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Sample records for based gene-gene interactions

  1. A gene-based information gain method for detecting gene-gene interactions in case-control studies.

    Science.gov (United States)

    Li, Jin; Huang, Dongli; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Jiang, Yongshuai; Lv, Hongchao; Wang, Limei

    2015-11-01

    Currently, most methods for detecting gene-gene interactions (GGIs) in genome-wide association studies are divided into SNP-based methods and gene-based methods. Generally, the gene-based methods can be more powerful than SNP-based methods. Some gene-based entropy methods can only capture the linear relationship between genes. We therefore proposed a nonparametric gene-based information gain method (GBIGM) that can capture both linear relationship and nonlinear correlation between genes. Through simulation with different odds ratio, sample size and prevalence rate, GBIGM was shown to be valid and more powerful than classic KCCU method and SNP-based entropy method. In the analysis of data from 17 genes on rheumatoid arthritis, GBIGM was more effective than the other two methods as it obtains fewer significant results, which was important for biological verification. Therefore, GBIGM is a suitable and powerful tool for detecting GGIs in case-control studies.

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

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    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

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

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    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.

  4. A genetic ensemble approach for gene-gene interaction identification

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    Ho Joshua WK

    2010-10-01

    Full Text Available Abstract Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA and an ensemble of classifiers (called genetic ensemble. Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR and is slightly better than Polymorphism Interaction Analysis (PIA, which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of

  5. 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...

  6. Testing for gene-gene interaction with AMMI models.

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    Barhdadi, Amina; Dubé, Marie-Pierre

    2010-01-01

    Studies have shown that many common diseases are influenced by multiple genes and their interactions. There is currently a strong interest in testing for association between combinations of these genes and disease, in particular because genes that affect the risk of disease only in the presence of another genetic variant may not be detected in marginal analysis. In this paper we propose the use of additive main effect and multiplicative interaction (AMMI) models to detect and to quantify gene-gene interaction effects for a quantitative trait. The objective of the present research is to demonstrate the practical advantages of these models to describe complex interaction between two unlinked loci. Although gene-gene interactions have often been defined as a deviance from additive genetic effects, the residual term has generally not been appropriately treated. The AMMI models allow for the analysis of a two way factorial data structure and combine the analysis of variance of the two main genotype effects with a principal component analysis of the residual multiplicative interaction. The AMMI models for gene-gene interaction presented here allow for the testing of non additivity between the two loci, and also describe how their interaction structure fits the existing non-additivity. Moreover, these models can be used to identify the specific two genotypes combinations that contribute to the significant gene-gene interaction. We describe the use of the biplot to display the structure of the interaction and evaluate the performance of the AMMI and the special cases of the AMMI previously described by Tukey and Mandel with simulated data sets. Our simulated study showed that the AMMI model is as powerful as general linear models when the interaction is not modeled in the presence of marginal effects. However, in the presence of pure epitasis, i.e. in the absence of marginal effects, the AMMI method was not found to be superior to other tested regression methods.

  7. Characterizing gene-gene interactions in a statistical epistasis network of twelve candidate genes for obesity

    OpenAIRE

    Rishika; Hu, Ting; Moore, Jason H.; Gilbert-Diamond, Diane

    2015-01-01

    Background Recent findings have reemphasized the importance of epistasis, or gene-gene interactions, as a contributing factor to the unexplained heritability of obesity. Network-based methods such as statistical epistasis networks (SEN), present an intuitive framework to address the computational challenge of studying pairwise interactions between thousands of genetic variants. In this study, we aimed to analyze pairwise interactions that are associated with Body Mass Index (BMI) between SNPs...

  8. Gene-gene and gene-environmental interactions of childhood asthma: a multifactor dimension reduction approach.

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    Ming-Wei Su

    Full Text Available BACKGROUND: The importance of gene-gene and gene-environment interactions on asthma is well documented in literature, but a systematic analysis on the interaction between various genetic and environmental factors is still lacking. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a population-based, case-control study comprised of seventh-grade children from 14 Taiwanese communities. A total of 235 asthmatic cases and 1,310 non-asthmatic controls were selected for DNA collection and genotyping. We examined the gene-gene and gene-environment interactions between 17 single-nucleotide polymorphisms in antioxidative, inflammatory and obesity-related genes, and childhood asthma. Environmental exposures and disease status were obtained from parental questionnaires. The model-free and non-parametrical multifactor dimensionality reduction (MDR method was used for the analysis. A three-way gene-gene interaction was elucidated between the gene coding glutathione S-transferase P (GSTP1, the gene coding interleukin-4 receptor alpha chain (IL4Ra and the gene coding insulin induced gene 2 (INSIG2 on the risk of lifetime asthma. The testing-balanced accuracy on asthma was 57.83% with a cross-validation consistency of 10 out of 10. The interaction of preterm birth and indoor dampness had the highest training-balanced accuracy at 59.09%. Indoor dampness also interacted with many genes, including IL13, beta-2 adrenergic receptor (ADRB2, signal transducer and activator of transcription 6 (STAT6. We also used likelihood ratio tests for interaction and chi-square tests to validate our results and all tests showed statistical significance. CONCLUSIONS/SIGNIFICANCE: The results of this study suggest that GSTP1, INSIG2 and IL4Ra may influence the lifetime asthma susceptibility through gene-gene interactions in schoolchildren. Home dampness combined with each one of the genes STAT6, IL13 and ADRB2 could raise the asthma risk.

  9. Extracting gene-gene interactions through curve fitting.

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    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

  10. Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis

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    Ueki Masao

    2012-05-01

    Full Text Available Abstract Background Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Individual hypothesis testing for SNP-SNP pairs as in common genome-wide association study (GWAS however involves difficulty in setting overall p-value due to complicated correlation structure, namely, the multiple testing problem that causes unacceptable false negative results. A large number of SNP-SNP pairs than sample size, so-called the large p small n problem, precludes simultaneous analysis using multiple regression. The method that overcomes above issues is thus needed. Results We adopt an up-to-date method for ultrahigh-dimensional variable selection termed the sure independence screening (SIS for appropriate handling of numerous number of SNP-SNP interactions by including them as predictor variables in logistic regression. We propose ranking strategy using promising dummy coding methods and following variable selection procedure in the SIS method suitably modified for gene-gene interaction analysis. We also implemented the procedures in a software program, EPISIS, using the cost-effective GPGPU (General-purpose computing on graphics processing units technology. EPISIS can complete exhaustive search for SNP-SNP interactions in standard GWAS dataset within several hours. The proposed method works successfully in simulation experiments and in application to real WTCCC (Wellcome Trust Case–control Consortium data. Conclusions Based on the machine-learning principle, the proposed method gives powerful and flexible genome-wide search for various patterns of gene-gene interaction.

  11. 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

  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.

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    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.

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    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. 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...

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

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    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

  18. 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...

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

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    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.

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

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    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

  1. 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.

  2. Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

    NARCIS (Netherlands)

    De, Rishika; Verma, Shefali S; Drenos, Fotios; Holzinger, Emily R; Holmes, Michael V; Hall, Molly A; Crosslin, David R; Carrell, David S; Hakonarson, Hakon; Jarvik, Gail; Larson, Eric; Pacheco, Jennifer A; Rasmussen-Torvik, Laura J; Moore, Carrie B; Asselbergs, Folkert W; Moore, Jason H; Ritchie, Marylyn D; Keating, Brendan J; Gilbert-Diamond, Diane

    2015-01-01

    BACKGROUND: Despite heritability estimates of 40-70 % for obesity, less than 2 % of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions are a plausible source to explain portions of the missing heritability of BMI

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

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    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.

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

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    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

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

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    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

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

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    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

  7. 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.

  8. 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...

  9. Gene-gene interaction and RNA splicing profiles of MAP2K4 gene in rheumatoid arthritis.

    Science.gov (United States)

    Shchetynsky, Klementy; Protsyuk, Darya; Ronninger, Marcus; Diaz-Gallo, Lina-Marcela; Klareskog, Lars; Padyukov, Leonid

    2015-05-01

    We performed gene-gene interaction analysis, with HLA-DRB1 shared epitope (SE) alleles for 195 SNPs within immunologically important MAP2K, MAP3K and MAP4K gene families, in 2010 rheumatoid arthritis (RA) patients and 2280 healthy controls. We found a significant statistical interaction for rs10468473 with SE alleles in autoantibody-positive RA. Individuals heterozygous for rs10468473 demonstrated higher expression of total MAP2K4 mRNA in blood, compared to A-allele homozygous. We discovered a novel, putatively translated, "cassette exon" RNA splice form of MAP2K4, differentially expressed in peripheral blood mononuclear cells from 88 RA cases and controls. Within the group of RA patients, we observed a correlation of MAP2K4 isoform expression with carried SE alleles, autoantibody, and rheumatoid factor profiles. TNF-dependent modulation of isoform expression pattern was detected in the Jurkat cell line. Our data suggest a genetic interaction between MAP2K4 and HLA-DRB1, and the importance of rs10468473 and MAP2K4 splice variants in the development of autoantibody-positive RA.

  10. 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...

  11. 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/.

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

    Science.gov (United States)

    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

    2012-11-01

    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 carrying the susceptible homozygous genotype were, on average, 7.2 months younger at diagnosis than those carrying the protective homozygous genotypes. In addition to protein tyrosine phosphatase nonreceptor type 22 (PTPN22), evidence of statistical interaction between HLA class II genotypes and rs3087243 at cytotoxic T-lymphocyte antigen 4 (CTLA4)/2q33.2 was obtained (P = 7.90 × 10⁻⁵). No evidence of differential risk by sex was obtained at any loci (P ≥ 0.01). Statistical interaction effects can be detected in type 1 diabetes although they provide a relatively small contribution to our understanding of the familial clustering of the disease. PMID:22891215

  13. 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

  14. 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.

  15. 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;

    2012-01-01

    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...... 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...

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

    DEFF Research Database (Denmark)

    Kopp, Tine Iskov

    single-gene mutations due to their low frequency in the general population. Overall, the contribution from hereditary factors to the causation of BC is only 27%, whereas genetics contributes to 35% and 42% for CRC and PC, respectively. Additionally, immigrations studies point to environmental factors...... 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......, such as alcohol consumption, smoking, obesity, inflammation and high meat intake; whereas other factors protect against cancer, such as high intake of dietary fibre, fruits and vegetables, and physical activity. Investigating the interactions between genetic variations and environmental factors, such as dietary...

  17. 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.

  18. 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

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

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    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

  20. 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

  1. CYP1A1, GCLC, AGT, AGTR1 gene-gene interactions in community-acquired pneumonia pulmonary complications.

    Science.gov (United States)

    Salnikova, Lyubov E; Smelaya, Tamara V; Golubev, Arkadiy M; Rubanovich, Alexander V; Moroz, Viktor V

    2013-11-01

    This study was conducted to establish the possible contribution of functional gene polymorphisms in detoxification/oxidative stress and vascular remodeling pathways to community-acquired pneumonia (CAP) susceptibility in the case-control study (350 CAP patients, 432 control subjects) and to predisposition to the development of CAP complications in the prospective study. All subjects were genotyped for 16 polymorphic variants in the 14 genes of xenobiotics detoxification CYP1A1, AhR, GSTM1, GSTT1, ABCB1, redox-status SOD2, CAT, GCLC, and vascular homeostasis ACE, AGT, AGTR1, NOS3, MTHFR, VEGFα. Risk of pulmonary complications (PC) in the single locus analysis was associated with CYP1A1, GCLC and AGTR1 genes. Extra PC (toxic shock syndrome and myocarditis) were not associated with these genes. We evaluated gene-gene interactions using multi-factor dimensionality reduction, and cumulative gene risk score approaches. The final model which included >5 risk alleles in the CYP1A1 (rs2606345, rs4646903, rs1048943), GCLC, AGT, and AGTR1 genes was associated with pleuritis, empyema, acute respiratory distress syndrome, all PC and acute respiratory failure (ARF). We considered CYP1A1, GCLC, AGT, AGTR1 gene set using Set Distiller mode implemented in GeneDecks for discovering gene-set relations via the degree of sharing descriptors within a given gene set. N-acetylcysteine and oxygen were defined by Set Distiller as the best descriptors for the gene set associated in the present study with PC and ARF. Results of the study are in line with literature data and suggest that genetically determined oxidative stress exacerbation may contribute to the progression of lung inflammation.

  2. Gene-gene interaction and functional impact of polymorphisms on innate immune genes in controlling Plasmodium falciparum blood infection level.

    Directory of Open Access Journals (Sweden)

    Madhumita Basu

    Full Text Available Genetic variations in toll-like receptors and cytokine genes of the innate immune pathways have been implicated in controlling parasite growth and the pathogenesis of Plasmodium falciparum mediated malaria. We previously published genetic association of TLR4 non-synonymous and TNF-α promoter polymorphisms with P.falciparum blood infection level and here we extend the study considerably by (i investigating genetic dependence of parasite-load on interleukin-12B polymorphisms, (ii reconstructing gene-gene interactions among candidate TLRs and cytokine loci, (iii exploring genetic and functional impact of epistatic models and (iv providing mechanistic insights into functionality of disease-associated regulatory polymorphisms. Our data revealed that carriage of AA (P = 0.0001 and AC (P = 0.01 genotypes of IL12B 3'UTR polymorphism was associated with a significant increase of mean log-parasitemia relative to rare homozygous genotype CC. Presence of IL12B+1188 polymorphism in five of six multifactor models reinforced its strong genetic impact on malaria phenotype. Elevation of genetic risk in two-component models compared to the corresponding single locus and reduction of IL12B (2.2 fold and lymphotoxin-α (1.7 fold expressions in patients'peripheral-blood-mononuclear-cells under TLR4Thr399Ile risk genotype background substantiated the role of Multifactor Dimensionality Reduction derived models. Marked reduction of promoter activity of TNF-α risk haplotype (C-C-G-G compared to wild-type haplotype (T-C-G-G with (84% and without (78% LPS stimulation and the loss of binding of transcription factors detected in-silico supported a causal role of TNF-1031. Significantly lower expression of IL12B+1188 AA (5 fold and AC (9 fold genotypes compared to CC and under-representation (P = 0.0048 of allele A in transcripts of patients' PBMCs suggested an Allele-Expression-Imbalance. Allele (A+1188C dependent differential stability (2 fold of IL12B-transcripts upon

  3. 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.

  4. 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.

  5. 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,

  6. 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.

  7. A systematic gene-gene and gene-environment interaction analysis of DNA repair genes XRCC1, XRCC2, XRCC3, XRCC4, and oral cancer risk.

    Science.gov (United States)

    Yang, Cheng-Hong; Lin, Yu-Da; Yen, Ching-Yui; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2015-04-01

    Oral cancer is the sixth most common cancer worldwide with a high mortality rate. Biomarkers that anticipate susceptibility, prognosis, or response to treatments are much needed. Oral cancer is a polygenic disease involving complex interactions among genetic and environmental factors, which require multifaceted analyses. Here, we examined in a dataset of 103 oral cancer cases and 98 controls from Taiwan the association between oral cancer risk and the DNA repair genes X-ray repair cross-complementing group (XRCCs) 1-4, and the environmental factors of smoking, alcohol drinking, and betel quid (BQ) chewing. We employed logistic regression, multifactor dimensionality reduction (MDR), and hierarchical interaction graphs for analyzing gene-gene (G×G) and gene-environment (G×E) interactions. We identified a significantly elevated risk of the XRCC2 rs2040639 heterozygous variant among smokers [adjusted odds ratio (OR) 3.7, 95% confidence interval (CI)=1.1-12.1] and alcohol drinkers [adjusted OR=5.7, 95% CI=1.4-23.2]. The best two-factor based G×G interaction of oral cancer included the XRCC1 rs1799782 and XRCC2 rs2040639 [OR=3.13, 95% CI=1.66-6.13]. For the G×E interaction, the estimated OR of oral cancer for two (drinking-BQ chewing), three (XRCC1-XRCC2-BQ chewing), four (XRCC1-XRCC2-age-BQ chewing), and five factors (XRCC1-XRCC2-age-drinking-BQ chewing) were 32.9 [95% CI=14.1-76.9], 31.0 [95% CI=14.0-64.7], 49.8 [95% CI=21.0-117.7] and 82.9 [95% CI=31.0-221.5], respectively. Taken together, the genotypes of XRCC1 rs1799782 and XRCC2 rs2040639 DNA repair genes appear to be significantly associated with oral cancer. These were enhanced by exposure to certain environmental factors. The observations presented here warrant further research in larger study samples to examine their relevance for routine clinical care in oncology.

  8. 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.

  9. Multivariate dimensionality reduction approaches to identify gene-gene and gene-environment interactions underlying multiple complex traits.

    Directory of Open Access Journals (Sweden)

    Hai-Ming Xu

    Full Text Available The elusive but ubiquitous multifactor interactions represent a stumbling block that urgently needs to be removed in searching for determinants involved in human complex diseases. The dimensionality reduction approaches are a promising tool for this task. Many complex diseases exhibit composite syndromes required to be measured in a cluster of clinical traits with varying correlations and/or are inherently longitudinal in nature (changing over time and measured dynamically at multiple time points. A multivariate approach for detecting interactions is thus greatly needed on the purposes of handling a multifaceted phenotype and longitudinal data, as well as improving statistical power for multiple significance testing via a two-stage testing procedure that involves a multivariate analysis for grouped phenotypes followed by univariate analysis for the phenotypes in the significant group(s. In this article, we propose a multivariate extension of generalized multifactor dimensionality reduction (GMDR based on multivariate generalized linear, multivariate quasi-likelihood and generalized estimating equations models. Simulations and real data analysis for the cohort from the Study of Addiction: Genetics and Environment are performed to investigate the properties and performance of the proposed method, as compared with the univariate method. The results suggest that the proposed multivariate GMDR substantially boosts statistical power.

  10. 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

  11. 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.

  12. Gene-gene interactions in psoriasis%银屑病基因-基因交互作用研究进展

    Institute of Scientific and Technical Information of China (English)

    江龙; 尹先勇; 杨森

    2014-01-01

    In recent years,significant breakthroughs have been made in the search for psoriasis susceptibility genes through genome-wide association studies (GWAS),and positive evidences have also been established for gene-gene interactions in the pathogenesis of psoriasis,both of which greatly increase the understanding of psoriasis pathogenesis.Moreover,these interactions mainly occur in the major histocompatibility complex (MHC) region and interleukin-23 (IL-23)/T helper 17 (Th17) pathway.The MHC region,the first susceptible region identified for psoriasis,is thought to be the most important region in the pathogenesis of psoriasis.Evidences have been found for the interactions between HLA-Cw6 and various genes including the endoplasmic reticulum aminopeptidase I (ERAP1) gene,cystatin A (CSTA) gene,LCE gene cluster,chromosome 19p13 region (PSORS6),etc.The IL-23/Th17 pathway is closely associated with the pathogenesis of several chronic inflammatory diseases,and multiple genes in this pathway are found to interact mutually in the initiation of psoriasis.%全基因组关联研究发现,对基因-基因交互作用在银屑病发病中的研究取得了积极进展,增进了对银屑病遗传学发病机制的认识.目前,银屑病基因-基因交互作用主要集中在主要组织相容性复合体易感区域和IL23/Th17信号通路.主要组织相容性复合体区域是最早被发现而且是银屑病发病机制中最重要的易感区域.研究表明,其与内质网氨基肽酶1(ERAP1)基因、抑半胱氨酸蛋白酶蛋白A(CSTA)基因、LCE基因簇及染色体19 p13区域(PSORS6)等存在相互作用.白介素23/Th17是一个与慢性炎症性疾病发病密切相关的重要通路,研究发现其中的多个基因在银屑病发病中存在交互作用.

  13. 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...

  14. 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

  15. Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models

    Science.gov (United States)

    Leaf shape traits have long been a focus of many disciplines, but searching for complex genetic and environmental interactive mechanisms regulating leaf shape variation has not yet been well developed. The question of the respective roles of gene and environment and how they interplay to modulate l...

  16. 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

  17. Antioxidant Defense Enzyme Genes and Asthma Susceptibility: Gender-Specific Effects and Heterogeneity in Gene-Gene Interactions between Pathogenetic Variants of the Disease

    Directory of Open Access Journals (Sweden)

    Alexey V. Polonikov

    2014-01-01

    Full Text Available Oxidative stress resulting from an increased amount of reactive oxygen species and an imbalance between oxidants and antioxidants plays an important role in the pathogenesis of asthma. The present study tested the hypothesis that genetic susceptibility to allergic and nonallergic variants of asthma is determined by complex interactions between genes encoding antioxidant defense enzymes (ADE. We carried out a comprehensive analysis of the associations between adult asthma and 46 single nucleotide polymorphisms of 34 ADE genes and 12 other candidate genes of asthma in Russian population using set association analysis and multifactor dimensionality reduction approaches. We found for the first time epistatic interactions between ADE genes underlying asthma susceptibility and the genetic heterogeneity between allergic and nonallergic variants of the disease. We identified GSR (glutathione reductase and PON2 (paraoxonase 2 as novel candidate genes for asthma susceptibility. We observed gender-specific effects of ADE genes on the risk of asthma. The results of the study demonstrate complexity and diversity of interactions between genes involved in oxidative stress underlying susceptibility to allergic and nonallergic asthma.

  18. Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value.

    Directory of Open Access Journals (Sweden)

    Stéphane Cauchi

    Full Text Available BACKGROUND: Recently, several Genome Wide Association (GWA studies in populations of European descent have identified and validated novel single nucleotide polymorphisms (SNPs, highly associated with type 2 diabetes (T2D. Our aims were to validate these markers in other European and non-European populations, then to assess their combined effect in a large French study comparing T2D and normal glucose tolerant (NGT individuals. METHODOLOGY/PRINCIPAL FINDINGS: In the same French population analyzed in our previous GWA study (3,295 T2D and 3,595 NGT, strong associations with T2D were found for CDKAL1 (OR(rs7756992 = 1.30[1.19-1.42], P = 2.3x10(-9, CDKN2A/2B (OR(rs10811661 = 0.74[0.66-0.82], P = 3.5x10(-8 and more modestly for IGFBP2 (OR(rs1470579 = 1.17[1.07-1.27], P = 0.0003 SNPs. These results were replicated in both Israeli Ashkenazi (577 T2D and 552 NGT and Austrian (504 T2D and 753 NGT populations (except for CDKAL1 but not in the Moroccan population (521 T2D and 423 NGT. In the overall group of French subjects (4,232 T2D and 4,595 NGT, IGFBP2 and CXCR4 synergistically interacted with (LOC38776, SLC30A8, HHEX and (NGN3, CDKN2A/2B, respectively, encoding for proteins presumably regulating pancreatic endocrine cell development and function. The T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24. With an area under the ROC curve of 0.86, only 15 novel loci were necessary to discriminate French individuals susceptible to develop T2D. CONCLUSIONS/SIGNIFICANCE: In addition to TCF7L2, SLC30A8 and HHEX, initially identified by the French GWA scan, CDKAL1, IGFBP2 and CDKN2A/2B strongly associate with T2D in French individuals, and mostly in populations of Central European descent but not in Moroccan subjects. Genes expressed in the pancreas interact together and their

  19. 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

  20. 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.

  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. Family-based study of HTR2A in suicide attempts: observed gene, gene × environment and parent-of-origin associations.

    Science.gov (United States)

    Ben-Efraim, Y J; Wasserman, D; Wasserman, J; Sokolowski, M

    2013-07-01

    While suicidal behavior is frequently accompanied by serotonergic system alterations, specific associations with genetic variation in the serotonin 2A receptor (HTR2A) gene have been inconsistent. Using a family-based study design of 660 offspring who have made a suicide attempt (SA) and both parents, we conducted an association and linkage analysis using single-nucleotide polymorphisms (SNPs) with extensive gene coverage, and included the study of parent-of-origin (POE) and gene-environment interaction (G × E), also using previously unstudied exposures. The main finding was a G × E between the exon 1 SNP rs6313 and exposure to cumulative types of lifetime stressful life events (SLEs), driven by overtransmission of CT and undertransmission of TT, both in relation to other genotypes. Further exploratory analysis revealed a significant POE in this G × E in female subjects, which followed a polar overdominant inheritance pattern. In addition, rs6310 and rs6305 were found to significantly associate with SA in the total sample. A G × E in female subjects (rs7322347 × physical assault in childhood/adolescence) confirmed features of a previously observed association with SA. Other potentially interesting nominally significant findings were observed, but like the G × E of rs7322347 did not pass a false-discovery rate cutoff. Taken together, this study found multiple associations of HTR2A SNPs on SA, with strongest statistical evidence for a G × E involving rs6313, and further suggested the importance of taking into account different inheritance patterns and G × Es with regard to HTR2A.

  3. 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

  4. Application of the interaction models between the polymorphism(s) of metabolic gene(s) and environmental exposure%代谢酶基因多态性与环境暴露交互作用的分析方法及其应用

    Institute of Scientific and Technical Information of China (English)

    沈靖; 王润田; 徐希平

    2001-01-01

    目的 以肿瘤易感基因谷胱苷肽-S-转硫酶(GST)M1缺失基因型为例,说明基因与环境暴露交互作用的分析方法以及应用。方法 采用社区为基础的病例对照研究方法,代谢酶基因多态性的检测用PCR技术,资料分析用多因素logistic回归模型。研究对象为1997年1月至1998年12月经扬中市人民医院确诊,肠型胃癌病例112例,以同期该地无上消化道肿瘤的“健康”人群为对照,共675例。结果 调整混杂因素后,GST M1缺失基因型与既往吸烟史的交互作用系数为3.38,OReg值达8.40,有极显著意义,为4型交互作用中的超相乘模型;GST M1缺失基因型与吸烟量的交互作用呈高暴露-基因效应,交互作用系数分别为0.995、2.085和2.157,即随着暴露剂量增加,交互作用强度也逐渐增加;与饮酒量呈低暴露-基因效应,交互作用系数分别为1.01和0.97,交互作用强度随暴露剂量增加而逐渐降低。结论 基于logistic模型的分析方法,可用于评价基因-环境之间的交互作用,以及剂量反应关系的暴露基因效应。%Objective Taking GST M1 as an example to introduce analytic method of interaction models between the polymorphism(s) of metabolic gene(s) and environmental exposure in stomach cancer susceptibility. Methods Using community-based case-control design, combined with molecular biological techniques (PCR) and multiple variables logistic regression models, we analyzed 112 intestinal types of stomach cancer cases with endoscopy and pathology diagnosis in the Yangzhong City Hospital during January 1997 and December 1998. A total of 675 controls were selected from persons who had no history of digestive system cancers. Results After adjustment of confounding variables with both GST M1 null genotype and history of ever tobacco smoking, the results showed a significant types of 4 gene-environment interaction. Interaction index (γ) value

  5. 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…

  6. Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium.

    Science.gov (United States)

    Verma, Shefali Setia; Cooke Bailey, Jessica N; Lucas, Anastasia; Bradford, Yuki; Linneman, James G; Hauser, Michael A; Pasquale, Louis R; Peissig, Peggy L; Brilliant, Murray H; McCarty, Catherine A; Haines, Jonathan L; Wiggs, Janey L; Vrabec, Tamara R; Tromp, Gerard; Ritchie, Marylyn D

    2016-09-01

    Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects of variants across the genome, it is believed that gene-gene interactions can help elucidate part of the missing heritability by allowing for the test of interactions between genetic variants to mimic the complex nature of biology. To explain the etiology of glaucoma, we first performed a genome-wide association study (GWAS) on glaucoma case-control samples obtained from electronic medical records (EMR) to establish the utility of EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype. Our findings from GWAS suggest consistent evidence of several known associations in POAG. We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value value value <0.001) among the top 17 gene-gene models identified in the discovery phase. Variants from gene-gene interaction analysis that we found to be associated with POAG explain 3.5% of additional genetic variance in eMERGE dataset above what is explained by the SNPs in genes that are replicated from previous GWAS studies (which was only 2.1% variance explained in eMERGE dataset); in the NEIGHBOR dataset, adding replicated SNPs from gene-gene interaction analysis explain 3.4% of total variance whereas GWAS SNPs alone explain only 2.8% of variance. Exploring gene-gene interactions may provide additional insights into many complex traits when explored in properly designed and powered association studies. PMID:27623284

  7. 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.

  8. 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...

  9. Immersion in Movement-Based Interaction

    Science.gov (United States)

    Pasch, Marco; Bianchi-Berthouze, Nadia; van Dijk, Betsy; Nijholt, Anton

    The phenomenon of immersing oneself into virtual environments has been established widely. Yet to date (to our best knowledge) the physical dimension has been neglected in studies investigating immersion in Human-Computer Interaction (HCI). In movement-based interaction the user controls the interface via body movements, e.g. direct manipulation of screen objects via gestures or using a handheld controller as a virtual tennis racket. It has been shown that physical activity affects arousal and that movement-based controllers can facilitate engagement in the context of video games. This paper aims at identifying movement features that influence immersion. We first give a brief survey on immersion and movement-based interfaces. Then, we report results from an interview study that investigates how users experience their body movements when interacting with movement-based interfaces. Based on the interviews, we identify four movement-specific features. We recommend them as candidates for further investigation.

  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. 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

  14. 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.

  15. Interactive Reliability-Based Optimal Design

    DEFF Research Database (Denmark)

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

    1994-01-01

    tasks, namely finite element analyses, sensitivity analyses, reliability analyses and application of an optimization algorithm. In the paper it is shown how these four tasks can be linked effectively and how existing information on design variables, Lagrange multipliers and the Hessian matrix can......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...... be used in interactive optimization....

  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. 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

  19. A new clinical evidence-based gene-environment interaction model of depression.

    Science.gov (United States)

    Bagdy, Gyorgy; Juhasz, Gabriella; Gonda, Xenia

    2012-12-01

    In our current understanding of mood disorders, the role of genes is diverse including the mediation of the effects of provoking and protective factors. Different or partially overlapping gene sets play a major role in the development of personality traits including also affective temperaments, in the mediation of the effects of environmental factors, and in the interaction of these elements in the development of depression. Certain genes are associated with personality traits and temperaments including e.g., neuroticism, impulsivity, openness, rumination and extroversion. Environmental factors consist of external (early and provoking life events, seasonal changes, social support etc.) and internal factors (hormones, biological rhythm generators, comorbid disorders etc). Some of these environmental factors, such as early life events and some prenatal events directly influence the development of personality traits and temperaments. In the NEWMOOD cohort polymorphisms of the genes of the serotonin transporter, 5-HT1A, 5-HT1B and 5-HT2A and endocannabinoid CB1 receptors, tryptophan hydroxylase, CREB1, BDNF and GIRK provide evidence for the involvement of these genes in the development of depression. Based on their role in this process they could be assigned to different gene sets. The role of certain genes, such as promoter polymorphisms of the serotonin transporter (5-HTTLPR) and CB1 receptor has been shown in more than one of the above factors. Furthermore, gene-gene interactions of these promoters associated with anxiety suggest the application of these polymorphisms in personalized medicine. In this review we introduce a new model including environmental factors, genes, trait and temperament markers based on human genetic studies.

  20. 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.

  1. Interactive physically-based sound simulation

    Science.gov (United States)

    Raghuvanshi, Nikunj

    The realization of interactive, immersive virtual worlds requires the ability to present a realistic audio experience that convincingly compliments their visual rendering. Physical simulation is a natural way to achieve such realism, enabling deeply immersive virtual worlds. However, physically-based sound simulation is very computationally expensive owing to the high-frequency, transient oscillations underlying audible sounds. The increasing computational power of desktop computers has served to reduce the gap between required and available computation, and it has become possible to bridge this gap further by using a combination of algorithmic improvements that exploit the physical, as well as perceptual properties of audible sounds. My thesis is a step in this direction. My dissertation concentrates on developing real-time techniques for both sub-problems of sound simulation: synthesis and propagation. Sound synthesis is concerned with generating the sounds produced by objects due to elastic surface vibrations upon interaction with the environment, such as collisions. I present novel techniques that exploit human auditory perception to simulate scenes with hundreds of sounding objects undergoing impact and rolling in real time. Sound propagation is the complementary problem of modeling the high-order scattering and diffraction of sound in an environment as it travels from source to listener. I discuss my work on a novel numerical acoustic simulator (ARD) that is hundred times faster and consumes ten times less memory than a high-accuracy finite-difference technique, allowing acoustic simulations on previously-intractable spaces, such as a cathedral, on a desktop computer. Lastly, I present my work on interactive sound propagation that leverages my ARD simulator to render the acoustics of arbitrary static scenes for multiple moving sources and listener in real time, while accounting for scene-dependent effects such as low-pass filtering and smooth attenuation

  2. 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…

  3. 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

  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. 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....

  7. 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...

  8. Designing Software-Based Interactive Installations

    DEFF Research Database (Denmark)

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

    2014-01-01

    considers the development of interactive installations for immersive experiences with emphasis on the special design challenges they present. How. The approach described includes four phases: exploration, design, construction, and exhibition. The aim of the exploration is to clarify the general behavior...... architecture as well as esthetic experience, artistic expression, and leisure aspects into focus. The approach presented here has this intended purpose. Where. Building on experience from conventional software development and with inspiration from interaction design and creative programming, this chapter...... of the installation using tools like sketching or storyboarding. The design involves a clarification of available and appropriate building blocks, as well as the linking of these blocks to provide an architectural framework comprising the intended external behavior. The construction phase takes a component...

  9. Contributions of renin-angiotensin system-related gene interactions to obesity in a Chinese population.

    Directory of Open Access Journals (Sweden)

    Jian-Bo Zhou

    Full Text Available BACKGROUND: Gene-gene interactions may be partly responsible for complex traits such as obesity. Increasing evidence suggests that the renin-angiotensin system (RAS contributes to the etiology of obesity. How the epistasis of genes in the RAS contributes to obesity is still under research. We aim to evaluate the contribution of RAS-related gene interactions to a predisposition of obesity in a Chinese population. METHODOLOGY AND PRINCIPAL FINDINGS: We selected six single nucleotide polymorphisms (SNPs located in angiotensin (AGT, angiotensin converting enzyme (ACE, angiotensin type 1 receptor (AGTR1, MAS1, nitric oxide synthase 3 (NOS3 and the bradykinin B2 receptor gene (BDKRB2, and genotyped them in 324 unrelated individuals with obesity (BMI ≥ 28 kg/m(2 and 373 non-obese controls (BMI 18.5 to <24 kg/m(2 from a large scale population-based cohort. We analyzed gene-gene interactions among 6 polymorphic loci using the Generalized Multifactor Dimensionality Reduction (GMDR method, which has been shown to be effective for detecting gene-gene interactions in case-control studies with relatively small samples. Then we used logistic regression models to confirm the best combination of loci identified in the GMDR. It showed a significant gene-gene interaction between the rs220721 polymorphism in the MAS1 gene and the rs1799722 polymorphism in the gene BDKB2R. The best two-locus combination scored 9 for cross-validation consistency and 9 for sign test (p = 0.0107. This interaction showed the maximum consistency and minimum prediction error among all gene-gene interaction models evaluated. Moreover, the combination of the MAS1 rs220721 and the BDKRB2 rs1799722 was associated with a significantly increased risk of obesity (OR 1.82, CI 95%: 1.15-2.88, p = 0.0103. CONCLUSIONS AND SIGNIFICANCE: These results suggest that the SNPs from the RAS-related genes may contribute to the risk of obesity in an interactive manner in a Chinese population. The gene-gene

  10. 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.

  11. 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.

  12. 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

  13. 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...

  14. 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,…

  15. Web-based Interactive Simulator for Rotating Machinery.

    Science.gov (United States)

    Sirohi, Vijayalaxmi

    1999-01-01

    Baroma (Balance of Rotating Machinery), the Web-based educational engineering interactive software for teaching/learning combines didactical and software ergonomical approaches. The software in tutorial form simulates a problem using Visual Interactive Simulation in graphic display, and animation is brought about through graphical user interface…

  16. 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"…

  17. 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

  18. 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.

  19. 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

  20. 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...

  1. 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.

  2. 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.

  3. Interacting with Visual Poems through AR-Based Digital Artwork

    Science.gov (United States)

    Lin, Hao-Chiang Koong; Hsieh, Min-Chai; Liu, Eric Zhi-Feng; Chuang, Tsung-Yen

    2012-01-01

    In this study, an AR-based digital artwork called "Mind Log" was designed and evaluated. The augmented reality technique was employed to create digital artwork that would present interactive poems. A digital poem was generated via the interplay between a video film and a text-based poem. This artwork was created following a rigorous design flow,…

  4. 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-...

  5. Interactive Multimedia Synchronization Model Based on Petri Nets

    Institute of Scientific and Technical Information of China (English)

    WANG Zhiqiang; PENG Xiaogang; JI Zhen

    2007-01-01

    The multimedia synchronization is used to coordinate the timing of each multimedia object in the multimedia system.After studying different multimedia synchronization systems that have been published, an Interactive Synchronization multimedia based on Petri Nets model (ISPN) is proposed in this paper. The system is capable of describing the dynamic timing actions of multimedia objects vividly as well as controlling them interactively to maintain the system level synchronization balance.

  6. 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.

  7. 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....

  8. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

    Directory of Open Access Journals (Sweden)

    Andrea Flannery

    2015-12-01

    Full Text Available Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i conventional carbohydrate or glycan microarrays; (ii whole mucin microarrays; and (iii microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments.

  9. Online approach to feature interaction problems in middleware based system

    Institute of Scientific and Technical Information of China (English)

    HUANG Gang; LIU XuanZhe; MEI Hong

    2008-01-01

    As a popular infrastructure for distributed systems running on the Internet, middle-ware has to support much more diverse and complex interactions for coping with the drastically increasing demand on information technology and the extremely open and dynamic nature of the Internet. These supporting mechanisms facilitate the development, deployment, and integration of distributed systems, as well as increase the occasions for distributed systems to interact in an undesired way. The undesired interactions may cause serious problems, such as quality violation, function loss, and even system crash. In this paper, the problem is studied from the perspective of the feature interaction problem (FIP) in telecom, and an online ap-proach to the detection and solution on runtime systems is proposed. Based on a classification of middleware enabled interactions, the existence of FIP in middle-ware based systems is illustrated by four real cases and a conceptual comparison between middleware based systems and telecom systems. After that, runtime soft-ware architecture is employed to facilitate the online detection and solution of FIP. The approach is demonstrated on J2EE (Java 2 Platform Enterprise Edition) and applied to detect and resolve all of the four real cases.

  10. Interactions between acid- and base-functionalized surfaces

    NARCIS (Netherlands)

    Giesbers, M.; Kleijn, J.M.; Cohen Stuart, M.A.

    2002-01-01

    In this paper we present an AFM force study on interactions between chemically modified surfaces. Surfaces with terminal groups of either NH2 or COOH were obtained by chemisorption of a silane-based compound (3-amino-propyltriethoxysilane) on silica or a thiol compound (11-mercapto undecanoic acid)

  11. 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…

  12. 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

  13. 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

  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. 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....

  16. 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.

  17. 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.

  18. WAVE: Interactive Wave-based Sound Propagation for Virtual Environments.

    Science.gov (United States)

    Mehra, Ravish; Rungta, Atul; Golas, Abhinav; Ming Lin; Manocha, Dinesh

    2015-04-01

    We present an interactive wave-based sound propagation system that generates accurate, realistic sound in virtual environments for dynamic (moving) sources and listeners. We propose a novel algorithm to accurately solve the wave equation for dynamic sources and listeners using a combination of precomputation techniques and GPU-based runtime evaluation. Our system can handle large environments typically used in VR applications, compute spatial sound corresponding to listener's motion (including head tracking) and handle both omnidirectional and directional sources, all at interactive rates. As compared to prior wave-based techniques applied to large scenes with moving sources, we observe significant improvement in runtime memory. The overall sound-propagation and rendering system has been integrated with the Half-Life 2 game engine, Oculus-Rift head-mounted display, and the Xbox game controller to enable users to experience high-quality acoustic effects (e.g., amplification, diffraction low-passing, high-order scattering) and spatial audio, based on their interactions in the VR application. We provide the results of preliminary user evaluations, conducted to study the impact of wave-based acoustic effects and spatial audio on users' navigation performance in virtual environments.

  19. 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.

  20. 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.

  1. 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...

  2. 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...

  3. A Moving Human Tracking Approach Based on Semantic Interaction

    Institute of Scientific and Technical Information of China (English)

    ZHOU Ning; FANG Bao-hong; SUN Fu-liang

    2007-01-01

    In order to deal with partical occlusion, a semantic interaction based moving human tracking approach is put forward. Firstly human is modeled as moving blobs which are described as blob descriptions. Then moving blobs are updated and verified by projecting these descriptions. The approach exploits improved fast gauss transform and chooses source and target samples to reduce compute cost. Multi-moving human can be tracked simply and part occlusion can be done well.

  4. 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....

  5. 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...

  6. 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...

  7. Improved physical stability of amorphous state through acid base interactions.

    Science.gov (United States)

    Telang, Chitra; Mujumdar, Siddharthya; Mathew, Michael

    2009-06-01

    To investigate role of specific interactions in aiding formation and stabilization of amorphous state in ternary and binary dispersions of a weakly acidic drug. Indomethacin (IMC), meglumine (MU), and polyvinyl pyrollidone (PVP) were the model drug, base, and polymer, respectively. Dispersions were prepared using solvent evaporation. Physical mixtures were cryogenically coground. XRPD, PLM, DSC, TGA, and FTIR were used for characterization. MU has a high crystallization tendency and is characterized by a low T(g) (17 degrees C). IMC crystallization was inhibited in ternary dispersion with MU compared to IMC/PVP alone. An amorphous state formed readily even in coground mixtures. Spectroscopic data are indicative of an IMC-MU amorphous salt and supports solid-state proton transfer. IMC-MU salt displays a low T(g) approximately 50 degrees C, but is more physically stable than IMC, which in molecular mixtures with MU, resisted crystallization even when present in stoichiometric excess of base. This is likely due to a disrupted local structure of amorphous IMC due to specific interactions. IMC showed improved physical stability on incorporating MU in polymer, in spite of low T(g) of the base indicating that chemical interactions play a dominant role in physical stabilization. Salt formation could be induced thermally and mechanically.

  8. 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.

  9. Quantification of Aromaticity Based on Interaction Coordinates: A New Proposal.

    Science.gov (United States)

    Pandey, Sarvesh Kumar; Manogaran, Dhivya; Manogaran, Sadasivam; Schaefer, Henry F

    2016-05-12

    Attempts to establish degrees of aromaticity in molecules are legion. In the present study, we begin with a fictitious fragment arising from only those atoms contributing to the aromatic ring and having a force field projected from the original system. For example, in benzene, we adopt a fictitious C6 fragment with a force field projected from the full benzene force field. When one bond or angle is stretched and kept fixed, followed by a partial optimization for all other internal coordinates, structures change from their respective equilibria. These changes are the responses of all other internal coordinates for constraining the bond or angle by unit displacements and relaxing the forces on all other internal coordinates. The "interaction coordinate" derived from the redundant internal coordinate compliance constants measures how a bond (its electron density) responds for constrained optimization when another bond or angle is stretched by a specified unit (its electron density is perturbed by a finite amount). The sum of interaction coordinates (responses) of all bonded neighbors for all internal coordinates of the fictitious fragment is a measure of the strength of the σ and π electron interactions leading to aromatic stability. This sum, based on interaction coordinates, appears to be successful as an aromaticity index for a range of chemical systems. Since the concept involves analyzing a fragment rather than the whole molecule, this idea is more general and is likely to lead to new insights.

  10. An interactive tutorial-based training technique for vertebral morphometry.

    Science.gov (United States)

    Gardner, J C; von Ingersleben, G; Heyano, S L; Chesnut, C H

    2001-01-01

    The purpose of this work was to develop a computer-based procedure for training technologists in vertebral morphometry. The utility of the resulting interactive, tutorial based training method was evaluated in this study. The training program was composed of four steps: (1) review of an online tutorial, (2) review of analyzed spine images, (3) practice in fiducial point placement and (4) testing. During testing, vertebral heights were measured from digital, lateral spine images containing osteoporotic fractures. Inter-observer measurement precision was compared between research technicians, and between technologists and radiologist. The technologists participating in this study had no prior experience in vertebral morphometry. Following completion of the online training program, good inter-observer measurement precision was seen between technologists, showing mean coefficients of variation of 2.33% for anterior, 2.87% for central and 2.65% for posterior vertebral heights. Comparisons between the technicians and radiologist ranged from 2.19% to 3.18%. Slightly better precision values were seen with height measurements compared with height ratios, and with unfractured compared with fractured vertebral bodies. The findings of this study indicate that self-directed, tutorial-based training for spine image analyses is effective, resulting in good inter-observer measurement precision. The interactive tutorial-based approach provides standardized training methods and assures consistency of instructional technique over time.

  11. 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.

  12. Interactive cell segmentation based on phase contrast optics.

    Science.gov (United States)

    Su, Hang; Su, Zhou; Zheng, Shibao; Yang, Hua; Wei, Sha

    2014-01-01

    Cell segmentation in phase contrast microscopy images lays a crucial foundation for numerous subsequent computer-aided cell image analysis, but it encounters many unsolved challenges due to image qualities and artifacts caused by phase contrast optics. Addressing the unsolved challenges, the authors propose an interactive cell segmentation scheme over phase retardation features. After partitioning the images into phase homogeneous atoms, human annotations are propagated to unlabeled atoms over an affinity graph that is learned based on discrimination analysis. Then, an active query strategy is proposed for which the most informative unlabeled atom is selected for annotation, which is also propagated to the other unlabeled atoms. Cell segmentation converges to quality results after several rounds of interactions involving both the user's intentions and characteristics of image features. Experimental results demonstrate that cells with different optical properties are well segmented via the proposed approach.

  13. 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

  14. 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.

  15. 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.

  16. Elucidating Interactions between DMSO and Chelate-Based Ionic Liquids.

    Science.gov (United States)

    Chen, Hang; Wang, Xinyu; Yao, Jia; Chen, Kexian; Guo, Yan; Zhang, Pengfei; Li, Haoran

    2015-12-21

    The C-D bond stretching vibrations of deuterated dimethyl sulfoxide ([D6 ]DMSO) and the C2 -H bond stretching vibrations of 1,1,1,5,5,5-hexafluoropentane-2,4-dione (hfac) ligand in anion are chosen as probes to elucidate the solvent-solute interaction between chelate-based ionic liquids (ILs) and DMSO by vibrational spectroscopic studies. The indirect effect from the interaction of the adjacent S=O functional group of DMSO with the cation [C10 mim](+) and anion [Mn(hfac)3 ](-) of the ILs leads to the blue-shift of the C-D stretching vibrations of DMSO. The C2 -H bond stretching vibrations in hfac ligand is closely related to the ionic hydrogen bond strength between the cation and anion of chelate-based ILs. EPR studies reveal that the crystal field of the central metal is kept when the chelate-based ILs are in different microstructure environment in the solution.

  17. [Expression of rice dwarf virus outer coat protein gene(S8) in insect cells].

    Science.gov (United States)

    Li, S; Liu, H; Chen, Z; Li, Y

    2001-04-01

    Outer coat protein gene(S8) of RDV was cloned into the transfer vector pVL 1393 to construct a recombinant vector pVL1393-S8. The recombinant vector pVL1393-S8 and the linear baculovirus RP23. LacZ were cotransfected into sf9 cells to produce the recombinant virus RP23-S8. RP23-S8 infected sf9 cells were collected and analysed by SDS-PAGE and Western-blot. The results showed that the S8 gene of RDV was expressed in sf9 cells and the expression level of sf9 cells was higher between 72-96 h after infected.

  18. 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.

  19. 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.

  20. Comparing Four Touch-Based Interaction Techniques for an Image-Based Audience Response System

    NARCIS (Netherlands)

    Jorritsma, Wiard; Prins, Jonatan T.; van Ooijen, Peter M. A.

    2015-01-01

    This study aimed to determine the most appropriate touch-based interaction technique for I2Vote, an image-based audience response system for radiology education in which users need to accurately mark a target on a medical image. Four plausible techniques were identified: land-on, take-off, zoom-poin

  1. 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.

  2. 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.

  3. 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

  4. 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.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    and sustained invitation to interaction afforded by the cyclic motion of a pendulum’s simple harmonic oscillation presents a new tangible interaction scenario for human computer interaction in 3D physical-digital-sonic environments. An investigation of Pendaphoncs tangible interaction scenario is articulated...

  6. 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).

  7. 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.

  8. 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.

  9. 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.

  10. An Interactive Web-based Environment using Human Companion

    Directory of Open Access Journals (Sweden)

    Tahar Bouhadada

    2006-01-01

    Full Text Available This paper describes the architecture of an Interactive Learning Environment (ILE on internet using companions, one of which is a human and geographically distant from the learning site. The achieved system rests on a 3-tier customer/server architecture (customer, web server, data and applications server where human and software actors can communicate via the internet and use the DTL learning strategy. It contains five main actors: a tutor actor in charge to guide the learner; a system actor whose role is to manage and to control the accesses to the system; a teacher actor in charge of the management and the updating of the different bases; a learner actor who represents the main actor of the system for whom is dedicated the teaching. Also, a learning companion actor whose role can be sometimes as an assistant, and other times as a troublemaker.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    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...... position data in order to trigger real-time sonic events via specified head gestures. These gestures are mapped to sound models that convey particular messages in order to control software on the mobile device or to another, simultaneous POKEHEAD user. The context for the project was motivated......, open source implementation. Our rapid prototype proved to be robust enough to work in performance for demonstration purposes and serves as a working proof of concept. In this paper we provide a technical description of our prototype, illustrate the context and motivation behind the project, and offer...

  12. 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...

  13. Evolving effective behaviours to interact with tag-based populations

    Science.gov (United States)

    Yucel, Osman; Crawford, Chad; Sen, Sandip

    2015-07-01

    Tags and other characteristics, externally perceptible features that are consistent among groups of animals or humans, can be used by others to determine appropriate response strategies in societies. This usage of tags can be extended to artificial environments, where agents can significantly reduce cognitive effort spent on appropriate strategy choice and behaviour selection by reusing strategies for interacting with new partners based on their tags. Strategy selection mechanisms developed based on this idea have successfully evolved stable cooperation in games such as the Prisoner's Dilemma game but relies upon payoff sharing and matching methods that limit the applicability of the tag framework. Our goal is to develop a general classification and behaviour selection approach based on the tag framework. We propose and evaluate alternative tag matching and adaptation schemes for a new, incoming individual to select appropriate behaviour against any population member of an existing, stable society. Our proposed approach allows agents to evolve both the optimal tag for the environment as well as appropriate strategies for existing agent groups. We show that these mechanisms will allow for robust selection of optimal strategies by agents entering a stable society and analyse the various environments where this approach is effective.

  14. 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.

  15. 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)

  16. 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.

  17. 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...

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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...

  4. 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...

  5. 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

  6. 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....

  7. Natural Interaction Based Online Military Boxing Learning System

    Science.gov (United States)

    Yang, Chenglei; Wang, Lu; Sun, Bing; Yin, Xu; Wang, Xiaoting; Liu, Li; Lu, Lin

    2013-01-01

    Military boxing, a kind of Chinese martial arts, is widespread and health beneficial. In this paper, the authors introduce a military boxing learning system realized by 3D motion capture, Web3D and 3D interactive technologies. The interactions with the system are natural and intuitive. Users can observe and learn the details of each action of the…

  8. 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.

  9. 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...

  10. 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...

  11. 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.

  12. Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    McAdams, Harley; AlQuraishi, Mohammed

    2015-04-21

    Techniques for determining values for a metric of microscale interactions include determining a mesoscale metric for a plurality of mesoscale interaction types, wherein a value of the mesoscale metric for each mesoscale interaction type is based on a corresponding function of values of the microscale metric for the plurality of the microscale interaction types. A plurality of observations that indicate the values of the mesoscale metric are determined for the plurality of mesoscale interaction types. Values of the microscale metric are determined for the plurality of microscale interaction types based on the plurality of observations and the corresponding functions and compressed sensing.

  13. 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.

  14. 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. ‎

  15. Agent based models for wealth distribution with preference in interaction

    CERN Document Server

    Goswami, Sanchari

    2014-01-01

    We propose a set of conservative models in which agents exchange wealth with a preference in the choice of interacting agents in different ways. The common feature in all the models is that the temporary values of financial status of agents is a deciding factor for interaction. Other factors which may play important role are past interactions and wealth possessed by individuals. Wealth distribution, network properties and activity are the main quantities which have been studied. Evidence of phase transitions and other interesting features are presented. The results show that certain observations of real economic system can be reproduced by the models.

  16. Component Based System Framework for Dynamic B2B Interaction

    OpenAIRE

    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 support different B2B protocols dynamically to enable interaction between diverse enterprises. This paper proposes a framework for dynamic B2B interaction. A B2B transaction is divided into the interacti...

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

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Witzner Hansen, Dan

    2011-01-01

    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......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...

  18. 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

  19. 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.

  20. 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....

  1. 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.

  2. 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)

  3. 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...

  4. 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

  5. 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.

  6. 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…

  7. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    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......, 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 performance which...

  8. 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 ......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...... also key figures in the philosophical discussions of nature and science - from philosophical tendencies like logical empiricism via critical rationalism to various neo-Kantian trends....

  9. 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.

  10. 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

  11. 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.

  12. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Trinoskey, P.A.; Camacho, P.I.; Wells, L.

    2000-01-18

    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

  14. Interactive image segmentation framework based on control theory

    Science.gov (United States)

    Zhu, Liangjia; Kolesov, Ivan; Ratner, Vadim; Karasev, Peter; Tannenbaum, Allen

    2015-03-01

    Segmentation of anatomical structures in medical imagery is a key step in a variety of clinical applications. Designing a generic, automated method that works for various structures and imaging modalities is a daunting task. Instead of proposing a new specific segmentation algorithm, in this paper, we present a general design principle on how to integrate user interactions from the perspective of control theory. In this formulation, Lyapunov stability analysis is employed to design an interactive segmentation system. The effectiveness and robustness of the proposed method are demonstrated.

  15. 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.

  16. Association, Haplotype, and Gene-Gene Interactions of the HPA Axis Genes with Suicidal Behaviour in Affective Disorders

    Directory of Open Access Journals (Sweden)

    Anna Leszczyńska-Rodziewicz

    2013-01-01

    Full Text Available Family twin and adoption studies have noted the heritability of specific biological factors that influence suicidal behaviour. Exposure to stress is one of the factors that strongly contribute to suicide attempts. The biological response to stress involves the hypothalamic-pituitary-adrenal axis (HPA. Therefore, we found it interesting to study polymorphisms of genes involved in the HPA axis (CRHR1, NR3C1, and AVPBR1. The study was performed on 597 patients, 225 of whom had a history of suicide attempts. We did not observe any significant differences in the studied polymorphisms between the group of patients with a history of suicide attempts and the control subjects. Our haplotype analysis of the AVPR1b gene revealed an association between the GCA haplotype and suicide attempts; however, this association was not significant after correcting for multiple testing. We did not observe any other association in haplotype and MDR analysis. We report here a comprehensive analysis of the HPA axis genes and a lack of association for genetic variations regarding the risk of suicide attempts in affective disorder patients. Nonetheless, the inconsistencies with the previously published results indicate the importance of the further investigation of these polymorphisms with respect to the risk of suicide attempts.

  17. Association, haplotype, and gene-gene interactions of the HPA axis genes with suicidal behaviour in affective disorders.

    Science.gov (United States)

    Leszczyńska-Rodziewicz, Anna; Szczepankiewicz, Aleksandra; Pawlak, Joanna; Dmitrzak-Weglarz, Monika; Hauser, Joanna

    2013-01-01

    Family twin and adoption studies have noted the heritability of specific biological factors that influence suicidal behaviour. Exposure to stress is one of the factors that strongly contribute to suicide attempts. The biological response to stress involves the hypothalamic-pituitary-adrenal axis (HPA). Therefore, we found it interesting to study polymorphisms of genes involved in the HPA axis (CRHR1, NR3C1, and AVPBR1). The study was performed on 597 patients, 225 of whom had a history of suicide attempts. We did not observe any significant differences in the studied polymorphisms between the group of patients with a history of suicide attempts and the control subjects. Our haplotype analysis of the AVPR1b gene revealed an association between the GCA haplotype and suicide attempts; however, this association was not significant after correcting for multiple testing. We did not observe any other association in haplotype and MDR analysis. We report here a comprehensive analysis of the HPA axis genes and a lack of association for genetic variations regarding the risk of suicide attempts in affective disorder patients. Nonetheless, the inconsistencies with the previously published results indicate the importance of the further investigation of these polymorphisms with respect to the risk of suicide attempts.

  18. 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

  19. 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

  20. An Agent Interaction Based Method for Nonlinear Process Plan Scheduling

    Institute of Scientific and Technical Information of China (English)

    GAO Qinglu; WU Bo; GUO Guang

    2006-01-01

    This article puts forward a scheduling method for nonlinear process plan shop floor. Task allocation and load balance are realized by bidding mechanism. Though the agent interaction process, the execution of tasks is determined and the coherence of manufacturing decision is verified. The employment of heuristic index can help to optimize the system performance.

  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. Referring Expression Generation in Interaction: A Graph-based perspective

    NARCIS (Netherlands)

    Krahmer, E.J.; Goudbeek, M.B.; Theune, M.; Stent, Amanda; Bangalore, Srinivas

    2014-01-01

    An informative and comprehensive overview of the state-of-the-art in natural language generation (NLG) for interactive systems, this guide serves to introduce graduate students and new researchers to the field of natural language processing and artificial intelligence, while inspiring them with idea

  4. 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...

  5. 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

  6. Interactive web-based Earth visualization telling the earth science story.

    Science.gov (United States)

    Stein, C.

    2006-12-01

    Interactive earth visualization applications provide a new level of understanding of complex spatial and time based environmental information. GeoFusion's earth visualization tools provide a web-based platform for sharing results of scientific research. One hundred years of predicted sea ice coverage is animated on an interactive globe in a web page. Watershed visualization comes alive with interactive control of terrain, map, satellite, and digital raster graph layers. Animating NASA's Blue Marble Next Generation half kilometer monthly datasets becomes a background for discussing yearly earth cycles. GeoFusion's tools are used for creating custom museum and web-based applications that engage users in an interactive exploration of environmental phenomena.

  7. 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 ...

  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. 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.

  10. Marker-Based Embodied Interaction for Handheld Augmented Reality Games

    Directory of Open Access Journals (Sweden)

    Michael Rohs

    2007-05-01

    Full Text Available This article deals with embodied user interfaces for handheld augmented reality games, which consist of both physical and virtual components. We have developed a number of spatial interaction techniques that optically capture the device’s movement and orientation relative to a visual marker. Such physical interactions in 3D space enable manipulative control of mobile games. In addition to acting as a physical controller that recognizes multiple game-dependent gestures, the mobile device augments the camera view with graphical overlays. We describe three game prototypes that use ubiquitous product packaging and other passive media as backgrounds for handheld augmentation. The prototypes can be realized on widely available off-the-shelf hardware and require only minimal setup and infrastructure support.

  11. 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

  12. 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...

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2015-01-01

    Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

  20. 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...

  1. Counting statistics for genetic switches based on effective interaction approximation

    CERN Document Server

    Ohkubo, Jun

    2012-01-01

    Applicability of counting statistics for a system with an infinite number of states is investigated. The counting statistics has been studied a lot for a system with a finite number of states. While it is possible to use the scheme in order to count specific transitions in a system with an infinite number of states in principle, we have non-closed equations in general. A simple genetic switch can be described by a master equation with an infinite number of states, and we use the counting statistics in order to count the number of transitions from inactive to active states in the gene. To avoid to have the non-closed equations, an effective interaction approximation is employed. As a result, it is shown that the switching problem can be treated as a simple two-state model approximately, which immediately indicates that the switching obeys non-Poisson statistics.

  2. Counting statistics for genetic switches based on effective interaction approximation

    Science.gov (United States)

    Ohkubo, Jun

    2012-09-01

    Applicability of counting statistics for a system with an infinite number of states is investigated. The counting statistics has been studied a lot for a system with a finite number of states. While it is possible to use the scheme in order to count specific transitions in a system with an infinite number of states in principle, we have non-closed equations in general. A simple genetic switch can be described by a master equation with an infinite number of states, and we use the counting statistics in order to count the number of transitions from inactive to active states in the gene. To avoid having the non-closed equations, an effective interaction approximation is employed. As a result, it is shown that the switching problem can be treated as a simple two-state model approximately, which immediately indicates that the switching obeys non-Poisson statistics.

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. 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

  8. 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...

  9. 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...

  10. 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...

  11. 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

  12. 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)

  13. 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.

  14. Experimental perspectives for systems based on long-range interactions

    CERN Document Server

    Bachelard, Romain; De Buyl, Pierre; Staniscia, F; Cataliotti, F S; De Ninno, G; Fanelli, Duccio; Piovella, Nicola

    2010-01-01

    The possibility of observing phenomena peculiar to long-range interactions, and more specifically in the so-called Quasi-Stationary State (QSS) regime is investigated within the framework of two devices, namely the Free-Electron Laser (FEL) and the Collective Atomic Recoil Laser (CARL). The QSS dynamics has been mostly studied using the Hamiltonian Mean-Field (HMF) toy model, demonstrating in particular the presence of first versus second order phase transitions from magnetized to unmagnetized regimes in the case of HMF. Here, we give evidence of the strong connections between the HMF model and the dynamics of the two mentioned devices, and we discuss the perspectives to observe some specific QSS features experimentally. In particular, a dynamical analog of the phase transition is present in the FEL and in the CARL in its conservative regime. Regarding the dissipative CARL, a formal link is established with the HMF model. For both FEL and CARL, calculations are performed with reference to existing experimenta...

  15. 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

  16. 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.

  17. Rydberg-interaction-based quantum gates free from blockade error

    CERN Document Server

    Shi, Xiao-Feng

    2016-01-01

    Accurate quantum gates are basic elements for building quantum computers. There has been great interest in designing quantum gates by using blockade effect of Rydberg atoms recently. The fidelity and operation speed of these gates, however, are fundamentally limited by the blockade error. Here we propose another type of quantum gates, which are based on Rydberg blockade effect, yet free from any blockade error. In contrast to the `blocking' method in previous schemes, we use Rydberg energy shift to realise a rational generalised Rabi frequency so that a novel $\\pi$ phase for one input state of the gate emerges. This leads to an accurate Rydberg-blockade based two-qubit quantum gate that can operate in a $0.1\\mu s$ timescale or faster thanks to that it operates by a Rabi frequency which is comparable to the blockade shift.

  18. Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control

    NARCIS (Netherlands)

    Dijk, van A.D.J.; Braak, ter C.J.F.; Immink, G.H.; Angenent, G.C.; Ham, van R.C.H.J.

    2008-01-01

    Motivation: Transcription factor interactions are the cornerstone of combinatorial control, which is a crucial aspect of the gene regulatory system. Understanding and predicting transcription factor interactions based on their sequence alone is difficult since they are often part of families of fact

  19. 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…

  20. 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...

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

    DEFF Research Database (Denmark)

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

    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...... for synthesizing any wavelength in the visible and ultraviolet light based sum frequency generation between two lasers is presented....

  2. 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.

  3. 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)...

  4. 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.

  5. 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.

  6. 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...

  7. 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.

  8. 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...... are treated in section 2.3. With respect to the reliability evalutation, the basic theory behind a reliability analysis and estimation of probability of failure by the First-Order Reliability Method (FORM) and the iterative Rackwitz-Fiessler (RF) algorithm are considered in section 2.5 in which...

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. The Interactions between Imidazolium-Based Ionic Liquids and Stable Nitroxide Radical Species: A Theoretical Study.

    Science.gov (United States)

    Zhang, Shaoze; Wang, Guimin; Lu, Yunxiang; Zhu, Weiliang; Peng, Changjun; Liu, Honglai

    2016-08-01

    In this work, the interactions between imidazolium-based ionic liquids and some stable radicals based on 2,2,6,6-tetramethylpiperidine-1-yloxyl (TEMPO) have been systematically investigated using density functional theory calculations at the level of M06-2x. Several different substitutions, such as hydrogen bonding formation substituent (OH) and ionic substituents (N(CH3)3(+) and OSO3(-)), are presented at the 4-position of the spin probe, which leads to additional hydrogen bonds or ionic interactions between these substitutions and ionic liquids. The interactions in the systems of the radicals containing ionic substitutions with ionic liquids are predicted much stronger than those in the systems of neutral radicals, resulting in a significant reduction of the mobility of ionic radicals in ionic liquids. To further understand the nature of these interactions, the natural bond order, atoms in molecules, noncovalent interaction index, electron density difference, energy decomposition analysis, and charge decomposition analysis schemes were employed. The additional ionic interactions between ionic radicals and counterions in ionic liquids are dominantly contributed from the electrostatic term, while the orbital interaction plays a major role in other interactions. The results reported herein are important to understand radical processes in ionic liquids and will be very useful in the design of task-specific ionic liquids to make the processes more efficient.

  20. 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 ...

  1. 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.

  2. 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

  3. 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.

  4. Reciprocity in computer-human interaction: source-based, norm-based, and affect-based explanations.

    Science.gov (United States)

    Lee, Seungcheol Austin; Liang, Yuhua Jake

    2015-04-01

    Individuals often apply social rules when they interact with computers, and this is known as the Computers Are Social Actors (CASA) effect. Following previous work, one approach to understand the mechanism responsible for CASA is to utilize computer agents and have the agents attempt to gain human compliance (e.g., completing a pattern recognition task). The current study focuses on three key factors frequently cited to influence traditional notions of compliance: evaluations toward the source (competence and warmth), normative influence (reciprocity), and affective influence (mood). Structural equation modeling assessed the effects of these factors on human compliance with computer request. The final model shows that norm-based influence (reciprocity) increased the likelihood of compliance, while evaluations toward the computer agent did not significantly influence compliance. PMID:25803145

  5. 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...

  6. 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

  7. 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.

  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. 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...

  10. Photoswitchable Adsorption in Metal-Organic Frameworks Based on Polar Guest-Host Interactions.

    Science.gov (United States)

    Wang, Zhengbang; Grosjean, Sylvain; Bräse, Stefan; Heinke, Lars

    2015-12-21

    Reversible remote-controlled switching of the properties of nanoporous metal-organic frameworks (MOFs) is enabled by incorporating photoswitchable azobenzene. The interaction of the host material with different guest molecules, which is crucial for all applications, is precisely studied using thin MOF films of the type Cu2 (BDC)2 (AzoBipyB). A molecule-specific effect of the photoswitching, based on dipole-dipole interactions, is found.

  11. 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.

  12. Genetics-based interactions among plants, pathogens, and herbivores define arthropod community structure.

    Science.gov (United States)

    Busby, Posy E; Lamit, Louis J; Keith, Arthur R; Newcombe, George; Gehring, Catherine A; Whitham, Thomas G; Dirzo, Rodolfo

    2015-07-01

    Plant resistance to pathogens or insect herbivores is common, but its potential for indirectly influencing plant-associated communities is poorly known. Here, we test whether pathogens' indirect effects on arthropod communities and herbivory depend on plant resistance to pathogens and/or herbivores, and address the overarching interacting foundation species hypothesis that genetics-based interactions among a few highly interactive species can structure a much larger community. In a manipulative field experiment using replicated genotypes of two Populus species and their interspecific hybrids, we found that genetic variation in plant resistance to both pathogens and insect herbivores modulated the strength of pathogens' indirect effects on arthropod communities and insect herbivory. First, due in part to the pathogens' differential impacts on leaf biomass among the two Populus species and the hybrids, the pathogen most strongly impacted arthropod community composition, richness, and abundance on the pathogen-susceptible tree species. Second, we found similar patterns comparing pathogen-susceptible and pathogen-resistant genotypes within species. Third, within a plant species, pathogens caused a fivefold greater reduction in herbivory on insect-herbivore-susceptible plant genotypes than on herbivore-resistant genotypes, demonstrating that the pathogen-herbivore interaction is genotype dependent. We conclude that interactions among plants, pathogens, and herbivores can structure multitrophic communities, supporting the interacting foundation species hypothesis. Because these interactions are genetically based, evolutionary changes in genetic resistance could result in ecological changes in associated communities, which may in turn feed back to affect plant fitness.

  13. 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. Spontaneous......Dialogic reading, in which the reader prompts the child to speak while listening to the story being read, represents a promising way to boost children’s lingual development but it is unclear how content interactivity and agency affect the technique. We used video interaction analysis to investigate...

  14. 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.

  15. 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

  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. 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.

  18. 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

  19. Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

    Directory of Open Access Journals (Sweden)

    Liao Li

    2010-10-01

    Full Text Available Abstract Background Protein-protein interaction (PPI plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs, based on domains represented as interaction profile hidden Markov models (ipHMM where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB. Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD. Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure, an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on

  20. 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

  1. 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.

  2. Specular Andreev reflection in graphene-based superconducting junction with substate-induced spin orbit interaction

    Science.gov (United States)

    Bai, Chunxu; Yang, Yanling

    2016-08-01

    Based on the Dirac-Bogoliubov-de Gennes equation, the chirality-resolved transport properties through a ballistic graphene-based superconducting heterojunction with both the Rashba and the Dresselhaus spin orbit interaction have been investigated. Our results show that, in contrast to the retro-Andreev reflection suppressed by the spin orbit interaction (SOI), the specular Andreev reflection (SAR) can be enhanced largely by the SOI. Moreover, the Fabry-Perot interferences in the barrier region lead to the oscillating feature of the tunneling conductance. It is anticipated to apply the qualitative different results to diagnose the SAR in single layer graphene in the presence of both kinds of the SOI.

  3. Stacking interaction in metal complexes with compositions of DNA and heteroaromatic N-bases

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The current development in the intramolecular aromatic-ring stacking i nteractions in the complexes with compositions of DNA and heteroaromatic N-bases has been reviewed to a great extent, especially the significant contributions i n several important systems about ternary mixed-ligand complexes, including nucl eotide-metal ion-po- lyaromatic amine, amino acid-metal ion-polyaromatic amine, nucleotide-metal ion-pyridine-like aromatic amine, nucleotide-metal ion-amino ac id, nucleotide-metal ion-nucleic acid base, nucleic acid base-metal ion, and the important factors affecting the intramolecular aromatic-ring stacking interacti ons in the complexes. Based on the study of stacking interaction in the complexe s, the mechanism of interaction between DNA molecules and complexes of heteroaro matic N-bases has been established, which is crucial for the design and synthesi s of the complexes acting as molecular devices of DNA.

  4. 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

  5. Improving Vision-Based Motor Rehabilitation Interactive Systems for Users with Disabilities Using Mirror Feedback

    Directory of Open Access Journals (Sweden)

    Antoni Jaume-i-Capó

    2014-01-01

    Full Text Available Observation is recommended in motor rehabilitation. For this reason, the aim of this study was to experimentally test the feasibility and benefit of including mirror feedback in vision-based rehabilitation systems: we projected the user on the screen. We conducted a user study by using a previously evaluated system that improved the balance and postural control of adults with cerebral palsy. We used a within-subjects design with the two defined feedback conditions (mirror and no-mirror with two different groups of users (8 with disabilities and 32 without disabilities using usability measures (time-to-start (Ts and time-to-complete (Tc. A two-tailed paired samples t-test confirmed that in case of disabilities the mirror feedback facilitated the interaction in vision-based systems for rehabilitation. The measured times were significantly worse in the absence of the user’s own visual feedback (Ts=7.09 (P<0.001 and Tc=4.48 (P<0.005. In vision-based interaction systems, the input device is the user’s own body; therefore, it makes sense that feedback should be related to the body of the user. In case of disabilities the mirror feedback mechanisms facilitated the interaction in vision-based systems for rehabilitation. Results recommends developers and researchers use this improvement in vision-based motor rehabilitation interactive systems.

  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. 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.

  10. Genome-wide interaction-based association analysis identified multiple new susceptibility Loci for common diseases.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2011-03-01

    Full Text Available Genome-wide interaction-based association (GWIBA analysis has the potential to identify novel susceptibility loci. These interaction effects could be missed with the prevailing approaches in genome-wide association studies (GWAS. However, no convincing loci have been discovered exclusively from GWIBA methods, and the intensive computation involved is a major barrier for application. Here, we developed a fast, multi-thread/parallel program named "pair-wise interaction-based association mapping" (PIAM for exhaustive two-locus searches. With this program, we performed a complete GWIBA analysis on seven diseases with stringent control for false positives, and we validated the results for three of these diseases. We identified one pair-wise interaction between a previously identified locus, C1orf106, and one new locus, TEC, that was specific for Crohn's disease, with a Bonferroni corrected P < 0.05 (P = 0.039. This interaction was replicated with a pair of proxy linked loci (P = 0.013 on an independent dataset. Five other interactions had corrected P < 0.5. We identified the allelic effect of a locus close to SLC7A13 for coronary artery disease. This was replicated with a linked locus on an independent dataset (P = 1.09 × 10⁻⁷. Through a local validation analysis that evaluated association signals, rather than locus-based associations, we found that several other regions showed association/interaction signals with nominal P < 0.05. In conclusion, this study demonstrated that the GWIBA approach was successful for identifying novel loci, and the results provide new insights into the genetic architecture of common diseases. In addition, our PIAM program was capable of handling very large GWAS datasets that are likely to be produced in the future.

  11. Stress-Corrosion Interactions in Zr-Based Bulk Metallic Glasses

    Directory of Open Access Journals (Sweden)

    Petre Flaviu Gostin

    2015-07-01

    Full Text Available Stress-corrosion interactions in materials may lead to early unpredictable catastrophic failure of structural parts, which can have dramatic effects. In Zr-based bulk metallic glasses, such interactions are particularly important as these have very high yield strength, limited ductility, and are relatively susceptible to localized corrosion in halide-containing aqueous environments. Relevant features of the mechanical and corrosion behavior of Zr-based bulk metallic glasses are described, and an account of knowledge regarding corrosion-deformation interactions gathered from ex situ experimental procedures is provided. Subsequently the literature on key phenomena including hydrogen damage, stress corrosion cracking, and corrosion fatigue is reviewed. Critical factors for such phenomena will be highlighted. The review also presents an outlook for the topic.

  12. 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.

  13. Towards a Semantics-based Framework for Meaning Construction in Constructivist Interactions

    DEFF Research Database (Denmark)

    Badie, Farshad

    2015-01-01

    in constructivist interactions based on my conceptualisation of Definition and Definiteness, Meaning and Meaningfully and Semantic Interpretation. In this research I will analyse meaning construction and meaningful comprehension production within constructivist interactions. I will employ some fundamentals from...... semantic loop that the learner and mentor as intentional participants move through, which organises their personal constructed conceptions in order to construct meanings and produce their meaningful comprehensions. This research will be concerned with meanings and definitions and proposes a new scheme......-structured knowledge and based on their personal knowings – actively participate in an interaction with each other in order to construct personal knowledge. The most significant objective of constructivism is construction of personal knowledge and its development, and producing the own understanding of a world...

  14. 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

  15. 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.

  16. 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...

  17. 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…

  18. 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…

  19. Project-Based Method as an Effective Means of Interdisciplinary Interaction While Teaching a Foreign Language

    Science.gov (United States)

    Bondar, Irina Alekseevna; Kulbakova, Renata Ivanovna; Svintorzhitskaja, Irina Andreevna; Pilat, Larisa Pavlovna; Zavrumov, Zaur Aslanovich

    2016-01-01

    The article explains how to use a project-based method as an effective means of interdisciplinary interaction when teaching a foreign language on the example of The Institute of service, tourism and design (branch) of the North Caucasus Federal University (Pyatigorsk, Stavropol Territory Russia). The article holds the main objectives of the…

  20. The Application Study of MCU in Visual Classroom Interactive Teaching Based on Virtual Experiment Platform

    Science.gov (United States)

    Ding, Diankuan; Li, Lixin

    Because many students are lacking in perceptual knowledge of MCU, they are difficult to engage themselves in classroom activities. The paper therefore offers an interactive teaching mode of proteus-based MCU virtual laboratory. The teaching mode is of help in arousing students' interests, improving their learning efficiency and practical abilities, and promoting the teaching reform of MCU subject.

  1. 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

  2. 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…

  3. Interaction Between Conceptual Level and Training Method in Computer Based Problem Solving.

    Science.gov (United States)

    Sustik, Joan M.; Brown, Bobby R.

    A study of 130 undergraduate students enrolled in a course on auiovisual techniques sought to determine whether heuristic or algorithmic computer-based problem solving training would be differentially effective for students varying in cognitive complexity as measured by the Educational Set Scale (ESS). The interaction was investigated between one…

  4. 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

  5. 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…

  6. Memory-Aware Query Routing in Interactive Web-based Information Systems

    NARCIS (Netherlands)

    Waas, F.; Kersten, M.L.

    2001-01-01

    Query throughput is one of the primary optimization goals in interactive web-based information systems in order to achieve the performance necessary to serve large user communities. Queries in this application domain differ significantly from those in traditional database applications: they are of l

  7. 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,…

  8. 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…

  9. Balancing Hydrogen Bonding and van der Waals Interactions in Cyclohexane-Based Bisamide and Bisurea Organogelators

    NARCIS (Netherlands)

    Zweep, Nick; Hopkinson, Andrew; Meetsma, Auke; Browne, Wesley R.; Feringa, Ben L.; van Esch, Jan H.; Zweep, Niek

    2009-01-01

    The solvent dependence of the gelation properties, the thermotropic behavior, and the melting enthalpy of a series of enantiomerically pure cyclohexane-based bisamide and bisurea compounds are reported. The two series of gelators examined are related structurally with the intermolecular interactions

  10. Understanding Manual-Based Behavior Therapy: Some Theoretical Foundations of Parent-Child Interaction Therapy.

    Science.gov (United States)

    Greco, Laurie A.; Sorrell, John T.; McNeil, Cheryl B.

    2001-01-01

    Provides a model of understanding and evaluating manualized treatments by beginning with a review of the theory and data-driven principles upon which one treatment, Parent-Child Interaction Therapy (PCIT), is based. As a point of illustration, several principles of PCIT, such as reinforcement, punishment, and stimulus control, are highlighted, and…

  11. 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.

  12. An Investigation of Interactive, Dialogue-Based Instruction for Undergraduate Art History

    Science.gov (United States)

    Gioffre, Penelope

    2012-01-01

    This paper explores the feasibility and efficacy of incorporating an interactive, discussion-based instructional approach into an undergraduate art history survey course and investigates effects of the new pedagogic strategy on students' demonstrated comprehension and retention of required content. The action research project follows a systematic…

  13. Wersync: A WEB-BASED PLATFORM FOR DISTRIBUTED MEDIA SYNCHRONIZATION AND SOCIAL INTERACTION

    NARCIS (Netherlands)

    Belda, J.; Montagud Climent, M.A.; Boronat, F.; Martinez, M.; Pastor, J.

    2015-01-01

    This paper presents Wersync, which is an adaptive and accurate web-based platform that enables distributed media synchronization and social interaction across remote users. By using Wersync, users can create or join on-going sessions for concurrently consuming the same media content with other remot

  14. 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...

  15. 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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Miguel edos Santos

    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.

  18. Physiologically Based Pharmacokinetic Modeling Framework for Quantitative Prediction of an Herb–Drug Interaction

    Science.gov (United States)

    Brantley, S J; Gufford, B T; Dua, R; Fediuk, D J; Graf, T N; Scarlett, Y V; Frederick, K S; Fisher, M B; Oberlies, N H; Paine, M F

    2014-01-01

    Herb–drug interaction predictions remain challenging. Physiologically based pharmacokinetic (PBPK) modeling was used to improve prediction accuracy of potential herb–drug interactions using the semipurified milk thistle preparation, silibinin, as an exemplar herbal product. Interactions between silibinin constituents and the probe substrates warfarin (CYP2C9) and midazolam (CYP3A) were simulated. A low silibinin dose (160 mg/day × 14 days) was predicted to increase midazolam area under the curve (AUC) by 1%, which was corroborated with external data; a higher dose (1,650 mg/day × 7 days) was predicted to increase midazolam and (S)-warfarin AUC by 5% and 4%, respectively. A proof-of-concept clinical study confirmed minimal interaction between high-dose silibinin and both midazolam and (S)-warfarin (9 and 13% increase in AUC, respectively). Unexpectedly, (R)-warfarin AUC decreased (by 15%), but this is unlikely to be clinically important. Application of this PBPK modeling framework to other herb–drug interactions could facilitate development of guidelines for quantitative prediction of clinically relevant interactions. PMID:24670388

  19. 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.

  20. A method for image-based shadow interaction with virtual objects

    Directory of Open Access Journals (Sweden)

    Hyunwoo Ha

    2015-01-01

    Full Text Available A lot of researchers have been investigating interactive portable projection systems such as a mini-projector. In addition, in exhibition halls and museums, there is a trend toward using interactive projection systems to make viewing more exciting and impressive. They can also be applied in the field of art, for example, in creating shadow plays. The key idea of the interactive portable projection systems is to recognize the user׳s gesture in real-time. In this paper, a vision-based shadow gesture recognition method is proposed for interactive projection systems. The gesture recognition method is based on the screen image obtained by a single web camera. The method separates only the shadow area by combining the binary image with an input image using a learning algorithm that isolates the background from the input image. The region of interest is recognized with labeling the shadow of separated regions, and then hand shadows are isolated using the defect, convex hull, and moment of each region. To distinguish hand gestures, Hu׳s invariant moment method is used. An optical flow algorithm is used for tracking the fingertip. Using this method, a few interactive applications are developed, which are presented in this paper.

  1. 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

  2. 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.

  3. 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.

  4. String-theory-based predictions for nonhydrodynamic collective modes in strongly interacting Fermi gases

    Science.gov (United States)

    Bantilan, H.; Brewer, J. T.; Ishii, T.; Lewis, W. E.; Romatschke, P.

    2016-09-01

    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 nonhydrodynamic 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 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.

  5. 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.

  6. 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)

  7. 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.

  8. 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/.

  9. 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

  10. 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

  11. 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.

  12. Interfacial Interaction in Coated Carbon Fibre Reinforced Aluminous Mg-based Composites

    Institute of Scientific and Technical Information of China (English)

    Kun LI; Nanlin SHI; Jun GON; Chao SUN

    2008-01-01

    Four kinds of Mg alloys reinforced with carbon fibres were fabricated by a gas pressure infiltration technique.The fibres were pre-coated a SiO2 layer prior to fabrication.Different microstructures and interactions in the fibre-matrix interface of these composites were observed by transmission electron microscopy (TEM).The results showed that the interracial interaction strongly depended on the content of Al in the Mg-based matrices.The microstructure of the interface could then be controlled by adjusting the Al content of the Mg-based matrix.In addition,fibres extracted from different Mg-based matrix all had some degradation owing to the interracial reaction and the fibre-matrix interdiffusion.

  13. 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.

  14. 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...

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions.

    Science.gov (United States)

    Syedbasha, Mohameedyaseen; Linnik, Janina; Santer, Deanna; O'Shea, Daire; Barakat, Khaled; Joyce, Michael; Khanna, Nina; Tyrrell, D Lorne; Houghton, Michael; Egli, Adrian

    2016-01-01

    A comprehensive understanding of signaling pathways requires detailed knowledge regarding ligand-receptor interaction. This article describes two fast and reliable point-by-point protocols of enzyme-linked immunosorbent assays (ELISAs) for the investigation of ligand-receptor interactions: the direct ligand-receptor interaction assay (LRA) and the competition LRA. As a case study, the ELISA based analysis of the interaction between different lambda interferons (IFNLs) and the alpha subunit of their receptor (IL28RA) is presented: the direct LRA is used for the determination of dissociation constants (KD values) between receptor and IFN ligands, and the competition LRA for the determination of the inhibitory capacity of an oligopeptide, which was designed to compete with the IFNLs at their receptor binding site. Analytical steps to estimate KD and half maximal inhibitory concentration (IC50) values are described. Finally, the discussion highlights advantages and disadvantages of the presented method and how the results enable a better molecular understanding of ligand-receptor interactions.

  7. 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.

  8. 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.

  9. 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

  10. Mass spectrometry–based metabolomics, analysis of metabolite-protein interactions, and imaging

    Science.gov (United States)

    Lee, Do Yup; Bowen, Benjamin P.; Northen, Trent R.

    2010-01-01

    Our understanding of biology has been greatly improved through recent developments in mass spectrometry, which is providing detailed information on protein and metabolite composition as well as protein-metabolite interactions. The high sensitivity and resolution of mass spectrometry achieved with liquid or gas chromatography allows for detection and quantification of hundreds to thousands of molecules in a single measurement. Where homogenization-based sample preparation and extraction methods result in a loss of spatial information, mass spectrometry imaging technologies provide the in situ distribution profiles of metabolites and proteins within tissues. Mass spectrometry–based analysis of metabolite abundance, protein-metabolite interactions, and spatial distribution of compounds facilitates the high-throughput screening of biochemical reactions, the reconstruction of metabolic networks, biomarker discovery, determination of tissue compositions, and functional annotation of both proteins and metabolites. PMID:20701590

  11. 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

  12. Consonant-vowel interactions in Modern Standard Latvian: a representational and constraint-based account

    Directory of Open Access Journals (Sweden)

    Olga Urek

    2016-07-01

    Full Text Available In this article I provide a representational and a constraint-based analysis of four interacting palatalization processes operative in Modern Standard Latvian: velar affrication, velar palatalization, yod-palatalization and front vowel raising. The main advantage of the representational account developed here is that it treats all of the mentioned Latvian processes as strictly assimilatory, and at the same time avoids purely stipulative mechanisms characteristic of many feature-geometric approaches to cross-category interactions. The article also contributes to the debate on the role of geometric subsegmental representations in constraint-based computational models, by demonstrating that a principled account of locality, transparency and blocking effects in Latvian palatalization requires the reference to hierarchical autosegmental structures.

  13. Parallel Processing Based on Ship Maneuvering in Identification of Interaction Force Coefficients

    Institute of Scientific and Technical Information of China (English)

    LIU Xiao-jian; HUANG Guo-liang; DENG De-heng

    2008-01-01

    The parallel processing based on the free running model test was adopted to predict the interac-tion force coefficients (flow straightening coefficient and wake fraction) of ship maneuvering. And the multi-population genetic algorithm (MPGA) based on real coding that can contemporarily process the data of freerunning model and simulation of ship maneuvering was applied to solve the problem. Accordingly the optimalindividual was obtained using the method of genetic algorithm. The parallel processing of multi-populationsolved the prematurity in the identification for single population, meanwhile, the parallel processing of the dataof ship maneuvering (turning motion and zigzag motion) is an attempt to solve the coefficient drift problem.In order to validate the method, the interaction force coefficients were verified by the procedure and thesecoefficients measured were compared with those ones identified. The maximum error is less than 5%, and theidentification is an effective method.

  14. 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.

  15. 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.

  16. Interaction of preosteoblasts with surface-immobilized collagen-based nanotubes.

    Science.gov (United States)

    Kalaskar, Deepak M; Demoustier-Champagne, Sophie; Dupont-Gillain, Christine C

    2013-11-01

    In a previous work, we demonstrated the successful use of electrophoretic deposition (EPD) to immobilize collagen-based nanotubes onto indium-tin-oxide-coated glass (ITO glass), leading to the creation of biointerfaces with protein-based chemistry and topography [1]. In this work, we present a first study of preosteoblasts behavior in contact with surface-immobilized collagen-based nanotubes. Changes in cell morphology after their interaction with ITO glass modified with collagen-based nanotubes were studied using fluorescence microscopy and compared to those observed on virgin ITO glass as well as on ITO glass on which a collagen layer was simply adsorbed. Scanning electron microscopy (SEM) was used to study interactions of cell filopodias with the deposited nanotubes. Cytotoxicity of these biointerfaces was examined as well in short term cultures, using Alamar blue assay. Cells showed particular morphologies on ITO glass coated with nanotubes compared to virgin ITO glass or collagen adsorbed layer on ITO glass. High resolution SEM images suggest that apart from cell morphology, length and thickness of filopodias seem to be significantly affected by surface modification with collagen-based nanotubes. Moreover, nanotube-coated ITO glass did not show any obvious cytotoxicity in short term culture, opening new perspectives for the surface modification of biomaterials. We show the versatility of the proposed surface modification procedure by tailoring biointerfaces with a mixture of micro- and nanometer-scale collagen-based tubes.

  17. 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.

  18. 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.

  19. 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.

  20. A Domain-Based Approach to Predict Protein-Protein Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Singhal, Mudita; Resat, Haluk

    2007-06-13

    Background:Understanding of biological processes necessitates knowing not only which proteins exist in a certain organism or cell type but also how these proteins interact with each other. However, the determination of the protein-protein interaction (PPI) networks is a daunting task and it has been the subject of extensive research. Despite the development of reasonably successful methods, serious technical difficulties still exist as is evident from the small overlap between the high-throughput experimental approaches. Results:In this manuscript we present DomainGA which is a Genetic Algorithm based method that optimizes the domain-domain interactions scores which can be used to predict protein-protein interactions (PPI). We show the robustness and insensitivity of the DomainGA method to the selection of the parameter sets, score ranges, and detection rules using the Yeast PPI data. In a two-fold cross-validation study, the DomainGA optimization achieves an explanation ratio of 99% and the cross validation test results are 97% and 88% for the positive and negative PPIs, respectively. We discuss how the DomainGA method significantly improves on the random predictions, particularly for predicting the non-interacting protein pairs. Based on our cross-verification tests on Human PPI, comparison of the optimized scores with the structurally observed domain interactions obtained from the iPFAM database, and sensitivity & specificity analysis; we conclude that our DomainGA method shows great promise to be applicable across multiple organisms. Conclusions:We envision the DomainGA as a first step of a multiple tier approach to constructing PPIs. As it is based on the fundamental structural information, DomainGA approach can be used to create the potential PPIs and the accuracy of the constructed interaction template can be improved later using complementary methods such as literature search or other prediction methods. Obtained explanation ratios during the reported test

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. Face to Face: Anthropometry-Based Interactive Face Shape Modeling Using Model Priors

    OpenAIRE

    Yu Zhang; Prakash, Edmond C.

    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 compon...

  6. Support for Interactive Features of E-learning Content Based on the Formal Theory

    Directory of Open Access Journals (Sweden)

    Oleg BISIKALO

    2014-03-01

    Full Text Available A formal theory based on a binary operator of directional associative relation is constructed in the article and an understanding of an associative normal form of image constructions is introduced. A model of a commutative semigroup, which provides a presentation of a sentence as three components of an interrogative linguistic image construction, is considered. Given examples demonstrate development of interactive features of e-Learning content.

  7. Three Nodes Acoustic Element for Fluid-Structure Interaction Based on a Parameterized Variational Principle

    Directory of Open Access Journals (Sweden)

    Correa S.

    2011-10-01

    Full Text Available This article presents a finite element formulation based on a parameterized variational principle for solving plane problems of fluid-structure interaction using the displacements as state variable for both solid and fluid media. The circular spurious modes, typical of displacement formulations are avoided. The penalty parameter is not random because it is selected according to energy criterion. Finally the formulation is not sensible to the definition of the normal direction in the fluid-structure interface.

  8. 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

  9. 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...

  10. 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...

  11. 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...

  12. 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.

  13. 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...

  14. Vector rectangular-shape laser based on reduced graphene oxide interacting with long fiber taper

    OpenAIRE

    Gao, Lei; Zhu, Tao; 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...

  15. 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...

  16. 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.

  17. Simultaneous structure and geometry detail completion based on interactive user sketches

    Institute of Scientific and Technical Information of China (English)

    YANG Shen; QI Yue; QIN Hong

    2012-01-01

    We articulate a novel approach to geometric model completion via interactive sketches in this paper.First,the initial incomplete model (with holes) is decomposed into a base model and a high-frequency component,which represents global rough shape and geometric details,respectively.We then repair the base model via smooth hole-filling,and compute the geometry detail image using high frequency information.One novel element of our approach is that we allow users to interactively sketch a few structural curves that span across hole regions,with a goal to repair both local geometric details and global structure.With the help of local parameterization,we convert detailed geometry into gradient-domain images which can propagate along user-specified sketches.By integrating recovered gradient-domain images and base shape,we can generate a complete model that faithfully recovers both global structure and local details.The salient contribution of this paper is the unified approach for user interaction,global structure,and geometry details towards high-fidelity model completion.We demonstrate our new approach using a number of examples that exhibit salient global structure as well as local geometry details.

  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)

    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.

  19. 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.

  20. A Context-Aware Infrastructure for Supporting Applications with Pen-Based Interaction

    Institute of Scientific and Technical Information of China (English)

    LI Yang(栗阳); GUAN ZhiWei(关志伟); DAI GuoZhong(戴国忠); REN XiangShi(任向实); HAN Yong(韩勇)

    2003-01-01

    Pen-based user interfaces which leverage the affordances of the pen provide userswith more flexibility and natural interaction. However, it is difficult to construct usable pen-baseduser interfaces because of the lack of support for their development. Toolkit-level support has beenexploited to solve this problem, but this approach makes it hard to gain platform independence,easy maintenance and easy extension. In this paper a context-aware infrastructure is created,called WEAVER, to provide pen interaction services for both novel pen-based applications andlegacy GUI-based applications. WEAVER aims to support the pen as another standard interactivedevice along with the keyboard and mouse and present a high-level access interface to pen input.It employs application context to tailor its service to different applications. By modeling theapplication context and registering the relevant action adapters, WEAVER can offer services,such as gesture recognition, continuous handwriting and other fundamental ink manipulations, toappropriate applications. One of the distinct features of WEAVER is that off-the-shelf GUI-basedsoftware packages can be easily enhanced with pen interaction without modifying the existing code.In this paper, the architecture and components of WEAVER are described. In addition, examplesand feedbacks of its use are presented.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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...

  6. An Open-Source Web-Based Tool for Resource-Agnostic Interactive Translation Prediction

    Directory of Open Access Journals (Sweden)

    Daniel Torregrosa

    2014-09-01

    Full Text Available We present a web-based open-source tool for interactive translation prediction (ITP and describe its underlying architecture. ITP systems assist human translators by making context-based computer-generated suggestions as they type. Most of the ITP systems in literature are strongly coupled with a statistical machine translation system that is conveniently adapted to provide the suggestions. Our system, however, follows a resource-agnostic approach and suggestions are obtained from any unmodified black-box bilingual resource. This paper reviews our ITP method and describes the architecture of Forecat, a web tool, partly based on the recent technology of web components, that eases the use of our ITP approach in any web application requiring this kind of translation assistance. We also evaluate the performance of our method when using an unmodified Moses-based statistical machine translation system as the bilingual resource.

  7. 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.

  8. Assessing interactions among multiple physiological systems during walking outside a laboratory: An Android based gait monitor.

    Science.gov (United States)

    Sejdić, E; Millecamps, A; Teoli, J; Rothfuss, M A; Franconi, N G; Perera, S; Jones, A K; Brach, J S; Mickle, M H

    2015-12-01

    Gait function is traditionally assessed using well-lit, unobstructed walkways with minimal distractions. In patients with subclinical physiological abnormalities, these conditions may not provide enough stress on their ability to adapt to walking. The introduction of challenging walking conditions in gait can induce responses in physiological systems in addition to the locomotor system. There is a need for a device that is capable of monitoring multiple physiological systems in various walking conditions. To address this need, an Android-based gait-monitoring device was developed that enabled the recording of a patient's physiological systems during walking. The gait-monitoring device was tested during self-regulated overground walking sessions of fifteen healthy subjects that included 6 females and 9 males aged 18-35 years. The gait-monitoring device measures the patient's stride interval, acceleration, electrocardiogram, skin conductance and respiratory rate. The data is stored on an Android phone and is analyzed offline through the extraction of features in the time, frequency and time-frequency domains. The analysis of the data depicted multisystem physiological interactions during overground walking in healthy subjects. These interactions included locomotion-electrodermal, locomotion-respiratory and cardiolocomotion couplings. The current results depicting strong interactions between the locomotion system and the other considered systems (i.e., electrodermal, respiratory and cardiovascular systems) warrant further investigation into multisystem interactions during walking, particularly in challenging walking conditions with older adults.

  9. 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.

  10. 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.

  11. Interactions of Aqueous Imidazolium-Based Ionic Liquid Mixtures with Solid-Supported Phospholipid Vesicles

    Science.gov (United States)

    Losada-Pérez, Patricia; Khorshid, Mehran; Renner, Frank Uwe

    2016-01-01

    Despite the environmentally friendly reputation of ionic liquids (ILs), their safety has been recently questioned given their potential as cytotoxic agents. The fundamental mechanisms underlying the interactions between ILs and cells are less studied and by far not completely understood. Biomimetic films are here important biophysical model systems to elucidate fundamental aspects and mechanisms relevant for a large range of biological interaction ranging from signaling to drug reception or toxicity. Here we use dissipative quartz crystal microbalance QCM-D to examine the effect of aqueous imidazolium-based ionic liquid mixtures on solid-supported biomimetic membranes. Specifically, we assess in real time the effect of the cation chain length and the anion nature on a supported vesicle layer of the model phospholipid DMPC. Results indicate that interactions are mainly driven by the hydrophobic components of the IL, which significantly distort the layer and promote vesicle rupture. Our analyses evidence the gradual decrease of the main phase transition temperature upon increasing IL concentration, reflecting increased disorder by weakening of lipid chain interactions. The degree of rupture is significant for ILs with long hydrophobic cation chains and large hydrophobic anions whose behavior is reminiscent of that of antimicrobial peptides. PMID:27684947

  12. A viral-human interactome based on structural motif-domain interactions captures the human infectome.

    Directory of Open Access Journals (Sweden)

    Aldo Segura-Cabrera

    Full Text Available Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB. The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome and non-infectious diseases (human diseasome. The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets.

  13. Efficient techniques for wave-based sound propagation in interactive applications

    Science.gov (United States)

    Mehra, Ravish

    Sound propagation techniques model the effect of the environment on sound waves and predict their behavior from point of emission at the source to the final point of arrival at the listener. Sound is a pressure wave produced by mechanical vibration of a surface that propagates through a medium such as air or water, and the problem of sound propagation can be formulated mathematically as a second-order partial differential equation called the wave equation. Accurate techniques based on solving the wave equation, also called the wave-based techniques, are too expensive computationally and memory-wise. Therefore, these techniques face many challenges in terms of their applicability in interactive applications including sound propagation in large environments, time-varying source and listener directivity, and high simulation cost for mid-frequencies. In this dissertation, we propose a set of efficient wave-based sound propagation techniques that solve these three challenges and enable the use of wave-based sound propagation in interactive applications. Firstly, we propose a novel equivalent source technique for interactive wave-based sound propagation in large scenes spanning hundreds of meters. It is based on the equivalent source theory used for solving radiation and scattering problems in acoustics and electromagnetics. Instead of using a volumetric or surface-based approach, this technique takes an object-centric approach to sound propagation. The proposed equivalent source technique generates realistic acoustic effects and takes orders of magnitude less runtime memory compared to prior wave-based techniques. Secondly, we present an efficient framework for handling time-varying source and listener directivity for interactive wave-based sound propagation. The source directivity is represented as a linear combination of elementary spherical harmonic sources. This spherical harmonic-based representation of source directivity can support analytical, data

  14. A Modified Adaptive Lasso for Identifying Interactions in the Cox Model with the Heredity Constraint.

    Science.gov (United States)

    Wang, Lu; Shen, Jincheng; Thall, Peter F

    2014-10-01

    In many biomedical studies, identifying effects of covariate interactions on survival is a major goal. Important examples are treatment-subgroup interactions in clinical trials, and gene-gene or gene-environment interactions in genomic studies. A common problem when implementing a variable selection algorithm in such settings is the requirement that the model must satisfy the strong heredity constraint, wherein an interaction may be included in the model only if the interaction's component variables are included as main effects. We propose a modified Lasso method for the Cox regression model that adaptively selects important single covariates and pairwise interactions while enforcing the strong heredity constraint. The proposed method is based on a modified log partial likelihood including two adaptively weighted penalties, one for main effects and one for interactions. A two-dimensional tuning parameter for the penalties is determined by generalized cross-validation. Asymptotic properties are established, including consistency and rate of convergence, and it is shown that the proposed selection procedure has oracle properties, given proper choice of regularization parameters. Simulations illustrate that the proposed method performs reliably across a range of different scenarios.

  15. 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.

  16. Aerosol-cloud interactions (ACI) viewed by satellite and ground-based remote sensing

    Science.gov (United States)

    Kim, Yoo-Jun; Kim, Byung-Gon

    2013-05-01

    Various aerosol and cloud microphysical properties have been compared and examined for several years using ground-based remote sensing data from Atmospheric Radiation Measurement (ARM), which showed that the clouds with strong above-cloud inversions are more immune to variations in the meteorological environment and the associated aerosol-cloud interactions appear to be more dominant in nearly adiabatic clouds by comparing different environmental conditions. Meanwhile, MODIS (Moderate-Resolution Imaging Spectroradiometer) and NCEP/NCAR (National Centers for Environmental Prediction/National Center for Atmospheric Research) reanalysis data from 2001 to 2008 have been analysed to understand long-term aerosol and cloud optical properties, and their relationships in East Asia. Specifically only relationships between aerosol optical depth (AOD) and cloud fraction (CF) for the low-level liquid-phase clouds exhibit the overall positive correlation, being consistent with cloud lifetime effect. The results imply that ground-based remote sensing is probably better for the study of aerosol-cloud microphysical interactions, whereas satellite remote sensing is more appropriate for the study of aerosol and cloud macroscopic interactions.

  17. 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.

  18. 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.

  19. Interaction Mechanism Insights on the Solvation of Fullerene B(80)with Choline-based Ionic Liquids.

    Science.gov (United States)

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2015-09-24

    Beyond carbon allotropes, other nanostructures such as fullerene B80 are attracting a growing interest due to their potential applications. The use of new materials based on fullerene B80 is still in a premature stage; however many of these applications would require the use of B80 in solution. This paper reports an unprecedented density functional theory (DFT) analysis on the interaction mechanism between B80 and two choline-based ionic liquids as a first insight for the fullerene B80 solvation by ionic liquids. The analysis of properties such as binding energies, charge distributions or intermolecular interactions shed light on the main features, which should govern interaction between ionic liquids and fullerene B80. In addition, the optimization of systems composed by six ionic pairs around a fullerene B80 has supplied some information about the first solvation shell at the molecular level. As a summary, this paper provides the first insights in the rational design of ionic liquids with suitable properties for the solvation of B80.

  20. 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.

  1. 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.

  2. 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.

  3. Interactions between Antibiotics and Graphene-Based Materials in Water: A Comparative Experimental and Theoretical Investigation.

    Science.gov (United States)

    Zhang, Xuntong; Shen, Jiachun; Zhuo, Ning; Tian, Ziqi; Xu, Peiran; Yang, Zhen; Yang, Weiben

    2016-09-14

    Complex interactions between antibiotics and graphene-based materials determine both the adsorption performance of graphene-based materials and the transport behaviors of antibiotics in water. In this work, such interactions were investigated through adsorption experiments, instrumental analyses and theoretical DFT calculations. Three typical antibiotics (norfloxacin (NOR), sulfadiazine (SDZ) and tetracycline (TC)) and different graphene-based materials (divided into two groups: graphene oxides-based ones (GOs) and reduced GOs (RGOs)) were employed. Optimal adsorption pHs for NOR, SDZ, and TC are 6.2, 4.0, and 4.0, respectively. At corresponding optimal pHs, NOR favored RGOs (adsorption capability: ∼50 mg/g) while SDZ preferred GOs (∼17 mg/g); All adsorbents exhibited similar uptake of TC (∼70 mg/g). Similar amounts of edge carboxyls of both GOs and RGOs wielded electrostatic attraction with NOR and TC, but not with SDZ. According to DFT-calculated most-stable-conformations of antibiotics-adsorbents complexes, the intrinsic distinction between GOs and RGOs was the different amounts of sp(2) and sp(3) hybridization regions: π-π electron donor-acceptor effect of antibiotic-sp(2)/sp(3) and H-bonds of antibiotic-sp(3) coexisted. Binding energy (BE) of the former was larger for NOR; the latter interaction was stronger for SDZ; two species of TC at the optimal pH, i.e., TC(+) and TC(0), possessed larger BE with sp(3) and sp(2) regions, respectively. PMID:27548426

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. Realization on the interactive remote video conference system based on multi-Agent

    Directory of Open Access Journals (Sweden)

    Zheng Yan

    2016-01-01

    Full Text Available To make people at different places participate in the same conference, speak and discuss freely, the interactive remote video conferencing system is designed and realized based on multi-Agent collaboration. FEC (forward error correction and tree P2P technology are firstly used to build a live conference structure to transfer audio and video data; then the branch conference port can participate to speak and discuss through the application of becoming a interactive focus; the introduction of multi-Agent collaboration technology improve the system robustness. The experiments showed that, under normal network conditions, the system can support 350 branch conference node simultaneously to make live broadcasting. The audio and video quality is smooth. It can carry out large-scale remote video conference.

  12. MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.

    Science.gov (United States)

    Berka, Karel; Hanák, Ondrej; Sehnal, David; Banás, Pavel; Navrátilová, Veronika; Jaiswal, Deepti; Ionescu, Crina-Maria; Svobodová Vareková, Radka; Koca, Jaroslav; Otyepka, Michal

    2012-07-01

    Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.

  13. Improving Human-Computer Interaction by Developing Culture-sensitive Applications based on Common Sense Knowledge

    CERN Document Server

    Anacleto, Junia Coutinho

    2010-01-01

    The advent of Web 3.0, claiming for personalization in interactive systems (Lassila & Hendler, 2007), and the need for systems capable of interacting in a more natural way in the future society flooded with computer systems and devices (Harper et al., 2008) show that great advances in HCI should be done. This chapter presents some contributions of LIA for the future of HCI, defending that using common sense knowledge is a possibility for improving HCI, especially because people assign meaning to their messages based on their common sense and, therefore, the use of this knowledge in developing user interfaces can make them more intuitive to the end-user. Moreover, as common sense knowledge varies from group to group of people, it can be used for developing applications capable of giving different feedback for different target groups, as the applications presented along this chapter illustrate, allowing, in this way, interface personalization taking into account cultural issues. For the purpose of using com...

  14. 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

  15. 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.

  16. Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions.

    Directory of Open Access Journals (Sweden)

    Ning Zhao

    Full Text Available Changes in intermolecular interactions (differential interactions may influence the progression of cancer. Specific genes and their regulatory networks may be more closely associated with cancer when taking their transcriptional and post-transcriptional levels and dynamic and static interactions into account simultaneously. In this paper, a differential interaction analysis was performed to detect lung adenocarcinoma-related genes. Furthermore, a miRNA-TF (transcription factor synergistic regulation network was constructed to identify three kinds of co-regulated motifs, namely, triplet, crosstalk and joint. Not only were the known cancer-related miRNAs and TFs (let-7, miR-15a, miR-17, TP53, ETS1, and so on were detected in the motifs, but also the miR-15, let-7 and miR-17 families showed a tendency to regulate the triplet, crosstalk and joint motifs, respectively. Moreover, several biological functions (i.e., cell cycle, signaling pathways and hemopoiesis associated with the three motifs were found to be frequently targeted by the drugs for lung adenocarcinoma. Specifically, the two 4-node motifs (crosstalk and joint based on co-expression and interaction had a closer relationship to lung adenocarcinoma, and so further research was performed on them. A 10-gene biomarker (UBC, SRC, SP1, MYC, STAT3, JUN, NR3C1, RB1, GRB2 and MAPK1 was selected from the joint motif, and a survival analysis indicated its significant association with survival. Among the ten genes, JUN, NR3C1 and GRB2 are our newly detected candidate lung adenocarcinoma-related genes. The genes, regulators and regulatory motifs detected in this work will provide potential drug targets and new strategies for individual therapy.

  17. 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

  18. 3D MODELLING AND INTERACTIVE WEB-BASED VISUALIZATION OF CULTURAL HERITAGE OBJECTS

    Directory of Open Access Journals (Sweden)

    M. N. Koeva

    2016-06-01

    Full Text Available 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Ni(II) complexes of arginine Schiff-bases and its interaction with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sallam, S.A., E-mail: shehabsallam@yahoo.com [Chemistry Department, Faculty of Science, Suez Canal University, Isamilia (Egypt); Abbas, A.M. [Chemistry Department, Faculty of Science, Suez Canal University, Isamilia (Egypt)

    2013-04-15

    Ni(II) complexes with Schiff-bases obtained by condensation of arginine with salicylaldehyde; 2,3-; 2,4-; 2,5-dihydroxybenzaldehyde and o-hydroxynaphthaldehyde have been synthesized using the template method in ethanol or ammonia media. They were characterized by elemental analyses, conductivity measurements, magnetic moment, UV, IR and {sup 1}H NMR spectra as well as thermal analysis (TG, DTG and DTA). The Schiff-bases are dibasic tridentate donors and the complexes have diamagnetic square planar and octahedral structures. The complexes decompose in three steps where kinetic and thermodynamic parameters of the decomposition steps were computed. The interactions of the formed complexes with FM-DNA were monitored by UV and fluorescence spectroscopy. -- Highlights: ► Arginine Schiff-bases and their nickel(II) complexes have been synthesized. ► Magnetic and spectral data show diamagnetic square planar and octahedral complexes. ► The complexes thermally decompose in three stages. Interaction with FM-DNA shows hyperchromism with blue shift.

  8. 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

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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...

  14. 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....

  15. Vector rectangular-shape laser based on reduced graphene oxide interacting with a long fiber taper.

    Science.gov (United States)

    Gao, Lei; Zhu, Tao; Huang, Wei; Zeng, Jing

    2014-10-01

    A vector dual-wavelength rectangular-shape laser (RSL) based on a long fiber taper deposited with reduced graphene oxide is proposed, where nonlinearity is enhanced due to a large evanescent-field-interacting length and strong field confinement of an 8 mm fiber taper with a waist diameter of 4 μm. 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 shows fast polarization switching in two orthogonal polarization directions, and temporal and spectral characteristics are investigated. PMID:25322232

  16. High-throughput and multiplexed regeneration buffer scouting for affinity-based interactions.

    Science.gov (United States)

    Geuijen, Karin P M; Schasfoort, Richard B; Wijffels, Rene H; Eppink, Michel H M

    2014-06-01

    Affinity-based analyses on biosensors depend partly on regeneration between measurements. Regeneration is performed with a buffer that efficiently breaks all interactions between ligand and analyte while maintaining the active binding site of the ligand. We demonstrated a regeneration buffer scouting using the combination of a continuous flow microspotter with a surface plasmon resonance imaging platform to simultaneously test 48 different regeneration buffers on a single biosensor. Optimal regeneration conditions are found within hours and consume little amounts of buffers, analyte, and ligand. This workflow can be applied to any ligand that is coupled through amine, thiol, or streptavidin immobilization.

  17. 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.

  18. [The study on the characters of membrane protein interaction and its network based on integrated intelligence method].

    Science.gov (United States)

    Shen, Yizhen; Ding, Yongsheng; Hao, Kuangrong

    2011-08-01

    Membrane protein and its interaction network have become a novel research direction in bioinformatics. In this paper, a novel membrane protein interaction network simulator is proposed for system biology studies by integrated intelligence method including spectrum analysis, fuzzy K-Nearest Neighbor(KNN) algorithm and so on. We consider biological system as a set of active computational components interacting with each other and with the external environment. Then we can use the network simulator to construct membrane protein interaction networks. Based on the proposed approach, we found that the membrane protein interaction network almost has some dynamic and collective characteristics, such as small-world network, scale free distributing, and hierarchical module structure. These properties are similar to those of other extensively studied protein interaction networks. The present studies on the characteristics of the membrane protein interaction network will be valuable for its relatively biological and medical studies. PMID:21936357

  19. Interaction model between capsule robot and intestine based on nonlinear viscoelasticity.

    Science.gov (United States)

    Zhang, Cheng; Liu, Hao; Tan, Renjia; Li, Hongyi

    2014-03-01

    Active capsule endoscope could also be called capsule robot, has been developed from laboratory research to clinical application. However, the system still has defects, such as poor controllability and failing to realize automatic checks. The imperfection of the interaction model between capsule robot and intestine is one of the dominating reasons causing the above problems. A model is hoped to be established for the control method of the capsule robot in this article. It is established based on nonlinear viscoelasticity. The interaction force of the model consists of environmental resistance, viscous resistance and Coulomb friction. The parameters of the model are identified by experimental investigation. Different methods are used in the experiment to obtain different values of the same parameter at different velocities. The model is proved to be valid by experimental verification. The achievement in this article is the attempted perfection of an interaction model. It is hoped that the model can optimize the control method of the capsule robot in the future.

  20. Interactions between students and tutor in problem-based learning: the significance of deep learning.

    Science.gov (United States)

    Azer, Samy A

    2009-05-01

    Problem-based learning (PBL) is an excellent opportunity for students to take responsibility for their learning and to develop a number of cognitive skills. These include identifying problems in the trigger, generating hypotheses, constructing mechanisms, developing an enquiry plan, ranking their hypotheses on the basis of available evidence, interpreting clinical and laboratory findings, identifying their learning needs, and dealing with uncertainty. Students also need to work collaboratively in their group, communicate effectively, and take active roles in the tutorials. Therefore, interaction in the group between students and their tutor is vital to ensure deep learning and successful outcomes. The aims of this paper are to discuss the key principles for successful interaction in PBL tutorials and to highlight the major symptoms of superficial learning and poor interactions. This comprises a wide range of symptoms for different group problems, including superficial learning. By early detection of such problems, tutors will be able to explore actions with the group and negotiate changes that can foster group dynamics and enforce deep learning.

  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. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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...

  10. 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.

  11. An object-based interaction framework for the operation of multiple field robots

    Science.gov (United States)

    Jones, Henry Lee, II

    Today's field robots, such as the Sojourner Mars rover or the Predator unmanned aerial vehicle, work alone to accomplish dirty, dull, or dangerous missions. Plans for the next generation of robotic systems call for multiple field robots to conduct these missions cooperatively under the direction of a single operator. This research examines the role of the operator in multiple-robot missions and creates a human-robot interaction framework that supports this role---a vital step toward the successful deployment of these future robots. In a typical user-centered approach to the development of a human-robot interaction framework, the work practices of the robot operator would be observed, characterized, and integrated into the design. Unfortunately, there are no settings where one can study the operator of multiple robots at work because no such systems have been deployed. As an alternative, this research incorporated a surrogate setting that could be used to inform the early interaction design of multiple-robot systems. Police Special Weapons and Tactics (SWAT) teams were chosen as this setting, and an ethnographic study of SWAT commanders was conducted. Concepts from the interdisciplinary study of geographically distributed work, including common ground, shared mental models, and information sharing, were used to understand and characterize the ethnographic observations. Using lessons learned from the surrogate setting, an implementation of a new human-robot interaction framework was demonstrated on the Micro Autonomous Rovers (MAR) platform in the Aerospace Robotics Laboratory at Stanford University. This interaction framework, which is based on the sensing and manipulation of physical objects by the robots, was derived from the finding that references to physical objects serve as an essential communication and coordination tool for SWAT commanders. A human-computer interface that utilizes direct manipulation techniques and three-dimensional computer graphics was

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Interactive and Symbolic Data Dependence AnalysisBased on Ranges of Expressions

    Institute of Scientific and Technical Information of China (English)

    杨博; 郑丰宙; 王鼎兴; 郑纬民

    2002-01-01

    Traditional data dependence testing algorithms have become very accurate and efficient for simple subscript expressions, but they cannot handle symbolic expressions because of the complexity of data-flow and lack of the semantic information of variables in programs. In this paper, a range-based testing and query approach, called DDTQ, is proposed to eliminate data dependence between array references with symbolic subscripts. DDTQ firstly extracts data dependence information from the symbolic subscripts, a testing algorithm is then used to disprove the dependence based on the ranges of expressions. The assumed dependence that cannot be handled by the disprover will be converted into simple questions by a question engine so that the compiler can solve them by user interaction in a friendly way. The experiment on perfect benchmarks indicates that DDTQ is effective in improving the parallelizing capability of the compiler.

  20. 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.

  1. 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.

  2. 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

    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...... home training of children with CP is an efficient way to deliver training, which can enable functional motor improvements and increased activity to perform daily activities. TRIAL REGISTRATION: ISRCTN13188513 . Date of registration: 04/12/2014....

  3. 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…

  4. Interaction potential for water dimer from symmetry-adapted perturbation theory based on density functional description of monomers

    NARCIS (Netherlands)

    Bukowski, R.; Szalewicz, K.; Groenenboom, G.C.; Avoird, A. van der

    2006-01-01

    A new six-dimensional interaction potential for the water dimer has been obtained by fitting interaction energies computed at 2510 geometries using a variant of symmetry-adapted perturbation theory (SAPT) based on density functional theory (DFT) description of monomers, referred to as SAPT(DFT). The

  5. 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.

  6. A 3D-video-based computerized analysis of social and sexual interactions in rats.

    Directory of Open Access Journals (Sweden)

    Jumpei Matsumoto

    Full Text Available A large number of studies have analyzed social and sexual interactions between rodents in relation to neural activity. Computerized video analysis has been successfully used to detect numerous behaviors quickly and objectively; however, to date only 2D video recording has been used, which cannot determine the 3D locations of animals and encounters difficulties in tracking animals when they are overlapping, e.g., when mounting. To overcome these limitations, we developed a novel 3D video analysis system for examining social and sexual interactions in rats. A 3D image was reconstructed by integrating images captured by multiple depth cameras at different viewpoints. The 3D positions of body parts of the rats were then estimated by fitting skeleton models of the rats to the 3D images using a physics-based fitting algorithm, and various behaviors were recognized based on the spatio-temporal patterns of the 3D movements of the body parts. Comparisons between the data collected by the 3D system and those by visual inspection indicated that this system could precisely estimate the 3D positions of body parts for 2 rats during social and sexual interactions with few manual interventions, and could compute the traces of the 2 animals even during mounting. We then analyzed the effects of AM-251 (a cannabinoid CB1 receptor antagonist on male rat sexual behavior, and found that AM-251 decreased movements and trunk height before sexual behavior, but increased the duration of head-head contact during sexual behavior. These results demonstrate that the use of this 3D system in behavioral studies could open the door to new approaches for investigating the neuroscience of social and sexual behavior.

  7. 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.

  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. Diffusion interaction and quantitative analysis of zinc dialkyldithiophosphate content in lube base oils in terahertz regime

    Institute of Scientific and Technical Information of China (English)

    Lu Tian; Kun Zhao; Qingli Zhou; Yulei Shi; Dongmei Zhao; Cunlin Zhang; Songqing Zhao

    2011-01-01

    We investigate the diffusion interaction and quantitative analysis of zinc dialkyldithiophosphate (ZDDP) mixed with lube base oil (LBO) at different concentrations using terahertz time-domain spectroscopy (THz-TDS). When the concentration exceeds 6.78%, the characteristic absorption peaks exhibit significantly shift, and the absorption coefficient peak value is nonlinear against concentration. Moreover, the absorption coefficients of mixed samples follow the Beer's law at a concentration below 6.78%. The quantitative analysis enables a strategy for monitoring the formulation of lubricating oil in real time.%Zinc dialkyldithiophosphate (ZDDP),as a multifunctional additive and inhibitor in petroleum industry,works mainly as antiwear,antioxidant,and anticorrosion agent[1,2].ZDDP mixed with lube base oils (LBOs)has been used to study the effect of concentration on lubrication boundary and tribological properties[3].The concentration of ZDDP in LBOs plays a crucial role in formulation,which is a balance of many different aspects of performance.Lubricating formulation generally results from a molecular diffusion mechanism due to the relative motion of molecules.Molecular diffusion in a steady-state and nonequilibrium system is divided into molecular motion and interaction.Molecular motion,containing the electronic motion,molecular vibration,and molecular rotation,is complicated and multibody.

  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. 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

  12. 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

  13. 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.

  14. 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

  15. 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...

  16. Interactive Web-based e-learning for Studying Flexible Manipulator Systems

    Directory of Open Access Journals (Sweden)

    Abul K. M. Azad

    2008-03-01

    Full Text Available Abstract— This paper presents a web-based e-leaning facility for simulation, modeling, and control of flexible manipulator systems. The simulation and modeling part includes finite difference and finite element simulations along with neural network and genetic algorithm based modeling strategies for flexible manipulator systems. The controller part constitutes a number of open-loop and closed-loop designs. Closed loop control designs include the classical, adaptive, and neuro-model based strategies. Matlab software package and its associated toolboxes are used to implement these. The Matlab web server is used as the gateway between the facility and web-access. ASP.NET technology and SQL database are utilized to develop web applications for access control, user account and password maintenance, administrative management, and facility utilization monitoring. The reported facility provides a flexible but effective approach of web-based interactive e-learning facility of an engineering system. This can be extended to incorporate additional engineering systems within the e-learning framework.

  17. Relative importance and interactions of furan precursors in sterilised, vegetable-based food systems.

    Science.gov (United States)

    Palmers, Stijn; Grauwet, Tara; Buvé, Carolien; Vanratingen, Koen; Kebede, Biniam T; Goos, Peter; Hendrickx, Marc E; Van Loey, Ann

    2016-01-01

    Mitigation strategies aimed at an intervention in the reaction pathways for furan formation (e.g., by adjusting precursor concentrations) might offer an additional route for furan reduction in sterilised, vegetable-based foods, without adverse effects on other food safety or quality attributes. As a first step towards product reformulation, the aim of the present study was to determine the relative importance and interactions of possible furan precursors in these types of foods. Based on an I-optimal experimental design, potato purée (naturally low in furan precursors) was spiked with known amounts of sugars, ascorbic acid, olive oil and β-carotene, and subjected to a thermal sterilisation. Significant correlations were observed between furan concentrations after thermal treatment and starting concentrations of ascorbic acid and monosaccharides (i.e., fructose and glucose). Ascorbic acid had a clear furan-reducing effect as an antioxidant by protecting (polyunsaturated) fatty acids against oxidative degradation. Fructose and glucose were the main precursors, which can most probably be attributed to their high, but realistic, concentrations in the product. The contributions of fatty acids and β-carotene were strongly dependent on redox interactions with other food constituents. In the same potato purées, only low concentrations (0-2 ng g(-1) purée) of 2-methylfuran were detected, indicating that the direct importance of the spiked food constituents as a precursor for methylfuran formation was rather small. Based on the results of this study, reducing the amount of monosaccharides or adjusting the redox conditions of the matrix are suggested as two possible approaches for furan mitigation on the product side. PMID:26605424

  18. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    Energy Technology Data Exchange (ETDEWEB)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I., E-mail: igalsz@northwestern.edu [Department of Biomedical Engineering, Department of Chemistry, and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3100 (United States)

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  19. Effects of surface charge on interfacial interactions related to membrane fouling in a submerged membrane bioreactor based on thermodynamic analysis.

    Science.gov (United States)

    Cai, Huihui; Fan, Hao; Zhao, Leihong; Hong, Huachang; Shen, Liguo; He, Yiming; Lin, Hongjun; Chen, Jianrong

    2016-03-01

    Effects of both membrane and sludge foulant surface zeta potentials on interfacial interactions between membrane and sludge foulant in different interaction scenarios were systematically investigated based on thermodynamic methods. Under conditions in this study, it was found that zeta potential had marginal effects on total interfacial interaction between two infinite planar surfaces, and the total interfacial interaction between foulant particles and membrane would be more repulsive with increase of absolute value of zeta potential. Adhesion of foulant particles on membrane surface should overcome an energy barrier. There exists a critical zeta potential below which energy barrier would disappear. Results also showed that rough surface membrane corresponded to significantly low strength of interfacial interactions. This study not only provided a series of methods to quantitatively assess the interfacial interactions between membrane and sludge foulants, but also reconciled the contradictory conclusions regarding effects of zeta potential in literature, giving important implications for membrane fouling mitigation.

  20. A prototype of an interactive web-based risk analysis tool for floods and landslides

    Science.gov (United States)

    Aye, Zar Chi; Jaboyedoff, Michel; Derron, Marc-Henri

    2015-04-01

    Within the framework of the European project CHANGES, we developed a prototype web-GIS based risk analysis tool for natural hazards, in particular for floods and landslides, based on open-source geospatial software and technologies. This tool is developed based on Boundless (Opengeo) framework and its client side SDK environment with customized plugins for the risk analysis and data management modules of the web based decision support platform. Free and open source components were applied: PostGIS spatial database, GeoServer and GeoWebCache for application servers with tile cache and GeoExt and OpenLayers for user interface development of the platform. The aim of the presented tool is to assist the experts (risk managers) in analyzing the impacts and consequences of a certain hazard event in the considered region as well as to support the responsible authorities and decision makers in making decisions for selection of risk management strategies to be implemented in the region. Within the platform, the users can provide (upload) the necessary maps and data such as hazard maps, elements at risk maps and vulnerability information. For the vulnerability component of the platform, the users can not only upload the vulnerability tables of a certain elements at risk for a given range of hazard intensity values but also create own vulnerability curves by giving the parameter values of a built-in vulnerability function of the platform. Based on these provided input information, the losses (amount of damages and number of people killed) of a certain hazard scenario are calculated on-the-fly and visualized interactively in the web-GIS interface of the platform. The annualized risk per year can also be obtained based on the combination of these calculated loss scenarios with different return periods of a hazard event. The application of the tool at a regional scale is demonstrated using one of the case study sites, Fella River of North Eastern Italy, of the CHANGES project.

  1. Protein–Protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM

    Indian Academy of Sciences (India)

    Brijesh Kumar Sriwastava; Subhadip Basu; Ujjwal Maulik

    2015-10-01

    Protein–protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

  2. PKQuest_Java: free, interactive physiologically based pharmacokinetic software package and tutorial

    Directory of Open Access Journals (Sweden)

    Levitt David G

    2009-08-01

    Full Text Available Abstract Background Physiologically based pharmacokinetics (PBPK uses a realistic organ model to describe drug kinetics. The blood-tissue exchange of each organ is characterized by its volume, perfusion, metabolism, capillary permeability and blood/tissue partition coefficient. PBPK applications require both sophisticated mathematical modeling software and a reliable complete set of physiological parameters. Currently there are no software packages available that combine ease of use with the versatility that is required of a general PBPK program. Findings The program is written in Java and is available for free download at http://www.pkquest.com/. Included in the download is a detailed tutorial that discusses the pharmacokinetics of 6 solutes (D2O, amoxicillin, desflurane, propofol, ethanol and thiopental illustrated using experimental human pharmacokinetic data. The complete PBPK description for each solute is stored in Excel spreadsheets that are included in the download. The main features of the program are: 1 Intuitive and versatile interactive interface; 2 Absolute and semi-logarithmic graphical output; 3 Pre-programmed optimized human parameter data set (but, arbitrary values can be input; 4 Time dependent changes in the PBPK parameters; 5 Non-linear parameter optimization; 6 Unique approach to determine the oral "first pass metabolism" of non-linear solutes (e.g. ethanol; 7 Pulmonary perfusion/ventilation heterogeneity for volatile solutes; 8 Input and output of Excel spreadsheet data; 9 Antecubital vein sampling. Conclusion PKQuest_Java is a free, easy to use, interactive PBPK software routine. The user can either directly use the pre-programmed optimized human or rat data set, or enter an arbitrary data set. It is designed so that drugs that are classified as "extracellular" or "highly fat soluble" do not require information about tissue/blood partition coefficients and can be modeled by a minimum of user input parameters. PKQuest

  3. Hubbard interactions in iron-based pnictides and chalcogenides: Slater parametrization, screening channels, and frequency dependence

    Science.gov (United States)

    van Roekeghem, Ambroise; Vaugier, Loïg; Jiang, Hong; Biermann, Silke

    2016-09-01

    We calculate the strength of the frequency-dependent on-site electronic interactions in the iron pnictides LaFeAsO, BaFe2As2 , BaRu2As2 , and LiFeAs and the chalcogenide FeSe from first principles within the constrained random phase approximation. We discuss the accuracy of an atomiclike parametrization of the two-index density-density interaction matrices based on the calculation of an optimal set of three independent Slater integrals, assuming that the angular part of the Fe d localized orbitals can be described within spherical harmonics as for isolated Fe atoms. We show that its quality depends on the ligand-metal bonding character rather than on the dimensionality of the lattice: it is excellent for ionic-like Fe-Se (FeSe) chalcogenides and a more severe approximation for more covalent Fe-As (LaFeAsO, BaFe2As2 ) pnictides. We furthermore analyze the relative importance of different screening channels, with similar conclusions for the different pnictides but a somewhat different picture for the benchmark oxide SrVO3: the ligand channel does not appear to be dominant in the pnictides, while oxygen screening is the most important process in the oxide. Finally, we analyze the frequency dependence of the interaction. In contrast to simple oxides, in iron pnictides its functional form cannot be simply modeled by a single plasmon, and the actual density of modes enters the construction of an effective Hamiltonian determining the low-energy properties.

  4. NMR-based approach to measure the free energy of transmembrane helix-helix interactions.

    Science.gov (United States)

    Mineev, Konstantin S; Lesovoy, Dmitry M; Usmanova, Dinara R; Goncharuk, Sergey A; Shulepko, Mikhail A; Lyukmanova, Ekaterina N; Kirpichnikov, Mikhail P; Bocharov, Eduard V; Arseniev, Alexander S

    2014-01-01

    Knowledge of the energetic parameters of transmembrane helix-helix interactions is necessary for the establishment of a structure-energy relationship for α-helical membrane domains. A number of techniques have been developed to measure the free energies of dimerization and oligomerization of transmembrane α-helices, and all of these have their advantages and drawbacks. In this study we propose a methodology to determine the magnitudes of the free energy of interactions between transmembrane helices in detergent micelles. The suggested approach employs solution nuclear magnetic resonance (NMR) spectroscopy to determine the population of the oligomeric states of the transmembrane domains and introduces a new formalism to describe the oligomerization equilibrium, which is based on the assumption that both the dimerization of the transmembrane domains and the dissociation of the dimer can occur only upon the collision of detergent micelles. The technique has three major advantages compared with other existing approaches: it may be used to analyze both weak and relatively strong dimerization/oligomerization processes, it works well for the analysis of complex equilibria, e.g. when monomer, dimer and high-order oligomer populations are simultaneously present in the solution, and it can simultaneously yield both structural and energetic characteristics of the helix-helix interaction under study. The proposed methodology was applied to investigate the oligomerization process of transmembrane domains of fibroblast growth factor receptor 3 (FGFR3) and vascular endothelium growth factor receptor 2 (VEGFR2), and allowed the measurement of the free energy of dimerization of both of these objects. In addition the proposed method was able to describe the multi-state oligomerization process of the VEGFR2 transmembrane domain. PMID:24036227

  5. Prediction of drug-target interactions for drug repositioning only based on genomic expression similarity.

    Directory of Open Access Journals (Sweden)

    Kejian Wang

    Full Text Available Small drug molecules usually bind to multiple protein targets or even unintended off-targets. Such drug promiscuity has often led to unwanted or unexplained drug reactions, resulting in side effects or drug repositioning opportunities. So it is always an important issue in pharmacology to identify potential drug-target interactions (DTI. However, DTI discovery by experiment remains a challenging task, due to high expense of time and resources. Many computational methods are therefore developed to predict DTI with high throughput biological and clinical data. Here, we initiatively demonstrate that the on-target and off-target effects could be characterized by drug-induced in vitro genomic expression changes, e.g. the data in Connectivity Map (CMap. Thus, unknown ligands of a certain target can be found from the compounds showing high gene-expression similarity to the known ligands. Then to clarify the detailed practice of CMap based DTI prediction, we objectively evaluate how well each target is characterized by CMap. The results suggest that (1 some targets are better characterized than others, so the prediction models specific to these well characterized targets would be more accurate and reliable; (2 in some cases, a family of ligands for the same target tend to interact with common off-targets, which may help increase the efficiency of DTI discovery and explain the mechanisms of complicated drug actions. In the present study, CMap expression similarity is proposed as a novel indicator of drug-target interactions. The detailed strategies of improving data quality by decreasing the batch effect and building prediction models are also effectively established. We believe the success in CMap can be further translated into other public and commercial data of genomic expression, thus increasing research productivity towards valid drug repositioning and minimal side effects.

  6. Fuzzy Integral-Based Gaze Control of a Robotic Head for Human Robot Interaction.

    Science.gov (United States)

    Yoo, Bum-Soo; Kim, Jong-Hwan

    2015-09-01

    During the last few decades, as a part of effort to enhance natural human robot interaction (HRI), considerable research has been carried out to develop human-like gaze control. However, most studies did not consider hardware implementation, real-time processing, and the real environment, factors that should be taken into account to achieve natural HRI. This paper proposes a fuzzy integral-based gaze control algorithm, operating in real-time and the real environment, for a robotic head. We formulate the gaze control as a multicriteria decision making problem and devise seven human gaze-inspired criteria. Partial evaluations of all candidate gaze directions are carried out with respect to the seven criteria defined from perceived visual, auditory, and internal inputs, and fuzzy measures are assigned to a power set of the criteria to reflect the user defined preference. A fuzzy integral of the partial evaluations with respect to the fuzzy measures is employed to make global evaluations of all candidate gaze directions. The global evaluation values are adjusted by applying inhibition of return and are compared with the global evaluation values of the previous gaze directions to decide the final gaze direction. The effectiveness of the proposed algorithm is demonstrated with a robotic head, developed in the Robot Intelligence Technology Laboratory at Korea Advanced Institute of Science and Technology, through three interaction scenarios and three comparison scenarios with another algorithm.

  7. Micellar interactions in water-AOT based droplet microemulsions containing hydrophilic and amphiphilic polymers

    Science.gov (United States)

    Appel, Markus; Spehr, Tinka Luise; Wipf, Robert; Moers, Christian; Frey, Holger; Stühn, Bernd

    2013-11-01

    We investigate the influence of addition of hydrophilic and amphiphilic polymer on percolation behavior and micellar interactions in AOT-based water-in-oil droplet microemulsions. We focus on two series of samples having constant molar water to surfactant ratio W = 20 and constant droplet volume fraction Φ = 30%, respectively. From dielectric spectroscopy experiments, we extract the bending rigidity of the surfactant shell by percolation temperature measurements. Depending on droplet size, we find stabilization and destabilization of the surfactant shell upon addition of hydrophilic poly(ethylene glycol) (PEG) (Mn = 3100 g mol-1) and amphiphilic poly(styrene)-b-poly(ethylene glycol) copolymer with comparable length of the hydrophilic block. Complementary small angle X-ray scattering experiments corroborate the finding of stabilization for smaller droplets and destabilization of larger droplets. Subsequent analysis of dielectric spectra enables us to extract detailed information about micellar interactions and clustering by evaluating the dielectric high frequency shell relaxation. We interpret the observed results as a possible modification of the inter-droplet charge transfer efficiency by addition of PEG polymer, while the amphiphilic polymer shows a comparable, but dampened effect.

  8. Clustering Gene Expression Data Based on Predicted Differential Effects of G V Interaction

    Institute of Scientific and Technical Information of China (English)

    Hai-Yan Pan; Jun Zhu; Dan-Fu Han

    2005-01-01

    Microarray has become a popular biotechnology in biological and medical research.However, systematic and stochastic variabilities in microarray data are expected and unavoidable, resulting in the problem that the raw measurements have inherent "noise" within microarray experiments. Currently, logarithmic ratios are usually analyzed by various clustering methods directly, which may introduce bias interpretation in identifying groups of genes or samples. In this paper, a statistical method based on mixed model approaches was proposed for microarray data cluster analysis. The underlying rationale of this method is to partition the observed total gene expression level into various variations caused by different factors using an ANOVA model, and to predict the differential effects of G V (gene by variety)interaction using the adjusted unbiased prediction (AUP) method. The predicted G V interaction effects can then be used as the inputs of cluster analysis. We illustrated the application of our method with a gene expression dataset and elucidated the utility of our approach using an external validation.

  9. A feature-based approach to modeling protein-DNA interactions.

    Directory of Open Access Journals (Sweden)

    Eilon Sharon

    Full Text Available Transcription factor (TF binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position specific scoring matrix (PSSM, which assumes independence between binding positions. However, in many cases, this simplifying assumption does not hold. Here, we present feature motif models (FMMs, a novel probabilistic method for modeling TF-DNA interactions, based on log-linear models. Our approach uses sequence features to represent TF binding specificities, where each feature may span multiple positions. We develop the mathematical formulation of our model and devise an algorithm for learning its structural features from binding site data. We also developed a discriminative motif finder, which discovers de novo FMMs that are enriched in target sets of sequences compared to background sets. We evaluate our approach on synthetic data and on the widely used TF chromatin immunoprecipitation (ChIP dataset of Harbison et al. We then apply our algorithm to high-throughput TF ChIP data from mouse and human, reveal sequence features that are present in the binding specificities of mouse and human TFs, and show that FMMs explain TF binding significantly better than PSSMs. Our FMM learning and motif finder software are available at http://genie.weizmann.ac.il/.

  10. NUMERICAL METHOD FOR MULTI-BODY FLUID INTERACTION BASED ON IMMERSED BOUNDARY METHOD

    Institute of Scientific and Technical Information of China (English)

    MING Ping-jian; ZHANG Wen-ping

    2011-01-01

    A Cartesian grid based on Immersed Boundary Method(IBM),proposed by the present authors,is extended to unstructured grids.The advantages of IBM and Body Fitted Grid(BFG)are taken to enhance the computation efficiency of the fluid structure interaction in a complex domain.There are many methods to generate the BFG,among which the unstructured grid method is the most popular.The concept of Volume Of Solid(VOS)is used to deal with the multi rigid body and fluid interaction.Each body surface is represented by a set of points which can be traced in an anti-clockwise order with the solid area on the left side of surface.An efficient Lagrange point tracking algorithm on the fixed grid is applied to search the moving boundary grid points.This method is verified by low Reynolds number flows in the range from Re =100 to 1 000 in the cavity with a moving lid.The results are in a good agreement with experimental data in literature.Finally,the flow past two moving cylinders is simulated to test the capability of the method.

  11. Prediction of Protein-Protein Interaction By Metasample-Based Sparse Representation

    Directory of Open Access Journals (Sweden)

    Xiuquan Du

    2015-01-01

    Full Text Available Protein-protein interactions (PPIs play key roles in many cellular processes such as transcription regulation, cell metabolism, and endocrine function. Understanding these interactions takes a great promotion to the pathogenesis and treatment of various diseases. A large amount of data has been generated by experimental techniques; however, most of these data are usually incomplete or noisy, and the current biological experimental techniques are always very time-consuming and expensive. In this paper, we proposed a novel method (metasample-based sparse representation classification, MSRC for PPIs prediction. A group of metasamples are extracted from the original training samples and then use the l1-regularized least square method to express a new testing sample as the linear combination of these metasamples. PPIs prediction is achieved by using a discrimination function defined in the representation coefficients. The MSRC is applied to PPIs dataset; it achieves 84.9% sensitivity, and 94.55% specificity, which is slightly lower than support vector machine (SVM and much higher than naive Bayes (NB, neural networks (NN, and k-nearest neighbor (KNN. The result shows that the MSRC is efficient for PPIs prediction.

  12. Energy spectra of KASCADE-Grande based on shower size measurements and different hadronic interaction models

    CERN Document Server

    Kang, D; Arteaga-Velazquez, J C; Bekk, K; Bertaina, M; Bluemer, J; Bozdog, H; Brancus, I M; Cantoni, E; Chiavassa, A; Cossavella, F; Curcio, C; Daumiller, K; de Souza, V; Di Pierro, F; Doll, P; Engel, R; Engler, J; Fuchs, B; Fuhrmann, D; Gils, H J; Glasstetter, R; Grupen, C; Haungs, A; Heck, D; Hoerandel, J R; Huber, D; Huege, T; Kampert, K -H; Klages, H O; Link, K; Luczak, P; Ludwig, M; Mathes, H J; Mayer, H J; Melissas, M; Milke, J; Mitrica, B; Morello, C; Oehlschlaeger, J; Ostapchenko, S; Palmieri, N; Petcu, M; Pierog, T; Rebel, H; Roth, M; Schieler, H; Schoo, S; Schroeder, F G; Sima, O; Toma, G; Trinchero, G C; Ulrich, H; Weindl, A; Wochele, D; Wochele, J

    2013-01-01

    KASCADE-Grande is dedicated for investigations of cosmic-ray air showers in the primary energy range from 10 PeV to 1 EeV. The multi-detector system allows us to reconstruct charged particles, electron and muon numbers for individual air showers with high accuracies. Based on the shower size ($N_{ch}$) spectra of the charged particle component, the all-particle energy spectrum of cosmic rays is reconstructed, where attenuation effects in the atmosphere are corrected by applying the constant intensity cut method. The energy calibration is performed by using CORSIKA simulations with high-energy interaction models QGSJET-II-2, QGSJET-II-4, EPOS 1.99 and SIBYLL 2.1, where FLUKA has been used as low-energy interaction model for all cases. In the different hadronic models, different abundances for shower particles are predicted. Such model differences in the observables will be compared and discussed in this contribution. Furthermore, by using data with increasing statistics, the updated energy spectra by means of ...

  13. Context-aware computing-based reducing cost of service method in resource discovery and interaction

    Institute of Scientific and Technical Information of China (English)

    TANG Shan-cheng; HOU Yi-bin

    2004-01-01

    Reducing cost of service is an important goal for resource discovery and interaction technologies. The shortcomings of transhipment-method and hibernation-method are to increase holistic cost of service and to slower resource discovery respectively. To overcome these shortcomings, a context-aware computing-based method is developed. This method, firstly,analyzes the courses of devices using resource discovery and interaction technologies to identify some types of context related to reducing cost of service, then, chooses effective methods such as stopping broadcast and hibernation to reduce cost of service according to information supplied by the context but not the transhipment-method's simple hibernations. The results of experiments indicate that under the worst condition this method overcomes the shortcomings of transhipment-method, makes the "poor" devices hibernate longer than hibernation-method to reduce cost of service more effectively, and discovers resources faster than hibernation-method; under the best condition it is far better than hibernation-method in all aspects.

  14. Interactions between excitation and extraction modes in an organic-based plasmon-emitting diode

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Nan-Fu, E-mail: nfchiu@ntnu.edu.tw [Institute of Electro-Optical Science and Technology, National Taiwan Normal University, Taipei 11677, Taiwan (China); Le Ster, Maxime [Institute of Electro-Optical Science and Technology, National Taiwan Normal University, Taipei 11677, Taiwan (China); Material Sciences and Engineering, Institut National des Sciences Appliquées de Rennes, Rennes 35708 (France); Yang, Cheng-Du [Institute of Electro-Optical Science and Technology, National Taiwan Normal University, Taipei 11677, Taiwan (China); Tseng, Ming-Hung; Tsai, Feng-Yu [Department of Material Science and Engineering, National Taiwan University, Taipei 10617, Taiwan (China)

    2015-03-30

    Highlights: • Directional emission properties give rise to a spectral band-gap response enhancement. • The subsequent emission intensity can increase by up to 3.5 times. • FWHM of approximately 60 nm in a defined direction is achieved. • SP coupling rate is approximately 80% on the metal grating structure. - Abstract: This study demonstrates the feasibility of enhancing an organic-based plasmon-emitting diode on the directional light beaming efficiency by near-field surface plasmon polaritons (SPPs) in both metal grating and polymer grating nanostructures. The interaction between organic/metal and PR/metal interfaces to cause SPPs can facilitate specific directional emission. Directional emission properties give rise to a spectral band-gap response enhancement. Our results also verify that efficient surface plasmon grating coupled emissions (SPGCEs) can improve directionality under index-mediated tuning. Experimental results indicate SP decoupling emission in the visible light. The subsequent emission intensity can increase by up to 3.5 times. Moreover, a narrow FWHM of approximately 60 nm in a defined direction is achieved, and an SP coupling rate is approximately 80% on the metal grating structure. The proposed method is highly promising for use as an active plasmonic emitter and discoloration biosensors with enhanced SPPs resonance energy, owing to interactions with the organic/metal nanostructure.

  15. A systematic identification of multiple toxin-target interactions based on chemical, genomic and toxicological data.

    Science.gov (United States)

    Zhou, Wei; Huang, Chao; Li, Yan; Duan, Jinyou; Wang, Yonghua; Yang, Ling

    2013-02-01

    Although the assessment of toxicity of various agents, -omics (genomic, proteomic, metabolomic, etc.) data has been accumulated largely, the acquirement of toxicity information of variety of molecules through experimental methods still remains a difficult task. Presently, a systems toxicology approach that integrates massive diverse chemical, genomic and toxicological information was developed for prediction of the toxin targets and their related networks. The procedures are: (1) by use of two powerful statistical methods, i.e., support vector machine (SVM) and random forest (RF), a systemic model for prediction of multiple toxin-target interactions using the extracted chemical and genomic features has been developed with its reliability and robustness estimated. And the qualitative classification of targets according to the phenotypic diseases has been taken into account to further uncover the biological meaning of the targets, as well as to validate the robustness of the in silico models. (2) Based on the predicted toxin-target interactions, a genome-scale toxin-target-disease network exampled by cardiovascular disease is generated. (3) A topological analysis of the network is carried out to identify those targets that are most susceptible in human to topical agents including the most critical toxins, as well as to uncover both the toxin-specific mechanisms and pathways. The methodologies presented herein for systems toxicology will make drug development, toxin environmental risk assessment more efficient, acceptable and cost-effective.

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

    Science.gov (United States)

    Ravikumar, Vaishnavi; Jers, Carsten; Mijakovic, Ivan

    2015-01-01

    Microbes with the capability to survive in the host tissue and efficiently subvert its innate immune responses can cause various health hazards. There is an inherent need to understand microbial infection patterns and mechanisms in order to develop efficient therapeutics. Microbial pathogens 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 can be efficiently applied to gain an insight into the molecular mechanisms involved. The measurement of the proteome and post-translationally modified proteome dynamics using mass spectrometry, results in a wide array of information, such as significant changes in protein expression, protein abundance, the modification status, the site occupancy level, interactors, functional significance of key players, potential drug targets, etc. This mini review discusses the potential of proteomics to investigate the involvement of post-translational modifications in bacterial pathogenesis and host–pathogen interactions. PMID:26635773

  17. A Multilayer Hidden Markov Models-Based Method for Human-Robot Interaction

    Directory of Open Access Journals (Sweden)

    Chongben Tao

    2013-01-01

    Full Text Available To achieve Human-Robot Interaction (HRI by using gestures, a continuous gesture recognition approach based on Multilayer Hidden Markov Models (MHMMs is proposed, which consists of two parts. One part is gesture spotting and segment module, the other part is continuous gesture recognition module. Firstly, a Kinect sensor is used to capture 3D acceleration and 3D angular velocity data of hand gestures. And then, a Feed-forward Neural Networks (FNNs and a threshold criterion are used for gesture spotting and segment, respectively. Afterwards, the segmented gesture signals are respectively preprocessed and vector symbolized by a sliding window and a K-means clustering method. Finally, symbolized data are sent into Lower Hidden Markov Models (LHMMs to identify individual gestures, and then, a Bayesian filter with sequential constraints among gestures in Upper Hidden Markov Models (UHMMs is used to correct recognition errors created in LHMMs. Five predefined gestures are used to interact with a Kinect mobile robot in experiments. The experimental results show that the proposed method not only has good effectiveness and accuracy, but also has favorable real-time performance.

  18. Sensitive voltammetric detection of yeast RNA based on its interaction with Victoria Blue B

    Directory of Open Access Journals (Sweden)

    WEI SUN

    2009-12-01

    Full Text Available Voltammetric studies of the interaction of yeast RNA (y-RNA with Victoria Blue B (VBB are described in this paper. Furthermore, a linear sweep voltammetric method for the detection of y-RNA was established. The reaction conditions, such as acidity and amount of buffer solution, the concentration of VBB, the reaction time and temperature, etc., were carefully investigated by second order derivative linear sweep voltammetry. Under the optimal conditions, the reduction peak current of VBB at –0.75 V decreased greatly after the addition of y-RNA to the solution without any shift of the reduction peak potential. Based on the decrease of the peak current, a new quantitative method for the determination of y-RNA was developed. The effects of co-existing substances on the determination were carefully investigated and three synthetic samples were determined with satisfactory results. The stoichiometry of the VBB–y-RNA complex was calculated by linear sweep voltammetry and the interaction mechanism is discussed.

  19. Interactive sculpting of product shape based on constraint manipulation in virtual environment

    Institute of Scientific and Technical Information of China (English)

    LIU Zhen-yu; TAN Jian-rong

    2005-01-01

    In product concept design, not only designers with professional CAD skills, but also final customers take part in the design and evaluation of product shape styling. Because customers usually lack surface modelling background and are not familiar with concrete operations of commercial CAD systems, it is difficult for them to express their change intentions of product shape through professional CAD tools if they are not satisfied with the current shape design. This paper puts forward a method for creating, dragging and manipulating constraint and load represented in form of icon entity in interactive sculpting of product shape in virtual environment. The method supports customers manipulation of sculpting constraints or loads on sculpting shapes in virtual reality interaction to control the deformation of product shape. Constraints management based on icon entity is similar to spline lofting operation that is familiar to engineers, so users do not need to know surface details or have any professional knowledge of surface modelling, by only using their physical and engineering experience, they can manipulate the sculpting of product shape intuitively.

  20. Fuzzy Integral-Based Gaze Control of a Robotic Head for Human Robot Interaction.

    Science.gov (United States)

    Yoo, Bum-Soo; Kim, Jong-Hwan

    2015-09-01

    During the last few decades, as a part of effort to enhance natural human robot interaction (HRI), considerable research has been carried out to develop human-like gaze control. However, most studies did not consider hardware implementation, real-time processing, and the real environment, factors that should be taken into account to achieve natural HRI. This paper proposes a fuzzy integral-based gaze control algorithm, operating in real-time and the real environment, for a robotic head. We formulate the gaze control as a multicriteria decision making problem and devise seven human gaze-inspired criteria. Partial evaluations of all candidate gaze directions are carried out with respect to the seven criteria defined from perceived visual, auditory, and internal inputs, and fuzzy measures are assigned to a power set of the criteria to reflect the user defined preference. A fuzzy integral of the partial evaluations with respect to the fuzzy measures is employed to make global evaluations of all candidate gaze directions. The global evaluation values are adjusted by applying inhibition of return and are compared with the global evaluation values of the previous gaze directions to decide the final gaze direction. The effectiveness of the proposed algorithm is demonstrated with a robotic head, developed in the Robot Intelligence Technology Laboratory at Korea Advanced Institute of Science and Technology, through three interaction scenarios and three comparison scenarios with another algorithm. PMID:25312975