methodology has the following distinctive features: i Each complex question was decomposed into a set of coherent finer subquestions by following the carefully designed criteria to maintain a delicate balance between guiding the students and inspiring them to think independently. This learning methodology enabled the students to solve the complex questions progressively in an inductive context. ii Facilitated by the utilization of our web-based learning systems, the teacher was able to interact with the students intensively and could allocate more teaching time to provide tailor-made feedback for individual student. The students were actively engaged in the learning activities, stimulated by the intensive interaction. iii The answers submitted by the students could be automatically consolidated in the report of the Moodle system in real-time. The teacher could adjust the teaching schedule and focus of the class to adapt to the learning progress of the students by analysing the automatically generated report and log files of the web-based learning system. As a result, the attendance rate of the students increased from about 50% to more than 90%, and the students’ learning motivation have been significantly enhanced.

  17. Microscopically based constitutive relations for damage mechanics and creep-plasticity interaction

    International Nuclear Information System (INIS)

    In this paper we put forward a new formulation of constitutive relations based on micromechanical analysis to describe the behavior of damaged materials and the creep-plasticity interaction effects at high temperature. The constitutive theory of Continuum Damage Mechanics (CDM) previously proposed by Fan Jinghong has been further developed on the foundation of large deformation endochronic plasticity and an elaborated analysis of the mechanical behavior of a microelement of damaged material in which different damage mechanisms are involved. The softening functions, obtained by the comparative study of microelement with and without a hole, have been introduced into the macroscopic constitutive equations to model the damage effects on material response. The comparison between the calculated results, based on the new constitutive description and corresponding finite element code, and the experimental data of carefully conducted tests on a notched specimen, has shown reasonable agreement. In this paper we also put forward microscopically based constitutive relations to describe the important creep-plasticity interaction for transient creep and steady-state creep. The theoretical analysis developed here has been compared with Ohashi's experimental results. It seems that the present theory could satisfactorily describe the creep-plasticity effects reported. (orig.)

  18. Ground-based remote sensing scheme for monitoring aerosol-cloud interactions

    Science.gov (United States)

    Sarna, Karolina; Russchenberg, Herman W. J.

    2016-03-01

    A new method for continuous observation of aerosol-cloud interactions with ground-based remote sensing instruments is presented. The main goal of this method is to enable the monitoring of the change of the cloud droplet size due to the change in the aerosol concentration. We use high-resolution measurements from a lidar, a radar and a radiometer, which allow us to collect and compare data continuously. This method is based on a standardised data format from Cloudnet and can be implemented at any observatory where the Cloudnet data set is available. Two example case studies were chosen from the Atmospheric Radiation Measurement (ARM) Program deployment on Graciosa Island, Azores, Portugal, in 2009 to present the method. We use the cloud droplet effective radius (re) to represent cloud microphysical properties and an integrated value of the attenuated backscatter coefficient (ATB) below the cloud to represent the aerosol concentration. All data from each case study are divided into bins of the liquid water path (LWP), each 10 g m-2 wide. For every LWP bin we present the correlation coefficient between ln re and ln ATB, as well as ACIr (defined as ACIr = -d ln re/d ln ATB, change in cloud droplet effective radius with aerosol concentration). Obtained values of ACIr are in the range 0.01-0.1. We show that ground-based remote sensing instruments used in synergy can efficiently and continuously monitor aerosol-cloud interactions.

  19. Web-based, Interactive, Nuclear Reactor Transient Analyzer using LabVIEW and RELAP5 (ATHENA)

    International Nuclear Information System (INIS)

    In nuclear engineering, large system analysis codes such as RELAP5, TRAC-M, etc. play an important role in evaluating a reactor system behavior during a wide range of transient conditions. One limitation that restricts their use on a wider scale is that these codes often have a complicated I/O structure. This has motivated the development of GUI tools for best estimate codes, such as SNAP and ViSA, etc. In addition to a user interface, a greater degree of freedom in simulation and analyses of nuclear transient phenomena can be achieved if computer codes and their outputs are accessible from anywhere through the web. Such a web-based interactive interface can be very useful for geographically distributed groups when there is a need to share real-time data. Using mostly off-the-shelf technology, such a capability - a web-based transient analyzer based on a best-estimate code - has been developed. Specifically, the widely used best-estimate code RELAP5 is linked with a graphical interface. Moreover, a capability to web-cast is also available. This has been achieved by using the LabVIEW virtual instruments (VIs). In addition to the graphical display of the results, interactive control functions have also been added that allow operator's actions as well as, if permitted, by a distant user through the web

  20. A unified set-based test with adaptive filtering for gene-environment interaction analyses.

    Science.gov (United States)

    Liu, Qianying; Chen, Lin S; Nicolae, Dan L; Pierce, Brandon L

    2016-06-01

    In genome-wide gene-environment interaction (GxE) studies, a common strategy to improve power is to first conduct a filtering test and retain only the SNPs that pass the filtering in the subsequent GxE analyses. Inspired by two-stage tests and gene-based tests in GxE analysis, we consider the general problem of jointly testing a set of parameters when only a few are truly from the alternative hypothesis and when filtering information is available. We propose a unified set-based test that simultaneously considers filtering on individual parameters and testing on the set. We derive the exact distribution and approximate the power function of the proposed unified statistic in simplified settings, and use them to adaptively calculate the optimal filtering threshold for each set. In the context of gene-based GxE analysis, we show that although the empirical power function may be affected by many factors, the optimal filtering threshold corresponding to the peak of the power curve primarily depends on the size of the gene. We further propose a resampling algorithm to calculate P-values for each gene given the estimated optimal filtering threshold. The performance of the method is evaluated in simulation studies and illustrated via a genome-wide gene-gender interaction analysis using pancreatic cancer genome-wide association data. PMID:26496228

  1. Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation

    Energy Technology Data Exchange (ETDEWEB)

    Rokitskaya, Tatyana I; Kotova, Elena A; Antonenko, Yuri N [Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991 (Russian Federation); Macrae, Michael X; Blake, Steven; Yang, Jerry [Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358 (United States); Egorova, Natalya S, E-mail: jerryyang@ucsd.ed, E-mail: antonen@genebee.msu.s [Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117871 Moscow (Russian Federation)

    2010-11-17

    Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors.

  2. Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation

    Science.gov (United States)

    Rokitskaya, Tatyana I.; Macrae, Michael X.; Blake, Steven; Egorova, Natalya S.; Kotova, Elena A.; Yang, Jerry; Antonenko, Yuri N.

    2010-11-01

    Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors.

  3. Interactive Web-based Floodplain Simulation System for Realistic Experiments of Flooding and Flood Damage

    Science.gov (United States)

    Demir, I.

    2013-12-01

    Recent developments in web technologies make it easy to manage and visualize large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The floodplain simulation system is a web-based 3D interactive flood simulation environment to create real world flooding scenarios. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create and modify predefined scenarios, control environmental parameters, and evaluate flood mitigation techniques. The web-based simulation system provides an environment to children and adults learn about the flooding, flood damage, and effects of development and human activity in the floodplain. The system provides various scenarios customized to fit the age and education level of the users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various flooding and land use scenarios.

  4. Lewis Acid–Base Interactions between Polysulfides and Metal Organic Framework in Lithium Sulfur Batteries

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Jianming; Tian, Jian; Wu, Dangxin; Gu, Meng; Xu, Wu; Wang, Chongmin; Gao, Fei; Engelhard, Mark H.; Zhang, Ji-Guang; Liu, Jun; Xiao, Jie

    2014-05-14

    Lithium–sulfur (Li–S) battery is one of the most promising energy storage systems because of its high specific capacity of 1675 mAh g–1 based on sulfur. However, the rapid capacity degradation, mainly caused by polysulfide dissolution, remains a significant challenge prior to practical applications. This work demonstrates that a novel Ni-based metal organic framework (Ni-MOF), Ni6(BTB)4(BP)3 (BTB = benzene-1,3,5-tribenzoate and BP = 4,4'-bipyridyl), can remarkably immobilize polysulfides within the cathode structure through physical and chemical interactions at molecular level. The capacity retention achieves up to 89% after 100 cycles at 0.1 C. Finally, the excellent performance is attributed to the synergistic effects of the interwoven mesopores (~2.8 nm) and micropores (~1.4 nm) of Ni-MOF, which first provide an ideal matrix to confine polysulfides, and the strong interactions between Lewis acidic Ni(II) center and the polysulfide base, which significantly slow down the migration of soluble polysulfides out of the pores, leading to the excellent cycling performance of Ni-MOF/S composite.

  5. Wearable Computing System with Input-Output Devices Based on Eye-Based Human Computer Interaction Allowing Location Based Web Services

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2013-08-01

    Full Text Available Wearable computing with Input-Output devices Base on Eye-Based Human Computer Interaction: EBHCI which allows location based web services including navigation, location/attitude/health condition monitoring is proposed. Through implementation of the proposed wearable computing system, all the functionality is confirmed. It is also found that the system does work well. It can be used easily and also is not expensive. Experimental results for EBHCI show excellent performance in terms of key-in accuracy as well as input speed. It is accessible to internet, obviously, and has search engine capability.

  6. Fluid-structure interaction-based biomechanical perception model for tactile sensing.

    Directory of Open Access Journals (Sweden)

    Zheng Wang

    Full Text Available The reproduced tactile sensation of haptic interfaces usually selectively reproduces a certain object attribute, such as the object's material reflected by vibration and its surface shape by a pneumatic nozzle array. Tactile biomechanics investigates the relation between responses to an external load stimulus and tactile perception and guides the design of haptic interface devices via a tactile mechanism. Focusing on the pneumatic haptic interface, we established a fluid-structure interaction-based biomechanical model of responses to static and dynamic loads and conducted numerical simulation and experiments. This model provides a theoretical basis for designing haptic interfaces and reproducing tactile textures.

  7. Dual-responsive colloidal microcapsules based on host-guest interaction on solid templates.

    Science.gov (United States)

    Li, Guangyu; Dong, Zhirui; Zhu, Yuting; Tong, Weijun; Gao, Changyou

    2016-08-01

    Colloidal microcapsules (MCs) have received considerable attention in the fields of microencapsulation, drug delivery as well as microreactors due to their unique nanoparticles-composed structure. In this study, dual-responsive colloidal MCs based on host-guest interaction were successfully fabricated via a layer-by-layer assembly method on sacrificial solid templates. Ferrocene-modified polyethylenimine (PEI-Fc) and cyclodextrin-modified polystyrene nanoparticles (PS-CD NPs) were used as building blocks for assembly. The colloidal MCs could be disassembled into nano-components upon addition of competitive adamantane (Ad) molecules or in the solution with a pH lower than 4. PMID:27175830

  8. Nanoscale switch based on interacting molecular dipoles: Cooperativity can improve the device characteristics

    Science.gov (United States)

    Mafé, , Salvador; Manzanares, , José A.; Reiss, Howard

    2011-02-01

    We propose a nanoscale switch, giving a nonlinear function with two conductive states separated by a sharp transition region, on the basis of an array of molecular dipoles. We show theoretically that the local interactions between dipoles result in cooperative phenomena that can significantly improve the switching characteristics. We demonstrate the general validity of the concept in the cases of (i) an electrical switch robust to the finite size and variability effects inherent to the nanoscale and (ii) a sensing layer based on the voltage and ligand concentration dependence of the dipole array conductance.

  9. Nuclear equation of state based on density dependent realistic effective NN interaction

    CERN Document Server

    Basu, D N

    2003-01-01

    A density dependent M3Y effective nucleon-nucleon (NN) interaction based on the G-matrix elements of the Reid-Elliott NN potential is used to determine the nuclear matter equation of state. The equilibrium density of the nuclear matter is determined by minimizing the energy per nucleon. The density dependence parameters are chosen to reproduce the saturation energy per nucleon and the saturation density of spin and isospin symmetric cold infinite nuclear matter. The nuclear matter equation of state thus obtained is then used to calculate the pressure, the energy density, the nuclear incompressibility and the velocity of sound in nuclear medium.

  10. A Web-based Interactive Real Laboratory for Process Engineering Education

    OpenAIRE

    Maher Chaabene; Kamel Mkaouar; Mohamed Ouali

    2007-01-01

    An online supervision and control of a laboratory designed for process engineering education was conceived. The principal aim was to minimise the time access of an operator when manipulating laboratory features. Hence, the Time delay due to Internet traffic was overcome by using a Web Embedded Server (WES). A human-computer interactive interface using JAVA Script was developed so as to control multi-user access. The multi-user management was ensured by means of a PHP-based dynamic pages using...

  11. Interaction of quinones with three pyrimidine bases: A laser flash photolysis study

    International Nuclear Information System (INIS)

    The interaction between three different pyrimidine bases, uracil (U), cytosine (C) and thymine (T) and two quinones, 2-methyl-1,4-naphthoquinone or menadione (MQ) and 9,10-anthraquinone (AQ) have been studied using laser flash photolysis technique in organic homogeneous medium. The three pyrimidines have revealed a difference in their extent of reactivity towards the quinones, which has been attributed to their structural difference. Our works have revealed that the difference in structural dimension of the quinones is also responsible for affecting the reactivity of these pyrimidines in homogeneous medium.

  12. Individualized, home-based interactive training of cerebral palsy children delivered through the Internet

    DEFF Research Database (Denmark)

    Bilde, Peder E; Kliim-Due, Mette; Rasmussen, Betina;

    2011-01-01

    The available health resources limit the amount of therapy that may be offered to children with cerebral palsy and the amount of training in each session may be insufficient to drive the neuroplastic changes, which are necessary for functional improvements to take place. The aim of this pilot study...... was to provide proof of concept that individualized and supervised interactive home-based training delivered through the internet may provide an efficient way of maintaining intensive training of children with cerebral palsy over prolonged periods....

  13. A Maneuvering Target Tracking Algorithm Based on the Interacting Multiple Models

    OpenAIRE

    Liu Yan-Chang; Zuo Xian-Gang

    2013-01-01

    In view of the limitation of the traditional Kalman filter with which the tracking has big calculation amount and low tracking precision base on the model of CV or CA movement, a algorithm is suggested in the present article which is the Interacting Multiple Models Kalman filter(IMM-KF) with the CV and CA model. Under keeping invariant of the tracking precision of linear motion, This method can make the tracking precision of curve motion approach the linear motion’s. The system simulation res...

  14. An interactive system for creating object models from range data based on simulated annealing

    International Nuclear Information System (INIS)

    In hazardous applications such as remediation of buried waste and dismantlement of radioactive facilities, robots are an attractive solution. Sensing to recognize and locate objects is a critical need for robotic operations in unstructured environments. An accurate 3-D model of objects in the scene is necessary for efficient high level control of robots. Drawing upon concepts from supervisory control, the authors have developed an interactive system for creating object models from range data, based on simulated annealing. Site modeling is a task that is typically performed using purely manual or autonomous techniques, each of which has inherent strengths and weaknesses. However, an interactive modeling system combines the advantages of both manual and autonomous methods, to create a system that has high operator productivity as well as high flexibility and robustness. The system is unique in that it can work with very sparse range data, tolerate occlusions, and tolerate cluttered scenes. The authors have performed an informal evaluation with four operators on 16 different scenes, and have shown that the interactive system is superior to either manual or automatic methods in terms of task time and accuracy

  15. Physiologically based pharmacokinetic modeling for assessing the clinical drug-drug interaction of alisporivir.

    Science.gov (United States)

    Xia, Binfeng; Barve, Avantika; Heimbach, Tycho; Zhang, Tao; Gu, Helen; Wang, Lai; Einolf, Heidi; Alexander, Natalya; Hanna, Imad; Ke, June; Mangold, James B; He, Handan; Sunkara, Gangadhar

    2014-10-15

    Alisporivir is a novel cyclophilin-binding molecule with potent anti-hepatitis C virus (HCV) activity. In vitro data from human liver microsomes suggest that alisporivir is a substrate and a time-dependent inhibitor (TDI) of CYP3A4. The aim of the current work was to develop a novel physiologically based pharmacokinetic (PBPK) model to quantitatively assess the magnitude of CYP3A4 mediated drug-drug interactions with alisporivir as the substrate or victim drug. Towards that, a Simcyp PBPK model was developed by integrating in vitro data with in vivo clinical findings to characterize the clinical pharmacokinetics of alisporivir and further assess the magnitude of drug-drug interactions. Incorporated with absorption, distribution, elimination, and TDI data, the model accurately predicted AUC, Cmax, and tmax values after single or multiple doses of alisporivir with a prediction deviation within ± 32%. The model predicted an alisporivir AUC increase by 9.4-fold and a decrease by 86% when alisporivir was co-administrated with ketoconazole (CYP3A4 inhibitor) or rifampin (CYP3A4 inducer), respectively. Predictions were within ± 20% of the observed changes. In conclusion, the PBPK model successfully predicted the alisporivir PK and the magnitude of drug-drug interactions. PMID:25008118

  16. a Method to Estimate Temporal Interaction in a Conditional Random Field Based Approach for Crop Recognition

    Science.gov (United States)

    Diaz, P. M. A.; Feitosa, R. Q.; Sanches, I. D.; Costa, G. A. O. P.

    2016-06-01

    This paper presents a method to estimate the temporal interaction in a Conditional Random Field (CRF) based approach for crop recognition from multitemporal remote sensing image sequences. This approach models the phenology of different crop types as a CRF. Interaction potentials are assumed to depend only on the class labels of an image site at two consecutive epochs. In the proposed method, the estimation of temporal interaction parameters is considered as an optimization problem, whose goal is to find the transition matrix that maximizes the CRF performance, upon a set of labelled data. The objective functions underlying the optimization procedure can be formulated in terms of different accuracy metrics, such as overall and average class accuracy per crop or phenological stages. To validate the proposed approach, experiments were carried out upon a dataset consisting of 12 co-registered LANDSAT images of a region in southeast of Brazil. Pattern Search was used as the optimization algorithm. The experimental results demonstrated that the proposed method was able to substantially outperform estimates related to joint or conditional class transition probabilities, which rely on training samples.

  17. Truck-based mobile wireless sensor networks for the experimental observation of vehicle-bridge interaction

    Science.gov (United States)

    Kim, Junhee; Lynch, Jerome P.; Lee, Jong-Jae; Lee, Chang-Geun

    2011-06-01

    Heavy vehicles driving over a bridge create a complex dynamic phenomenon known as vehicle-bridge interaction. In recent years, interest in vehicle-bridge interaction has grown because a deeper understanding of the phenomena can lead to improvements in bridge design methods while enhancing the accuracy of structural health monitoring techniques. The mobility of wireless sensors can be leveraged to directly monitor the dynamic coupling between the moving vehicle and the bridge. In this study, a mobile wireless sensor network is proposed for installation on a heavy truck to capture the vertical acceleration, horizontal acceleration and gyroscopic pitching of the truck as it crosses a bridge. The vehicle-based wireless monitoring system is designed to interact with a static, permanent wireless monitoring system installed on the bridge. Specifically, the mobile wireless sensors time-synchronize with the bridge's wireless sensors before transferring the vehicle response data. Vertical acceleration and gyroscopic pitching measurements of the vehicle are combined with bridge accelerations to create a time-synchronized vehicle-bridge response dataset. In addition to observing the vehicle vibrations, Kalman filtering is adopted to accurately track the vehicle position using the measured horizontal acceleration of the vehicle and positioning information derived from piezoelectric strip sensors installed on the bridge deck as part of the bridge monitoring system. Using the Geumdang Bridge (Korea), extensive field testing of the proposed vehicle-bridge wireless monitoring system is conducted. Experimental results verify the reliability of the wireless system and the accuracy of the vehicle positioning algorithm.

  18. GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

    Science.gov (United States)

    Nemoto, Wataru; Yamanishi, Yoshihiro; Limviphuvadh, Vachiranee; Saito, Akira; Toh, Hiroyuki

    2016-09-01

    G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases. GPCR oligomerization is now recognized as an important event in various biological phenomena, and many researchers are investigating this subject. We have developed a support vector machine (SVM)-based method to predict interacting pairs for GPCR oligomerization, by integrating the structure and sequence information of GPCRs. The performance of our method was evaluated by the Receiver Operating Characteristic (ROC) curve. The corresponding area under the curve was 0.938. As far as we know, this is the only prediction method for interacting pairs among GPCRs. Our method could accelerate the analyses of these interactions, and contribute to the elucidation of the global structures of the GPCR networks in membranes. Proteins 2016; 84:1224-1233. © 2016 Wiley Periodicals, Inc. PMID:27191053

  19. An interactive system for creating object models from range data based on simulated annealing

    Energy Technology Data Exchange (ETDEWEB)

    Hoff, W.A.; Hood, F.W.; King, R.H. [Colorado School of Mines, Golden, CO (United States). Center for Robotics and Intelligent Systems

    1997-05-01

    In hazardous applications such as remediation of buried waste and dismantlement of radioactive facilities, robots are an attractive solution. Sensing to recognize and locate objects is a critical need for robotic operations in unstructured environments. An accurate 3-D model of objects in the scene is necessary for efficient high level control of robots. Drawing upon concepts from supervisory control, the authors have developed an interactive system for creating object models from range data, based on simulated annealing. Site modeling is a task that is typically performed using purely manual or autonomous techniques, each of which has inherent strengths and weaknesses. However, an interactive modeling system combines the advantages of both manual and autonomous methods, to create a system that has high operator productivity as well as high flexibility and robustness. The system is unique in that it can work with very sparse range data, tolerate occlusions, and tolerate cluttered scenes. The authors have performed an informal evaluation with four operators on 16 different scenes, and have shown that the interactive system is superior to either manual or automatic methods in terms of task time and accuracy.

  20. Improving the Performance of Interactive TCP Applications using End-point Based and Network Level Techniques

    Directory of Open Access Journals (Sweden)

    Varun G Menon

    2012-04-01

    Full Text Available Recent measurement based studies reveal that most of the Internet connections are short in terms of the amount of traffic they carry, while a small fraction of the connections are carrying a largeportion of the traffic.. Most of these short flows are from interactive applications like telnet, gaming that use TCP protocol for connection establishment and data transfer. These short TCP flows suffer from severe response-time performance degradations when multiplexed with long-lived flows during times of network congestion. The reasons for this problem is that, in the absence of large number of packets the short flows are unable to get a detailed knowledge about the level of underlying network congestion and even a single packet loss forces long retransmission timeouts. Also as the numbers of packets are less they are not able to develop large congestion windows and thus unable to jumpstart the next data burst. Due to this, clients of interactive applications suffer from increased response time for data packets sent and they try to upgrade their short flows to long flows by sending dummy packets into the network even when they do not have any data to send. This behavior can lead to severe congestion in the network and causes harm to statistical multiplexing in the Internet. This paper aims at providing easy to implement techniques that can be used by the clients of interactive applications to get much better performance without causing any serious congestion in the network.

  1. Truck-based mobile wireless sensor networks for the experimental observation of vehicle–bridge interaction

    International Nuclear Information System (INIS)

    Heavy vehicles driving over a bridge create a complex dynamic phenomenon known as vehicle–bridge interaction. In recent years, interest in vehicle–bridge interaction has grown because a deeper understanding of the phenomena can lead to improvements in bridge design methods while enhancing the accuracy of structural health monitoring techniques. The mobility of wireless sensors can be leveraged to directly monitor the dynamic coupling between the moving vehicle and the bridge. In this study, a mobile wireless sensor network is proposed for installation on a heavy truck to capture the vertical acceleration, horizontal acceleration and gyroscopic pitching of the truck as it crosses a bridge. The vehicle-based wireless monitoring system is designed to interact with a static, permanent wireless monitoring system installed on the bridge. Specifically, the mobile wireless sensors time-synchronize with the bridge's wireless sensors before transferring the vehicle response data. Vertical acceleration and gyroscopic pitching measurements of the vehicle are combined with bridge accelerations to create a time-synchronized vehicle–bridge response dataset. In addition to observing the vehicle vibrations, Kalman filtering is adopted to accurately track the vehicle position using the measured horizontal acceleration of the vehicle and positioning information derived from piezoelectric strip sensors installed on the bridge deck as part of the bridge monitoring system. Using the Geumdang Bridge (Korea), extensive field testing of the proposed vehicle–bridge wireless monitoring system is conducted. Experimental results verify the reliability of the wireless system and the accuracy of the vehicle positioning algorithm

  2. Aggregator-Based Interactive Charging Management System for Electric Vehicle Charging

    Directory of Open Access Journals (Sweden)

    Mingchao Xia

    2016-03-01

    Full Text Available With the ongoing large-scale implementation of electric vehicles (EVs, the exploration of a more flexible approach to maintain fair interaction between EVs and the power grid is urgently required. This paper presents an aggregator-based interactive charging management scheme adopting interruptible load (IL pricing, in which the EV aggregator will respond to the load control command of the grid in an EV interactive mode. Charging managements are carried out according to battery state-of-charge and the EV departure time in EV charging stations. A power-altering charging (PAC control method is proposed to dispatch the EVs charging fairly in a station and guarantee EV owners’ preferences. The method does not require classical iterative procedures or heavy computations; furthermore, it is beneficial for EVs to depart earlier than expected for reasons beyond keeping homeostatic charging. The proposed scheme, which is tested to charge individual EVs well according to its preference, was implemented as part of an “EV Beijing” project. The proposed management scheme provides new insight into EV charging strategy and provides another choice to EV users.

  3. Finite element based evaluation of stress intensity factors for interactive semi-elliptic surface cracks

    International Nuclear Information System (INIS)

    A finite thickness plate with two coplanar self-same shallow and deep semi-elliptical surface cracks subjected to remote tensile surface traction is considered for fracture analysis. Based on three-dimensional (3D) finite element solutions, stress intensity factors (SIFs) are evaluated along the entire crack front using a force method. The line spring model has also been used to evaluate crack depth point SIFs using shell finite element analysis. A wide range of geometric dimensions and crack configurations viz. crack shape aspect ratio (0.3≤a/c≤1.2), crack depth ratio (1.25≤t/a≤6), relative crack location (0.33≤2c/d≤0.9) and normalized location on the crack front (0≤2phi/π≤2) are considered for numerical estimation of crack interaction factors. SIFs evaluated at the depth point using the force method from the 3D finite element results are compared with SIFs evaluated using the line spring model. Finally, using finite element results, an empirical relation is proposed for the evaluation of crack interaction factors. For the ranges considered, the proposed empirical relation predicts crack interaction factors at critical locations within ±2% of the 3D finite element solutions

  4. Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis

    OpenAIRE

    Grange, Laura; Bureau, Jean-François; Nikolayeva, Iryna; Paul, Richard; Van Steen, Kristel; Schwikowski, Benno; Sakuntabhai, Anavaj

    2015-01-01

    Background Deciphering the genetic architecture of complex traits is still a major challenge for human genetics. In most cases, genome-wide association studies have only partially explained the heritability of traits and diseases. Epistasis, one potentially important cause of this missing heritability, is difficult to explore at the genome-wide level. Here, we develop and assess a tool based on interactive odds ratios (IOR), Fast Odds Ratio-based sCan for Epistasis (FORCE), as a novel approac...

  5. MORPHOLOGICAL AND SEMANTIC ANALYSIS OF TURKISH LANGUAGE FOR TEXT BASED DIALOGUE SYSTEM AS A TOOL OF HUMAN-COMPUTER INTERACTION

    OpenAIRE

    ÖZYURT, Hacer; ÖZYURT, Özcan

    2010-01-01

    Natural Language Processing (NLP) is one of the most important research and application fields in artificial intelligence. According to known the most important tool of human-computer interaction is language, in the near future the language will be an important tool for human-computer interaction. In this sense, the rules of a language must be known and must be analyzed by computer. In this study, a Turkish text based dialogue system has been developed to ensure human-computer interaction. Th...

  6. The nature of interactions between [Cu2Cl3]−-based ionic liquid and thiophene – A theoretical study

    Directory of Open Access Journals (Sweden)

    Renqing Lü

    2016-05-01

    Full Text Available In an effort to deepen the understanding of nature of interactions between CuCl-based ionic liquids and thiophene, the electronic and topological properties of interactions between 1-butyl-3-methylimidazolium ([BMIM]+[Cu2Cl3]− and thiophene (TS have been investigated by the density functional theory. The occurrence of interactions caused by resonance effects between virtual orbitals of Cu and virtual orbitals of thiophene has been corroborated at the molecular level.

  7. Design of a New Virtual Interaction Based PLC Training Using Virtual Sensors and Actuators: System and Its Application

    OpenAIRE

    Yoon Sang Kim; Hak-Man Kim

    2013-01-01

    This paper proposes a new virtual interaction based programmable logic controller (PLC) training system using virtual sensors and actuators. The proposed system is composed of four components including virtual sensors (for interacting between user and input devices), virtual actuators (for manipulating and controlling device or equipment), virtual PLC (for programming and generating command), and virtual networks (for interfacing the interactions and transferring the data between all the comp...

  8. MPQ-cytometry: a magnetism-based method for quantification of nanoparticle-cell interactions

    Science.gov (United States)

    Shipunova, V. O.; Nikitin, M. P.; Nikitin, P. I.; Deyev, S. M.

    2016-06-01

    Precise quantification of interactions between nanoparticles and living cells is among the imperative tasks for research in nanobiotechnology, nanotoxicology and biomedicine. To meet the challenge, a rapid method called MPQ-cytometry is developed, which measures the integral non-linear response produced by magnetically labeled nanoparticles in a cell sample with an original magnetic particle quantification (MPQ) technique. MPQ-cytometry provides a sensitivity limit 0.33 ng of nanoparticles and is devoid of a background signal present in many label-based assays. Each measurement takes only a few seconds, and no complicated sample preparation or data processing is required. The capabilities of the method have been demonstrated by quantification of interactions of iron oxide nanoparticles with eukaryotic cells. The total amount of targeted nanoparticles that specifically recognized the HER2/neu oncomarker on the human cancer cell surface was successfully measured, the specificity of interaction permitting the detection of HER2/neu positive cells in a cell mixture. Moreover, it has been shown that MPQ-cytometry analysis of a HER2/neu-specific iron oxide nanoparticle interaction with six cell lines of different tissue origins quantitatively reflects the HER2/neu status of the cells. High correlation of MPQ-cytometry data with those obtained by three other commonly used in molecular and cell biology methods supports consideration of this method as a prospective alternative for both quantifying cell-bound nanoparticles and estimating the expression level of cell surface antigens. The proposed method does not require expensive sophisticated equipment or highly skilled personnel and it can be easily applied for rapid diagnostics, especially under field conditions.Precise quantification of interactions between nanoparticles and living cells is among the imperative tasks for research in nanobiotechnology, nanotoxicology and biomedicine. To meet the challenge, a rapid method

  9. Interactions of selected policy-stakeholder groups implementing middle school science standards-based systemic reform

    Science.gov (United States)

    Boydston, Theodore Lewis, III

    1999-12-01

    This research is an interpretive inquiry into the views and interactions of stakeholders in a district office of a large school system responsible for implementing science systemic reform. Three major sources of data were used in this research: surveys, stakeholder interviews, and autobiographical reflection on experiences as part of the reform initiative. This is an emergent research that is evident in the shift in the focus of research questions and their supporting assumptions during the research. The literature review describes standards-based reform, arguments about reform, and the major dimensions of reform research. The results of the survey of stakeholders revealed that the views among the stakeholder groups followed the system hierarchy and could be separated into two large groups; staff responsible for implementing the reform initiative and the other stakeholder groups. Each of these groups was composed of identifiable subgroups. The interviews with stakeholders revealed how their different attitudes, values, and beliefs frame the context of stakeholder interactions. An over reliance on an authoritarian view of decision-making leaves many stakeholders feeling disempowered and critical of others. This atmosphere promotes blaming, which inhibits collegial interaction. Work experiences in the district office revealed how stakeholders' unaddressed assumptions, attitudes, and beliefs promote fragmentation and competition rather than cooperation. Hidden assumptions about management by control and mandate, competition, and teaching and learning appear to restrain the interactions of stakeholders. Support of the National Science Education Standards was identified as a unifying view among the stakeholders, yet the professional development program focused on content and pedagogical knowledge without addressing stakeholder concerns and beliefs about the intended constructivist framework of the program. Stakeholders' attitudes about the issue of equity demonstrated

  10. Gene-environment interactions on growth trajectories.

    Science.gov (United States)

    Wang, Shuang; Xiong, Wei; Ma, Weiping; Chanock, Stephen; Jedrychowski, Wieslaw; Wu, Rongling; Perera, Frederica P

    2012-04-01

    It has been suggested that children with larger brains tend to perform better on IQ tests or cognitive function tests. Prenatal head growth and head growth in infancy are two crucial periods for subsequent intelligence. Studies have shown that environmental exposure to air pollutants during pregnancy is associated with fetal growth reduction, developmental delay, and reduced IQ. Meanwhile, genetic polymorphisms may modify the effect of environment on head growth. However, studies on gene-environment or gene-gene interactions on growth trajectories have been quite limited partly due to the difficulty to quantitatively measure interactions on growth trajectories. Moreover, it is known that assessing the significance of gene-environment or gene-gene interactions on cross-sectional outcomes empirically using the permutation procedures may bring substantial errors in the tests. We proposed a score that quantitatively measures interactions on growth trajectories and developed an algorithm with a parametric bootstrap procedure to empirically assess the significance of the interactions on growth trajectories under the likelihood framework. We also derived a Wald statistic to test for interactions on growth trajectories and compared it to the proposed parametric bootstrap procedure. Through extensive simulation studies, we demonstrated the feasibility and power of the proposed testing procedures. We applied our method to a real dataset with head circumference measures from birth to age 7 on a cohort currently being conducted by the Columbia Center for Children's Environmental Health (CCCEH) in Krakow, Poland, and identified several significant gene-environment interactions on head circumference growth trajectories. PMID:22311237

  11. Web-based (HTML5) interactive graphics for fusion research and collaboration

    International Nuclear Information System (INIS)

    Highlights: ► Interactive data visualization is supported via the Web without a browser plugin and provides users easy, real-time access to data of different types from various locations. ► Crosshair, zoom, pan as well as toggling dimensionality and a slice bar for multi-dimensional data are available. ► Data with PHP API can be applied: MDSplus and SQL have been tested. ► Modular in design, this has been deployed to support both the experimental and the simulation research arenas. - Abstract: With the continuing development of web technologies, it is becoming feasible for websites to operate a lot like a scientific desktop application. This has opened up more possibilities for utilizing the web browser for interactive scientific research and providing new means of on-line communication and collaboration. This paper describes the research and deployment for utilizing these enhanced web graphics capabilities on the fusion research tools which has led to a general toolkit that can be deployed as required. It allows users to dynamically create, interact with and share with others, the large sets of data generated by the fusion experiments and simulations. Hypertext Preprocessor (PHP), a general-purpose scripting language for the Web, is used to process a series of inputs, and determine the data source types and locations to fetch and organize the data. Protovis, a Javascript and SVG based web graphics package, then quickly draws the interactive graphs and makes it available to the worldwide audience. This toolkit has been deployed to both the simulation and experimental arenas. The deployed applications will be presented as well as the architecture and technologies used in producing the general graphics toolkit.

  12. Web-based (HTML5) interactive graphics for fusion research and collaboration

    Energy Technology Data Exchange (ETDEWEB)

    Kim, E.N., E-mail: kimny@fusion.gat.com [General Atomics, P.O. Box 85608, San Diego, CA (United States); Schissel, D.P.; Abla, G.; Flanagan, S.; Lee, X. [General Atomics, P.O. Box 85608, San Diego, CA (United States)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer Interactive data visualization is supported via the Web without a browser plugin and provides users easy, real-time access to data of different types from various locations. Black-Right-Pointing-Pointer Crosshair, zoom, pan as well as toggling dimensionality and a slice bar for multi-dimensional data are available. Black-Right-Pointing-Pointer Data with PHP API can be applied: MDSplus and SQL have been tested. Black-Right-Pointing-Pointer Modular in design, this has been deployed to support both the experimental and the simulation research arenas. - Abstract: With the continuing development of web technologies, it is becoming feasible for websites to operate a lot like a scientific desktop application. This has opened up more possibilities for utilizing the web browser for interactive scientific research and providing new means of on-line communication and collaboration. This paper describes the research and deployment for utilizing these enhanced web graphics capabilities on the fusion research tools which has led to a general toolkit that can be deployed as required. It allows users to dynamically create, interact with and share with others, the large sets of data generated by the fusion experiments and simulations. Hypertext Preprocessor (PHP), a general-purpose scripting language for the Web, is used to process a series of inputs, and determine the data source types and locations to fetch and organize the data. Protovis, a Javascript and SVG based web graphics package, then quickly draws the interactive graphs and makes it available to the worldwide audience. This toolkit has been deployed to both the simulation and experimental arenas. The deployed applications will be presented as well as the architecture and technologies used in producing the general graphics toolkit.

  13. Structure and Magnetic Interactions in the Organic-based Ferromagnet Decamethylferrocenium Tetracyanoethenide

    International Nuclear Information System (INIS)

    The structures of three temperature-dependent polymorphs of solvent-free decamethylferrocenium tetracyanoethenide, (FeCp*2)(TCNE), are determined from high-resolution synchrotron powder diffraction data. (FeCp*2)(TCNE) is the first organic-based ferromagnetic material to be synthesized and is known to have two structural phase transitions at 249 and 282 K. The low-temperature phase, which exhibits spontaneous ferromagnetic order below 4.8 K, was determined at 12 K. At that temperature, it has monoclinic space group P21/c (a = 9.6637(4) A, b = 14.1217(5) A, c = 18.6256(7) A, ? = 113.231(2) degrees, Z = 4) and consists of parallel chains of alternating (Fe(C5Me5)2) + and (TCNE) - ions, with an intrachain Fe Fe distance of 10.45 A. Structures of the intermediate and ambient temperature phases, also studied here, are characterized by increasing disorder. At 250 K, the unit cell space group is P21/m (a = 9.7100(3) A, b = 14.4926(4) A, c = 9.4997(3) A, ? = 113.153(1) degrees, Z = 2). At ambient temperature, the lattice, albeit quite disordered, belongs to the orthorhombic space group Cmcm (a = 10.629(1) A, b = 16.128(1) A, c = 14.593(1) A, Z = 4). Nearest-neighbor magnetic interactions were evaluated for the 12 K structure by CASSCF and CASSCF/MCQDPT calculations (a methodology similar to the CASPT2 method). Similar trends are observed in computations with and without inclusion of spin-orbit coupling. The strongest are two intrachain (FeCp*2)- (TCNE) - interactions (ferromagnetic with values of 45 and 29 cm-1), although weaker, nonnegligible, ferro- or antiferromagnetic interchain interactions of less than ± 0.2 cm-1 are also present. Magnetic interactions that lead to ordering are therefore three-dimensional, despite the vastly different intra- and interchain coupling strengths.

  14. Titin-Actin Interaction: PEVK-Actin-Based Viscosity in a Large Animal

    Directory of Open Access Journals (Sweden)

    Charles S. Chung

    2011-01-01

    Full Text Available Titin exhibits an interaction between its PEVK segment and the actin filament resulting in viscosity, a speed dependent resistive force, which significantly influences diastolic filling in mice. While diastolic disease is clinically pervasive, humans express a more compliant titin (N2BA:N2B ratio ~0.5–1.0 than mice (N2BA:N2B ratio ~0.2. To examine PEVK-actin based viscosity in compliant titin-tissues, we used pig cardiac tissue that expresses titin isoforms similar to that in humans. Stretch-hold experiments were performed at speeds from 0.1 to 10 lengths/s from slack sarcomere lengths (SL to SL of 2.15 μm. Viscosity was calculated from the slope of stress-relaxation vs stretch speed. Recombinant PEVK was added to compete off native interactions and this found to reduce the slope by 35%, suggesting that PEVK-actin interactions are a strong contributor of viscosity. Frequency sweeps were performed at frequencies of 0.1–400 Hz and recombinant protein reduced viscous moduli by 40% at 2.15 μm and by 50% at 2.25 μm, suggesting a SL-dependent nature of viscosity that might prevent SL ``overshoot’’ at long diastolic SLs. This study is the first to show that viscosity is present at physiologic speeds in the pig and supports the physiologic relevance of PEVK-actin interactions in humans in both health and disease.

  15. Amperometric glucose biosensor based on glucose oxidase-lectin biospecific interaction.

    Science.gov (United States)

    Zhang, Juanjuan; Wang, Chengyan; Chen, Shihong; Yuan, Dehua; Zhong, Xia

    2013-03-01

    An amperometric glucose biosensor based on high electrocatalytic activity of gold/platinum hybrid functionalized zinc oxide nanorods (Pt-Au@ZnONRs) and glucose oxidase (GOx)-lectin biospecific interaction was proposed. The Pt-Au@ZnONRs, which were prepared through a multiple-step chemosynthesis, were modified onto the surface of glassy carbon electrode (GCE) by a simple casting method due to the excellent film forming ability of the Pt-Au@ZnONRs suspension. Subsequently, a layer of porous gold nanocrystals (pAu) film was assembled onto the Pt-Au@ZnONRs film by immersing the electrode in HAuCl(4) solution to perform the electrochemical deposition at a constant potential of -0.2V. Following that, Concanavalin A (ConA) was immobilized onto the surface of pAu film through physical adsorption and covalent binding interactions between gold nanomaterials and the amino groups or thiol groups of ConA protein. Finally, the GOx was easily immobilized on the ConA/pAu/Pt-Au@ZnONRs/GCE by the biospecific interaction between GOx and ConA. The Pt-Au@ZnONRs composites were characterized using transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). Cyclic voltammetry (CV) was used to characterize the assembly process of the modified electrode. Proposed biosensor showed a high electrocatalytic activity to the glucose with a wide linear range covering from 1.8 μM to 5.15 mM, a low detection limit of 0.6 μM and a low apparent Michaelis-Menten constant (K(M)(app)) of 0.41 mM. Furthermore, the biosensor exhibited good reproducibility and long-term stability, as well as high selectivity. The integration of Pt-Au@ZnONRs and GOx-lectin biospecific interaction would offer potential promise for the fabrication of biosensors and biocatalysts. PMID:23410923

  16. Vector rectangular-shape laser based on reduced graphene oxide interacting with long fiber taper

    CERN Document Server

    Gao, Lei; Zeng, Jing; Huang, Wei; Liu, Min

    2014-01-01

    A vector dual-wavelength rectangular-shape laser (RSL) based on a long fiber taper deposited with reduced graphene oxide is proposed, where the nonlinearity is enhanced due to large evanescent-field-interacting length and strong field confinement of a 8 mm fiber taper with a waist diameter of 4 micronmeters. Graphene flakes are deposited uniformly on the taper waist with light pressure effect, so this structure guarantees both excellent saturable absorption and high nonlinearity. The RSL with a repetition rate of 7.9 MHz exhibits fast polarization switching in two orthogonal polarization directions, and the temporal and spectral characteristics are investigated. The results suggest that the long taper-based graphene structure is an efficient choice for nonlinear devices.

  17. FRIAA: A FRamework for Web-based Interactive Astronomy Analysis using AMQP Messaging

    Science.gov (United States)

    Young, M. D.; Gopu, A.; Hayashi, S.; Cox, J. A.

    2013-10-01

    This paper describes a web-based FRamework for Interactive Astronomy Analysis (FRIAA) being developed as part of the One Degree Imager - Pipeline, Portal, and Archive (ODI-PPA) Science Gateway. The framework provides astronomers with the ability to invoke data processing modules including IRAF and SExtractor on large data within their ODI-PPA web account without requiring them to download the data or to access remote compute resources. Currently available functionality includes contour plots, point source detection and photometry, surface photometry, and catalog source matching. The web browser front-end developed using the Zend PHP platform and the Bootstrap library makes Remote Procedure Calls (RPC) to the back-end modules using AMQP based messaging. The compute-intensive data processing codes are executed on powerful and dedicated nodes on a compute cluster at Indiana University.

  18. Interactive Web service choice-making based on extended QoS model

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Quality of Service (QoS) is a key factor in Web service advertising, choosing and runtime monitoring. Web service QoS is multi-faceted, fuzzy and dynamic. Current researches focus on implementation level performance assurance, ignoring domain specific or application level metrics which are also very important to service users. Industry Web service standards lack QoS expression. The support for QoS based service choice-making is very limited. We proposed an extended Web service QoS model based on configurable fuzzy synthetic evaluation system. Web service QoS is evaluated dynamically according to the service context. A QoS requirement description model is also given for service QoS requirement definition. An interactive Web service choice-making process is described, which takes QoS as a key factor when choosing from functionally equivalent services.

  19. Web- and system-code based, interactive, nuclear power plant simulators

    International Nuclear Information System (INIS)

    Using two different approaches, on-line, web- and system-code based graphical user interfaces have been developed for reactor system analysis. Both are LabVIEW (graphical programming language developed by National Instruments) based systems that allow local users as well as those at remote sites to run, interact and view the results of the system code in a web browser. In the first approach, only the data written by the system code in a tab separated ASCII output file is accessed and displayed graphically. In the second approach, LabVIEW virtual instruments are coupled with the system code as dynamic link libraries (DLL). RELAP5 is used as the system code to demonstrate the capabilities of these approaches. From collaborative projects between teams in geographically remote locations to providing system code experience to distance education students, these tools can be very beneficial in many areas of teaching and R and D. (authors)

  20. Interactive Collision Avoidance Based on Surrounding Mobility Type for an Intelligent Powered Wheelchair

    Directory of Open Access Journals (Sweden)

    Takuma Ito

    2013-05-01

    Full Text Available Electric powered wheelchairs have been developed for people with disabilities and the elderly who have difficulties walking and participating in social activities. However, for users with decreased cognitive abilities and judgment due to further aging, mobility aids that are not only powered but also intelligent are required. Intelligent powered wheelchairs with autonomous locomotion functions are one solution to this problem. This research focused on the complexity of coexisting ʺmobility typesʺ on sidewalks and a prototype intelligent wheelchair equipped with interactive strategies for collision avoidance based on the surrounding mobility type was developed. In order to classify the mobility type of coexisting traffic participants, image‐processing components combined with LIDAR were developed. Based on the classification results, the wheelchair selected and executed either a changing‐lanes strategy or deceleration strategy autonomously.

  1. The human interactome knowledge base (hint-kb): An integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique

    KAUST Repository

    Theofilatos, Konstantinos A.

    2013-07-12

    Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about experimentally and computationally detected human PPIs as well as their corresponding annotation data. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (http://biotools.ceid.upatras.gr/hint-kb/), a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, cal-culatesasetoffeaturesofinterest and computesaconfidence score for every candidate protein interaction. This confidence score is essential for filtering the false positive interactions which are present in existing databases, predicting new protein interactions and measuring the frequency of each true protein interaction. For this reason, a novel machine learning hybrid methodology, called (Evolutionary Kalman Mathematical Modelling—EvoKalMaModel), was used to achieve an accurate and interpretable scoring methodology. The experimental results indicated that the proposed scoring scheme outperforms existing computational methods for the prediction of PPIs.

  2. Prediction of drug-target interactions and drug repositioning via network-based inference.

    Directory of Open Access Journals (Sweden)

    Feixiong Cheng

    Full Text Available Drug-target interaction (DTI is the basis of drug discovery and design. It is time consuming and costly to determine DTI experimentally. Hence, it is necessary to develop computational methods for the prediction of potential DTI. Based on complex network theory, three supervised inference methods were developed here to predict DTI and used for drug repositioning, namely drug-based similarity inference (DBSI, target-based similarity inference (TBSI and network-based inference (NBI. Among them, NBI performed best on four benchmark data sets. Then a drug-target network was created with NBI based on 12,483 FDA-approved and experimental drug-target binary links, and some new DTIs were further predicted. In vitro assays confirmed that five old drugs, namely montelukast, diclofenac, simvastatin, ketoconazole, and itraconazole, showed polypharmacological features on estrogen receptors or dipeptidyl peptidase-IV with half maximal inhibitory or effective concentration ranged from 0.2 to 10 µM. Moreover, simvastatin and ketoconazole showed potent antiproliferative activities on human MDA-MB-231 breast cancer cell line in MTT assays. The results indicated that these methods could be powerful tools in prediction of DTIs and drug repositioning.

  3. Nuclear Spin Relaxation and Molecular Interactions of a Novel Triazolium-Based Ionic Liquid

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Jesse J; Schneider, Yanika; Kail, Brian W; Luebke, David R; Nulwala, Hunaid; Damodaran, Krishnan

    2013-04-11

    Nuclear spin relaxation, small-angle X-ray scattering (SAXS), and electrospray ionization mass spectrometry (ESI-MS) techniques are used to determine supramolecular arrangement of 3-methyl-1-octyl-4-phenyl-1H-triazol-1,2,3-ium bis(trifluoromethanesulfonyl)imide [OMPhTz][Tf{sub 2}N], an example of a triazolium-based ionic liquid. The results obtained showed first-order thermodynamic dependence for nuclear spin relaxation of the anion. First-order relaxation dependence is interpreted as through-bond dipolar relaxation. Greater than first-order dependence was found in the aliphatic protons, aromatic carbons (including nearest neighbors), and carbons at the end of the aliphatic tail. Greater than first order thermodynamic dependence of spin relaxation rates is interpreted as relaxation resulting from at least one mechanism additional to through-bond dipolar relaxation. In rigid portions of the cation, an additional spin relaxation mechanism is attributed to anisotropic effects, while greater than first order thermodynamic dependence of the octyl side chain’s spin relaxation rates is attributed to cation–cation interactions. Little interaction between the anion and the cation was observed by spin relaxation studies or by ESI-MS. No extended supramolecular structure was observed in this study, which was further supported by MS and SAXS. nuclear Overhauser enhancement (NOE) factors are used in conjunction with spin–lattice relaxation time (T{sub 1}) measurements to calculate rotational correlation times for C–H bonds (the time it takes for the vector represented by the bond between the two atoms to rotate by one radian). The rotational correlation times are used to represent segmental reorientation dynamics of the cation. A combination of techniques is used to determine the segmental interactions and dynamics of this example of a triazolium-based ionic liquid.

  4. Interactive dose shaping - efficient strategies for CPU-based real-time treatment planning

    International Nuclear Information System (INIS)

    Conventional intensity modulated radiation therapy (IMRT) treatment planning is based on the traditional concept of iterative optimization using an objective function specified by dose volume histogram constraints for pre-segmented VOIs. This indirect approach suffers from unavoidable shortcomings: i) The control of local dose features is limited to segmented VOIs. ii) Any objective function is a mathematical measure of the plan quality, i.e., is not able to define the clinically optimal treatment plan. iii) Adapting an existing plan to changed patient anatomy as detected by IGRT procedures is difficult. To overcome these shortcomings, we introduce the method of Interactive Dose Shaping (IDS) as a new paradigm for IMRT treatment planning. IDS allows for a direct and interactive manipulation of local dose features in real-time. The key element driving the IDS process is a two-step Dose Modification and Recovery (DMR) strategy: A local dose modification is initiated by the user which translates into modified fluence patterns. This also affects existing desired dose features elsewhere which is compensated by a heuristic recovery process. The IDS paradigm was implemented together with a CPU-based ultra-fast dose calculation and a 3D GUI for dose manipulation and visualization. A local dose feature can be implemented via the DMR strategy within 1-2 seconds. By imposing a series of local dose features, equal plan qualities could be achieved compared to conventional planning for prostate and head and neck cases within 1-2 minutes. The idea of Interactive Dose Shaping for treatment planning has been introduced and first applications of this concept have been realized.

  5. Interactive Dose Shaping - efficient strategies for CPU-based real-time treatment planning

    Science.gov (United States)

    Ziegenhein, P.; Kamerling, C. P.; Oelfke, U.

    2014-03-01

    Conventional intensity modulated radiation therapy (IMRT) treatment planning is based on the traditional concept of iterative optimization using an objective function specified by dose volume histogram constraints for pre-segmented VOIs. This indirect approach suffers from unavoidable shortcomings: i) The control of local dose features is limited to segmented VOIs. ii) Any objective function is a mathematical measure of the plan quality, i.e., is not able to define the clinically optimal treatment plan. iii) Adapting an existing plan to changed patient anatomy as detected by IGRT procedures is difficult. To overcome these shortcomings, we introduce the method of Interactive Dose Shaping (IDS) as a new paradigm for IMRT treatment planning. IDS allows for a direct and interactive manipulation of local dose features in real-time. The key element driving the IDS process is a two-step Dose Modification and Recovery (DMR) strategy: A local dose modification is initiated by the user which translates into modified fluence patterns. This also affects existing desired dose features elsewhere which is compensated by a heuristic recovery process. The IDS paradigm was implemented together with a CPU-based ultra-fast dose calculation and a 3D GUI for dose manipulation and visualization. A local dose feature can be implemented via the DMR strategy within 1-2 seconds. By imposing a series of local dose features, equal plan qualities could be achieved compared to conventional planning for prostate and head and neck cases within 1-2 minutes. The idea of Interactive Dose Shaping for treatment planning has been introduced and first applications of this concept have been realized.

  6. Student Interaction and Knowledge Construction in Case-Based Learning in Educational Psychology Using Online Discussions: The Role of Structure

    Science.gov (United States)

    Pena-Shaff, Judith; Altman, William

    2015-01-01

    We analyzed students' patterns of participation, interaction and knowledge construction in asynchronous online case-based discussions in two Educational Psychology classes with different participation and interaction guidelines. We conducted quantitative analyses of the outlines of postings and transcripts of online messages from these group…

  7. Comparison of Interactive Computer-Based and Classroom Training on Human Rights Awareness in Persons with Intellectual Disabilities

    Science.gov (United States)

    Tardif-Williams, Christine Y.; Owen, Frances; Feldman, Maurice; Tarulli, Donato; Griffiths, Dorothy; Sales, Carol; McQueen-Fuentes, Glenys; Stoner, Karen

    2007-01-01

    We tested the effectiveness of an interactive, video CD-ROM in teaching persons with intellectual disabilities (ID) about their human rights. Thirty-nine participants with ID were trained using both a classroom activity-based version of the training program and the interactive CD-ROM in a counterbalanced presentation. All individuals were pre- and…

  8. Agent-based financial dynamics model from stochastic interacting epidemic system and complexity analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Yunfan, E-mail: yunfanlu@yeah.net; Wang, Jun; Niu, Hongli

    2015-06-12

    An agent-based financial stock price model is developed and investigated by a stochastic interacting epidemic system, which is one of the statistical physics systems and has been used to model the spread of an epidemic or a forest fire. Numerical and statistical analysis are performed on the simulated returns of the proposed financial model. Complexity properties of the financial time series are explored by calculating the correlation dimension and using the modified multiscale entropy method. In order to verify the rationality of the financial model, the real stock market indexes, Shanghai Composite Index and Shenzhen Component Index, are studied in comparison with the simulation data of the proposed model for the different infectiousness parameters. The empirical research reveals that this financial model can reproduce some important features of the real stock markets. - Highlights: • A new agent-based financial price model is developed by stochastic interacting epidemic system. • The structure of the proposed model allows to simulate the financial dynamics. • Correlation dimension and MMSE are applied to complexity analysis of financial time series. • Empirical results show the rationality of the proposed financial model.

  9. GIS - Based data presentation and interactive communication system for public involvement in EIA

    International Nuclear Information System (INIS)

    The data presentation and interactive communication system has as main task to integrate technical and administrative information, as well as to ensure an efficient public participation. The system can achieve desired inter-operability between specialists, government and public in decision-making and environmental impact assessment (EIA). It incorporates different modules relative to specific types of parameters and authorities involved. The GIS-based system provides mapping, database, automatic information collection and advanced presentation techniques. It includes a graphically oriented executive support, which has the ability to present information by geographical representation of the zones on the map. The public opinion is taking into account by consideration of alternatives and providing access to the monitoring of environmental effects. The system offers an effective way to avoid negative reactions by interactive communication based on real-time information exchange. The system can be integrated into national or international management systems, being a useful tool for an efficient communication, handling and exchanging a vast amount of information. (authors)

  10. Development and practice for a PACS-based interactive teaching model for CT image

    International Nuclear Information System (INIS)

    Objective: To explore the interactive teaching model for CT imaging based on PACS, and provide the clinician and young radiologist with continued medical education. Methods: 100 M trunk net was adopted in PACS and 10 M was exchanged on desktop. Teaching model was installed in browse and diagnosis workstation. Teaching contents were classified according to region and managed according to branch model. Text data derived from authoritative textbooks, monograph, and periodicals. Imaging data derived from cases proved by pathology and clinic. The data were obtained through digital camera and scanner or from PACS. After edited and transformed into standard digital image through DICOM server, they were saved in HD of PACS image server with file form. Results: Teaching model for CT imaging provided kinds of cases of CT sign, clinic characteristics, pathology and distinguishing diagnosis. Normal section anatomy, typical image, and its notation could be browsed real time. Teaching model for CT imaging could provide reference to teaching, diagnosis and report. Conclusion: PACS-based teaching model for CT imaging could provide interactive teaching and scientific research tool and improve work quality and efficiency

  11. Web-based interactive visualization of 3D video mosaics using X3D standard

    Institute of Scientific and Technical Information of China (English)

    CHON Jaechoon; LEE Yang-Won; SHIBASAKI Ryosuke

    2006-01-01

    We present a method of 3D image mosaicing for real 3D representation of roadside buildings, and implement a Web-based interactive visualization environment for the 3D video mosaics created by 3D image mosaicing. The 3D image mosaicing technique developed in our previous work is a very powerful method for creating textured 3D-GIS data without excessive data processing like the laser or stereo system. For the Web-based open access to the 3D video mosaics, we build an interactive visualization environment using X3D, the emerging standard of Web 3D. We conduct the data preprocessing for 3D video mosaics and the X3D modeling for textured 3D data. The data preprocessing includes the conversion of each frame of 3D video mosaics into concatenated image files that can be hyperlinked on the Web. The X3D modeling handles the representation of concatenated images using necessary X3D nodes. By employing X3D as the data format for 3D image mosaics, the real 3D representation of roadside buildings is extended to the Web and mobile service systems.

  12. Agent-based financial dynamics model from stochastic interacting epidemic system and complexity analysis

    International Nuclear Information System (INIS)

    An agent-based financial stock price model is developed and investigated by a stochastic interacting epidemic system, which is one of the statistical physics systems and has been used to model the spread of an epidemic or a forest fire. Numerical and statistical analysis are performed on the simulated returns of the proposed financial model. Complexity properties of the financial time series are explored by calculating the correlation dimension and using the modified multiscale entropy method. In order to verify the rationality of the financial model, the real stock market indexes, Shanghai Composite Index and Shenzhen Component Index, are studied in comparison with the simulation data of the proposed model for the different infectiousness parameters. The empirical research reveals that this financial model can reproduce some important features of the real stock markets. - Highlights: • A new agent-based financial price model is developed by stochastic interacting epidemic system. • The structure of the proposed model allows to simulate the financial dynamics. • Correlation dimension and MMSE are applied to complexity analysis of financial time series. • Empirical results show the rationality of the proposed financial model

  13. Lipid-based nanocarrier for quercetin delivery: system characterization and molecular interactions studies.

    Science.gov (United States)

    Hädrich, Gabriela; Monteiro, Samantha Oliveira; Rodrigues, Marisa Raquel; de Lima, Vânia Rodrigues; Putaux, Jean-Luc; Bidone, Juliana; Teixeira, Helder Ferreira; Muccillo-Baisch, Ana Luiza; Dora, Cristiana Lima

    2016-07-01

    The flavonoid quercetin (QU) is a naturally occurring compound with several biological activities. However, the oral bioavailability of this compound is very low due to the high pre-systemic metabolism in the colon and liver and its low water solubility. In this context, the development of QU-loaded nanocarriers (NEs) is a promising approach to improve the drug oral bioavailability. This study investigates the variation of the concentration of 12-hydroxystearic acid-polyethylene glycol copolymer, lecithin and castor oil (CO) as to increase the amount of QU encapsulated while maintaining physicochemical characteristics described in previous studies. To better understand the ability to load and release the drug, we investigated the molecular interactions between QU and NE. Lipid-based NEs were prepared using CO as oily phase and PEG 660-stearate and lecithin as surfactants. Hot solvent diffusion and phase inversion temperature were methods employed to produce NEs. The QU-NEs were investigated for physicochemical characteristics and in vitro drug release. Molecular interactions between QU and the NEs were monitored through the complementary infrared (Fourier transform infrared) and NMR. The results revealed that it was possible to incorporate higher amounts of QU in a lipid-based NE with a reduced size (20 nm). The system developed allow a sustained release of QU probably due to the shell formed by the surfactants around the NE and the flavonoid ordering effect in the emulsion hydrophobic regions, which may reduce the system permeability. PMID:26571009

  14. UTOPIAN: user-driven topic modeling based on interactive nonnegative matrix factorization.

    Science.gov (United States)

    Choo, Jaegul; Lee, Changhyun; Reddy, Chandan K; Park, Haesun

    2013-12-01

    Topic modeling has been widely used for analyzing text document collections. Recently, there have been significant advancements in various topic modeling techniques, particularly in the form of probabilistic graphical modeling. State-of-the-art techniques such as Latent Dirichlet Allocation (LDA) have been successfully applied in visual text analytics. However, most of the widely-used methods based on probabilistic modeling have drawbacks in terms of consistency from multiple runs and empirical convergence. Furthermore, due to the complicatedness in the formulation and the algorithm, LDA cannot easily incorporate various types of user feedback. To tackle this problem, we propose a reliable and flexible visual analytics system for topic modeling called UTOPIAN (User-driven Topic modeling based on Interactive Nonnegative Matrix Factorization). Centered around its semi-supervised formulation, UTOPIAN enables users to interact with the topic modeling method and steer the result in a user-driven manner. We demonstrate the capability of UTOPIAN via several usage scenarios with real-world document corpuses such as InfoVis/VAST paper data set and product review data sets. PMID:24051765

  15. Secondary Neutron Production from Space Radiation Interactions: Advances in Model and Experimental Data Base Development

    Science.gov (United States)

    Heilbronn, Lawrence H.; Townsend, Lawrence W.; Braley, G. Scott; Iwata, Yoshiyuki; Iwase, Hiroshi; Nakamura, Takashi; Ronningen, Reginald M.; Cucinotta, Francis A.

    2003-01-01

    For humans engaged in long-duration missions in deep space or near-Earth orbit, the risk from exposure to galactic and solar cosmic rays is an important factor in the design of spacecraft, spacesuits, and planetary bases. As cosmic rays are transported through shielding materials and human tissue components, a secondary radiation field is produced. Neutrons are an important component of that secondary field, especially in thickly-shielded environments. Calculations predict that 50% of the dose-equivalent in a lunar or Martian base comes from neutrons, and a recent workshop held at the Johnson Space Center concluded that as much as 30% of the dose in the International Space Station may come from secondary neutrons. Accelerator facilities provide a means for measuring the effectiveness of various materials in their ability to limit neutron production, using beams and energies that are present in cosmic radiation. The nearly limitless range of beams, energies, and target materials that are present in space, however, means that accelerator-based experiments will not provide a complete database of cross sections and thick-target yields that are necessary to plan and design long-duration missions. As such, accurate nuclear models of neutron production are needed, as well as data sets that can be used to compare with, and verify, the predictions from such models. Improvements in a model of secondary neutron production from heavy-ion interactions are presented here, along with the results from recent accelerator-based measurements of neutron-production cross sections. An analytical knockout-ablation model capable of predicting neutron production from high-energy hadron-hadron interactions (both nucleon-nucleus and nucleus-nucleus collisions) has been previously developed. In the knockout stage, the collision between two nuclei result in the emission of one or more nucleons from the projectile and/or target. The resulting projectile and target remnants, referred to as

  16. Gene-Gene and Gene-Environment Interactions in HIV-Associated Nephropathy: a Focus on the MYH9 Nephropathy Susceptibility Gene

    OpenAIRE

    Núñez, Marina; Saran, Anita M.; Freedman, Barry I.

    2010-01-01

    Human immunodeficiency virus-associated nephropathy (HIVAN) is a leading cause of end-stage renal disease in African Americans. The HIV-1 virus infects podocytes, cells integral to formation of the glomerular filtration barrier, often leading to focal segmental glomerulosclerosis. HIVAN is typically a complication of late-stage HIV infection, associated with low CD4 cell counts and elevated serum HIV RNA levels. Highly active antiretroviral therapy (HAART) is partially protective and has alte...

  17. Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

    OpenAIRE

    Kool, J.; N. Jonker; Irth, H.; Niessen, W.M.A.

    2011-01-01

    This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of prote...

  18. Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences

    OpenAIRE

    Park Yungki

    2009-01-01

    Abstract Background Protein-protein interactions underlie many important biological processes. Computational prediction methods can nicely complement experimental approaches for identifying protein-protein interactions. Recently, a unique category of sequence-based prediction methods has been put forward - unique in the sense that it does not require homologous protein sequences. This enables it to be universally applicable to all protein sequences unlike many of previous sequence-based predi...

  19. Struct2Net: a web service to predict protein–protein interactions using a structure-based approach

    OpenAIRE

    Singh, Rohit; Park, Daniel; Xu, Jinbo; Hosur, Raghavendra; Berger, Bonnie

    2010-01-01

    Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein–protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate. We believe that Struct2Net is the first community-wide resource to provide structure-based PPI predictions that go beyond homology modeling...

  20. THE EFFECTS OF DIFFERENT INTERACTION TYPES IN WEB-BASED TEACHING ON THE ATTITUDES OF LEARNERS TOWARDS WEB BASED TEACHING AND INTERNET

    Directory of Open Access Journals (Sweden)

    Ozgen KORKMAZ

    2013-04-01

    Full Text Available It might be said that attitudes impact success directly in web-based teaching and timely and appropriate fulfillment of learners’ expectations bear utmost significance for their success. From this perspective a properly designed web supported teaching application can provide positive contribution as well to learners’ attitudes towards web supported teaching and internet. Based on this premise, the objective of present research is to explore the effects of different interaction types in web-based teaching setting on the attitudes of learners towards web-based teaching and internet. An experimental pattern with pretest-posttest control group was used in the study. Study group of research consists of 77 students. Research data have been compiled via Attitude towards Internet Scale (α=0,77 and Attitude towards Web-based Learning Scale (α=0,86. In one of the experimental groups, synchronous web-based training interaction and in the other group asynchronous web-based training interaction and in the control group learner-content only interaction has been provided. In data analysis; standard deviation, arithmetical means, one-way variance analysis and LSD tests have been employed. As a result: Web-based training applications with synchronous interaction, compared to web-based training application with learner-content only interaction, have significantly higher contribution on learners’ attitudes towards web-based teaching. In Web-based teaching settings different types of interaction have no effect on learners’ attitudes towards internet which may be attributed to the fact that learners’ attitudes towards internet were already in quite high levels prior to the procedure.