Inhibitory Mechanism of Apigenin on α-Glucosidase and Synergy Analysis of Flavonoids.

PubMed

Zeng, Li; Zhang, Guowen; Lin, Suyun; Gong, Deming

2016-09-21

Inhibition of α-glucosidase activity may suppress postprandial hyperglycemia. The inhibition kinetic analysis showed that apigenin reversibly inhibited α-glucosidase activity with an IC50 value of (10.5 ± 0.05) × 10(-6) mol L(-1), and the inhibition was in a noncompetitive manner through a monophasic kinetic process. The fluorescence quenching and conformational changes determined by fluorescence and circular dichroism were due to the formation of an α-glucosidase-apigenin complex, and the binding was mainly driven by hydrophobic interactions and hydrogen bonding. The molecular simulation showed that apigenin bound to a site close to the active site of α-glucosidase, which may induce the channel closure to prevent the access of substrate, eventually leading to the inhibition of α-glucosidase. Isobolographic analysis of the interaction between myricetin and apigenin or morin showed that both of them exhibited synergistic effects at low concentrations and tended to exhibit additive or antagonistic interaction at high concentrations.

Interaction between polymorphisms in aspirin metabolic pathways, regular aspirin use and colorectal cancer risk: A case-control study in unselected white European populations.

PubMed

Sheth, Harsh; Northwood, Emma; Ulrich, Cornelia M; Scherer, Dominique; Elliott, Faye; Barrett, Jennifer H; Forman, David; Wolf, C Roland; Smith, Gillian; Jackson, Michael S; Santibanez-Koref, Mauro; Haile, Robert; Casey, Graham; Jenkins, Mark; Win, Aung Ko; Hopper, John L; Marchand, Loic Le; Lindor, Noralane M; Thibodeau, Stephen N; Potter, John D; Burn, John; Bishop, D Timothy

2018-01-01

Regular aspirin use is associated with reduced risk of colorectal cancer (CRC). Variation in aspirin's chemoprevention efficacy has been attributed to the presence of single nucleotide polymorphisms (SNPs). We conducted a meta-analysis using two large population-based case-control datasets, the UK-Leeds Colorectal Cancer Study Group and the NIH-Colon Cancer Family Registry, having a combined total of 3325 cases and 2262 controls. The aim was to assess 42 candidate SNPs in 15 genes whose association with colorectal cancer risk was putatively modified by aspirin use, in the literature. Log odds ratios (ORs) and standard errors were estimated for each dataset separately using logistic regression adjusting for age, sex and study site, and dataset-specific results were combined using random effects meta-analysis. Meta-analysis showed association between SNPs rs6983267, rs11694911 and rs2302615 with CRC risk reduction (All P<0.05). Association for SNP rs6983267 in the CCAT2 gene only was noteworthy after multiple test correction (P = 0.001). Site-specific analysis showed association between SNPs rs1799853 and rs2302615 with reduced colon cancer risk only (P = 0.01 and P = 0.004, respectively), however neither reached significance threshold following multiple test correction. Meta-analysis of SNPs rs2070959 and rs1105879 in UGT1A6 gene showed interaction between aspirin use and CRC risk (Pinteraction = 0.01 and 0.02, respectively); stratification by aspirin use showed an association for decreased CRC risk for aspirin users having a wild-type genotype (rs2070959 OR = 0.77, 95% CI = 0.68-0.86; rs1105879 OR = 0.77 95% CI = 0.69-0.86) compared to variant allele cariers. The direction of the interaction however is in contrast to that published in studies on colorectal adenomas. Both SNPs showed potential site-specific interaction with aspirin use and colon cancer risk only (Pinteraction = 0.006 and 0.008, respectively), with the direction of association similar to that observed for CRC. Additionally, they showed interaction between any non-steroidal anti-inflammatory drugs (including aspirin) use and CRC risk (Pinteraction = 0.01 for both). All gene x environment (GxE) interactions however were not significant after multiple test correction. Candidate gene investigation indicated no evidence of GxE interaction between genetic variants in genes involved in aspirin pathways, regular aspirin use and colorectal cancer risk.

Interaction between polymorphisms in aspirin metabolic pathways, regular aspirin use and colorectal cancer risk: A case-control study in unselected white European populations

PubMed Central

Ulrich, Cornelia M.; Scherer, Dominique; Elliott, Faye; Barrett, Jennifer H.; Forman, David; Wolf, C. Roland; Smith, Gillian; Jackson, Michael S.; Santibanez-Koref, Mauro; Haile, Robert; Casey, Graham; Jenkins, Mark; Win, Aung Ko; Hopper, John L.; Marchand, Loic Le; Lindor, Noralane M.; Thibodeau, Stephen N.; Potter, John D.; Burn, John; Bishop, D. Timothy

2018-01-01

Regular aspirin use is associated with reduced risk of colorectal cancer (CRC). Variation in aspirin’s chemoprevention efficacy has been attributed to the presence of single nucleotide polymorphisms (SNPs). We conducted a meta-analysis using two large population-based case-control datasets, the UK-Leeds Colorectal Cancer Study Group and the NIH-Colon Cancer Family Registry, having a combined total of 3325 cases and 2262 controls. The aim was to assess 42 candidate SNPs in 15 genes whose association with colorectal cancer risk was putatively modified by aspirin use, in the literature. Log odds ratios (ORs) and standard errors were estimated for each dataset separately using logistic regression adjusting for age, sex and study site, and dataset-specific results were combined using random effects meta-analysis. Meta-analysis showed association between SNPs rs6983267, rs11694911 and rs2302615 with CRC risk reduction (All P<0.05). Association for SNP rs6983267 in the CCAT2 gene only was noteworthy after multiple test correction (P = 0.001). Site-specific analysis showed association between SNPs rs1799853 and rs2302615 with reduced colon cancer risk only (P = 0.01 and P = 0.004, respectively), however neither reached significance threshold following multiple test correction. Meta-analysis of SNPs rs2070959 and rs1105879 in UGT1A6 gene showed interaction between aspirin use and CRC risk (Pinteraction = 0.01 and 0.02, respectively); stratification by aspirin use showed an association for decreased CRC risk for aspirin users having a wild-type genotype (rs2070959 OR = 0.77, 95% CI = 0.68–0.86; rs1105879 OR = 0.77 95% CI = 0.69–0.86) compared to variant allele cariers. The direction of the interaction however is in contrast to that published in studies on colorectal adenomas. Both SNPs showed potential site-specific interaction with aspirin use and colon cancer risk only (Pinteraction = 0.006 and 0.008, respectively), with the direction of association similar to that observed for CRC. Additionally, they showed interaction between any non-steroidal anti-inflammatory drugs (including aspirin) use and CRC risk (Pinteraction = 0.01 for both). All gene x environment (GxE) interactions however were not significant after multiple test correction. Candidate gene investigation indicated no evidence of GxE interaction between genetic variants in genes involved in aspirin pathways, regular aspirin use and colorectal cancer risk. PMID:29425227

Agent Interaction with Human Systems in Complex Environments: Requirements for Automating the Function of CapCom in Apollo 17

NASA Technical Reports Server (NTRS)

Clancey, William J.

2003-01-01

A human-centered approach to computer systems design involves reframing analysis in terms of people interacting with each other, not only human-machine interaction. The primary concern is not how people can interact with computers, but how shall we design computers to help people work together? An analysis of astronaut interactions with CapCom on Earth during one traverse of Apollo 17 shows what kind of information was conveyed and what might be automated today. A variety of agent and robotic technologies are proposed that deal with recurrent problems in communication and coordination during the analyzed traverse.

Systematic analysis of video data from different human-robot interaction studies: a categorization of social signals during error situations.

PubMed

Giuliani, Manuel; Mirnig, Nicole; Stollnberger, Gerald; Stadler, Susanne; Buchner, Roland; Tscheligi, Manfred

2015-01-01

Human-robot interactions are often affected by error situations that are caused by either the robot or the human. Therefore, robots would profit from the ability to recognize when error situations occur. We investigated the verbal and non-verbal social signals that humans show when error situations occur in human-robot interaction experiments. For that, we analyzed 201 videos of five human-robot interaction user studies with varying tasks from four independent projects. The analysis shows that there are two types of error situations: social norm violations and technical failures. Social norm violations are situations in which the robot does not adhere to the underlying social script of the interaction. Technical failures are caused by technical shortcomings of the robot. The results of the video analysis show that the study participants use many head movements and very few gestures, but they often smile, when in an error situation with the robot. Another result is that the participants sometimes stop moving at the beginning of error situations. We also found that the participants talked more in the case of social norm violations and less during technical failures. Finally, the participants use fewer non-verbal social signals (for example smiling, nodding, and head shaking), when they are interacting with the robot alone and no experimenter or other human is present. The results suggest that participants do not see the robot as a social interaction partner with comparable communication skills. Our findings have implications for builders and evaluators of human-robot interaction systems. The builders need to consider including modules for recognition and classification of head movements to the robot input channels. The evaluators need to make sure that the presence of an experimenter does not skew the results of their user studies.

Systematic analysis of video data from different human–robot interaction studies: a categorization of social signals during error situations

PubMed Central

Giuliani, Manuel; Mirnig, Nicole; Stollnberger, Gerald; Stadler, Susanne; Buchner, Roland; Tscheligi, Manfred

2015-01-01

Human–robot interactions are often affected by error situations that are caused by either the robot or the human. Therefore, robots would profit from the ability to recognize when error situations occur. We investigated the verbal and non-verbal social signals that humans show when error situations occur in human–robot interaction experiments. For that, we analyzed 201 videos of five human–robot interaction user studies with varying tasks from four independent projects. The analysis shows that there are two types of error situations: social norm violations and technical failures. Social norm violations are situations in which the robot does not adhere to the underlying social script of the interaction. Technical failures are caused by technical shortcomings of the robot. The results of the video analysis show that the study participants use many head movements and very few gestures, but they often smile, when in an error situation with the robot. Another result is that the participants sometimes stop moving at the beginning of error situations. We also found that the participants talked more in the case of social norm violations and less during technical failures. Finally, the participants use fewer non-verbal social signals (for example smiling, nodding, and head shaking), when they are interacting with the robot alone and no experimenter or other human is present. The results suggest that participants do not see the robot as a social interaction partner with comparable communication skills. Our findings have implications for builders and evaluators of human–robot interaction systems. The builders need to consider including modules for recognition and classification of head movements to the robot input channels. The evaluators need to make sure that the presence of an experimenter does not skew the results of their user studies. PMID:26217266

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

PubMed

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

Tertiary structure-based analysis of microRNA–target interactions

PubMed Central

Gan, Hin Hark; Gunsalus, Kristin C.

2013-01-01

Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis. Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression. We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex–Argonaute protein complexes into a pipeline to model and predict miRNA–target duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the Poisson–Boltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA–target duplexes to an accuracy of ∼3.8 Å root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA–target duplexes agree with titration calorimetry data. Analysis of duplex–Argonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-based methods. PMID:23417009

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes

PubMed Central

Singh, Parmit Kumar; Plumb, Matthew R.; Ferris, Andrea L.; Iben, James R.; Wu, Xiaolin; Fadel, Hind J.; Luke, Brian T.; Esnault, Caroline; Poeschla, Eric M.; Hughes, Stephen H.; Kvaratskhelia, Mamuka; Levin, Henry L.

2015-01-01

The host chromatin-binding factor LEDGF/p75 interacts with HIV-1 integrase and directs integration to active transcription units. To understand how LEDGF/p75 recognizes transcription units, we sequenced 1 million HIV-1 integration sites isolated from cultured HEK293T cells. Analysis of integration sites showed that cancer genes were preferentially targeted, raising concerns about using lentivirus vectors for gene therapy. Additional analysis led to the discovery that introns and alternative splicing contributed significantly to integration site selection. These correlations were independent of transcription levels, size of transcription units, and length of the introns. Multivariate analysis with five parameters previously found to predict integration sites showed that intron density is the strongest predictor of integration density in transcription units. Analysis of previously published HIV-1 integration site data showed that integration density in transcription units in mouse embryonic fibroblasts also correlated strongly with intron number, and this correlation was absent in cells lacking LEDGF. Affinity purification showed that LEDGF/p75 is associated with a number of splicing factors, and RNA sequencing (RNA-seq) analysis of HEK293T cells lacking LEDGF/p75 or the LEDGF/p75 integrase-binding domain (IBD) showed that LEDGF/p75 contributes to splicing patterns in half of the transcription units that have alternative isoforms. Thus, LEDGF/p75 interacts with splicing factors, contributes to exon choice, and directs HIV-1 integration to transcription units that are highly spliced. PMID:26545813

Lifestyle Factors and Metabolic Syndrome among Workers: The Role of Interactions between Smoking and Alcohol to Nutrition and Exercise

PubMed Central

Huang, Jui-Hua; Li, Ren-Hau; Huang, Shu-Ling; Sia, Hon-Ke; Chen, Yu-Ling; Tang, Feng-Cheng

2015-01-01

This study aimed to investigate (1) relations of smoking and alcohol to metabolic syndrome (MetS) and its components, with nutrition and exercise controlled; and (2) interactions between smoking/alcohol and nutrition/exercise on MetS. This cross-sectional study enrolled 4025 workers. Self-reported lifestyles, anthropometric values, blood pressure (BP), and biochemical determinations were obtained. Among males, smoking significantly increased the risk of low high-density lipoprotein cholesterol (HDL-C), high triglyceride, abdominal obesity (AO), and MetS. Additionally, smoking showed significant interaction effects with nutrition on high BP, AO, and MetS; after further analysis, nutrition did not decrease above-mentioned risks for smokers. However, there was no significant interaction of smoking with exercise on any metabolic parameter. Alcohol increased the risk of AO, but decreased low HDL-C. It also showed an interaction effect with exercise on AO; after further analysis, exercise decreased AO risk for drinkers. Among females, alcohol significantly decreased the risk of high fasting blood glucose, but did not show significant interaction with nutrition/exercise on any metabolic parameter. In conclusion, in males, smoking retained significant associations with MetS and its components, even considering benefits of nutrition; exercise kept predominance on lipid parameters regardless of smoking status. Alcohol showed inconsistencies on metabolic parameters for both genders. PMID:26694434

Lifestyle Factors and Metabolic Syndrome among Workers: The Role of Interactions between Smoking and Alcohol to Nutrition and Exercise.

PubMed

Huang, Jui-Hua; Li, Ren-Hau; Huang, Shu-Ling; Sia, Hon-Ke; Chen, Yu-Ling; Tang, Feng-Cheng

2015-12-16

This study aimed to investigate (1) relations of smoking and alcohol to metabolic syndrome (MetS) and its components, with nutrition and exercise controlled; and (2) interactions between smoking/alcohol and nutrition/exercise on MetS. This cross-sectional study enrolled 4025 workers. Self-reported lifestyles, anthropometric values, blood pressure (BP), and biochemical determinations were obtained. Among males, smoking significantly increased the risk of low high-density lipoprotein cholesterol (HDL-C), high triglyceride, abdominal obesity (AO), and MetS. Additionally, smoking showed significant interaction effects with nutrition on high BP, AO, and MetS; after further analysis, nutrition did not decrease above-mentioned risks for smokers. However, there was no significant interaction of smoking with exercise on any metabolic parameter. Alcohol increased the risk of AO, but decreased low HDL-C. It also showed an interaction effect with exercise on AO; after further analysis, exercise decreased AO risk for drinkers. Among females, alcohol significantly decreased the risk of high fasting blood glucose, but did not show significant interaction with nutrition/exercise on any metabolic parameter. In conclusion, in males, smoking retained significant associations with MetS and its components, even considering benefits of nutrition; exercise kept predominance on lipid parameters regardless of smoking status. Alcohol showed inconsistencies on metabolic parameters for both genders.

Characterizing Interactive Engagement Activities in a Flipped Introductory Physics Class

ERIC Educational Resources Information Center

Wood, Anna K.; Galloway, Ross K.; Donnelly, Robyn; Hardy, Judy

2016-01-01

Interactive engagement activities are increasingly common in undergraduate physics teaching. As research efforts move beyond simply showing that interactive engagement pedagogies work towards developing an understanding of "how" they lead to improved learning outcomes, a detailed analysis of the way in which these activities are used in…

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

Exploring pathway interactions in insulin resistant mouse liver

PubMed Central

2011-01-01

Background Complex phenotypes such as insulin resistance involve different biological pathways that may interact and influence each other. Interpretation of related experimental data would be facilitated by identifying relevant pathway interactions in the context of the dataset. Results We developed an analysis approach to study interactions between pathways by integrating gene and protein interaction networks, biological pathway information and high-throughput data. This approach was applied to a transcriptomics dataset to investigate pathway interactions in insulin resistant mouse liver in response to a glucose challenge. We identified regulated pathway interactions at different time points following the glucose challenge and also studied the underlying protein interactions to find possible mechanisms and key proteins involved in pathway cross-talk. A large number of pathway interactions were found for the comparison between the two diet groups at t = 0. The initial response to the glucose challenge (t = 0.6) was typed by an acute stress response and pathway interactions showed large overlap between the two diet groups, while the pathway interaction networks for the late response were more dissimilar. Conclusions Studying pathway interactions provides a new perspective on the data that complements established pathway analysis methods such as enrichment analysis. This study provided new insights in how interactions between pathways may be affected by insulin resistance. In addition, the analysis approach described here can be generally applied to different types of high-throughput data and will therefore be useful for analysis of other complex datasets as well. PMID:21843341

Using concurrent think-aloud and protocol analysis to explore student nurses' social learning information communication technology knowledge and skill development.

PubMed

Todhunter, Fern

2015-06-01

Observations obtained through concurrent think-aloud and protocol analysis offer new understanding about the influence of social learning on student nurses' acquisition of Information and Communication Technology (ICT) knowledge and skills. The software used provides a permanent record of the underpinning study method, events and analyses. The emerging themes reflect the dimensions of social engagement, and the characteristics of positive and negative reactions to ICT. The evidence shows that given the right conditions, stronger learners will support and guide their peers. To explore the use of concurrent think-aloud and protocol analysis as a method to examine how student nurses approach ICT. To identify the benefits and challenges of using observational technology to capture learning behaviours. To show the influence of small group arrangement and student interactions on their ICT knowledge and skills development. Previous studies examining social interaction between students show how they work together and respond to interactive problem solving. Social interaction has been shown to enhance skills in both ICT and collaborative decision making. Structured observational analysis using concurrent think-aloud and protocol analysis. Students displayed varying degrees of pastoral support and emotional need, leadership, reflection, suggestion and experimentation skills. Encouraging student nurses to work in small mixed ability groups can be conducive for social and ICT skill and knowledge development. Observational software gives a permanent record of the proceedings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

PubMed

Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

2016-04-01

To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

Theoretical evidence of charge transfer interaction between SO₂ and deep eutectic solvents formed by choline chloride and glycerol.

PubMed

Li, Hongping; Chang, Yonghui; Zhu, Wenshuai; Wang, Changwei; Wang, Chao; Yin, Sheng; Zhang, Ming; Li, Huaming

2015-11-21

The nature of the interaction between deep eutectic solvents (DESs), formed by ChCl and glycerol, and SO2 has been systematically investigated using the M06-2X density functional combined with cluster models. Block-localized wave function energy decomposition (BLW-ED) analysis shows that the interaction between SO2 and DESs is dominated by a charge transfer interaction. After this interaction, the SO2 molecule becomes negatively charged, whereas the ChCl-glycerol molecule is positively charged, which is the result of Lewis acid-base interaction. The current result affords a theoretical proof that it is highly useful and efficient to manipulate the Lewis acidity of absorbents for SO2 capture. Moreover, hydrogen bonding as well as electrostatic interactions may also contribute to the stability of the complex. Structure analysis shows that solvent molecules will adjust their geometries to interact with SO2. In addition, the structure of SO2 is barely changed after interaction. The interaction energy between different cluster models and SO2 ranges from -6.8 to -14.4 kcal mol(-1). It is found that the interaction energy is very sensitive to the solvent structure. The moderate interaction between ChCl-glycerol and SO2 is consistent with the concept that highly efficient solvents for SO2 absorption should not only be solvable but also regenerable.

Levels and Patterns of Participation and Social Interaction in an Online Learning Community for Learning to Teach

ERIC Educational Resources Information Center

Tsai, I-Chun

2011-01-01

This study investigates how pre-service and in-service teachers participate in an online community for learning to teach. Members' levels and patterns of participation and social interaction were examined via social network analysis of activity logs and content analysis of interviews. The results of the analyses show that (a) members' levels and…

How memory of direct animal interactions can lead to territorial pattern formation.

PubMed

Potts, Jonathan R; Lewis, Mark A

2016-05-01

Mechanistic home range analysis (MHRA) is a highly effective tool for understanding spacing patterns of animal populations. It has hitherto focused on populations where animals defend their territories by communicating indirectly, e.g. via scent marks. However, many animal populations defend their territories using direct interactions, such as ritualized aggression. To enable application of MHRA to such populations, we construct a model of direct territorial interactions, using linear stability analysis and energy methods to understand when territorial patterns may form. We show that spatial memory of past interactions is vital for pattern formation, as is memory of 'safe' places, where the animal has visited but not suffered recent territorial encounters. Additionally, the spatial range over which animals make decisions to move is key to understanding the size and shape of their resulting territories. Analysis using energy methods, on a simplified version of our system, shows that stability in the nonlinear system corresponds well to predictions of linear analysis. We also uncover a hysteresis in the process of territory formation, so that formation may depend crucially on initial space-use. Our analysis, in one dimension and two dimensions, provides mathematical groundwork required for extending MHRA to situations where territories are defended by direct encounters. © 2016 The Author(s).

Cell Division in genus Corynebacterium: protein-protein interaction and molecular docking of SepF and FtsZ in the understanding of cytokinesis in pathogenic species.

PubMed

Oliveira, Alberto F; Folador, Edson L; Gomide, Anne C P; Goes-Neto, Aristóteles; Azevedo, Vasco A C; Wattam, Alice R

2018-02-15

The genus Corynebacterium includes species of great importance in medical, veterinary and biotechnological fields. The genus-specific families (PLfams) from PATRIC have been used to observe conserved proteins associated to all species. Our results showed a large number of conserved proteins that are associated with the cellular division process. Was not observe in our results other proteins like FtsA and ZapA that interact with FtsZ. Our findings point that SepF overlaps the function of this proteins explored by molecular docking, protein-protein interaction and sequence analysis. Transcriptomic analysis showed that these two (Sepf and FtsZ) proteins can be expressed in different conditions together. The work presents novelties on molecules participating in the cell division event, from the interaction of FtsZ and SepF, as new therapeutic targets.

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

NASA Astrophysics Data System (ADS)

Prasanna, M. D.; Row, T. N. Guru

2001-05-01

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Robustness of meta-analyses in finding gene × environment interactions

PubMed Central

Shi, Gang; Nehorai, Arye

2017-01-01

Meta-analyses that synthesize statistical evidence across studies have become important analytical tools for genetic studies. Inspired by the success of genome-wide association studies of the genetic main effect, researchers are searching for gene × environment interactions. Confounders are routinely included in the genome-wide gene × environment interaction analysis as covariates; however, this does not control for any confounding effects on the results if covariate × environment interactions are present. We carried out simulation studies to evaluate the robustness to the covariate × environment confounder for meta-regression and joint meta-analysis, which are two commonly used meta-analysis methods for testing the gene × environment interaction or the genetic main effect and interaction jointly. Here we show that meta-regression is robust to the covariate × environment confounder while joint meta-analysis is subject to the confounding effect with inflated type I error rates. Given vast sample sizes employed in genome-wide gene × environment interaction studies, non-significant covariate × environment interactions at the study level could substantially elevate the type I error rate at the consortium level. When covariate × environment confounders are present, type I errors can be controlled in joint meta-analysis by including the covariate × environment terms in the analysis at the study level. Alternatively, meta-regression can be applied, which is robust to potential covariate × environment confounders. PMID:28362796

Missing continuous outcomes under covariate dependent missingness in cluster randomised trials

PubMed Central

Diaz-Ordaz, Karla; Bartlett, Jonathan W

2016-01-01

Attrition is a common occurrence in cluster randomised trials which leads to missing outcome data. Two approaches for analysing such trials are cluster-level analysis and individual-level analysis. This paper compares the performance of unadjusted cluster-level analysis, baseline covariate adjusted cluster-level analysis and linear mixed model analysis, under baseline covariate dependent missingness in continuous outcomes, in terms of bias, average estimated standard error and coverage probability. The methods of complete records analysis and multiple imputation are used to handle the missing outcome data. We considered four scenarios, with the missingness mechanism and baseline covariate effect on outcome either the same or different between intervention groups. We show that both unadjusted cluster-level analysis and baseline covariate adjusted cluster-level analysis give unbiased estimates of the intervention effect only if both intervention groups have the same missingness mechanisms and there is no interaction between baseline covariate and intervention group. Linear mixed model and multiple imputation give unbiased estimates under all four considered scenarios, provided that an interaction of intervention and baseline covariate is included in the model when appropriate. Cluster mean imputation has been proposed as a valid approach for handling missing outcomes in cluster randomised trials. We show that cluster mean imputation only gives unbiased estimates when missingness mechanism is the same between the intervention groups and there is no interaction between baseline covariate and intervention group. Multiple imputation shows overcoverage for small number of clusters in each intervention group. PMID:27177885

Missing continuous outcomes under covariate dependent missingness in cluster randomised trials.

PubMed

Hossain, Anower; Diaz-Ordaz, Karla; Bartlett, Jonathan W

2017-06-01

Attrition is a common occurrence in cluster randomised trials which leads to missing outcome data. Two approaches for analysing such trials are cluster-level analysis and individual-level analysis. This paper compares the performance of unadjusted cluster-level analysis, baseline covariate adjusted cluster-level analysis and linear mixed model analysis, under baseline covariate dependent missingness in continuous outcomes, in terms of bias, average estimated standard error and coverage probability. The methods of complete records analysis and multiple imputation are used to handle the missing outcome data. We considered four scenarios, with the missingness mechanism and baseline covariate effect on outcome either the same or different between intervention groups. We show that both unadjusted cluster-level analysis and baseline covariate adjusted cluster-level analysis give unbiased estimates of the intervention effect only if both intervention groups have the same missingness mechanisms and there is no interaction between baseline covariate and intervention group. Linear mixed model and multiple imputation give unbiased estimates under all four considered scenarios, provided that an interaction of intervention and baseline covariate is included in the model when appropriate. Cluster mean imputation has been proposed as a valid approach for handling missing outcomes in cluster randomised trials. We show that cluster mean imputation only gives unbiased estimates when missingness mechanism is the same between the intervention groups and there is no interaction between baseline covariate and intervention group. Multiple imputation shows overcoverage for small number of clusters in each intervention group.

[Mannheim Rating Scales for the analysis of mother-child interaction in toddlers].

PubMed

Dinter-Jörg, M; Polowczyk, M; Herrle, J; Esser, G; Laucht, M; Schmidt, M H

1997-12-01

As part of a prospective study on child development from birth to age 11 the Mannheim Rating Scales for the Analysis of Mother-Child Interaction in Toddlers was constructed. Ten-minute interactions of 352 mothers and their toddlers were videotaped in the laboratory and evaluated with micro- and macroanalytic techniques. The instrument consists of a combination of second-by-second codings and dimensional ratings of 5-second to 1 minute periods. Interrater reliability, assessed by having two raters analyze 16 mother-child dyads, proved satisfactory. Psychosocial risk showed different patterns from those at low risk. Interactions of mothers and daughters seemed to be more harmonious than interactions of mothers and sons.

Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity.

PubMed

Silva, Daniel-Adriano; Domínguez-Ramírez, Lenin; Rojo-Domínguez, Arturo; Sosa-Peinado, Alejandro

2011-07-01

The molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G-protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L-lysine, L-arginine, L-ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr-14 and Phe-52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation-π interaction with Tyr-14 and Phe-52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand-dependent conformational plasticity not explained by the previous crystallographic data. Copyright © 2011 Wiley-Liss, Inc.

Molecular properties of metal difluorides and their interactions with CO2 and H2O molecules: a DFT investigation.

PubMed

Arokiyanathan, Agnes Lincy; Lakshmipathi, Senthilkumar

2017-11-18

A computational study of metal difluorides (MF 2 ; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca-F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn-Teller effect in nonlinear MF 2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO 2 with ScF 2 (Scc3 geometry) and TiF 2 (Tic2 geometry) caused CO 2 to shift from its usual linear geometry to a bent geometry (η 2 (C=O) binding mode), while it retained its linear geometry (η 1 (O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H 2 O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO 2 . Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO 2 capture under moist conditions. Graphical abstract Interaction of metal difluorides with carbon dioxide and water.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Some dynamical aspects of interacting quintessence model

NASA Astrophysics Data System (ADS)

Choudhury, Binayak S.; Mondal, Himadri Shekhar; Chatterjee, Devosmita

2018-04-01

In this paper, we consider a particular form of coupling, namely B=σ (\\dot{ρ _m}-\\dot{ρ _φ }) in spatially flat (k=0) Friedmann-Lemaitre-Robertson-Walker (FLRW) space-time. We perform phase-space analysis for this interacting quintessence (dark energy) and dark matter model for different numerical values of parameters. We also show the phase-space analysis for the `best-fit Universe' or concordance model. In our analysis, we observe the existence of late-time scaling attractors.

Wake Geometry Effects on Rotor Blade-Vortex Interaction Noise Directivity

NASA Technical Reports Server (NTRS)

Martin, R. M.; Marcolini, Michael A.; Splettstoesser, W. R.; Schultz, K.-J.

1990-01-01

Acoustic measurements from a model rotor wind tunnel test are presented which show that the directionality of rotor blade vortex interaction (BVI) noise is strongly dependent on the rotor advance ratio and disk attitude. A rotor free wake analysis is used to show that the general locus of interactions on the rotor disk is also strongly dependent on advance ratio and disk attitude. A comparison of the changing directionality of the BVI noise with changes in the interaction locations shows that the strongest noise radiation occurs in the direction of motion normal to the blade span at the time of interaction, for both advancing and retreating side BVI. For advancing side interactions, the BVI radiation angle down from the tip-path plane appears relatively insensitive to rotor operating condition and is typically between 40 and 55 deg below the disk. However, the azimuthal radiation direction shows a clear trend with descent speed, moving towards the right of the flight path with increasing descent speed. The movement of the strongest radiation direction is attributed to the movement of the interaction locations on the rotor disk with increasing descent speed.

Blade row interaction effects on flutter and forced response

NASA Technical Reports Server (NTRS)

Buffum, Daniel H.

1993-01-01

In the flutter or forced response analysis of a turbomachine blade row, the blade row in question is commonly treated as if it is isolated from the neigboring blade rows. Disturbances created by vibrating blades are then free to propagate away from this blade row without being disturbed. In reality, neighboring blade rows will reflect some portion of this wave energy back toward the vibrating blades, causing additional unsteady forces on them. It is of fundamental importance to determine whether or not these reflected waves can have a significant effect on the aeroelastic stability or forced response of a blade row. Therefore, a procedure to calculate intra-blade-row unsteady aerodynamic interactions was developed which relies upon results available from isolated blade row unsteady aerodynamic analyses. In addition, an unsteady aerodynamic influence coefficient technique is used to obtain a model for the vibratory response in which the neighboring blade rows are also flexible. The flutter analysis shows that interaction effects can be destabilizing, and the forced response analysis shows that interaction effects can result in a significant increase in the resonant response of a blade row.

Anisotropic surface-state-mediated RKKY interaction between adatoms on a hexagonal lattice

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Einstein, T. L.

2012-01-01

Motivated by recent numerical studies of Ag on Pt(111), we derive an expression for the RKKY interaction mediated by surface states, considering the effect of anisotropy in the Fermi edge. Our analysis is based on a stationary phase approximation. The main contribution to the interaction comes from electrons whose Fermi velocity vF is parallel to the vector R connecting the interacting adatoms; we show that, in general, the corresponding Fermi wave vector kF is not parallel to R. The interaction is oscillatory; the amplitude and wavelength of oscillations have angular dependence arising from the anisotropy of the surface-state band structure. The wavelength, in particular, is determined by the projection of this kF (corresponding to vF) onto the direction of R. Our analysis is easily generalized to other systems. For Ag on Pt(111), our results indicate that the RKKY interaction between pairs of adatoms should be nearly isotropic and so cannot account for the anisotropy found in the studies motivating our work. However, for metals with surface-state dispersions similar to Be(101¯0), we show that the RKKY interaction should have considerable anisotropy.

Students' and teachers' focus of attention in classroom interaction — subtle sources for the reproduction of social disparities

NASA Astrophysics Data System (ADS)

Vogler, Anna-Marietha; Prediger, Susanne; Quasthoff, Uta; Heller, Vivien

2018-01-01

Mathematics classroom interaction has often been described as an important context for involving all students. However, this article shows that teacher-student-interaction is still not really in the focus of teachers' attention. Based on classroom video studies, some authors hypothesize that the implicitness of establishing norms and practices is, among others, an obstacle for students with low socio-economic status. The article intends to put this hypothesis into perspective by investigating teachers' and students' focus of attention on classroom interaction in video-stimulated group discussions (six discussions with 5-6 students, four discussions with 5-9 teachers). The data analysis used inductive procedures of category development, frequency analysis, and deeper qualitative analysis of the transcripts. For students' focus of attention, differential patterns could be extrapolated: Whereas students of high socio-economic status seem to be more attentive to teacher's contextual expectations, the students of low socio-economic status seem to be more focused on general norms without taking into account contextual expectations. For the teachers, the analysis shows that interactive mechanisms of teacher-student exchanges in classrooms are usually not in the teachers' focus of attention. Additionally, the teachers address, but rarely problematize the implicitness by which norms and practices are established. Together with the differential findings on students' attention, these findings are discussed with respect to equity concerns and consequences for professional development of teachers.

Three-dimensional isobolographic analysis of interactions between lamotrigine and clonazepam in maximal electroshock-induced seizures in mice.

PubMed

Luszczki, Jarogniew J; Czuczwar, Stanislaw J

2004-11-01

The anticonvulsant effects of lamotrigine (LTG) and clonazepam (CZP) and combinations thereof against maximal electroshock (MES)-induced seizures in mice were investigated using three-dimensional (3D) isobolographic analysis. With this method, the doses of fixed-ratio combinations of the drugs (1:3, 1:1 and 3:1) that elicited 16, 50 and 84% of the maximum anticonvulsant effect were determined. Additionally, to evaluate the characteristics of interactions observed with 3D isobolography, the brain concentrations of both drugs were verified pharmacokinetically. The 3D isobolographic analysis showed that LTG and CZP combined at the fixed ratios of 3:1 and 1:1 interacted synergistically in the MES test for all anticonvulsant effects between 16% and 84% of maximum. In contrast, the combination of LTG and CZP at the fixed ratio of 1:3 showed only pure additivity for all estimated effects in 3D isobolography. Moreover, none of the examined antiepileptic drugs altered the brain concentrations of the coadministered drug, so the observed interactions in the MES test are of a pharmacodynamic nature. The 3D isobolographic findings suggest that in epilepsy therapy, increased efficacy of seizure control (synergistic interaction) might be achieved by using LTG and CZP in combination. In this study, some important problems and assumptions related to statistical analysis of data in 3D isobolography are discussed.

Multi-frequency data analysis in AFM by wavelet transform

NASA Astrophysics Data System (ADS)

Pukhova, V.; Ferrini, G.

2017-10-01

Interacting cantilevers in AFM experiments generate non-stationary, multi-frequency signals consisting of numerous excited flexural and torsional modes and their harmonics. The analysis of such signals is challenging, requiring special methodological approaches and a powerful mathematical apparatus. The most common approach to the signal analysis is to apply Fourier transform analysis. However, FT gives accurate spectra for stationary signals, and for signals changing their spectral content over time, FT provides only an averaged spectrum. Hence, for non-stationary and rapidly varying signals, such as those from interacting cantilevers, a method that shows the spectral evolution in time is needed. One of the most powerful techniques, allowing detailed time-frequency representation of signals, is the wavelet transform. It is a method of analysis that allows representation of energy associated to the signal at a particular frequency and time, providing correlation between the spectral and temporal features of the signal, unlike FT. This is particularly important in AFM experiments because signals nonlinearities contains valuable information about tip-sample interactions and consequently surfaces properties. The present work is aimed to show the advantages of wavelet transform in comparison with FT using as an example the force curve analysis in dynamic force spectroscopy.

Chandra Interactive Analysis of Observations (CIAO)

NASA Technical Reports Server (NTRS)

Dobrzycki, Adam

2000-01-01

The Chandra (formerly AXAF) telescope, launched on July 23, 1999, provides X-rays data with unprecedented spatial and spectral resolution. As part of the Chandra scientific support, the Chandra X-ray Observatory Center provides a new data analysis system, CIAO ("Chandra Interactive Analysis of Observations"). We will present the main components of the system: "First Look" analysis; SHERPA: a multi-dimensional, multi-mission modeling and fitting application; Chandra Imaging and Plotting System; Detect package-source detection algorithms; and DM package generic data manipulation tools, We will set up a demonstration of the portable version of the system and show examples of Chandra Data Analysis.

Nuclear factor-kappaB bioluminescence imaging-guided transcriptomic analysis for the assessment of host-biomaterial interaction in vivo.

PubMed

Hsiang, Chien-Yun; Chen, Yueh-Sheng; Ho, Tin-Yun

2009-06-01

Establishment of a comprehensive platform for the assessment of host-biomaterial interaction in vivo is an important issue. Nuclear factor-kappaB (NF-kappaB) is an inducible transcription factor that is activated by numerous stimuli. Therefore, NF-kappaB-dependent luminescent signal in transgenic mice carrying the luciferase genes was used as the guide to monitor the biomaterials-affected organs, and transcriptomic analysis was further applied to evaluate the complex host responses in affected organs in this study. In vivo imaging showed that genipin-cross-linked gelatin conduit (GGC) implantation evoked the strong NF-kappaB activity at 6h in the implanted region, and transcriptomic analysis showed that the expressions of interleukin-6 (IL-6), IL-24, and IL-1 family were up-regulated. A strong luminescent signal was observed in spleen on 14 d, suggesting that GGC implantation might elicit the biological events in spleen. Transcriptomic analysis of spleen showed that 13 Kyoto Encyclopedia of Genes and Genomes pathways belonging to cell cycles, immune responses, and metabolism were significantly altered by GGC implants. Connectivity Map analysis suggested that the gene signatures of GGC were similar to those of compounds that affect lipid or glucose metabolism. GeneSetTest analysis further showed that host responses to GGC implants might be related to diseases states, especially the metabolic and cardiovascular diseases. In conclusion, our data provided a concept of molecular imaging-guided transcriptomic platform for the evaluation and the prediction of host-biomaterial interaction in vivo.

Differential proteome profiling in the hippocampus of amnesic mice.

PubMed

Baghel, Meghraj Singh; Thakur, Mahendra Kumar

2017-08-01

Amnesia or memory loss is associated with brain aging and several neurodegenerative pathologies including Alzheimer's disease (AD). This can be induced by a cholinergic antagonist scopolamine but the underlying molecular mechanism is poorly understood. This study of proteome profiling in the hippocampus could provide conceptual insights into the molecular mechanisms involved in amnesia. To reveal this, mice were administered scopolamine to induce amnesia and memory impairment was validated by novel object recognition test. Using two-dimensional gel electrophoresis coupled with MALDI-MS/MS, we have analyzed the hippocampal proteome and identified 18 proteins which were differentially expressed. Out of these proteins, 11 were downregulated and 7 were upregulated in scopolamine-treated mice as compared to control. In silico analysis showed that the majority of identified proteins are involved in metabolism, catalytic activity, and cytoskeleton architectural functions. STRING interaction network analysis revealed that majority of identified proteins exhibit common association with Actg1 cytoskeleton and Vdac1 energy transporter protein. Furthermore, interaction map analysis showed that Fascin1 and Coronin 1b individually interact with Actg1 and regulate the actin filament dynamics. Vdac1 was significantly downregulated in amnesic mice and showed interaction with other proteins in interaction network. Therefore, we silenced Vdac1 in the hippocampus of normal young mice and found similar impairment in recognition memory of Vdac1 silenced and scopolamine-treated mice. Thus, these findings suggest that Vdac1-mediated disruption of energy metabolism and cytoskeleton architecture might be involved in scopolamine-induced amnesia. © 2017 Wiley Periodicals, Inc.

Cluster Approach to Network Interaction in Pedagogical University

ERIC Educational Resources Information Center

Chekaleva, Nadezhda V.; Makarova, Natalia S.; Drobotenko, Yulia B.

2016-01-01

The study presented in the article is devoted to the analysis of theory and practice of network interaction within the framework of education clusters. Education clusters are considered to be a novel form of network interaction in pedagogical education in Russia. The aim of the article is to show the advantages and disadvantages of the cluster…

Unconditional analyses can increase efficiency in assessing gene-environment interaction of the case-combined-control design.

PubMed

Goldstein, Alisa M; Dondon, Marie-Gabrielle; Andrieu, Nadine

2006-08-01

A design combining both related and unrelated controls, named the case-combined-control design, was recently proposed to increase the power for detecting gene-environment (GxE) interaction. Under a conditional analytic approach, the case-combined-control design appeared to be more efficient and feasible than a classical case-control study for detecting interaction involving rare events. We now propose an unconditional analytic strategy to further increase the power for detecting gene-environment (GxE) interactions. This strategy allows the estimation of GxE interaction and exposure (E) main effects under certain assumptions (e.g. no correlation in E between siblings and the same exposure frequency in both control groups). Only the genetic (G) main effect cannot be estimated because it is biased. Using simulations, we show that unconditional logistic regression analysis is often more efficient than conditional analysis for detecting GxE interaction, particularly for a rare gene and strong effects. The unconditional analysis is also at least as efficient as the conditional analysis when the gene is common and the main and joint effects of E and G are small. Under the required assumptions, the unconditional analysis retains more information than does the conditional analysis for which only discordant case-control pairs are informative leading to more precise estimates of the odds ratios.

A critical analysis of computational protein design with sparse residue interaction graphs

PubMed Central

Georgiev, Ivelin S.

2017-01-01

Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently find the GMEC, protein design algorithms must methodically reduce the conformational search space. By applying distance and energy cutoffs, the protein system to be designed can thus be represented using a sparse residue interaction graph, where the number of interacting residue pairs is less than all pairs of mutable residues, and the corresponding GMEC is called the sparse GMEC. However, ignoring some pairwise residue interactions can lead to a change in the energy, conformation, or sequence of the sparse GMEC vs. the original or the full GMEC. Despite the widespread use of sparse residue interaction graphs in protein design, the above mentioned effects of their use have not been previously analyzed. To analyze the costs and benefits of designing with sparse residue interaction graphs, we computed the GMECs for 136 different protein design problems both with and without distance and energy cutoffs, and compared their energies, conformations, and sequences. Our analysis shows that the differences between the GMECs depend critically on whether or not the design includes core, boundary, or surface residues. Moreover, neglecting long-range interactions can alter local interactions and introduce large sequence differences, both of which can result in significant structural and functional changes. Designs on proteins with experimentally measured thermostability show it is beneficial to compute both the full and the sparse GMEC accurately and efficiently. To this end, we show that a provable, ensemble-based algorithm can efficiently compute both GMECs by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine sparse residue interaction graphs with provable, ensemble-based algorithms to reap the benefits of sparse residue interaction graphs while avoiding their potential inaccuracies. PMID:28358804

Aggregation state and magnetic properties of magnetite nanoparticles controlled by an optimized silica coating

NASA Astrophysics Data System (ADS)

Pérez, Nicolás; Moya, C.; Tartaj, P.; Labarta, A.; Batlle, X.

2017-01-01

The control of magnetic interactions is becoming essential to expand/improve the applicability of magnetic nanoparticles (NPs). Here, we show that an optimized microemulsion method can be used to obtain homogenous silica coatings on even single magnetic nuclei of highly crystalline Fe3-xO4 NPs (7 and 16 nm) derived from a high-temperature method. We show that the thickness of this coating is controlled almost at will allowing much higher average separation among particles as compared to the oleic acid coating present on pristine NPs. Magnetic susceptibility studies show that the thickness of the silica coating allows the control of magnetic interactions. Specifically, as this effect is better displayed for the smallest particles, we show that dipole-dipole interparticle interactions can be tuned progressively for the 7 nm NPs, from almost non-interacting to strongly interacting particles at room temperature. The quantitative analysis of the magnetic properties unambiguously suggests that dipolar interactions significantly broaden the effective distribution of energy barriers by spreading the distribution of activation magnetic volumes.

Docking analysis of verteporfin with YAP WW domain.

PubMed

Kandoussi, Ilham; Lakhlili, Wiame; Taoufik, Jamal; Ibrahimi, Azeddine

2017-01-01

The YAP oncogene is a known cancer target. Therefore, it is of interest to understand the molecular docking interaction of verteporfin (a derivative of benzo-porphyrin) with the WW domain of YAP (clinically used for photo-dynamic therapy in macular degeneration) as a potential WW domain-ligand modulator by inhibition. A homology protein SWISS MODEL of the human YAP protein was constructed to dock (using AutoDock vina) with the PubChem verteporfin structure for interaction analysis. The docking result shows the possibilities of verteporfin interaction with the oncogenic transcription cofactor YAP having WW1 and WW2 domains. Thus, the ability of verteporfin to bind with the YAP WW domain having modulator activity is implied in this analysis.

Dynamic interactions between Pit-1 and C/EBPalpha in the pituitary cell nucleus.

PubMed

Demarco, Ignacio A; Voss, Ty C; Booker, Cynthia F; Day, Richard N

2006-11-01

The homeodomain (HD) transcription factors are a structurally conserved family of proteins that, through networks of interactions with other nuclear proteins, control patterns of gene expression during development. For example, the network interactions of the pituitary-specific HD protein Pit-1 control the development of anterior pituitary cells and regulate the expression of the hormone products in the adult cells. Inactivating mutations in Pit-1 disrupt these processes, giving rise to the syndrome of combined pituitary hormone deficiency. Pit-1 interacts with CCAAT/enhancer-binding protein alpha (C/EBPalpha) to regulate prolactin transcription. Here, we used the combination of biochemical analysis and live-cell microscopy to show that two different point mutations in Pit-1, which disrupted distinct activities, affected the dynamic interactions between Pit-1 and C/EBPalpha in different ways. The results showed that the first alpha-helix of the POU-S domain is critical for the assembly of Pit-1 with C/EBPalpha, and they showed that DNA-binding activity conferred by the HD is critical for the final intranuclear positioning of the metastable complex. This likely reflects more general mechanisms that govern cell-type-specific transcriptional control, and the results from the analysis of the point mutations could indicate an important link between the mislocalization of transcriptional complexes and disease processes.

Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.

PubMed

Houser, Josef; Kozmon, Stanislav; Mishra, Deepti; Mishra, Sushil K; Romano, Patrick R; Wimmerová, Michaela; Koča, Jaroslav

2017-01-01

Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp-carbohydrate complexes, which would suggest no substantial preference for one conformation over another.

Electron-phonon interaction in efficient perovskite blue emitters

NASA Astrophysics Data System (ADS)

Gong, Xiwen; Voznyy, Oleksandr; Jain, Ankit; Liu, Wenjia; Sabatini, Randy; Piontkowski, Zachary; Walters, Grant; Bappi, Golam; Nokhrin, Sergiy; Bushuyev, Oleksandr; Yuan, Mingjian; Comin, Riccardo; McCamant, David; Kelley, Shana O.; Sargent, Edward H.

2018-06-01

Low-dimensional perovskites have—in view of their high radiative recombination rates—shown great promise in achieving high luminescence brightness and colour saturation. Here we investigate the effect of electron-phonon interactions on the luminescence of single crystals of two-dimensional perovskites, showing that reducing these interactions can lead to bright blue emission in two-dimensional perovskites. Resonance Raman spectra and deformation potential analysis show that strong electron-phonon interactions result in fast non-radiative decay, and that this lowers the photoluminescence quantum yield (PLQY). Neutron scattering, solid-state NMR measurements of spin-lattice relaxation, density functional theory simulations and experimental atomic displacement measurements reveal that molecular motion is slowest, and rigidity greatest, in the brightest emitter. By varying the molecular configuration of the ligands, we show that a PLQY up to 79% and linewidth of 20 nm can be reached by controlling crystal rigidity and electron-phonon interactions. Designing crystal structures with electron-phonon interactions in mind offers a previously underexplored avenue to improve optoelectronic materials' performance.

Extended GTST-MLD for aerospace system safety analysis.

PubMed

Guo, Chiming; Gong, Shiyu; Tan, Lin; Guo, Bo

2012-06-01

The hazards caused by complex interactions in the aerospace system have become a problem that urgently needs to be settled. This article introduces a method for aerospace system hazard interaction identification based on extended GTST-MLD (goal tree-success tree-master logic diagram) during the design stage. GTST-MLD is a functional modeling framework with a simple architecture. Ontology is used to extend the ability of system interaction description in GTST-MLD by adding the system design knowledge and the past accident experience. From the level of functionality and equipment, respectively, this approach can help the technician detect potential hazard interactions. Finally, a case is used to show the method. © 2011 Society for Risk Analysis.

Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

NASA Astrophysics Data System (ADS)

Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

2016-05-01

Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

Phase transitions and thermodynamic properties of antiferromagnetic Ising model with next-nearest-neighbor interactions on the Kagomé lattice

NASA Astrophysics Data System (ADS)

Ramazanov, M. K.; Murtazaev, A. K.; Magomedov, M. A.; Badiev, M. K.

2018-06-01

We study phase transitions and thermodynamic properties in the two-dimensional antiferromagnetic Ising model with next-nearest-neighbor interaction on a Kagomé lattice by Monte Carlo simulations. A histogram data analysis shows that a second-order transition occurs in the model. From the analysis of obtained data, we can assume that next-nearest-neighbor ferromagnetic interactions in two-dimensional antiferromagnetic Ising model on a Kagomé lattice excite the occurrence of a second-order transition and unusual behavior of thermodynamic properties on the temperature dependence.

Simulation of self-induced unsteady motion in the near wake of a Joukowski airfoil

NASA Technical Reports Server (NTRS)

Ghia, K. N.; Osswald, G. A.; Ghia, U.

1986-01-01

The unsteady Navier-Stokes analysis is shown to be capable of analyzing the massively separated, persistently unsteady flow in the post-stall regime of a Joukowski airfoil for an angle of attack as high as 53 degrees. The analysis has provided the detailed flow structure, showing the complex vortex interaction for this configuration. The aerodynamic coefficients for lift, drag, and moment were calculated. So far only the spatial structure of the vortex interaction was computed. It is now important to potentially use the large-scale vortex interactions, an additional energy source, to improve the aerodynamic performance.

Investigating cardiorespiratory interaction by cross-spectral analysis of event series

NASA Astrophysics Data System (ADS)

Schäfer, Carsten; Rosenblum, Michael G.; Pikovsky, Arkady S.; Kurths, Jürgen

2000-02-01

The human cardiovascular and respiratory systems interact with each other and show effects of modulation and synchronization. Here we present a cross-spectral technique that specifically considers the event-like character of the heartbeat and avoids typical restrictions of other spectral methods. Using models as well as experimental data, we demonstrate how modulation and synchronization can be distinguished. Finally, we compare the method to traditional techniques and to the analysis of instantaneous phases.

Transforming Parent-Child Interaction in Family Routines: Longitudinal Analysis with Families of Children with Developmental Disabilities.

PubMed

Lucyshyn, Joseph M; Fossett, Brenda; Bakeman, Roger; Cheremshynski, Christy; Miller, Lynn; Lohrmann, Sharon; Binnendyk, Lauren; Khan, Sophia; Chinn, Stephen; Kwon, Samantha; Irvin, Larry K

2015-12-01

The efficacy and consequential validity of an ecological approach to behavioral intervention with families of children with developmental disabilities was examined. The approach aimed to transform coercive into constructive parent-child interaction in family routines. Ten families participated, including 10 mothers and fathers and 10 children 3-8 years old with developmental disabilities. Thirty-six family routines were selected (2 to 4 per family). Dependent measures included child problem behavior, routine steps completed, and coercive and constructive parent-child interaction. For each family, a single case, multiple baseline design was employed with three phases: baseline, intervention, and follow-up. Visual analysis evaluated the functional relation between intervention and improvements in child behavior and routine participation. Nonparametric tests across families evaluated the statistical significance of these improvements. Sequential analyses within families and univariate analyses across families examined changes from baseline to intervention in the percentage and odds ratio of coercive and constructive parent-child interaction. Multiple baseline results documented functional or basic effects for 8 of 10 families. Nonparametric tests showed these changes to be significant. Follow-up showed durability at 11 to 24 months postintervention. Sequential analyses documented the transformation of coercive into constructive processes for 9 of 10 families. Univariate analyses across families showed significant improvements in 2- and 4-step coercive and constructive processes but not in odds ratio. Results offer evidence of the efficacy of the approach and consequential validity of the ecological unit of analysis, parent-child interaction in family routines. Future studies should improve efficiency, and outcomes for families experiencing family systems challenges.

Supramolecular interactions between triphenylphosphine oxide and benzamide evaluated by positron annihilation lifetime spectroscopy

NASA Astrophysics Data System (ADS)

Oliveira, F. C.; Denadai, A. M. L.; Fulgêncio, F.; Oliveira, A. M.; Andrade, A. C. A.; Melo, A. C. A.; Yoshida, M. I.; Windmöller, D.; Magalhães, W. F.

2017-04-01

In the present work, intermolecular interactions between triphenylphosphine oxide (TPPO) and benzamide (BZM) has been studied in solid state by Positron Annihilation Lifetime Spectroscopy (PALS) and supported by several analytical techniques (in solid state and in solution) and by computational modeling (in gaseous phase). Isothermal Titration Calorimetry (ITC) in ethyl acetate solvent showed that complexation is a stepwise process, with 2:1 and 1:1 TPPO/BZM stoichiometries, both driven by entropy. HPLC analysis of isolated single crystal confirmed the existence of a 2:1 TPPO/BZM crystalline complex in solid state. The results of thermal analysis (TGA, DTA and DSC) and FTIR spectroscopy showed that the interactions in the complexes are relatively weaker than those found in pure precursors. Finally, PALS showed higher positronium formation probability (I3) at [TPPO0.62·BZM0.38] and [TPPO0.25·BZM0.75] molar fractions, corroborating the existence of two stoichiometries for the TPPO/BZM system and suggesting greater electronic availability of n- and π-electrons in heterosynton complexes, as resulting of interactions, bring forward new evidences of the participation of electronic excited states on the positronium formation mechanism.

Factors affecting quality of social interaction park in Jakarta

NASA Astrophysics Data System (ADS)

Mangunsong, N. I.

2018-01-01

The existence of social interactions park in Jakarta is an oasis in the middle of a concrete jungle. Parks is a response to the need for open space as a place of recreation and community interaction. Often the social interaction parks built by the government does not function as expected, but other functions such as a place to sell, trash, unsafe so be rarely visited by visitors. The purpose of this study was to analyze the factors that affect the quality of social interaction parks in Jakarta by conducting descriptive analysis and correlation analysis of the variables assessment. The results of the analysis can give an idea of social interactions park based on community needs and propose the development of social interactioncity park. The object of study are 25 social interaction parks in 5 municipalities of Jakarta. The method used is descriptive analysis method, correlation analysis using SPSS 19 and using crosstab, chi-square tests. The variables are 5 aspects of Design, Plants composition: Selection type of plant (D); the beauty and harmony (Ind); Maintenance and fertility (P); Cleanliness and Environmental Health (BS); Specificity (Drainage, Multi Function garden, Means, Concern/Mutual cooperation, in dense settlements) (K). The results of analysis show that beauty is the most significant correlation with the value of the park followed by specificity, cleanliness and maintenance. Design was not the most significant variable affecting the quality of the park. The results of this study can be used by the Department of Parks and Cemeteries as input in managing park existing or to be developed and to improve the quality of social interaction park in Jakarta.

Interacting with Users in Social Networks: The Follow-back Problem

DTIC Science & Technology

2016-05-02

interacting with the friends of the target(s). Because forming a connection is known as following in social networks such as Twitter , we refer to this as...of an interaction resulting in a follow-back, we conduct an empirical analysis of several thousand interactions in Twitter . We build a model of the...define as the followback score. We show through simulation that these heuristic policies perform well on real Twitter graphs. Thesis Supervisor: Dr

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis.

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches.

Web-Exclusive--Exposing Technomyths: Getting Technical about Technology and Teaching / A Solid Foundation of Success: Research Supports the Effectiveness of Interactive Whiteboards

ERIC Educational Resources Information Center

Phillips, Linda M.; Lovell, Meridith A.; Jones, Heather Sadler

2012-01-01

In some provinces, Interactive White Boards (IWBs) have been recommended for every classroom. The primary and alluring claim made in the promotional and anecdotal literature is that IWBs promote interactivity, which in turn is the crux of three secondary claims of achievement, engagement, and motivation. Careful analysis of research shows these…

Numerical Analysis of Intra-Cavity and Power-Stream Flow Interaction in Multiple Gas-Turbine Disk-Cavities

NASA Technical Reports Server (NTRS)

Athavale, M. M.; Przekwas, A. J.; Hendricks, R. C.; Steinetz, B. M.

1995-01-01

A numerical analysis methodology and solutions of the interaction between the power stream and multiply-connected multi-cavity sealed secondary flow fields are presented. Flow solutions for a multi-cavity experimental rig were computed and compared with experimental data of Daniels and Johnson. The flow solutions illustrate the complex coupling between the main-path and the cavity flows as well as outline the flow thread that exists throughout the subplatform multiple cavities and seals. The analysis also shows that the de-coupled solutions on single cavities is inadequate. The present results show trends similar to the T-700 engine data that suggests the changes in the CDP seal altered the flow fields throughout the engine and affected the engine performance.

Functional interaction analysis of GM1-related carbohydrates and Vibrio cholerae toxins using carbohydrate microarray.

PubMed

Kim, Chang Sup; Seo, Jeong Hyun; Cha, Hyung Joon

2012-08-07

The development of analytical tools is important for understanding the infection mechanisms of pathogenic bacteria or viruses. In the present work, a functional carbohydrate microarray combined with a fluorescence immunoassay was developed to analyze the interactions of Vibrio cholerae toxin (ctx) proteins and GM1-related carbohydrates. Ctx proteins were loaded onto the surface-immobilized GM1 pentasaccharide and six related carbohydrates, and their binding affinities were detected immunologically. The analysis of the ctx-carbohydrate interactions revealed that the intrinsic selectivity of ctx was GM1 pentasaccharide ≫ GM2 tetrasaccharide > asialo GM1 tetrasaccharide ≥ GM3trisaccharide, indicating that a two-finger grip formation and the terminal monosaccharides play important roles in the ctx-GM1 interaction. In addition, whole cholera toxin (ctxAB(5)) had a stricter substrate specificity and a stronger binding affinity than only the cholera toxin B subunit (ctxB). On the basis of the quantitative analysis, the carbohydrate microarray showed the sensitivity of detection of the ctxAB(5)-GM1 interaction with a limit-of-detection (LOD) of 2 ng mL(-1) (23 pM), which is comparable to other reported high sensitivity assay tools. In addition, the carbohydrate microarray successfully detected the actual toxin directly secreted from V. cholerae, without showing cross-reactivity to other bacteria. Collectively, these results demonstrate that the functional carbohydrate microarray is suitable for analyzing toxin protein-carbohydrate interactions and can be applied as a biosensor for toxin detection.

The role of environmental heterogeneity in meta-analysis of gene-environment interactions with quantitative traits.

PubMed

Li, Shi; Mukherjee, Bhramar; Taylor, Jeremy M G; Rice, Kenneth M; Wen, Xiaoquan; Rice, John D; Stringham, Heather M; Boehnke, Michael

2014-07-01

With challenges in data harmonization and environmental heterogeneity across various data sources, meta-analysis of gene-environment interaction studies can often involve subtle statistical issues. In this paper, we study the effect of environmental covariate heterogeneity (within and between cohorts) on two approaches for fixed-effect meta-analysis: the standard inverse-variance weighted meta-analysis and a meta-regression approach. Akin to the results in Simmonds and Higgins (), we obtain analytic efficiency results for both methods under certain assumptions. The relative efficiency of the two methods depends on the ratio of within versus between cohort variability of the environmental covariate. We propose to use an adaptively weighted estimator (AWE), between meta-analysis and meta-regression, for the interaction parameter. The AWE retains full efficiency of the joint analysis using individual level data under certain natural assumptions. Lin and Zeng (2010a, b) showed that a multivariate inverse-variance weighted estimator retains full efficiency as joint analysis using individual level data, if the estimates with full covariance matrices for all the common parameters are pooled across all studies. We show consistency of our work with Lin and Zeng (2010a, b). Without sacrificing much efficiency, the AWE uses only univariate summary statistics from each study, and bypasses issues with sharing individual level data or full covariance matrices across studies. We compare the performance of the methods both analytically and numerically. The methods are illustrated through meta-analysis of interaction between Single Nucleotide Polymorphisms in FTO gene and body mass index on high-density lipoprotein cholesterol data from a set of eight studies of type 2 diabetes. © 2014 WILEY PERIODICALS, INC.

Docking analysis of verteporfin with YAP WW domain

PubMed Central

Kandoussi, Ilham; Lakhlili, Wiame; Taoufik, Jamal; Ibrahimi, Azeddine

2017-01-01

The YAP oncogene is a known cancer target. Therefore, it is of interest to understand the molecular docking interaction of verteporfin (a derivative of benzo-porphyrin) with the WW domain of YAP (clinically used for photo-dynamic therapy in macular degeneration) as a potential WW domain-ligand modulator by inhibition. A homology protein SWISS MODEL of the human YAP protein was constructed to dock (using AutoDock vina) with the PubChem verteporfin structure for interaction analysis. The docking result shows the possibilities of verteporfin interaction with the oncogenic transcription cofactor YAP having WW1 and WW2 domains. Thus, the ability of verteporfin to bind with the YAP WW domain having modulator activity is implied in this analysis. PMID:28943729

Cloning, expression analysis, and chromosomal localization of HIP1R, an isolog of huntingtin interacting protein (HIP1).

PubMed

Seki, N; Muramatsu, M; Sugano, S; Suzuki, Y; Nakagawara, A; Ohhira, M; Hayashi, A; Hori, T; Saito, T

1998-01-01

Huntington disease (HD) is an inherited neurodegenerative disorder which is associated with CAG expansion in the coding region of the gene for huntingtin protein. Recently, a huntingtin interacting protein, HIP1, was isolated by the yeast two-hybrid system. Here we report the isolation of a cDNA clone for HIP1R (huntingtin interacting protein-1 related), which encodes a predicted protein product sharing a striking homology with HIP1. RT-PCR analysis showed that the messenger RNA was ubiquitously expressed in various human tissues. Based on PCR-assisted analysis of a radiation hybrid panel and fluorescence in situ hybridization, HIP1R was localized to the q24 region of chromosome 12.

Evaluation of interaction dynamics of concurrent processes

NASA Astrophysics Data System (ADS)

Sobecki, Piotr; Białasiewicz, Jan T.; Gross, Nicholas

2017-03-01

The purpose of this paper is to present the wavelet tools that enable the detection of temporal interactions of concurrent processes. In particular, the determination of interaction coherence of time-varying signals is achieved using a complex continuous wavelet transform. This paper has used electrocardiogram (ECG) and seismocardiogram (SCG) data set to show multiple continuous wavelet analysis techniques based on Morlet wavelet transform. MATLAB Graphical User Interface (GUI), developed in the reported research to assist in quick and simple data analysis, is presented. These software tools can discover the interaction dynamics of time-varying signals, hence they can reveal their correlation in phase and amplitude, as well as their non-linear interconnections. The user-friendly MATLAB GUI enables effective use of the developed software what enables to load two processes under investigation, make choice of the required processing parameters, and then perform the analysis. The software developed is a useful tool for researchers who have a need for investigation of interaction dynamics of concurrent processes.

A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis.

PubMed

Astani, Elahe K; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L

2016-07-01

A theoretical study at the level of density functional theory (DFT) was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond interactions, in the active site of enzyme human androsterone sulphotransferase (SULT2A1/ADT). Geometry optimization, interaction energy, (2)H, (14)N, and (17)O electric field gradient (EFG) tensors, (1)H, (13)C, (17)O, and (15)N chemical shielding (CS) tensors, Natural Bonding Orbital (NBO) analysis, and quantum theory of atoms in molecules (QTAIM) analysis of this active site were investigated. It was found that androsterone (ADT) is able to form hydrogen bonds with residues Ser80, Ile82, and His99 of the active site. The interaction energy calculations and NBO analysis revealed that the ADT molecule forms the strongest hydrogen bond with Ser80. Results revealed that ADT interacts with the other residues through electrostatic and Van der Waals interactions. Results showed that these hydrogen bonds influence on the calculated (2)H, (14)N, and (17)O quadrupole coupling constants (QCCs), as well as (1)H, (13)C, (17)O, and (15)N CS tensors. The magnitude of the QCC and CS changes at each nucleus depends directly on its amount of contribution to the hydrogen bond interaction. Copyright © 2016 Elsevier Inc. All rights reserved.

Effect of stoichiometry on magnetic and transport properties in polycrystalline Y2Ir2O7

NASA Astrophysics Data System (ADS)

Dwivedi, Vinod Kumar; Mukhopadhyay, Soumik

2018-05-01

In this paper we discuss synthesis of polycrystalline Y2Ir2O7 by solid state reaction route. XRD analysis shows deviation from stoichiometry which is also confirmed by SEM-EDX analysis. SEM analysis indicates average particle size ranging from 100 nm to 800 µm. EDX analysis gives clear evidence for deviation of stoichiometry of the product. Magnetic analysis is indicating effect of stoichiometry and showing ferromagnetic interaction unlike antiferromagnetic feature. Electrical resistivity is showing similar behavior as reported earlier and reveals no effect of different size of grains or grain boundaries from room temperature to 125 K.

Critical behavior in graphene with Coulomb interactions.

PubMed

Wang, Jianhui; Fertig, H A; Murthy, Ganpathy

2010-05-07

We demonstrate that, in the presence of Coulomb interactions, electrons in graphene behave like a critical system, supporting power law correlations with interaction-dependent exponents. An asymptotic analysis shows that the origin of this behavior lies in particle-hole scattering, for which the Coulomb interaction induces anomalously close approaches. With increasing interaction strength the relevant power law changes from real to complex, leading to an unusual instability characterized by a complex-valued susceptibility in the thermodynamic limit. Measurable quantities, as well as the connection to classical two-dimensional systems, are discussed.

The Interaction between Multimedia Data Analysis and Theory Development in Design Research

ERIC Educational Resources Information Center

van Nes, Fenna; Doorman, Michiel

2010-01-01

Mathematics education researchers conducting instruction experiments using a design research methodology are challenged with the analysis of often complex and large amounts of qualitative data. In this paper, we present two case studies that show how multimedia analysis software can greatly support video data analysis and theory development in…

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

PubMed Central

Burger, Lukas; van Nimwegen, Erik

2008-01-01

Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

Supporting self-efficacy through interactive discussion in online communities of weight loss.

PubMed

Wang, Ye; Willis, Erin

2016-06-01

By conducting a content analysis of online communities connected by the Weight Watchers' online message boards, this study examined the relationship between conversational interactivity and consumer-generated content about consumer health information, self-efficacious content, and experiences with dieting and physical activities. The results showed that discussion about successful experiences with weight loss tended to be more interactive. Discussion about consumer health information tended to be non-interactive. The findings suggest that online communities generate social support through interactive discussion about successful experiences, and the interactive discussion, in return, sustains active participation in the community.

Study of a tri-trophic prey-dependent food chain model of interacting populations.

PubMed

Haque, Mainul; Ali, Nijamuddin; Chakravarty, Santabrata

2013-11-01

The current paper accounts for the influence of intra-specific competition among predators in a prey dependent tri-trophic food chain model of interacting populations. We offer a detailed mathematical analysis of the proposed food chain model to illustrate some of the significant results that has arisen from the interplay of deterministic ecological phenomena and processes. Biologically feasible equilibria of the system are observed and the behaviours of the system around each of them are described. In particular, persistence, stability (local and global) and bifurcation (saddle-node, transcritical, Hopf-Andronov) analysis of this model are obtained. Relevant results from previous well known food chain models are compared with the current findings. Global stability analysis is also carried out by constructing appropriate Lyapunov functions. Numerical simulations show that the present system is capable enough to produce chaotic dynamics when the rate of self-interaction is very low. On the other hand such chaotic behaviour disappears for a certain value of the rate of self interaction. In addition, numerical simulations with experimented parameters values confirm the analytical results and shows that intra-specific competitions bears a potential role in controlling the chaotic dynamics of the system; and thus the role of self interactions in food chain model is illustrated first time. Finally, a discussion of the ecological applications of the analytical and numerical findings concludes the paper. Copyright © 2013 Elsevier Inc. All rights reserved.

Socializing Children to Honorifics in Japanese: Identity and Stance in Interaction

ERIC Educational Resources Information Center

Burdelski, Matthew

2013-01-01

This paper examines socialization of honorifics in Japanese. Drawing upon audiovisual recordings of interaction in households and a preschool, the paper details ways caregivers use honorifics with children and ways children use honorifics with caregivers and peers. The analysis shows ways caregivers use referent and addressee honorifics within…

Emergent Readers' Social Interaction Styles and Their Comprehension Processes during Buddy Reading

ERIC Educational Resources Information Center

Christ, Tanya; Wang, X. Christine; Chiu, Ming Ming

2015-01-01

To examine the relations between emergent readers' social interaction styles and their comprehension processes, we adapted sociocultural and transactional views of learning and reading, and conducted statistical discourse analysis of 1,359 conversation turns transcribed from 14 preschoolers' 40 buddy reading events. Results show that interaction…

Classroom "Families": Cooperating or Competing--Girls' and Boys' Interactional Styles in a Bilingual Classroom.

ERIC Educational Resources Information Center

Cook-Gumperz, Jenny; Szymanski, Margaret

2001-01-01

Examines how students use gendered discourse practices in small peer group settings to accomplish their school tasks. The analysis contributes to the separate worlds hypothesis by showing how Latino children interactionally orient to their peer group as a gendered context. (Author/VWL)

Reconsideration of dynamic force spectroscopy analysis of streptavidin-biotin interactions.

PubMed

Taninaka, Atsushi; Takeuchi, Osamu; Shigekawa, Hidemi

2010-05-13

To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) is a technique that enables us to study the interaction between molecules at the single-molecule level. However, the obtained results differ among previous studies, which is considered to be caused by the differences in the measurement conditions. We have developed an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS. After verifying the performance of this technique, we carried out measurements to determine the landscapes of streptavidin-biotin interactions. The obtained results showed good agreement with theoretical predictions. Lifetimes were also well analyzed. Using a combination of cross-linkers and the atomic force microscope that we developed, site-selective measurement was carried out, and the steps involved in bonding due to microscopic interactions are discussed using the results obtained by site-selective analysis.

Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network.

PubMed

Yang, Huiying; Ke, Yuehua; Wang, Jian; Tan, Yafang; Myeni, Sebenzile K; Li, Dong; Shi, Qinghai; Yan, Yanfeng; Chen, Hui; Guo, Zhaobiao; Yuan, Yanzhi; Yang, Xiaoming; Yang, Ruifu; Du, Zongmin

2011-11-01

A Yersinia pestis-human protein interaction network is reported here to improve our understanding of its pathogenesis. Up to 204 interactions between 66 Y. pestis bait proteins and 109 human proteins were identified by yeast two-hybrid assay and then combined with 23 previously published interactions to construct a protein-protein interaction network. Topological analysis of the interaction network revealed that human proteins targeted by Y. pestis were significantly enriched in the proteins that are central in the human protein-protein interaction network. Analysis of this network showed that signaling pathways important for host immune responses were preferentially targeted by Y. pestis, including the pathways involved in focal adhesion, regulation of cytoskeleton, leukocyte transendoepithelial migration, and Toll-like receptor (TLR) and mitogen-activated protein kinase (MAPK) signaling. Cellular pathways targeted by Y. pestis are highly relevant to its pathogenesis. Interactions with host proteins involved in focal adhesion and cytoskeketon regulation pathways could account for resistance of Y. pestis to phagocytosis. Interference with TLR and MAPK signaling pathways by Y. pestis reflects common characteristics of pathogen-host interaction that bacterial pathogens have evolved to evade host innate immune response by interacting with proteins in those signaling pathways. Interestingly, a large portion of human proteins interacting with Y. pestis (16/109) also interacted with viral proteins (Epstein-Barr virus [EBV] and hepatitis C virus [HCV]), suggesting that viral and bacterial pathogens attack common cellular functions to facilitate infections. In addition, we identified vasodilator-stimulated phosphoprotein (VASP) as a novel interaction partner of YpkA and showed that YpkA could inhibit in vitro actin assembly mediated by VASP.

Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks.

PubMed

Nariai, N; Kim, S; Imoto, S; Miyano, S

2004-01-01

We propose a statistical method to estimate gene networks from DNA microarray data and protein-protein interactions. Because physical interactions between proteins or multiprotein complexes are likely to regulate biological processes, using only mRNA expression data is not sufficient for estimating a gene network accurately. Our method adds knowledge about protein-protein interactions to the estimation method of gene networks under a Bayesian statistical framework. In the estimated gene network, a protein complex is modeled as a virtual node based on principal component analysis. We show the effectiveness of the proposed method through the analysis of Saccharomyces cerevisiae cell cycle data. The proposed method improves the accuracy of the estimated gene networks, and successfully identifies some biological facts.

Time-Frequency Analysis Reveals Pairwise Interactions in Insect Swarms

NASA Astrophysics Data System (ADS)

Puckett, James G.; Ni, Rui; Ouellette, Nicholas T.

2015-06-01

The macroscopic emergent behavior of social animal groups is a classic example of dynamical self-organization, and is thought to arise from the local interactions between individuals. Determining these interactions from empirical data sets of real animal groups, however, is challenging. Using multicamera imaging and tracking, we studied the motion of individual flying midges in laboratory mating swarms. By performing a time-frequency analysis of the midge trajectories, we show that the midge behavior can be segmented into two distinct modes: one that is independent and composed of low-frequency maneuvers, and one that consists of higher-frequency nearly harmonic oscillations conducted in synchrony with another midge. We characterize these pairwise interactions, and make a hypothesis as to their biological function.

Label-free quantitative secretome analysis of Xanthomonas oryzae pv. oryzae highlights the involvement of a novel cysteine protease in its pathogenicity.

PubMed

Wang, Yiming; Gupta, Ravi; Song, Wei; Huh, Hyun-Hye; Lee, So Eui; Wu, Jingni; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kang, Kyu Young; Park, Sang-Ryeol; Kim, Sun Tae

2017-10-03

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases resulting in a huge loss of the total rice productivity. The initial interaction between rice and Xoo takes place in the host apoplast and is mediated primarily by secretion of various proteins from both partners. Yet, such secretory proteins remain to be largely identified and characterized. This study employed a label-free quantitative proteomics approach and identified 404 and 323 Xoo-secreted proteins from in vitro suspension-cultured cells and in planta systems, respectively. Gene Ontology analysis showed their involvement primarily in catalytic, transporter, and ATPase activities. Of a particular interest was a Xoo cysteine protease (XoCP), which showed dramatic increase in its protein abundance in planta upon Xoo interaction with a susceptible rice cultivar. Knock-out mutants of XoCP showed reduced pathogenicity on rice, highlighting its potential involvement in Xoo virulence. Besides, a parallel analysis of in planta rice-secreted proteins resulted in identification of 186 secretory proteins mainly associated with the catalytic, antioxidant, and electron carrier activities. Identified secretory proteins were exploited to shed light on their possible role in the rice-Xoo interaction, and that further deepen our understanding of such interaction. Xanthomonas oryzae pv. oryzae (Xoo), causative agent of bacterial blight disease, results in a huge loss of the total rice productivity. Using a label-free quantitative proteomics approach, we identified 727 Xoo- and 186 rice-secreted proteins. Functional annotation showed Xoo secreted proteins were mainly associated with the catalytic, transporter, and ATPase activities while the rice secreted proteins were mainly associated with the catalytic, antioxidant, and electron carrier activities. A novel Xoo cysteine protease (XoCP) was identified, showing dramatic increase in its protein abundance in planta upon Xoo interaction with a susceptible rice cultivar. Knock-out mutants of XoCP showed reduced pathogenicity on rice, highlighting its potential involvement in Xoo virulence. Copyright © 2017 Elsevier B.V. All rights reserved.

Differential gene expression analysis in glioblastoma cells and normal human brain cells based on GEO database.

PubMed

Wang, Anping; Zhang, Guibin

2017-11-01

The differentially expressed genes between glioblastoma (GBM) cells and normal human brain cells were investigated to performed pathway analysis and protein interaction network analysis for the differentially expressed genes. GSE12657 and GSE42656 gene chips, which contain gene expression profile of GBM were obtained from Gene Expression Omniub (GEO) database of National Center for Biotechnology Information (NCBI). The 'limma' data packet in 'R' software was used to analyze the differentially expressed genes in the two gene chips, and gene integration was performed using 'RobustRankAggreg' package. Finally, pheatmap software was used for heatmap analysis and Cytoscape, DAVID, STRING and KOBAS were used for protein-protein interaction, Gene Ontology (GO) and KEGG analyses. As results: i) 702 differentially expressed genes were identified in GSE12657, among those genes, 548 were significantly upregulated and 154 were significantly downregulated (p<0.01, fold-change >1), and 1,854 differentially expressed genes were identified in GSE42656, among the genes, 1,068 were significantly upregulated and 786 were significantly downregulated (p<0.01, fold-change >1). A total of 167 differentially expressed genes including 100 upregulated genes and 67 downregulated genes were identified after gene integration, and the genes showed significantly different expression levels in GBM compared with normal human brain cells (p<0.05). ii) Interactions between the protein products of 101 differentially expressed genes were identified using STRING and expression network was established. A key gene, called CALM3, was identified by Cytoscape software. iii) GO enrichment analysis showed that differentially expressed genes were mainly enriched in 'neurotransmitter:sodium symporter activity' and 'neurotransmitter transporter activity', which can affect the activity of neurotransmitter transportation. KEGG pathway analysis showed that the differentially expressed genes were mainly enriched in 'protein processing in endoplasmic reticulum', which can affect protein processing in endoplasmic reticulum. The results showed that: i) 167 differentially expressed genes were identified from two gene chips after integration; and ii) protein interaction network was established, and GO and KEGG pathway analyses were successfully performed to identify and annotate the key gene, which provide new insights for the studies on GBN at gene level.

A new 1D manganese(II) coordination polymer with end-to-end azide bridge and isonicotinoylhydrazone Schiff base ligand: Crystal structure, Hirshfeld surface, NBO and thermal analyses

NASA Astrophysics Data System (ADS)

Khani, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

2018-02-01

A new manganese (II) coordination polymer, [MnL2 (μ-1,3-N3)2]n, with co-ligands including azide anion and Schiff base based on isonicotinoylhydrazone has been synthesized and characterized. The crystal structure determination shows that the azide ligand acts as end-to-end (EE) bridging ligand and generates a one-dimensional coordination polymer. In this compound, each manganes (II) metal center is hexa-coordinated by four azide nitrogens and two pyridinic nitrogens for the formation of octahedral geometry. The analysis of crystal packing indicates that the 1D chain of [MnL2 (μ-1,3-N3)2]n, is stabilized as a 3D supramolecular network by intra- and inter-chain intermolecular interactions of X-H···Y (X = N and C, Y = O and N). Hirshfeld surface analysis and 2D fingerprint plots have been used for a more detailed investigation of intermolecular interactions. Also, natural bond orbital (NBO) analysis was performed to get information about atomic charge distributions, hybridizations and the strength of interactions. Finally, thermal analysis of compound showed its complete decomposition during three thermal steps.

Molecular interactions in the complexes of toluene with butyronitrile: A DFT approach

NASA Astrophysics Data System (ADS)

Karthick, N. K.; Arivazhagan, G.

2018-04-01

Density Functional Theory (DFT) has been employed to investigate the self association of butyronitrile and the heterointeractions in the 1:2 (toluene: butyronitrile) and 1:1 complexes of toluene with butyronitrile. For this investigation the B3LYP functional with Grimme's dispersion correction (D3) term and ωB97XD functionals were used. The theoretical frequency analysis shows the unsuitability of B3LYP with D3 for the present investigation. Therefore, Natural Bonding Orbital analysis was done at the functional ωB97XD. It is found through this work that only the methylene hydrogens of butyronitrile are responsible for the self association among the butyronitrile molecules. In 1:1 complex, the red shift in the butyronitrile methyl asymmetric stretching mode is not due to the active participation of this group in heterointeractions and it is solely due to the other interactions happening in its vicinity. Only the interaction (TOL) C - H ⋯ N(BN) is present in the complex. In 1:2 complex the butyronitrile methyl/methylene hydrogens interact with the delocalized electron cloud of toluene and the toluene hydrogens interact with the butyronitrile nitrogen. Comparison of interaction energies shows that the stability of 1:2 complex is more than that of butyronitrile dimer and 1:1 complex.

Markov Logic Networks in the Analysis of Genetic Data

PubMed Central

Sakhanenko, Nikita A.

2010-01-01

Abstract Complex, non-additive genetic interactions are common and can be critical in determining phenotypes. Genome-wide association studies (GWAS) and similar statistical studies of linkage data, however, assume additive models of gene interactions in looking for genotype-phenotype associations. These statistical methods view the compound effects of multiple genes on a phenotype as a sum of influences of each gene and often miss a substantial part of the heritable effect. Such methods do not use any biological knowledge about underlying mechanisms. Modeling approaches from the artificial intelligence (AI) field that incorporate deterministic knowledge into models to perform statistical analysis can be applied to include prior knowledge in genetic analysis. We chose to use the most general such approach, Markov Logic Networks (MLNs), for combining deterministic knowledge with statistical analysis. Using simple, logistic regression-type MLNs we can replicate the results of traditional statistical methods, but we also show that we are able to go beyond finding independent markers linked to a phenotype by using joint inference without an independence assumption. The method is applied to genetic data on yeast sporulation, a complex phenotype with gene interactions. In addition to detecting all of the previously identified loci associated with sporulation, our method identifies four loci with smaller effects. Since their effect on sporulation is small, these four loci were not detected with methods that do not account for dependence between markers due to gene interactions. We show how gene interactions can be detected using more complex models, which can be used as a general framework for incorporating systems biology with genetics. PMID:20958249

Using Networks To Understand Medical Data: The Case of Class III Malocclusions

PubMed Central

Scala, Antonio; Auconi, Pietro; Scazzocchio, Marco; Caldarelli, Guido; McNamara, James A.; Franchi, Lorenzo

2012-01-01

A system of elements that interact or regulate each other can be represented by a mathematical object called a network. While network analysis has been successfully applied to high-throughput biological systems, less has been done regarding their application in more applied fields of medicine; here we show an application based on standard medical diagnostic data. We apply network analysis to Class III malocclusion, one of the most difficult to understand and treat orofacial anomaly. We hypothesize that different interactions of the skeletal components can contribute to pathological disequilibrium; in order to test this hypothesis, we apply network analysis to 532 Class III young female patients. The topology of the Class III malocclusion obtained by network analysis shows a strong co-occurrence of abnormal skeletal features. The pattern of these occurrences influences the vertical and horizontal balance of disharmony in skeletal form and position. Patients with more unbalanced orthodontic phenotypes show preponderance of the pathological skeletal nodes and minor relevance of adaptive dentoalveolar equilibrating nodes. Furthermore, by applying Power Graphs analysis we identify some functional modules among orthodontic nodes. These modules correspond to groups of tightly inter-related features and presumably constitute the key regulators of plasticity and the sites of unbalance of the growing dentofacial Class III system. The data of the present study show that, in their most basic abstraction level, the orofacial characteristics can be represented as graphs using nodes to represent orthodontic characteristics, and edges to represent their various types of interactions. The applications of this mathematical model could improve the interpretation of the quantitative, patient-specific information, and help to better targeting therapy. Last but not least, the methodology we have applied in analyzing orthodontic features can be applied easily to other fields of the medical science. PMID:23028552

Understanding interactions in virtual HIV communities: a social network analysis approach.

PubMed

Shi, Jingyuan; Wang, Xiaohui; Peng, Tai-Quan; Chen, Liang

2017-02-01

This study investigated the driving mechanism of building interaction ties among the people living with HIV/AIDS in one of the largest virtual HIV communities in China using social network analysis. Specifically, we explained the probability of forming interaction ties with homophily and popularity characteristics. The exponential random graph modeling results showed that members in this community tend to form homophilous ties in terms of shared location and interests. Moreover, we found a tendency away from popularity effect. This suggests that in this community, resources and information were not disproportionally received by a few of members, which could be beneficial to the overall community.

Network-Induced Classification Kernels for Gene Expression Profile Analysis

PubMed Central

Dror, Gideon; Shamir, Ron

2012-01-01

Abstract Computational classification of gene expression profiles into distinct disease phenotypes has been highly successful to date. Still, robustness, accuracy, and biological interpretation of the results have been limited, and it was suggested that use of protein interaction information jointly with the expression profiles can improve the results. Here, we study three aspects of this problem. First, we show that interactions are indeed relevant by showing that co-expressed genes tend to be closer in the network of interactions. Second, we show that the improved performance of one extant method utilizing expression and interactions is not really due to the biological information in the network, while in another method this is not the case. Finally, we develop a new kernel method—called NICK—that integrates network and expression data for SVM classification, and demonstrate that overall it achieves better results than extant methods while running two orders of magnitude faster. PMID:22697242

A strategy to apply quantitative epistasis analysis on developmental traits.

PubMed

Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

2017-05-15

Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

The Multiple Correspondence Analysis Method and Brain Functional Connectivity: Its Application to the Study of the Non-linear Relationships of Motor Cortex and Basal Ganglia.

PubMed

Rodriguez-Sabate, Clara; Morales, Ingrid; Sanchez, Alberto; Rodriguez, Manuel

2017-01-01

The complexity of basal ganglia (BG) interactions is often condensed into simple models mainly based on animal data and that present BG in closed-loop cortico-subcortical circuits of excitatory/inhibitory pathways which analyze the incoming cortical data and return the processed information to the cortex. This study was aimed at identifying functional relationships in the BG motor-loop of 24 healthy-subjects who provided written, informed consent and whose BOLD-activity was recorded by MRI methods. The analysis of the functional interaction between these centers by correlation techniques and multiple linear regression showed non-linear relationships which cannot be suitably addressed with these methods. The multiple correspondence analysis (MCA), an unsupervised multivariable procedure which can identify non-linear interactions, was used to study the functional connectivity of BG when subjects were at rest. Linear methods showed different functional interactions expected according to current BG models. MCA showed additional functional interactions which were not evident when using lineal methods. Seven functional configurations of BG were identified with MCA, two involving the primary motor and somatosensory cortex, one involving the deepest BG (external-internal globus pallidum, subthalamic nucleus and substantia nigral), one with the input-output BG centers (putamen and motor thalamus), two linking the input-output centers with other BG (external pallidum and subthalamic nucleus), and one linking the external pallidum and the substantia nigral. The results provide evidence that the non-linear MCA and linear methods are complementary and should be best used in conjunction to more fully understand the nature of functional connectivity of brain centers.

rs1495741 as a tag single nucleotide polymorphism of N-acetyltransferase 2 acetylator phenotype associates bladder cancer risk and interacts with smoking: A systematic review and meta-analysis.

PubMed

Ma, Chong; Gu, Liyan; Yang, Mingyuan; Zhang, Zhensheng; Zeng, Shuxiong; Song, Ruixiang; Xu, Chuanliang; Sun, Yinghao

2016-08-01

Rs1495741 has been identified to infer N-acetyltransferase 2 (NAT2) acetylator phenotype, and to decrease the risk of bladder cancer. However, a number of studies conducted in various regions showed controversial results. To quantify the association between rs1495741 and the risk of bladder cancer and to estimate the interaction effect of this genetic variant with smoking, we performed a systematic literature review and meta-analysis involving 14,815 cases and 58,282 controls from 29 studies. Our results indicates rs1495741 significantly associated with bladder cancer risk (OR = 0.85, 95% CI = 0.82-0.89, test for heterogeneity P = 0.36, I = 7.0%). And we verified this association in populations from Europe, America, and Asia. Further, our stratified meta-analysis showed rs1495741's role is typically evident only in ever smokers, which suggests its interaction with smoking. This study may provide new insight into gene-environment study on bladder cancer.

Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

PubMed Central

Jothi, Raja; Cherukuri, Praveen F.; Tasneem, Asba; Przytycka, Teresa M.

2006-01-01

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the noninteracting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain–domain interactions. Given a protein–protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain–domain interactions, and used known domain–domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain–domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites. PMID:16949097

Gene-based interaction analysis shows GABAergic genes interacting with parenting in adolescent depressive symptoms.

PubMed

Van Assche, Evelien; Moons, Tim; Cinar, Ozan; Viechtbauer, Wolfgang; Oldehinkel, Albertine J; Van Leeuwen, Karla; Verschueren, Karine; Colpin, Hilde; Lambrechts, Diether; Van den Noortgate, Wim; Goossens, Luc; Claes, Stephan; van Winkel, Ruud

2017-12-01

Most gene-environment interaction studies (G × E) have focused on single candidate genes. This approach is criticized for its expectations of large effect sizes and occurrence of spurious results. We describe an approach that accounts for the polygenic nature of most psychiatric phenotypes and reduces the risk of false-positive findings. We apply this method focusing on the role of perceived parental support, psychological control, and harsh punishment in depressive symptoms in adolescence. Analyses were conducted on 982 adolescents of Caucasian origin (M age (SD) = 13.78 (.94) years) genotyped for 4,947 SNPs in 263 genes, selected based on a literature survey. The Leuven Adolescent Perceived Parenting Scale (LAPPS) and the Parental Behavior Scale (PBS) were used to assess perceived parental psychological control, harsh punishment, and support. The Center for Epidemiologic Studies Depression Scale (CES-D) was the outcome. We used gene-based testing taking into account linkage disequilibrium to identify genes containing SNPs exhibiting an interaction with environmental factors yielding a p-value per single gene. Significant results at the corrected p-value of p < 1.90 × 10 -4 were examined in an independent replication sample of Dutch adolescents (N = 1354). Two genes showed evidence for interaction with perceived support: GABRR1 (p = 4.62 × 10 -5 ) and GABRR2 (p = 9.05 × 10 -6 ). No genes interacted significantly with psychological control or harsh punishment. Gene-based analysis was unable to confirm the interaction of GABRR1 or GABRR2 with support in the replication sample. However, for GABRR2, but not GABRR1, the correlation of the estimates between the two datasets was significant (r (46) = .32; p = .027) and a gene-based analysis of the combined datasets supported GABRR2 × support interaction (p = 1.63 × 10 -4 ). We present a gene-based method for gene-environment interactions in a polygenic context and show that genes interact differently with particular aspects of parenting. This accentuates the importance of polygenic approaches and the need to accurately assess environmental exposure in G × E. © 2017 Association for Child and Adolescent Mental Health.

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

PubMed Central

Lopes, Anne; Sacquin-Mora, Sophie; Dimitrova, Viktoriya; Laine, Elodie; Ponty, Yann; Carbone, Alessandra

2013-01-01

Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to evaluate whether proteins in the environment, competing with the true partner, affect its identification. We found three populations of proteins: strongly competing, never competing, and interacting with different levels of strength. Populations and levels of strength are numerically characterized and provide a signature for the behavior of a protein in the crowded environment. We showed that partner identification, to some extent, does not depend on the competing partners present in the environment, that certain biochemical classes of proteins are intrinsically easier to analyze than others, and that small proteins are not more promiscuous than large ones. Our approach brings to light that the knowledge of the binding site can be used to reduce the high computational cost of docking simulations with no consequence in the quality of the results, demonstrating the possibility to apply coarse-grain docking to datasets made of thousands of proteins. Comparison with all available large-scale analyses aimed to partner predictions is realized. We release the complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary sequence analysis leading to binding site predictions. Download site: http://www.lgm.upmc.fr/CCDMintseris/ PMID:24339765

Structural and computational analysis of intermolecular interactions in a new 2-thiouracil polymorph.

PubMed

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Sanković, Krešimir

2017-12-01

The crystallization and characterization of a new polymorph of 2-thiouracil by single-crystal X-ray diffraction, Hirshfeld surface analysis and periodic density functional theory (DFT) calculations are described. The previously published polymorph (A) crystallizes in the triclinic space group P\\overline{1}, while that described herein (B) crystallizes in the monoclinic space group P2 1 /c. Periodic DFT calculations showed that the energies of polymorphs A and B, compared to the gas-phase geometry, were -108.8 and -29.4 kJ mol -1 , respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O...H and S...H contacts cover over 50% of the noncovalent contacts in both of the polymorphs; however, they are quite different in strength. Hydrogen bonds of the N-H...O and N-H...S types were found in polymorph A, whereas in polymorph B, only those of the N-H...O type are present, resulting in a different packing in the unit cell. QTAIM (quantum theory of atoms in molecules) computational analysis showed that the interaction energies for these weak-to-medium strength hydrogen bonds with a noncovalent or mixed interaction character were estimated to fall within the ranges 5.4-10.2 and 4.9-9.2 kJ mol -1 for polymorphs A and B, respectively. Also, the NCI (noncovalent interaction) plots revealed weak stacking interactions. The interaction energies for these interactions were in the ranges 3.5-4.1 and 3.1-5.5 kJ mol -1 for polymorphs A and B, respectively, as shown by QTAIM analysis.

The PLIN4 Variant rs8887 Modulates Obesity Related Phenotypes in Humans through Creation of a Novel miR-522 Seed Site

PubMed Central

Richardson, Kris; Louie-Gao, Qiong; Arnett, Donna K.; Parnell, Laurence D.; Lai, Chao-Qiang; Davalos, Alberto; Fox, Caroline S.; Demissie, Serkalem; Cupples, L. Adrienne; Fernandez-Hernando, Carlos; Ordovas, Jose M.

2011-01-01

PLIN4 is a member of the PAT family of lipid storage droplet (LSD) proteins. Associations between seven single nucleotide polymorphisms (SNPs) at human PLIN4 with obesity related phenotypes were investigated using meta-analysis followed by a determination if these phenotypes are modulated by interactions between PLIN4 SNPs and dietary PUFA. Samples consisted of subjects from two populations of European ancestry. We demonstrated association of rs8887 with anthropometrics. Meta-analysis demonstrated significant interactions between the rs8887 minor allele with PUFA n3 modulating anthropometrics. rs884164 showed interaction with both n3 and n6 PUFA modulating anthropometric and lipid phenotypes. In silico analysis of the PLIN4 3′UTR sequence surrounding the rs8887 minor A allele predicted a seed site for the human microRNA-522 (miR-522), suggesting a functional mechanism. Our data showed that a PLIN4 3′UTR luciferase reporter carrying the A allele of rs8887 was reduced in response to miR-522 mimics compared to the G allele. These results suggest variation at the PLIN4 locus, and its interaction with PUFA as a modulator of obesity related phenotypes, acts in part through creation of a miR-522 regulatory site. PMID:21533135

Biplot evaluation of test environments and identification of mega-environment for sugarcane cultivars in China

PubMed Central

Luo, Jun; Pan, Yong-Bao; Que, Youxiong; Zhang, Hua; Grisham, Michael Paul; Xu, Liping

2015-01-01

Test environments and classification of regional ecological zones into mega environments are the two key components in regional testing of sugarcane cultivars. This study aims to provide the theoretical basis for test environment evaluation and ecological zone division for sugarcane cultivars. In the present study, sugarcane yield data from a three-year nationwide field trial involving 21 cultivars and 14 pilot test locations were analysed using both analysis of variance (ANOVA) and heritability adjusted-genotype main effect plus genotype-environment interaction (HA-GGE) biplot. The results showed that among the interactive factors, the GE interaction had the greatest impact, while the genotype and year interaction showed the lowest impact. Kaiyuan, Lincang and Baoshan of Yunnan, Zhangzhou and Fuzhou of Fujian, and Hechi, Liuzhou and Chongzuo of Guangxi, and Lingao of Hainan were ideal test environments with a demonstrated high efficiency in selecting new cultivars with a wide adaptability, whereas Baise of Guangxi was not. Based on HA-GGE biplot analysis, there are three ecological sugarcane production zones in China, the Southern China Inland Zone, the Southwestern Plateau Zone, and the Southern Coastal Zone. The HA-GGE biplot analysis here presents the ideal test environments and also identifies the mega-environment for sugarcane cultivars in China. PMID:26489689

Biplot evaluation of test environments and identification of mega-environment for sugarcane cultivars in China.

PubMed

Luo, Jun; Pan, Yong-Bao; Que, Youxiong; Zhang, Hua; Grisham, Michael Paul; Xu, Liping

2015-10-22

Test environments and classification of regional ecological zones into mega environments are the two key components in regional testing of sugarcane cultivars. This study aims to provide the theoretical basis for test environment evaluation and ecological zone division for sugarcane cultivars. In the present study, sugarcane yield data from a three-year nationwide field trial involving 21 cultivars and 14 pilot test locations were analysed using both analysis of variance (ANOVA) and heritability adjusted-genotype main effect plus genotype-environment interaction (HA-GGE) biplot. The results showed that among the interactive factors, the GE interaction had the greatest impact, while the genotype and year interaction showed the lowest impact. Kaiyuan, Lincang and Baoshan of Yunnan, Zhangzhou and Fuzhou of Fujian, and Hechi, Liuzhou and Chongzuo of Guangxi, and Lingao of Hainan were ideal test environments with a demonstrated high efficiency in selecting new cultivars with a wide adaptability, whereas Baise of Guangxi was not. Based on HA-GGE biplot analysis, there are three ecological sugarcane production zones in China, the Southern China Inland Zone, the Southwestern Plateau Zone, and the Southern Coastal Zone. The HA-GGE biplot analysis here presents the ideal test environments and also identifies the mega-environment for sugarcane cultivars in China.

Three-dimensional viscous rotor flow calculations using a viscous-inviscid interaction approach

NASA Technical Reports Server (NTRS)

Chen, Ching S.; Bridgeman, John O.

1990-01-01

A three-dimensional viscous-inviscid interaction analysis was developed to predict the performance of rotors in hover and in forward flight at subsonic and transonic tip speeds. The analysis solves the full-potential and boundary-layer equations by finite-difference numerical procedures. Calculations were made for several different model rotor configurations. The results were compared with predictions from a two-dimensional integral method and with experimental data. The comparisons show good agreement between predictions and test data.

Identification of expression quantitative trait loci by the interaction analysis using genetic algorithm.

PubMed

Namkung, Junghyun; Nam, Jin-Wu; Park, Taesung

2007-01-01

Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient and robust algorithm is needed. The genetic algorithm (GA) is useful in searching for the optimal solution from a very large searchable space. In this study, we show that genome-wide interaction analysis using GA and a statistical interaction model can provide a practical method to detect biologically interacting loci. We focus our search on transcriptional regulators by analyzing gene x gene interactions for cancer-related genes. The expression values of three cancer-related genes were selected from the expression data of the Genetic Analysis Workshop 15 Problem 1 data set. We implemented a GA to identify the expression quantitative trait loci that are significantly associated with expression levels of the cancer-related genes. The time complexity of the GA was compared with that of an exhaustive search algorithm. As a result, our GA, which included heuristic methods, such as archive, elitism, and local search, has greatly reduced computational time in a genome-wide search for gene x gene interactions. In general, the GA took one-fifth the computation time of an exhaustive search for the most significant pair of single-nucleotide polymorphisms.

Identification of expression quantitative trait loci by the interaction analysis using genetic algorithm

PubMed Central

Namkung, Junghyun; Nam, Jin-Wu; Park, Taesung

2007-01-01

Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient and robust algorithm is needed. The genetic algorithm (GA) is useful in searching for the optimal solution from a very large searchable space. In this study, we show that genome-wide interaction analysis using GA and a statistical interaction model can provide a practical method to detect biologically interacting loci. We focus our search on transcriptional regulators by analyzing gene × gene interactions for cancer-related genes. The expression values of three cancer-related genes were selected from the expression data of the Genetic Analysis Workshop 15 Problem 1 data set. We implemented a GA to identify the expression quantitative trait loci that are significantly associated with expression levels of the cancer-related genes. The time complexity of the GA was compared with that of an exhaustive search algorithm. As a result, our GA, which included heuristic methods, such as archive, elitism, and local search, has greatly reduced computational time in a genome-wide search for gene × gene interactions. In general, the GA took one-fifth the computation time of an exhaustive search for the most significant pair of single-nucleotide polymorphisms. PMID:18466570

Trophic and Non-Trophic Interactions in a Biodiversity Experiment Assessed by Next-Generation Sequencing

PubMed Central

Tiede, Julia; Wemheuer, Bernd; Traugott, Michael; Daniel, Rolf; Tscharntke, Teja; Ebeling, Anne; Scherber, Christoph

2016-01-01

Plant diversity affects species richness and abundance of taxa at higher trophic levels. However, plant diversity effects on omnivores (feeding on multiple trophic levels) and their trophic and non-trophic interactions are not yet studied because appropriate methods were lacking. A promising approach is the DNA-based analysis of gut contents using next generation sequencing (NGS) technologies. Here, we integrate NGS-based analysis into the framework of a biodiversity experiment where plant taxonomic and functional diversity were manipulated to directly assess environmental interactions involving the omnivorous ground beetle Pterostichus melanarius. Beetle regurgitates were used for NGS-based analysis with universal 18S rDNA primers for eukaryotes. We detected a wide range of taxa with the NGS approach in regurgitates, including organisms representing trophic, phoretic, parasitic, and neutral interactions with P. melanarius. Our findings suggest that the frequency of (i) trophic interactions increased with plant diversity and vegetation cover; (ii) intraguild predation increased with vegetation cover, and (iii) neutral interactions with organisms such as fungi and protists increased with vegetation cover. Experimentally manipulated plant diversity likely affects multitrophic interactions involving omnivorous consumers. Our study therefore shows that trophic and non-trophic interactions can be assessed via NGS to address fundamental questions in biodiversity research. PMID:26859146

Modeling eye gaze patterns in clinician-patient interaction with lag sequential analysis.

PubMed

Montague, Enid; Xu, Jie; Chen, Ping-Yu; Asan, Onur; Barrett, Bruce P; Chewning, Betty

2011-10-01

The aim of this study was to examine whether lag sequential analysis could be used to describe eye gaze orientation between clinicians and patients in the medical encounter. This topic is particularly important as new technologies are implemented into multiuser health care settings in which trust is critical and nonverbal cues are integral to achieving trust. This analysis method could lead to design guidelines for technologies and more effective assessments of interventions. Nonverbal communication patterns are important aspects of clinician-patient interactions and may affect patient outcomes. The eye gaze behaviors of clinicians and patients in 110 videotaped medical encounters were analyzed using the lag sequential method to identify significant behavior sequences. Lag sequential analysis included both event-based lag and time-based lag. Results from event-based lag analysis showed that the patient's gaze followed that of the clinician, whereas the clinician's gaze did not follow the patient's. Time-based sequential analysis showed that responses from the patient usually occurred within 2 s after the initial behavior of the clinician. Our data suggest that the clinician's gaze significantly affects the medical encounter but that the converse is not true. Findings from this research have implications for the design of clinical work systems and modeling interactions. Similar research methods could be used to identify different behavior patterns in clinical settings (physical layout, technology, etc.) to facilitate and evaluate clinical work system designs.

Modeling Eye Gaze Patterns in Clinician-Patient Interaction with Lag Sequential Analysis

PubMed Central

Montague, E; Xu, J; Asan, O; Chen, P; Chewning, B; Barrett, B

2011-01-01

Objective The aim of this study was to examine whether lag-sequential analysis could be used to describe eye gaze orientation between clinicians and patients in the medical encounter. This topic is particularly important as new technologies are implemented into multi-user health care settings where trust is critical and nonverbal cues are integral to achieving trust. This analysis method could lead to design guidelines for technologies and more effective assessments of interventions. Background Nonverbal communication patterns are important aspects of clinician-patient interactions and may impact patient outcomes. Method Eye gaze behaviors of clinicians and patients in 110-videotaped medical encounters were analyzed using the lag-sequential method to identify significant behavior sequences. Lag-sequential analysis included both event-based lag and time-based lag. Results Results from event-based lag analysis showed that the patients’ gaze followed that of clinicians, while clinicians did not follow patients. Time-based sequential analysis showed that responses from the patient usually occurred within two seconds after the initial behavior of the clinician. Conclusion Our data suggest that the clinician’s gaze significantly affects the medical encounter but not the converse. Application Findings from this research have implications for the design of clinical work systems and modeling interactions. Similar research methods could be used to identify different behavior patterns in clinical settings (physical layout, technology, etc.) to facilitate and evaluate clinical work system designs. PMID:22046723

Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

PubMed

Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

2016-10-07

Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

Does the growth response of woody plants to elevated CO2 increase with temperature? A model-oriented meta-analysis.

PubMed

Baig, Sofia; Medlyn, Belinda E; Mercado, Lina M; Zaehle, Sönke

2015-12-01

The temperature dependence of the reaction kinetics of the Rubisco enzyme implies that, at the level of a chloroplast, the response of photosynthesis to rising atmospheric CO2 concentration (Ca ) will increase with increasing air temperature. Vegetation models incorporating this interaction predict that the response of net primary productivity (NPP) to elevated CO2 (eCa ) will increase with rising temperature and will be substantially larger in warm tropical forests than in cold boreal forests. We tested these model predictions against evidence from eCa experiments by carrying out two meta-analyses. Firstly, we tested for an interaction effect on growth responses in factorial eCa  × temperature experiments. This analysis showed a positive, but nonsignificant interaction effect (95% CI for above-ground biomass response = -0.8, 18.0%) between eCa and temperature. Secondly, we tested field-based eCa experiments on woody plants across the globe for a relationship between the eCa effect on plant biomass and mean annual temperature (MAT). This second analysis showed a positive but nonsignificant correlation between the eCa response and MAT. The magnitude of the interactions between CO2 and temperature found in both meta-analyses were consistent with model predictions, even though both analyses gave nonsignificant results. Thus, we conclude that it is not possible to distinguish between the competing hypotheses of no interaction vs. an interaction based on Rubisco kinetics from the available experimental database. Experiments in a wider range of temperature zones are required. Until such experimental data are available, model predictions should aim to incorporate uncertainty about this interaction. © 2015 John Wiley & Sons Ltd.

Tin-Platinum catalysts interactions on titania and silica

NASA Astrophysics Data System (ADS)

Nava, N.; Del Angel, P.; Salmones, J.; Baggio-Saitovitch, E.; Santiago, P.

2007-09-01

Pt-Sn was supported on titania and silica, and the resulting interactions between the components in prepared samples and the resulting interactions between the components before and after treatment with hydrogen were characterized by Mössbauer spectroscopy, X-ray diffraction, Rietveld refinement, high-resolution transmission electron microscopy (HRTEM) and catalytic tests data. Results show the presence of Pt and SnO 2 after calcinations, and Pt 3Sn, PtSn and PtSn 3 after reduction. Rietveld analysis shows that some Ti 4+ are replaced by Sn 4+ atoms in the titania structure. Finally, HRTEM and the practically absence of activity observed confirms that metallic platinum is encapsulated.

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

PubMed

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

2016-07-01

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

The long-time dynamics of two hydrodynamically-coupled swimming cells.

PubMed

Michelin, Sébastien; Lauga, Eric

2010-05-01

Swimming microorganisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where fluid-mediated interactions can be treated rigorously, the long-time hydrodynamics of a collection of cells result from interactions with many other cells, and as such typically eludes an analytical approach. Here, we consider the only case where such problem can be treated rigorously analytically, namely when the cells have spatially confined trajectories, such as the spermatozoa of some marine invertebrates. We consider two spherical cells swimming, when isolated, with arbitrary circular trajectories, and derive the long-time kinematics of their relative locomotion. We show that in the dilute limit where the cells are much further away than their size, and the size of their circular motion, a separation of time scale occurs between a fast (intrinsic) swimming time, and a slow time where hydrodynamic interactions lead to change in the relative position and orientation of the swimmers. We perform a multiple-scale analysis and derive the effective dynamical system--of dimension two--describing the long-time behavior of the pair of cells. We show that the system displays one type of equilibrium, and two types of rotational equilibrium, all of which are found to be unstable. A detailed mathematical analysis of the dynamical systems further allows us to show that only two cell-cell behaviors are possible in the limit of t-->infinity, either the cells are attracted to each other (possibly monotonically), or they are repelled (possibly monotonically as well), which we confirm with numerical computations. Our analysis shows therefore that, even in the dilute limit, hydrodynamic interactions lead to new modes of cell-cell locomotion.

Automated identification of social interaction criteria in Drosophila melanogaster.

PubMed

Schneider, J; Levine, J D

2014-10-01

The study of social behaviour within groups has relied on fixed definitions of an 'interaction'. Criteria used in these definitions often involve a subjectively defined cut-off value for proximity, orientation and time (e.g. courtship, aggression and social interaction networks) and the same numerical values for these criteria are applied to all of the treatment groups within an experiment. One universal definition of an interaction could misidentify interactions within groups that differ in life histories, study treatments and/or genetic mutations. Here, we present an automated method for determining the values of interaction criteria using a pre-defined rule set rather than pre-defined values. We use this approach and show changing social behaviours in different manipulations of Drosophila melanogaster. We also show that chemosensory cues are an important modality of social spacing and interaction. This method will allow a more robust analysis of the properties of interacting groups, while helping us understand how specific groups regulate their social interaction space. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family*

PubMed Central

Li, Ping-Yi; Chen, Xiu-Lan; Ji, Peng; Li, Chun-Yang; Wang, Peng; Zhang, Yi; Xie, Bin-Bin; Qin, Qi-Long; Su, Hai-Nan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Zhang, Xi-Ying

2015-01-01

Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp202 and Phe203 in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability. PMID:25771540

Studies on interaction of insect repellent compounds with odorant binding receptor proteins by in silico molecular docking approach.

PubMed

Gopal, J Vinay; Kannabiran, K

2013-12-01

The aim of the study was to identify the interactions between insect repellent compounds and target olfactory proteins. Four compounds, camphor (C10H16O), carvacrol (C10H14O), oleic acid (C18H34O2) and firmotox (C22H28O5) were chosen as ligands. Seven olfactory proteins of insects with PDB IDs: 3K1E, 1QWV, 1TUJ, 1OOF, 2ERB, 3R1O and OBP1 were chosen for docking analysis. Patch dock was used and pymol for visualizing the structures. The interactions of these ligands with few odorant binding proteins showed binding energies. The ligand camphor had showed a binding energy of -136 kcal/mol with OBP1 protein. The ligand carvacrol interacted with 1QWV and 1TUJ proteins with a least binding energy of -117.45 kcal/mol and -21.78 kcal/mol respectively. The ligand oleic acid interacted with 1OOF, 2ERB, 3R1O and OBP1 with least binding energies. Ligand firmotox interacted with OBP1 and showed least binding energies. Three ligands (camphor, oleic acid and firmotox) had one, two, three interactions with a single protein OBP1 of Nilaparvatha lugens (Rice pest). From this in silico study we identified the interaction patterns for insect repellent compounds with the target insect odarant proteins. The results of our study revealed that the chosen ligands showed hydrogen bond interactions with the target olfactory receptor proteins.

Fuel swelling and interaction layer formation in the SELENIUM Si and ZrN coated U(Mo) dispersion fuel plates irradiated at high power in BR2

NASA Astrophysics Data System (ADS)

Leenaers, A.; Van den Berghe, S.; Koonen, E.; Kuzminov, V.; Detavernier, C.

2015-03-01

In the framework of the SELENIUM project two full size flat fuel plates were produced with respectively Si and ZrN coated U(Mo) particles and irradiated in the BR2 reactor at SCK•CEN. Non-destructive analysis of the plates showed that the fuel swelling profiles of both SELENIUM plates were very similar to each other and none of the plates showed signs of pillowing or excessive swelling at the end of irradiation at the highest power position (local maximum 70% 235U). The microstructural analysis showed that the Si coated fuel has less interaction phase formation at low burn-up but at the highest burn-ups, defects start to develop on the IL-matrix interface. The ZrN coated fuel, shows a virtual absence of reaction between the U(Mo) and the Al, up to high fission densities after which the interaction layer formation starts and defects develop in the matrix near the U(Mo) particles. It was found and is confirmed by the SELENIUM (Surface Engineering of Low ENrIched Uranium-Molybdenum) experiment that there are two phenomena at play that need to be controlled: the formation of an interaction layer and swelling of the fuel. As the interaction layer formation occurs at the U(Mo)-matrix interface, applying a diffusion barrier (coating) at that interface should prevent the interaction between U(Mo) and the matrix. The U(Mo) swelling, observed to proceed at an accelerating rate with respect to fission density accumulation, is governed by linear solid state swelling and fission gas bubble swelling due to recrystallization of the fuel. The examination of the SELENIUM fuel plates clearly show that for the U(Mo) dispersion fuel to be qualified, the swelling rate at high burn-up needs to be reduced.

Effects of reward and punishment on task performance, mood and autonomic nervous function, and the interaction with personality.

PubMed

Sakuragi, Sokichi; Sugiyama, Yoshiki

2009-06-01

The effects of reward and punishment are different, and there are individual differences in sensitivity to reward and punishment. The purpose of this study was to investigate the effects of reward and punishment on task performance, mood, and autonomic nervous function, along with the interaction with personality. Twenty-one healthy female subjects volunteered for the experiment. The task performance was evaluated by required time and total errors while performing a Wisconsin Card Sorting Test. We assessed their personalities using the Minnesota Multiphasic Personality Inventory (MMPI) questionnaire, and mood states by a profile of mood states. Autonomic nervous function was estimated by a spectral analysis of heart rate variability, baroreflex sensitivity, and blood pressure. Repeated measures analysis of variance (ANOVA) revealed significant interaction of condition x time course on mood and autonomic nervous activity, which would indicate a less stressed state under the rewarding condition, but revealed no significant interaction of condition x time course on the task performance. The interactions with personality were further analyzed by repeated measures ANOVA applying the clinical scales of MMPI as independent variables, and significant interactions of condition x time course x Pt (psychasthenia) on task performance, mood, and blood pressure, were revealed. That is, the high Pt group, whose members tend to be sensitive and prone to worry, showed gradual improvement of task performance under the punishing situation with slight increase in systolic blood pressure, while showed no improvement under the rewarding situation with fatigue sense attenuation. In contrast, the low Pt group, whose members tend to be adaptive and self-confident, showed gradual improvement under the rewarding situation. Therefore, we should carefully choose the strategy of reward or punishment, considering the interaction with personality as well as the context in which it is given.

Matrix metalloproteinase 20-dentin sialophosphoprotein interaction in oral cancer.

PubMed

Saxena, G; Koli, K; de la Garza, J; Ogbureke, K U E

2015-04-01

Matrix metalloproteinase 20 (MMP-20), widely regarded as tooth specific, participates with MMP-2 in processing dentin sialophosphoprotein (DSPP) into dentin sialoprotein, dentin phosphoprotein, and dentin glycoprotein. In biochemical system, MMP-2, MMP-3, and MMP-9 bind with high affinity to, and are activated by, specific small integrin-binding ligand N-linked glycoproteins (SIBLINGs): bone sialoprotein, osteopontin, and dentin matrix protein 1, respectively. Subsequent reports documented possible biological relevance of SIBLING-MMP interaction in vivo by showing that SIBLINGs are always coexpressed with their MMP partners. However, the cognate MMPs for 2 other SIBLINGs-DSPP and matrix extracellular phosphogylcoprotein-are yet to be identified. Our goal was to investigate MMP-20 expression and to explore preliminary evidence of its interaction with DSPP in oral squamous cell carcinomas (OSCCs). Immunohistochemistry analysis of sections from 21 cases of archived human OSCC tissues showed immunoreactivity for MMP-20 in 18 (86%) and coexpression with DSPP in all 15 cases (71%) positive for DSPP. Similarly, 28 (93%) of 30 cases of oral epithelial dysplasia were positive for MMP-20. Western blot and quantitative real-time polymerase chain reaction analysis on OSCC cell lines showed upregulation of MMP-20 protein and mRNA, respectively, while immunofluorescence showed coexpression of MMP-20 and DSPP. Colocalization and potential interaction of MMP-20 with dentin sialoprotein was confirmed by coimmunoprecipitation and mass spectrometry analysis of immunoprecipitation product from OSCC cell lysate, and in situ proximity ligation assays. Significantly, results of chromatin immunoprecipation revealed a 9-fold enrichment of DSPP at MMP-20 promoter-proximal elements. Our data provide evidence that MMP-20 has a wider tissue distribution than previously acknowledged. MMP-20-DSPP specific interaction, excluding other MMP-20-SIBLING pairings, identifies MMP-20 as DSPP cognate MMP. Furthermore, the strong DSPP enrichment at the MMP-20 promoter suggests a regulatory role in MMP-20 transcription. These novel findings provide the foundation to explore the mechanisms and significance of DSPP-MMP-20 interaction in oral carcinogenesis. © International & American Associations for Dental Research 2015.

A model-based approach to monitor complex road-vehicle interactions through first principles

NASA Astrophysics Data System (ADS)

Chakravarty, T.; Srinivasarengan, K.; Roy, S.; Bilal, S.; Balamuralidhar, P.

2013-02-01

The increasing availability of portable computing devices and their interaction with physical systems ask for designing compact models and simulations to understand and characterize such interactions. For instance, monitoring a road's grade using accelerometer stationed inside a moving ground vehicle is an emerging trend in city administration. Typically the focus has largely been to develop algorithms to articulate meaning from that. But, the experimentation cannot provide with an exhaustive analysis of all scenarios and the characteristics of them. We propose an approach of modeling these interactions of physical systems with gadgets through first principles, in a compact manner to focus on limited number of interactions. We derive an approach to model the vehicle interaction with a pothole on a road, a specific case, but allowing for selectable car parameters like natural damped frequency, tire size etc, thus generalizing it. Different road profiles are also created to represent rough road with sharp irregularities. These act as excitation to the moving vehicle and the interaction is computed to determine the vertical/ lateral vibration of the system i.e vehicle with sensors using joint time-frequency signal analysis methods. The simulation is compared with experimental data for validation. We show some directions as to how simulation of such models can reveal different characteristics of the interaction through analysis of their frequency spectrum. It is envisioned that the proposed models will get enriched further as and when large data set of real life data is captured and appropriate sensitivity analysis is done.

A case study on the communication of older adolescents.

PubMed

Davis, Lauren; Spencer, Elizabeth; Ferguson, Alison

2011-11-01

This study compared the communication of two older male adolescents (aged 17 and 19 years) with each other (peer interaction) and with a teacher (non-peer interaction) in three different types of activity (casual conversation, providing/listening to a recount and collaborative problem-solving). Conversation analysis, selected analyses from the perspective of systemic functional linguistics and social psychology (communication accommodation theory) were applied in data analysis. Peer interaction showed fewer questions, fewer challenging moves and the absence of divergent accommodation strategies. In the non-peer interaction, the teacher's higher number of turns, questions and interruptions appeared to influence the opportunity for adolescent contribution to the interactions. Some aspects of language use by each adolescent - mean turn length, use of one-word utterances and sarcasm - were consistent across communication partner and activity. The methodology is suggested to provide a suitable procedure for use in similar research with older adolescents who have traumatic brain injury.

Pedagogical Distance: Explaining Misalignment in Student-Driven Online Learning Activities Using Activity Theory

ERIC Educational Resources Information Center

Westberry, Nicola; Franken, Margaret

2015-01-01

This paper provides an Activity Theory analysis of two online student-driven interactive learning activities to interrogate assumptions that such groups can effectively learn in the absence of the teacher. Such an analysis conceptualises learning tasks as constructed objects that drive pedagogical activity. The analysis shows a disconnect between…

Origin of attraction in p-benzoquinone complexes with benzene and p-hydroquinone.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Ono, Taizo

2017-08-30

The origin of the attraction in charge-transfer complexes (a p-hydroquinone-p-benzoquinone complex and benzene complexes with benzoquinone, tetracyanoethylene and Br 2 ) was analyzed using distributed multipole analysis and symmetry-adapted perturbation theory. Both methods show that the dispersion interactions are the primary source of the attraction in these charge-transfer complexes followed by the electrostatic interactions. The natures of the intermolecular interactions in these complexes are close to the π/π interactions of neutral aromatic molecules. The electrostatic interactions play important roles in determining the magnitude of the attraction. The contribution of charge-transfer interactions to the attraction is not large compared with the dispersion interactions in these complexes.

Conservation laws, bilinear forms and solitons for a fifth-order nonlinear Schrödinger equation for the attosecond pulses in an optical fiber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chai, Jun; Tian, Bo, E-mail: tian_bupt@163.com; Zhen, Hui-Ling

Under investigation in this paper is a fifth-order nonlinear Schrödinger equation, which describes the propagation of attosecond pulses in an optical fiber. Based on the Lax pair, infinitely-many conservation laws are derived. With the aid of auxiliary functions, bilinear forms, one-, two- and three-soliton solutions in analytic forms are generated via the Hirota method and symbolic computation. Soliton velocity varies linearly with the coefficients of the high-order terms. Head-on interaction between the bidirectional two solitons and overtaking interaction between the unidirectional two solitons as well as the bound state are depicted. For the interactions among the three solitons, two head-onmore » and one overtaking interactions, three overtaking interactions, an interaction between a bound state and a single soliton and the bound state are displayed. Graphical analysis shows that the interactions between the two solitons are elastic, and interactions among the three solitons are pairwise elastic. Stability analysis yields the modulation instability condition for the soliton solutions.« less

A deeper look at two concepts of measuring gene-gene interactions: logistic regression and interaction information revisited.

PubMed

Mielniczuk, Jan; Teisseyre, Paweł

2018-03-01

Detection of gene-gene interactions is one of the most important challenges in genome-wide case-control studies. Besides traditional logistic regression analysis, recently the entropy-based methods attracted a significant attention. Among entropy-based methods, interaction information is one of the most promising measures having many desirable properties. Although both logistic regression and interaction information have been used in several genome-wide association studies, the relationship between them has not been thoroughly investigated theoretically. The present paper attempts to fill this gap. We show that although certain connections between the two methods exist, in general they refer two different concepts of dependence and looking for interactions in those two senses leads to different approaches to interaction detection. We introduce ordering between interaction measures and specify conditions for independent and dependent genes under which interaction information is more discriminative measure than logistic regression. Moreover, we show that for so-called perfect distributions those measures are equivalent. The numerical experiments illustrate the theoretical findings indicating that interaction information and its modified version are more universal tools for detecting various types of interaction than logistic regression and linkage disequilibrium measures. © 2017 WILEY PERIODICALS, INC.

On the molecular origins of biomass recalcitrance: the interaction network and solvation structures of cellulose microfibrils.

PubMed

Gross, Adam S; Chu, Jhih-Wei

2010-10-28

Biomass recalcitrance is a fundamental bottleneck to producing fuels from renewable sources. To understand its molecular origin, we characterize the interaction network and solvation structures of cellulose microfibrils via all-atom molecular dynamics simulations. The network is divided into three components: intrachain, interchain, and intersheet interactions. Analysis of their spatial dependence and interaction energetics indicate that intersheet interactions are the most robust and strongest component and do not display a noticeable dependence on solvent exposure. Conversely, the strength of surface-exposed intrachain and interchain hydrogen bonds is significantly reduced. Comparing the interaction networks of I(β) and I(α) cellulose also shows that the number of intersheet interactions is a clear descriptor that distinguishes the two allomorphs and is consistent with the observation that I(β) is the more stable form. These results highlight the dominant role of the often-overlooked intersheet interactions in giving rise to biomass recalcitrance. We also analyze the solvation structures around the surfaces of microfibrils and show that the structural and chemical features at cellulose surfaces constrict water molecules into specific density profiles and pair correlation functions. Calculations of water density and compressibility in the hydration shell show noticeable but not drastic differences. Therefore, specific solvation structures are more prominent signatures of different surfaces.

Dynamic Network-Based Epistasis Analysis: Boolean Examples

PubMed Central

Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

2011-01-01

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and single-path assumption, but also by demonstrating the importance of considering temporal dynamics, and specifically introducing the usefulness of Boolean network models and also reviewing some key properties of network approaches. PMID:22645556

Diet and Colorectal Cancer: Analysis of a Candidate Pathway Using SNPS, Haplotypes, and Multi-Gene Assessment

PubMed Central

Slattery, Martha L.; Lundgreen, Abbie; Herrick, Jennifer S.; Caan, Bette J.; Potter, John D.; Wolff, Roger K.

2012-01-01

There is considerable biologic plausibility to the hypothesis that genetic variability in pathways involved in insulin signaling and energy homeostasis may modulate dietary risk associated with colorectal cancer. We utilized data from 2 population-based case-control studies of colon (n = 1,574 cases, 1,970 controls) and rectal (n = 791 cases, 999 controls) cancer to evaluate genetic variation in candidate SNPs identified from 9 genes in a candidate pathway: PDK1, RP6KA1, RPS6KA2, RPS6KB1, RPS6KB2, PTEN, FRAP1 (mTOR), TSC1, TSC2, Akt1, PIK3CA, and PRKAG2 with dietary intake of total energy, carbohydrates, fat, and fiber. We employed SNP, haplotype, and multiple-gene analysis to evaluate associations. PDK1 interacted with dietary fat for both colon and rectal cancer and with dietary carbohydrates for colon cancer. Statistically significant interaction with dietary carbohydrates and rectal cancer was detected by haplotype analysis of PDK1. Evaluation of dietary interactions with multiple genes in this candidate pathway showed several interactions with pairs of genes: Akt1 and PDK1, PDK1 and PTEN, PDK1 and TSC1, and PRKAG2 and PTEN. Analyses show that genetic variation influences risk of colorectal cancer associated with diet and illustrate the importance of evaluating dietary interactions beyond the level of single SNPs or haplotypes when a biologically relevant candidate pathway is examined. PMID:21999454

Pilot study on real-time motion detection in UAS video data by human observer and image exploitation algorithm

NASA Astrophysics Data System (ADS)

Hild, Jutta; Krüger, Wolfgang; Brüstle, Stefan; Trantelle, Patrick; Unmüßig, Gabriel; Voit, Michael; Heinze, Norbert; Peinsipp-Byma, Elisabeth; Beyerer, Jürgen

2017-05-01

Real-time motion video analysis is a challenging and exhausting task for the human observer, particularly in safety and security critical domains. Hence, customized video analysis systems providing functions for the analysis of subtasks like motion detection or target tracking are welcome. While such automated algorithms relieve the human operators from performing basic subtasks, they impose additional interaction duties on them. Prior work shows that, e.g., for interaction with target tracking algorithms, a gaze-enhanced user interface is beneficial. In this contribution, we present an investigation on interaction with an independent motion detection (IDM) algorithm. Besides identifying an appropriate interaction technique for the user interface - again, we compare gaze-based and traditional mouse-based interaction - we focus on the benefit an IDM algorithm might provide for an UAS video analyst. In a pilot study, we exposed ten subjects to the task of moving target detection in UAS video data twice, once performing with automatic support, once performing without it. We compare the two conditions considering performance in terms of effectiveness (correct target selections). Additionally, we report perceived workload (measured using the NASA-TLX questionnaire) and user satisfaction (measured using the ISO 9241-411 questionnaire). The results show that a combination of gaze input and automated IDM algorithm provides valuable support for the human observer, increasing the number of correct target selections up to 62% and reducing workload at the same time.

Dispersed fluorescence spectroscopy of the SiCN A ˜ 2 Δ - X ˜ 2 Π system: Observation of some vibrational levels with chaotic characteristics

NASA Astrophysics Data System (ADS)

Fukushima, Masaru; Ishiwata, Takashi

2016-12-01

The laser induced fluorescence (LIF) spectrum of the A ˜ 2Δ - X ˜ 2Π transition was obtained for SiCN generated by laser ablation under supersonic free jet expansion. The vibrational structures of the dispersed fluorescence (DF) spectra from single vibronic levels (SVL's) were analyzed with consideration of the Renner-Teller (R-T) interaction. Analysis of the pure bending (ν2) structure by a perturbation approach including R-T, anharmonicity, spin-orbit (SO), and Herzberg-Teller (H-T) interactions indicated considerably different spin splitting for the μ and κ levels of the X ˜ 2Π state of SiCN, in contrast to identical spin splitting for general species derived from the perturbation approach, where μ and κ specify the lower and upper levels, respectively, separated by R-T. Further analysis of the vibrational structure including R-T, anharmonicity, SO, H-T, Fermi, and Sears interactions was carried out via a direct diagonalization procedure, where Sears resonance is a second-order interaction combined from SO and H-T interactions with Δ K = ± 1, ΔΣ = ∓1, and Δ P = 0, and where P is a quantum number, P = K + Σ. The later numerical analysis reproduced the observed structure, not only the pure ν2 structure but also the combination structure of the ν2 and the Si-CN stretching (ν3) modes. As an example, the analysis demonstrates Sears resonance between vibronic levels, (0110) κ Σ(+) and ( 0 2 0 0 ) μ Π /1 2 , with Δ K = ± 1 and Δ P = 0. On the basis of coefficients of their eigen vectors derived from the numerical analysis, it is interpreted as an almost one-to-one mixing between the two levels. The mixing coefficients of the two vibronic levels agree with those obtained from computational studies. The numerical analysis also indicates that some of the vibronic levels show chaotic characteristics in view of the two-dimensional harmonic oscillator (2D-HO) basis which is used as the basis function in the present numerical analysis; i.e., the eigen vectors for some of the observed levels have several components of the basis, and we have not been able to give precise vibronic assignments for the levels, but just vibronically labeled, referring the largest component in their vectors. (To emphasize this situation, we do not use the word "assignment," but prefer to use "label" as the meaning of just "label," but not "assign," throughout this paper.) The latter shows that the vibronic labels of the levels are meaningless, and the P quantum number and the order of their eigen states in the P matrix block derived in the numerical analysis only characterize the vibronic levels. Comparing the constants obtained for all of the interactions with those of species showing Sears resonance and studied previously, it is found that none of them are strong, but are moderate. It is thus concluded that the chaotic appearance is not derived by any strong interaction, but is induced by complex and accidental proximities of the vibronic levels caused by the moderate interactions.

Simulation of Shock-Shock Interaction in Parsec-Scale Jets

NASA Astrophysics Data System (ADS)

Fromm, Christian M.; Perucho, Manel; Ros, Eduardo; Mimica, Petar; Savolainen, Tuomas; Lobanov, Andrei P.; Zensus, J. Anton

The analysis of the radio light curves of the blazar CTA 102 during its 2006 flare revealed a possible interaction between a standing shock wave and a traveling one. In order to better understand this highly non-linear process, we used a relativistic hydrodynamic code to simulate the high energy interaction and its related emission. The calculated synchrotron emission from these simulations showed an increase in turnover flux density, Sm, and turnover frequency, νm, during the interaction and decrease to its initial values after the passage of the traveling shock wave.

Network topological analysis reveals the functional cohesiveness for the newly discovered links by Yeast 2 Hybrid approach

NASA Astrophysics Data System (ADS)

Ghiassian, Susan; Pevzner, Sam; Rolland, Thomas; Tassan, Murat; Barabasi, Albert Laszlo; Vidal, Mark; CCNR, Northeastern University Collaboration; Dana Farber Cancer Institute Collaboration

2014-03-01

Protein-protein interaction maps and interactomes are the blueprint of Network Medicine and systems biology and are being experimentally studied by different groups. Despite the wide usage of Literature Curated Interactome (LCI), these sources are biased towards different parameters such as highly studied proteins. Yeast two hybrid method is a high throughput experimental setup which screens proteins in an unbiased fashion. Current knowledge of protein interactions is far from complete. In fact the previous offered data from Y2H method (2005), is estimated to offer only 5% of all potential protein interactions. Currently this coverage has increased to 20% of what is known as reference HI In this work we study the topological properties of Y2H protein-protein interactions network with LCI and show although they both agree on some properties, LCI shows a clear unbiased nature of interaction selections. Most importantly, we assess the properties of PPI as it evolves with increasing the coverage. We show that, the newly discovered interactions tend to connect proteins that have been closer than average in the previous PPI release. reinforcing the modular structure of PPI. Furthermore, we show, some unseen effects on PPI (as opposed to LCI) can be explained by its incompleteness.

Interactive Visualization of Parking Orbits Around the Moon: An X3D Application for a NASA Lunar Mission Study

NASA Technical Reports Server (NTRS)

Murphy, Douglas G.; Qu, Min; Salas, Andrea O.

2006-01-01

The NASA Integrated Modeling and Simulation (IM&S) project aims to develop a collaborative engineering system to include distributed analysis, integrated tools, and web-enabled graphics. Engineers on the IM&S team were tasked with applying IM&S capabilities to an orbital mechanics analysis for a lunar mission study. An interactive lunar globe was created to show 7 landing sites, contour lines depicting the energy required to reach a given site, and the optimal lunar orbit orientation to meet the mission constraints. Activation of the lunar globe rotation shows the change of the angle between the landing site latitude and the orbit plane. A heads-up-display was used to embed straightforward interface elements.

Interactions of different carrageenan isoforms and flour components in breadmaking.

PubMed

León, A E; Ribotta, P D; Ausar, S F; Fernández, C; Lanada, C A; Beltramo, D M

2000-07-01

The aim of this study was to compare the effects of carrageenans with different sulfate contents on bread volume and dough rheological properties. Results showed that only lambda carrageenan, the most sulfated isoform, produced a significant increase in bread volume. In contrast, the different carrageenans induced a negative effect on the cookie factor. Alveographic and farinographic analyses indicated that dough rheological properties were differentially modified depending on whether lambda carrageenan was added to flour and then hydrated or vice versa. Analysis of the interaction between lambda carrageenan and flour components by infrared spectroscopy and SDS-PAGE indicated that a pool of low molecular weight hydrophobic gluten proteins interact with carrageenan. This interaction drastically changes their physicochemical properties since carrageenan-gluten protein complexes show a hydrophilic behavior. In addition, the results indicate that carrageenan sulfate groups and probably the amino groups of glutamines present in the primary structure of gluten proteins are involved in the interaction.

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks

PubMed Central

Ulitsky, Igor; Shamir, Ron

2007-01-01

The biological interpretation of genetic interactions is a major challenge. Recently, Kelley and Ideker proposed a method to analyze together genetic and physical networks, which explains many of the known genetic interactions as linking different pathways in the physical network. Here, we extend this method and devise novel analytic tools for interpreting genetic interactions in a physical context. Applying these tools on a large-scale Saccharomyces cerevisiae data set, our analysis reveals 140 between-pathway models that explain 3765 genetic interactions, roughly doubling those that were previously explained. Model genes tend to have short mRNA half-lives and many phosphorylation sites, suggesting that their stringent regulation is linked to pathway redundancy. We also identify ‘pivot' proteins that have many physical interactions with both pathways in our models, and show that pivots tend to be essential and highly conserved. Our analysis of models and pivots sheds light on the organization of the cellular machinery as well as on the roles of individual proteins. PMID:17437029

Numerical simulation and analysis of the flow in a two-staged axial fan

NASA Astrophysics Data System (ADS)

Xu, J. Q.; Dou, H. S.; Jia, H. X.; Chen, X. P.; Wei, Y. K.; Dong, M. W.

2016-05-01

In this paper, numerical simulation was performed for the internal three-dimensional turbulent flow field in the two-stage axial fan using steady three-dimensional in-compressible Navier-Stokes equations coupled with the Realizable turbulent model. The numerical simulation results of the steady analysis were combined with the flow characteristics of two- staged axial fan, the influence of the mutual effect between the blade and the vane on the flow of the two inter-stages was analyzed emphatically. This paper studied how the flow field distribution in inter-stage is influenced by the wake interaction and potential flow interaction of mutual effect in the impeller-vane inter-stage and the vane-impeller inter-stage. The results showed that: Relatively, wake interaction has an advantage over potential flow interaction in the impeller-vane inter-stage; potential flow interaction has an advantage over wake interaction in the vane-impeller inter-stage. In other words, distribution of flow field in the two interstages is determined by the rotating component.

Genetic and physical interaction of the B-cell systemic lupus erythematosus-associated genes BANK1 and BLK.

PubMed

Castillejo-López, Casimiro; Delgado-Vega, Angélica M; Wojcik, Jerome; Kozyrev, Sergey V; Thavathiru, Elangovan; Wu, Ying-Yu; Sánchez, Elena; Pöllmann, David; López-Egido, Juan R; Fineschi, Serena; Domínguez, Nicolás; Lu, Rufei; James, Judith A; Merrill, Joan T; Kelly, Jennifer A; Kaufman, Kenneth M; Moser, Kathy L; Gilkeson, Gary; Frostegård, Johan; Pons-Estel, Bernardo A; D'Alfonso, Sandra; Witte, Torsten; Callejas, José Luis; Harley, John B; Gaffney, Patrick M; Martin, Javier; Guthridge, Joel M; Alarcón-Riquelme, Marta E

2012-01-01

Altered signalling in B cells is a predominant feature of systemic lupus erythematosus (SLE). The genes BANK1 and BLK were recently described as associated with SLE. BANK1 codes for a B-cell-specific cytoplasmic protein involved in B-cell receptor signalling and BLK codes for an Src tyrosine kinase with important roles in B-cell development. To characterise the role of BANK1 and BLK in SLE, a genetic interaction analysis was performed hypothesising that genetic interactions could reveal functional pathways relevant to disease pathogenesis. The GPAT16 method was used to analyse the gene-gene interactions of BANK1 and BLK. Confocal microscopy was used to investigate co-localisation, and immunoprecipitation was used to verify the physical interaction of BANK1 and BLK. Epistatic interactions between BANK1 and BLK polymorphisms associated with SLE were observed in a discovery set of 279 patients and 515 controls from northern Europe. A meta-analysis with 4399 European individuals confirmed the genetic interactions between BANK1 and BLK. As BANK1 was identified as a binding partner of the Src tyrosine kinase LYN, the possibility that BANK1 and BLK could also show a protein-protein interaction was tested. The co-immunoprecipitation and co-localisation of BLK and BANK1 were demonstrated. In a Daudi cell line and primary naive B cells endogenous binding was enhanced upon B-cell receptor stimulation using anti-IgM antibodies. This study shows a genetic interaction between BANK1 and BLK, and demonstrates that these molecules interact physically. The results have important consequences for the understanding of SLE and other autoimmune diseases and identify a potential new signalling pathway.

Genetic and Physical Interaction of the B-Cell SLE-Associated Genes BANK1 and BLK

PubMed Central

Castillejo-López, Casimiro; Delgado-Vega, Angélica M.; Wojcik, Jerome; Kozyrev, Sergey V.; Thavathiru, Elangovan; Wu, Ying-Yu; Sánchez, Elena; Pöllmann, David; López-Egido, Juan R.; Fineschi, Serena; Domínguez, Nicolás; Lu, Rufei; James, Judith A.; Merrill, Joan T.; Kelly, Jennifer A.; Kaufman, Kenneth M.; Moser, Kathy; Gilkeson, Gary; Frostegård, Johan; Pons-Estel, Bernardo A.; D’Alfonso, Sandra; Witte, Torsten; Callejas, José Luis; Harley, John B.; Gaffney, Patrick; Martin, Javier; Guthridge, Joel M.; Alarcón-Riquelme, Marta E.

2012-01-01

Objectives Altered signaling in B-cells is a predominant feature of systemic lupus erythematosus (SLE). The genes BANK1 and BLK were recently described as associated with SLE. BANK1 codes for a B-cell-specific cytoplasmic protein involved in B-cell receptor signaling and BLK codes for an Src tyrosine kinase with important roles in B-cell development. To characterize the role of BANK1 and BLK in SLE, we performed a genetic interaction analysis hypothesizing that genetic interactions could reveal functional pathways relevant to disease pathogenesis. Methods We Used the method GPAT16 to analyze the gene-gene interactions of BANK1 and BLK. Confocal microscopy was used to investigate co-localization, and immunoprecipitation was used to verify the physical interaction of BANK1 and BLK. Results Epistatic interactions between BANK1 and BLK polymorphisms associated with SLE were observed in a discovery set of 279 patients and 515 controls from Northern Europe. A meta-analysis with 4399 European individuals confirmed the genetic interactions between BANK1 and BLK. As BANK1 was identified as a binding partner of the Src tyrosine kinase LYN, we tested the possibility that BANK1 and BLK could also show a protein-protein interaction. We demonstrated co-immunoprecipitation and co-localization of BLK and BANK1. In a Daudi cell line and primary naïve B-cells the endogenous binding was enhanced upon B-cell receptor stimulation using anti-IgM antibodies. Conclusions Here, we show a genetic interaction between BANK1 and BLK, and demonstrate that these molecules interact physically. Our results have important consequences for the understanding of SLE and other autoimmune diseases and identify a potential new signaling pathway. PMID:21978998

A novel non-contact radar sensor for affective and interactive analysis.

PubMed

Lin, Hong-Dun; Lee, Yen-Shien; Shih, Hsiang-Lan; Chuang, Bor-Nian

2013-01-01

Currently, many physiological signal sensing techniques have been applied for affective analysis in Human-Computer Interaction applications. Most known maturely developed sensing methods (EEG/ECG/EMG/Temperature/BP etc. al.) replied on contact way to obtain desired physiological information for further data analysis. However, those methods might cause some inconvenient and uncomfortable problems, and not easy to be used for affective analysis in interactive performing. To improve this issue, a novel technology based on low power radar technology (Nanosecond Pulse Near-field Sensing, NPNS) with 300 MHz radio-frequency was proposed to detect humans' pulse signal by the non-contact way for heartbeat signal extraction. In this paper, a modified nonlinear HRV calculated algorithm was also developed and applied on analyzing affective status using extracted Peak-to-Peak Interval (PPI) information from detected pulse signal. The proposed new affective analysis method is designed to continuously collect the humans' physiological signal, and validated in a preliminary experiment with sound, light and motion interactive performance. As a result, the mean bias between PPI (from NPNS) and RRI (from ECG) shows less than 1ms, and the correlation is over than 0.88, respectively.

Effect of occupational exposures on lung cancer susceptibility: a study of gene-environment interaction analysis.

PubMed

Malhotra, Jyoti; Sartori, Samantha; Brennan, Paul; Zaridze, David; Szeszenia-Dabrowska, Neonila; Świątkowska, Beata; Rudnai, Peter; Lissowska, Jolanta; Fabianova, Eleonora; Mates, Dana; Bencko, Vladimir; Gaborieau, Valerie; Stücker, Isabelle; Foretova, Lenka; Janout, Vladimir; Boffetta, Paolo

2015-03-01

Occupational exposures are known risk factors for lung cancer. Role of genetically determined host factors in occupational exposure-related lung cancer is unclear. We used genome-wide association (GWA) data from a case-control study conducted in 6 European countries from 1998 to 2002 to identify gene-occupation interactions and related pathways for lung cancer risk. GWA analysis was performed for each exposure using logistic regression and interaction term for genotypes, and exposure was included in this model. Both SNP-based and gene-based interaction P values were calculated. Pathway analysis was performed using three complementary methods, and analyses were adjusted for multiple comparisons. We analyzed 312,605 SNPs and occupational exposure to 70 agents from 1,802 lung cancer cases and 1,725 cancer-free controls. Mean age of study participants was 60.1 ± 9.1 years and 75% were male. Largest number of significant associations (P ≤ 1 × 10(-5)) at SNP level was demonstrated for nickel, brick dust, concrete dust, and cement dust, and for brick dust and cement dust at the gene-level (P ≤ 1 × 10(-4)). Approximately 14 occupational exposures showed significant gene-occupation interactions with pathways related to response to environmental information processing via signal transduction (P < 0.001 and FDR < 0.05). Other pathways that showed significant enrichment were related to immune processes and xenobiotic metabolism. Our findings suggest that pathways related to signal transduction, immune process, and xenobiotic metabolism may be involved in occupational exposure-related lung carcinogenesis. Our study exemplifies an integrative approach using pathway-based analysis to demonstrate the role of genetic variants in occupational exposure-related lung cancer susceptibility. Cancer Epidemiol Biomarkers Prev; 24(3); 570-9. ©2015 AACR. ©2015 American Association for Cancer Research.

Comparison of Elementary School Children's Interaction in Teacher-Led and Student-Led Small Groups. Abstract.

ERIC Educational Resources Information Center

Wilcox, Mary Anastole

This study examined interaction among members in small groups under different leadership conditions: leadership by teacher, by untrained student, and by trained student. Small groups of low-income fifth- and sixth-grade students were videotaped as they discussed solutions to problem-solving stories. Analysis of the tapes shows that trained…

Metal-ligand bond directionality in the M2-NH3 complexes (M = Cu, Ag and Au)

NASA Astrophysics Data System (ADS)

Eskandari, K.; Ebadinejad, F.

2018-05-01

The metal-ligand bonds in the M2-NH3 complexes (M = Au, Ag and Cu) are directional and the M-M-N angles tend to be linear. Natural energy decomposition analysis (NEDA) and localised molecular orbital energy decomposition analysis (LMOEDA) approaches indicate that the metal-ligand bonds in these complexes are mainly electrostatic in nature, however, the electrostatic is not the cause of the linearity of M-M-N arrangements. Instead, NEDA shows that the charge transfer and core repulsion are mainly responsible for the directionality of these bonds. In the LMOEDA point of view, the repulsion term is the main reason for the linearity of these complexes. Interacting quantum atoms (IQA) analysis shows that inter-atomic and inter-fragment interactions favour the nonlinear arrangements; however, these terms are compensated by the atomic self-energies, which stabilise the linear structure.

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

NASA Astrophysics Data System (ADS)

Zhang, Rui; Jiang, Shuai; Liu, Yi-Rong; Wen, Hui; Feng, Ya-Juan; Huang, Teng; Huang, Wei

2018-05-01

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid's weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

Functional analysis of inappropriate social interactions in students with Asperger's syndrome.

PubMed

Roantree, Christina F; Kennedy, Craig H

2012-01-01

We analyzed the inappropriate social interactions of 3 students with Asperger's syndrome whose behavior was maintained by social positive reinforcement. We tested whether inappropriate social behavior was sensitive to social positive reinforcement contingencies and whether such contingencies could be reversed to increase the probability of socially appropriate responding. Our results show that social positive reinforcers can be identified for inappropriate social interactions and that appropriate social behaviors can be sensitive to reinforcement contingency reversals.

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

DOE PAGES

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-11

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local Structure of Ion Pair Interaction in Lapatinib Amorphous Dispersions characterized by Synchrotron X-Ray diffraction and Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-01

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contacts for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Finally, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (Δ) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.

Number-squeezed and fragmented states of strongly interacting bosons in a double well

NASA Astrophysics Data System (ADS)

Corbo, Joel C.; DuBois, Jonathan L.; Whaley, K. Birgitta

2017-11-01

We present a systematic study of the phenomena of number squeezing and fragmentation for a repulsive Bose-Einstein condensate (BEC) in a three-dimensional double-well potential over a range of interaction strengths and barrier heights, including geometries that exhibit appreciable overlap in the one-body wave functions localized in the left and right wells. We compute the properties of the condensate with numerically exact, full-dimensional path-integral ground-state (PIGS) quantum Monte Carlo simulations and compare with results obtained from using two- and eight-mode truncated basis models. The truncated basis models are found to agree with the numerically exact PIGS simulations for weak interactions, but fail to correctly predict the amount of number squeezing and fragmentation exhibited by the PIGS simulations for strong interactions. We find that both number squeezing and fragmentation of the BEC show nonmonotonic behavior at large values of interaction strength a . The number squeezing shows a universal scaling with the product of number of particles and interaction strength (N a ), but no such universal behavior is found for fragmentation. Detailed analysis shows that the introduction of repulsive interactions not only suppresses number fluctuations to enhance number squeezing, but can also enhance delocalization across wells and tunneling between wells, each of which may suppress number squeezing. This results in a dynamical competition whose resolution shows a complex dependence on all three physical parameters defining the system: interaction strength, number of particles, and barrier height.

Development of sustainable dye adsorption system using nutraceutical industrial fennel seed spent-studies using Congo red dye.

PubMed

Taqui, Syed Noeman; Yahya, Rosiyah; Hassan, Aziz; Nayak, Nayan; Syed, Akheel Ahmed

2017-07-03

Fennel seed spent (FSS)-an inexpensive nutraceutical industrial spent has been used as an efficient biosorbent for the removal of Congo red (CR) from aqueous media. Results show that the conditions for maximum adsorption would be pH 2-4 and 30°C were ideal for maximum adsorption. Based on regression fitting of the data, it was determined that the Sips isotherm (R 2 = 0.994, χ 2 = 0.5) adequately described the mechanism of adsorption, suggesting that the adsorption occurs homogeneously with favorable interaction between layers with favorable interaction between layers. Thermodynamic analysis showed that the adsorption is favorable (negative values for ΔG°) and endothermic (ΔH° = 12-20 kJ mol -1 ) for initial dye concentrations of 25, 50, and 100 ppm. The low ΔH° value indicates that the adsorption is a physical process involving weak chemical interactions like hydrogen bonds and van der Waals interactions. The kinetics revealed that the adsorption process showed pseudo-second-order tendencies with the equal influence of intraparticle as well as film diffusion. The scanning electron microscopy images of FSS show a highly fibrous matrix with a hierarchical porous structure. The Fourier transform infrared spectroscopy analysis of the spent confirmed the presence of cellulosic and lignocellulosic matter, giving it both hydrophilic and hydrophobic properties. The investigations indicate that FSS is a cost-effective and efficient biosorbent for the remediation of toxic CR dye.

Analysis of candidates for interacting galaxy clusters. I. A1204 and A2029/A2033

NASA Astrophysics Data System (ADS)

Gonzalez, Elizabeth Johana; de los Rios, Martín; Oio, Gabriel A.; Lang, Daniel Hernández; Tagliaferro, Tania Aguirre; Domínguez R., Mariano J.; Castellón, José Luis Nilo; Cuevas L., Héctor; Valotto, Carlos A.

2018-04-01

Context. Merging galaxy clusters allow for the study of different mass components, dark and baryonic, separately. Also, their occurrence enables to test the ΛCDM scenario, which can be used to put constraints on the self-interacting cross-section of the dark-matter particle. Aim. It is necessary to perform a homogeneous analysis of these systems. Hence, based on a recently presented sample of candidates for interacting galaxy clusters, we present the analysis of two of these cataloged systems. Methods: In this work, the first of a series devoted to characterizing galaxy clusters in merger processes, we perform a weak lensing analysis of clusters A1204 and A2029/A2033 to derive the total masses of each identified interacting structure together with a dynamical study based on a two-body model. We also describe the gas and the mass distributions in the field through a lensing and an X-ray analysis. This is the first of a series of works which will analyze these type of system in order to characterize them. Results: Neither merging cluster candidate shows evidence of having had a recent merger event. Nevertheless, there is dynamical evidence that these systems could be interacting or could interact in the future. Conclusions: It is necessary to include more constraints in order to improve the methodology of classifying merging galaxy clusters. Characterization of these clusters is important in order to properly understand the nature of these systems and their connection with dynamical studies.

Biological Evaluation in Vitro and in Silico of Azetidin-2-one Derivatives as Potential Anticancer Agents.

PubMed

Olazaran, Fabián E; Rivera, Gildardo; Pérez-Vázquez, Alondra M; Morales-Reyes, Cynthia M; Segura-Cabrera, Aldo; Balderas-Rentería, Isaías

2017-01-12

Potential anticancer activity of 16 azetidin-2-one derivatives was evaluated showing that compound 6 [ N -( p -methoxy-phenyl)-2-( p -methyl-phenyl)-3-phenoxy-azetidin-2-one] presented cytotoxic activity in SiHa cells and B16F10 cells. The caspase-3 assay in B16F10 cells displayed that azetidin-2-one derivatives induce apoptosis. Microarray and molecular analysis showed that compound 6 was involved on specific gene overexpression of cytoskeleton regulation and apoptosis due to the inhibition of some cell cycle genes. From the 16 derivatives, compound 6 showed the highest selectivity to neoplastic cells, it was an inducer of apoptosis, and according to an in silico analysis of chemical interactions with colchicine binding site of human α/β-tubulin, the mechanism of action could be a molecular interaction involving the amino acids outlining such binding site.

Biological Evaluation in Vitro and in Silico of Azetidin-2-one Derivatives as Potential Anticancer Agents

PubMed Central

2016-01-01

Potential anticancer activity of 16 azetidin-2-one derivatives was evaluated showing that compound 6 [N-(p-methoxy-phenyl)-2-(p-methyl-phenyl)-3-phenoxy-azetidin-2-one] presented cytotoxic activity in SiHa cells and B16F10 cells. The caspase-3 assay in B16F10 cells displayed that azetidin-2-one derivatives induce apoptosis. Microarray and molecular analysis showed that compound 6 was involved on specific gene overexpression of cytoskeleton regulation and apoptosis due to the inhibition of some cell cycle genes. From the 16 derivatives, compound 6 showed the highest selectivity to neoplastic cells, it was an inducer of apoptosis, and according to an in silico analysis of chemical interactions with colchicine binding site of human α/β-tubulin, the mechanism of action could be a molecular interaction involving the amino acids outlining such binding site. PMID:28105271

Final-state interactions in semi-inclusive deep inelastic scattering off the Deuteron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wim Cosyn, Misak Sargsian

2011-07-01

Semi-inclusive deep inelastic scattering off the Deuteron with production of a slow nucleon in recoil kinematics is studied in the virtual nucleon approximation, in which the final state interaction (FSI) is calculated within general eikonal approximation. The cross section is derived in a factorized approach, with a factor describing the virtual photon interaction with the off-shell nucleon and a distorted spectral function accounting for the final-state interactions. One of the main goals of the study is to understand how much the general features of the diffractive high energy soft rescattering accounts for the observed features of FSI in deep inelasticmore » scattering (DIS). Comparison with the Jefferson Lab data shows good agreement in the covered range of kinematics. Most importantly, our calculation correctly reproduces the rise of the FSI in the forward direction of the slow nucleon production angle. By fitting our calculation to the data we extracted the W and Q{sup 2} dependences of the total cross section and slope factor of the interaction of DIS products, X, off the spectator nucleon. This analysis shows the XN scattering cross section rising with W and decreasing with an increase of Q{sup 2}. Finally, our analysis points at a largely suppressed off-shell part of the rescattering amplitude.« less

A Viral-Human Interactome Based on Structural Motif-Domain Interactions Captures the Human Infectome

PubMed Central

Guo, Xianwu; Rodríguez-Pérez, Mario A.

2013-01-01

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. PMID:23951184

Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data.

PubMed

Tang, Hongwei; Wei, Peng; Duell, Eric J; Risch, Harvey A; Olson, Sara H; Bueno-de-Mesquita, H Bas; Gallinger, Steven; Holly, Elizabeth A; Petersen, Gloria; Bracci, Paige M; McWilliams, Robert R; Jenab, Mazda; Riboli, Elio; Tjønneland, Anne; Boutron-Ruault, Marie Christine; Kaaks, Rudolph; Trichopoulos, Dimitrios; Panico, Salvatore; Sund, Malin; Peeters, Petra H M; Khaw, Kay-Tee; Amos, Christopher I; Li, Donghui

2014-05-01

Cigarette smoking is the best established modifiable risk factor for pancreatic cancer. Genetic factors that underlie smoking-related pancreatic cancer have previously not been examined at the genome-wide level. Taking advantage of the existing Genome-wide association study (GWAS) genotype and risk factor data from the Pancreatic Cancer Case Control Consortium, we conducted a discovery study in 2028 cases and 2109 controls to examine gene-smoking interactions at pathway/gene/single nucleotide polymorphism (SNP) level. Using the likelihood ratio test nested in logistic regression models and ingenuity pathway analysis (IPA), we examined 172 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, 3 manually curated gene sets, 3 nicotine dependency gene ontology pathways, 17 912 genes and 468 114 SNPs. None of the individual pathway/gene/SNP showed significant interaction with smoking after adjusting for multiple comparisons. Six KEGG pathways showed nominal interactions (P < 0.05) with smoking, and the top two are the pancreatic secretion and salivary secretion pathways (major contributing genes: RAB8A, PLCB and CTRB1). Nine genes, i.e. ZBED2, EXO1, PSG2, SLC36A1, CLSTN1, MTHFSD, FAT2, IL10RB and ATXN2 had P interaction < 0.0005. Five intergenic region SNPs and two SNPs of the EVC and KCNIP4 genes had P interaction < 0.00003. In IPA analysis of genes with nominal interactions with smoking, axonal guidance signaling $$\\left(P=2.12\\times 1{0}^{-7}\\right)$$ and α-adrenergic signaling $$\\left(P=2.52\\times 1{0}^{-5}\\right)$$ genes were significantly overrepresented canonical pathways. Genes contributing to the axon guidance signaling pathway included the SLIT/ROBO signaling genes that were frequently altered in pancreatic cancer. These observations need to be confirmed in additional data set. Once confirmed, it will open a new avenue to unveiling the etiology of smoking-associated pancreatic cancer.

Meta-analysis identifies gene-by-environment interactions as demonstrated in a study of 4,965 mice.

PubMed

Kang, Eun Yong; Han, Buhm; Furlotte, Nicholas; Joo, Jong Wha J; Shih, Diana; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar

2014-01-01

Identifying environmentally-specific genetic effects is a key challenge in understanding the structure of complex traits. Model organisms play a crucial role in the identification of such gene-by-environment interactions, as a result of the unique ability to observe genetically similar individuals across multiple distinct environments. Many model organism studies examine the same traits but under varying environmental conditions. For example, knock-out or diet-controlled studies are often used to examine cholesterol in mice. These studies, when examined in aggregate, provide an opportunity to identify genomic loci exhibiting environmentally-dependent effects. However, the straightforward application of traditional methodologies to aggregate separate studies suffers from several problems. First, environmental conditions are often variable and do not fit the standard univariate model for interactions. Additionally, applying a multivariate model results in increased degrees of freedom and low statistical power. In this paper, we jointly analyze multiple studies with varying environmental conditions using a meta-analytic approach based on a random effects model to identify loci involved in gene-by-environment interactions. Our approach is motivated by the observation that methods for discovering gene-by-environment interactions are closely related to random effects models for meta-analysis. We show that interactions can be interpreted as heterogeneity and can be detected without utilizing the traditional uni- or multi-variate approaches for discovery of gene-by-environment interactions. We apply our new method to combine 17 mouse studies containing in aggregate 4,965 distinct animals. We identify 26 significant loci involved in High-density lipoprotein (HDL) cholesterol, many of which are consistent with previous findings. Several of these loci show significant evidence of involvement in gene-by-environment interactions. An additional advantage of our meta-analysis approach is that our combined study has significantly higher power and improved resolution compared to any single study thus explaining the large number of loci discovered in the combined study.

Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice

PubMed Central

Joo, Jong Wha J.; Shih, Diana; Davis, Richard C.; Lusis, Aldons J.; Eskin, Eleazar

2014-01-01

Identifying environmentally-specific genetic effects is a key challenge in understanding the structure of complex traits. Model organisms play a crucial role in the identification of such gene-by-environment interactions, as a result of the unique ability to observe genetically similar individuals across multiple distinct environments. Many model organism studies examine the same traits but under varying environmental conditions. For example, knock-out or diet-controlled studies are often used to examine cholesterol in mice. These studies, when examined in aggregate, provide an opportunity to identify genomic loci exhibiting environmentally-dependent effects. However, the straightforward application of traditional methodologies to aggregate separate studies suffers from several problems. First, environmental conditions are often variable and do not fit the standard univariate model for interactions. Additionally, applying a multivariate model results in increased degrees of freedom and low statistical power. In this paper, we jointly analyze multiple studies with varying environmental conditions using a meta-analytic approach based on a random effects model to identify loci involved in gene-by-environment interactions. Our approach is motivated by the observation that methods for discovering gene-by-environment interactions are closely related to random effects models for meta-analysis. We show that interactions can be interpreted as heterogeneity and can be detected without utilizing the traditional uni- or multi-variate approaches for discovery of gene-by-environment interactions. We apply our new method to combine 17 mouse studies containing in aggregate 4,965 distinct animals. We identify 26 significant loci involved in High-density lipoprotein (HDL) cholesterol, many of which are consistent with previous findings. Several of these loci show significant evidence of involvement in gene-by-environment interactions. An additional advantage of our meta-analysis approach is that our combined study has significantly higher power and improved resolution compared to any single study thus explaining the large number of loci discovered in the combined study. PMID:24415945

Desorption of oxygen from alloyed Ag/Pt(111)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jankowski, Maciej; Wormeester, Herbert, E-mail: h.wormeester@utwente.nl; Zandvliet, Harold J. W.

2014-06-21

We have investigated the interaction of oxygen with the Ag/Pt(111) surface alloy by thermal desorption spectroscopy (TDS). The surface alloy was formed during the deposition of sub-monolayer amounts of silver on Pt(111) at 800 K and subsequent cooling to 300 K. The low-temperature phase of the surface alloy is composed of nanometer-sized silver rich stripes, embedded within platinum-rich domains, which were characterized with spot profile analysis low energy electron diffraction. The TDS measurements show that oxygen adsorption is blocked on Ag sites: the saturation coverage of oxygen decreases with increasing Ag coverage. Also, the activation energy for desorption (E{sub des})more » decreases with Ag coverage. The analysis of the desorption spectra from clean Pt(111) shows a linear decay of E{sub des} with oxygen coverage, which indicates repulsive interactions between the adsorbed oxygen atoms. In contrast, adsorption on alloyed Ag/Pt(111) leads to an attractive interaction between adsorbed oxygen atoms.« less

Association of HS6ST3 gene polymorphisms with obesity and triglycerides: gene x gender interaction.

PubMed

Wang, Ke-Sheng; Wang, Liang; Liu, Xuefeng; Zeng, Min

2013-12-01

The heparan sulfate 6-O-sulfotransferase 3 (HS6ST3) gene is involved in heparan sulphate and heparin metabolism, and has been reported to be associated with diabetic retinopathy in type 2 diabetes.We hypothesized that HS6ST3 gene polymorphisms might play an important role in obesity and related phenotypes (such as triglycerides). We examined genetic associations of 117 single-nucleotide polymorphisms (SNPs) within the HS6ST3 gene with obesity and triglycerides using two Caucasian samples: the Marshfield sample (1442 obesity cases and 2122 controls), and the Health aging and body composition (Health ABC) sample (305 cases and 1336 controls). Logistic regression analysis of obesity as a binary trait and linear regression analysis of triglycerides as a continuous trait, adjusted for age and sex, were performed using PLINK. Single marker analysis showed that six SNPs in the Marshfield sample and one SNP in the Health ABC sample were associated with obesity (P < 0.05). SNP rs535812 revealed a stronger association with obesity in meta-analysis of these two samples (P = 0.0105). The T-A haplotype from rs878950 and rs9525149 revealed significant association with obesity in the Marshfield sample (P = 0.012). Moreover, nine SNPs showed associations with triglycerides in the Marshfield sample (P < 0.05) and the best signal was rs1927796 (P = 0.00858). In addition, rs7331762 showed a strong gene x gender interaction (P = 0.00956) for obesity while rs1927796 showed a strong gene x gender interaction (P = 0.000625) for triglycerides in the Marshfield sample. These findings contribute new insights into the pathogenesis of obesity and triglycerides and demonstrate the importance of gender differences in the aetiology.

Applications of hydrophilic interaction chromatography to amino acids, peptides, and proteins.

PubMed

Periat, Aurélie; Krull, Ira S; Guillarme, Davy

2015-02-01

This review summarizes the recent advances in the analysis of amino acids, peptides, and proteins using hydrophilic interaction chromatography. Various reports demonstrate the successful analysis of amino acids under such conditions. However, a baseline resolution of the 20 natural amino acids has not yet been published and for this reason, there is often a need to use mass spectrometry for detection to further improve selectivity. Hydrophilic interaction chromatography is also recognized as a powerful technique for peptide analysis, and there are a lot of papers showing its applicability for proteomic applications (peptide mapping). It is expected that its use for peptide mapping will continue to grow in the future, particularly because this analytical strategy can be combined with reversed-phase liquid chromatography, in a two-dimensional setup, to reach very high resolving power. Finally, the interest in hydrophilic interaction chromatography for intact proteins analysis is less evident due to possible solubility issues and a lack of suitable hydrophilic interaction chromatography stationary phases. To date, it has been successfully employed only for the characterization of membrane proteins, histones, and the separation of glycosylated isoforms of an intact glycoprotein. From our point of view, the number of hydrophilic interaction chromatography columns compatible with intact proteins (higher upper temperature limit, large pore size, etc.) is still too limited. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Validation of the Spanish version of the Frankfurt Emotion Work Scales].

PubMed

Ortiz Bonnín, Silvia; Navarro Guzmán, Capilla; García Buades, Esther; Ramis Palmer, Carmen; Manassero Mas, M Antonia

2012-05-01

This study presents the validity and reliability analysis of a questionnaire that assesses emotion work in the service sector. Emotion work is a term introduced by Hochschild (1983) and it refers to the expression of organizationally desirable emotions to influence the interactions with clients at work. The results show a 6-factor structure: Requirement to display Positive, Negative and Neutral Emotions, Sensitivity Requirements, Interaction Control and Emotional Dissonance. The analysis of the sub-scale scores reveals that the most frequently expressed emotions are positive, whereas negative emotions are expressed less frequently.

Modeling the reflection of Photosynthetically active radiation in a monodominant floodable forest in the Pantanal of Mato Grosso State using multivariate statistics and neural networks.

PubMed

Curado, Leone F A; Musis, Carlo R DE; Cunha, Cristiano R DA; Rodrigues, Thiago R; Pereira, Vinicius M R; Nogueira, José S; Sanches, Luciana

2016-09-01

The study of radiation entrance and exit dynamics and energy consumption in a system is important for understanding the environmental processes that rule the biosphere-atmosphere interactions of all ecosystems. This study provides an analysis of the interaction of energy in the form of photosynthetically active radiation (PAR) in the Pantanal, a Brazilian wetland forest, by studying the variation of PAR reflectance and its interaction with local rainfall. The study site is located in Private Reserve of Natural Heritage, Mato Grosso State, Brazil, where the vegetation is a monodominant forest of Vochysia divergens Phol. The results showed a high correlation between the reflection of visible radiation and rainfall; however, the behavior was not the same at the three heights studied. An analysis of the hourly variation of the reflected waves also showed the seasonality of these phenomena in relation to the dry and rainy seasons. A predictive model for PAR was developed with a neural network that has a hidden layer, and it showed a determination coefficient of 0.938. This model showed that the Julian day and time of measurements had an inverse association with the wind profile and a direct association with the relative humidity profile.

A combined spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of quercetin with β-casein nanoparticles.

PubMed

Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Parastar, Hadi

2013-10-05

The interaction of quercetin with β-casein nanoparticle micelle was studied at various temperatures in order to do a complete thermodynamic and molecular analysis on the binding process. The results of fluorescence studies showed the possibility of fluorescence energy transfer between excited tryptophan and quercetin. The determined values of critical transfers distance and the mean distance of ligand from Trp-143 residues in β-casein micelle represents a non-radiative energy transfer mechanism for quenching and the existence of a significant interaction between this flavonoid and β-casein nanoparticle. The equilibrium binding of quercetin with β-casein micelle at different temperatures was studied by using UV-Vis absorption spectroscopy. The chemometric analysis (principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods) on spectrophotometric data revealed the existence of two components in solution (quercetin and β-casein-quercetin complex) and resolved their pure concentration and spectral profiles. This information let us to calculate the equilibrium binding constant at various temperatures and the relevant thermodynamic parameters of interaction (enthalpy, entropy and Gibbs free energy) with low uncertainty. The negative values of entropy and enthalpy changes represent the predominate role of hydrogen binding and van der Waals interactions in the binding process. Docking calculations showed the probable binding site of quercetin is located in the hydrophobic core of β-casein where the quercetin molecule is lined by hydrophobic residues and make five hydrogen bonds and several van der Waals contacts with them. Moreover, molecular dynamic (MD) simulation results suggested that this flavonoid can interact with β-casein, without affecting the secondary structure of β-casein. Simulations, molecular docking and experimental data reciprocally supported each other. Copyright © 2013 Elsevier B.V. All rights reserved.

[Evaluate drug interaction of multi-components in Morus alba leaves based on α-glucosidase inhibitory activity].

PubMed

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

2016-06-01

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

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

PubMed Central

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-01-01

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting.

PubMed

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-02-17

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes.

Hydrogen bonded supra-molecular framework in inorganic-organic hybrid compounds: Syntheses, structures, and photoluminescent properties

NASA Astrophysics Data System (ADS)

Yan, Li; Liu, Wei; Li, Chuanbi; Wang, Yifei; Ma, Li; Dong, Qinqin

2013-03-01

Two novel compounds constructed from aromatic acid and N-Heterocyclic ligands have been synthesized by hydrothermal reaction: [Cd(mip)(1,8-NDC)(H2O)]2 (1) [mip = 2-(3-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline, 1,8-NDC = naphthalene-1,8-dicarboxylic acid] and Cd(mip)2(NTC)2 (2) [NTC = nicotinic acid]. Compounds 1 and 2 are characterized by elemental analysis, IR, single crystal X-ray diffraction and thermogravimetric analysis (TGA). Single-crystal X-ray investigation reveals that compounds 1-2 are 0 dimensional (0D) structures, and the existence of hydrogen bonds and π-π interactions lead the 0D to 2D novel framework. Hydrogen bonds and π-π interactions are powerful non-covalent intermolecular interactions for directing supra-molecular architectures. TG analysis shows clear courses of weight loss, which corresponds to the decomposition of different ligands. At room temperature, compound 1 exhibits emission at 449 nm upon excitation at 325 nm, and compound 2 shows a strong emission at 656 nm upon excitation at 350 nm. Fluorescent spectrum displays that compounds 1 and 2 are potential luminescent materials.

Coilin phosphorylation mediates interaction with SMN and SmB'.

PubMed

Toyota, Cory G; Davis, Misty D; Cosman, Angela M; Hebert, Michael D

2010-04-01

Cajal bodies (CBs) are subnuclear domains that participate in spliceosomal small nuclear ribonucleoprotein (snRNP) biogenesis and play a part in the assembly of the spliceosomal complex. The CB marker protein, coilin, interacts with survival of motor neuron (SMN) and Sm proteins. Several coilin phosphoresidues have been identified by mass spectrometric analysis. Phosphorylation of coilin affects its self-interaction and localization in the nucleus. We hypothesize that coilin phosphorylation also impacts its binding to SMN and Sm proteins. In vitro binding studies with a C-terminal fragment of coilin and corresponding phosphomimics show that SMN binds preferentially to dephosphorylated analogs and that SmB' binds preferentially to phosphomimetic constructs. Bacterially expressed full-length coilin binds more SMN and SmB' than does the C-terminal fragment. Co-immunoprecipitation and phosphatase experiments show that SMN also binds dephosphorylated coilin in vivo. These data show that phosphorylation of coilin influences interaction with its target proteins and, thus, may be significant in managing the flow of snRNPs through the CB.

Coilin phosphorylation mediates interaction with SMN and SmB′

PubMed Central

Toyota, Cory G.; Davis, Misty D.; Cosman, Angela M.; Hebert, Michael D.

2010-01-01

Cajal bodies (CBs) are subnuclear domains that participate in spliceosomal small nuclear ribonucleoprotein (snRNP) biogenesis and play a part in the assembly of the spliceosomal complex. The CB marker protein, coilin, interacts with survival of motor neuron (SMN) and Sm proteins. Several coilin phosphoresidues have been identified by mass spectrometric analysis. Phosphorylation of coilin affects its self-interaction and localization in the nucleus. We hypothesize that coilin phosphorylation also impacts its binding to SMN and Sm proteins. In vitro binding studies with a C-terminal fragment of coilin and corresponding phosphomimics show that SMN binds preferentially to dephosphorylated analogs and that SmB′ binds preferentially to phosphomimetic constructs. Bacterially expressed full-length coilin binds more SMN and SmB′ than does the C-terminal fragment. Co-immunoprecipitation and phosphatase experiments show that SMN also binds dephosphorylated coilin in vivo. These data show that phosphorylation of coilin influences interaction with its target proteins and, thus, may be significant in managing the flow of snRNPs through the CB. PMID:19997741

Indications of a late-time interaction in the dark sector.

PubMed

Salvatelli, Valentina; Said, Najla; Bruni, Marco; Melchiorri, Alessandro; Wands, David

2014-10-31

We show that a general late-time interaction between cold dark matter and vacuum energy is favored by current cosmological data sets. We characterize the strength of the coupling by a dimensionless parameter q(V) that is free to take different values in four redshift bins from the primordial epoch up to today. This interacting scenario is in agreement with measurements of cosmic microwave background temperature anisotropies from the Planck satellite, supernovae Ia from Union 2.1 and redshift space distortions from a number of surveys, as well as with combinations of these different data sets. Our analysis of the 4-bin interaction shows that a nonzero interaction is likely at late times. We then focus on the case q(V)≠0 in a single low-redshift bin, obtaining a nested one parameter extension of the standard ΛCDM model. We study the Bayesian evidence, with respect to ΛCDM, of this late-time interaction model, finding moderate evidence for an interaction starting at z=0.9, dependent upon the prior range chosen for the interaction strength parameter q(V). For this case the null interaction (q(V)=0, i.e., ΛCDM) is excluded at 99% C.L.

Genome-wide interaction study of smoking and bladder cancer risk

PubMed Central

Figueroa, Jonine D.; Han, Summer S.; Garcia-Closas, Montserrat; Baris, Dalsu; Jacobs, Eric J.; Kogevinas, Manolis; Schwenn, Molly; Malats, Nuria; Johnson, Alison; Purdue, Mark P.; Caporaso, Neil; Landi, Maria Teresa; Prokunina-Olsson, Ludmila; Wang, Zhaoming; Hutchinson, Amy; Burdette, Laurie; Wheeler, William; Vineis, Paolo; Siddiq, Afshan; Cortessis, Victoria K.; Kooperberg, Charles; Cussenot, Olivier; Benhamou, Simone; Prescott, Jennifer; Porru, Stefano; Bueno-de-Mesquita, H.Bas; Trichopoulos, Dimitrios; Ljungberg, Börje; Clavel-Chapelon, Françoise; Weiderpass, Elisabete; Krogh, Vittorio; Dorronsoro, Miren; Travis, Ruth; Tjønneland, Anne; Brenan, Paul; Chang-Claude, Jenny; Riboli, Elio; Conti, David; Gago-Dominguez, Manuela; Stern, Mariana C.; Pike, Malcolm C.; Van Den Berg, David; Yuan, Jian-Min; Hohensee, Chancellor; Rodabough, Rebecca; Cancel-Tassin, Geraldine; Roupret, Morgan; Comperat, Eva; Chen, Constance; De Vivo, Immaculata; Giovannucci, Edward; Hunter, David J.; Kraft, Peter; Lindstrom, Sara; Carta, Angela; Pavanello, Sofia; Arici, Cecilia; Mastrangelo, Giuseppe; Karagas, Margaret R.; Schned, Alan; Armenti, Karla R.; Hosain, G.M.Monawar; Haiman, Chris A.; Fraumeni, Joseph F.; Chanock, Stephen J.; Chatterjee, Nilanjan; Rothman, Nathaniel; Silverman, Debra T.

2014-01-01

Bladder cancer is a complex disease with known environmental and genetic risk factors. We performed a genome-wide interaction study (GWAS) of smoking and bladder cancer risk based on primary scan data from 3002 cases and 4411 controls from the National Cancer Institute Bladder Cancer GWAS. Alternative methods were used to evaluate both additive and multiplicative interactions between individual single nucleotide polymorphisms (SNPs) and smoking exposure. SNPs with interaction P values < 5 × 10− 5 were evaluated further in an independent dataset of 2422 bladder cancer cases and 5751 controls. We identified 10 SNPs that showed association in a consistent manner with the initial dataset and in the combined dataset, providing evidence of interaction with tobacco use. Further, two of these novel SNPs showed strong evidence of association with bladder cancer in tobacco use subgroups that approached genome-wide significance. Specifically, rs1711973 (FOXF2) on 6p25.3 was a susceptibility SNP for never smokers [combined odds ratio (OR) = 1.34, 95% confidence interval (CI) = 1.20–1.50, P value = 5.18 × 10− 7]; and rs12216499 (RSPH3-TAGAP-EZR) on 6q25.3 was a susceptibility SNP for ever smokers (combined OR = 0.75, 95% CI = 0.67–0.84, P value = 6.35 × 10− 7). In our analysis of smoking and bladder cancer, the tests for multiplicative interaction seemed to more commonly identify susceptibility loci with associations in never smokers, whereas the additive interaction analysis identified more loci with associations among smokers—including the known smoking and NAT2 acetylation interaction. Our findings provide additional evidence of gene–environment interactions for tobacco and bladder cancer. PMID:24662972

Automated Video Analysis of Non-verbal Communication in a Medical Setting.

PubMed

Hart, Yuval; Czerniak, Efrat; Karnieli-Miller, Orit; Mayo, Avraham E; Ziv, Amitai; Biegon, Anat; Citron, Atay; Alon, Uri

2016-01-01

Non-verbal communication plays a significant role in establishing good rapport between physicians and patients and may influence aspects of patient health outcomes. It is therefore important to analyze non-verbal communication in medical settings. Current approaches to measure non-verbal interactions in medicine employ coding by human raters. Such tools are labor intensive and hence limit the scale of possible studies. Here, we present an automated video analysis tool for non-verbal interactions in a medical setting. We test the tool using videos of subjects that interact with an actor portraying a doctor. The actor interviews the subjects performing one of two scripted scenarios of interviewing the subjects: in one scenario the actor showed minimal engagement with the subject. The second scenario included active listening by the doctor and attentiveness to the subject. We analyze the cross correlation in total kinetic energy of the two people in the dyad, and also characterize the frequency spectrum of their motion. We find large differences in interpersonal motion synchrony and entrainment between the two performance scenarios. The active listening scenario shows more synchrony and more symmetric followership than the other scenario. Moreover, the active listening scenario shows more high-frequency motion termed jitter that has been recently suggested to be a marker of followership. The present approach may be useful for analyzing physician-patient interactions in terms of synchrony and dominance in a range of medical settings.

Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots

PubMed Central

Cheruiyot, Erick Kimutai; Othira, Jacktone Odongo; Njuguna, Virginia Wanjiku; Macharia, Joseph Kinyoro; Owuoche, James; Oyier, Moses; Kange, Alex Machio

2016-01-01

The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P < 0.05) affected by environments (E), genotypes (G) and genotype by environment interaction (GEI). GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield. PMID:27777968

Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots.

PubMed

Rono, Justice Kipkorir; Cheruiyot, Erick Kimutai; Othira, Jacktone Odongo; Njuguna, Virginia Wanjiku; Macharia, Joseph Kinyoro; Owuoche, James; Oyier, Moses; Kange, Alex Machio

2016-01-01

The genotype and environment interaction influences the selection criteria of sorghum ( Sorghum bicolor ) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly ( P < 0.05) affected by environments (E), genotypes (G) and genotype by environment interaction (GEI). GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield.

Fourier's law of heat conduction: quantum mechanical master equation analysis.

PubMed

Wu, Lian-Ao; Segal, Dvira

2008-06-01

We derive the macroscopic Fourier's Law of heat conduction from the exact gain-loss time convolutionless quantum master equation under three assumptions for the interaction kernel. To second order in the interaction, we show that the first two assumptions are natural results of the long time limit. The third assumption can be satisfied by a family of interactions consisting of an exchange effect. The pure exchange model directly leads to energy diffusion in a weakly coupled spin- 12 chain.

Dimensionality of consumer search space drives trophic interaction strengths.

PubMed

Pawar, Samraat; Dell, Anthony I; Savage, Van M

2012-06-28

Trophic interactions govern biomass fluxes in ecosystems, and stability in food webs. Knowledge of how trophic interaction strengths are affected by differences among habitats is crucial for understanding variation in ecological systems. Here we show how substantial variation in consumption-rate data, and hence trophic interaction strengths, arises because consumers tend to encounter resources more frequently in three dimensions (3D) (for example, arboreal and pelagic zones) than two dimensions (2D) (for example, terrestrial and benthic zones). By combining new theory with extensive data (376 species, with body masses ranging from 5.24 × 10(-14) kg to 800 kg), we find that consumption rates scale sublinearly with consumer body mass (exponent of approximately 0.85) for 2D interactions, but superlinearly (exponent of approximately 1.06) for 3D interactions. These results contradict the currently widespread assumption of a single exponent (of approximately 0.75) in consumer-resource and food-web research. Further analysis of 2,929 consumer-resource interactions shows that dimensionality of consumer search space is probably a major driver of species coexistence, and the stability and abundance of populations.

The Role of Father Involvement and Marital Satisfaction in the Development of Family Interactive Abilities: A Multilevel Approach.

PubMed

Simonelli, Alessandra; Parolin, Micol; Sacchi, Chiara; De Palo, Francesca; Vieno, Alessio

2016-01-01

The study aims to investigate the development of family interactions from pregnancy to preschool age in a longitudinal perspective, using multilevel analysis. Also, it explored the impact of couple relationship and father involvement in childcare on the developmental trend of the quality of mother-father-child interactions. One hundred and three primiparous families were assessed at 7th month of pregnancy, 4th, 9th, and 18th months of child's life and during preschool age (36-48th), using the observational procedure named, Lausanne Trilogue Play. Parents' perception of marital satisfaction was assessed with the Dyadic Adjustment Scale at each point of measure; moreover, in the postnatal assessment, parents completed the Father Involvement Questionnaire. Results showed that family interactions increase over time. Secondly, a decrease of marital adjustment is associated with an improvement of the quality of family interactions. Moreover, father involvement predicts the quality of family interactions from the earliest stages of child's life. In a longitudinal perspective, family interactions and marital quality show opposite developmental trends and father's involvement represents a particularly important feature of the family.

Tailoring the Interfacial Chemical Interaction for High-Efficiency Perovskite Solar Cells.

PubMed

Zuo, Lijian; Chen, Qi; De Marco, Nicholas; Hsieh, Yao-Tsung; Chen, Huajun; Sun, Pengyu; Chang, Sheng-Yung; Zhao, Hongxiang; Dong, Shiqi; Yang, Yang

2017-01-11

The ionic nature of perovskite photovoltaic materials makes it easy to form various chemical interactions with different functional groups. Here, we demonstrate that interfacial chemical interactions are a critical factor in determining the optoelectronic properties of perovskite solar cells. By depositing different self-assembled monolayers (SAMs), we introduce different functional groups onto the SnO 2 surface to form various chemical interactions with the perovskite layer. It is observed that the perovskite solar cell device performance shows an opposite trend to that of the energy level alignment theory, which shows that chemical interactions are the predominant factor governing the interfacial optoelectronic properties. Further analysis verifies that proper interfacial interactions can significantly reduce trap state density and facilitate the interfacial charge transfer. Through use of the 4-pyridinecarboxylic acid SAM, the resulting perovskite solar cell exhibits striking improvements to the reach the highest efficiency of 18.8%, which constitutes an ∼10% enhancement compared to those without SAMs. Our work highlights the importance of chemical interactions at perovskite/electrode interfaces and paves the way for further optimizing performances of perovskite solar cells.

Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?

PubMed Central

2017-01-01

Halogens are present in a significant number of drugs, contributing favorably to ligand–protein binding. Currently, the contribution of halogens, most notably chlorine and bromine, is largely attributed to halogen bonds involving favorable interactions with hydrogen bond acceptors. However, we show that halogens acting as hydrogen bond acceptors potentially make a more favorable contribution to ligand binding than halogen bonds based on quantum mechanical calculations. In addition, bioinformatics analysis of ligand–protein crystal structures shows the presence of significant numbers of such interactions. It is shown that interactions between halogens and hydrogen bond donors (HBDs) are dominated by perpendicular C–X···HBD orientations. Notably, the orientation dependence of the halogen–HBD (X–HBD) interactions is minimal over greater than 100° with favorable interaction energies ranging from −2 to −14 kcal/mol. This contrasts halogen bonds in that X–HBD interactions are substantially more favorable, being comparable to canonical hydrogen bonds, with a smaller orientation dependence, such that they make significant, favorable contributions to ligand–protein binding and, therefore, should be actively considered during rational ligand design. PMID:28657759

An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

PubMed

Mallik, Mrinmay Kumar

2018-02-07

Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that is indicative of their strong influence in the protein protein interaction network. Similarly the newly proposed GEADCA helped identify the transcription factors with high centrality values indicative of their key roles in transcriptional regulation. The enrichment studies provided a list of molecular functions, biological processes and biochemical pathways associated with the constructed network. The study shows how pathway based databases may be used to create and analyze a relevant protein interaction network in glioma cancer stem cells and identify the essential elements within it to gather insights into the molecular interactions that regulate the properties of glioma stem cells. How these insights may be utilized to help the development of future research towards formulation of new management strategies have been discussed from a theoretical standpoint. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Laughter Differs in Children with Autism: An Acoustic Analysis of Laughs Produced by Children with and without the Disorder

ERIC Educational Resources Information Center

Hudenko, William J.; Stone, Wendy; Bachorowski, Jo-Anne

2009-01-01

Few studies have examined vocal expressions of emotion in children with autism. We tested the hypothesis that during social interactions, children diagnosed with autism would exhibit less extreme laugh acoustics than their nonautistic peers. Laughter was recorded during a series of playful interactions with an examiner. Results showed that…

Code Switching in the Classroom: A Case Study of Economics and Management Students at the University of Sfax, Tunisia

ERIC Educational Resources Information Center

Bach Baoueb, Sallouha Lamia; Toumi, Naouel

2012-01-01

This case study explores the motivations for code switching (CS) in the interactions of Tunisian students at the faculty of Economics and Management in Sfax, Tunisia. The study focuses on students' (EMSs) classroom conversations and out-of-classroom peer interactions. The analysis of the social motivations of EMSs' CS behaviour shows that…

Serine Proteases-Like Genes in the Asian Rice Gall Midge Show Differential Expression in Compatible and Incompatible Interactions with Rice

PubMed Central

Sinha, Deepak Kumar; Lakshmi, Mulagondla; Anuradha, Ghanta; Rahman, Shaik J.; Siddiq, Ebrahimali A.; Bentur, Jagadish S.; Nair, Suresh

2011-01-01

The Asian rice gall midge, Orseolia oryzae (Wood-Mason), is a serious pest of rice. Investigations into the gall midge-rice interaction will unveil the underlying molecular mechanisms which, in turn, can be used as a tool to assist in developing suitable integrated pest management strategies. The insect gut is known to be involved in various physiological and biological processes including digestion, detoxification and interaction with the host. We have cloned and identified two genes, OoprotI and OoprotII, homologous to serine proteases with the conserved His87, Asp136 and Ser241 residues. OoProtI shared 52.26% identity with mosquito-type trypsin from Hessian fly whereas OoProtII showed 52.49% identity to complement component activated C1s from the Hessian fly. Quantitative real time PCR analysis revealed that both the genes were significantly upregulated in larvae feeding on resistant cultivar than in those feeding on susceptible cultivar. These results provide an opportunity to understand the gut physiology of the insect under compatible or incompatible interactions with the host. Phylogenetic analysis grouped these genes in the clade containing proteases of phytophagous insects away from hematophagous insects. PMID:21686154

NMR structural study of the intracellular loop 3 of the serotonin 5-HT(1A) receptor and its interaction with calmodulin.

PubMed

Chen, Angela Shuyi; Kim, Young Mee; Gayen, Shovanlal; Huang, Qiwei; Raida, Manfred; Kang, Congbao

2011-09-01

The serotonin (5-HT(1A)) receptor, a G-protein-coupled receptor (GPCR), plays important roles in serotonergic signaling in the central nervous system. The third intracellular loop (ICL3) of the 5-HT(1A) receptor has been shown to be important for the regulation of this receptor through interactions with proteins such as G-proteins and calmodulin. In this study, the ICL3 of 5-HT(1A) receptor was expressed in E. coli and purified. Gel filtration and mass spectrometry were used to confirm the molecular weight of the purified ICL3. Secondary structure analysis using circular dichroism (CD) demonstrated the presence of α-helical structures. Backbone assignment of ICL3 was achieved using three-dimensional experiments. A chemical shift index and Talos+ analysis showed that residues E326 to R339 form α-helical structure. Residues G256 to S269 of ICL3 were shown to be a novel region that has a molecular interaction with calmodulin in titration assays. Peptide derived from the ICL3 containing residues from G256 to S269 also showed molecular interaction with calmodulin. Copyright © 2011 Elsevier B.V. All rights reserved.

A Missense Mutation in the Aggrecan C-type Lectin Domain Disrupts Extracellular Matrix Interactions and Causes Dominant Familial Osteochondritis Dissecans

PubMed Central

Stattin, Eva-Lena; Wiklund, Fredrik; Lindblom, Karin; Önnerfjord, Patrik; Jonsson, Björn-Anders; Tegner, Yelverton; Sasaki, Takako; Struglics, André; Lohmander, Stefan; Dahl, Niklas; Heinegård, Dick; Aspberg, Anders

2010-01-01

Osteochondritis dissecans is a disorder in which fragments of articular cartilage and subchondral bone dislodge from the joint surface. We analyzed a five-generation family in which affected members had autosomal-dominant familial osteochondritis dissecans. A genome-wide linkage analysis identified aggrecan (ACAN) as a prime candidate gene for the disorder. Sequence analysis of ACAN revealed heterozygosity for a missense mutation (c.6907G > A) in affected individuals, resulting in a p.V2303M amino acid substitution in the aggrecan G3 domain C-type lectin, which mediates interactions with other proteins in the cartilage extracellular matrix. Binding studies with recombinant mutated and wild-type G3 proteins showed loss of fibulin-1, fibulin-2, and tenascin-R interactions for the V2303M protein. Mass spectrometric analyses of aggrecan purified from patient cartilage verified that V2303M aggrecan is produced and present in the tissue. Our results provide a molecular mechanism for the etiology of familial osteochondritis dissecans and show the importance of the aggrecan C-type lectin interactions for cartilage function in vivo. PMID:20137779

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.

PubMed

Fujimoto, Takeshi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2013-01-31

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Chemical bonding in silicon-carbene complexes.

PubMed

Liu, Z

2009-06-04

The bonding situations in the newly synthesized silicon-carbene complexes with formulas L:SiCl4, L:(Cl)Si-Si(Cl):L, and L:Si=Si:L (where L: is an N-heterocyclic carbene), are reported using density functional theory at the BP86/TZ2P level. The bonding analysis clearly shows that the bonding situation in the silicon-carbene complexes cannot be described in terms of donor-acceptor interactions depicted in the Dewar-Chatt-Duncanson model. The energy decomposition analysis (EDA) shows that the electrostatic attraction plays an important or even dominant role for the Si-C(carbene) binding interactions in the silicon-carbene complexes. That the molecular orbitals of the silicon-carbene complexes are lower in energy than the parent orbitals of carbenes indicates that these complexes are better described as stabilized carbene complexes.

Provoking Reflective Thinking in Post Observation Conversations

ERIC Educational Resources Information Center

Kim, Younhee; Silver, Rita Elaine

2016-01-01

We present a micro-analysis of post observation conversations between classroom teachers and mentors. Using the approach of conversation analysis, we show how the sequential organization of an episode (i.e., who initiates the interaction, question format used by mentors) could potentially serve to provoke or hinder teacher reflection. Our analysis…

Natural three-qubit interactions in one-way quantum computing

NASA Astrophysics Data System (ADS)

Tame, M. S.; Paternostro, M.; Kim, M. S.; Vedral, V.

2006-02-01

We address the effects of natural three-qubit interactions on the computational power of one-way quantum computation. A benefit of using more sophisticated entanglement structures is the ability to construct compact and economic simulations of quantum algorithms with limited resources. We show that the features of our study are embodied by suitably prepared optical lattices, where effective three-spin interactions have been theoretically demonstrated. We use this to provide a compact construction for the Toffoli gate. Information flow and two-qubit interactions are also outlined, together with a brief analysis of relevant sources of imperfection.

Carbene-aerogen bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Sabouri, Ayda

2017-04-01

Through the use of ab initio calculations, the possibility of formation of σ-hole interaction between ZO3 (Z = Ar, Kr and Xe) and carbene species is investigated. Since singlet carbenes show a negative electrostatic potential on their divalent carbon atom, they can favourably interact with the positive electrostatic potential generated by the σ-hole of Z atom of ZO3. The characteristic of this interaction, termed as 'carbene-aerogen' bond, is analysed in terms of geometric, interaction energies and electronic features. The energy decomposition analysis indicates that for all complexes analysed here, the electrostatic energy is more negative than the polarisation or dispersion energy term. According to the electron density analysis, some partial covalent character can be ascribed to XeṡṡṡC interactions. In addition, the carbene-aerogen bond exhibits cooperative effects with the HṡṡṡO hydrogen-bonding interaction in ternary complexes where both interactions coexist. For a given carbene, the amount of these cooperative effects increases with the size of the Z atom. The results obtained in this work may be helpful for the extension and future application of σ-hole intermolecular interactions as well as coordination chemistry.

Repetition, response mobilization, and face: Analysis of group interactions with a 19-year-old with Asperger syndrome.

PubMed

Bottema-Beutel, Kristen; Louick, Rebecca; White, Rachael

2015-01-01

This Conversation Analytic study examined the talk of an adolescent with Asperger syndrome (under previously used diagnostic criteria), Nathan, as he interacts with peers in a small group setting. We focused on Nathan's repetition aimed at pursuing response, and rely on analytical frameworks including response mobilization, face-work, and agreement preference. We found that while Nathan's repetitions resembled 'topic perseveration' previously described in the literature, they showed evidence of interactional awareness as they were employed when peers offered little or no response to his original utterance. However, we also found that while much of Nathan's talk was sophisticatedly structured, his repetition to pursue response eschewed interaction rituals that work to maintain social cohesion. As a result, Nathan's interactional priorities appeared mis-aligned with those of his peers, and failed to produce extended interactions in most cases. Readers will be able to describe features of conversational interaction, including response mobilization, agreement preference, and face work. They will understand the relevance of conversation analysis to the study of interaction in individuals with autism spectrum disorder. Lastly, they will be able to describe the conditions under which the subject used repetition within peer interactions, and the effects of his repetition on interaction. Copyright © 2015 Elsevier Inc. All rights reserved.

ICAP - An Interactive Cluster Analysis Procedure for analyzing remotely sensed data

NASA Technical Reports Server (NTRS)

Wharton, S. W.; Turner, B. J.

1981-01-01

An Interactive Cluster Analysis Procedure (ICAP) was developed to derive classifier training statistics from remotely sensed data. ICAP differs from conventional clustering algorithms by allowing the analyst to optimize the cluster configuration by inspection, rather than by manipulating process parameters. Control of the clustering process alternates between the algorithm, which creates new centroids and forms clusters, and the analyst, who can evaluate and elect to modify the cluster structure. Clusters can be deleted, or lumped together pairwise, or new centroids can be added. A summary of the cluster statistics can be requested to facilitate cluster manipulation. The principal advantage of this approach is that it allows prior information (when available) to be used directly in the analysis, since the analyst interacts with ICAP in a straightforward manner, using basic terms with which he is more likely to be familiar. Results from testing ICAP showed that an informed use of ICAP can improve classification, as compared to an existing cluster analysis procedure.

Finding brain oscillations with power dependencies in neuroimaging data.

PubMed

Dähne, Sven; Nikulin, Vadim V; Ramírez, David; Schreier, Peter J; Müller, Klaus-Robert; Haufe, Stefan

2014-08-01

Phase synchronization among neuronal oscillations within the same frequency band has been hypothesized to be a major mechanism for communication between different brain areas. On the other hand, cross-frequency communications are more flexible allowing interactions between oscillations with different frequencies. Among such cross-frequency interactions amplitude-to-amplitude interactions are of a special interest as they show how the strength of spatial synchronization in different neuronal populations relates to each other during a given task. While, previously, amplitude-to-amplitude correlations were studied primarily on the sensor level, we present a source separation approach using spatial filters which maximize the correlation between the envelopes of brain oscillations recorded with electro-/magnetoencephalography (EEG/MEG) or intracranial multichannel recordings. Our approach, which is called canonical source power correlation analysis (cSPoC), is thereby capable of extracting genuine brain oscillations solely based on their assumed coupling behavior even when the signal-to-noise ratio of the signals is low. In addition to using cSPoC for the analysis of cross-frequency interactions in the same subject, we show that it can also be utilized for studying amplitude dynamics of neuronal oscillations across subjects. We assess the performance of cSPoC in simulations as well as in three distinctively different analysis scenarios of real EEG data, each involving several subjects. In the simulations, cSPoC outperforms unsupervised state-of-the-art approaches. In the analysis of real EEG recordings, we demonstrate excellent unsupervised discovery of meaningful power-to-power couplings, within as well as across subjects and frequency bands. Copyright © 2014 Elsevier Inc. All rights reserved.

An enrichment method based on synergistic and reversible covalent interactions for large-scale analysis of glycoproteins.

PubMed

Xiao, Haopeng; Chen, Weixuan; Smeekens, Johanna M; Wu, Ronghu

2018-04-27

Protein glycosylation is ubiquitous in biological systems and essential for cell survival. However, the heterogeneity of glycans and the low abundance of many glycoproteins complicate their global analysis. Chemical methods based on reversible covalent interactions between boronic acid and glycans have great potential to enrich glycopeptides, but the binding affinity is typically not strong enough to capture low-abundance species. Here, we develop a strategy using dendrimer-conjugated benzoboroxole to enhance the glycopeptide enrichment. We test the performance of several boronic acid derivatives, showing that benzoboroxole markedly increases glycopeptide coverage from human cell lysates. The enrichment is further improved by conjugating benzoboroxole to a dendrimer, which enables synergistic benzoboroxole-glycan interactions. This robust and simple method is highly effective for sensitive glycoproteomics analysis, especially capturing low-abundance glycopeptides. Importantly, the enriched glycopeptides remain intact, making the current method compatible with mass-spectrometry-based approaches to identify glycosylation sites and glycan structures.

'Understanding' as a practical issue in sexual health education for people with intellectual disabilities: a study using two qualitative methods.

PubMed

Finlay, W M L; Rohleder, Poul; Taylor, Natalie; Culfear, Hollie

2015-04-01

Sexual health education is important in addressing the health and social inequalities faced by people with intellectual disabilities. However, provision of health-related advice and education to people with various types and degrees of linguistic and learning difficulties involves addressing complex issues of language and comprehension. This article reports an exploratory study using 2 qualitative methods to examine the delivery of sexual health education to people with intellectual disabilities. Four video-recordings of sexual health education sessions were collected. Conversation analysis was used to examine in detail how such education occurs as a series of interactions between educators and learners. Interviews with 4 educators were carried out and analyzed using thematic analysis. The analysis shows how educators anticipate problems of comprehension and how they respond when there is evidence that a person does not understand the activity or the educational message. This occurs particularly when verbal prompts involve long sentences and abstract concepts. We show a characteristic pattern that arises in these situations, in which both educator and learner jointly produce a superficially correct response. Although interviews allows us some insight into contextual issues, strategy, and aspects of sexual health education that occur outside of the actual teaching sessions, analysis of actual interactions can show us patterns that occur in interactions between educators and learners when comprehension is in question. Addressing how sexual health education is delivered in practice and in detail provides valuable lessons about how such education can be improved. (c) 2015 APA, all rights reserved).

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.

PubMed

Lambert, Jean-Philippe; Ivosev, Gordana; Couzens, Amber L; Larsen, Brett; Taipale, Mikko; Lin, Zhen-Yuan; Zhong, Quan; Lindquist, Susan; Vidal, Marc; Aebersold, Ruedi; Pawson, Tony; Bonner, Ron; Tate, Stephen; Gingras, Anne-Claude

2013-12-01

Characterizing changes in protein-protein interactions associated with sequence variants (e.g., disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies in which cost and time are major considerations. We have coupled AP to data-independent mass spectrometric acquisition (sequential window acquisition of all theoretical spectra, SWATH) and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. We used AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes and propose a scalable pipeline for systems biology studies.

Neurofibromin interacts with CRMP-2 and CRMP-4 in rat brain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Y.-L.; Hsueh, Y.-P., E-mail: yph@gate.sinica.edu.tw

Neurofibromin, encoded by the neurofibromatosis type 1 (NF1) gene, regulates the Ras and cAMP pathways and plays a role in proliferation and neuronal morphogenesis. The details of the molecular mechanism of neurofibromin action in these processes are still unclear. In this study, immunoprecipitation and proteomics were used to identify novel proteins from rat brain that interact with neurofibromin. Mass spectrometry analysis showed that two proteins, the collapsin response mediator protein-2 (CRMP-2) and propionyl-CoA carboxylase alpha chain (PCCA), associated with neurofibromin. Immunoprecipitation-immunoblotting analysis confirmed the interactions between neurofibromin and CRMP-2 and CRMP-4, but not CRMP-1, in rat brain. CDK5, a kinasemore » that regulates CRMP-2 in axonal outgrowth, was required for the interaction between neurofibromin and CRMP-2. Since both neurofibromin and CRMP proteins are involved in proliferation and axonal morphogenesis, these results suggest that the interaction with CRMPs contributes to the function of neurofibromin in tumorigenesis and neuronal morphogenesis.« less

Living with dementia: communicating with an older person and her family.

PubMed

Long, A; Slevin, E

1999-01-01

This article is designed to explore and examine the key components of communication that emerged during the interactional analysis of a role play that took place in the classroom. The 'actors' were nurses who perceived the interaction to reflect an everyday encounter in a hospital ward. Permission to tape the interaction was sought and given by all persons involved. The principal 'players' in the scenario were: the patient, a 70-year-old-woman who had been admitted with dementia, her son and daughter, and the nurse in charge of the ward. The fundamental dynamics of the use of power and restriction, truth telling, family stress, interpersonal conflict, ageism, sexism, empathy and humanism surfaced during the analysis. The findings show that therapeutic communication should be the foundation on which nursing should stand. The article continues with an exploration of the theoretical frameworks that guided the analysis of interaction and concludes by suggesting tentatively some meaningful implications for nursing practice. It plans to furnish provocative new insights into the sometimes covert communication dynamics occurring within the nurse-patient relationship. Finally, it aims to generate discussion on this little-charted realm of human social interaction.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

PubMed Central

Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

2009-01-01

We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

Synthesis, spectroscopic characterization, crystal structure, DNA interaction study and invitro biological screenings of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid

NASA Astrophysics Data System (ADS)

Sirajuddin, Muhammad; Nooruddin; Ali, Saqib; McKee, Vickie; Khan, Shahan Zeb; Malook, Khan

2015-01-01

The titled compound, 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid was synthesized and characterized by various techniques like elemental analyses, FT-IR, NMR (1H, and 13C) and single crystal X-ray structural analysis. The appearance of the OH peak of the carboxylic acid in the FT-IR and NMR spectra conform the formation of the compound. A good agreement was found between the calculated values of C, H, N and found values in elemental analysis that show the purity of the compound. Protons H2 and H3 are in cis conformation with each other as conformed both from 1H NMR as well as from single crystal X-ray analysis. The molecular structure of the title compound, C10H10NO3Cl, is stabilized by short intramolecular Osbnd H- - -O hydrogen bonds within the molecule. In the crystal structure, intermolecular Nsbnd H- - -O hydrogen bonds link molecules into zigzag chains resulting in a dendrimer like structure. The title compound was screened for biological activities like interaction with DNA, cytotoxicity, antitumor and antioxidant activities. DNA interaction study reveals that the binding mode of interaction of the compound with SS-DNA is intercalative as it results in hypochromism along with significant red shift of 5 nm. It was also found to be effective antioxidant of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and show almost comparable antioxidant activity to that of the standard and known antioxidant, ascorbic acid, at higher concentration. The antitumor activity data of the compound shows that it can be used as potent antitumor agent.

Interaction of Kelvin waves and nonlocality of energy transfer in superfluids

NASA Astrophysics Data System (ADS)

Laurie, Jason; L'Vov, Victor S.; Nazarenko, Sergey; Rudenko, Oleksii

2010-03-01

We argue that the physics of interacting Kelvin Waves (KWs) is highly nontrivial and cannot be understood on the basis of pure dimensional reasoning. A consistent theory of KW turbulence in superfluids should be based upon explicit knowledge of their interactions. To achieve this, we present a detailed calculation and comprehensive analysis of the interaction coefficients for KW turbuelence, thereby, resolving previous mistakes stemming from unaccounted contributions. As a first application of this analysis, we derive a local nonlinear (partial differential) equation. This equation is much simpler for analysis and numerical simulations of KWs than the Biot-Savart equation, and in contrast to the completely integrable local induction approximation (in which the energy exchange between KWs is absent), describes the nonlinear dynamics of KWs. Second, we show that the previously suggested Kozik-Svistunov energy spectrum for KWs, which has often been used in the analysis of experimental and numerical data in superfluid turbulence, is irrelevant, because it is based upon an erroneous assumption of the locality of the energy transfer through scales. Moreover, we demonstrate the weak nonlocality of the inverse cascade spectrum with a constant particle-number flux and find resulting logarithmic corrections to this spectrum.

Risk analysis based on hazards interactions

NASA Astrophysics Data System (ADS)

Rossi, Lauro; Rudari, Roberto; Trasforini, Eva; De Angeli, Silvia; Becker, Joost

2017-04-01

Despite an increasing need for open, transparent, and credible multi-hazard risk assessment methods, models, and tools, the availability of comprehensive risk information needed to inform disaster risk reduction is limited, and the level of interaction across hazards is not systematically analysed. Risk assessment methodologies for different hazards often produce risk metrics that are not comparable. Hazard interactions (consecutive occurrence two or more different events) are generally neglected, resulting in strongly underestimated risk assessment in the most exposed areas. This study presents cases of interaction between different hazards, showing how subsidence can affect coastal and river flood risk (Jakarta and Bandung, Indonesia) or how flood risk is modified after a seismic event (Italy). The analysis of well documented real study cases, based on a combination between Earth Observation and in-situ data, would serve as basis the formalisation of a multi-hazard methodology, identifying gaps and research frontiers. Multi-hazard risk analysis is performed through the RASOR platform (Rapid Analysis and Spatialisation Of Risk). A scenario-driven query system allow users to simulate future scenarios based on existing and assumed conditions, to compare with historical scenarios, and to model multi-hazard risk both before and during an event (www.rasor.eu).

Design of copper DNA intercalators with leishmanicidal activity.

PubMed

Navarro, Maribel; Cisneros-Fajardo, Efrén José; Sierralta, Aníbal; Fernández-Mestre, Mercedes; Silva, Pedro; Arrieche, Dwight; Marchán, Edgar

2003-04-01

The complexes [Cu(dppz)(NO(3))]NO(3) (1), [Cu(dppz)(2)(NO(3))]NO(3) (2), [Cu(dpq)(NO(3))]NO(3) (3), and [Cu(dpq)(2)(NO(3))]NO(3) (4) were synthesized and characterized by elemental analysis, FAB-mass spectrometry, EPR, UV, and IR spectroscopies, and molar conductivity. DNA interaction studies showed that intercalation is an important way of interacting with DNA for these complexes. The biological activity of these copper complexes was evaluated on Leishmania braziliensis promastigotes, and the results showed leishmanicidal activity. Preliminary ultrastructural studies with the most active complex (2) at 1 h revealed parasite swelling and binucleated cells. This finding suggests that the leishmanicidal activity of the copper complexes could be associated with their interaction with the parasitic DNA.

Study on fluid-structure interaction in liquid oxygen feeding pipe systems using finite volume method

NASA Astrophysics Data System (ADS)

Wei, Xin; Sun, Bing

2011-10-01

The fluid-structure interaction may occur in space launch vehicles, which would lead to bad performance of vehicles, damage equipments on vehicles, or even affect astronauts' health. In this paper, analysis on dynamic behavior of liquid oxygen (LOX) feeding pipe system in a large scale launch vehicle is performed, with the effect of fluid-structure interaction (FSI) taken into consideration. The pipe system is simplified as a planar FSI model with Poisson coupling and junction coupling. Numerical tests on pipes between the tank and the pump are solved by the finite volume method. Results show that restrictions weaken the interaction between axial and lateral vibrations. The reasonable results regarding frequencies and modes indicate that the FSI affects substantially the dynamic analysis, and thus highlight the usefulness of the proposed model. This study would provide a reference to the pipe test, as well as facilitate further studies on oscillation suppression.

Insight into the binding mechanism of imipenem to human serum albumin by spectroscopic and computational approaches.

PubMed

Rehman, Md Tabish; Shamsi, Hira; Khan, Asad U

2014-06-02

The mechanism of interaction between imipenem and HSA was investigated by various techniques like fluorescence, UV.vis absorbance, FRET, circular dichroism, urea denaturation, enzyme kinetics, ITC, and molecular docking. We found that imipenem binds to HSA at a high affinity site located in subdomain IIIA (Sudlow's site I) and a low affinity site located in subdomain IIA.IIB. Electrostatic interactions played a vital role along with hydrogen bonding and hydrophobic interactions in stabilizing the imipenem.HSA complex at subdomain IIIA, while only electrostatic and hydrophobic interactions were present at subdomain IIA.IIB. The binding and thermodynamic parameters obtained by ITC showed that the binding of imipenem to HSA was a spontaneous process (ΔGD⁰(D)= -32.31 kJ mol(-1) for high affinity site and ΔGD⁰(D) = -23.02 kJ mol(-1) for low affinity site) with binding constants in the range of 10(4)-10(5) M(-1). Spectroscopic investigation revealed only one binding site of imipenem on HSA (Ka∼10(4) M(-1)). FRET analysis showed that the binding distance between imipenem and HSA (Trp-214) was optimal (r = 4.32 nm) for quenching to occur. Decrease in esterase-like activity of HSA in the presence of imipenem showed that Arg-410 and Tyr-411 of subdomain IIIA (Sudlow's site II) were directly involved in the binding process. CD spectral analysis showed altered conformation of HSA upon imipenem binding. Moreover, the binding of imipenem to subdomain IIIA (Sudlow's site II) of HSA also affected its folding pathway as clear from urea-induced denaturation studies.

Ecological network analysis on global virtual water trade.

PubMed

Yang, Zhifeng; Mao, Xufeng; Zhao, Xu; Chen, Bin

2012-02-07

Global water interdependencies are likely to increase with growing virtual water trade. To address the issues of the indirect effects of water trade through the global economic circulation, we use ecological network analysis (ENA) to shed insight into the complicated system interactions. A global model of virtual water flow among agriculture and livestock production trade in 1995-1999 is also built as the basis for network analysis. Control analysis is used to identify the quantitative control or dependency relations. The utility analysis provides more indicators for describing the mutual relationship between two regions/countries by imitating the interactions in the ecosystem and distinguishes the beneficiary and the contributor of virtual water trade system. Results show control and utility relations can well depict the mutual relation in trade system, and direct observable relations differ from integral ones with indirect interactions considered. This paper offers a new way to depict the interrelations between trade components and can serve as a meaningful start as we continue to use ENA in providing more valuable implications for freshwater study on a global scale.

Negotiating towards a next turn: phonetic resources for 'doing the same'.

PubMed

Sikveland, Rein Ove

2012-03-01

This paper investigates hearers' use of response tokens (back-channels), in maintaining and differentiating their actions. Initial observations suggest that hearers produce a sequence of phonetically similar responses to disengage from the current topic, and dissimilar responses to engage with the current topic. This is studied systematically by combining detailed interactional and phonetic analysis in a collection of naturally-occurring talk in Norwegian. The interactional analysis forms the basis for labeling actions as maintained ('doing the same') and differentiated ('NOT doing the same'), which is then used as a basis for phonetic analysis. The phonetic analysis shows that certain phonetic characteristics, including pitch, loudness, voice quality and articulatory characteristics, are associated with 'doing the same', as different from 'NOT doing the same'. Interactional analysis gives further evidence of how this differentiation is of systematic relevance in the negotiations of a next turn. This paper addresses phonetic variation and variability by focusing on the relationship between sequence and phonetics in the turn-by-turn development of meaning. This has important implications for linguistic/phonetic research, and for the study of back-channels.

Energy component analysis of π interactions.

PubMed

Sherrill, C David

2013-04-16

Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively unimportant. In general, a nitrogen heteroatom contracts the electron density, reducing the magnitude of both the London dispersion and the exchange-repulsion terms, but with an overall net increase in attraction. Finally, using recent advances in SAPT algorithms, researchers can now perform SAPT computations on systems with 200 atoms or more. We discuss a recent study of the intercalation complex of proflavine with a trinucleotide duplex of DNA. Here, London dispersion forces are the strongest contributors to binding, as is typical for π-π interactions. However, the electrostatic terms are larger than usual on a fractional basis, which likely results from the positive charge on the intercalator and its location between two electron-rich base pairs. These cation-π interactions also increase the induction term beyond those of typical noncovalent π-interactions.

Interaction entropy for protein-protein binding

NASA Astrophysics Data System (ADS)

Sun, Zhaoxi; Yan, Yu N.; Yang, Maoyou; Zhang, John Z. H.

2017-03-01

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interaction entropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interaction entropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

An examination of the earthquake behaviour of a retaining wall considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Köktan, Utku; Demir, Gökhan; Kerem Ertek, M.

2017-04-01

The earthquake behavior of retaining walls is commonly calculated with pseudo static approaches based on Mononobe-Okabe method. The seismic ground pressure acting on the retaining wall by the Mononobe-Okabe method does not give a definite idea of the distribution of the seismic ground pressure because it is obtained by balancing the forces acting on the active wedge behind the wall. With this method, wave propagation effects and soil-structure interaction are neglected. The purpose of this study is to examine the earthquake behavior of a retaining wall taking into account the soil-structure interaction. For this purpose, time history seismic analysis of the soil-structure interaction system using finite element method has been carried out considering 3 different soil conditions. Seismic analysis of the soil-structure model was performed according to the earthquake record of "1971, San Fernando Pacoima Dam, 196 degree" existing in the library of MIDAS GTS NX software. The results obtained from the analyses show that the soil-structure interaction is very important for the seismic design of a retaining wall. Keywords: Soil-structure interaction, Finite element model, Retaining wall

Clinicopathologic significance of minichromosome maintenance protein 2 and Tat-interacting protein 30 expression in benign and malignant lesions of the gallbladder.

PubMed

Liu, Dong-cai; Yang, Zhu-lin

2011-11-01

Gallbladder cancers are aggressive tumors with a poor prognosis and high mortality rate. To find specific biological markers for early diagnosis and prognosis and to develop possible alternative treatment strategies, we examined minichromosome maintenance protein 2 (MCM2) and Tat-interacting protein 30 (TIP30) expression in 108 gallbladder adenocarcinomas, 15 gallbladder polyps, 35 chronic cholecystitis tissues, and 46 peritumoral tissues using immunohistochemistry. Expression of MCM2 was significantly higher in adenocarcinomas than in peritumoral tissues (χ² = 8.41; P < .01), adenomatous polyps (χ² = 6.81; P < .01), and chronic cholecystitis (χ² = 21.00; P < .01). In contrast, Tat-interacting protein 30 expression was significantly less in adenocarcinomas than in peritumoral tissues (χ² = 13.26; P < .01), adenomatous polyps (χ² = 4.76; P < .05), and chronic cholecystitis (χ² = 18.93; P < .01). The benign lesions in gallbladder epithelium with positive MCM2 or negative Tat-interacting protein 30 expression showed moderate to severe atypical hyperplasia. Expression of MCM2 and absence of Tat-interacting protein 30 were significantly associated with poor differentiation, large tumor mass, lymph node metastasis, and invasion of adenocarcinoma. Univariate Kaplan-Meier analysis showed that either elevated MCM2 (P = .006) or lowered Tat-interacting protein 30 (P = .006) expression was closely associated with shorter overall survival. Multivariate Cox regression analysis revealed that expression of MCM2 (P = .007) or nonexpression of Tat-interacting protein 30 (P = .009) was an independent predictor of a poor prognosis in adenocarcinoma. Our results suggest that overexpression of MCM2 or loss of expression of Tat-interacting protein 30 is closely related to carcinogenesis, progression, biological behavior, and prognosis of gallbladder adenocarcinoma. Copyright © 2011 Elsevier Inc. All rights reserved.

Changes in divergence-free grid turbulence interacting with a weak spherical shock wave

NASA Astrophysics Data System (ADS)

Kitamura, T.; Nagata, K.; Sakai, Y.; Sasoh, A.; Ito, Y.

2017-06-01

The characteristics of divergence-free grid turbulence interacting with a weak spherical shock wave with a Mach number of 1.05 are experimentally investigated. Turbulence-generating grids are used to generate nearly isotropic, divergence-free turbulence. The turbulent Reynolds number based on the Taylor microscale R eλ and the turbulent Mach number Mt are 49 ≤R eλ≤159 and 0.709 × 1 0-3≤Mt≤2.803 ×1 0-3, respectively. A spherical shock wave is generated by a diaphragmless shock tube. The instantaneous streamwise velocity before and after the interaction is measured by a hot wire probe. The results show that the root-mean-square value of streamwise velocity fluctuations (r.m.s velocity) increases and the streamwise integral length scale decreases after the interaction. The changes in the r.m.s velocity become small with the increase in R eλ and Mt for the same strength of the shock wave. This tendency is similar to that of the streamwise integral length scale. The continuous wavelet analysis shows that high intensity appears mainly in the low-frequency region and positive and negative wavelet coefficients appear periodically in time before the interaction, whereas such high intensity appears in both the low- and high-frequency regions after the interaction. The spectral analysis reveals that the energy at high wavenumbers increases after the interaction. The change in turbulence after the interaction is explained from the viewpoint of the initial turbulent Mach number. It is suggested that the change is more significant for initial divergence-free turbulence than for curl-free turbulence.

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

PubMed Central

Memišević, Vesna; Zavaljevski, Nela; Rajagopala, Seesandra V.; Kwon, Keehwan; Pieper, Rembert; DeShazer, David; Reifman, Jaques; Wallqvist, Anders

2015-01-01

Burkholderia pathogenicity relies on protein virulence factors to control and promote bacterial internalization, survival, and replication within eukaryotic host cells. We recently used yeast two-hybrid (Y2H) screening to identify a small set of novel Burkholderia proteins that were shown to attenuate disease progression in an aerosol infection animal model using the virulent Burkholderia mallei ATCC 23344 strain. Here, we performed an extended analysis of primarily nine B. mallei virulence factors and their interactions with human proteins to map out how the bacteria can influence and alter host processes and pathways. Specifically, we employed topological analyses to assess the connectivity patterns of targeted host proteins, identify modules of pathogen-interacting host proteins linked to processes promoting infectivity, and evaluate the effect of crosstalk among the identified host protein modules. Overall, our analysis showed that the targeted host proteins generally had a large number of interacting partners and interacted with other host proteins that were also targeted by B. mallei proteins. We also introduced a novel Host-Pathogen Interaction Alignment (HPIA) algorithm and used it to explore similarities between host-pathogen interactions of B. mallei, Yersinia pestis, and Salmonella enterica. We inferred putative roles of B. mallei proteins based on the roles of their aligned Y. pestis and S. enterica partners and showed that up to 73% of the predicted roles matched existing annotations. A key insight into Burkholderia pathogenicity derived from these analyses of Y2H host-pathogen interactions is the identification of eukaryotic-specific targeted cellular mechanisms, including the ubiquitination degradation system and the use of the focal adhesion pathway as a fulcrum for transmitting mechanical forces and regulatory signals. This provides the mechanisms to modulate and adapt the host-cell environment for the successful establishment of host infections and intracellular spread. PMID:25738731

Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms.

PubMed

Memišević, Vesna; Zavaljevski, Nela; Rajagopala, Seesandra V; Kwon, Keehwan; Pieper, Rembert; DeShazer, David; Reifman, Jaques; Wallqvist, Anders

2015-03-01

Burkholderia pathogenicity relies on protein virulence factors to control and promote bacterial internalization, survival, and replication within eukaryotic host cells. We recently used yeast two-hybrid (Y2H) screening to identify a small set of novel Burkholderia proteins that were shown to attenuate disease progression in an aerosol infection animal model using the virulent Burkholderia mallei ATCC 23344 strain. Here, we performed an extended analysis of primarily nine B. mallei virulence factors and their interactions with human proteins to map out how the bacteria can influence and alter host processes and pathways. Specifically, we employed topological analyses to assess the connectivity patterns of targeted host proteins, identify modules of pathogen-interacting host proteins linked to processes promoting infectivity, and evaluate the effect of crosstalk among the identified host protein modules. Overall, our analysis showed that the targeted host proteins generally had a large number of interacting partners and interacted with other host proteins that were also targeted by B. mallei proteins. We also introduced a novel Host-Pathogen Interaction Alignment (HPIA) algorithm and used it to explore similarities between host-pathogen interactions of B. mallei, Yersinia pestis, and Salmonella enterica. We inferred putative roles of B. mallei proteins based on the roles of their aligned Y. pestis and S. enterica partners and showed that up to 73% of the predicted roles matched existing annotations. A key insight into Burkholderia pathogenicity derived from these analyses of Y2H host-pathogen interactions is the identification of eukaryotic-specific targeted cellular mechanisms, including the ubiquitination degradation system and the use of the focal adhesion pathway as a fulcrum for transmitting mechanical forces and regulatory signals. This provides the mechanisms to modulate and adapt the host-cell environment for the successful establishment of host infections and intracellular spread.

Quint: An R package for the identification of subgroups of clients who differ in which treatment alternative is best for them.

PubMed

Dusseldorp, Elise; Doove, Lisa; Mechelen, Iven van

2016-06-01

In the analysis of randomized controlled trials (RCTs), treatment effect heterogeneity often occurs, implying differences across (subgroups of) clients in treatment efficacy. This phenomenon is typically referred to as treatment-subgroup interactions. The identification of subgroups of clients, defined in terms of pretreatment characteristics that are involved in a treatment-subgroup interaction, is a methodologically challenging task, especially when many characteristics are available that may interact with treatment and when no comprehensive a priori hypotheses on relevant subgroups are available. A special type of treatment-subgroup interaction occurs if the ranking of treatment alternatives in terms of efficacy differs across subgroups of clients (e.g., for one subgroup treatment A is better than B and for another subgroup treatment B is better than A). These are called qualitative treatment-subgroup interactions and are most important for optimal treatment assignment. The method QUINT (Qualitative INteraction Trees) was recently proposed to induce subgroups involved in such interactions from RCT data. The result of an analysis with QUINT is a binary tree from which treatment assignment criteria can be derived. The implementation of this method, the R package quint, is the topic of this paper. The analysis process is described step-by-step using data from the Breast Cancer Recovery Project, showing the reader all functions included in the package. The output is explained and given a substantive interpretation. Furthermore, an overview is given of the tuning parameters involved in the analysis, along with possible motivational concerns associated with choice alternatives that are available to the user.

Cooperativity of anion⋯π and π⋯π interactions regulates the self-assembly of a series of carbene proligands: Towards quantitative analysis of intermolecular interactions with Hirshfeld surface

NASA Astrophysics Data System (ADS)

Samanta, Tapastaru; Dey, Lingaraj; Dinda, Joydev; Chattopadhyay, Shyamal Kumar; Seth, Saikat Kumar

2014-06-01

The cooperative effect of weak non-covalent forces between anions and electron deficient aromatics by π⋯π stacking of a series of carbene proligands (1-3) have been thoroughly explored by crystallographic studies. Structural analysis revealed that the anion⋯π and π⋯π interactions along with intermolecular hydrogen bonding mutually cooperate to facilitate the assembling of the supramolecular framework. The π⋯π and corresponding anion⋯π interactions have been investigated in the title carbene proligands despite their association with counter ions. The presence of the anion in the vicinity of the π-system leads to the formation of anion⋯π/π⋯π/π⋯anion network for an inductive stabilization of the assemblies. To assess the dimensionality of the supramolecular framework consolidated by cooperative anion⋯π/π⋯π interactions and hydrogen bonding, different substituent effects in the carbene backbone have been considered to tune these interactions. These facts show that the supramolecular framework based on these cooperative weak forces may be robust enough for application in molecular recognition. The investigation of close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented in order to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within each crystal.

Building Interactional Space in an ESL Classroom to Foster Bilingual Identity and Linguistic Repertoires

ERIC Educational Resources Information Center

Welch, Irene

2015-01-01

This article draws on data from a yearlong case study of a Mexican American ESL teacher's practice in a K-5 school in the southeastern United States. The study examines how the teacher established bilingual interactional space in her ESL pullout class consisting of six 9- to 11-year old students of Mexican descent. The analysis shows the ways in…

Using a Complexity Approach to Study the Interpersonal Dynamics in Teacher-­Student Interactions: A Case Study of Two Teachers

ERIC Educational Resources Information Center

Pennings, Helena J. M.

2017-01-01

In the present study, complex dynamic systems theory and interpersonal theory are combined to describe the teacher-student interactions of two teachers with different interpersonal styles. The aim was to show and explain the added value of looking at different steps in the analysis of behavioral time-series data (i.e., observations of teacher and…

Interactive visual exploration and analysis of origin-destination data

NASA Astrophysics Data System (ADS)

Ding, Linfang; Meng, Liqiu; Yang, Jian; Krisp, Jukka M.

2018-05-01

In this paper, we propose a visual analytics approach for the exploration of spatiotemporal interaction patterns of massive origin-destination data. Firstly, we visually query the movement database for data at certain time windows. Secondly, we conduct interactive clustering to allow the users to select input variables/features (e.g., origins, destinations, distance, and duration) and to adjust clustering parameters (e.g. distance threshold). The agglomerative hierarchical clustering method is applied for the multivariate clustering of the origin-destination data. Thirdly, we design a parallel coordinates plot for visualizing the precomputed clusters and for further exploration of interesting clusters. Finally, we propose a gradient line rendering technique to show the spatial and directional distribution of origin-destination clusters on a map view. We implement the visual analytics approach in a web-based interactive environment and apply it to real-world floating car data from Shanghai. The experiment results show the origin/destination hotspots and their spatial interaction patterns. They also demonstrate the effectiveness of our proposed approach.

Molecular tweezers modulate 14-3-3 protein-protein interactions

NASA Astrophysics Data System (ADS)

Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

2013-03-01

Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes.

PubMed

Uchikoga, Nobuyuki; Hirokawa, Takatsugu

2010-05-11

Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG), CaM kinase kinase (CaMKK) and the plasma membrane Ca2+ ATPase pump (PMCA), and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

Numerical modelling of the reinforced concrete influence on a combined system of tunnel support

NASA Astrophysics Data System (ADS)

Grujić, Bojana; Jokanović, Igor; Grujić, Žarko; Zeljić, Dragana

2017-12-01

The paper presents the experimental, laboratory determined rheological-dynamic analysis of the properties of fiber reinforced concrete, which was then utilized to show nonlinear analysis of combined system of tunnel support structure. According to the performed experiments and calculations, different processes of destructive behavior of tunnel lining were simulated in combination with elastic and elastic-plastic behavior of materials taking into account the tunnel loading, the interaction between the fiber reinforced concrete and soil, as well as the interaction between the fiber reinforced concrete and the inner lining of the tunnel.

Kernel canonical-correlation Granger causality for multiple time series

NASA Astrophysics Data System (ADS)

Wu, Guorong; Duan, Xujun; Liao, Wei; Gao, Qing; Chen, Huafu

2011-04-01

Canonical-correlation analysis as a multivariate statistical technique has been applied to multivariate Granger causality analysis to infer information flow in complex systems. It shows unique appeal and great superiority over the traditional vector autoregressive method, due to the simplified procedure that detects causal interaction between multiple time series, and the avoidance of potential model estimation problems. However, it is limited to the linear case. Here, we extend the framework of canonical correlation to include the estimation of multivariate nonlinear Granger causality for drawing inference about directed interaction. Its feasibility and effectiveness are verified on simulated data.

Equilibrium denaturation and preferential interactions of an RNA tetraloop with urea

DOE PAGES

Miner, Jacob Carlson; García, Angel Enrique

2017-02-09

Urea is an important organic cosolute with implications in maintaining osmotic stress in cells and differentially stabilizing ensembles of folded biomolecules. We report an equilibrium study of urea-induced denaturation of a hyperstable RNA tetraloop through unbiased replica exchange molecular dynamics. We find that, in addition to destabilizing the folded state, urea smooths the RNA free energy landscape by destabilizing specific configurations, and forming favorable interactions with RNA nucleobases. A linear concentration-dependence of the free energy (m-value) is observed, in agreement with the results of other RNA hairpins and proteins. Additionally, analysis of the hydrogen-bonding and stacking interactions within RNA primarilymore » show temperature-dependence, while interactions between RNA and urea primarily show concentration-dependence. Lastly, our findings provide valuable insight into the effects of urea on RNA folding and describe the thermodynamics of a basic RNA hairpin as a function of solution chemistry.« less

Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dou, Wei-Dong; Center of Super-Diamond and Advanced Films; Huang, Shu-Ping

2015-10-07

Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc andmore » CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.« less

[Interactive patterns detection in family communication with adolescents].

PubMed

Gimeno Collado, Adelina; Anguera Argilaga, M Teresa; Berzosa Sanz, Amparo; Ramírez Ramírez, Luis

2006-11-01

Interactive patterns detection in family communication with adolescents. Nondistant communication is a relevant indicator for family functionality valuation. The goal of this study is to analyze this communication in order to identify specific kinds of leadership, interaction patterns and the relation between verbal and nonverbal elements in communication. The observational design exposed is an idiographic one, punctual and multidimensional, which uses field format as observation instrument. Participants were seven standardized families made up of both ancestors and an adolescent son or daughter. According to the family models analyzed, results show a predominantly democratic communication style in adults with recurrent support expressions. The sequential analysis incorporates only categories from the emitter point of view, and detects relevant sequences which show symmetric interaction between all three family members. Verbal and nonverbal channels provide complementary information. Depending on adolescents' gender different patterns in behaviour can be identified as well.

Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop with Urea.

PubMed

Miner, Jacob C; García, Angel E

2017-04-20

Urea is an important organic cosolute with implications in maintaining osmotic stress in cells and differentially stabilizing ensembles of folded biomolecules. We report an equilibrium study of urea-induced denaturation of a hyperstable RNA tetraloop through unbiased replica exchange molecular dynamics. We find that, in addition to destabilizing the folded state, urea smooths the RNA free energy landscape by destabilizing specific configurations, and forming favorable interactions with RNA nucleobases. A linear concentration-dependence of the free energy (m-value) is observed, in agreement with the results of other RNA hairpins and proteins. Additionally, analysis of the hydrogen-bonding and stacking interactions within RNA primarily show temperature-dependence, while interactions between RNA and urea primarily show concentration-dependence. Our findings provide valuable insight into the effects of urea on RNA folding and describe the thermodynamics of a basic RNA hairpin as a function of solution chemistry.

Equilibrium denaturation and preferential interactions of an RNA tetraloop with urea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miner, Jacob Carlson; García, Angel Enrique

Urea is an important organic cosolute with implications in maintaining osmotic stress in cells and differentially stabilizing ensembles of folded biomolecules. We report an equilibrium study of urea-induced denaturation of a hyperstable RNA tetraloop through unbiased replica exchange molecular dynamics. We find that, in addition to destabilizing the folded state, urea smooths the RNA free energy landscape by destabilizing specific configurations, and forming favorable interactions with RNA nucleobases. A linear concentration-dependence of the free energy (m-value) is observed, in agreement with the results of other RNA hairpins and proteins. Additionally, analysis of the hydrogen-bonding and stacking interactions within RNA primarilymore » show temperature-dependence, while interactions between RNA and urea primarily show concentration-dependence. Lastly, our findings provide valuable insight into the effects of urea on RNA folding and describe the thermodynamics of a basic RNA hairpin as a function of solution chemistry.« less

Dementia, distributed interactional competence and social membership.

PubMed

Gjernes, Trude; Måseide, Per

2015-12-01

The article analyzes how a person with dementia playing a guitar collaborates with other people in a joint activity. The analysis shows that a person with dementia may gain social membership in a group of persons with and without dementia through social interaction, collaboration, scaffolding and use of material anchors. It shows that interactional skills as well as skills as guitar player are not only products of a mind-body system, but also a product of collaboration between different actors with different participant statuses in a particular situation. The guitar player's mind emerges in the social context of the joint activity and scaffolding. Scaffolding comes from interactive moves from the other participants without dementia and from the guitar. The guitar represents a material anchor. It is a tool for participation, experiences of pleasure, and coping, but it is also a challenge that requires management of face threatening events. Copyright © 2015 Elsevier Inc. All rights reserved.

Creating history: documents and patient participation in nurse-patient interviews.

PubMed

Jones, Aled

2009-09-01

Strongly worded directives regarding the need for increased patient participation during nursing interaction with patients have recently appeared in a range of 'best-practice' documents. This paper focuses on one area of nurse-patient communication, the hospital admission interview, which has been put forward as an ideal arena for increased patient participation. It uses data from a total of 27 admission interviews, extensive periods of participant observation and analysis of nursing records to examine how hospital admission interviews are performed by nurses and patients. Analysis shows that topics discussed during admission closely follow the layout of the admission document which nurses complete during the interview. Whilst it is tempting to describe the admission document as a 'super technological power' in influencing the interaction and restricting patient participation, this analysis attempts a more rounded reading of the data. Findings demonstrate that, whilst opportunities for patient participation were rare, admission interviews are complex interactional episodes that often belie simplistic or prescriptive guidance regarding interaction between nurses and patients. In particular, issue is taken with the lack of contextual and conceptual clarity with which best-practice guidelines are written.

Roles for Agent Assistants in Field Science: Understanding Personal Projects and Collaboration

NASA Technical Reports Server (NTRS)

Clancey, William J.

2003-01-01

A human-centered approach to computer systems design involves reframing analysis in terms of the people interacting with each other. The primary concern is not how people can interact with computers, but how shall we design work systems (facilities, tools, roles, and procedures) to help people pursue their personal projects, as they work independently and collaboratively? Two case studies provide empirical requirements. First, an analysis of astronaut interactions with CapCom on Earth during one traverse of Apollo 17 shows what kind of information was conveyed and what might be automated today. A variety of agent and robotic technologies are proposed that deal with recurrent problems in communication and coordination during the analyzed traverse. Second, an analysis of biologists and a geologist working at Haughton Crater in the High Canadian Arctic reveals how work interactions between people involve independent personal projects, sensitively coordinated for mutual benefit. In both cases, an agent or robotic system's role would be to assist people, rather than collaborating, because today's computer systems lack the identity and purpose that consciousness provides.

Collaborative real-time motion video analysis by human observer and image exploitation algorithms

NASA Astrophysics Data System (ADS)

Hild, Jutta; Krüger, Wolfgang; Brüstle, Stefan; Trantelle, Patrick; Unmüßig, Gabriel; Heinze, Norbert; Peinsipp-Byma, Elisabeth; Beyerer, Jürgen

2015-05-01

Motion video analysis is a challenging task, especially in real-time applications. In most safety and security critical applications, a human observer is an obligatory part of the overall analysis system. Over the last years, substantial progress has been made in the development of automated image exploitation algorithms. Hence, we investigate how the benefits of automated video analysis can be integrated suitably into the current video exploitation systems. In this paper, a system design is introduced which strives to combine both the qualities of the human observer's perception and the automated algorithms, thus aiming to improve the overall performance of a real-time video analysis system. The system design builds on prior work where we showed the benefits for the human observer by means of a user interface which utilizes the human visual focus of attention revealed by the eye gaze direction for interaction with the image exploitation system; eye tracker-based interaction allows much faster, more convenient, and equally precise moving target acquisition in video images than traditional computer mouse selection. The system design also builds on prior work we did on automated target detection, segmentation, and tracking algorithms. Beside the system design, a first pilot study is presented, where we investigated how the participants (all non-experts in video analysis) performed in initializing an object tracking subsystem by selecting a target for tracking. Preliminary results show that the gaze + key press technique is an effective, efficient, and easy to use interaction technique when performing selection operations on moving targets in videos in order to initialize an object tracking function.

Facilitating an L2 Book Club: A Conversation-Analytic Study of Task Management

ERIC Educational Resources Information Center

Ro, Eunseok

2018-01-01

This study employs conversation analysis to examine a facilitator's interactional practices in the post-expansion phase of students' presentations in the context of a book club for second language learning. The analysis shows how the facilitator establishes intersubjectivity with regard to the ongoing task and manages students' task performance.…

Universality and tails of long-range interactions in one dimension

NASA Astrophysics Data System (ADS)

Valiente, Manuel; Öhberg, Patrik

2017-07-01

Long-range interactions and, in particular, two-body potentials with power-law long-distance tails are ubiquitous in nature. For two bosons or fermions in one spatial dimension, the latter case being formally equivalent to three-dimensional s -wave scattering, we show how generic asymptotic interaction tails can be accounted for in the long-distance limit of scattering wave functions. This is made possible by introducing a generalization of the collisional phase shifts to include space dependence. We show that this distance dependence is universal, in that it does not depend on short-distance details of the interaction. The energy dependence is also universal, and is fully determined by the asymptotic tails of the two-body potential. As an important application of our findings, we describe how to eliminate finite-size effects with long-range potentials in the calculation of scattering phase shifts from exact diagonalization. We show that even with moderately small system sizes it is possible to accurately extract phase shifts that would otherwise be plagued with finite-size errors. We also consider multichannel scattering, focusing on the estimation of open channel asymptotic interaction strengths via finite-size analysis.

Techniques of EMG signal analysis: detection, processing, classification and applications

PubMed Central

Hussain, M.S.; Mohd-Yasin, F.

2006-01-01

Electromyography (EMG) signals can be used for clinical/biomedical applications, Evolvable Hardware Chip (EHW) development, and modern human computer interaction. EMG signals acquired from muscles require advanced methods for detection, decomposition, processing, and classification. The purpose of this paper is to illustrate the various methodologies and algorithms for EMG signal analysis to provide efficient and effective ways of understanding the signal and its nature. We further point up some of the hardware implementations using EMG focusing on applications related to prosthetic hand control, grasp recognition, and human computer interaction. A comparison study is also given to show performance of various EMG signal analysis methods. This paper provides researchers a good understanding of EMG signal and its analysis procedures. This knowledge will help them develop more powerful, flexible, and efficient applications. PMID:16799694

Gender Differences in Genetic Risk Profiles for Cardiovascular Disease

PubMed Central

Silander, Kaisa; Saarela, Olli; Ripatti, Samuli; Auro, Kirsi; Karvanen, Juha; Kulathinal, Sangita; Niemelä, Matti; Ellonen, Pekka; Vartiainen, Erkki; Jousilahti, Pekka; Saarela, Janna; Kuulasmaa, Kari; Evans, Alun; Perola, Markus; Salomaa, Veikko; Peltonen, Leena

2008-01-01

Background Cardiovascular disease (CVD) incidence, complications and burden differ markedly between women and men. Although there is variation in the distribution of lifestyle factors between the genders, they do not fully explain the differences in CVD incidence and suggest the existence of gender-specific genetic risk factors. We aimed to estimate whether the genetic risk profiles of coronary heart disease (CHD), ischemic stroke and the composite end-point of CVD differ between the genders. Methodology/Principal Findings We studied in two Finnish population cohorts, using the case-cohort design the association between common variation in 46 candidate genes and CHD, ischemic stroke, CVD, and CVD-related quantitative risk factors. We analyzed men and women jointly and also conducted genotype-gender interaction analysis. Several allelic variants conferred disease risk for men and women jointly, including rs1801020 in coagulation factor XII (HR = 1.31 (1.08–1.60) for CVD, uncorrected p = 0.006 multiplicative model). Variant rs11673407 in the fucosyltransferase 3 gene was strongly associated with waist/hip ratio (uncorrected p = 0.00005) in joint analysis. In interaction analysis we found statistical evidence of variant-gender interaction conferring risk of CHD and CVD: rs3742264 in the carboxypeptidase B2 gene, p(interaction) = 0.009 for CHD, and rs2774279 in the upstream stimulatory factor 1 gene, p(interaction) = 0.007 for CHD and CVD, showed strong association in women but not in men, while rs2069840 in interleukin 6 gene, p(interaction) = 0.004 for CVD, showed strong association in men but not in women (uncorrected p-values). Also, two variants in the selenoprotein S gene conferred risk for ischemic stroke in women, p(interaction) = 0.003 and 0.007. Importantly, we identified a larger number of gender-specific effects for women than for men. Conclusions/Significance A false discovery rate analysis suggests that we may expect half of the reported findings for combined gender analysis to be true positives, while at least third of the reported genotype-gender interaction results are true positives. The asymmetry in positive findings between the genders could imply that genetic risk loci for CVD are more readily detectable in women, while for men they are more confounded by environmental/lifestyle risk factors. The possible differences in genetic risk profiles between the genders should be addressed in more detail in genetic studies of CVD, and more focus on female CVD risk is also warranted in genome-wide association studies. PMID:18974842

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

PubMed

Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

2017-06-01

The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

A Preliminary Examination of the Relationship Between Social Networking Interactions, Internet Use, and Thwarted Belongingness.

PubMed

Moberg, Fallon B; Anestis, Michael D

2015-01-01

Joiner's (2005) interpersonal-psychological theory of suicide hypothesizes that suicidal desire develops in response to the joint presence of thwarted belongingness and perceived burdensomeness. To consider the potential influence of online interactions and behaviors on these outcomes. To address this, we administered an online protocol assessing suicidal desire and online interactions in a sample of 305 undergraduates (83.6% female). We hypothesized negative interactions on social networking sites and a preference for online social interactions would be associated with thwarted belongingness. We also conducted an exploratory analysis examining the associations between Internet usage and perceived burdensomeness. Higher levels of negative interactions on social networking sites, but no other variables, significantly predicted thwarted belongingness. Our exploratory analysis showed that none of our predictors were associated with perceived burdensomeness after accounting for demographics, depression, and thwarted belongingness. Our findings indicate that a general tendency to have negative interactions on social networking sites could possibly impact suicidal desire and that these effects are significant above and beyond depression symptoms. Furthermore, no other aspect of problematic Internet use significantly predicted our outcomes in multivariate analyses, indicating that social networking in particular may have a robust effect on thwarted belongingness.

A Large-Scale Analysis of Variance in Written Language.

PubMed

Johns, Brendan T; Jamieson, Randall K

2018-01-22

The collection of very large text sources has revolutionized the study of natural language, leading to the development of several models of language learning and distributional semantics that extract sophisticated semantic representations of words based on the statistical redundancies contained within natural language (e.g., Griffiths, Steyvers, & Tenenbaum, ; Jones & Mewhort, ; Landauer & Dumais, ; Mikolov, Sutskever, Chen, Corrado, & Dean, ). The models treat knowledge as an interaction of processing mechanisms and the structure of language experience. But language experience is often treated agnostically. We report a distributional semantic analysis that shows written language in fiction books varies appreciably between books from the different genres, books from the same genre, and even books written by the same author. Given that current theories assume that word knowledge reflects an interaction between processing mechanisms and the language environment, the analysis shows the need for the field to engage in a more deliberate consideration and curation of the corpora used in computational studies of natural language processing. Copyright © 2018 Cognitive Science Society, Inc.

Application of clustering methods: Regularized Markov clustering (R-MCL) for analyzing dengue virus similarity

NASA Astrophysics Data System (ADS)

Lestari, D.; Raharjo, D.; Bustamam, A.; Abdillah, B.; Widhianto, W.

2017-07-01

Dengue virus consists of 10 different constituent proteins and are classified into 4 major serotypes (DEN 1 - DEN 4). This study was designed to perform clustering against 30 protein sequences of dengue virus taken from Virus Pathogen Database and Analysis Resource (VIPR) using Regularized Markov Clustering (R-MCL) algorithm and then we analyze the result. By using Python program 3.4, R-MCL algorithm produces 8 clusters with more than one centroid in several clusters. The number of centroid shows the density level of interaction. Protein interactions that are connected in a tissue, form a complex protein that serves as a specific biological process unit. The analysis of result shows the R-MCL clustering produces clusters of dengue virus family based on the similarity role of their constituent protein, regardless of serotypes.

Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis

NASA Astrophysics Data System (ADS)

Tripathi, Shubhandra; Srivastava, Gaurava; Singh, Aastha; Prakasham, A. P.; Negi, Arvind S.; Sharma, Ashok

2018-03-01

Colchicine site inhibitors are microtubule destabilizers having promising role in cancer therapeutics. In the current study, four such indanone derivatives (t1, t9, t14 and t17) with 3,4,5-trimethoxyphenyl fragment (ring A) and showing significant microtubule destabilization property have been explored. The interaction mechanism and conformational modes triggered by binding of these indanone derivatives and combretastatin at colchicine binding site (CBS) of αβ-tubulin dimer were studied using molecular dynamics (MD) simulation, principle component analysis and free energy landscape analysis. In the MD results, t1 showed binding similar to colchicine interacting in the deep hydrophobic core at the CBS. While t9, t14 and t17 showed binding conformation similar to combretastatin, with ring A superficially binding at the CBS. Results demonstrated that ring A played a vital role in binding via hydrophobic interactions and got anchored between the S8 and S9 sheets, H8 helix and T7 loop at the CBS. Conformational modes study revealed that twisting and bending conformational motions (as found in the apo system) were nearly absent in the ligand bound systems. Absence of twisting motion might causes loss of lateral contacts in microtubule, thus promoting microtubule destabilization. This study provides detailed account of microtubule destabilization mechanism by indanone ligands and combretastatin, and would be helpful for designing microtubule destabilizers with higher activity.

Nonequilibrium localization and the interplay between disorder and interactions.

PubMed

Mascarenhas, Eduardo; Bragança, Helena; Drumond, R; Aguiar, M C O; França Santos, M

2016-05-18

We study the nonequilibrium interplay between disorder and interactions in a closed quantum system. We base our analysis on the notion of dynamical state-space localization, calculated via the Loschmidt echo. Although real-space and state-space localization are independent concepts in general, we show that both perspectives may be directly connected through a specific choice of initial states, namely, maximally localized states (ML-states). We show numerically that in the noninteracting case the average echo is found to be monotonically increasing with increasing disorder; these results are in agreement with an analytical evaluation in the single particle case in which the echo is found to be inversely proportional to the localization length. We also show that for interacting systems, the length scale under which equilibration may occur is upper bounded and such bound is smaller the greater the average echo of ML-states. When disorder and interactions, both being localization mechanisms, are simultaneously at play the echo features a non-monotonic behaviour indicating a non-trivial interplay of the two processes. This interplay induces delocalization of the dynamics which is accompanied by delocalization in real-space. This non-monotonic behaviour is also present in the effective integrability which we show by evaluating the gap statistics.

Computational Framework for Analysis of Prey–Prey Associations in Interaction Proteomics Identifies Novel Human Protein–Protein Interactions and Networks

PubMed Central

Saha, Sudipto; Dazard, Jean-Eudes; Xu, Hua; Ewing, Rob M.

2013-01-01

Large-scale protein–protein interaction data sets have been generated for several species including yeast and human and have enabled the identification, quantification, and prediction of cellular molecular networks. Affinity purification-mass spectrometry (AP-MS) is the preeminent methodology for large-scale analysis of protein complexes, performed by immunopurifying a specific “bait” protein and its associated “prey” proteins. The analysis and interpretation of AP-MS data sets is, however, not straightforward. In addition, although yeast AP-MS data sets are relatively comprehensive, current human AP-MS data sets only sparsely cover the human interactome. Here we develop a framework for analysis of AP-MS data sets that addresses the issues of noise, missing data, and sparsity of coverage in the context of a current, real world human AP-MS data set. Our goal is to extend and increase the density of the known human interactome by integrating bait–prey and cocomplexed preys (prey–prey associations) into networks. Our framework incorporates a score for each identified protein, as well as elements of signal processing to improve the confidence of identified protein–protein interactions. We identify many protein networks enriched in known biological processes and functions. In addition, we show that integrated bait–prey and prey–prey interactions can be used to refine network topology and extend known protein networks. PMID:22845868

A National Study Assessing the Teaching and Learning of Introductory Astronomy; Part II: Analysis of Student Demographics

NASA Astrophysics Data System (ADS)

Prather, E. E.; Consiglio, D.; Rudolph, A. L.; Brissenden, G.

2011-09-01

This is the second in a series of reports on a national study of the teaching and learning of astronomy in general education, non-science major, introductory astronomy courses (Astro 101). We report here on the analysis of how individual student characteristics affect student learning in these classes, and whether the demonstrated positive effect of interactive learning strategies on student learning differs based on these characteristics. This analysis was conducted using data from nearly 2000 students enrolled in 69 Astro 101 classes taught across the country. These students completed a 15-question demographic survey, in addition to completing the 26-question Light and Spectroscopy Concept Inventory (LSCI) pre- and post-instruction. The LSCI was used to determine student learning via a normalized gain calculated for each student. A multivariate regression analysis was conducted to determine how ascribed characteristics (personal demographic and family characteristics), obtained characteristics (academic achievement and student major), and the use of interactive learning strategies predict student learning in these classes. The results show dramatic improvement in student learning with increased use of interactive learning strategies even after controlling for individual characteristics. In addition, we find that the positive effects of interactive learning strategies are the same for strong and weak students, men and women, across ethnicities, and regardless of primary language. The research strongly suggests all students benefit from interactive learning strategies.

Finite element for rotor/stator interactive forces in general engine dynamic simulation. Part 1: Development of bearing damper element

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1980-01-01

A general purpose squeeze-film damper interactive force element was developed, coded into a software package (module) and debugged. This software package was applied to nonliner dynamic analyses of some simple rotor systems. Results for pressure distributions show that the long bearing (end sealed) is a stronger bearing as compared to the short bearing as expected. Results of the nonlinear dynamic analysis, using a four degree of freedom simulation model, showed that the orbit of the rotating shaft increases nonlinearity to fill the bearing clearance as the unbalanced weight increases.

Examining reference frame interaction in spatial memory using a distribution analysis.

PubMed

Street, Whitney N; Wang, Ranxiao Frances

2016-02-01

Previous research showed competition among reference frames in spatial attention and language. The present studies developed a new distribution analysis to examine reference frame interactions in spatial memory. Participants viewed virtual arrays of colored pegs and were instructed to remember them either from their own perspective or from the perspective aligned with the rectangular floor. Then they made judgments of relative directions from their respective encoding orientation. Those taking the floor-axis perspective showed systematic bias in the signed errors toward their egocentric perspective, while those taking their own perspective showed no systematic bias, both for random and symmetrical object arrays. The bias toward the egocentric perspective was observed when learning a real symmetric regular object array with strong environmental cues for the aligned axis. These results indicate automatic processing of the self reference while taking the floor-axis perspective but not vice versa, and suggest that research on spatial memory needs to consider the implications of competition effects in reference frame use.

Interactive computer graphics and its role in control system design of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1985-01-01

This paper attempts to show the relevance of interactive computer graphics in the design of control systems to maintain attitude and shape of large space structures to accomplish the required mission objectives. The typical phases of control system design, starting from the physical model such as modeling the dynamics, modal analysis, and control system design methodology are reviewed and the need of the interactive computer graphics is demonstrated. Typical constituent parts of large space structures such as free-free beams and free-free plates are used to demonstrate the complexity of the control system design and the effectiveness of the interactive computer graphics.

Pectins filled with LDH-antimicrobial molecules: preparation, characterization and physical properties.

PubMed

Gorrasi, Giuliana; Bugatti, Valeria; Vittoria, Vittoria

2012-06-05

Nanohybrids of layered double hydroxide (LDH) with intercalated active molecules: benzoate, 2,4-dichlorobenzoate, para-hydroxybenzoate and ortho-hydroxybenzoate, were incorporated into pectins from apples through high energy ball milling in the presence of water. Cast films were obtained and analysed. X-ray diffraction analysis showed a complete destructuration of all nanohybrids in the pectin matrix. Thermogravimetric analysis showed a better thermal resistance of pectin in the presence of fillers, especially para-hydroxybenzoate and ortho-hydroxybenzoate. Mechanical properties showed an improvement of elastic modulus in particular for LDH-para-hydroxybenzoate nanohybrid, due probably to a better interaction between pectin matrix and nanohybrid layers. Barrier properties (sorption and diffusion) to water vapour showed improvement in the dependence on the intercalated active molecule, the best improvement was achieved for composites containing para-hydroxybenzoate molecules, suggesting that the interaction between the filler phase and the polymer plays an important role in sorption and diffusion phenomena. Incorporation of these active molecules gave antimicrobial properties to the composite films giving opportunities in the field of active packaging. Copyright © 2012 Elsevier Ltd. All rights reserved.

Automated Video Analysis of Non-verbal Communication in a Medical Setting

PubMed Central

Hart, Yuval; Czerniak, Efrat; Karnieli-Miller, Orit; Mayo, Avraham E.; Ziv, Amitai; Biegon, Anat; Citron, Atay; Alon, Uri

2016-01-01

Non-verbal communication plays a significant role in establishing good rapport between physicians and patients and may influence aspects of patient health outcomes. It is therefore important to analyze non-verbal communication in medical settings. Current approaches to measure non-verbal interactions in medicine employ coding by human raters. Such tools are labor intensive and hence limit the scale of possible studies. Here, we present an automated video analysis tool for non-verbal interactions in a medical setting. We test the tool using videos of subjects that interact with an actor portraying a doctor. The actor interviews the subjects performing one of two scripted scenarios of interviewing the subjects: in one scenario the actor showed minimal engagement with the subject. The second scenario included active listening by the doctor and attentiveness to the subject. We analyze the cross correlation in total kinetic energy of the two people in the dyad, and also characterize the frequency spectrum of their motion. We find large differences in interpersonal motion synchrony and entrainment between the two performance scenarios. The active listening scenario shows more synchrony and more symmetric followership than the other scenario. Moreover, the active listening scenario shows more high-frequency motion termed jitter that has been recently suggested to be a marker of followership. The present approach may be useful for analyzing physician-patient interactions in terms of synchrony and dominance in a range of medical settings. PMID:27602002

A laser scanning confocal imaging-surface plasmon resonance system application in real time detection of antibody-antigen interaction

NASA Astrophysics Data System (ADS)

Zhang, H. Y.; Yang, L. Q.; Liu, W. M.

2011-12-01

The laser scanning confocal microscope (LSCM) offers several advantages over conventional optical microscopy, but most LSCM work is qualitative analysis and it is very hard to achieve quantitative detection directly with the changing of the fluorescent intensity. A new real time sensor system for the antibody-antigen interaction detection was built integrating with a LSCM and a wavelength-dependent surface plasmon resonance (SPR) sensor. The system was applied to detect the bonding process of human IgG and fluorescent-labeled affinity purified antibody in real time. The fluorescence images changing is well with that of SPR wavelengths in real time, and the trend of the resonance wavelength shift with the concentrations of antibody is similar to that of the fluorescent intensity changing. The results show that SPR makes up the short of quantificational analysis with LSCM with the high spatial resolution. The sensor system shows the merits of the of the LSCM and SPR synergetic application, which are of great importance for practical application in biosensor and life science for interesting local interaction.

Haemophilus parasuis encodes two functional cytolethal distending toxins: CdtC contains an atypical cholesterol recognition/interaction region.

PubMed

Zhou, Mingguang; Zhang, Qiang; Zhao, Jianping; Jin, Meilin

2012-01-01

Haemophilus parasuis is the causative agent of Glässer's disease of pigs, a disease associated with fibrinous polyserositis, polyarthritis and meningitis. We report here H. parasuis encodes two copies of cytolethal distending toxins (Cdts), which these two Cdts showed the uniform toxin activity in vitro. We demonstrate that three Cdt peptides can form an active tripartite holotoxin that exhibits maximum cellular toxicity, and CdtA and CdtB form a more active toxin than CdtB and CdtC. Moreover, the cellular toxicity is associated with the binding of Cdt subunits to cells. Further analysis indicates that CdtC subunit contains an atypical cholesterol recognition/interaction amino acid consensus (CRAC) region. The mutation of CRAC site resulted in decreased cell toxicity. Finally, western blot analysis show all the 15 H. parasuis reference strains and 109 clinical isolates expressed CdtB subunit, indicating that Cdt is a conservative putative virulence factor for H. parasuis. This is the first report of the molecular and cellular basis of Cdt host interactions in H. parasuis.

Analysis and modeling of heat-labile enterotoxins of Escherichia coli suggests a novel space with insights into receptor preference.

PubMed

Krishna Raja, M; Ghosh, Asit Ranjan; Vino, S; Sajitha Lulu, S

2015-01-01

Features of heat-labile enterotoxins of Escherichia coli which make them fit to use as novel receptors for antidiarrheals are not completely explored. Data-set of 14 different serovars of enterotoxigenic Escherichia coli producing heat-labile toxins were taken from NCBI Genbank database and used in the study. Sequence analysis showed mutations in different subunits and also at their interface residues. As these toxins lack crystallography structures, homology modeling using Modeller 9.11 led to the structural approximation for the E. coli producing heat-labile toxins. Interaction of modeled toxin subunits with proanthocyanidin, an antidiarrheal showed several strong hydrogen bonding interactions at the cost of minimized energy. The hits were subsequently characterized by molecular dynamics simulation studies to monitor their binding stabilities. This study looks into novel space where the ligand can choose the receptor preference not as a whole but as an individual subunit. Mutation at interface residues and interaction among subunits along with the binding of ligand to individual subunits would help to design a non-toxic labile toxin and also to improve the therapeutics.

Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome.

PubMed

Chang, Dong W; Hayashi, Shinichi; Gharib, Sina A; Vaisar, Tomas; King, S Trevor; Tsuchiya, Mitsuhiro; Ruzinski, John T; Park, David R; Matute-Bello, Gustavo; Wurfel, Mark M; Bumgarner, Roger; Heinecke, Jay W; Martin, Thomas R

2008-10-01

Acute lung injury causes complex changes in protein expression in the lungs. Whereas most prior studies focused on single proteins, newer methods allowing the simultaneous study of many proteins could lead to a better understanding of pathogenesis and new targets for treatment. The purpose of this study was to examine the changes in protein expression in the bronchoalveolar lavage fluid (BALF) of patients during the course of the acute respiratory distress syndrome (ARDS). Using two-dimensional difference gel electrophoresis (DIGE), the expression of proteins in the BALF from patients on Days 1 (n = 7), 3 (n = 8), and 7 (n = 5) of ARDS were compared with findings in normal volunteers (n = 9). The patterns of protein expression were analyzed using principal component analysis (PCA). Biological processes that were enriched in the BALF proteins of patients with ARDS were identified using Gene Ontology (GO) analysis. Protein networks that model the protein interactions in the BALF were generated using Ingenuity Pathway Analysis. An average of 991 protein spots were detected using DIGE. Of these, 80 protein spots, representing 37 unique proteins in all of the fluids, were identified using mass spectrometry. PCA confirmed important differences between the proteins in the ARDS and normal samples. GO analysis showed that these differences are due to the enrichment of proteins involved in inflammation, infection, and injury. The protein network analysis showed that the protein interactions in ARDS are complex and redundant, and revealed unexpected central components in the protein networks. Proteomics and protein network analysis reveals the complex nature of lung protein interactions in ARDS. The results provide new insights about protein networks in injured lungs, and identify novel mediators that are likely to be involved in the pathogenesis and progression of acute lung injury.

Interaction between early-life stress and FKBP5 gene variants in major depressive disorder and post-traumatic stress disorder: A systematic review and meta-analysis.

PubMed

Wang, Qingzhong; Shelton, Richard C; Dwivedi, Yogesh

2018-01-01

Gene-environment interaction contributes to the risks of psychiatric disorders. Interactions between FKBP5 gene variants and early-life stress may enhance the risk not only for mood disorder, but also for a number of other behavioral phenotypes. The aim of the present study was to review and conduct a meta-analysis on the results from published studies examining interaction between FKBP5 gene variants and early-life stress and their associations with stress-related disorders such as major depression and PTSD. A literature search was conducted using PsychINFO and PubMed databases until May 2017. A total of 14 studies with a pooled total of 15109 participants met the inclusion criteria, the results of which were combined and a meta-analysis was performed using the differences in correlations as the effect measure. Based on literature, rs1360780, rs3800373, and rs9470080 SNPs were selected within the FKBP5 gene and systematic review was conducted. Based on the Comprehensive Meta-Analysis software, no publication bias was detected. Sensitivity analysis and credibility of meta-analysis results also indicated that the analyses were stable. The meta-analysis showed that individuals who carry T allele of rs1360780, C-allele of rs3800373 or T-allele of rs9470080 exposed to early-life trauma had higher risks for depression or PTSD. The effects of ethnicity, age, sex, and different stress measures were not examined due to limited sample size. These results provide strong evidence of interactions between FKBP5 genotypes and early-life stress, which could pose a significant risk factor for stress-associated disorders such as major depression and PTSD. Copyright © 2017 Elsevier B.V. All rights reserved.

Cloning and characterization of carboxyl terminus of heat shock cognate 70-interacting protein gene from the silkworm, Bombyx mori.

PubMed

Ohsawa, Takeshi; Fujimoto, Shota; Tsunakawa, Akane; Shibano, Yuka; Kawasaki, Hideki; Iwanaga, Masashi

2016-11-01

Carboxyl terminus of heat shock cognate 70-interacting protein (CHIP) is an evolutionarily conserved E3 ubiquitin ligase across different eukaryotic species and is known to play a key role in protein quality control. CHIP has two distinct functional domains, an N-terminal tetratricopeptide repeat (TPR) and a C-terminal U-box domain, which are required for the ubiquitination of numerous labile client proteins that are chaperoned by heat shock proteins (HSPs) and heat shock cognate proteins (HSCs). During our screen for CHIP-like proteins in the Bombyx mori databases, we found a novel silkworm gene, Bombyx mori CHIP. Phylogenetic analysis showed that BmCHIP belongs to Lepidopteran lineages. Quantitative reverse transcription-PCR analysis indicated that BmCHIP was relatively highly expressed in the gonad and fat body. A pull-down experiment and auto-ubiquitination assay showed that BmCHIP interacted with BmHSC70 and had E3 ligase activity. Additionally, immunohistochemical analysis revealed that BmCHIP was partially co-localized with ubiquitin in BmN4 cells. These data support that BmCHIP plays an important role in the ubiquitin proteasome system as an E3 ubiquitin ligase in B. mori. Copyright © 2016 Elsevier Inc. All rights reserved.

Multi-variant study of obesity risk genes in African Americans: The Jackson Heart Study.

PubMed

Liu, Shijian; Wilson, James G; Jiang, Fan; Griswold, Michael; Correa, Adolfo; Mei, Hao

2016-11-30

Genome-wide association study (GWAS) has been successful in identifying obesity risk genes by single-variant association analysis. For this study, we designed steps of analysis strategy and aimed to identify multi-variant effects on obesity risk among candidate genes. Our analyses were focused on 2137 African American participants with body mass index measured in the Jackson Heart Study and 657 common single nucleotide polymorphisms (SNPs) genotyped at 8 GWAS-identified obesity risk genes. Single-variant association test showed that no SNPs reached significance after multiple testing adjustment. The following gene-gene interaction analysis, which was focused on SNPs with unadjusted p-value<0.10, identified 6 significant multi-variant associations. Logistic regression showed that SNPs in these associations did not have significant linear interactions; examination of genetic risk score evidenced that 4 multi-variant associations had significant additive effects of risk SNPs; and haplotype association test presented that all multi-variant associations contained one or several combinations of particular alleles or haplotypes, associated with increased obesity risk. Our study evidenced that obesity risk genes generated multi-variant effects, which can be additive or non-linear interactions, and multi-variant study is an important supplement to existing GWAS for understanding genetic effects of obesity risk genes. Copyright © 2016 Elsevier B.V. All rights reserved.

An analysis of commitment strategies in planning: The details

NASA Technical Reports Server (NTRS)

Minton, Steven; Bresina, John; Drummond, Mark; Philips, Andrew B.

1991-01-01

We compare the utility of different commitment strategies in planning. Under a 'least commitment strategy', plans are represented as partial orders and operators are ordered only when interactions are detected. We investigate claims of the inherent advantages of planning with partial orders, as compared to planning with total orders. By focusing our analysis on the issue of operator ordering commitment, we are able to carry out a rigorous comparative analysis of two planners. We show that partial-order planning can be more efficient than total-order planning, but we also show that this is not necessarily so.

Voltage-spike analysis for a free-running parallel inverter

NASA Technical Reports Server (NTRS)

Lee, F. C. Y.; Wilson, T. G.

1974-01-01

Unwanted and sometimes damaging high-amplitude voltage spikes occur during each half cycle in many transistor saturable-core inverters at the moment when the core saturates and the transistors switch. The analysis shows that spikes are an intrinsic characteristic of certain types of inverters even with negligible leakage inductance and purely resistive load. The small but unavoidable after-saturation inductance of the saturable-core transformer plays an essential role in creating these undesired thigh-voltage spikes. State-plane analysis provides insight into the complex interaction between core and transistors, and shows the circuit parameters upon which the magnitude of these spikes depends.

Lessons from life: Learning from exhibits, animals and interaction in a museum

NASA Astrophysics Data System (ADS)

Goldowsky, Alexander Noah

This study examines the effect of interaction on visitor behavior at a public aquarium, experimentally comparing one exhibit under interactive and noninteractive conditions. A quantitative analysis showed that the time visitor groups spent in the study area significantly increased in the interactive condition (median 73 vs. 32 seconds). Further, this effect extended only to those groups within the interactive condition in which at least one member operated the exhibit (median 102 vs. 36 seconds). Both median times and survival curves are compared, and the analysis controlled for group size, age and sex ratios, visitor density, queuing time, and animal activity. Qualitative analyses focused on visitors' spontaneous conversation at the exhibit. Interactive visitors were found to engage in more in-depth exploration, including conducting informal experiments. The amount of discussion was found to correlate with stay time (r = 0.47). Visitor discussion centered on the exhibit, with frequent observations of penguin behavior. Greater enthusiasm was observed for interactive visitors, and coding showed interactive visitors laughed more frequently, and were significantly more likely to speculate on the penguins' reactions and motivations for behaviors. The experimental setup included a control condition consisting of a typical aquarium exhibit, including live penguins, naturalistic habitat, and graphics. The interactive condition added a device designed to mediate a two-way interaction between the visitors and penguins: visitors moved a light beam across the bottom of the pool. The penguins, intern, chased the light. This exhibit was designed both to benefit visitors and to serve as behavioral enrichment for the penguins. A third condition employed an automatically moving light, which elicited similar penguin behaviors, but without allowing visitor interaction. Videotaped data was analyzed for 301 visitor groups (756 individuals). A supplemental study employed video recall interviews. The study concludes that interaction is fundamental to the way in which humans investigate their world, and should play a major role in shaping the educational design of zoo and aquarium exhibits. Interactivity can encourage investigation and experimentation with phenomena, increase exhibit feedback, enhance the psychological dimensions of choice and control, and support visitors' desire for relationships with animals.

Mapping regions of Epstein-Barr virus (EBV) glycoprotein B (gB) important for fusion function with gH/gL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plate, Aileen E.; Reimer, Jessica J.; Jardetzky, Theodore S.

Glycoproteins gB and gH/gL are required for entry of Epstein-Barr virus (EBV) into cells, but the role of each glycoprotein and how they function together to mediate fusion is unclear. Analysis of the functional homology of gB from the closely related primate gammaherpesvirus, rhesus lymphocryptovirus (Rh-LCV), showed that EBV gB could not complement Rh gB due to a species-specific dependence between gB and gL. To map domains of gB required for this interaction, we constructed a panel of EBV/Rh gB chimeric proteins. Analysis showed that insertion of Rh gB from residues 456 to 807 restored fusion function of EBV gBmore » with Rh gH/gL, suggesting this region of gB is important for interaction with gH/gL. Split YFP bimolecular complementation (BiFC) provided evidence of an interaction between EBV gB and gH/gL. Together, our results suggest the importance of a gB-gH/gL interaction in EBV-mediated fusion with B cells requiring the region of EBV gB from 456 to 807.« less

Insulating phase in Sr2IrO4: An investigation using critical analysis and magnetocaloric effect

NASA Astrophysics Data System (ADS)

Bhatti, Imtiaz Noor; Pramanik, A. K.

2017-01-01

The nature of insulating phase in 5d based Sr2IrO4 is quite debated as the theoretical as well as experimental investigations have put forward evidences in favor of both magnetically driven Slater-type and interaction driven Mott-type insulator. To understand this insulating behavior, we have investigated the nature of magnetic state in Sr2IrO4 through studying critical exponents, low temperature thermal demagnetization and magnetocaloric effect. The estimated critical exponents do not exactly match with any universality class, however, the values obey the scaling behavior. The exponent values suggest that spin interaction in present material is close to mean-field model. The analysis of low temperature thermal demagnetization data, however, shows dual presence of localized- and itinerant-type of magnetic interaction. Moreover, field dependent change in magnetic entropy indicates magnetic interaction is close to mean-field type. While this material shows an insulating behavior across the magnetic transition, yet a distinct change in slope in resistivity is observed around Tc. We infer that though the insulating phase in Sr2IrO4 is more close to be Slater-type but the simultaneous presence of both Slater- and Mott-type is the likely scenario for this material.

Social support and social interaction ties on internet addiction: integrating online and offline contexts.

PubMed

Wang, Edward Shih-Tse; Wang, Michael Chih-Hung

2013-11-01

This study explores the relationship between social support and social interaction ties on Internet addiction by integrating both online and offline social encounters. A total of 1,642 members of online social communities participated in this research, for which structural equation modeling was used for analysis. The findings show that social support is positively associated with social interaction ties in both online and offline contexts. In addition, online social support and online social interaction ties are positively associated with Internet addiction, whereas offline social support and social interaction ties on Internet addiction are negatively associated. This finding has important implications not only for understanding the cause of Internet addiction but also for understanding the diminishing Internet addiction due to social support and social interaction ties.

Synthesis, structure, computational and in-silico anticancer studies of N,N-diethyl-N‧-palmitoylthiourea

NASA Astrophysics Data System (ADS)

Asegbeloyin, Jonnie Niyi; Oyeka, Ebube Evaristus; Okpareke, Obinna; Ibezim, Akachukwu

2018-02-01

A new potential ONS donor ligand N,N-diethyl-N‧-palmitoylthiourea (PACDEA) with the molecular formular C21H42N2OS has been synthesized and characterized by ESI-MS, UV, FTIR 1H and 13C NMR spectroscopy and single X-ray crystallography. The asymmetric molecules crystallized in the centrosymmetric structure of monoclinic crystal system with space group P21/c. In the crystal structure of the compound, molecules are linked in a continuous chain by intermolecular Nsbnd H⋯Odbnd C hydrogen bonds, which stabilized the crystal structure. The palmitoyl moiety and N (2)-ethyl group lie on a plane, while the thiocarbonyl moiety is twisted and lying othorgonal to the plane. Non-covalent interaction (NCI) analysis on the hydrogen bonded solid state structure of the molecule revealed the presence of a significant number of non-covalent interactions including intermolecular hydrogen bonding interactions, Csbnd Hsbnd -lone pair interactions, weak Van der Waals interactions, and steric/ring closure interactions. The NCI analysis also showed the presence of intramolecular stabilizing Csbnd H⋯Odbnd C and Csbnd H⋯Sdbnd C interactions. Docking simulation revealed that the compound interacted favourably with ten selected validated anticancer drug targets, which is an indication that the compound could possess some anticancer properties.

Two-dimensional nonlinear finite element analysis of well damage due to reservoir compaction, well-to-well interactions, and localization on weak layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hilbert, L.B. Jr.; Fredrich, J.T.; Bruno, M.S.

1996-05-01

In this paper the authors present the results of a coupled nonlinear finite element geomechanics model for reservoir compaction and well-to-well interactions for the high-porosity, low strength diatomite reservoirs of the Belridge field near Bakersfield, California. They show that well damage and failures can occur under the action of two distinct mechanisms: shear deformations induced by pore compaction, and subsidence, and shear deformations due to well-to-well interactions during production or water injection. They show such casting damage or failure can be localized to weak layers that slide or slip under shear due to subsidence. The magnitude of shear displacements andmore » surface subsidence agree with field observations.« less

Epistasis Analysis for Estrogen Metabolic and Signaling Pathway Genes on Young Ischemic Stroke Patients

PubMed Central

Hsieh, Yi-Chen; Jeng, Jiann-Shing; Lin, Huey-Juan; Hu, Chaur-Jong; Yu, Chia-Chen; Lien, Li-Ming; Peng, Giia-Sheun; Chen, Chin-I; Tang, Sung-Chun; Chi, Nai-Fang; Tseng, Hung-Pin; Chern, Chang-Ming; Hsieh, Fang-I; Bai, Chyi-Huey; Chen, Yi-Rhu; Chiou, Hung-Yi; Jeng, Jiann-Shing; Tang, Sung-Chun; Yeh, Shin-Joe; Tsai, Li-Kai; Kong, Shin; Lien, Li-Ming; Chiu, Hou-Chang; Chen, Wei-Hung; Bai, Chyi-Huey; Huang, Tzu-Hsuan; Chi-Ieong, Lau; Wu, Ya-Ying; Yuan, Rey-Yue; Hu, Chaur-Jong; Sheu, Jau- Jiuan; Yu, Jia-Ming; Ho, Chun-Sum; Chen, Chin-I; Sung, Jia-Ying; Weng, Hsing-Yu; Han, Yu-Hsuan; Huang, Chun-Ping; Chung, Wen-Ting; Ke, Der-Shin; Lin, Huey-Juan; Chang, Chia-Yu; Yeh, Poh-Shiow; Lin, Kao-Chang; Cheng, Tain-Junn; Chou, Chih-Ho; Yang, Chun-Ming; Peng, Giia-Sheun; Lin, Jiann-Chyun; Hsu, Yaw-Don; Denq, Jong-Chyou; Lee, Jiunn-Tay; Hsu, Chang-Hung; Lin, Chun-Chieh; Yen, Che-Hung; Cheng, Chun-An; Sung, Yueh-Feng; Chen, Yuan-Liang; Lien, Ming-Tung; Chou, Chung-Hsing; Liu, Chia-Chen; Yang, Fu-Chi; Wu, Yi-Chung; Tso, An-Chen; Lai, Yu- Hua; Chiang, Chun-I; Tsai, Chia-Kuang; Liu, Meng-Ta; Lin, Ying-Che; Hsu, Yu-Chuan; Chen, Chih-Hung; Sung, Pi-Shan; Chern, Chang-Ming; Hu, Han-Hwa; Wong, Wen-Jang; Luk, Yun-On; Hsu, Li-Chi; Chung, Chih-Ping; Tseng, Hung-Pin; Liu, Chin-Hsiung; Lin, Chun-Liang; Lin, Hung-Chih; Hu, Chaur-Jong

2012-01-01

Background Endogenous estrogens play an important role in the overall cardiocirculatory system. However, there are no studies exploring the hormone metabolism and signaling pathway genes together on ischemic stroke, including sulfotransferase family 1E (SULT1E1), catechol-O-methyl-transferase (COMT), and estrogen receptor α (ESR1). Methods A case-control study was conducted on 305 young ischemic stroke subjects aged ≦ 50 years and 309 age-matched healthy controls. SULT1E1 -64G/A, COMT Val158Met, ESR1 c.454−397 T/C and c.454−351 A/G genes were genotyped and compared between cases and controls to identify single nucleotide polymorphisms associated with ischemic stroke susceptibility. Gene-gene interaction effects were analyzed using entropy-based multifactor dimensionality reduction (MDR), classification and regression tree (CART), and traditional multiple regression models. Results COMT Val158Met polymorphism showed a significant association with susceptibility of young ischemic stroke among females. There was a two-way interaction between SULT1E1 -64G/A and COMT Val158Met in both MDR and CART analysis. The logistic regression model also showed there was a significant interaction effect between SULT1E1 -64G/A and COMT Val158Met on ischemic stroke of the young (P for interaction = 0.0171). We further found that lower estradiol level could increase the risk of young ischemic stroke for those who carry either SULT1E1 or COMT risk genotypes, showing a significant interaction effect (P for interaction = 0.0174). Conclusions Our findings support that a significant epistasis effect exists among estrogen metabolic and signaling pathway genes and gene-environment interactions on young ischemic stroke subjects. PMID:23112845

Linkage and association analysis of obesity traits reveals novel loci and interactions with dietary n-3 fatty acids in an Alaska Native (Yup’ik) population

PubMed Central

Vaughan, Laura Kelly; Wiener, Howard W.; Aslibekyan, Stella; Allison, David B.; Havel, Peter J.; Stanhope, Kimber L.; O’Brien, Diane M.; Hopkins, Scarlett E.; Lemas, Dominick J.; Boyer, Bert B.; Tiwari, Hemant K.

2015-01-01

Objective To identify novel genetic markers of obesity-related traits and to identify gene-diet interactions with n-3 polyunsaturated fatty acid (n-3 PUFA) intake in Yup’ik people. Material and Methods We measured body composition, plasma adipokines and ghrelin in 982 participants enrolled in the Center for Alaska Native Health Research (CANHR) Study. We conducted a genome-wide SNP linkage scan and targeted association analysis, fitting additional models to investigate putative gene-diet interactions. Finally, we performed bioinformatic analysis to uncover likely candidate genes within the identified linkage peaks. Results We observed evidence of linkage for all obesity-related traits, replicating previous results and identifying novel regions of interest for adiponectin (10q26.13-2) and thigh circumference (8q21.11-13). Bioinformatic analysis revealed DOCK1, PTPRE (10q26.13-2) and FABP4 (8q21.11-13) as putative candidate genes in the newly identified regions. Targeted SNP analysis under the linkage peaks identified associations between three SNPs and obesity-related traits: rs1007750 on chromosome 8 and thigh circumference (P=0.0005), rs878953 on chromosome 5 and thigh skinfold (P=0.0004), and rs1596854 on chromosome 11 for waist circumference (P=0.0003). Finally, we showed that n-3 PUFA modified the association between obesity related traits and two additional variants (rs2048417 on chromosome 3 for adiponectin, P for interaction=0.0006 and rs730414 on chromosome 11 for percentage body fat, P for interaction=0.0004). Conclusions This study presents evidence of novel genomic regions and gene-diet interactions that may contribute to the pathophysiology of obesity-related traits among Yup’ik people. PMID:25772781

Linkage and association analysis of obesity traits reveals novel loci and interactions with dietary n-3 fatty acids in an Alaska Native (Yup'ik) population.

PubMed

Vaughan, Laura Kelly; Wiener, Howard W; Aslibekyan, Stella; Allison, David B; Havel, Peter J; Stanhope, Kimber L; O'Brien, Diane M; Hopkins, Scarlett E; Lemas, Dominick J; Boyer, Bert B; Tiwari, Hemant K

2015-06-01

To identify novel genetic markers of obesity-related traits and to identify gene-diet interactions with n-3 polyunsaturated fatty acid (n-3 PUFA) intake in Yup'ik people. We measured body composition, plasma adipokines and ghrelin in 982 participants enrolled in the Center for Alaska Native Health Research (CANHR) Study. We conducted a genome-wide SNP linkage scan and targeted association analysis, fitting additional models to investigate putative gene-diet interactions. Finally, we performed bioinformatic analysis to uncover likely candidate genes within the identified linkage peaks. We observed evidence of linkage for all obesity-related traits, replicating previous results and identifying novel regions of interest for adiponectin (10q26.13-2) and thigh circumference (8q21.11-13). Bioinformatic analysis revealed DOCK1, PTPRE (10q26.13-2) and FABP4 (8q21.11-13) as putative candidate genes in the newly identified regions. Targeted SNP analysis under the linkage peaks identified associations between three SNPs and obesity-related traits: rs1007750 on chromosome 8 and thigh circumference (P=0.0005), rs878953 on chromosome 5 and thigh skinfold (P=0.0004), and rs1596854 on chromosome 11 for waist circumference (P=0.0003). Finally, we showed that n-3 PUFA modified the association between obesity related traits and two additional variants (rs2048417 on chromosome 3 for adiponectin, P for interaction=0.0006 and rs730414 on chromosome 11 for percentage body fat, P for interaction=0.0004). This study presents evidence of novel genomic regions and gene-diet interactions that may contribute to the pathophysiology of obesity-related traits among Yup'ik people. Copyright © 2015 Elsevier Inc. All rights reserved.

Universal Power Law Governing Pedestrian Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karamouzas, Ioannis; Skinner, Brian; Guy, Stephen J.

2014-12-01

Human crowds often bear a striking resemblance to interacting particle systems, and this has prompted many researchers to describe pedestrian dynamics in terms of interaction forces and potential energies. The correct quantitative form of this interaction, however, has remained an open question. Here, we introduce a novel statistical-mechanical approach to directly measure the interaction energy between pedestrians. This analysis, when applied to a large collection of human motion data, reveals a simple power-law interaction that is based not on the physical separation between pedestrians but on their projected time to a potential future collision, and is therefore fundamentally anticipatory inmore » nature. Remarkably, this simple law is able to describe human interactions across a wide variety of situations, speeds, and densities. We further show, through simulations, that the interaction law we identify is sufficient to reproduce many known crowd phenomena.« less

Theoretical study of interactions between cysteine and perfluoropropanoic acid in gas and aqueous phase

NASA Astrophysics Data System (ADS)

Holmes, Tiffani M.; Doskocz, Jacek; Wright, Terrance; Hill, Glake A.

The interaction of perfluoropropanoic acid (PFPA) with the amino acid cysteine was investigated using density functional theory. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur-containing amino acids. We present conformational analysis of the interactions of PFPA, a small model of perfluorooctanoic acid, with the sulfur-containing amino acid which occur by the process of hydrogen bonding, in which the hydrogen of the sulfhydryl group interacts with the carboxyl oxygen, and the amino nitrogen forms a hydrogen bond with the hydrogen of the bond OH group of the fluorinated alkyl. We also show in our structures a recently characterized weak nonbonded interaction between divalent sulfur and a main chain carboxyl oxygen in proteins. B3LYP calculated free energies and interaction energies predict low-energy, high-interaction conformations for complex systems of perfluorinated fatty acid interactions with cysteine.

Position space analysis of the AdS (in)stability problem

NASA Astrophysics Data System (ADS)

Dimitrakopoulos, Fotios V.; Freivogel, Ben; Lippert, Matthew; Yang, I.-Sheng

2015-08-01

We investigate whether arbitrarily small perturbations in global AdS space are generically unstable and collapse into black holes on the time scale set by gravitational interactions. We argue that current evidence, combined with our analysis, strongly suggests that a set of nonzero measure in the space of initial conditions does not collapse on this time scale. We perform an analysis in position space to study this puzzle, and our formalism allows us to directly study the vanishing-amplitude limit. We show that gravitational self-interaction leads to tidal deformations which are equally likely to focus or defocus energy, and we sketch the phase diagram accordingly. We also clarify the connection between gravitational evolution in global AdS and holographic thermalization.

Interactions between cadmium and decabrominated diphenyl ether on blood cells count in rats-Multiple factorial regression analysis.

PubMed

Curcic, Marijana; Buha, Aleksandra; Stankovic, Sanja; Milovanovic, Vesna; Bulat, Zorica; Đukić-Ćosić, Danijela; Antonijević, Evica; Vučinić, Slavica; Matović, Vesna; Antonijevic, Biljana

2017-02-01

The objective of this study was to assess toxicity of Cd and BDE-209 mixture on haematological parameters in subacutely exposed rats and to determine the presence and type of interactions between these two chemicals using multiple factorial regression analysis. Furthermore, for the assessment of interaction type, an isobologram based methodology was applied and compared with multiple factorial regression analysis. Chemicals were given by oral gavage to the male Wistar rats weighing 200-240g for 28days. Animals were divided in 16 groups (8/group): control vehiculum group, three groups of rats were treated with 2.5, 7.5 or 15mg Cd/kg/day. These doses were chosen on the bases of literature data and reflect relatively high Cd environmental exposure, three groups of rats were treated with 1000, 2000 or 4000mg BDE-209/kg/bw/day, doses proved to induce toxic effects in rats. Furthermore, nine groups of animals were treated with different mixtures of Cd and BDE-209 containing doses of Cd and BDE-209 stated above. Blood samples were taken at the end of experiment and red blood cells, white blood cells and platelets counts were determined. For interaction assessment multiple factorial regression analysis and fitted isobologram approach were used. In this study, we focused on multiple factorial regression analysis as a method for interaction assessment. We also investigated the interactions between Cd and BDE-209 by the derived model for the description of the obtained fitted isobologram curves. Current study indicated that co-exposure to Cd and BDE-209 can result in significant decrease in RBC count, increase in WBC count and decrease in PLT count, when compared with controls. Multiple factorial regression analysis used for the assessment of interactions type between Cd and BDE-209 indicated synergism for the effect on RBC count and no interactions i.e. additivity for the effects on WBC and PLT counts. On the other hand, isobologram based approach showed slight antagonism for the effects on RBC and WBC while no interactions were proved for the joint effect on PLT count. These results confirm that the assessment of interactions between chemicals in the mixture greatly depends on the concept or method used for this evaluation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

MiR-132 regulated olfactory bulb proteins linked to olfactory learning in greater short-nosed fruit bat Cynopterus sphinx.

PubMed

Mukilan, Murugan; Rajathei, David Mary; Jeyaraj, Edwin; Kayalvizhi, Nagarajan; Rajan, Koilmani Emmanuvel

2018-05-30

Earlier, we showed that micro RNA-132 (miR-132) regulate the immediate early genes (IEGs) in the olfactory bulb (OB) of fruit bat Cynopterus sphinx during olfactory learning. This study was designed to examine whether the miR-132 regulate other proteins in OB during olfactory learning. To test this, miR-132 anti-sense oligodeoxynucleotide (AS-ODN) was delivered to the OB and then trained to novel odor. The 2-dimensional gel electrophoresis analysis showed that inhibition of miR-132 altered olfactory training induced expression of 321 proteins. Further, liquid chromatography-mass spectrometry (LC-MS/MS) analysis reveals the identity of differently expressed proteins such as phosphoribosyl transferase domain containing protein (PRTFDC 1), Sorting nexin-8 (SNX8), Creatine kinase B-type (CKB) and Annexin A11 (ANX A11). Among them PRTFDC 1 showing 189 matching peptides with highest sequence coverage (67.0%) and protein-protein interaction analysis showed that PRTFDC 1 is a homolog of hypoxanthine phosphoribosyltransferase-1 (HPRT-1). Subsequent immunohistochemical analysis (IHC) showed that inhibition of miR-132 down-regulated HPRT expression in OB of C. sphinx. In addition, western blot analysis depicts that HPRT, serotonin transporter (SERT), N-methyl-d-asparate (NMDA) receptors (2A,B) were down-regulated, but not altered in OB of non-sense oligodeoxynucleotide (NS-ODN) infused groups. These analyses suggest that miR-132 regulates the process of olfactory learning and memory formation through SERT and NMDA receptors signalling, which is possibly associated with the PRTFDC1-HPRT interaction. Copyright © 2017. Published by Elsevier B.V.

Structural studies reveal an important role for the pleiotrophin C-terminus in mediating interactions with chondroitin sulfate.

PubMed

Ryan, Eathen; Shen, Di; Wang, Xu

2016-04-01

Pleiotrophin (PTN) is a potent glycosaminoglycan-binding cytokine that is important in neural development, angiogenesis and tissue regeneration. Much of its activity is attributed to its interactions with the chondroitin sulfate (CS) proteoglycan, receptor type protein tyrosine phosphatase ζ (PTPRZ). However, there is little high resolution structural information on the interactions between PTN and CS, nor is it clear why the C-terminal tail of PTN is necessary for signaling through PTPRZ, even though it does not contribute to heparin binding. We determined the first structure of PTN and analyzed its interactions with CS. Our structure shows that PTN possesses large basic surfaces on both of its structured domains and also that residues in the hinge segment connecting the domains have significant contacts with the C-terminal domain. Our analysis of PTN-CS interactions showed that the C-terminal tail of PTN is essential for maintaining stable interactions with chondroitin sulfate A, the type of CS commonly found on PTPRZ. These results offer the first possible explanation of why truncated PTN missing the C-terminal tail is unable to signal through PTPRZ. NMR analysis of the interactions of PTN with CS revealed that the C-terminal domain and hinge of PTN make up the major CS-binding site in PTN, and that removal of the C-terminal tail weakened the affinity of the site for CSA but not for other high sulfation density CS. Coordinates of the ensemble of ten PTN structures have been deposited in RCSB under accession number 2n6f. Chemical shifts assignments and structural constraints have been deposited in BMRB under accession number 25762. © 2016 Federation of European Biochemical Societies.

A simple and efficient method for predicting protein-protein interaction sites.

PubMed

Higa, R H; Tozzi, C L

2008-09-23

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).

Perceived usefulness, perceived ease of use, and perceived enjoyment as drivers for the user acceptance of interactive mobile maps

NASA Astrophysics Data System (ADS)

Hussain, Azham; Mkpojiogu, Emmanuel O. C.; Yusof, Muhammad Mat

2016-08-01

This study examines the user perception of usefulness, ease of use and enjoyment as drivers for the users' complex interaction with map on mobile devices. TAM model was used to evaluate users' intention to use and their acceptance of interactive mobile map using the above three beliefs as antecedents. Quantitative research (survey) methodology was employed and the analysis and findings showed that all the three explanatory variables used in this study, explain the variability in the user acceptance of interactive mobile map technology. Perceived usefulness, perceived ease of use, and perceived enjoyment each have significant positive influence on user acceptance of interactive mobile maps. This study further validates the TAM model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Arvind, E-mail: arvindsharma230771@gmail.com; Nagar, A. K., E-mail: ajaya.nagar@gmail.com

We investigate the interaction of optical vector soliton with a symmetric thin-film gallium-silica waveguide structure using the equivalent particle theory. The relevant nonlinear Schrodinger equation has been solved by the method of phase plane analysis. The analysis shows beam break up into transmitted, reflected and nonlinear surface waves at the interface. The stability properties of the solitons so formed have been discussed.

NASA TLA workload analysis support. Volume 3: FFD autopilot scenario validation data

NASA Technical Reports Server (NTRS)

Sundstrom, J. L.

1980-01-01

The data used to validate a seven time line analysis of forward flight deck autopilot mode for the pilot and copilot for NASA B737 terminal configured vehicle are presented. Demand workloads are given in two forms: workload histograms and workload summaries (bar graphs). A report showing task length and task interaction is also presented.

Perceived Status and Value: The Student-Customer Relationship Inflected by the Inherent Challenges of University-Industry Collaboration

ERIC Educational Resources Information Center

Heikkinen, Juho; Isomöttönen, Ville

2017-01-01

This article examines how students in a multidisciplinary project-based learning course involving real customers perceive their interactions with their customers. The authors conducted a qualitative study and analysed students' learning reports by means of a thematic network analysis. The analysis shows how students perceive their status in…

Ratio-of-Mediator-Probability Weighting for Causal Mediation Analysis in the Presence of Treatment-by-Mediator Interaction

ERIC Educational Resources Information Center

Hong, Guanglei; Deutsch, Jonah; Hill, Heather D.

2015-01-01

Conventional methods for mediation analysis generate biased results when the mediator-outcome relationship depends on the treatment condition. This article shows how the ratio-of-mediator-probability weighting (RMPW) method can be used to decompose total effects into natural direct and indirect effects in the presence of treatment-by-mediator…

Ratio-of-Mediator-Probability Weighting for Causal Mediation Analysis in the Presence of Treatment-by-Mediator Interaction

ERIC Educational Resources Information Center

Hong, Guanglei; Deutsch, Jonah; Hill, Heather D.

2015-01-01

Conventional methods for mediation analysis generate biased results when the mediator--outcome relationship depends on the treatment condition. This article shows how the ratio-of-mediator-probability weighting (RMPW) method can be used to decompose total effects into natural direct and indirect effects in the presence of treatment-by-mediator…

Working at Community Boundaries: A Micro-Analysis of the Activist's Role in Participatory Learning Networks

ERIC Educational Resources Information Center

Thorpe, Mary; Kubiak, Chris

2005-01-01

The interaction of agency and context in workplace learning is explored through a micro-analysis of the implementation of networked learning communities in schools in England. Interviews with local activists show evidence of co-participation between individuals' responses and their workplace roles and experience as they take up the opportunity to…

Genes-environment interactions in obesity- and diabetes-associated pancreatic cancer: a GWAS data analysis.

PubMed

Tang, Hongwei; Wei, Peng; Duell, Eric J; Risch, Harvey A; Olson, Sara H; Bueno-de-Mesquita, H Bas; Gallinger, Steven; Holly, Elizabeth A; Petersen, Gloria M; Bracci, Paige M; McWilliams, Robert R; Jenab, Mazda; Riboli, Elio; Tjønneland, Anne; Boutron-Ruault, Marie Christine; Kaaks, Rudolf; Trichopoulos, Dimitrios; Panico, Salvatore; Sund, Malin; Peeters, Petra H M; Khaw, Kay-Tee; Amos, Christopher I; Li, Donghui

2014-01-01

Obesity and diabetes are potentially alterable risk factors for pancreatic cancer. Genetic factors that modify the associations of obesity and diabetes with pancreatic cancer have previously not been examined at the genome-wide level. Using genome-wide association studies (GWAS) genotype and risk factor data from the Pancreatic Cancer Case Control Consortium, we conducted a discovery study of 2,028 cases and 2,109 controls to examine gene-obesity and gene-diabetes interactions in relation to pancreatic cancer risk by using the likelihood-ratio test nested in logistic regression models and Ingenuity Pathway Analysis (IPA). After adjusting for multiple comparisons, a significant interaction of the chemokine signaling pathway with obesity (P = 3.29 × 10(-6)) and a near significant interaction of calcium signaling pathway with diabetes (P = 1.57 × 10(-4)) in modifying the risk of pancreatic cancer were observed. These findings were supported by results from IPA analysis of the top genes with nominal interactions. The major contributing genes to the two top pathways include GNGT2, RELA, TIAM1, and GNAS. None of the individual genes or single-nucleotide polymorphism (SNP) except one SNP remained significant after adjusting for multiple testing. Notably, SNP rs10818684 of the PTGS1 gene showed an interaction with diabetes (P = 7.91 × 10(-7)) at a false discovery rate of 6%. Genetic variations in inflammatory response and insulin resistance may affect the risk of obesity- and diabetes-related pancreatic cancer. These observations should be replicated in additional large datasets. A gene-environment interaction analysis may provide new insights into the genetic susceptibility and molecular mechanisms of obesity- and diabetes-related pancreatic cancer.

Study binding of Al-curcumin complex to ds-DNA, monitoring by multispectroscopic and voltammetric techniques

NASA Astrophysics Data System (ADS)

Ahmadi, F.; Alizadeh, A. A.; Shahabadi, N.; Rahimi-Nasrabadi, M.

2011-09-01

In this work a complex of Al 3+ with curcumin ([Al(curcumin) (EtOH) 2](NO 3) 2) was synthesized and characterized by UV-vis, FT-IR, elemental analysis and spectrophotometric titration techniques. The mole ratio plot revealed a 1:1 complex between Al 3+ and curcumin in solution. For binding studies of this complex to calf thymus-DNA various methods such as: UV-vis, fluorescence, circular dichroism (CD), FT-IR spectroscopy and cyclic voltammetry were used. The intrinsic binding constant of ACC with DNA at 25 °C was calculated by UV-vis and cyclic voltammetry as 2.1 × 10 4 and 2.6 × 10 4, respectively. The thermodynamic studies showed that the reaction is enthalpy and entropy favored. The CD results showed that only the Δ-ACC interacts with DNA and the Δ-ACC form has not any tendency to interact with DNA, also the pure curcumin has not any stereoselective interaction with CT-DNA. Fluorimetric studies showed that fluorescence enhancement was initiated by a static process in the ground state. The cyclic voltammetry showed that ACC interact with DNA with a binding site size of 2. From the FT-IR we concluded that the Δ-ACC interacts with DNA via partial electrostatic and minor groove binding. In comparison with previous works it was concluded that curcumin significantly reduced the affinity of Al 3+ to the DNA.

Interactions between toxic chemicals and natural environmental factors--a meta-analysis and case studies.

PubMed

Laskowski, Ryszard; Bednarska, Agnieszka J; Kramarz, Paulina E; Loureiro, Susana; Scheil, Volker; Kudłek, Joanna; Holmstrup, Martin

2010-08-15

The paper addresses problems arising from effects of natural environmental factors on toxicity of pollutants to organisms. Most studies on interactions between toxicants and natural factors, including those completed in the EU project NoMiracle (Novel Methods for Integrated Risk Assessment of Cumulative Stressors in Europe) described herein, showed that effects of toxic chemicals on organisms can differ vastly depending purely on external conditions. We compiled data from 61 studies on effects of temperature, moisture and dissolved oxygen on toxicity of a range of chemicals representing pesticides, polycyclic aromatic hydrocarbons, plant protection products of bacterial origin and trace metals. In 62.3% cases significant interactions (p< or =0.05 or less) between natural factors and chemicals were found, reaching 100% for the effect of dissolved oxygen on toxicity of waterborne chemicals. The meta-analysis of the 61 studies showed that the null hypothesis assuming no interactions between toxic chemicals and natural environmental factors should be rejected at p=2.7 x 10(-82) (truncated product method probability). In a few cases of more complex experimental designs, also second-order interactions were found, indicating that natural factors can modify interactions among chemicals. Such data emphasize the necessity of including information on natural factors and their variation in time and across geographic regions in ecological risk assessment. This can be done only if appropriate ecotoxicological test designs are used, in which test organisms are exposed to toxicants at a range of environmental conditions. We advocate designing such tests for the second-tier ecological risk assessment procedures. Copyright 2010 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun-Hao; Liu, Shun; Zheng, Ling-Ling

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown. Recent advances in high-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq) provide powerful ways to identify biologically relevant protein–lncRNA interactions. In this study, by analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBP–lncRNA regulatory relationships. We found that one single lncRNA will generally be bound and regulated by one or multiple RBPs, the combination of which may coordinately regulatemore » gene expression. We also revealed the expression correlation of these interaction networks by mining expression profiles of over 6000 normal and tumor samples from 14 cancer types. Our combined analysis of CLIP-Seq data and genome-wide association studies data discovered hundreds of disease-related single nucleotide polymorphisms resided in the RBP binding sites of lncRNAs. Finally, we developed interactive web implementations to provide visualization, analysis, and downloading of the aforementioned large-scale datasets. Our study represented an important step in identification and analysis of RBP–lncRNA interactions and showed that these interactions may play crucial roles in cancer and genetic diseases.« less

Phthalic acid chemical probes synthesized for protein-protein interaction analysis.

PubMed

Liang, Shih-Shin; Liao, Wei-Ting; Kuo, Chao-Jen; Chou, Chi-Hsien; Wu, Chin-Jen; Wang, Hui-Min

2013-06-24

Plasticizers are additives that are used to increase the flexibility of plastic during manufacturing. However, in injection molding processes, plasticizers cannot be generated with monomers because they can peel off from the plastics into the surrounding environment, water, or food, or become attached to skin. Among the various plasticizers that are used, 1,2-benzenedicarboxylic acid (phthalic acid) is a typical precursor to generate phthalates. In addition, phthalic acid is a metabolite of diethylhexyl phthalate (DEHP). According to Gene_Ontology gene/protein database, phthalates can cause genital diseases, cardiotoxicity, hepatotoxicity, nephrotoxicity, etc. In this study, a silanized linker (3-aminopropyl triethoxyslane, APTES) was deposited on silicon dioxides (SiO2) particles and phthalate chemical probes were manufactured from phthalic acid and APTES-SiO2. These probes could be used for detecting proteins that targeted phthalic acid and for protein-protein interactions. The phthalic acid chemical probes we produced were incubated with epithelioid cell lysates of normal rat kidney (NRK-52E cells) to detect the interactions between phthalic acid and NRK-52E extracted proteins. These chemical probes interacted with a number of chaperones such as protein disulfide-isomerase A6, heat shock proteins, and Serpin H1. Ingenuity Pathways Analysis (IPA) software showed that these chemical probes were a practical technique for protein-protein interaction analysis.

Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Talukder, Srijeeta; Sen, Shrabani; Chaudhury, Pinaki, E-mail: pinakc@rediffmail.com

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε{sub hb}(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stackingmore » interaction ε{sub st}(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.« less

In silico study of protein to protein interaction analysis of AMP-activated protein kinase and mitochondrial activity in three different farm animal species

NASA Astrophysics Data System (ADS)

Prastowo, S.; Widyas, N.

2018-03-01

AMP-activated protein kinase (AMPK) is cellular energy censor which works based on ATP and AMP concentration. This protein interacts with mitochondria in determine its activity to generate energy for cell metabolism purposes. For that, this paper aims to compare the protein to protein interaction of AMPK and mitochondrial activity genes in the metabolism of known animal farm (domesticated) that are cattle (Bos taurus), pig (Sus scrofa) and chicken (Gallus gallus). In silico study was done using STRING V.10 as prominent protein interaction database, followed with biological function comparison in KEGG PATHWAY database. Set of genes (12 in total) were used as input analysis that are PRKAA1, PRKAA2, PRKAB1, PRKAB2, PRKAG1, PRKAG2, PRKAG3, PPARGC1, ACC, CPT1B, NRF2 and SOD. The first 7 genes belong to gene in AMPK family, while the last 5 belong to mitochondrial activity genes. The protein interaction result shows 11, 8 and 5 metabolism pathways in Bos taurus, Sus scrofa and Gallus gallus, respectively. The top pathway in Bos taurus is AMPK signaling pathway (10 genes), Sus scrofa is Adipocytokine signaling pathway (8 genes) and Gallus gallus is FoxO signaling pathway (5 genes). Moreover, the common pathways found in those 3 species are Adipocytokine signaling pathway, Insulin signaling pathway and FoxO signaling pathway. Genes clustered in Adipocytokine and Insulin signaling pathway are PRKAA2, PPARGC1A, PRKAB1 and PRKAG2. While, in FoxO signaling pathway are PRKAA2, PRKAB1, PRKAG2. According to that, we found PRKAA2, PRKAB1 and PRKAG2 are the common genes. Based on the bioinformatics analysis, we can demonstrate that protein to protein interaction shows distinct different of metabolism in different species. However, further validation is needed to give a clear explanation.

Spectral analysis and quantum chemical studies of chair and twist-boat conformers of cycloheximide in gas and solution phases

NASA Astrophysics Data System (ADS)

Tokatli, A.; Ucun, F.; Sütçü, K.; Osmanoğlu, Y. E.; Osmanoğlu, Ş.

2018-02-01

In this study the conformational behavior of cycloheximide in the gas and solution (CHCl3) phases has theoretically been investigated by spectroscopic and quantum chemical properties using density functional theory (wB97X-D) method with 6-31++G(d,p) basis set, for the first time. The calculated IR results reveal that in the ground state the molecule exits as a mixture of the chair and twist-boat conformers in the gas phase, while the calculated NMR results reveal that it only exits as the chair conformer in the solution phase. In order to obtain the contributions coming from intramolecular interactions to the stability of the conformers in the gas and solution phases, the quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI) method, and natural bond orbital analysis (NBO) have been employed. The QTAIM and NCI methods indicated that by intramolecular interactions with bond critical point (BCP) the twist-boat conformer is more stabilized than the chair conformer, while by steric interactions it is more destabilized. Considering that these interactions balance each other, the stabilities of the conformers are understood to be dictated by the van der Waals interactions. The NBO analyses show that the hyperconjugative and steric effects play an important role in the stabilization in the gas and solution phases. Furthermore, to get a better understanding of the chemical behavior of this important antibiotic drug we have evaluated and, commented the global and local reactivity descriptors of the both conformers. Finally, the EPR analysis of γ-irradiated cycloheximide has been done. The comparison of the experimental and calculated data have showed the inducement of a radical structure of (CH2)2ĊCH2 in the molecule. The experimental EPR spectrum has also confirmed that the molecule simultaneously exists in the chair and twist-boat conformers in the solid phase.

Proteomic Analysis of Virus-Host Interactions in an Infectious Context Using Recombinant Viruses*

PubMed Central

Komarova, Anastassia V.; Combredet, Chantal; Meyniel-Schicklin, Laurène; Chapelle, Manuel; Caignard, Grégory; Camadro, Jean-Michel; Lotteau, Vincent; Vidalain, Pierre-Olivier; Tangy, Frédéric

2011-01-01

RNA viruses exhibit small-sized genomes encoding few proteins, but still establish complex networks of interactions with host cell components to achieve replication and spreading. Ideally, these virus-host protein interactions should be mapped directly in infected cell culture, but such a high standard is often difficult to reach when using conventional approaches. We thus developed a new strategy based on recombinant viruses expressing tagged viral proteins to capture both direct and indirect physical binding partners during infection. As a proof of concept, we engineered a recombinant measles virus (MV) expressing one of its virulence factors, the MV-V protein, with a One-STrEP amino-terminal tag. This allowed virus-host protein complex analysis directly from infected cells by combining modified tandem affinity chromatography and mass spectrometry analysis. Using this approach, we established a prosperous list of 245 cellular proteins interacting either directly or indirectly with MV-V, and including four of the nine already known partners of this viral factor. These interactions were highly specific of MV-V because they were not recovered when the nucleoprotein MV-N, instead of MV-V, was tagged. Besides key components of the antiviral response, cellular proteins from mitochondria, ribosomes, endoplasmic reticulum, protein phosphatase 2A, and histone deacetylase complex were identified for the first time as prominent targets of MV-V and the critical role of the later protein family in MV replication was addressed. Most interestingly, MV-V showed some preferential attachment to essential proteins in the human interactome network, as assessed by centrality and interconnectivity measures. Furthermore, the list of MV-V interactors also showed a massive enrichment for well-known targets of other viruses. Altogether, this clearly supports our approach based on reverse genetics of viruses combined with high-throughput proteomics to probe the interaction network that viruses establish in infected cells. PMID:21911578

Interactive Visualization of Healthcare Data Using Tableau.

PubMed

Ko, Inseok; Chang, Hyejung

2017-10-01

Big data analysis is receiving increasing attention in many industries, including healthcare. Visualization plays an important role not only in intuitively showing the results of data analysis but also in the whole process of collecting, cleaning, analyzing, and sharing data. This paper presents a procedure for the interactive visualization and analysis of healthcare data using Tableau as a business intelligence tool. Starting with installation of the Tableau Desktop Personal version 10.3, this paper describes the process of understanding and visualizing healthcare data using an example. The example data of colon cancer patients were obtained from health insurance claims in years 2012 and 2013, provided by the Health Insurance Review and Assessment Service. To explore the visualization of healthcare data using Tableau for beginners, this paper describes the creation of a simple view for the average length of stay of colon cancer patients. Since Tableau provides various visualizations and customizations, the level of analysis can be increased with small multiples, view filtering, mark cards, and Tableau charts. Tableau is a software that can help users explore and understand their data by creating interactive visualizations. The software has the advantages that it can be used in conjunction with almost any database, and it is easy to use by dragging and dropping to create an interactive visualization expressing the desired format.

Modeling of intracerebral interictal epileptic discharges: Evidence for network interactions.

PubMed

Meesters, Stephan; Ossenblok, Pauly; Colon, Albert; Wagner, Louis; Schijns, Olaf; Boon, Paul; Florack, Luc; Fuster, Andrea

2018-06-01

The interictal epileptic discharges (IEDs) occurring in stereotactic EEG (SEEG) recordings are in general abundant compared to ictal discharges, but difficult to interpret due to complex underlying network interactions. A framework is developed to model these network interactions. To identify the synchronized neuronal activity underlying the IEDs, the variation in correlation over time of the SEEG signals is related to the occurrence of IEDs using the general linear model. The interdependency is assessed of the brain areas that reflect highly synchronized neural activity by applying independent component analysis, followed by cluster analysis of the spatial distributions of the independent components. The spatiotemporal interactions of the spike clusters reveal the leading or lagging of brain areas. The analysis framework was evaluated for five successfully operated patients, showing that the spike cluster that was related to the MRI-visible brain lesions coincided with the seizure onset zone. The additional value of the framework was demonstrated for two more patients, who were MRI-negative and for whom surgery was not successful. A network approach is promising in case of complex epilepsies. Analysis of IEDs is considered a valuable addition to routine review of SEEG recordings, with the potential to increase the success rate of epilepsy surgery. Copyright © 2018 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Electro-osmosis over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions

NASA Astrophysics Data System (ADS)

Ghosh, Uddipta; Chakraborty, Suman

2016-06-01

In this study, we attempt to bring out a generalized formulation for electro-osmotic flows over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions. To this end, we start with modified electro-chemical potential of the individual species and subsequently use it to derive modified Nernst-Planck equation accounting for the ionic fluxes generated because of the presence of non-electrostatic potential. We establish what we refer to as the Poisson-Helmholtz-Nernst-Planck equations, coupled with the Navier-Stokes equations, to describe the complete transport process. Our analysis shows that the presence of non-electrostatic interactions between the ions results in an excess body force on the fluid, and modifies the osmotic pressure as well, which has hitherto remained unexplored. We further apply our analysis to a simple geometry, in an effort to work out the Smoluchowski slip velocity for thin electrical double layer limits. To this end, we employ singular perturbation and develop a general framework for the asymptotic analysis. Our calculations reveal that the final expression for slip velocity remains the same as that without accounting for non-electrostatic interactions. However, the presence of non-electrostatic interactions along with ion specificity can significantly change the quantitative behavior of Smoluchowski slip velocity. We subsequently demonstrate that the presence of non-electrostatic interactions may significantly alter the effective interfacial potential, also termed as the "Zeta potential." Our analysis can potentially act as a guide towards the prediction and possibly quantitative determination of the implications associated with the existence of non-electrostatic potential, in an electrokinetic transport process.

Characterization of non-classical Csbnd Br⋯π interactions in (E)-1,3-dibromo-5-(2-(ferrocenyl)vinyl)benzene and related derivatives of ferrocene

NASA Astrophysics Data System (ADS)

Shukla, Rahul; Panini, Piyush; McAdam, C. John; Robinson, Brian H.; Simpson, Jim; Tagg, Tei; Chopra, Deepak

2017-03-01

Amongst the halogens, the involvement of bromine atoms in various types of intermolecular interactions is comparatively the least studied. In this manuscript, we report the formation of Csbnd Br⋯π interactions, with the π-rings being the cyclopentadienyl (Cp) rings of a ferrocene molecule in a newly synthesized compound (E)-1,3-dibromo-5-(2-(ferrocenyl)vinyl)benzene. We have also performed a detailed quantitative analysis on Csbnd Br⋯π interactions observed in the synthesized molecule and in several related molecules found in the Cambridge Structure Database (CSD) showing the presence of these interactions. A topological analysis based upon QTAIM theory and electrostatic potential ESP mapped on the Hirshfeld surface of these molecules confirm that these interactions are better described as "halogen bonds" wherein the electropositive region (σ-hole) on the Br-atom interacts with the electronegative region over the Cp-ring of the ferrocene. Further, the electronegative region on the bromine atom (perpendicular to the Csbnd Br bond) was observed to be involved in the formation of highly directional Csbnd H⋯Br interactions with the ∠Csbnd Br⋯H close to 90°. Thus the bromine atom is acting as both a "halogen bond donor" and "hydrogen bond acceptor" in the crystal packing with the two interactions being mutually orthogonal.

Accumulation of transcription factors and cell signaling-related proteins in the nucleus during citrus-Xanthomonas interaction.

PubMed

Rani, T Swaroopa; Durgeshwar, P; Podile, Appa Rao

2015-07-20

The nucleus is the maestro of the cell and is involved in the modulation of cell signaling during stress. We performed a comprehensive nuclear proteome analysis of Citrus sinensis during interaction with host (Xanthomonas citri pv. citri-Xcc) and non-host (Xanthomonas oryzae pv. oryzae-Xoo) pathogens. The nuclear proteome was obtained using a sequential method of organelle enrichment and determined by nano-LC-MS/MS analysis. A total of 243 proteins accumulated differentially during citrus-Xanthomonas interaction, belonging to 11 functional groups, with signaling and transcription-related proteins dominating. MADS-box transcription factors, DEAD-box RNA helicase and leucine aminopeptidase, mainly involved in jasmonic acid (JA) responses, were in high abundance during non-host interaction (Xoo). Signaling-related proteins like serine/threonine kinase, histones (H3.2, H2A), phosphoglycerate kinase, dynamin, actin and aldolase showed increased accumulation early during Xoo interaction. Our results suggest that there is a possible involvement of JA-triggered defense responses during non-host resistance, with early recognition of the non-host pathogen. Copyright © 2015. Published by Elsevier GmbH.

Protein interactions and ligand binding: from protein subfamilies to functional specificity.

PubMed

Rausell, Antonio; Juan, David; Pazos, Florencio; Valencia, Alfonso

2010-02-02

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.

Structural and electronic properties of OsB2 : A hard metallic material

NASA Astrophysics Data System (ADS)

Chen, Z. Y.; Xiang, H. J.; Yang, Jinlong; Hou, J. G.; Zhu, Qingshi

2006-07-01

We calculate the structural and electronic properties of OsB2 using density functional theory with or without taking into account the spin-orbit (SO) interaction. Our results show that the bulk modulus with and without SO interactions are 364 and 365GPa , respectively, both are in good agreement with experiment (365-395GPa) . The evidence of covalent bonding of Os-B, which plays an important role to form a hard material, is indicated both in charge density, atoms in molecules analysis, and density of states analysis. The good metallicity and hardness of OsB2 might suggest its potential application as hard conductors.

Social support and support groups among people with HIV/AIDS in Ghana.

PubMed

Abrefa-Gyan, Tina; Wu, Liyun; Lewis, Marilyn W

2016-01-01

HIV/AIDS, a chronic burden in Ghana, poses social and health outcome concerns to those infected. Examining the Medical Outcome Study Social Support Survey (MOS-SSS) instrument among 300 Ghanaians from a cross-sectional design, Principal Component Analysis yielded four factors (positive interaction, trust building, information giving, and essential support), which accounted for 85.73% of the total variance in the MOS-SSS. A logistic regression analysis showed that essential support was the strongest predictor of the length of time an individual stayed in the support group, whereas positive interaction indicated negative association. The study's implications for policy, research, and practice were discussed.

Relative Displacement Method for Track-Structure Interaction

PubMed Central

Ramos, Óscar Ramón; Pantaleón, Marcos J.

2014-01-01

The track-structure interaction effects are usually analysed with conventional FEM programs, where it is difficult to implement the complex track-structure connection behaviour, which is nonlinear, elastic-plastic and depends on the vertical load. The authors developed an alternative analysis method, which they call the relative displacement method. It is based on the calculation of deformation states in single DOF element models that satisfy the boundary conditions. For its solution, an iterative optimisation algorithm is used. This method can be implemented in any programming language or analysis software. A comparison with ABAQUS calculations shows a very good result correlation and compliance with the standard's specifications. PMID:24634610

Vibrational Spectra and Density functional calculation of Organic Nonlinear Optic Crystal p-Amino Acetanilide

NASA Astrophysics Data System (ADS)

Saja, D.; Joe, I. Hubert; Jayakumar, V. S.

2006-01-01

The NIR-FT Raman, FT-IR spectral analysis of potential NLO material P-Amino Acetanilide is carried out by density functional computations. The optimized geometry shows that NH2 and NHCOCH3 groups substituted in para position of phenyl ring are non-planar which predicts maximum conjugation of molecule with donor and acceptor groups. Vibrational analysis reveals that simultaneous IR and Raman activation of the phenyl ring modes also provide evidence for the charge transfer interaction between the donors and the acceptor can make the molecule highly polarized and the intra molecular charge transfer interaction must be responsible for the NLO properties of PAA.

The interaction between Pseudomonas aeruginosa cells and cationic PC:Chol:DOTAP liposomal vesicles versus outer-membrane structure and envelope properties of bacterial cell.

PubMed

Drulis-Kawa, Zuzanna; Dorotkiewicz-Jach, Agata; Gubernator, Jerzy; Gula, Grzegorz; Bocer, Tomasz; Doroszkiewicz, Wlodzimierz

2009-02-09

The interactions between cationic liposomal formulations (PC:Chol:DOTAP 3:4:3) and 23 Pseudomonas aeruginosa strains were tested. The study was undertaken because different antimicrobial results had been obtained by the authors for Pseudomonas aeruginosa strains and liposomal antibiotics (Drulis-Kawa, Z., Gubernator, J., Dorotkiewicz-Jach, A., Doroszkiewicz, W., Kozubek, A., 2006. The comparison of in vitro antimicrobial activity of liposomes containing meropenem and gentamicin. Cell. Mol. Biol. Lett., 11, 360-375; Drulis-Kawa, Z., Gubernator, J., Dorotkiewicz-Jach, A., Doroszkiewicz W., Kozubek, A., 2006. In vitro antimicrobial activity of liposomal meropenem against Pseudomonas aeruginosa strains. Int. J. Pharm., 315, 59-66). The experiments evaluate the roles of the bacterial outer-membrane structure, especially outer-membrane proteins and LPS, and envelope properties (hydrophobicity and electrostatic potential) in the interactions/fusion process between cells and lipid vesicles. The interactions were examined by fluorescent microscopy using PE-rhodamine-labelled liposomes. Some of the strains exhibited red-light emission (fusion with vesicles or vesicles surrounding the cell) and some showed negative reaction (no red-light emission). The main aim of the study was to determine what kinds of bacterial structure or envelope properties have a major influence on the fusion process. Negatively charged cells and hydrophobic properties promote interaction with cationic lipid vesicles, but no specific correlation was noted for the tested strains. A similar situation concerned LPS structure, where parent strains and their mutants possessing identical ladder-like band patterns in SDS-PAGE analysis exhibited totally different results with fluorescent microscopy. Outer-membrane protein analysis showed that an 18-kDA protein occurred in the isolates showing fusion with rhodamine-labelled vesicles and, conversely, strains lacking the 18-kDA protein exhibited no positive reaction (red emission). This suggests that even one protein may be responsible for favouring stronger interactions between Pseudomonas aeruginosa cells and cationic liposomal formulations (PC:Chol:DOTAP 3:4:3).

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.

PubMed

Falconi, M; Oteri, F; Eliseo, T; Cicero, D O; Desideri, A

2008-08-01

The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.

A spin-frustrated trinuclear copper complex based on triaminoguanidine with an energetically well-separated degenerate ground state.

PubMed

Spielberg, Eike T; Gilb, Aksana; Plaul, Daniel; Geibig, Daniel; Hornig, David; Schuch, Dirk; Buchholz, Axel; Ardavan, Arzhang; Plass, Winfried

2015-04-06

We present the synthesis and crystal structure of the trinuclear copper complex [Cu3(saltag)(bpy)3]ClO4·3DMF [H5saltag = tris(2-hydroxybenzylidene)triaminoguanidine; bpy = 2,2'-bipyridine]. The complex crystallizes in the trigonal space group R3̅, with all copper ions being crystallographically equivalent. Analysis of the temperature dependence of the magnetic susceptibility shows that the triaminoguanidine ligand mediates very strong antiferromagnetic interactions (JCuCu = -324 cm(-1)). Detailed analysis of the magnetic susceptibility and magnetization data as well as X-band electron spin resonance spectra, all recorded on both powdered samples and single crystals, show indications of neither antisymmetric exchange nor symmetry lowering, thus indicating only a very small splitting of the degenerate S = (1)/2 ground state. These findings are corroborated by density functional theory calculations, which explain both the strong isotropic and negligible antisymmetric exchange interactions.

Interactions between Impacting Particles and Target in Two-Phase Flow

NASA Astrophysics Data System (ADS)

Kang, Sang-Wook; Chow, Tze-Show

1996-11-01

The time-dependent interaction phenomena between a target and the incident solid particles borne by supersonic gas-jet stream have been numerically analyzed. In particular, the analysis dealt with particles such as aluminum, copper, and uranium ipinging on aluminum, copper, or uranium targets at various impact velocities ranging from 200 m/s to 1,000 m/s. Typical particle sizes were 50 to 100 micrometers. Results show considerable deformation of both the incident particles and the target when the velocity is greater than 500 m/s. Experiments performed on copper particles impacting an aluminum target demonstrate that under certain conditions (such as a supersonic gas jet issuing from a nozzle carrying solid particles) the impacts not only deform but also cause deposition of the particles on the surface. The present analysis shows the plausibility of such behavior when the particles impact the target at high velocities.

The study of interaction between PFOA/PFOS and uracil by topology quality and spectroscopic analysis

NASA Astrophysics Data System (ADS)

Xu, Hui-Ying; Zhu, Jian-Qing; Wang, Wei; Xu, Xiao-Lu; Lu, Yin

2014-02-01

It has been established that perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) can be considered as emerging persistent organic pollutants. In recent years, there was increasing distribution of PFOA/PFOS in environmental systems, and accumulation and toxic effects of PFOA/PFOS in human body. In this paper, quantum chemistry methods were employed to study the interaction between perfluorinated organic pollutants and base (uracil). The results showed that there were four stable binding modes between the two perfluorinated compounds with uracil, especially the second mode which caused the most detrimental physiological functional response. NBO analysis showed that reactive hydrogen in the two perfluorinated compounds had the greatest effect on the hydrogen bond. The nature of the hydrogen bond formed between the two perfluorinated compounds and base was investigated using the AIM theory. The changes of spectroscopic properties in complexes were analyzed by IR and NMR spectra.

Transcriptome-Based Characterization of Interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in Lactose-Grown Chemostat Cocultures

PubMed Central

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J. H.; Luttik, Marijke A. H.; Pronk, Jack T.; Smid, Eddy J.; Bron, Peter A.

2013-01-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations. PMID:23872557

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach

NASA Astrophysics Data System (ADS)

Saeed, Aamer; Ifzan Arshad, M.; Bolte, Michael; Fantoni, Adolfo C.; Delgado Espinoza, Zuly Y.; Erben, Mauricio F.

2016-03-01

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, 1H and 13C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···Odbnd C hydrogen bond occurring between the carbonyl (-Cdbnd O) and the hydrazone -Cdbnd N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1 → σ*(N2-H) remote interaction between the C2dbnd O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.

Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures.

PubMed

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J H; Luttik, Marijke A H; Pronk, Jack T; Smid, Eddy J; Bron, Peter A; Daran-Lapujade, Pascale

2013-10-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations.

Effect of amino acid mutations on intra-dimer tubulin-tubulin binding strength of microtubules.

PubMed

Liu, Ning; Pidaparti, Ramana; Wang, Xianqiao

2017-12-11

Energetic interactions inside αβ-tubulin dimers of a microtubule (MT) with atomic resolutions are of importance in determining the mechanical properties and structural stability of the MT as well as designing self-assembled functional structures from it. Here, we carry out several comprehensive atomistic simulations to investigate the interaction properties within αβ-tubulin dimers and effect of residue mutations on the intra-dimer tubulin-tubulin (IDTT) binding strength. Results indicate that the force-displacement responses of the dimer could be roughly divided into three stages involving increasing, decreasing, and fluctuating forces. Energetic analysis shows that electrostatic interactions dominate the IDTT binding strength. Further per-residue energetic analysis shows that the major part of the interface interaction energy (approximately 72% for α-tubulin and 62% for β-tubulin) comes from amino acid residues with net charges, namely arginine (ARG), lysine (LYS), glutamic acid (GLU), aspartic acid (ASP). Residue mutations are completed for ARG105 on α-tubulin and ASP251 on β-tubulin to study the effect of mutations on the IDTT binding strength. Results indicate that stiffness, rupture force, and interface interaction energy of αβ-tubulin dimer can be improved by up to 28%, 13% and 28%, respectively. Overall, our results provide a thorough atomistic understanding of the IDTT binding strength within αβ-tubulin heterodimers and help pave the way for eventually designing and controlling the self-assembled functional structures from MTs.

In-cell SHAPE uncovers dynamic interactions between the untranslated regions of the foot-and-mouth disease virus RNA.

PubMed

Diaz-Toledano, Rosa; Lozano, Gloria; Martinez-Salas, Encarnacion

2017-02-17

The genome of RNA viruses folds into 3D structures that include long-range RNA–RNA interactions relevant to control critical steps of the viral cycle. In particular, initiation of translation driven by the IRES element of foot-and-mouth disease virus is stimulated by the 3΄UTR. Here we sought to investigate the RNA local flexibility of the IRES element and the 3΄UTR in living cells. The SHAPE reactivity observed in vivo showed statistically significant differences compared to the free RNA, revealing protected or exposed positions within the IRES and the 3΄UTR. Importantly, the IRES local flexibility was modified in the presence of the 3΄UTR, showing significant protections at residues upstream from the functional start codon. Conversely, presence of the IRES element in cis altered the 3΄UTR local flexibility leading to an overall enhanced reactivity. Unlike the reactivity changes observed in the IRES element, the SHAPE differences of the 3΄UTR were large but not statistically significant, suggesting multiple dynamic RNA interactions. These results were supported by covariation analysis, which predicted IRES-3΄UTR conserved helices in agreement with the protections observed by SHAPE probing. Mutational analysis suggested that disruption of one of these interactions could be compensated by alternative base pairings, providing direct evidences for dynamic long-range interactions between these distant elements of the viral genome.

Fluid-structure Interaction Modeling of Aneurysmal Conditions with High and Normal Blood Pressures

NASA Astrophysics Data System (ADS)

Torii, Ryo; Oshima, Marie; Kobayashi, Toshio; Takagi, Kiyoshi; Tezduyar, Tayfun E.

2006-09-01

Hemodynamic factors like the wall shear stress play an important role in cardiovascular diseases. To investigate the influence of hemodynamic factors in blood vessels, the authors have developed a numerical fluid-structure interaction (FSI) analysis technique. The objective is to use numerical simulation as an effective tool to predict phenomena in a living human body. We applied the technique to a patient-specific arterial model, and with that we showed the effect of wall deformation on the WSS distribution. In this paper, we compute the interaction between the blood flow and the arterial wall for a patient-specific cerebral aneurysm with various hemodynamic conditions, such as hypertension. We particularly focus on the effects of hypertensive blood pressure on the interaction and the WSS, because hypertension is reported to be a risk factor in rupture of aneurysms. We also aim to show the possibility of FSI computations with hemodynamic conditions representing those risk factors in cardiovascular disease. The simulations show that the transient behavior of the interaction under hypertensive blood pressure is significantly different from the interaction under normal blood pressure. The transient behavior of the blood-flow velocity, and the resulting WSS and the mechanical stress in the aneurysmal wall, are significantly affected by hypertension. The results imply that hypertension affects the growth of an aneurysm and the damage in arterial tissues.

Titin Based Viscosity in Ventricular Physiology: An Integrative Investigation of PEVK-Actin Interactions

PubMed Central

Chung, Charles S; Methawasin, Methajit; Nelson, O Lynne; Radke, Michael H; Hidalgo, Carlos G; Gotthardt, Michael; Granzier, Henk L

2011-01-01

Viscosity is proposed to modulate diastolic function, but only limited understanding of the source(s) of viscosity exists. In-vitro experiments have shown that the proline-glutamic acid-valine-lysine (PEVK) rich element of titin interacts with actin, causing a viscous force in the sarcomere. It is unknown whether this mechanism contributes to viscosity in-vivo. We tested the hypothesis that PEVK-actin interaction causes cardiac viscosity and is important in-vivo via an integrative physiological study on a unique PEVK-knockout (KO) model. Both skinned cardiomyocytes and papillary muscle fibers were isolated from wildtype (WT) and PEVK KO mice and passive viscosity was examined using stretch-hold-release and sinusoidal analysis. Viscosity was reduced by ~60% in KO myocytes and ~50% in muscle fibers at room temperature. The PEVK-actin interaction was not modulated by temperature or diastolic calcium, but was increased by lattice compression. Stretch-hold and sinusoidal frequency protocols on intact isolated mouse hearts showed a smaller, 30–40% reduction in viscosity, possibly due to actomyosin interactions, and showed that microtubules did not contribute to viscosity. Transmitral Doppler echocardiography similarly revealed a 40% decrease in LV chamber viscosity in the PEVK KO in-vivo. This integrative study is the first to quantify the influence of a specific molecular (PEVK-actin) viscosity in-vivo and shows that PEVK-actin interactions are an important physiological source of viscosity. PMID:21708170

Find the Hidden Object. Understanding Play in Psychological Assessments

PubMed Central

Fasulo, Alessandra; Shukla, Janhavi; Bennett, Stephanie

2017-01-01

Standardized psychological assessments are extensively used by practitioners to determine rate and level of development in different domains of ability in both typical and atypical children. The younger the children, the more likely the trials will resemble play activities. However, mode of administration, timing and use of objects involved are constrained. The purpose of this study is to explore what kind of play is play in psychological assessments, what are the expectations about children's performance and what are the abilities supporting the test activities. Conversation Analysis (CA) was applied to the videorecording of an interaction between a child and a practitioner during the administration of the Bayley Scale of Infant and Toddler Development, III edition. The analysis focuses on a 2′07″ long sequence relative to the administration of the test item “Find the hidden object” to a 23 months old child with Down syndrome. The analysis of the sequence shows that the assessor promotes the child's engagement by couching the actions required to administer the item in utterances with marked child-directed features. The analysis also shows that the objects constituting the test item did not suggest to the child a unique course of action, leading to the assessor's modeling of the successful sequence. We argue that when a play frame is activated by an interactional partner, the relational aspect of the activity is foregrounded and the co-player becomes a source of cues for ways in which playing can develop. We discuss the assessment interaction as orienting the child toward a right-or-wrong interpretation, leaving the realm of play, which is inherently exploratory and inventive, to enter that of instructional activities. Finally, we argue that the sequential analysis of the interaction and of the mutual sense-making procedures that partners put in place during the administration of an assessment could be used in the design and evaluation of tests for a finer understanding of the abilities involved. PMID:28392771

Find the Hidden Object. Understanding Play in Psychological Assessments.

PubMed

Fasulo, Alessandra; Shukla, Janhavi; Bennett, Stephanie

2017-01-01

Standardized psychological assessments are extensively used by practitioners to determine rate and level of development in different domains of ability in both typical and atypical children. The younger the children, the more likely the trials will resemble play activities. However, mode of administration, timing and use of objects involved are constrained. The purpose of this study is to explore what kind of play is play in psychological assessments, what are the expectations about children's performance and what are the abilities supporting the test activities. Conversation Analysis (CA) was applied to the videorecording of an interaction between a child and a practitioner during the administration of the Bayley Scale of Infant and Toddler Development, III edition. The analysis focuses on a 2'07″ long sequence relative to the administration of the test item "Find the hidden object" to a 23 months old child with Down syndrome. The analysis of the sequence shows that the assessor promotes the child's engagement by couching the actions required to administer the item in utterances with marked child-directed features. The analysis also shows that the objects constituting the test item did not suggest to the child a unique course of action, leading to the assessor's modeling of the successful sequence. We argue that when a play frame is activated by an interactional partner, the relational aspect of the activity is foregrounded and the co-player becomes a source of cues for ways in which playing can develop. We discuss the assessment interaction as orienting the child toward a right-or-wrong interpretation, leaving the realm of play, which is inherently exploratory and inventive, to enter that of instructional activities. Finally, we argue that the sequential analysis of the interaction and of the mutual sense-making procedures that partners put in place during the administration of an assessment could be used in the design and evaluation of tests for a finer understanding of the abilities involved.

Dynamical system analysis of interacting models

NASA Astrophysics Data System (ADS)

Carneiro, S.; Borges, H. A.

2018-01-01

We perform a dynamical system analysis of a cosmological model with linear dependence between the vacuum density and the Hubble parameter, with constant-rate creation of dark matter. We show that the de Sitter spacetime is an asymptotically stable critical point, future limit of any expanding solution. Our analysis also shows that the Minkowski spacetime is an unstable critical point, which eventually collapses to a singularity. In this way, such a prescription for the vacuum decay not only predicts the correct future de Sitter limit, but also forbids the existence of a stable Minkowski universe. We also study the effect of matter creation on the growth of structures and their peculiar velocities, showing that it is inside the current errors of redshift space distortions observations.

Spin Hamiltonian Analysis of the SMM V15 Using High Field ESR

NASA Astrophysics Data System (ADS)

Martens, Mathew; van Tol, Hans; Bertaina, Sylvain; Barbara, Bernard; Muller, Achim; Chiorescu, Irinel

2014-03-01

We have studied molecular magnets using high field / high frequency Electron Spin Resonance. Such molecular structures contain many quantum spins linked by exchange interactions and consequently their energy structure is often complex and require a good understanding of the molecular spin Hamiltonian. In particular, we studied the V15 molecule, comprised of 15 spins 1/2 and a total spin 1/2, which is a system that recently showed quantum Rabi oscillations of its total quantum spin. This type of molecule is an essential system for advancing molecular structures into quantum computing. We used high frequency characterization techniques (of hundreds of GHz) to gain insight into the exchange anisotropy interactions, crystal field, and anti-symmetric interactions present in this system. We analyzed the data using a detailed numerical analysis of spin interactions and our findings regarding the V15 spin Hamiltonian will be discussed. Supported by the NSF Cooperative Agreement Grant No. DMR-0654118 and No. NHMFL UCGP 5059, NSF grant No. DMR-0645408.

Studies of supersonic, radiative plasma jet interaction with gases at the Prague Asterix Laser System facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicolaie, Ph.; Stenz, C.; Tikhonchuk, V.

2008-08-15

The interaction of laser driven jets with gas puffs at various pressures is investigated experimentally and is analyzed by means of numerical tools. In the experiment, a combination of two complementary diagnostics allowed to characterize the main structures in the interaction zone. By changing the gas composition and its density, the plasma cooling time can be controlled and one can pass from a quasiadiabatic outflow to a strongly radiation cooling jet. This tuning yields hydrodynamic structures very similar to those seen in astrophysical objects; the bow shock propagating through the gas, the shocked materials, the contact discontinuity, and the Machmore » disk. From a dimensional analysis, a scaling is made between both systems and shows the study relevance for the jet velocity, the Mach number, the jet-gas density ratio, and the dissipative processes. The use of a two-dimensional radiation hydrodynamic code, confirms the previous analysis and provides detailed structure of the interaction zone and energy repartition between jet and surrounding gases.« less

A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids

NASA Astrophysics Data System (ADS)

Tang, Qingjie; Guo, Zhenfu; Li, Qingzhong

2014-03-01

The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X = Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The Osbnd H and Osbnd X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.

Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

NASA Astrophysics Data System (ADS)

Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

2018-04-01

The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

Electrostatic Interactions Between Glycosaminoglycan Molecules

NASA Astrophysics Data System (ADS)

Song, Fan; Moyne, Christian; Bai, Yi-Long

2005-02-01

The electrostatic interactions between nearest-neighbouring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains are obtained on the bottle brush conformation of proteoglycan aggrecan based on an asymptotic solution of the Poisson-Boltzmann equation the CS-GAGs satisfy under the physiological conditions of articular cartilage. The present results show that the interactions are associated intimately with the minimum separation distance and mutual angle between the molecular chains themselves. Further analysis indicates that the electrostatic interactions are not only expressed to be purely exponential in separation distance and decrease with the increasing mutual angle but also dependent sensitively on the saline concentration in the electrolyte solution within the tissue, which is in agreement with the existed relevant conclusions.

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.

PubMed

Du, Tianchuan; Liao, Li; Wu, Cathy H

2016-12-01

Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact matrix for a pair of interacting proteins are two computational tasks at different levels of an in-depth analysis of protein-protein interaction. Various methods for solving these two problems have been reported in the literature. However, the interacting residue prediction and contact matrix prediction were handled by and large independently in those existing methods, though intuitively good prediction of interacting residues will help with predicting the contact matrix. In this work, we developed a novel protein interacting residue prediction system, contact matrix-interaction profile hidden Markov model (CM-ipHMM), with the integration of contact matrix prediction and the ipHMM interaction residue prediction. We propose to leverage what is learned from the contact matrix prediction and utilize the predicted contact matrix as "feedback" to enhance the interaction residue prediction. The CM-ipHMM model showed significant improvement over the previous method that uses the ipHMM for predicting interaction residues only. It indicates that the downstream contact matrix prediction could help the interaction site prediction.

Extreme disorder in an ultrahigh-affinity protein complex

NASA Astrophysics Data System (ADS)

Borgia, Alessandro; Borgia, Madeleine B.; Bugge, Katrine; Kissling, Vera M.; Heidarsson, Pétur O.; Fernandes, Catarina B.; Sottini, Andrea; Soranno, Andrea; Buholzer, Karin J.; Nettels, Daniel; Kragelund, Birthe B.; Best, Robert B.; Schuler, Benjamin

2018-03-01

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

Interaction effects of metals and salinity on biodegradation of a complex hydrocarbon waste.

PubMed

Amatya, Prasanna L; Hettiaratchi, Joseph Patrick A; Joshi, Ramesh C

2006-02-01

The presence of high levels of salts because of produced brine water disposal at flare pits and the presence of metals at sufficient concentrations to impact microbial activity are of concern to bioremediation of flare pit waste in the upstream oil and gas industry. Two slurry-phase biotreatment experiments based on three-level factorial statistical experimental design were conducted with a flare pit waste. The experiments separately studied the primary effect of cadmium [Cd(II)] and interaction effect between Cd(II) and salinity and the primary effect of zinc [Zn(II)] and interaction effect between Zn(II) and salinity on hydrocarbon biodegradation. The results showed 42-52.5% hydrocarbon removal in slurries spiked with Cd and 47-62.5% in the slurries spiked with Zn. The analysis of variance showed that the primary effects of Cd and Cd-salinity interaction were statistically significant on hydrocarbon degradation. The primary effects of Zn and the Zn-salinity interaction were statistically insignificant, whereas the quadratic effect of Zn was highly significant on hydrocarbon degradation. The study on effects of metallic chloro-complexes showed that the total aqueous concentration of Cd or Zn does not give a reliable indication of overall toxicity to the microbial activity in the presence of high salinity levels.

Multiple protein–protein interactions converging on the Prp38 protein during activation of the human spliceosome

PubMed Central

Schütze, Tonio; Ulrich, Alexander K.C.; Apelt, Luise; Will, Cindy L.; Bartlick, Natascha; Seeger, Martin; Weber, Gert; Lührmann, Reinhard; Stelzl, Ulrich; Wahl, Markus C.

2016-01-01

Spliceosomal Prp38 proteins contain a conserved amino-terminal domain, but only higher eukaryotic orthologs also harbor a carboxy-terminal RS domain, a hallmark of splicing regulatory SR proteins. We show by crystal structure analysis that the amino-terminal domain of human Prp38 is organized around three pairs of antiparallel α-helices and lacks similarities to RNA-binding domains found in canonical SR proteins. Instead, yeast two-hybrid analyses suggest that the amino-terminal domain is a versatile protein–protein interaction hub that possibly binds 12 other spliceosomal proteins, most of which are recruited at the same stage as Prp38. By quantitative, alanine surface-scanning two-hybrid screens and biochemical analyses we delineated four distinct interfaces on the Prp38 amino-terminal domain. In vitro interaction assays using recombinant proteins showed that Prp38 can bind at least two proteins simultaneously via two different interfaces. Addition of excess Prp38 amino-terminal domain to in vitro splicing assays, but not of an interaction-deficient mutant, stalled splicing at a precatalytic stage. Our results show that human Prp38 is an unusual SR protein, whose amino-terminal domain is a multi-interface protein–protein interaction platform that might organize the relative positioning of other proteins during splicing. PMID:26673105

Cell-free formation and interactome analysis of caveolae.

PubMed

Jung, WooRam; Sierecki, Emma; Bastiani, Michele; O'Carroll, Ailis; Alexandrov, Kirill; Rae, James; Johnston, Wayne; Hunter, Dominic J B; Ferguson, Charles; Gambin, Yann; Ariotti, Nicholas; Parton, Robert G

2018-06-04

Caveolae have been linked to the regulation of signaling pathways in eukaryotic cells through direct interactions with caveolins. Here, we describe a cell-free system based on Leishmania tarentolae ( Lt ) extracts for the biogenesis of caveolae and show its use for single-molecule interaction studies. Insertion of expressed caveolin-1 (CAV1) into Lt membranes was analogous to that of caveolin in native membranes. Electron tomography showed that caveolins generate domains of precise size and curvature. Cell-free caveolae were used in quantitative assays to test the interaction of membrane-inserted caveolin with signaling proteins and to determine the stoichiometry of interactions. Binding of membrane-inserted CAV1 to several proposed binding partners, including endothelial nitric-oxide synthase, was negligible, but a small number of proteins, including TRAF2, interacted with CAV1 in a phosphorylation-(CAV1 Y14 )-stimulated manner. In cells subjected to oxidative stress, phosphorylated CAV1 recruited TRAF2 to the early endosome forming a novel signaling platform. These findings lead to a novel model for cellular stress signaling by CAV1. © 2018 Jung et al.

Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2014-01-01

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

Endosomal Interactions during Root Hair Growth

PubMed Central

von Wangenheim, Daniel; Rosero, Amparo; Komis, George; Šamajová, Olga; Ovečka, Miroslav; Voigt, Boris; Šamaj, Jozef

2016-01-01

The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth. PMID:26858728

Endosomal Interactions during Root Hair Growth.

PubMed

von Wangenheim, Daniel; Rosero, Amparo; Komis, George; Šamajová, Olga; Ovečka, Miroslav; Voigt, Boris; Šamaj, Jozef

2015-01-01

The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes-termed herein as dancing-endosomes-which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth.

Shape and size variation on the wing of Drosophila mediopunctata: influence of chromosome inversions and genotype-environment interaction.

PubMed

Hatadani, Luciane Mendes; Klaczko, Louis Bernard

2008-07-01

The second chromosome of Drosophila mediopunctata is highly polymorphic for inversions. Previous work reported a significant interaction between these inversions and collecting date on wing size, suggesting the presence of genotype-environment interaction. We performed experiments in the laboratory to test for the joint effects of temperature and chromosome inversions on size and shape of the wing in D. mediopunctata. Size was measured as the centroid size, and shape was analyzed using the generalized least squares Procrustes superimposition followed by discriminant analysis and canonical variates analysis of partial warps and uniform components scores. Our findings show that wing size and shape are influenced by temperature, sex, and karyotype. We also found evidence suggestive of an interaction between the effects of karyotype and temperature on wing shape, indicating the existence of genotype-environment interaction for this trait in D. mediopunctata. In addition, the association between wing size and chromosome inversions is in agreement with previous results indicating that these inversions might be accumulating alleles adapted to different temperatures. However, no significant interaction between temperature and karyotype for size was found--in spite of the significant presence of temperature-genotype (cross) interaction. We suggest that other ecological factors--such as larval crowding--or seasonal variation of genetic content within inversions may explain the previous results.

Identifying the regional-scale groundwater-surface water interaction on the Sanjiang Plain, Northeast China.

PubMed

Wang, Xihua; Zhang, Guangxin; Xu, Y Jun; Sun, Guangzhi

2015-11-01

Assessment on the interaction between groundwater and surface water (GW-SW) can generate information that is critical to regional water resource management, especially for regions that are highly dependent on groundwater resources for irrigation. This study investigated such interaction on China's Sanjiang Plain (10.9 × 10(4) km(2)) and produced results to assist sustainable regional water management for intensive agricultural activities. Methods of hierarchical cluster analysis (HCA), principal component analysis (PCA), and statistical analysis were used in this study. One hundred two water samplings (60 from shallow groundwater, 7 from deep groundwater, and 35 from surface water) were collected and grouped into three clusters and seven sub-clusters during the analyses. The PCA analysis identified four principal components of the interaction, which explained 85.9% variance of total database, attributed to the dissolution and evolution of gypsum, feldspar, and other natural minerals in the region that was affected by anthropic and geological (sedimentary rock mineral) activities. The analyses showed that surface water in the upper region of the Sanjiang Plain gained water from local shallow groundwater, indicating that the surface water in the upper region was relatively more resilient to withdrawal for usage, whereas in the middle region, there was only a weak interaction between shallow groundwater and surface water. In the lower region of the Sanjiang Plain, surface water lost water to shallow groundwater, indicating that the groundwater was vulnerable to pollution by pesticides and fertilizers from terrestrial sources.

Landau instability and mobility edges of the interacting one-dimensional Bose gas in weak random potentials

NASA Astrophysics Data System (ADS)

Cherny, Alexander Yu; Caux, Jean-Sébastien; Brand, Joachim

2018-01-01

We study the frictional force exerted on the trapped, interacting 1D Bose gas under the influence of a moving random potential. Specifically we consider weak potentials generated by optical speckle patterns with finite correlation length. We show that repulsive interactions between bosons lead to a superfluid response and suppression of frictional force, which can inhibit the onset of Anderson localisation. We perform a quantitative analysis of the Landau instability based on the dynamic structure factor of the integrable Lieb-Liniger model and demonstrate the existence of effective mobility edges.

Mathematical Analysis of a Coarsening Model with Local Interactions

NASA Astrophysics Data System (ADS)

Helmers, Michael; Niethammer, Barbara; Velázquez, Juan J. L.

2016-10-01

We consider particles on a one-dimensional lattice whose evolution is governed by nearest-neighbor interactions where particles that have reached size zero are removed from the system. Concentrating on configurations with infinitely many particles, we prove existence of solutions under a reasonable density assumption on the initial data and show that the vanishing of particles and the localized interactions can lead to non-uniqueness. Moreover, we provide a rigorous upper coarsening estimate and discuss generic statistical properties as well as some non-generic behavior of the evolution by means of heuristic arguments and numerical observations.

Hamiltonian dynamics for complex food webs

NASA Astrophysics Data System (ADS)

Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno

2016-03-01

We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.

Leader charisma and affective team climate: the moderating role of the leader's influence and interaction.

PubMed

Hernández Baeza, Ana; Araya Lao, Cristina; García Meneses, Juliana; González Romá, Vicente

2009-11-01

In this study, we evaluate the role of leader charisma in fostering positive affective team climate and preventing negative affective climate. The analysis of a longitudinal database of 137 bank branches by means of hierarchical moderated regression shows that leader charisma has a stronger effect on team optimism than on team tension. In addition, the leader's influence and the frequency of leader-team interaction moderate the relationship between charisma and affective climate. However, whereas the leader's influence enhances the relationship between leader charisma and positive affective climate, the frequency of interaction has counterproductive effects.

When Age and Culture Interact in an Easy and Yet Cognitively Demanding Task: Older Adults, But Not Younger Adults, Showed the Expected Cultural Differences

PubMed Central

Na, Jinkyung; Huang, Chih-Mao; Park, Denise C.

2017-01-01

The interaction between age and culture can have various implications for cognition as age represents the effect of biological processes whereas culture represents the effect of sustaining experiences. Nevertheless, their interaction has rarely been examined. Thus, based on the fact that Asians are more intuitive in reasoning than Americans, we examined how this cultural difference might interact with age. Young and old participants from the US and Singapore performed a categorization task (living vs. non-living). To measure their reliance on intuition, we manipulated the typicality of targets (animate vs. inanimate). We showed that (1) RTs for inanimate organisms were slower than RTs for animate organisms (atypicality cost), (2) the cost was particularly large for older adults and (3) an age × culture interaction was observed such that cultural differences in the cost (Singaporeans > Americans) was found only among older participants. Further, we demonstrated that the age effect was associated with cognitive function and the culture effect among older adults was associated with cultural values. Finally, a moderated mediation analysis suggests that cognitive function and cultural values interact with each other in order to jointly influence one’s cognition. PMID:28396649

When Age and Culture Interact in an Easy and Yet Cognitively Demanding Task: Older Adults, But Not Younger Adults, Showed the Expected Cultural Differences.

PubMed

Na, Jinkyung; Huang, Chih-Mao; Park, Denise C

2017-01-01

The interaction between age and culture can have various implications for cognition as age represents the effect of biological processes whereas culture represents the effect of sustaining experiences. Nevertheless, their interaction has rarely been examined. Thus, based on the fact that Asians are more intuitive in reasoning than Americans, we examined how this cultural difference might interact with age. Young and old participants from the US and Singapore performed a categorization task (living vs. non-living). To measure their reliance on intuition, we manipulated the typicality of targets (animate vs. inanimate). We showed that (1) RTs for inanimate organisms were slower than RTs for animate organisms (atypicality cost), (2) the cost was particularly large for older adults and (3) an age × culture interaction was observed such that cultural differences in the cost (Singaporeans > Americans) was found only among older participants. Further, we demonstrated that the age effect was associated with cognitive function and the culture effect among older adults was associated with cultural values. Finally, a moderated mediation analysis suggests that cognitive function and cultural values interact with each other in order to jointly influence one's cognition.

The modular architecture of protein-protein binding interfaces.

PubMed

Reichmann, D; Rahat, O; Albeck, S; Meged, R; Dym, O; Schreiber, G

2005-01-04

Protein-protein interactions are essential for life. Yet, our understanding of the general principles governing binding is not complete. In the present study, we show that the interface between proteins is built in a modular fashion; each module is comprised of a number of closely interacting residues, with few interactions between the modules. The boundaries between modules are defined by clustering the contact map of the interface. We show that mutations in one module do not affect residues located in a neighboring module. As a result, the structural and energetic consequences of the deletion of entire modules are surprisingly small. To the contrary, within their module, mutations cause complex energetic and structural consequences. Experimentally, this phenomenon is shown on the interaction between TEM1-beta-lactamase and beta-lactamase inhibitor protein (BLIP) by using multiple-mutant analysis and x-ray crystallography. Replacing an entire module of five interface residues with Ala created a large cavity in the interface, with no effect on the detailed structure of the remaining interface. The modular architecture of binding sites, which resembles human engineering design, greatly simplifies the design of new protein interactions and provides a feasible view of how these interactions evolved.

Highly biocompatible collagen-Delonix regia seed polysaccharide hybrid scaffolds for antimicrobial wound dressing.

PubMed

Cheirmadurai, Kalirajan; Thanikaivelan, Palanisamy; Murali, Ragothaman

2016-02-10

Biomaterials based entirely on biological resources are ideal for tissue engineering applications. Here we report the preparation of hybrid collagen scaffolds comprising gulmohar seed polysaccharide (GSP) and cinnamon bark extract as cross-linking agent. (1)H NMR spectrum of GSP confirms the presence of galactose and mannose in the ratio of 1:1.54, which was further corroborated using FT-IR. The hybrid scaffolds show better enzyme and thermal stability in contrast to pure collagen scaffold probably due to weak interactions from GSP and covalent interaction through cinnamaldehyde. Gas permeability and scanning electron microscopic analysis show that the porosity of the hybrid scaffolds is slightly reduced with the increase in the concentration of GSP. The infrared and circular dichroic spectral studies show that the secondary structure of the collagen did not change after the interaction with GSP and cinnamaldehyde. The hybrid scaffolds stabilized with cinnamaldehyde show good antimicrobial activity against the common multi-drug resistant wound pathogens. These results suggest that the prepared hybrid scaffolds have great potential for antimicrobial wound dressing applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Emergent dark energy via decoherence in quantum interactions

NASA Astrophysics Data System (ADS)

Altamirano, Natacha; Corona-Ugalde, Paulina; Khosla, Kiran E.; Milburn, Gerard J.; Mann, Robert B.

2017-06-01

In this work we consider a recent proposal that gravitational interactions are mediated via classical information and apply it to a relativistic context. We study a toy model of a quantized Friedman-Robertson-Walker (FRW) universe with the assumption that any test particles must feel a classical metric. We show that such a model results in decoherence in the FRW state that manifests itself as a dark energy fluid that fills the spacetime. Analysis of the resulting fluid, shows the equation of state asymptotically oscillates around the value w  =  -1/3, regardless of the spatial curvature, which provides the bound between accelerating and decelerating expanding FRW cosmologies. Motivated with quantum-classical interactions this model is yet another example of theories with violation of energy-momentum conservation whose signature could have significant consequences for the observable universe.

Displays of paternal mouse pup retrieval following communicative interaction with maternal mates.

PubMed

Liu, Hong-Xiang; Lopatina, Olga; Higashida, Chiharu; Fujimoto, Hiroko; Akther, Shirin; Inzhutova, Alena; Liang, Mingkun; Zhong, Jing; Tsuji, Takahiro; Yoshihara, Toru; Sumi, Kohei; Ishiyama, Mizuho; Ma, Wen-Jie; Ozaki, Mitsunori; Yagitani, Satoshi; Yokoyama, Shigeru; Mukaida, Naofumi; Sakurai, Takeshi; Hori, Osamu; Yoshioka, Katsuji; Hirao, Atsushi; Kato, Yukio; Ishihara, Katsuhiko; Kato, Ichiro; Okamoto, Hiroshi; Cherepanov, Stanislav M; Salmina, Alla B; Hirai, Hirokazu; Asano, Masahide; Brown, David A; Nagano, Isamu; Higashida, Haruhiro

2013-01-01

Compared with the knowledge of maternal care, much less is known about the factors required for paternal parental care. Here we report that new sires of laboratory mice, though not spontaneously parental, can be induced to show maternal-like parental care (pup retrieval) using signals from dams separated from their pups. During this interaction, the maternal mates emit 38-kHz ultrasonic vocalizations to their male partners, which are equivalent to vocalizations that occur following pheromone stimulation. Without these signals or in the absence of maternal mates, the sires do not retrieve their pups within 5 min. These results show that, in mice, the maternal parent communicates to the paternal parent to encourage pup care. This new paradigm may be useful in the analysis of the parental brain during paternal care induced by interactive communication.

Feedback control of an interacting Bose-Einstein condensate using phase-contrast imaging

NASA Astrophysics Data System (ADS)

Szigeti, S. S.; Hush, M. R.; Carvalho, A. R. R.; Hope, J. J.

2010-10-01

The linewidth of an atom laser is limited by density fluctuations in the Bose-Einstein condensate (BEC) from which the atom laser beam is outcoupled. In this paper we show that a stable spatial mode for an interacting BEC can be generated using a realistic control scheme that includes the effects of the measurement backaction. This model extends the feedback theory, based on a phase-contrast imaging setup, presented by Szigeti, Hush, Carvalho, and Hope [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.013614 80, 013614 (2009)]. In particular, it is applicable to a BEC with large interatomic interactions and solves the problem of inadequacy of the mean-field (coherent state) approximation by utilizing a fixed number state approximation. Our numerical analysis shows the control to be more effective for a condensate with a large nonlinearity.

Feedback control of an interacting Bose-Einstein condensate using phase-contrast imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szigeti, S. S.; Hush, M. R.; Carvalho, A. R. R.

2010-10-15

The linewidth of an atom laser is limited by density fluctuations in the Bose-Einstein condensate (BEC) from which the atom laser beam is outcoupled. In this paper we show that a stable spatial mode for an interacting BEC can be generated using a realistic control scheme that includes the effects of the measurement backaction. This model extends the feedback theory, based on a phase-contrast imaging setup, presented by Szigeti, Hush, Carvalho, and Hope [Phys. Rev. A 80, 013614 (2009)]. In particular, it is applicable to a BEC with large interatomic interactions and solves the problem of inadequacy of the mean-fieldmore » (coherent state) approximation by utilizing a fixed number state approximation. Our numerical analysis shows the control to be more effective for a condensate with a large nonlinearity.« less

Integrating Household Risk Mitigation Behavior in Flood Risk Analysis: An Agent-Based Model Approach.

PubMed

Haer, Toon; Botzen, W J Wouter; de Moel, Hans; Aerts, Jeroen C J H

2017-10-01

Recent studies showed that climate change and socioeconomic trends are expected to increase flood risks in many regions. However, in these studies, human behavior is commonly assumed to be constant, which neglects interaction and feedback loops between human and environmental systems. This neglect of human adaptation leads to a misrepresentation of flood risk. This article presents an agent-based model that incorporates human decision making in flood risk analysis. In particular, household investments in loss-reducing measures are examined under three economic decision models: (1) expected utility theory, which is the traditional economic model of rational agents; (2) prospect theory, which takes account of bounded rationality; and (3) a prospect theory model, which accounts for changing risk perceptions and social interactions through a process of Bayesian updating. We show that neglecting human behavior in flood risk assessment studies can result in a considerable misestimation of future flood risk, which is in our case study an overestimation of a factor two. Furthermore, we show how behavior models can support flood risk analysis under different behavioral assumptions, illustrating the need to include the dynamic adaptive human behavior of, for instance, households, insurers, and governments. The method presented here provides a solid basis for exploring human behavior and the resulting flood risk with respect to low-probability/high-impact risks. © 2016 The Authors Risk Analysis published by Wiley Periodicals, Inc. on behalf of Society for Risk Analysis.

Spectral, optical, thermal, Hirshfeld, antimicrobial studies and computational calculations of a new organic crystal, 1H-benzo[d]imidazol-3-ium-3,5-dinitrobenzoate

NASA Astrophysics Data System (ADS)

Sathya, K.; Dhamodharan, P.; Dhandapani, M.

2017-06-01

Single crystals of 1H-benzo[d]imidazol-3-ium-3,5-dinitrobenzoate (BDNB) were grown by reacting 3,5-dinitrobenzoic acid and benzimidazole by slow evaporation method. UV-Vis-NIR spectral studies of the BDNB show that the crystal is excellently transparent in entire visible region. Chemically and magnetically equivalent protons in BDNB were identified by 1H NMR technique. The carbon frame work of the molecule was established by 13C NMR spectroscopy. Proton transfer mechanism was confirmed by the presence of N+H group in BDNB by FT-IR spectroscopic technique. TG/DTA analyses confirmed that the crystal is stable up to172 °C. Single crystal XRD analysis was carried out to ascertain the molecular structure and the crystal belongs to monoclinic system with space group P21/c. Computational studies that include optimization of molecular geometry, natural bond analysis, Mulliken population analysis and HOMO-LUMO analysis were performed using B3LYP method at 6-31 g level. The low HOMO-LUMO energy gap of BDNB confirms high reactivity of BDNB. Hirshfeld analysis expose that O⋯H/H⋯O interactions are the prominent interactions. Theoretical calculations indicate that first order hyperpolarizability is 16 times greater than urea. The results show that the BDNB may be used for opto-electronic applications. The antimicrobial and antioxidant analyses shows concentration of the compound increases inhibition activity also increases.

Framed School--Frame Factors, Frames and the Dynamics of Social Interaction in School

ERIC Educational Resources Information Center

Persson, Anders

2015-01-01

This paper aims to show how the Goffman frame perspective can be used in an analysis of school and education and how it can be combined, in such analysis, with the frame factor perspective. The latter emphasizes factors that are determined outside the teaching process, while the former stresses how actors organize their experiences and define…

The Effect of Communication Skills Training for Generalist Palliative Care Providers on Patient-Reported Outcomes and Clinician Behaviors: A Systematic Review and Meta-analysis.

PubMed

Selman, Lucy Ellen; Brighton, Lisa J; Hawkins, Amy; McDonald, Christine; O'Brien, Suzanne; Robinson, Vicky; Khan, Shaheen A; George, Rob; Ramsenthaler, Christine; Higginson, Irene J; Koffman, Jonathan

2017-09-01

As most end-of-life care is provided by health care providers who are generalists rather than specialists in palliative care, effective communication skills training for generalists is essential. To determine the effect of communication training interventions for generalist palliative care providers on patient-reported outcomes and trainee behaviors. Systematic review from searches of 10 databases to December 2015 (MEDLINE, EMBASE, PsycINFO, ERIC, CINAHL, CENTRAL, Web of Science, ICTRP, CORDIS, and OpenGrey) plus hand searching. Randomized controlled trials of training interventions intended to enhance generalists' communication skills in end-of-life care were included. Two authors independently assessed eligibility after screening, extracted data, and graded quality. Data were pooled for meta-analysis using a random-effects model. PRISMA guidelines were followed. Nineteen of 11,441 articles were eligible, representing 14 trials. Eleven were included in meta-analyses (patients n = 3144, trainees n = 791). Meta-analysis showed no effect on patient outcomes (standardized mean difference [SMD] = 0.10, 95% CI -0.05 to 0.24) and high levels of heterogeneity (chi-square = 21.32, degrees of freedom [df] = 7, P = 0.003; I 2  = 67%). The effect on trainee behaviors in simulated interactions (SMD = 0.50, 95% CI 0.19-0.81) was greater than in real patient interactions (SMD = 0.21, 95% CI -0.01 to 0.43) with moderate heterogeneity (chi-square = 8.90, df = 5, P = 0.11; I 2  = 44%; chi-square = 5.96, df = 3, P = 0.11; I 2  = 50%, respectively). Two interventions with medium effects on showing empathy in real patient interactions included personalized feedback on recorded interactions. The effect of communication skills training for generalists on patient-reported outcomes remains unclear. Training can improve clinicians' ability to show empathy and discuss emotions, at least in simulated consultations. Personalized feedback on recorded patient interactions may be beneficial. CRD42014014777. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Multiple Component Event-Related Potential (mcERP) Estimation

NASA Technical Reports Server (NTRS)

Knuth, K. H.; Clanton, S. T.; Shah, A. S.; Truccolo, W. A.; Ding, M.; Bressler, S. L.; Trejo, L. J.; Schroeder, C. E.; Clancy, Daniel (Technical Monitor)

2002-01-01

We show how model-based estimation of the neural sources responsible for transient neuroelectric signals can be improved by the analysis of single trial data. Previously, we showed that a multiple component event-related potential (mcERP) algorithm can extract the responses of individual sources from recordings of a mixture of multiple, possibly interacting, neural ensembles. McERP also estimated single-trial amplitudes and onset latencies, thus allowing more accurate estimation of ongoing neural activity during an experimental trial. The mcERP algorithm is related to informax independent component analysis (ICA); however, the underlying signal model is more physiologically realistic in that a component is modeled as a stereotypic waveshape varying both in amplitude and onset latency from trial to trial. The result is a model that reflects quantities of interest to the neuroscientist. Here we demonstrate that the mcERP algorithm provides more accurate results than more traditional methods such as factor analysis and the more recent ICA. Whereas factor analysis assumes the sources are orthogonal and ICA assumes the sources are statistically independent, the mcERP algorithm makes no such assumptions thus allowing investigators to examine interactions among components by estimating the properties of single-trial responses.

Large explosive basaltic eruptions at Katla volcano, Iceland: Fragmentation, grain size and eruption dynamics

NASA Astrophysics Data System (ADS)

Schmith, Johanne; Höskuldsson, Ármann; Holm, Paul Martin; Larsen, Guðrún

2018-04-01

Katla volcano in Iceland produces hazardous large explosive basaltic eruptions on a regular basis, but very little quantitative data for future hazard assessments exist. Here details on fragmentation mechanism and eruption dynamics are derived from a study of deposit stratigraphy with detailed granulometry and grain morphology analysis, granulometric modeling, componentry and the new quantitative regularity index model of fragmentation mechanism. We show that magma/water interaction is important in the ash generation process, but to a variable extent. By investigating the large explosive basaltic eruptions from 1755 and 1625, we document that eruptions of similar size and magma geochemistry can have very different fragmentation dynamics. Our models show that fragmentation in the 1755 eruption was a combination of magmatic degassing and magma/water-interaction with the most magma/water-interaction at the beginning of the eruption. The fragmentation of the 1625 eruption was initially also a combination of both magmatic and phreatomagmatic processes, but magma/water-interaction diminished progressively during the later stages of the eruption. However, intense magma/water interaction was reintroduced during the final stages of the eruption dominating the fine fragmentation at the end. This detailed study of fragmentation changes documents that subglacial eruptions have highly variable interaction with the melt water showing that the amount and access to melt water changes significantly during eruptions. While it is often difficult to reconstruct the progression of eruptions that have no quantitative observational record, this study shows that integrating field observations and granulometry with the new regularity index can form a coherent model of eruption evolution.

Arabidopsis miR171-Targeted Scarecrow-Like Proteins Bind to GT cis-Elements and Mediate Gibberellin-Regulated Chlorophyll Biosynthesis under Light Conditions

PubMed Central

Ma, Zhaoxue; Hu, Xupeng; Cai, Wenjuan; Huang, Weihua; Zhou, Xin; Luo, Qian; Yang, Hongquan; Wang, Jiawei; Huang, Jirong

2014-01-01

An extraordinarily precise regulation of chlorophyll biosynthesis is essential for plant growth and development. However, our knowledge on the complex regulatory mechanisms of chlorophyll biosynthesis is very limited. Previous studies have demonstrated that miR171-targeted scarecrow-like proteins (SCL6/22/27) negatively regulate chlorophyll biosynthesis via an unknown mechanism. Here we showed that SCLs inhibit the expression of the key gene encoding protochlorophyllide oxidoreductase (POR) in light-grown plants, but have no significant effect on protochlorophyllide biosynthesis in etiolated seedlings. Histochemical analysis of β-glucuronidase (GUS) activity in transgenic plants expressing pSCL27::rSCL27-GUS revealed that SCL27-GUS accumulates at high levels and suppresses chlorophyll biosynthesis at the leaf basal proliferation region during leaf development. Transient gene expression assays showed that the promoter activity of PORC is indeed regulated by SCL27. Consistently, chromatin immunoprecipitation and quantitative PCR assays showed that SCL27 binds to the promoter region of PORC in vivo. An electrophoretic mobility shift assay revealed that SCL27 is directly interacted with G(A/G)(A/T)AA(A/T)GT cis-elements of the PORC promoter. Furthermore, genetic analysis showed that gibberellin (GA)-regulated chlorophyll biosynthesis is mediated, at least in part, by SCLs. We demonstrated that SCL27 interacts with DELLA proteins in vitro and in vivo by yeast-two-hybrid and coimmunoprecipitation analysis and found that their interaction reduces the binding activity of SCL27 to the PORC promoter. Additionally, we showed that SCL27 activates MIR171 gene expression, forming a feedback regulatory loop. Taken together, our data suggest that the miR171-SCL module is critical for mediating GA-DELLA signaling in the coordinate regulation of chlorophyll biosynthesis and leaf growth in light. PMID:25101599

Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain.

PubMed

Hou, Tingjun; Zhang, Wei; Case, David A; Wang, Wei

2008-02-29

Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decomposition analysis to characterize domain-peptide interactions and the molecular interaction energy components (MIECs), including van der Waals, electrostatic, and desolvation energy between residue pairs on the binding interface. We show a proof-of-concept study on the amphiphysin-1 SH3 domain interacting with its peptide ligands. The structures of the human amphiphysin-1 SH3 domain complexed with 884 peptides were first modeled using virtual mutagenesis and optimized by molecular mechanics (MM) minimization. Next, the MIECs between domain and peptide residues were computed using the MM/generalized Born decomposition analysis. We conducted two types of statistical analyses on the MIECs to demonstrate their usefulness for predicting binding affinities of peptides and for classifying peptides into binder and non-binder categories. First, combining partial least squares analysis and genetic algorithm, we fitted linear regression models between the MIECs and the peptide binding affinities on the training data set. These models were then used to predict binding affinities for peptides in the test data set; the predicted values have a correlation coefficient of 0.81 and an unsigned mean error of 0.39 compared with the experimentally measured ones. The partial least squares-genetic algorithm analysis on the MIECs revealed the critical interactions for the binding specificity of the amphiphysin-1 SH3 domain. Next, a support vector machine (SVM) was employed to build classification models based on the MIECs of peptides in the training set. A rigorous training-validation procedure was used to assess the performances of different kernel functions in SVM and different combinations of the MIECs. The best SVM classifier gave satisfactory predictions for the test set, indicated by average prediction accuracy rates of 78% and 91% for the binding and non-binding peptides, respectively. We also showed that the performance of our approach on both binding affinity prediction and binder/non-binder classification was superior to the performances of the conventional MM/Poisson-Boltzmann solvent-accessible surface area and MM/generalized Born solvent-accessible surface area calculations. Our study demonstrates that the analysis of the MIECs between peptides and the SH3 domain can successfully characterize the binding interface, and it provides a framework to derive integrated prediction models for different domain-peptide systems.

Silver nanoparticle-human hemoglobin interface: time evolution of the corona formation and interaction phenomenon

NASA Astrophysics Data System (ADS)

Bhunia, A. K.; Kamilya, T.; Saha, S.

2017-10-01

In this paper, we have used spectroscopic and electron microscopic analysis to monitor the time evolution of the silver nanoparticles (Ag NP)-human hemoglobin (Hb) corona formation and to characterize the interaction of the Ag NPs with Hb. The time constants for surface plasmon resonance binding and reorganization are found to be 9.51 and 118.48 min, respectively. The drop of surface charge and the increase of the hydrodynamic diameter indicated the corona of Hb on the Ag NP surface. The auto correlation function is found to broaden with the increasing time of the corona formation. Surface zeta potential revealed that positively charged Hb interact electrostatically with negatively charged Ag NP surfaces. The change in α helix and β sheet depends on the corona formation time. The visualization of the Hb corona from HRTEM showed large number of Hb domains aggregate containing essentially Ag NPs and without Ag NPs. Emission study showed the tertiary deformation, energy transfer, nature of interaction and quenching under three different temperatures.

Silver nanoparticle-human hemoglobin interface: time evolution of the corona formation and interaction phenomenon.

PubMed

Bhunia, A K; Kamilya, T; Saha, S

2017-01-01

In this paper, we have used spectroscopic and electron microscopic analysis to monitor the time evolution of the silver nanoparticles (Ag NP)-human hemoglobin (Hb) corona formation and to characterize the interaction of the Ag NPs with Hb. The time constants for surface plasmon resonance binding and reorganization are found to be 9.51 and 118.48 min, respectively. The drop of surface charge and the increase of the hydrodynamic diameter indicated the corona of Hb on the Ag NP surface. The auto correlation function is found to broaden with the increasing time of the corona formation. Surface zeta potential revealed that positively charged Hb interact electrostatically with negatively charged Ag NP surfaces. The change in α helix and β sheet depends on the corona formation time. The visualization of the Hb corona from HRTEM showed large number of Hb domains aggregate containing essentially Ag NPs and without Ag NPs. Emission study showed the tertiary deformation, energy transfer, nature of interaction and quenching under three different temperatures.

Identification of non-classical C-H···M interactions in early and late transition metal complexes containing the CH(ArO)3 ligand.

PubMed

Lein, Matthias; Harrison, John A; Nielson, Alastair J

2013-08-14

The fully optimised DFT structure of the d(0) complex [{CH(ArO)3}Ti(NEt2)] (2) at the B3LYP level compares well with the distorted tetrahedral geometry shown by the X-ray crystal structure. QTAIM analysis of the electron density associated with the C-H···Ti interaction shows a well defined bond critical point, a bond path between the hydrogen and titanium centres and a negative value for the energy density indicative of covalency. A natural bond orbital (NBO) picture of the interaction shows that the C-H σ bond electron density donates to a d hybrid orbital on the metal in a linear fashion. Calculated IR and NMR data for the components of the interaction are consistent with experiment. The computed structures for [{CH(ArO)3}Ti(OPh)] (3), [{CH(ArO)3}Zr(NEt2)] (4), [{CH(ArO)3}Hf(NEt2)] (5), show tetrahedral geometries and QTAIM and NBO properties similar to (2). [{CH(ArO)3}Mo(NEt2)] (6) shows distortion of the tripodal ligand and a reduced C-H···M bond angle with properties more consistent with a C-H···M side-on donor interaction. In [{CH(ArO)3}Fe(NEt2)] (7) the C-H···M bond angle is linear and involves a donor interaction. An energy minimised structure maintaining the three fold coordination to the tripodal ligand was not obtained for [{CH(ArO)3}Ni(NEt2)](2-) but changing from a diethyl amide ligand to phenolato gave energy minimised [{CH(ArO)3}Ni(OPh)](2-) (8). This structure shows a distorted square planar geometry with a substantially bent phenoxo ligand and a near linear C-H···M covalent interaction with donor and back bonding properties. The work shows that linear C-H···M interactions can have both agostic and weak hydrogen bond-like covalency.

The USP1-UAF1 complex interacts with RAD51AP1 to promote homologous recombination repair.

PubMed

Cukras, Scott; Lee, Euiho; Palumbo, Emily; Benavidez, Pamela; Moldovan, George-Lucian; Kee, Younghoon

2016-10-01

USP1 deubiquitinating enzyme and its stoichiometric binding partner UAF1 play an essential role in promoting DNA homologous recombination (HR) repair in response to various types of DNA damaging agents. Deubiquitination of FANCD2 may be attributed to the key role of USP1-UAF1 complex in regulating HR repair, however whether USP1-UAF1 promotes HR repair independently of FANCD2 deubiquitination is not known. Here we show evidence that the USP1-UAF1 complex has a FANCD2-independent function in promoting HR repair. Proteomic search of UAF1-interacting proteins revealed that UAF1 associates with RAD51AP1, a RAD51-interacting protein implicated in HR repair. We show that UAF1 mediates the interaction between USP1 and RAD51AP1, and that depletion of USP1 or UAF1 led to a decreased stability of RAD51AP1. Protein interaction mapping analysis identified some key residues within RAD51AP1 required for interacting with the USP1-UAF1 complex. Cells expressing the UAF1 interaction-deficient mutant of RAD51AP1 show increased chromosomal aberrations in response to Mitomycin C treatment. Moreover, similar to the RAD51AP1 depleted cells, the cells expressing UAF1-interaction deficient RAD51AP1 display persistent RAD51 foci following DNA damage exposure, indicating that these factors regulate a later step during the HR repair. These data altogether suggest that the USP1-UAF1 complex promotes HR repair via multiple mechanisms: through FANCD2 deubiquitination, as well as by interacting with RAD51AP1.

The USP1-UAF1 complex interacts with RAD51AP1 to promote homologous recombination repair

PubMed Central

Cukras, Scott; Lee, Euiho; Palumbo, Emily; Benavidez, Pamela; Moldovan, George-Lucian; Kee, Younghoon

2016-01-01

ABSTRACT USP1 deubiquitinating enzyme and its stoichiometric binding partner UAF1 play an essential role in promoting DNA homologous recombination (HR) repair in response to various types of DNA damaging agents. Deubiquitination of FANCD2 may be attributed to the key role of USP1-UAF1 complex in regulating HR repair, however whether USP1-UAF1 promotes HR repair independently of FANCD2 deubiquitination is not known. Here we show evidence that the USP1-UAF1 complex has a FANCD2-independent function in promoting HR repair. Proteomic search of UAF1-interacting proteins revealed that UAF1 associates with RAD51AP1, a RAD51-interacting protein implicated in HR repair. We show that UAF1 mediates the interaction between USP1 and RAD51AP1, and that depletion of USP1 or UAF1 led to a decreased stability of RAD51AP1. Protein interaction mapping analysis identified some key residues within RAD51AP1 required for interacting with the USP1-UAF1 complex. Cells expressing the UAF1 interaction-deficient mutant of RAD51AP1 show increased chromosomal aberrations in response to Mitomycin C treatment. Moreover, similar to the RAD51AP1 depleted cells, the cells expressing UAF1-interaction deficient RAD51AP1 display persistent RAD51 foci following DNA damage exposure, indicating that these factors regulate a later step during the HR repair. These data altogether suggest that the USP1-UAF1 complex promotes HR repair via multiple mechanisms: through FANCD2 deubiquitination, as well as by interacting with RAD51AP1. PMID:27463890

A male-specific QTL for social interaction behavior in mice mapped with automated pattern detection by a hidden Markov model incorporated into newly developed freeware.

PubMed

Arakawa, Toshiya; Tanave, Akira; Ikeuchi, Shiho; Takahashi, Aki; Kakihara, Satoshi; Kimura, Shingo; Sugimoto, Hiroki; Asada, Nobuhiko; Shiroishi, Toshihiko; Tomihara, Kazuya; Tsuchiya, Takashi; Koide, Tsuyoshi

2014-08-30

Owing to their complex nature, social interaction tests normally require the observation of video data by a human researcher, and thus are difficult to use in large-scale studies. We previously established a statistical method, a hidden Markov model (HMM), which enables the differentiation of two social states ("interaction" and "indifference"), and three social states ("sniffing", "following", and "indifference"), automatically in silico. Here, we developed freeware called DuoMouse for the rapid evaluation of social interaction behavior. This software incorporates five steps: (1) settings, (2) video recording, (3) tracking from the video data, (4) HMM analysis, and (5) visualization of the results. Using DuoMouse, we mapped a genetic locus related to social interaction. We previously reported that a consomic strain, B6-Chr6C(MSM), with its chromosome 6 substituted for one from MSM/Ms, showed more social interaction than C57BL/6 (B6). We made four subconsomic strains, C3, C5, C6, and C7, each of which has a shorter segment of chromosome 6 derived from B6-Chr6C, and conducted social interaction tests on these strains. DuoMouse indicated that C6, but not C3, C5, and C7, showed higher interaction, sniffing, and following than B6, specifically in males. The data obtained by human observation showed high concordance to those from DuoMouse. The results indicated that the MSM-derived chromosomal region present in C6-but not in C3, C5, and C7-associated with increased social behavior. This method to analyze social interaction will aid primary screening for difference in social behavior in mice. Copyright © 2014 Elsevier B.V. All rights reserved.

Detecting treatment-subgroup interactions in clustered data with generalized linear mixed-effects model trees.

PubMed

Fokkema, M; Smits, N; Zeileis, A; Hothorn, T; Kelderman, H

2017-10-25

Identification of subgroups of patients for whom treatment A is more effective than treatment B, and vice versa, is of key importance to the development of personalized medicine. Tree-based algorithms are helpful tools for the detection of such interactions, but none of the available algorithms allow for taking into account clustered or nested dataset structures, which are particularly common in psychological research. Therefore, we propose the generalized linear mixed-effects model tree (GLMM tree) algorithm, which allows for the detection of treatment-subgroup interactions, while accounting for the clustered structure of a dataset. The algorithm uses model-based recursive partitioning to detect treatment-subgroup interactions, and a GLMM to estimate the random-effects parameters. In a simulation study, GLMM trees show higher accuracy in recovering treatment-subgroup interactions, higher predictive accuracy, and lower type II error rates than linear-model-based recursive partitioning and mixed-effects regression trees. Also, GLMM trees show somewhat higher predictive accuracy than linear mixed-effects models with pre-specified interaction effects, on average. We illustrate the application of GLMM trees on an individual patient-level data meta-analysis on treatments for depression. We conclude that GLMM trees are a promising exploratory tool for the detection of treatment-subgroup interactions in clustered datasets.

GraphSAW: a web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data.

PubMed

Shoshi, Alban; Hoppe, Tobias; Kormeier, Benjamin; Ogultarhan, Venus; Hofestädt, Ralf

2015-02-28

Adverse drug reactions are one of the most common causes of death in industrialized Western countries. Nowadays, empirical data from clinical studies for the approval and monitoring of drugs and molecular databases is available. The integration of database information is a promising method for providing well-based knowledge to avoid adverse drug reactions. This paper presents our web-based decision support system GraphSAW which analyzes and evaluates drug interactions and side effects based on data from two commercial and two freely available molecular databases. The system is able to analyze single and combined drug-drug interactions, drug-molecule interactions as well as single and cumulative side effects. In addition, it allows exploring associative networks of drugs, molecules, metabolic pathways, and diseases in an intuitive way. The molecular medication analysis includes the capabilities of the upper features. A statistical evaluation of the integrated data and top 20 drugs concerning drug interactions and side effects is performed. The results of the data analysis give an overview of all theoretically possible drug interactions and side effects. The evaluation shows a mismatch between pharmaceutical and molecular databases. The concordance of drug interactions was about 12% and 9% of drug side effects. An application case with prescribed data of 11 patients is presented in order to demonstrate the functionality of the system under real conditions. For each patient at least two interactions occured in every medication and about 8% of total diseases were possibly induced by drug therapy. GraphSAW (http://tunicata.techfak.uni-bielefeld.de/graphsaw/) is meant to be a web-based system for health professionals and researchers. GraphSAW provides comprehensive drug-related knowledge and an improved medication analysis which may support efforts to reduce the risk of medication errors and numerous drastic side effects.

New insights into organic-inorganic hybrid perovskite CH₃NH₃PbI₃ nanoparticles. An experimental and theoretical study of doping in Pb²⁺ sites with Sn²⁺, Sr²⁺, Cd²⁺ and Ca²⁺.

PubMed

Navas, Javier; Sánchez-Coronilla, Antonio; Gallardo, Juan Jesús; Hernández, Norge Cruz; Piñero, Jose Carlos; Alcántara, Rodrigo; Fernández-Lorenzo, Concha; De los Santos, Desireé M; Aguilar, Teresa; Martín-Calleja, Joaquín

2015-04-14

This paper presents the synthesis of the organic-inorganic hybrid perovskite, CH3NH3PbI3, doped in the Pb(2+) position with Sn(2+), Sr(2+), Cd(2+) and Ca(2+). The incorporation of the dopants into the crystalline structure was analysed, observing how the characteristics of the dopant affected properties such as the crystalline phase, emission and optical properties. XRD showed how doping with Sn(2+), Sr(2+) and Cd(2+) did not modify the normal tetragonal phase. When doping with Ca(2+), the cubic phase was obtained. Moreover, DR-UV-Vis spectroscopy showed how the band gap decreased with the dopants, the values following the trend Sr(2+) < Cd(2+) < Ca(2+) < CH3NH3PbI3 ≈ Sn(2+). The biggest decrease was generated by Sr(2+), which reduced the CH3NH3PbI3 value by 4.5%. In turn, cathodoluminescence (CL) measurements confirmed the band gap obtained. Periodic-DFT calculations were performed to understand the experimental structures. The DOS analysis confirmed the experimental results obtained using UV-Vis spectroscopy, with the values calculated following the trend Sn(2+) ≈ Pb(2+) > Cd(2+) > Sr(2+) for the tetragonal structure and Pb(2+) > Ca(2+) for the cubic phase. The electron localization function (ELF) analysis showed similar electron localizations for undoped and Sn(2+)-doped tetragonal structures, which were different from those doped with Sr(2+) and Cd(2+). Furthermore, when Cd(2+) was incorporated, the Cd-I interaction was strengthened. For Ca(2+) doping, the Ca-I interaction had a greater ionic nature than Cd-I. Finally, an analysis based on the non-covalent interaction (NCI) index is presented to determine the weak-type interactions of the CH3NH3 groups with the dopant and I atoms. To our knowledge, this kind of analysis with these hybrid systems has not been performed previously.

An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant

NASA Astrophysics Data System (ADS)

Sanusi, Zainab K.; Govender, Thavendran; Maguire, Glenn E. M.; Maseko, Sibusiso B.; Lin, Johnson; Kruger, Hendrik G.; Honarparvar, Bahareh

2018-03-01

The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host-guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.

Temporal scaling of groundwater level fluctuations near a stream

USGS Publications Warehouse

Schilling, K.E.; Zhang, Y.-K.

2012-01-01

Temporal scaling in stream discharge and hydraulic heads in riparian wells was evaluated to determine the feasibility of using spectral analysis to identify potential surface and groundwater interaction. In floodplains where groundwater levels respond rapidly to precipitation recharge, potential interaction is established if the hydraulic head (h) spectrum of riparian groundwater has a power spectral density similar to stream discharge (Q), exhibiting a characteristic breakpoint between high and low frequencies. At a field site in Walnut Creek watershed in central Iowa, spectral analysis of h in wells located 1 m from the channel edge showed a breakpoint in scaling very similar to the spectrum of Q (~20 h), whereas h in wells located 20 and 40 m from the channel showed temporal scaling from 1 to 10,000 h without a well-defined breakpoint. The spectral exponent (??) in the riparian zone decreased systematically from the channel into the floodplain as groundwater levels were increasingly dominated by white noise groundwater recharge. The scaling pattern of hydraulic head was not affected by land cover type, although the number of analyses was limited and site conditions were variable among sites. Spectral analysis would not replace quantitative tracer or modeling studies, but the method may provide a simple means of confirming potential interaction at some sites. ?? 2011, The Author(s). Ground Water ?? 2011, National Ground Water Association.

Temporal scaling of groundwater level fluctuations near a stream.

PubMed

Schilling, Keith E; Zhang, You-Kuan

2012-01-01

Temporal scaling in stream discharge and hydraulic heads in riparian wells was evaluated to determine the feasibility of using spectral analysis to identify potential surface and groundwater interaction. In floodplains where groundwater levels respond rapidly to precipitation recharge, potential interaction is established if the hydraulic head (h) spectrum of riparian groundwater has a power spectral density similar to stream discharge (Q), exhibiting a characteristic breakpoint between high and low frequencies. At a field site in Walnut Creek watershed in central Iowa, spectral analysis of h in wells located 1 m from the channel edge showed a breakpoint in scaling very similar to the spectrum of Q (∼20 h), whereas h in wells located 20 and 40 m from the channel showed temporal scaling from 1 to 10,000 h without a well-defined breakpoint. The spectral exponent (β) in the riparian zone decreased systematically from the channel into the floodplain as groundwater levels were increasingly dominated by white noise groundwater recharge. The scaling pattern of hydraulic head was not affected by land cover type, although the number of analyses was limited and site conditions were variable among sites. Spectral analysis would not replace quantitative tracer or modeling studies, but the method may provide a simple means of confirming potential interaction at some sites. © 2011, The Author(s). Ground Water © 2011, National Ground Water Association.

The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity.

PubMed

Zhao, Huaying; Balbo, Andrea; Brown, Patrick H; Schuck, Peter

2011-05-01

Sedimentation velocity (SV) experiments of heterogeneous interacting systems exhibit characteristic boundary structures that can usually be very easily recognized and quantified. For slowly interacting systems, the boundaries represent concentrations of macromolecular species sedimenting at different rates, and they can be interpreted directly with population models based solely on the mass action law. For fast reactions, migration and chemical reactions are coupled, and different, but equally easily discernable boundary structures appear. However, these features have not been commonly utilized for data analysis, for the lack of an intuitive and computationally simple model. The recently introduced effective particle theory (EPT) provides a suitable framework. Here, we review the motivation and theoretical basis of EPT, and explore practical aspects for its application. We introduce an EPT-based design tool for SV experiments of heterogeneous interactions in the software SEDPHAT. As a practical tool for the first step of data analysis, we describe how the boundary resolution of the sedimentation coefficient distribution c(s) can be further improved with a Bayesian adjustment of maximum entropy regularization to the case of heterogeneous interactions between molecules that have been previously studied separately. This can facilitate extracting the characteristic boundary features by integration of c(s). In a second step, these are assembled into isotherms as a function of total loading concentrations and fitted with EPT. Methods for addressing concentration errors in isotherms are discussed. Finally, in an experimental model system of alpha-chymotrypsin interacting with soybean trypsin inhibitor, we show that EPT provides an excellent description of the experimental sedimentation boundary structure of fast interacting systems. Published by Elsevier Inc.

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

PubMed Central

Shi, Wan; Quan, Mingyang; Du, Qingzhang; Zhang, Deqiang

2017-01-01

Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0.62), suggesting that the interaction of NERDL with its putative target might be involved in wood formation. We conducted association mapping in a natural population of P. tomentosa (435 unrelated individuals) to evaluate genetic variation and the interaction of the lncRNA NERDL with PtoNERD. Using additive and dominant models, we identified 30 SNPs (P < 0.01) associated with five tree growth and wood property traits. Each SNP explained 3.90–8.57% of phenotypic variance, suggesting that NERDL and its putative target play a common role in wood formation. Epistasis analysis uncovered nine SNP-SNP association pairs between NERDL and PtoNERD, with an information gain of -7.55 to 2.16%, reflecting the strong interactions between NERDL and its putative target. This analysis provides a powerful method for deciphering the genetic interactions of lncRNAs with mRNA and dissecting the complex genetic network of quantitative traits in trees. PMID:28674544

Constrained Kinematics of ICMEs from Multi-point in Situ and Heliospheric Imaging Data

NASA Astrophysics Data System (ADS)

Rollett, T.; Temmer, M.; Moestl, C.; Veronig, A. M.; Lugaz, N.; Vrsnak, B.; Farrugia, C. J.; Amerstorfer, U.

2013-12-01

The constrained harmonic mean (CHM) method is used to calculate the direction of motion of ICMEs and their kinematical profiles. Combining single spacecraft white-light observations from STEREO/HI with supplementary in situ data, it is possible to derive the propagation speed varying with heliocentric distance. This is a big advantage against other single-viewpoint methods, i.e. fitting methods, which assume a constant propagation speed. We show two different applications for the CHM method: first, an analysis of the interaction between the solar wind and ICMEs, and second, the interaction between two ICMEs. For analyzing interaction processes it is crucial to use a method that has the ability to investigate the corresponding effects on ICME kinematics. Additionally, we show the analysis of an outstanding fast ICME event of March 2012, which was detected in situ by Venus Express, Messenger and Wind and also observed by STEREO-A/HI. Due to these multiple in situ measurements it was possible to constrain the ICME kinematics by three different boundary values. These studies are fundamental in order to deepen the understanding of ICME evolution and to enhance existing forecasting methods. This work has received funding from the European Commission FP7 Project COMESEP (263252).

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

The gravitational self-interaction of the Earth's tidal bulge

NASA Astrophysics Data System (ADS)

Norsen, Travis; Dreese, Mackenzie; West, Christopher

2017-09-01

According to a standard, idealized analysis, the Moon would produce a 54 cm equilibrium tidal bulge in the Earth's oceans. This analysis omits many factors (beyond the scope of the simple idealized model) that dramatically influence the actual height and timing of the tides at different locations, but it is nevertheless an important foundation for more detailed studies. Here, we show that the standard analysis also omits another factor—the gravitational interaction of the tidal bulge with itself—which is entirely compatible with the simple, idealized equilibrium model and which produces a surprisingly non-trivial correction to the predicted size of the tidal bulge. Our analysis uses ideas and techniques that are familiar from electrostatics, and should thus be of interest to teachers and students of undergraduate E&M, Classical Mechanics (and/or other courses that cover the tides), and geophysics courses that cover the closely related topic of Earth's equatorial bulge.

A Global Meta-Analysis of the Value of Ecosystem Services Provided by Lakes.

PubMed

Reynaud, Arnaud; Lanzanova, Denis

2017-07-01

This study presents the first meta-analysis on the economic value of ecosystem services delivered by lakes. A worldwide data set of 699 observations drawn from 133 studies combines information reported in primary studies with geospatial data. The meta-analysis explores antagonisms and synergies between ecosystem services. This is the first meta-analysis to incorporate simultaneously external geospatial data and ecosystem service interactions. We first show that it is possible to reliably predict the value of ecosystem services provided by lakes based on their physical and geographic characteristics. Second, we demonstrate that interactions between ecosystem services appear to be significant for explaining lake ecosystem service values. Third, we provide an estimation of the average value of ecosystem services provided by lakes: between 106 and 140 USD$2010 per respondent per year for non-hedonic price studies and between 169 and 403 USD$2010 per property per year for hedonic price studies.

Automatic Identification of Character Types from Film Dialogs

PubMed Central

Skowron, Marcin; Trapp, Martin; Payr, Sabine; Trappl, Robert

2016-01-01

ABSTRACT We study the detection of character types from fictional dialog texts such as screenplays. As approaches based on the analysis of utterances’ linguistic properties are not sufficient to identify all fictional character types, we develop an integrative approach that complements linguistic analysis with interactive and communication characteristics, and show that it can improve the identification performance. The interactive characteristics of fictional characters are captured by the descriptive analysis of semantic graphs weighted by linguistic markers of expressivity and social role. For this approach, we introduce a new data set of action movie character types with their corresponding sequences of dialogs. The evaluation results demonstrate that the integrated approach outperforms baseline approaches on the presented data set. Comparative in-depth analysis of a single screenplay leads on to the discussion of possible limitations of this approach and to directions for future research. PMID:29118463

Psychological, emotional studies of Mir space station missions show Russians fared better than Americans.

PubMed

Boyd, K

2001-06-01

Weekly surveys gathered from crewmembers and mission control personnel during NASA missions to the Mir space station were used to rate mood, work environment, and interactions with the rest of the crew. Analysis of the surveys indicated that Americans were less satisfied with their group interactions and work environments than Russians. Also, mission control workers reported higher levels of tension, fatigue, confusion, and overall negative feelings than the astronauts and cosmonauts.

Dynamical network interactions in distributed control of robots

NASA Astrophysics Data System (ADS)

Buscarino, Arturo; Fortuna, Luigi; Frasca, Mattia; Rizzo, Alessandro

2006-03-01

In this paper the dynamical network model of the interactions within a group of mobile robots is investigated and proposed as a possible strategy for controlling the robots without central coordination. Motivated by the results of the analysis of our simple model, we show that the system performance in the presence of noise can be improved by including long-range connections between the robots. Finally, a suitable strategy based on this model to control exploration and transport is introduced.

Nonlinear and Dissipation Characteristics of Ocean Surface Waves in Estuarine Environments

DTIC Science & Technology

2010-01-01

determines the time scale over which the interactions occur, in the manner of Hill and Foda (1998) and Jamali et al. (2003). RESULTS Contrary to...the intermediate-depth work of Hill and Foda (1998) and Jamali et al. (2003), the interactions in this wealky-dispersive, weakly-nonlinear model...occur very quickly. Figure 1 shows the amplitude of one surface wave mode and two interface mode as a function of time resulting from the analysis . We

Functional analysis of the Hikeshi-like protein and its interaction with HSP70 in Arabidopsis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koizumi, Shinya; Ohama, Naohiko; Mizoi, Junya

2014-07-18

Highlights: • HKL, a Hikeshi homologous gene is identified in Arabidopsis. • HKL interacts with two HSP70 isoforms and regulates the subcellular localization of HSC70-1. • The two HSP70 translocate into nucleus in response to heat stress. • Overexpression of HKL confers thermotolerance in transgenic plants. - Abstract: Heat shock proteins (HSPs) refold damaged proteins and are an essential component of the heat shock response. Previously, the 70 kDa heat shock protein (HSP70) has been reported to translocate into the nucleus in a heat-dependent manner in many organisms. In humans, the heat-induced translocation of HSP70 requires the nuclear carrier proteinmore » Hikeshi. In the Arabidopsis genome, only one gene encodes a protein with high homology to Hikeshi, and we named this homolog Hikeshi-like (HKL) protein. In this study, we show that two Arabidopsis HSP70 isoforms accumulate in the nucleus in response to heat shock and that HKL interacts with these HSP70s. Our histochemical analysis revealed that HKL is predominantly expressed in meristematic tissues, suggesting the potential importance of HKL during cell division in Arabidopsis. In addition, we show that HKL regulates HSP70 localization, and HKL overexpression conferred thermotolerance to transgenic Arabidopsis plants. Our results suggest that HKL plays a positive role in the thermotolerance of Arabidopsis plants and cooperatively interacts with HSP70.« less

Interaction study of rice stripe virus proteins reveals a region of the nucleocapsid protein (NP) required for NP self-interaction and nuclear localization.

PubMed

Lian, Sen; Cho, Won Kyong; Jo, Yeonhwa; Kim, Sang-Min; Kim, Kook-Hyung

2014-04-01

Rice stripe virus (RSV), which belongs to the genus Tenuivirus, is an emergent virus problem. The RSV genome is composed of four single-strand RNAs (RNA1-RNA4) and encodes seven proteins. We investigated interactions between six of the RSV proteins by yeast-two hybrid (Y2H) assay in vitro and by bimolecular fluorescence complementation (BiFC) in planta. Y2H identified self-interaction of the nucleocapsid protein (NP) and NS3, while BiFC revealed self-interaction of NP, NS3, and NCP. To identify regions(s) and/or crucial amino acid (aa) residues required for NP self-interaction, we generated various truncated and aa substitution mutants. Y2H assay showed that the N-terminal region of NP (aa 1-56) is necessary for NP self-interaction. Further analysis with substitution mutants demonstrated that additional aa residues located at 42-47 affected their interaction with full-length NP. These results indicate that the N-terminal region (aa 1-36 and 42-47) is required for NP self-interaction. BiFC and co-localization studies showed that the region required for NP self-interaction is also required for NP localization at the nucleus. Overall, our results indicate that the N-terminal region (aa 1-47) of the NP is important for NP self-interaction and that six aa residues (42-47) are essential for both NP self-interaction and nuclear localization. Copyright © 2014 Elsevier B.V. All rights reserved.

Thiophenic compounds adsorption on Na(I)Y and rare earth exchanged Y zeolites: a density functional theory study.

PubMed

Gao, Xionghou; Geng, Wei; Zhang, Haitao; Zhao, Xuefei; Yao, Xiaojun

2013-11-01

We have theoretically investigated the adsorption of thiophene, benzothiophene, dibenzothiophene on Na(I)Y and rare earth exchanged La(III)Y, Ce(III)Y, Pr(III)Y Nd(III)Y zeolites by density functional theory calculations. The calculated results show that except benzothiophene adsorbed on Na(I)Y with a stand configuration, the stable adsorption structures of other thiophenic compounds on zeolites exhibit lying configurations. Adsorption energies of thiophenic compounds on the Na(I)Y are very low, and decrease with the increase of the number of benzene rings in thiophenic compounds. All rare earth exchanged zeolites exhibit strong interaction with thiophene. La(III)Y and Nd(III)Y zeolites are found to show enhanced adsorption energies to benzothiophene and Pr(III)Y zeolites are favorable for dibenzothiophene adsorption. The analysis of the electronic total charge density and electron orbital overlaps show that the thiophenic compounds interact with zeolites by π-electrons of thiophene ring and exchanged metal atom. Mulliken charge populations analysis reveals that adsorption energies are strongly dependent on the charge transfer of thiophenic molecule and exchanged metal atom.

Interaction between HLA-B60 and HLA-B27 as a Better Predictor of Ankylosing Spondylitis in a Taiwanese Population

PubMed Central

Hsu, Yu-Wen; Wen, Ya-Feng; Wang, Wen-Chang; Wong, Ruey-Hong; Lu, Hsing-Fang; van Gaalen, Floris A.; Chang, Wei-Chiao

2015-01-01

Objective Ankylosing spondylitis (AS) is a form of chronic inflammatory spondyloarthritis (SpA) that causes pain and stiffness in spines or joints. Human leukocyte antigen B27 (HLA-B27) and B60 (HLA-B60) have been reported as major genetic risk factors of AS. In addition, rs13202464, located on major histocompatibility complex (MHC) region, showed high sensitivity (98.7%) and specificity (98.0%) for HLA-B27. Design The aim of our study is to test whether the interaction between HLA-B60 and HLA-B27 (rs13202464) can serve as a better predictor of AS. We have genotyped HLA-B60 and rs13202464 among 471 patients with AS and 557 healthy subjects. Combined risk factors were investigated to test the biological interaction. Results Our results indicated that the relative risk (RR) for HLA-B27+/HLA-B60− was 152 (95% CI 91 to 255) and it increased to 201 (95% CI 85 to 475) in HLA-B27+/HLA-B60+ patients (with HLA-B27−/HLA-B60− as reference). Combinational analysis of two risk factors (HLA-B27+/HLA-B60+) showed a relative excess risk due to interaction (RERI) of 46.79 (95% CI: -117.58 to 211.16), attributable proportion (AP) of 0.23 (95% CI: -0.41 to 0.88) and a synergy index (S) of 1.31 (95% CI: 0.56 to 3.04). Conclusion In conclusion, genetic interaction analysis revealed that the interaction between HLA-B60 and HLA-B27 is a better marker for the risk of AS susceptibility in a Taiwanese population. PMID:26469786

Interaction between HLA-B60 and HLA-B27 as a Better Predictor of Ankylosing Spondylitis in a Taiwanese Population.

PubMed

Wei, James Cheng-Chung; Sung-Ching, Henry Wong; Hsu, Yu-Wen; Wen, Ya-Feng; Wang, Wen-Chang; Wong, Ruey-Hong; Lu, Hsing-Fang; Gaalen, Floris A van; Chang, Wei-Chiao

2015-01-01

Ankylosing spondylitis (AS) is a form of chronic inflammatory spondyloarthritis (SpA) that causes pain and stiffness in spines or joints. Human leukocyte antigen B27 (HLA-B27) and B60 (HLA-B60) have been reported as major genetic risk factors of AS. In addition, rs13202464, located on major histocompatibility complex (MHC) region, showed high sensitivity (98.7%) and specificity (98.0%) for HLA-B27. The aim of our study is to test whether the interaction between HLA-B60 and HLA-B27 (rs13202464) can serve as a better predictor of AS. We have genotyped HLA-B60 and rs13202464 among 471 patients with AS and 557 healthy subjects. Combined risk factors were investigated to test the biological interaction. Our results indicated that the relative risk (RR) for HLA-B27+/HLA-B60- was 152 (95% CI 91 to 255) and it increased to 201 (95% CI 85 to 475) in HLA-B27+/HLA-B60+ patients (with HLA-B27-/HLA-B60- as reference). Combinational analysis of two risk factors (HLA-B27+/HLA-B60+) showed a relative excess risk due to interaction (RERI) of 46.79 (95% CI: -117.58 to 211.16), attributable proportion (AP) of 0.23 (95% CI: -0.41 to 0.88) and a synergy index (S) of 1.31 (95% CI: 0.56 to 3.04). In conclusion, genetic interaction analysis revealed that the interaction between HLA-B60 and HLA-B27 is a better marker for the risk of AS susceptibility in a Taiwanese population.

A microphysical pathway analysis to investigate aerosol effects on convective clouds

NASA Astrophysics Data System (ADS)

Heikenfeld, Max; White, Bethan; Labbouz, Laurent; Stier, Philip

2017-04-01

The impact of aerosols on ice- and mixed-phase processes in convective clouds remains highly uncertain, which has strong implications for estimates of the role of aerosol-cloud interactions in the climate system. The wide range of interacting microphysical processes are still poorly understood and generally not resolved in global climate models. To understand and visualise these processes and to conduct a detailed pathway analysis, we have added diagnostic output of all individual process rates for number and mass mixing ratios to two commonly-used cloud microphysics schemes (Thompson and Morrison) in WRF. This allows us to investigate the response of individual processes to changes in aerosol conditions and the propagation of perturbations throughout the development of convective clouds. Aerosol effects on cloud microphysics could strongly depend on the representation of these interactions in the model. We use different model complexities with regard to aerosol-cloud interactions ranging from simulations with different levels of fixed cloud droplet number concentration (CDNC) as a proxy for aerosol, to prognostic CDNC with fixed modal aerosol distributions. Furthermore, we have implemented the HAM aerosol model in WRF-chem to also perform simulations with a fully interactive aerosol scheme. We employ a hierarchy of simulation types to understand the evolution of cloud microphysical perturbations in atmospheric convection. Idealised supercell simulations are chosen to present and test the analysis methods for a strongly confined and well-studied case. We then extend the analysis to large case study simulations of tropical convection over the Amazon rainforest. For both cases we apply our analyses to individually tracked convective cells. Our results show the impact of model uncertainties on the understanding of aerosol-convection interactions and have implications for improving process representation in models.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

PubMed Central

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

The fading affect bias shows positive outcomes at the general but not the individual level of analysis in the context of social media.

PubMed

Gibbons, Jeffrey A; Horowitz, Kyle A; Dunlap, Spencer M

2017-08-01

Unpleasant affect fades faster than pleasant affect (e.g., Walker, Vogl, & Thompson, 1997); this effect is referred to as the Fading Affect Bias (FAB; Walker, Skowronski, Gibbons, Vogl, & Thompson, 2003a). Research shows that the FAB is consistently related to positive/healthy outcomes at a general but not at a specific level of analysis based on event types and individual differences (e.g., Gibbons et al., 2013). Based on the positive outcomes for FAB and negative outcomes for social media (Bolton et al., 2013; Huang, 2010), the current study examined FAB in the context of social media events along with related individual differences. General positive outcomes were shown in the form of robust FAB effects across social media and non-social media events, a larger FAB for non-social media events than for social media events, negative correlations of FAB with depression, anxiety, and stress as well as a positive correlation of FAB with self-esteem. However, the lack of a negative correlation between FAB and anxiety for social media events in a 3-way interaction did not show positive outcomes at a specific level of analysis. Rehearsal ratings mediated the 3-way interaction. Implications are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

Land-Sea-Atmosphere Interaction and Their Association with Drought Conditions

NASA Astrophysics Data System (ADS)

Singh, R. P.; Nath, A.

2017-12-01

Detailed analysis of satellite data for the period 2002-2016 provides an understanding of the land-sea interaction and its association with the vegetation conditions over the Indian continent. The Indian Ocean dipole (IOD) phenomenon is also considered to understand the atmospheric dynamics and meteorological parameters. GPS water vapor and meteorological parameters (relative humidity and water vapor) from the Indian Institute of Science (IISC) Bangalore have been considered for meteorological data for the period 2008-2016. Atmospheric parameters (water vapor, precipitation rate, land temperature, total ozone column) have been considered using through NASA Giovanni portal and GPS water vapor through SoumiNet data to study relation between Sea Surface temperature (SST) from Indian Ocean, Bay of Bengal and Arabian Sea. Our detailed analysis shows that SST has strong impact on the NDVI at different locations, the maximum impact of SST is observed at lower latitudes. The NDVI over the central and northern India (Indo-Gangetic plains (IGP) is not affected. The SST and NDVI shows high correlation in the central and northern parts, whereas the correlation is poor in the southern parts i.e. close to the ocean. The detailed analysis of NDVI data provides progression of the drought conditions especially in the southern parts of India and also shows impact of the El Nino during 2015-2016.

Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex.

PubMed

Wang, Jingwen; Zhao, Yuqi; Wang, Yanjie; Huang, Jingfei

2013-01-16

Coevolution between proteins is crucial for understanding protein-protein interaction. Simultaneous changes allow a protein complex to maintain its overall structural-functional integrity. In this study, we combined statistical coupling analysis (SCA) and molecular dynamics simulations on the CDK6-CDKN2A protein complex to evaluate coevolution between proteins. We reconstructed an inter-protein residue coevolution network, consisting of 37 residues and 37 interactions. It shows that most of the coevolved residue pairs are spatially proximal. When the mutations happened, the stable local structures were broken up and thus the protein interaction was decreased or inhibited, with a following increased risk of melanoma. The identification of inter-protein coevolved residues in the CDK6-CDKN2A complex can be helpful for designing protein engineering experiments. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Structural analysis of nucleosomal barrier to transcription.

PubMed

Gaykalova, Daria A; Kulaeva, Olga I; Volokh, Olesya; Shaytan, Alexey K; Hsieh, Fu-Kai; Kirpichnikov, Mikhail P; Sokolova, Olga S; Studitsky, Vasily M

2015-10-27

Thousands of human and Drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. However, the molecular mechanisms of formation of the nucleosomal barrier to transcribing RNA polymerase II (Pol II) and nucleosome survival during/after transcription remain unknown. Here we show that both DNA-histone interactions and Pol II backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely occurs through allosterically stabilized histone-histone interactions. Structural analysis indicates that after Pol II encounters the barrier, the enzyme backtracks and nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state. DNA is displaced from one of the H2A/H2B dimers that remains associated with the octamer. The data reveal the importance of intranucleosomal DNA-protein and protein-protein interactions during conformational changes in the nucleosome structure on transcription. Mechanisms of nucleosomal barrier formation and nucleosome survival during transcription are proposed.

Man-machine interfaces in LACIE/ERIPS

NASA Technical Reports Server (NTRS)

Duprey, B. B. (Principal Investigator)

1979-01-01

One of the most important aspects of the interactive portion of the LACIE/ERIPS software system is the way in which the analysis and decision-making capabilities of a human being are integrated with the speed and accuracy of a computer to produce a powerful analysis system. The three major man-machine interfaces in the system are (1) the use of menus for communications between the software and the interactive user; (2) the checkpoint/restart facility to recreate in one job the internal environment achieved in an earlier one; and (3) the error recovery capability which would normally cause job termination. This interactive system, which executes on an IBM 360/75 mainframe, was adapted for use in noninteractive (batch) mode. A case study is presented to show how the interfaces work in practice by defining some fields based on an image screen display, noting the field definitions, and obtaining a film product of the classification map.

Interaction of aromatic amines with iron oxides: implications for prebiotic chemistry.

PubMed

Shanker, Uma; Singh, Gurinder; Kamaluddin

2013-06-01

The interaction of aromatic amines (aniline, p-chloroaniline, p-toludine and p-anisidine) with iron oxides (goethite, akaganeite and hematite) has been studied. Maximum uptake of amines was observed around pH 7. The adsorption data obtained at neutral pH were found to follow Langmuir adsorption. Anisidine was found to be a better adsorbate probably due to its higher basicity. In alkaline medium (pH > 8), amines reacted on goethite and akaganeite to give colored products. Analysis of the products by GC-MS showed benzoquinone and azobenzene as the reaction products of aniline while p-anisidine afforded a dimer. IR analysis of the amine-iron oxide hydroxide adduct suggests that the surface acidity of iron oxide hydroxides is responsible for the interaction. The present study suggests that iron oxide hydroxides might have played a role in the stabilization of organic molecules through their surface activity and in prebiotic condensation reactions.

Relationship between mediation analysis and the structured life course approach

PubMed Central

Howe, Laura D; Smith, Andrew D; Macdonald-Wallis, Corrie; Anderson, Emma L; Galobardes, Bruna; Lawlor, Debbie A; Ben-Shlomo, Yoav; Hardy, Rebecca; Cooper, Rachel; Tilling, Kate; Fraser, Abigail

2016-01-01

Abstract Many questions in life course epidemiology involve mediation and/or interaction because of the long latency period between exposures and outcomes. In this paper, we explore how mediation analysis (based on counterfactual theory and implemented using conventional regression approaches) links with a structured approach to selecting life course hypotheses. Using theory and simulated data, we show how the alternative life course hypotheses assessed in the structured life course approach correspond to different combinations of mediation and interaction parameters. For example, an early life critical period model corresponds to a direct effect of the early life exposure, but no indirect effect via the mediator and no interaction between the early life exposure and the mediator. We also compare these methods using an illustrative real-data example using data on parental occupational social class (early life exposure), own adult occupational social class (mediator) and physical capability (outcome). PMID:27681097

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Weizhou, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn; Zhang, Yu; Sun, Tao

High-level coupled cluster singles, doubles, and perturbative triples [CCSD(T)] computations with up to the aug-cc-pVQZ basis set (1924 basis functions) and various extrapolations toward the complete basis set (CBS) limit are presented for the sandwich, T-shaped, and parallel-displaced benzene⋯naphthalene complex. Using the CCSD(T)/CBS interaction energies as a benchmark, the performance of some newly developed wave function and density functional theory methods has been evaluated. The best performing methods were found to be the dispersion-corrected PBE0 functional (PBE0-D3) and spin-component scaled zeroth-order symmetry-adapted perturbation theory (SCS-SAPT0). The success of SCS-SAPT0 is very encouraging because it provides one method for energy componentmore » analysis of π-stacked complexes with 200 atoms or more. Most newly developed methods do, however, overestimate the interaction energies. The results of energy component analysis show that interaction energies are overestimated mainly due to the overestimation of dispersion energy.« less

Mechanistic approach to study conjugation of nanoparticles for biomedical applications.

PubMed

Uddin, Imran

2018-05-16

Interaction of nanoparticles with biological systems turns out to be vibrant for their efficient application in biomedical field. Here, we have shown antibiotic amakicin loaded nanoparticles are responsible for the dual role as reducing and stabilizing the silver nanoparticles without the use of any undesired chemicals. Synthesized nanoparticles are well-dispersed having quasi spherical morphology with an average particle size around 10-11 nm. Crystallinity of nanoparticles was measured using selected area electron diffraction (SAED) and powder XRD analysis which show that particles are perfectly crystalline with cubic phase of geometry. UV-Vis, FTIR and circular dichroism (CD) analysis explained the presence and interaction of antibiotic on the nanoparticle's surface. Amakicin functionalized Ag nanoparticles used in this study have shown enhanced antibacterial activity against E. coli. These studies will help in designing an in-depth understanding that how nanostructures can possibly interact with biological systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Directionality of coupling of physiological subsystems: age-related changes of cardiorespiratory interaction during different sleep stages in babies.

PubMed

Mrowka, Ralf; Cimponeriu, Laura; Patzak, Andreas; Rosenblum, Michael G

2003-12-01

Activity of many physiological subsystems has a well-expressed rhythmic character. Often, a dependency between physiological rhythms is established due to interaction between the corresponding subsystems. Traditional methods of data analysis allow one to quantify the strength of interaction but not the causal interrelation that is indispensable for understanding the mechanisms of interaction. Here we present a recently developed method for quantification of coupling direction and apply it to an important problem. Namely, we study the mutual influence of respiratory and cardiovascular rhythms in healthy newborns within the first 6 mo of life in quiet and active sleep. We find an age-related change of the coupling direction: the interaction is nearly symmetric during the first days and becomes practically unidirectional (from respiration to heart rhythm) at the age of 6 mo. Next, we show that the direction of interaction is mainly determined by respiratory frequency. If the latter is less than approximately 0.6 Hz, the interaction occurs dominantly from respiration to heart. With higher respiratory frequencies that only occur at very young ages, the dominating direction is less pronounced or even abolished. The observed dependencies are not related to sleep stage, suggesting that the coupling direction is determined by system-inherent dynamical processes, rather than by functional modulations. The directional analysis may be applied to other interacting narrow band oscillatory systems, e.g., in the central nervous system. Thus it is an important step forward in revealing and understanding causal mechanisms of interactions.

Measuring interdisciplinary research and education outcomes in the Vienna Doctoral Programme on Water Resource Systems

NASA Astrophysics Data System (ADS)

Carr, Gemma; Loucks, Daniel Pete; Blaschke, Alfred Paul; Bucher, Christian; Farnleitner, Andreas; Fürnkranz-Prskawetz, Alexia; Parajka, Juraj; Pfeifer, Norbert; Rechberger, Helmut; Wagner, Wolfgang; Zessner, Matthias; Blöschl, Günter

2015-04-01

The interdisciplinary postgraduate research and education programme - the Vienna Doctoral Programme on Water Resource Systems - was initiated in 2009. To date, 35 research students, three post-docs and ten faculty members have been engaged in the Programme, from ten research fields (aquatic microbiology, hydrology, hydro-climatology, hydro-geology, mathematical economics, photogrammetry, remote sensing, resource management, structural mechanics, and water quality). The Programme aims to develop research students with the capacity to work across the disciplines, to conduct cutting edge research and foster an international perspective. To do this, a variety of mechanisms are adopted that include research cluster groups, joint study sites, joint supervision, a basic study programme and a research semester abroad. The Programme offers a unique case study to explore if and how these mechanisms lead to research and education outcomes. Outcomes are grouped according to whether they are tangible (publications with co-authors from more than one research field, analysis of graduate profiles and career destinations) or non-tangible (interaction between researchers, networks and trust). A mixed methods approach that includes bibliometric analysis combined with interviews with students is applied. Bibliometric analysis shows that as the Programme has evolved the amount of multi-disciplinary work has increased (32% of the 203 full papers produced by the programme's researchers have authors from more than one research field). Network analysis to explore which research fields collaborate most frequently show that hydrology plays a significant role and has collaborated with seven of the ten research fields. Hydrology researchers seem to interact the most strongly with other research fields as they contribute understanding on water system processes. Network analysis to explore which individuals collaborate shows that much joint work takes place through the five research cluster groups (water resource management, land-surface processes, Hydrological Open Air Laboratory, water and health, modelling and risk). Student interviews highlight that trust between colleagues and supervisors, and the role of spaces for interaction (joint study sites, cluster group meetings, shared offices etc.) are important for joint work. Graduate analysis shows that students develop skills and confidence to work across disciplines through collaborating on their doctoral research. Working collaboratively during the doctorate appears to be strongly correlated with continuing to work in this way after graduation.

An unsteady rotor/fuselage interaction method

NASA Technical Reports Server (NTRS)

Egolf, T. Alan; Lorber, Peter F.

1987-01-01

An analytical method has been developed to treat unsteady helicopter rotor, wake, and fuselage interaction aerodynamics. An existing lifting line/prescribed wake rotor analysis and a source panel fuselage analysis were modified to predict vibratory fuselage airloads. The analyses were coupled through the induced flow velocities of the rotor and wake on the fuselage and the fuselage on the rotor. A prescribed displacement technique was used to distort the rotor wake about the fuselage. Sensitivity studies were performed to determine the influence of wake and body geometry on the computed airloads. Predicted and measured mean and unsteady pressures on a cylindrical body in the wake of a two-bladed rotor were compared. Initial results show good qualitative agreement.

Estimating the quality of pasturage in the municipality of Paragominas (PA) by means of automatic analysis of LANDSAT data

NASA Technical Reports Server (NTRS)

Dejesusparada, N. (Principal Investigator); Dossantos, A. P.; Novo, E. M. L. D.; Duarte, V.

1981-01-01

The use of LANDSAT data to evaluate pasture quality in the Amazon region is demonstrated. Pasture degradation in deforested areas of a traditional tropical forest cattle-raising region was estimated. Automatic analysis using interactive multispectral analysis (IMAGE-100) shows that 24% of the deforested areas were occupied by natural vegetation regrowth, 24% by exposed soil, 15% by degraded pastures, and 46% was suitable grazing land.

Enabling Community Through Social Media

PubMed Central

Haythornthwaite, Caroline

2013-01-01

Background Social network analysis provides a perspective and method for inquiring into the structures that comprise online groups and communities. Traces from interaction via social media provide the opportunity for understanding how a community is formed and maintained online. Objective The paper aims to demonstrate how social network analysis provides a vocabulary and set of techniques for examining interaction patterns via social media. Using the case of the #hcsmca online discussion forum, this paper highlights what has been and can be gained by approaching online community from a social network perspective, as well as providing an inside look at the structure of the #hcsmca community. Methods Social network analysis was used to examine structures in a 1-month sample of Twitter messages with the hashtag #hcsmca (3871 tweets, 486 unique posters), which is the tag associated with the social media–supported group Health Care Social Media Canada. Network connections were considered present if the individual was mentioned, replied to, or had a post retweeted. Results Network analyses revealed patterns of interaction that characterized the community as comprising one component, with a set of core participants prominent in the network due to their connections with others. Analysis showed the social media health content providers were the most influential group based on in-degree centrality. However, there was no preferential attachment among people in the same professional group, indicating that the formation of connections among community members was not constrained by professional status. Conclusions Network analysis and visualizations provide techniques and a vocabulary for understanding online interaction, as well as insights that can help in understanding what, and who, comprises and sustains a network, and whether community emerges from a network of online interactions. PMID:24176835

[Effect of occupational stress on mental health].

PubMed

Yu, Shan-fa; Zhang, Rui; Ma, Liang-qing; Gu, Gui-zhen; Yang, Yan; Li, Kui-rong

2003-02-01

To study the effect of job psychological demands and job control on mental health and their interaction. 93 male freight train dispatchers were evaluated by using revised Job Demand-Control Scale and 7 strain scales. Stepwise regression analysis, Univariate ANOVA, Kruskal-Wallis H and Modian methods were used in statistic analysis. Kruskal-Wallis H and Modian methods analysis revealed the difference in mental health scores among groups of decision latitude (mean rank 55.57, 47.95, 48.42, 33.50, P < 0.05), the differences in scores of mental health (37.45, 40.01, 58.35), job satisfaction (53.18, 46.91, 32.43), daily life strains (33.00, 44.96, 56.12) and depression (36.45, 42.25, 53.61) among groups of job time demands (P < 0.05) were all statistically significant. ANOVA showed that job time demands and decision latitude had interaction effects on physical complains (R(2) = 0.24), state-anxiety (R(2) = 0.26), and daytime fatigue (R(2) = 0.28) (P < 0.05). Regression analysis revealed a significant job time demands and job decision latitude interaction effect as well as significant main effects of the some independent variables on different job strains (R(2) > 0.05). Job time demands and job decision latitude have direct and interactive effects on psychosomatic health, the more time demands, the more psychological strains, the effect of job time demands is greater than that of job decision latitude.

Gene fusion analysis in the battle against the African endemic sleeping sickness.

PubMed

Trimpalis, Philip; Koumandou, Vassiliki Lila; Pliakou, Evangelia; Anagnou, Nicholas P; Kossida, Sophia

2013-01-01

The protozoan Trypanosoma brucei causes African Trypanosomiasis or sleeping sickness in humans, which can be lethal if untreated. Most available pharmacological treatments for the disease have severe side-effects. The purpose of this analysis was to detect novel protein-protein interactions (PPIs), vital for the parasite, which could lead to the development of drugs against this disease to block the specific interactions. In this work, the Domain Fusion Analysis (Rosetta Stone method) was used to identify novel PPIs, by comparing T. brucei to 19 organisms covering all major lineages of the tree of life. Overall, 49 possible protein-protein interactions were detected, and classified based on (a) statistical significance (BLAST e-value, domain length etc.), (b) their involvement in crucial metabolic pathways, and (c) their evolutionary history, particularly focusing on whether a protein pair is split in T. brucei and fused in the human host. We also evaluated fusion events including hypothetical proteins, and suggest a possible molecular function or involvement in a certain biological process. This work has produced valuable results which could be further studied through structural biology or other experimental approaches so as to validate the protein-protein interactions proposed here. The evolutionary analysis of the proteins involved showed that, gene fusion or gene fission events can happen in all organisms, while some protein domains are more prone to fusion and fission events and present complex evolutionary patterns.

Beyond Lecture and Non-Lecture Classrooms: LA-student interactions in Active Learning Classrooms

NASA Astrophysics Data System (ADS)

Gonzalez, Dayana; Kornreich, Hagit; Rodriguez, Idaykis; Monslave, Camila; Pena-Flores, Norma

Our expanded multi-site study on active learning classrooms supported by Learning Assistants (LAs) aims to understand the connections between three classroom elements: the activity, student learning, and how LAs support the learning process in the classroom. At FIU, LAs are used in a variety of active learning settings, from large auditorium settings to studio classroom with movable tables. Our study uses the COPUS observation protocol as a way to characterize LAs behaviors in these classrooms. With a focus on LA-student interactions, our analysis of how LAs interact with students during a 'learning session' generated new observational codes for specific new categories of LA roles. Preliminary results show that LAs spend more time interacting with students in some classes, regardless of the classroom setting, while in other classrooms, LA-student interactions are mostly brief. We discuss how LA-student interactions contribute to the dynamics and mechanism of the socially shared learning activity.

A cysteine-rich plant protein potentiates Potyvirus movement through an interaction with the virus genome-linked protein VPg.

PubMed

Dunoyer, P; Thomas, C; Harrison, S; Revers, F; Maule, A

2004-03-01

We have identified a cellular factor that interacts with the virus genome-linked proteins (VPgs) of a diverse range of potyviruses. The factor, called Potyvirus VPg-interacting protein (PVIP), is a plant-specific protein with homologues in all the species examined, i.e., pea, Arabidopsis thaliana, and Nicotiana benthamiana. The sequence of PVIP does not identify a specific function, although the existence of a "PHD finger" domain may implicate the protein in transcriptional control through chromatin remodeling. Deletion analysis using the yeast two-hybrid system showed that the determinants of the interaction lay close to the N terminus of VPg; indeed, the N-terminal 16 amino acids were shown to be both necessary and sufficient for the interaction with at least one PVIP protein. From a sequence comparison of different potyvirus VPg proteins, a specific amino acid at position 12 was directly implicated in the interaction. This part of VPg is distinct from regions associated with other functional roles of VPg. Through mutation of Turnip mosaic virus (TuMV) at VPg position 12, we showed that the interaction with PVIP affected systemic symptoms in infected plants. This resulted from reduced cell-to-cell and systemic movement more than reduced virus replication, as visualized by comparing green fluorescent protein-tagged wild-type and mutant viruses. Furthermore, by using RNA interference of PVIP in Arabidopsis, we showed that reduced expression of PVIP genes reduced susceptibility to TuMV infection. We conclude that PVIP functions as an ancillary factor to support potyvirus movement in plants.

Specificity of molecular interactions in transient protein-protein interaction interfaces.

PubMed

Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

2006-11-15

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of antibody-antigen complexes, the sign is somewhat ambiguous. From the evolutionary perspective, while protease-inhibitors and sig-naling proteins have optimized their interfaces to suit their biological functions, antibody-antigen interactions are the happenstance, implying that antibody-antigen complexes do not show distinctive interaction types. Persistent interaction types such as pi...pi, amide-carbonyl, and hydroxyl-carbonyl interaction, are also investigated. Analyzing the structural orientations of the pi...pi stacking interactions, we find that herringbone shape is a major configuration in transient protein-protein interfaces. This result is different from that of protein core, where parallel-displaced configurations are the major configuration. We also analyze overall trend of amide-carbonyl and hydroxyl-carbonyl interactions. It is noticeable that nearly 82% of the interfaces have at least one hydroxyl-carbonyl interactions. (c) 2006 Wiley-Liss, Inc.

TP53 mutations, expression and interaction networks in human cancers

PubMed Central

Wang, Xiaosheng; Sun, Qingrong

2017-01-01

Although the associations of p53 dysfunction, p53 interaction networks and oncogenesis have been widely explored, a systematic analysis of TP53 mutations and its related interaction networks in various types of human cancers is lacking. Our study explored the associations of TP53 mutations, gene expression, clinical outcomes, and TP53 interaction networks across 33 cancer types using data from The Cancer Genome Atlas (TCGA). We show that TP53 is the most frequently mutated gene in a number of cancers, and its mutations appear to be early events in cancer initiation. We identified genes potentially repressed by p53, and genes whose expression correlates significantly with TP53 expression. These gene products may be especially important nodes in p53 interaction networks in human cancers. This study shows that while TP53-truncating mutations often result in decreased TP53 expression, other non-truncating TP53 mutations result in increased TP53 expression in some cancers. Survival analyses in a number of cancers show that patients with TP53 mutations are more likely to have worse prognoses than TP53-wildtype patients, and that elevated TP53 expression often leads to poor clinical outcomes. We identified a set of candidate synthetic lethal (SL) genes for TP53, and validated some of these SL interactions using data from the Cancer Cell Line Project. These predicted SL genes are promising candidates for experimental validation and the development of personalized therapeutics for patients with TP53-mutated cancers. PMID:27880943

TP53 mutations, expression and interaction networks in human cancers.

PubMed

Wang, Xiaosheng; Sun, Qingrong

2017-01-03

Although the associations of p53 dysfunction, p53 interaction networks and oncogenesis have been widely explored, a systematic analysis of TP53 mutations and its related interaction networks in various types of human cancers is lacking. Our study explored the associations of TP53 mutations, gene expression, clinical outcomes, and TP53 interaction networks across 33 cancer types using data from The Cancer Genome Atlas (TCGA). We show that TP53 is the most frequently mutated gene in a number of cancers, and its mutations appear to be early events in cancer initiation. We identified genes potentially repressed by p53, and genes whose expression correlates significantly with TP53 expression. These gene products may be especially important nodes in p53 interaction networks in human cancers. This study shows that while TP53-truncating mutations often result in decreased TP53 expression, other non-truncating TP53 mutations result in increased TP53 expression in some cancers. Survival analyses in a number of cancers show that patients with TP53 mutations are more likely to have worse prognoses than TP53-wildtype patients, and that elevated TP53 expression often leads to poor clinical outcomes. We identified a set of candidate synthetic lethal (SL) genes for TP53, and validated some of these SL interactions using data from the Cancer Cell Line Project. These predicted SL genes are promising candidates for experimental validation and the development of personalized therapeutics for patients with TP53-mutated cancers.

Assessing Technology in the Absence of Proof: Trust Based on the Interplay of Others' Opinions and the Interaction Process.

PubMed

de Vries, Peter W; van den Berg, Stéphanie M; Midden, Cees

2015-12-01

The present research addresses the question of how trust in systems is formed when unequivocal information about system accuracy and reliability is absent, and focuses on the interaction of indirect information (others' evaluations) and direct (experiential) information stemming from the interaction process. Trust in decision-supporting technology, such as route planners, is important for satisfactory user interactions. Little is known, however, about trust formation in the absence of outcome feedback, that is, when users have not yet had opportunity to verify actual outcomes. Three experiments manipulated others' evaluations ("endorsement cues") and various forms of experience-based information ("process feedback") in interactions with a route planner and measured resulting trust using rating scales and credits staked on the outcome. Subsequently, an overall analysis was conducted. Study 1 showed that effectiveness of endorsement cues on trust is moderated by mere process feedback. In Study 2, consistent (i.e., nonrandom) process feedback overruled the effect of endorsement cues on trust, whereas inconsistent process feedback did not. Study 3 showed that although the effects of consistent and inconsistent process feedback largely remained regardless of face validity, high face validity in process feedback caused higher trust than those with low face validity. An overall analysis confirmed these findings. Experiential information impacts trust even if outcome feedback is not available, and, moreover, overrules indirect trust cues-depending on the nature of the former. Designing systems so that they allow novice users to make inferences about their inner workings may foster initial trust. © 2015, Human Factors and Ergonomics Society.

The effect of habitat modification on plant-pollinator network

NASA Astrophysics Data System (ADS)

Aminatun, Tien; Putra, Nugroho Susetya

2017-08-01

The research aimed to determine; (1) the mutualism interaction pattern of plant-pollinator on several habitat modifications; and (2) the habitat modification which showed the most stable pattern of interaction. The study was conducted in one planting season with 20 plots which each plot had 2x2 m2 width and 2 m spacing among plots, and each plot was planted with the same variety of tomato plants, i.e. "intan". Nitrogen manipulation treatment was conducted with four kinds of fertilizers, i.e. NPK (code PU), compost (code PKM), vermicompost (code PC), and manure (code PK). Each treatment had 5 plot replications. We observed the growth of tomato plants, weed and arthropod populationstwo weekly while pollinator visitation twice a week during tomato plant flowering with counting population and visitation frequence of each pollinator on each sample of tomato plants. The nectar of tomato plant flower of each treatment was tested in laboratory to see its reducing sugar and sucrose. Oganic matter and nitrogen of the soil samples of each treatment were tested in laboratory in the beginning and the end of this research. We analized the plant-pollinator network with bipartite program in R-statistics, and the abiotic and other biotic factors with descriptive analysis. The results of the research were; (1) the mutualism interaction pattern of plant-pollinator network of four treatments were varied, and (2) The pattern of plant-pollinator network of NPK fertilizer treatment showed the more stable interaction based on analysis of interaction evenness, Shannon diversity, frequency and longevity of pollinator visitation.

Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption.

PubMed

Hadzic, Ermin; Catillon, Marie; Halavatyi, Aliaksandr; Medves, Sandrine; Van Troys, Marleen; Moes, Michèle; Baird, Michelle A; Davidson, Michael W; Schaffner-Reckinger, Elisabeth; Ampe, Christophe; Friederich, Evelyne

2015-01-01

Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading.

Patterns of mother-infant interaction from 3 to 12 months among dyads with substance abuse and psychiatric problems.

PubMed

Siqveland, Torill S; Haabrekke, Kristin; Wentzel-Larsen, Tore; Moe, Vibeke

2014-11-01

The aim of this study was to investigate the development of mother-infant interaction patterns from 3 to 12 months among three groups of mother-baby pairs recruited during pregnancy: one group from residential substance abuse treatment (n=28), a second group from psychiatric outpatient treatment (n=22), and a third group from well-baby clinics (n=30). The mother-infant interaction at 3 and 12 months was assessed by the Parent-Child Early Relational Assessment (PCERA), which consists of maternal, child and dyadic subscales (Clark, 2006). Linear mixed effects models were used to analyze group differences and the changes in mother-infant interaction from 3 to 12 months. At 3 months, pairwise comparisons showed that the group with psychiatric problems had significantly more difficulties in the mother-infant interaction than the two other groups. The group with substance abuse problems was not significantly different from the two other groups. At 12 months, the mother-infant pairs in the substance abuse group showed significantly more relational disturbances than the non-clinical pairs, as well as a poorer affective quality of interaction than the dyads in the group with psychiatric problems. Analysis of change from 3 to 12 months showed that difficulties in the interaction increased among the mother-baby pairs in the substance abuse group, while improvements were displayed in the two other groups. These results underline that mother-infant pairs at double risk due to maternal substance abuse and other non-optimal factors, are in need for long-term follow up in order to prevent the development of negative interactional patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption

PubMed Central

Hadzic, Ermin; Catillon, Marie; Halavatyi, Aliaksandr; Medves, Sandrine; Van Troys, Marleen; Moes, Michèle; Baird, Michelle A.; Davidson, Michael W.; Schaffner-Reckinger, Elisabeth; Ampe, Christophe; Friederich, Evelyne

2015-01-01

Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading. PMID:26509500

Effect of interacting second- and third-order stimulus-dependent correlations on population-coding asymmetries.

PubMed

Montangie, Lisandro; Montani, Fernando

2016-10-01

Spike correlations among neurons are widely encountered in the brain. Although models accounting for pairwise interactions have proved able to capture some of the most important features of population activity at the level of the retina, the evidence shows that pairwise neuronal correlation analysis does not resolve cooperative population dynamics by itself. By means of a series expansion for short time scales of the mutual information conveyed by a population of neurons, the information transmission can be broken down into firing rate and correlational components. In a proposed extension of this framework, we investigate the information components considering both second- and higher-order correlations. We show that the existence of a mixed stimulus-dependent correlation term defines a new scenario for the interplay between pairwise and higher-than-pairwise interactions in noise and signal correlations that would lead either to redundancy or synergy in the information-theoretic sense.

Stability in Real Food Webs: Weak Links in Long Loops

NASA Astrophysics Data System (ADS)

Neutel, Anje-Margriet; Heesterbeek, Johan A. P.; de Ruiter, Peter C.

2002-05-01

Increasing evidence that the strengths of interactions among populations in biological communities form patterns that are crucial for system stability requires clarification of the precise form of these patterns, how they come about, and why they influence stability. We show that in real food webs, interaction strengths are organized in trophic loops in such a way that long loops contain relatively many weak links. We show and explain mathematically that this patterning enhances stability, because it reduces maximum ``loop weight'' and thus reduces the amount of intraspecific interaction needed for matrix stability. The patterns are brought about by biomass pyramids, a feature common to most ecosystems. Incorporation of biomass pyramids in 104 food-web descriptions reveals that the low weight of the long loops stabilizes complex food webs. Loop-weight analysis could be a useful tool for exploring the structure and organization of complex communities.

Graphene oxide as an optimal candidate material for methane storage.

PubMed

Chouhan, Rajiv K; Ulman, Kanchan; Narasimhan, Shobhana

2015-07-28

Methane, the primary constituent of natural gas, binds too weakly to nanostructured carbons to meet the targets set for on-board vehicular storage to be viable. We show, using density functional theory calculations, that replacing graphene by graphene oxide increases the adsorption energy of methane by 50%. This enhancement is sufficient to achieve the optimal binding strength. In order to gain insight into the sources of this increased binding, that could also be used to formulate design principles for novel storage materials, we consider a sequence of model systems that progressively take us from graphene to graphene oxide. A careful analysis of the various contributions to the weak binding between the methane molecule and the graphene oxide shows that the enhancement has important contributions from London dispersion interactions as well as electrostatic interactions such as Debye interactions, aided by geometric curvature induced primarily by the presence of epoxy groups.

Understanding children's science identity through classroom interactions

NASA Astrophysics Data System (ADS)

Kim, Mijung

2018-01-01

Research shows that various stereotypes about science and science learning, such as science being filled with hard and dry content, laboratory experiments, and male-dominated work environments, have resulted in feelings of distance from science in students' minds. This study explores children's experiences of science learning and science identity. It asks how children conceive of doing science like scientists and how they develop views of science beyond the stereotypes. This study employs positioning theory to examine how children and their teacher position themselves in science learning contexts and develop science identity through classroom interactions. Fifteen students in grades 4-6 science classrooms in Western Canada participated in this study. Classroom activities and interactions were videotaped, transcribed, and analysed to examine how the teacher and students position each other as scientists in the classroom. A descriptive explanatory case analysis showed how the teacher's positioning acted to develop students' science identity with responsibilities of knowledge seeking, perseverance, and excitement about science.

Differential C3NET reveals disease networks of direct physical interactions

PubMed Central

2011-01-01

Background Genes might have different gene interactions in different cell conditions, which might be mapped into different networks. Differential analysis of gene networks allows spotting condition-specific interactions that, for instance, form disease networks if the conditions are a disease, such as cancer, and normal. This could potentially allow developing better and subtly targeted drugs to cure cancer. Differential network analysis with direct physical gene interactions needs to be explored in this endeavour. Results C3NET is a recently introduced information theory based gene network inference algorithm that infers direct physical gene interactions from expression data, which was shown to give consistently higher inference performances over various networks than its competitors. In this paper, we present, DC3net, an approach to employ C3NET in inferring disease networks. We apply DC3net on a synthetic and real prostate cancer datasets, which show promising results. With loose cutoffs, we predicted 18583 interactions from tumor and normal samples in total. Although there are no reference interactions databases for the specific conditions of our samples in the literature, we found verifications for 54 of our predicted direct physical interactions from only four of the biological interaction databases. As an example, we predicted that RAD50 with TRF2 have prostate cancer specific interaction that turned out to be having validation from the literature. It is known that RAD50 complex associates with TRF2 in the S phase of cell cycle, which suggests that this predicted interaction may promote telomere maintenance in tumor cells in order to allow tumor cells to divide indefinitely. Our enrichment analysis suggests that the identified tumor specific gene interactions may be potentially important in driving the growth in prostate cancer. Additionally, we found that the highest connected subnetwork of our predicted tumor specific network is enriched for all proliferation genes, which further suggests that the genes in this network may serve in the process of oncogenesis. Conclusions Our approach reveals disease specific interactions. It may help to make experimental follow-up studies more cost and time efficient by prioritizing disease relevant parts of the global gene network. PMID:21777411

Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks

PubMed Central

2011-01-01

Background Gene co-expression, in the form of a correlation coefficient, has been valuable in the analysis, classification and prediction of protein-protein interactions. However, it is susceptible to bias from a few samples having a large effect on the correlation coefficient. Gene co-expression stability is a means of quantifying this bias, with high stability indicating robust, unbiased co-expression correlation coefficients. We assess the utility of gene co-expression stability as an additional measure to support the co-expression correlation in the analysis of protein-protein interaction networks. Results We studied the patterns of co-expression correlation and stability in interacting proteins with respect to their interaction promiscuity, levels of intrinsic disorder, and essentiality or disease-relatedness. Co-expression stability, along with co-expression correlation, acts as a better classifier of hub proteins in interaction networks, than co-expression correlation alone, enabling the identification of a class of hubs that are functionally distinct from the widely accepted transient (date) and obligate (party) hubs. Proteins with high levels of intrinsic disorder have low co-expression correlation and high stability with their interaction partners suggesting their involvement in transient interactions, except for a small group that have high co-expression correlation and are typically subunits of stable complexes. Similar behavior was seen for disease-related and essential genes. Interacting proteins that are both disordered have higher co-expression stability than ordered protein pairs. Using co-expression correlation and stability, we found that transient interactions are more likely to occur between an ordered and a disordered protein while obligate interactions primarily occur between proteins that are either both ordered, or disordered. Conclusions We observe that co-expression stability shows distinct patterns in structurally and functionally different groups of proteins and interactions. We conclude that it is a useful and important measure to be used in concert with gene co-expression correlation for further insights into the characteristics of proteins in the context of their interaction network. PMID:22369639

Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation.

PubMed

Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto; Pazos, Florencio

2013-01-01

Intrinsically disordered proteins/regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.

Bilinearization of the generalized coupled nonlinear Schrödinger equation with variable coefficients and gain and dark-bright pair soliton solutions.

PubMed

Chakraborty, Sushmita; Nandy, Sudipta; Barthakur, Abhijit

2015-02-01

We investigate coupled nonlinear Schrödinger equations (NLSEs) with variable coefficients and gain. The coupled NLSE is a model equation for optical soliton propagation and their interaction in a multimode fiber medium or in a fiber array. By using Hirota's bilinear method, we obtain the bright-bright, dark-bright combinations of a one-soliton solution (1SS) and two-soliton solutions (2SS) for an n-coupled NLSE with variable coefficients and gain. Crucial properties of two-soliton (dark-bright pair) interactions, such as elastic and inelastic interactions and the dynamics of soliton bound states, are studied using asymptotic analysis and graphical analysis. We show that a bright 2-soliton, in addition to elastic interactions, also exhibits multiple inelastic interactions. A dark 2-soliton, on the other hand, exhibits only elastic interactions. We also observe a breatherlike structure of a bright 2-soliton, a feature that become prominent with gain and disappears as the amplitude acquires a minimum value, and after that the solitons remain parallel. The dark 2-soliton, however, remains parallel irrespective of the gain. The results found by us might be useful for applications in soliton control, a fiber amplifier, all optical switching, and optical computing.

Assessment of genetic and nongenetic interactions for the prediction of depressive symptomatology: an analysis of the Wisconsin Longitudinal Study using machine learning algorithms.

PubMed

Roetker, Nicholas S; Page, C David; Yonker, James A; Chang, Vicky; Roan, Carol L; Herd, Pamela; Hauser, Taissa S; Hauser, Robert M; Atwood, Craig S

2013-10-01

We examined depression within a multidimensional framework consisting of genetic, environmental, and sociobehavioral factors and, using machine learning algorithms, explored interactions among these factors that might better explain the etiology of depressive symptoms. We measured current depressive symptoms using the Center for Epidemiologic Studies Depression Scale (n = 6378 participants in the Wisconsin Longitudinal Study). Genetic factors were 78 single nucleotide polymorphisms (SNPs); environmental factors-13 stressful life events (SLEs), plus a composite proportion of SLEs index; and sociobehavioral factors-18 personality, intelligence, and other health or behavioral measures. We performed traditional SNP associations via logistic regression likelihood ratio testing and explored interactions with support vector machines and Bayesian networks. After correction for multiple testing, we found no significant single genotypic associations with depressive symptoms. Machine learning algorithms showed no evidence of interactions. Naïve Bayes produced the best models in both subsets and included only environmental and sociobehavioral factors. We found no single or interactive associations with genetic factors and depressive symptoms. Various environmental and sociobehavioral factors were more predictive of depressive symptoms, yet their impacts were independent of one another. A genome-wide analysis of genetic alterations using machine learning methodologies will provide a framework for identifying genetic-environmental-sociobehavioral interactions in depressive symptoms.

Genome-wide identification, classification and expression analysis in fungal-plant interactions of cutinase gene family and functional analysis of a putative ClCUT7 in Curvularia lunata.

PubMed

Liu, Tong; Hou, Jumei; Wang, Yuying; Jin, Yazhong; Borth, Wayne; Zhao, Fengzhou; Liu, Zheng; Hu, John; Zuo, Yuhu

2016-06-01

Cutinase is described as playing various roles in fungal-plant pathogen interactions, such as eliciting host-derived signals, fungal spore attachment and carbon acquisition during saprophytic growth. However, the characteristics of the cutinase genes, their expression in compatible interactions and their roles in pathogenesis have not been reported in Curvularia lunata, an important leaf spot pathogen of maize in China. Therefore, a cutinase gene family analysis could have profound significance. In this study, we identified 13 cutinase genes (ClCUT1 to ClCUT13) in the C. lunata genome. Multiple sequence alignment showed that most fungal cutinase proteins had one highly conserved GYSQG motif and a similar DxVCxG[ST]-[LIVMF](3)-x(3)H motif. Gene structure analyses of the cutinases revealed a complex intron-exon pattern with differences in the position and number of introns and exons. Based on phylogenetic relationship analysis, C. lunata cutinases and 78 known cutinase proteins from other fungi were classified into four groups with subgroups, but the C. lunata cutinases clustered in only three of the four groups. Motif analyses showed that each group of cutinases from C. lunata had a common motif. Real-time PCR indicated that transcript levels of the cutinase genes in a compatible interaction between pathogen and host had varied expression patterns. Interestingly, the transcript levels of ClCUT7 gradually increased during early pathogenesis with the most significant up-regulation at 3 h post-inoculation. When ClCUT7 was deleted, pathogenicity of the mutant decreased on unwounded maize (Zea mays) leaves. On wounded maize leaves, however, the mutant caused symptoms similar to the wild-type strain. Moreover, the ClCUT7 mutant had an approximately 10 % reduction in growth rate when cutin was the sole carbon source. In conclusion, we identified and characterized the cutinase family genes of C. lunata, analyzed their expression patterns in a compatible host-pathogen interaction, and explored the role of ClCUT7 in pathogenicity. This work will increase our understanding of cutinase genes in other fungal-plant pathogens.

15q11.2–13.3 chromatin analysis reveals epigenetic regulation of CHRNA7 with deficiencies in Rett and autism brain

PubMed Central

Yasui, Dag H.; Scoles, Haley A.; Horike, Shin-ichi; Meguro-Horike, Makiko; Dunaway, Keith W.; Schroeder, Diane I.; LaSalle, Janine M.

2011-01-01

Copy number variations (CNVs) within human 15q11.2–13.3 show reduced penetrance and variable expressivity in a range of neurologic disorders. Therefore, characterizing 15q11.2–13.3 chromatin structure is important for understanding the regulation of this locus during normal neuronal development. Deletion of the Prader–Willi imprinting center (PWS-IC) within 15q11.2–13.3 disrupts long-range imprinted gene expression resulting in Prader–Willi syndrome. Previous results establish that MeCP2 binds to the PWS-IC and is required for optimal expression of distal GABRB3 and UBE3A. To examine the hypothesis that MeCP2 facilitates 15q11.2–13.3 transcription by linking the PWS-IC with distant elements, chromosome capture conformation on chip (4C) analysis was performed in human SH-SY5Y neuroblastoma cells. SH-SY5Y neurons had 2.84-fold fewer 15q11.2–13.3 PWS-IC chromatin interactions than undifferentiated SH-SY5Y neuroblasts, revealing developmental chromatin de-condensation of the locus. Out of 68 PWS-IC interactions with15q11.2–13.3 identified by 4C analysis and 62 15q11.2–13.3 MeCP2-binding sites identified by previous ChIP-chip studies, only five sites showed overlap. Remarkably, two of these overlapping PWS-IC- and MeCP2-bound sites mapped to sites flanking CHRNA7 (cholinergic receptor nicotinic alpha 7) encoding the cholinergic receptor, nicotinic, alpha 7. PWS-IC interaction with CHRNA7 in neurons was independently confirmed by fluorescent in situ hybridization analysis. Subsequent quantitative transcriptional analyses of frontal cortex from Rett syndrome and autism patients revealed significantly reduced CHRNA7 expression compared with controls. Together, these results suggest that transcription of CHRNA7 is modulated by chromatin interactions with the PWS-IC. Thus, loss of long-range chromatin interactions within 15q11.2–13.3 may contribute to multiple human neurodevelopmental disorders. PMID:21840925

15q11.2-13.3 chromatin analysis reveals epigenetic regulation of CHRNA7 with deficiencies in Rett and autism brain.

PubMed

Yasui, Dag H; Scoles, Haley A; Horike, Shin-Ichi; Meguro-Horike, Makiko; Dunaway, Keith W; Schroeder, Diane I; Lasalle, Janine M

2011-11-15

Copy number variations (CNVs) within human 15q11.2-13.3 show reduced penetrance and variable expressivity in a range of neurologic disorders. Therefore, characterizing 15q11.2-13.3 chromatin structure is important for understanding the regulation of this locus during normal neuronal development. Deletion of the Prader-Willi imprinting center (PWS-IC) within 15q11.2-13.3 disrupts long-range imprinted gene expression resulting in Prader-Willi syndrome. Previous results establish that MeCP2 binds to the PWS-IC and is required for optimal expression of distal GABRB3 and UBE3A. To examine the hypothesis that MeCP2 facilitates 15q11.2-13.3 transcription by linking the PWS-IC with distant elements, chromosome capture conformation on chip (4C) analysis was performed in human SH-SY5Y neuroblastoma cells. SH-SY5Y neurons had 2.84-fold fewer 15q11.2-13.3 PWS-IC chromatin interactions than undifferentiated SH-SY5Y neuroblasts, revealing developmental chromatin de-condensation of the locus. Out of 68 PWS-IC interactions with15q11.2-13.3 identified by 4C analysis and 62 15q11.2-13.3 MeCP2-binding sites identified by previous ChIP-chip studies, only five sites showed overlap. Remarkably, two of these overlapping PWS-IC- and MeCP2-bound sites mapped to sites flanking CHRNA7 (cholinergic receptor nicotinic alpha 7) encoding the cholinergic receptor, nicotinic, alpha 7. PWS-IC interaction with CHRNA7 in neurons was independently confirmed by fluorescent in situ hybridization analysis. Subsequent quantitative transcriptional analyses of frontal cortex from Rett syndrome and autism patients revealed significantly reduced CHRNA7 expression compared with controls. Together, these results suggest that transcription of CHRNA7 is modulated by chromatin interactions with the PWS-IC. Thus, loss of long-range chromatin interactions within 15q11.2-13.3 may contribute to multiple human neurodevelopmental disorders.

Antecedents and Consequences of Verbal Disagreements during Small-Group Learning.

ERIC Educational Resources Information Center

Lindow, Janet A.; And Others

1985-01-01

Controversy, an aspect of small-group interactions, was investigated in 10 mixed-ability, mixed-sex, elementary math groups through analysis of dissension episodes. Results showed that boys and higher-ability students had significantly more prevailing answers and demonstrations. (Author/LMO)

Variational analysis of SPM- and IPM-based interactions in cubic non-local nonlinear media

NASA Astrophysics Data System (ADS)

Maleshkov, G.; Bezuhanov, Kalojan; Dreischuh, Aleksander A.

2005-04-01

We analytically show the non-locality of cubic nonlinear media causes an increase of the critical power for self- and induced focusing and influences the condition for signal beam attraction/repulsion in an off-axis geometry.

Interactive Behaviors in Adolescent Conversation Dyads.

ERIC Educational Resources Information Center

Turkstra, Lyn; Ciccia, Angela; Seaton, Christine

2003-01-01

This study collected normative behavioral data from extemporaneous 3-minute conversations of 50 typically developing adolescents. Analysis found the following high frequency behaviors: directing gaze at the partner, nodding and showing neutral and positive facial expressions, using back-channel responses, and giving contingent responses.…

Stacking and T-shape competition in aromatic-aromatic amino acid interactions.

PubMed

Chelli, Riccardo; Gervasio, Francesco Luigi; Procacci, Piero; Schettino, Vincenzo

2002-05-29

The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

Animal Robot Assisted-therapy for Rehabilitation of Patient with Post-Stroke Depression

NASA Astrophysics Data System (ADS)

Zikril Zulkifli, Winal; Shamsuddin, Syamimi; Hwee, Lim Thiam

2017-06-01

Recently, the utilization of therapeutic animal robots has expanded. This research aims to explore robotics application for mental healthcare in Malaysia through human-robot interaction (HRI). PARO, the robotic seal PARO was developed to give psychological effects on humans. Major Depressive Disorder (MDD) is a common but severe mood disorder. This study focuses on the interaction protocol between PARO and patients with MDD. Initially, twelve rehabilitation patients gave subjective evaluation on their first interaction with PARO. Next, therapeutic interaction environment was set-up with PARO in it to act as an augmentation strategy with other psychological interventions for post-stroke depression. Patient was exposed to PARO for 20 minutes. The results of behavioural analysis complemented with information from HRI survey question. The analysis also observed that the individual interactors engaged with the robot in diverse ways based on their needs Results show positive reaction toward the acceptance of an animal robot. Next, therapeutic interaction is set-up for PARO to contribute as an augmentation strategy with other psychological interventions for post-stroke depression. The outcome is to reduce the stress level among patients through facilitated therapy session with PARO

A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex.

PubMed

Armour, Sean M; Bennett, Eric J; Braun, Craig R; Zhang, Xiao-Yong; McMahon, Steven B; Gygi, Steven P; Harper, J Wade; Sinclair, David A

2013-04-01

Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex.

Using Discursis to enhance the qualitative analysis of hospital pharmacist-patient interactions.

PubMed

Chevalier, Bernadette A M; Watson, Bernadette M; Barras, Michael A; Cottrell, William N; Angus, Daniel J

2018-01-01

Pharmacist-patient communication during medication counselling has been successfully investigated using Communication Accommodation Theory (CAT). Communication researchers in other healthcare professions have utilised Discursis software as an adjunct to their manual qualitative analysis processes. Discursis provides a visual, chronological representation of communication exchanges and identifies patterns of interactant engagement. The aim of this study was to describe how Discursis software was used to enhance previously conducted qualitative analysis of pharmacist-patient interactions (by visualising pharmacist-patient speech patterns, episodes of engagement, and identifying CAT strategies employed by pharmacists within these episodes). Visual plots from 48 transcribed audio recordings of pharmacist-patient exchanges were generated by Discursis. Representative plots were selected to show moderate-high and low- level speaker engagement. Details of engagement were investigated for pharmacist application of CAT strategies (approximation, interpretability, discourse management, emotional expression, and interpersonal control). Discursis plots allowed for identification of distinct patterns occurring within pharmacist-patient exchanges. Moderate-high pharmacist-patient engagement was characterised by multiple off-diagonal squares while alternating single coloured squares depicted low engagement. Engagement episodes were associated with multiple CAT strategies such as discourse management (open-ended questions). Patterns reflecting pharmacist or patient speaker dominance were dependant on clinical setting. Discursis analysis of pharmacist-patient interactions, a novel application of the technology in health communication, was found to be an effective visualisation tool to pin-point episodes for CAT analysis. Discursis has numerous practical and theoretical applications for future health communication research and training. Researchers can use the software to support qualitative analysis where large data sets can be quickly reviewed to identify key areas for concentrated analysis. Because Discursis plots are easily generated from audio recorded transcripts, they are conducive as teaching tools for both students and practitioners to assess and develop their communication skills.

Artifact-free dynamic atomic force microscopy reveals monotonic dissipation for a simple confined liquid

NASA Astrophysics Data System (ADS)

Kaggwa, G. B.; Kilpatrick, J. I.; Sader, J. E.; Jarvis, S. P.

2008-07-01

We present definitive interaction measurements of a simple confined liquid (octamethylcyclotetrasiloxane) using artifact-free frequency modulation atomic force microscopy. We use existing theory to decouple the conservative and dissipative components of the interaction, for a known phase offset from resonance (90° phase shift), that has been deliberately introduced into the experiment. Further we show the qualitative influence on the conservative and dissipative components of the interaction of a phase error deliberately introduced into the measurement, highlighting that artifacts, such as oscillatory dissipation, can be readily observed when the phase error is not compensated for in the force analysis.

Characterization of an Irradiated RERTR-7 Fuel Plate Using Transmission Electron Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. Gan; D. D. Keiser, Jr.; B. D. Miller

2010-03-01

Transmission electron microscopy (TEM) has been used to characterize an irradiated fuel plate with Al-2Si matrix from the RERTR-7 experiment that was irradiated under moderate reactor conditions. The results of this work showed the presence of a bubble superlattice within the U-7Mo grains that accommodated fission gases (e.g., Xe). The presence of this structure helps the U-7Mo exhibit a stable swelling behaviour during irradiation. Furthermore, TEM analysis showed that the Si-rich interaction layers that develop around the fuel particles at the U-7Mo/matrix interface during fuel plate fabrication and irradiation become amorphous during irradiation, and in regions of the interaction layermore » that have relatively high Si concentrations the fission gas bubbles remain small and contained within the layer but in areas with lower Si concentrations the bubbles grow in size. An important question that remains to be answered about the irradiation behaviour of U-Mo dispersion fuels, is how do more aggressive irradiation conditions affect the behaviour of fission gases within the U-7Mo fuel particles and in the amorphous interaction layers on the microstructural scale that can be characterized using TEM? This paper discusses the results of TEM analysis that was performed on a sample taken from an irradiated RERTR-7 fuel plate with Al-2Si matrix. This plate was exposed to more aggressive irradiation conditions than was the sample taken from the RERTR-6 plate. The microstructural features present within the U-7Mo and the amorphous interaction layers will be discussed. The results of this analysis will be compared to what was observed in the earlier RERTR-6 fuel plate characterization.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Wenfei; Wang, Ying; Wang, Nianshuang

Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Here, we report identification of critical residues on hDPP4 for RBD binding and virus entry through analysis of a panel of hDPP4 mutants. Based on the RBD–hDPP4 crystal structure we reported, the mutated residues were located at the interface between RBD and hDPP4, which potentially changed the polarity, hydrophobic or hydrophilic properties of hDPP4, thereby interfering or disrupting their interaction with RBD. Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay,more » we showed that several residues in hDPP4–RBD binding interface were important on hDPP4–RBD binding and viral entry. These results provide atomic insights into the features of interactions between hDPP4 and MERS-CoV RBD, and also provide potential explanation for cellular and species tropism of MERS-CoV infection. - Highlights: • It has been demonstrated that MERS-CoV infects host cells through binding its envelope spike (S) glycoprotein to the host cellular receptor dipeptidyl peptidase 4 (DPP4). • To identify the critical residues on hDPP4 for RBD binding and virus entry, we constructed a panel of hDPP4 mutants based on structure-guided mutagenesis. • Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues on hDPP4 had significant impacts on virus/receptor interactions and viral entry. • Our study has provided new insights into the features of interactions between hDPP4 and MERS-CoV RBD, and provides potential explanation for cellular and species tropism of MERS-CoV infection.« less

A computational study of Na behavior on graphene

NASA Astrophysics Data System (ADS)

Malyi, Oleksandr I.; Sopiha, Kostiantyn; Kulish, Vadym V.; Tan, Teck L.; Manzhos, Sergei; Persson, Clas

2015-04-01

We present the first ab initio and molecular dynamics study of Na adsorption and diffusion on ideal graphene that considers Na-Na interaction and dispersion forces. From density functional theory (DFT) calculations using the generalized gradient approximation (GGA), the binding energy (vs. the vacuum reference state) of -0.75 eV is higher than the cohesive energy of Na metal (E

An exploratory analysis of emotion dynamics between mothers and adolescents during conflict discussions.

PubMed

Main, Alexandra; Paxton, Alexandra; Dale, Rick

2016-09-01

Dynamic patterns of influence between parents and children have long been considered key to understanding family relationships. Despite this, most observational research on emotion in parent-child interactions examines global behaviors at the expense of exploring moment-to-moment fluctuations in emotions that are important for relational outcomes. Using recurrence quantification analysis (RQA) and growth curve analysis, this investigation explored emotion dynamics during parent-adolescent conflict interactions, focusing not only on concurrently shared emotional states but also on time-lagged synchrony of parents' and adolescents' emotions relative to one another. Mother-adolescent dyads engaged in a 10-min conflict discussion and reported on their satisfaction with the process and outcome of the discussion. Emotions were coded using the Specific Affect Coding System (SPAFF) and were collapsed into the following categories: negativity, positivity, and validation/interest. RQA and growth curve analyses revealed that negative and positive emotions were characterized by a concurrently synchronous pattern across all dyads, with the highest recurrence rates occurring around simultaneity. However, lower levels of concurrent synchrony of negative emotions were associated with higher discussion satisfaction. We also found that patterns of negativity differed with age: Mothers led negativity in dyads with younger adolescents, and adolescents led negativity in dyads with older adolescents. In contrast to negative and positive emotions, validation/interest showed the time-lagged pattern characteristic of turn-taking, and more highly satisfied dyads showed stronger patterns of time-lagged coordination in validation/interest. Our findings underscore the dynamic nature of emotions in parent-adolescent interactions and highlight the important contributions of these moment-to-moment dynamics toward overall interaction quality. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Axelrod's Metanorm Games on Networks

PubMed Central

Galán, José M.; Łatek, Maciej M.; Rizi, Seyed M. Mussavi

2011-01-01

Metanorms is a mechanism proposed to promote cooperation in social dilemmas. Recent experimental results show that network structures that underlie social interactions influence the emergence of norms that promote cooperation. We generalize Axelrod's analysis of metanorms dynamics to interactions unfolding on networks through simulation and mathematical modeling. Network topology strongly influences the effectiveness of the metanorms mechanism in establishing cooperation. In particular, we find that average degree, clustering coefficient and the average number of triplets per node play key roles in sustaining or collapsing cooperation. PMID:21655211

Spectroscopic investigation of the spectroscopic signatures of 2,4-DNT and 2,6-DNT: their interactions with sand particles

NASA Astrophysics Data System (ADS)

Blanco, Alejandro; Mina, Nairmen; Castro, Miguel E.; Castillo-Chara, Jairo; Hernandez-Rivera, Samuel P.

2004-09-01

Raman Spectroscopy is a well established tool for vibrational spectroscopy analysis. Interactions of explosives with different substrates can be measured by using quantitative vibrational signal shift information of scattered Raman light associated with these interactions. A vibrational spectroscopic study has been carried out on 2,4-DNT and 2,6-DNT crystals. Raman Microscopy spectrometers equipped with 514 nm and 785 nm laser excitation lines were used. The samples were recrystallized on different solvents (water, methanol and acetonitrile) and allowed to interact with soil samples. The interaction with sand and soil samples doped with the nitroaromatic compounds showed significant shifts in its peaks. The above information was used to detect DNT in soil using Raman Microscopy. These results will make possible the development of highly sensitive sensors for detection of explosives materials.

Extended family and friendship support and suicidality among African Americans.

PubMed

Nguyen, Ann W; Taylor, Robert Joseph; Chatters, Linda M; Taylor, Harry Owen; Lincoln, Karen D; Mitchell, Uchechi A

2017-03-01

This study examined the relationship between informal social support from extended family and friends and suicidality among African Americans. Logistic regression analysis was based on a nationally representative sample of African Americans from the National Survey of American Life (N = 3263). Subjective closeness and frequency of contact with extended family and friends and negative family interaction were examined in relation to lifetime suicide ideation and attempts. Subjective closeness to family and frequency of contact with friends were negatively associated with suicide ideation and attempts. Subjective closeness to friends and negative family interaction were positively associated with suicide ideation and attempts. Significant interactions between social support and negative interaction showed that social support buffers against the harmful effects of negative interaction on suicidality. Findings are discussed in relation to the functions of positive and negative social ties in suicidality.

In silico studies to explore the mutagenic ability of 5-halo/oxy/li-oxy-uracil bases with guanine of DNA base pairs.

PubMed

Jana, Kalyanashis; Ganguly, Bishwajit

2014-10-16

DNA nucleobases are reactive in nature and undergo modifications by deamination, oxidation, alkylation, or hydrolysis processes. Many such modified bases are susceptible to mutagenesis when formed in cellular DNA. The mutagenesis can occur by mispairing with DNA nucleobases by a DNA polymerase during replication. We have performed a study of mispairing of DNA bases with unnatural bases computationally. 5-Halo uracils have been studied as mispairs in mutagenesis; however, the reports on their different forms are scarce in the literature. The stability of mispairs with keto form, enol form, and ionized form of 5-halo-uracil has been computed with the M06-2X/6-31+G** level of theory. The enol form of 5-halo-uracil showed remarkable stability toward DNA mispair compared to the corresponding keto and ionized forms. (F)U-G mispair showed the highest stability in the series and (Halo)(U(enol/ionized)-G mispair interactions energies are more stable than the natural G-C basepair of DNA. To enhance the stability of DNA mispairs, we have introduced the hydroxyl group in the place of halogen atoms, which provides additional hydrogen-bonding interactions in the system while forming the 5-membered ring. The study has been further extended with lithiated 5-hydroxymethyl-uracil to stabilize the DNA mispair. (CH2OLi)U(ionized)-G mispair has shown the highest stability (ΔG = -32.4 kcal/mol) with multi O-Li interactions. AIM (atoms in molecules) and EDA (energy decomposition analysis) analysis has been performed to examine the nature of noncovalent interactions in such mispairs. EDA analysis has shown that electrostatic energy mainly contributes toward the interaction energy of mispairs. The higher stability achieved in these studied mispairs can play a pivotal role in the mutagenesis and can help to attain the mutation for many desired biological processes.

Sensitivity in forward modeled hyperspectral reflectance due to phytoplankton groups

NASA Astrophysics Data System (ADS)

Manzo, Ciro; Bassani, Cristiana; Pinardi, Monica; Giardino, Claudia; Bresciani, Mariano

2016-04-01

Phytoplankton is an integral part of the ecosystem, affecting trophic dynamics, nutrient cycling, habitat condition, and fisheries resources. The types of phytoplankton and their concentrations are used to describe the status of water and the processes inside of this. This study investigates bio-optical modeling of phytoplankton functional types (PFT) in terms of pigment composition demonstrating the capability of remote sensing to recognize freshwater phytoplankton. In particular, a sensitivity analysis of simulated hyperspectral water reflectance (with band setting of HICO, APEX, EnMAP, PRISMA and Sentinel-3) of productive eutrophic waters of Mantua lakes (Italy) environment is presented. The bio-optical model adopted for simulating the hyperspectral water reflectance takes into account the reflectance dependency on geometric conditions of light field, on inherent optical properties (backscattering and absorption coefficients) and on concentrations of water quality parameters (WQPs). The model works in the 400-750nm wavelength range, while the model parametrization is based on a comprehensive dataset of WQP concentrations and specific inherent optical properties of the study area, collected in field surveys carried out from May to September of 2011 and 2014. The following phytoplankton groups, with their specific absorption coefficients, a*Φi(λ), were used during the simulation: Chlorophyta, Cyanobacteria with phycocyanin, Cyanobacteria and Cryptophytes with phycoerythrin, Diatoms with carotenoids and mixed phytoplankton. The phytoplankton absorption coefficient aΦ(λ) is modelled by multiplying the weighted sum of the PFTs, Σpia*Φi(λ), with the chlorophyll-a concentration (Chl-a). To highlight the variability of water reflectance due to variation of phytoplankton pigments, the sensitivity analysis was performed by keeping constant the WQPs (i.e., Chl-a=80mg/l, total suspended matter=12.58g/l and yellow substances=0.27m-1). The sensitivity analysis was based on the decomposition of the output reflectance variance in partial variances of the output due to each functional group. This approach considers the sensitivity analysis of the model to each variable on its own and the corresponding interaction with the other variables, allowing identifying the single variability as well as the spectral interaction index. The analysis recognized three spectral ranges with specific level of interactions between the inputs. The first part of the spectrum up to 500 nm had average level of 10% of interaction; the second up to 600nm showed values of 5% with a peak around 580nm; the third showed an increasing interaction level until 15% near 715nm. The results presented in this study provide information relating the sensitivity of hyperspectral water reflectance as observable with band setting of the latest generation space- and air-borne sensors depending on different phytoplankton groups. In particular PRISMA was the best in the spectral sensitivity definition in the first part of the spectrum, while APEX in the second and third domain. The Sentinel 3 showed lower performances although in the third domain it was able to identify some spectral features. Results showed the Chlorophyta had high main effect at 440 nm and 480nm; sensitivity indices of phycoerythrin showed peaks at 550-580nm the range and near 680nm; phycocyanin showed high influence at 620-640nm. The research activity is part of the EU FP7 INFORM (Grant No. 606865, http://www.copernicus-inform.eu/).

Content relatedness in the social web based on social explicit semantic analysis

NASA Astrophysics Data System (ADS)

Ntalianis, Klimis; Otterbacher, Jahna; Mastorakis, Nikolaos

2017-06-01

In this paper a novel content relatedness algorithm for social media content is proposed, based on the Explicit Semantic Analysis (ESA) technique. The proposed scheme takes into consideration social interactions. In particular starting from the vector space representation model, similarity is expressed by a summation of term weight products. In this paper, term weights are estimated by a social computing method, where the strength of each term is calculated by the attention the terms receives. For this reason each post is split into two parts, title and comments area, while attention is defined by the number of social interactions such as likes and shares. The overall approach is named Social Explicit Semantic Analysis. Experimental results on real data show the advantages and limitations of the proposed approach, while an initial comparison between ESA and S-ESA is very promising.

Teaching and Learning Science in Authoritative Classrooms: Teachers' Power and Students' Approval in Korean Elementary Classrooms

NASA Astrophysics Data System (ADS)

Lee, Jeong-A.; Kim, Chan-Jong

2017-09-01

This study aims to understand interactions in Korean elementary science classrooms, which are heavily influenced by Confucianism. Ethnographic observations of two elementary science teachers' classrooms in Korea are provided. Their classes are fairly traditional teaching, which mean teacher-centered interactions are dominant. To understand the power and approval in science classroom discourse, we have adopted Critical Discourse Analysis (CDA). Based on CDA, form and function analysis was adopted. After the form and function analysis, all episodes were analyzed in terms of social distance. The results showed that both teachers exercised their power while teaching. However, their classes were quite different in terms of getting approval by students. When a teacher got students' approval, he could conduct the science lesson more effectively. This study highlights the importance of getting approval by students in Korean science classrooms.

Pathway-based discovery of genetic interactions in breast cancer

PubMed Central

Xu, Zack Z.; Boone, Charles; Lange, Carol A.

2017-01-01

Breast cancer is the second largest cause of cancer death among U.S. women and the leading cause of cancer death among women worldwide. Genome-wide association studies (GWAS) have identified several genetic variants associated with susceptibility to breast cancer, but these still explain less than half of the estimated genetic contribution to the disease. Combinations of variants (i.e. genetic interactions) may play an important role in breast cancer susceptibility. However, due to a lack of statistical power, the current tests for genetic interactions from GWAS data mainly leverage prior knowledge to focus on small sets of genes or SNPs that are known to have an association with breast cancer. Thus, many genetic interactions, particularly among novel variants, remain understudied. Reverse-genetic interaction screens in model organisms have shown that genetic interactions frequently cluster into highly structured motifs, where members of the same pathway share similar patterns of genetic interactions. Based on this key observation, we recently developed a method called BridGE to search for such structured motifs in genetic networks derived from GWAS studies and identify pathway-level genetic interactions in human populations. We applied BridGE to six independent breast cancer cohorts and identified significant pathway-level interactions in five cohorts. Joint analysis across all five cohorts revealed a high confidence consensus set of genetic interactions with support in multiple cohorts. The discovered interactions implicated the glutathione conjugation, vitamin D receptor, purine metabolism, mitotic prometaphase, and steroid hormone biosynthesis pathways as major modifiers of breast cancer risk. Notably, while many of the pathways identified by BridGE show clear relevance to breast cancer, variants in these pathways had not been previously discovered by traditional single variant association tests, or single pathway enrichment analysis that does not consider SNP-SNP interactions. PMID:28957314

Thematic content analysis of work-family interactions: Retired cosmonauts’ reflections

NASA Astrophysics Data System (ADS)

Johnson, Phyllis J.; Asmaro, Deyar; Suedfeld, Peter; Gushin, Vadim

2012-12-01

Anecdotal evidence and qualitative research attest to the importance of work-family interactions pre-, during and post-missions. This study uses thematic content analysis to quantify characteristics of work-family interactions and how these changed by stage of cosmonauts' career, identifying the effect of space career variables (e.g., time in space and station) on such interactions during and post-career. Using a thematic scoring scheme developed for this study, we coded work-family interactions identified from interviews with 20 retired male cosmonauts. The majority of work-family interactions were ones in which work overlapped into family life and work hindered or interfered with the family situation. The most common resolution was that family adjusted to work, and the mood or tone about this outcome was almost equally divided among negative, positive and neutral. Changes in work-family interactions and their resolution over the cosmonaut's life showed that the significant interactions were most evident during the cosmonaut career. Although the cosmonaut career has high work demands, it did adjust for family when the need arose. The Russian Space Agency (RKS) eased the impact of the periodic absences, especially through regular communication sessions. Positive work-family interactions, i.e., work or family helping the opposite role, were more likely for those who had been on ISS, not Mir, and for those whose last flight was after 2000. Our data reflect retired cosmonauts' recollections of work-family interactions during their career. Examples of work overlapping into family life and work viewed as interfering with family life were possibly more salient or better remembered than work or family helping the other role.

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks.

PubMed

Deeter, Anthony; Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.

One-stage individual participant data meta-analysis models: estimation of treatment-covariate interactions must avoid ecological bias by separating out within-trial and across-trial information.

PubMed

Hua, Hairui; Burke, Danielle L; Crowther, Michael J; Ensor, Joie; Tudur Smith, Catrin; Riley, Richard D

2017-02-28

Stratified medicine utilizes individual-level covariates that are associated with a differential treatment effect, also known as treatment-covariate interactions. When multiple trials are available, meta-analysis is used to help detect true treatment-covariate interactions by combining their data. Meta-regression of trial-level information is prone to low power and ecological bias, and therefore, individual participant data (IPD) meta-analyses are preferable to examine interactions utilizing individual-level information. However, one-stage IPD models are often wrongly specified, such that interactions are based on amalgamating within- and across-trial information. We compare, through simulations and an applied example, fixed-effect and random-effects models for a one-stage IPD meta-analysis of time-to-event data where the goal is to estimate a treatment-covariate interaction. We show that it is crucial to centre patient-level covariates by their mean value in each trial, in order to separate out within-trial and across-trial information. Otherwise, bias and coverage of interaction estimates may be adversely affected, leading to potentially erroneous conclusions driven by ecological bias. We revisit an IPD meta-analysis of five epilepsy trials and examine age as a treatment effect modifier. The interaction is -0.011 (95% CI: -0.019 to -0.003; p = 0.004), and thus highly significant, when amalgamating within-trial and across-trial information. However, when separating within-trial from across-trial information, the interaction is -0.007 (95% CI: -0.019 to 0.005; p = 0.22), and thus its magnitude and statistical significance are greatly reduced. We recommend that meta-analysts should only use within-trial information to examine individual predictors of treatment effect and that one-stage IPD models should separate within-trial from across-trial information to avoid ecological bias. © 2016 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. © 2016 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd.

Social interaction in management group meetings: a case study of Finnish hospital.

PubMed

Laapotti, Tomi; Mikkola, Leena

2016-06-20

Purpose - The purpose of this paper is to understand the role of management group meetings (MGMs) in hospital organization by examining the social interaction in these meetings. Design/methodology/approach - This case study approaches social interaction from a structuration point of view. Social network analysis and qualitative content analysis are applied. Findings - The findings show that MGMs are mainly forums for information sharing. Meetings are not held for problem solving or decision making, and operational coordinating is limited. Meeting interaction is very much focused on the chair, and most of the discussion takes place between the chair and one other member, not between members. The organizational structures are maintained and reproduced in the meeting interaction, and they appear to limit discussion. Meetings appear to fulfil their goals as a part of the organization's information structure and to some extent as an instrument for management. The significance of the relational side of MGMs was recognized. Research limitations/implications - The results of this study provide a basis for future research on hospital MGMs with wider datasets and other methodologies. Especially the relational role of MGMs needs more attention. Practical implications - The goals of MGMs should be reviewed and MG members should be made aware of meeting interaction structures. Originality/value - The paper provides new knowledge about interaction networks in hospital MGMs, and describes the complexity of the importance of MGMs for hospitals.

Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome.

PubMed

Schütze, Tonio; Ulrich, Alexander K C; Apelt, Luise; Will, Cindy L; Bartlick, Natascha; Seeger, Martin; Weber, Gert; Lührmann, Reinhard; Stelzl, Ulrich; Wahl, Markus C

2016-02-01

Spliceosomal Prp38 proteins contain a conserved amino-terminal domain, but only higher eukaryotic orthologs also harbor a carboxy-terminal RS domain, a hallmark of splicing regulatory SR proteins. We show by crystal structure analysis that the amino-terminal domain of human Prp38 is organized around three pairs of antiparallel α-helices and lacks similarities to RNA-binding domains found in canonical SR proteins. Instead, yeast two-hybrid analyses suggest that the amino-terminal domain is a versatile protein-protein interaction hub that possibly binds 12 other spliceosomal proteins, most of which are recruited at the same stage as Prp38. By quantitative, alanine surface-scanning two-hybrid screens and biochemical analyses we delineated four distinct interfaces on the Prp38 amino-terminal domain. In vitro interaction assays using recombinant proteins showed that Prp38 can bind at least two proteins simultaneously via two different interfaces. Addition of excess Prp38 amino-terminal domain to in vitro splicing assays, but not of an interaction-deficient mutant, stalled splicing at a precatalytic stage. Our results show that human Prp38 is an unusual SR protein, whose amino-terminal domain is a multi-interface protein-protein interaction platform that might organize the relative positioning of other proteins during splicing. © 2016 Schütze et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Factors affecting the viscosity in high concentration solutions of different monoclonal antibodies.

PubMed

Yadav, Sandeep; Shire, Steven J; Kalonia, Devendra S

2010-12-01

The viscosity profiles of four different IgG(1) molecules were studied as a function of concentration at pH 6.0. At high concentrations, MAb-H and -A showed significantly higher viscosities as compared to MAb-G and -E. Zeta Potential (ξ) measurements showed that all the IgG(1) molecules carried a net positive charge at this pH. MAb-G showed the highest positive zeta potential followed by MAb-E, -H, and -A. A consistent interpretation of the impact of net charge on viscosity for these MAbs is not possible, suggesting that electroviscous effects cannot explain the differences in viscosity. Values of k(D) (dynamic light scattering) indicated that the intermolecular interactions were repulsive for MAb-E and -G; and attractive for MAb-H and -A. Solution storage modulus (G') in high concentration solutions was consistent with attractive intermolecular interactions for MAb-H and -A, and repulsive interactions for MAb-G and -E. Effect of salt addition on solution G' and k(D) indicated that the interactions were primarily electrostatic in nature. The concentration dependent viscosity data were analyzed using a modified Ross and Minton equation. The analysis explicitly differentiates between the effect of molecular shape, size, self-crowding, and electrostatic intermolecular interactions in governing high concentration viscosity behavior. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association

The interaction between constituent year and within-1-year effects in elite German youth basketball.

PubMed

Steingröver, C; Wattie, N; Baker, J; Helsen, W F; Schorer, J

2017-06-01

The current state of research on relative age effects in basketball shows an uneven picture. These mixed results might be caused by the interaction of constituent year and within-year effects. Our aim was to examine constituent and within-1-year effects in elite German youth basketball. The sample (n = 4400) included players competing in the JBBL (Under-16 first division) and the NBBL (Under-19 first division) from 2011/2012 until 2013/2014. A multi-way frequency analysis revealed an interaction of constituent year effects and within-1-year effects for the JBBL, χ 2 (6, 2590) = 12.76, P < 0.05. NBBL data showed significant constituent year effects, χ 2 (2, n = 1810) = 25.32, P < 0.01, and within-1-year effects for all three age bands but no interaction. The interaction between constituent year and within-1-year effects in the JBBL showed reduced within-1-year effects with increasing age. Once players enter the system in the JBBL, relatively younger players seem less likely to drop out of the system. Results offer new insight regarding how the regulations of this talent development system may influence athletes' opportunities to enter the system and their likelihood of staying at the highest levels of competition. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Semiconducting polymers for gas detection

NASA Technical Reports Server (NTRS)

Byrd, N. R.; Sheratte, M. B.

1975-01-01

Conjugated polyenes, and polyesters containing phthalocyanine in their backbone, were synthesized. These polymers were characterized by chemical analysis, thermogravimetric analysis, spectral analysis, and X-ray diffraction studies for crystallinity, as well as for their film-forming capability and gas/polymer interactions. Most of the polymers were relatively insensitive to water vapor up to 50 percent relative humidity, but the polyester/phthalocyanine (iron) polymer was relatively insensitive up to 100 percent RH. On the other hand, poly(p-dimethylaminophenylacetylene) was too conductive at 100 percent RH. Of the gases tested, the only ones that gave any evidence of interacting with the polymers were SO2, NOx, HCN and NH3. Poly(imidazole)/thiophene responded to each of these gases at all relative humidities, while the other polymers gave varying response, depending upon the RH. Thus, since most of these gases were electron-accepting, the electron-donating character of poly(imidazole)/thiophene substantiates the concept of electronegativity being the operating principle for interaction effects. Of the six polymers prepared, poly(imidazole)/thiophene first showed a very good response to smoldering cotton, but it later became nonresponsive; presumably due to oxidation effects.

Creep-Fatigue Interaction and Cyclic Strain Analysis in P92 Steel Based on Test

NASA Astrophysics Data System (ADS)

Ji, Dongmei; Zhang, Lai-Chang; Ren, Jianxing; Wang, Dexian

2015-04-01

This work focused on the interaction of creep and fatigue and cyclic strain analysis in high-chromium ferritic P92 steel based on load-controlled creep-fatigue (CF) tests and conventional creep test at 873 K. Mechanical testing shows that the cyclic load inhibits the propagation of creep damage in the P92 steel and CF interaction becomes more severe with the decrease in the holding period duration and stress ratio. These results are also verified by the analysis of cyclic strain. The fatigue lifetime reduces with the increasing of the holding period duration and it does not reduce much with the increasing stress ratio especially under the conditions of long holding period duration. The cyclic strains (i.e., the strain range and creep strain) of CF tests consist of three stages, which is the same as those for the conventional creep behavior. The microscopic fracture surface observations illustrated that two different kinds of voids are observed at the fracture surfaces and Laves phase precipitates at the bottom of the voids.

Parental and Infant Gender Factors in Parent-Infant Interaction: State-Space Dynamic Analysis.

PubMed

Cerezo, M Angeles; Sierra-García, Purificación; Pons-Salvador, Gemma; Trenado, Rosa M

2017-01-01

This study aimed to investigate the influence of parental gender on their interaction with their infants, considering, as well, the role of the infant's gender. The State Space Grid (SSG) method, a graphical tool based on the non-linear dynamic system (NDS) approach was used to analyze the interaction, in Free-Play setting, of 52 infants, aged 6 to 10 months, divided into two groups: half of the infants interacted with their fathers and half with their mothers. There were 50% boys in each group. MANOVA results showed no differential parenting of boys and girls. Additionally, mothers and fathers showed no differences in the Diversity of behavioral dyadic states nor in Predictability. However, differences associated with parent's gender were found in that the paternal dyads were more "active" than the maternal dyads: they were faster in the rates per second of behavioral events and transitions or change of state. In contrast, maternal dyads were more repetitive because, once they visited a certain dyadic state, they tend to be involved in more events. Results showed a significant discriminant function on the parental groups, fathers and mothers. Specifically, the content analyses carried out for the three NDS variables, that previously showed differences between groups, showed particular dyadic behavioral states associated with the rate of Transitions and the Events per Visit ratio. Thus, the transitions involving 'in-out' of 'Child Social Approach neutral - Sensitive Approach neutral' state and the repetitions of events in the dyadic state 'Child Play-Sensitive Approach neutral' distinguished fathers from mothers. The classification of dyads (with fathers and mothers) based on this discriminant function identified 73.10% (19/26) of the father-infant dyads and 88.5% (23/26) of the mother-infant dyads. The study of father-infant interaction using the SSG approach offers interesting possibilities because it characterizes and quantifies the actual moment-to-moment flow of parent-infant interactive dynamics. Our findings showed how observational methods applied to natural contexts offer new facets in father vs. mother interactive behavior with their infants that can inform further developments in this field.

Versatility of Cooperative Transcriptional Activation: A Thermodynamical Modeling Analysis for Greater-Than-Additive and Less-Than-Additive Effects

PubMed Central

Frank, Till D.; Carmody, Aimée M.; Kholodenko, Boris N.

2012-01-01

We derive a statistical model of transcriptional activation using equilibrium thermodynamics of chemical reactions. We examine to what extent this statistical model predicts synergy effects of cooperative activation of gene expression. We determine parameter domains in which greater-than-additive and less-than-additive effects are predicted for cooperative regulation by two activators. We show that the statistical approach can be used to identify different causes of synergistic greater-than-additive effects: nonlinearities of the thermostatistical transcriptional machinery and three-body interactions between RNA polymerase and two activators. In particular, our model-based analysis suggests that at low transcription factor concentrations cooperative activation cannot yield synergistic greater-than-additive effects, i.e., DNA transcription can only exhibit less-than-additive effects. Accordingly, transcriptional activity turns from synergistic greater-than-additive responses at relatively high transcription factor concentrations into less-than-additive responses at relatively low concentrations. In addition, two types of re-entrant phenomena are predicted. First, our analysis predicts that under particular circumstances transcriptional activity will feature a sequence of less-than-additive, greater-than-additive, and eventually less-than-additive effects when for fixed activator concentrations the regulatory impact of activators on the binding of RNA polymerase to the promoter increases from weak, to moderate, to strong. Second, for appropriate promoter conditions when activator concentrations are increased then the aforementioned re-entrant sequence of less-than-additive, greater-than-additive, and less-than-additive effects is predicted as well. Finally, our model-based analysis suggests that even for weak activators that individually induce only negligible increases in promoter activity, promoter activity can exhibit greater-than-additive responses when transcription factors and RNA polymerase interact by means of three-body interactions. Overall, we show that versatility of transcriptional activation is brought about by nonlinearities of transcriptional response functions and interactions between transcription factors, RNA polymerase and DNA. PMID:22506020

Portfolio analysis of layered security measures.

PubMed

Chatterjee, Samrat; Hora, Stephen C; Rosoff, Heather

2015-03-01

Layered defenses are necessary for protecting the public from terrorist attacks. Designing a system of such defensive measures requires consideration of the interaction of these countermeasures. In this article, we present an analysis of a layered security system within the lower Manhattan area. It shows how portfolios of security measures can be evaluated through portfolio decision analysis. Consideration is given to the total benefits and costs of the system. Portfolio diagrams are created that help communicate alternatives among stakeholders who have differing views on the tradeoffs between security and economic activity. © 2014 Society for Risk Analysis.

Identification and In Silico Analysis of Major Redox Modulated Proteins from Brassica juncea Seedlings Using 2D Redox SDS PAGE (2-Dimensional Diagonal Redox Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis).

PubMed

Chaurasia, Satya Prakash; Deswal, Renu

2017-02-01

The thiol-disulphide exchange regulates the activity of proteins by redox modulation. Many studies to analyze reactive oxygen species (ROS), particularly, hydrogen peroxide (H 2 O 2 ) induced changes in the gene expression have been reported, but efforts to detect H 2 O 2 modified proteins are comparatively few. Two-dimensional diagonal redox sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) was used to detect polypeptides which undergo thiol-disulphide exchange in Brassica juncea seedlings following H 2 O 2 (10 mM) treatment for 30 min. Eleven redox responsive polypeptides were identified which included cruciferin, NLI [Nuclear LIM (Lin11, Isl-1 & Mec-3 domains)] interacting protein phosphatase, RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) large subunit, and myrosinase. Redox modulation of RuBisCO large subunit was further confirmed by western blotting. However, the small subunit of RuBisCO was not affected by these redox changes. All redox modulated targets except NLI interacting protein (although it contains two cysteines) showed oxidation sensitive cysteines by in silico analysis. Interestingly, interactome of cruciferin and myrosinase indicated that they may have additional function(s) beside their well-known roles in the seedling development and abiotic stress respectively. Cruciferin showed interactions with stress associated proteins like defensing-like protein 192 and 2-cys peroxiredoxin. Similarly, myrosinase showed interactions with nitrilase and cytochrome p450 which are involved in nitrogen metabolism and/or hormone biosynthesis. This simple procedure can be used to detect major stress mediated redox changes in other plants.

A cis-phase interaction study of genetic variants within the MAOA gene in major depressive disorder.

PubMed

Zhang, JieXu; Chen, YanBo; Zhang, KeRang; Yang, Hong; Sun, Yan; Fang, Yue; Shen, Yan; Xu, Qi

2010-11-01

The genetic basis of major depressive disorder (MDD) has been explored extensively, but the mode of transmission of the disease has yet to be established. To better understand the mechanism by which the monoamine oxidase A (MAOA) gene may play a role in developing MDD, the present work examined the cis-phase interaction between genetic variants within the MAOA gene for the pathogenesis of MDD. A variable number tandem repeat (VNTR) and 19 single nucleotide polymorphisms (SNPs) within the gene were genotyped in 512 unrelated patients with MDD and 567 unrelated control subjects among a Chinese population. Quantitative real-time polymerase chain reaction analysis was applied to test the effect of genetic variants on expression of the MAOA gene in MDD. Neither the VNTR polymorphism nor seven informative SNPs showed allelic association with MDD, but the cis-acting interactions between the VNTR polymorphism and four individual SNPs were strongly associated with MDD risk, of which the VNTR-rs1465107 combination showed the strongest association (p = .000011). Quantitative real-time polymerase chain reaction analysis showed that overall relative quantity of MAOA messenger RNA was significantly higher in patients with MDD than in control subjects (fold change = 5.28, p = 1.7 × 10⁻⁷) and that in the male subjects carrying the VNTR-L, rs1465107-A, rs6323-G, rs2072743-A, or rs1137070-T alleles, expression of MAOA messenger RNA was significantly higher in the patient group than in the control group. The cis-phase interaction between the VNTR polymorphism and functional SNPs may contribute to the etiology of MDD. Copyright © 2010 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

miR-122-SOCS1-JAK2 axis regulates allergic inflammation and allergic inflammation-promoted cellular interactions

PubMed Central

Kim, Hanearl; Kim, Hyuna; Byun, Jaehwan; Park, Yeongseo; Lee, Hansoo; Lee, Yun Sil; Choe, Jongseon; Kim, Young Myeong; Jeoung, Dooil

2017-01-01

The regulatory role of suppressor of cytokine signaling 1 (SOCS1) in inflammation has been reported. However, its role in allergic inflammation has not been previously reported. SOCS1 mediated in vitro and in vivo allergic inflammation. Histone deacetylase-3 (HDAC3), a mediator of allergic inflammation, interacted with SOCS1, and miR-384 inhibitor, a positive regulator of HDAC3, induced features of allergic inflammation in an SOCS1-dependent manner. miRNA array analysis showed that the expression of miR-122 was decreased by antigen-stimulation. TargetScan analysis predicted the binding of miR-122 to the 3′-UTR of SOCS1. miR-122 inhibitor induced in vitro and in vivo allergic features in SOCS1-dependent manner. SOCS1 was necessary for allergic inflammation-promoted enhanced tumorigenic and metastatic potential of cancer cells. SOCS1 and miR-122 regulated cellular interactions involving cancer cells, mast cells and macrophages during allergic inflammation. SOCS1 mimetic peptide, D-T-H-F-R-T-F-R-S-H-S-D-Y-R-R-I, inhibited in vitro and in vivo allergic inflammation, allergic inflammation-promoted enhanced tumorigenic and metastatic potential of cancer cells, and cellular interactions during allergic inflammation. Janus kinase 2 (JAK2) exhibited binding to SOCS1 mimetic peptide and mediated allergic inflammation. Transforming growth factor- Δ1 (TGF-Δ1) was decreased during allergic inflammation and showed an anti-allergic effect. SOCS1 and JAK2 regulated the production of anti-allergic TGF-Δ1. Taken together, our results show that miR-122-SOCS1 feedback loop can be employed as a target for the development of anti-allergic and anti-cancer drugs. PMID:28968979

A strategy for the study of the interactions between metal-dyes and proteins with QM/MM approaches: the case of iron-gall dye.

PubMed

Jurinovich, Sandro; Degano, Ilaria; Mennucci, Benedetta

2012-11-15

Historical textiles dyed with tannins usually show more extended degradation than fabrics dyed with other coloring materials. In order to shed light on this phenomenon we investigated the molecular interactions between tannin dyes and protein-based textiles using quantum-mechanical tools. In particular, we focused on the iron-gall complex with a fragment of α-helix wool keratin. We developed a step by step protocol which moves from the simplest ternary complexes with free amino acids (all treated quantum mechanically) to the more realistic system of the polypeptide fragment (treated at QM/MM level), passing through an intermediate model of interacting sites to evaluate the local environmental effects. The analysis of the interactions between the iron-gall complexes and free amino acids allowed us to identify possible coordination modes as well as determining their relative geometries. However, we also showed that only with the addition of the proteic environment a detailed picture of the interaction sites and binding modes can be achieved. An important role is in fact played by the microenvironment which can favor specific coordinations with respect to others due to both structural and electronic changes in the possible interaction sites.

Disability assessment: the efficacy of multimedia interactive nurse education.

PubMed

Chiang, Hui-Chaun; Lin, Feng-Yu; Hwu, Yueh-Juen

2013-06-01

Nearly 3% of the population in Taiwan is classified as disabled. Disability assessment directly relates to long-term care quality and resource allocation. The purpose of this study was to explore the effects of a multimedia interactive DVD on enhancing nurse knowledgeand disability assessment skills. The study was a quasi-experimental design. The experimental group received multimedia interactive DVD, and the control group received conventional classroom education. The study gathered data using scales assessing knowledge related to disability assessment and case studies. Scales were implemented before and after multimedia interactive DVD interventions at weeks 2 and 4. In-depth interviews with voice recording were used to collect qualitative data to elicit differences in perception between the experimental and control groups. This study found significant improvements in the experimental group in terms of disability assessment knowledge and case study assessment skills. These improvements lasted through at least 1-month posttest. Analysis of interview data for the experimental group showed that the multimedia interactive DVD provided a more flexible approach to learning than classroom education and improved participant self-confidence to conduct disability assessments. The study showed the effectiveness of the developed multimedia interactive DVD in significantly improving the disability assessment confidences of nurses. Study findings can be used as a reference guide for continuing educational efforts in long-term care settings.

Analysis of a summary network of co-infection in humans reveals that parasites interact most via shared resources

PubMed Central

Griffiths, Emily C.; Pedersen, Amy B.; Fenton, Andy; Petchey, Owen L.

2014-01-01

Simultaneous infection by multiple parasite species (viruses, bacteria, helminths, protozoa or fungi) is commonplace. Most reports show co-infected humans to have worse health than those with single infections. However, we have little understanding of how co-infecting parasites interact within human hosts. We used data from over 300 published studies to construct a network that offers the first broad indications of how groups of co-infecting parasites tend to interact. The network had three levels comprising parasites, the resources they consume and the immune responses they elicit, connected by potential, observed and experimentally proved links. Pairs of parasite species had most potential to interact indirectly through shared resources, rather than through immune responses or other parasites. In addition, the network comprised 10 tightly knit groups, eight of which were associated with particular body parts, and seven of which were dominated by parasite–resource links. Reported co-infection in humans is therefore structured by physical location within the body, with bottom-up, resource-mediated processes most often influencing how, where and which co-infecting parasites interact. The many indirect interactions show how treating an infection could affect other infections in co-infected patients, but the compartmentalized structure of the network will limit how far these indirect effects are likely to spread. PMID:24619434

Physical and Visual Accessibilities in Intensive Care Units: A Comparative Study of Open-Plan and Racetrack Units.

PubMed

Rashid, Mahbub; Khan, Nayma; Jones, Belinda

2016-01-01

This study compared physical and visual accessibilities and their associations with staff perception and interaction behaviors in 2 intensive care units (ICUs) with open-plan and racetrack layouts. For the study, physical and visual accessibilities were measured using the spatial analysis techniques of Space Syntax. Data on staff perception were collected from 81 clinicians using a questionnaire survey. The locations of 2233 interactions, and the location and length of another 339 interactions in these units were collected using systematic field observation techniques. According to the study, physical and visual accessibilities were different in the 2 ICUs, and clinicians' primary workspaces were physically and visually more accessible in the open-plan ICU. Physical and visual accessibilities affected how well clinicians' knew their peers and where their peers were located in these units. Physical and visual accessibilities also affected clinicians' perception of interaction and communication and of teamwork and collaboration in these units. Additionally, physical and visual accessibilities showed significant positive associations with interaction behaviors in these units, with the open-plan ICU showing stronger associations. However, physical accessibilities were less important than visual accessibilities in relation to interaction behaviors in these ICUs. The implications of these findings for ICU design are discussed.

Analysis of a summary network of co-infection in humans reveals that parasites interact most via shared resources.

PubMed

Griffiths, Emily C; Pedersen, Amy B; Fenton, Andy; Petchey, Owen L

2014-05-07

Simultaneous infection by multiple parasite species (viruses, bacteria, helminths, protozoa or fungi) is commonplace. Most reports show co-infected humans to have worse health than those with single infections. However, we have little understanding of how co-infecting parasites interact within human hosts. We used data from over 300 published studies to construct a network that offers the first broad indications of how groups of co-infecting parasites tend to interact. The network had three levels comprising parasites, the resources they consume and the immune responses they elicit, connected by potential, observed and experimentally proved links. Pairs of parasite species had most potential to interact indirectly through shared resources, rather than through immune responses or other parasites. In addition, the network comprised 10 tightly knit groups, eight of which were associated with particular body parts, and seven of which were dominated by parasite-resource links. Reported co-infection in humans is therefore structured by physical location within the body, with bottom-up, resource-mediated processes most often influencing how, where and which co-infecting parasites interact. The many indirect interactions show how treating an infection could affect other infections in co-infected patients, but the compartmentalized structure of the network will limit how far these indirect effects are likely to spread.

Correlational approach to study interactions between dust Brownian particles in a plasma

NASA Astrophysics Data System (ADS)

Lisin, E. A.; Vaulina, O. S.; Petrov, O. F.

2018-01-01

A general approach to the correlational analysis of Brownian motion of strongly coupled particles in open dissipative systems is described. This approach can be applied to the theoretical description of various non-ideal statistically equilibrium systems (including non-Hamiltonian systems), as well as for the analysis of experimental data. In this paper, we consider an application of the correlational approach to the problem of experimental exploring the wake-mediated nonreciprocal interactions in complex plasmas. We derive simple analytic equations, which allows one to calculate the gradients of forces acting on a microparticle due to each of other particles as well as the gradients of external field, knowing only the information on time-averaged correlations of particles displacements and velocities. We show the importance of taking dissipative and random processes into account, without which consideration of a system with a nonreciprocal interparticle interaction as linearly coupled oscillators leads to significant errors in determining the characteristic frequencies in a system. In the examples of numerical simulations, we demonstrate that the proposed original approach could be an effective instrument in exploring the longitudinal wake structure of a microparticle in a plasma. Unlike the previous attempts to study the wake-mediated interactions in complex plasmas, our method does not require any external perturbations and is based on Brownian motion analysis only.

Meta-analysis confirms the LCE3C_LCE3B deletion as a risk factor for psoriasis in several ethnic groups and finds interaction with HLA-Cw6

PubMed Central

Riveira-Munoz, Eva; He, Su-Min; Escaramís, Georgia; Stuart, Philip E; Hüffmeier, Ulrike; Lee, Catherine; Kirby, Brian; Oka, Akira; Giardina, Emiliano; Liao, Wilson; Bergboer, Judith; Kainu, Kati; de Cid, Rafael; Munkhbat, Batmunkh; Zeeuwen, Patrick L J M; Armour, John A L; Poon, Annie; Mabuchi, Tomotaka; Ozawa, Akira; Zawirska, Agnieszka; Burden, David A; Barker, Jonathan N; Capon, Francesca; Traupe, Heiko; Sun, Liang-Dan; Cui, Yong; Yin, Xian-Yong; Chen, Gang; Lim, Henry; Nair, Rajan; Voorhess, John; Tejasvi, Trilokraj; Pujol, Ramón; Munkhtuvshin, Namid; Fischer, Judith; Kere, Juha; Schalkwijk, Joost; Bowcock, Anne; Kwok, Pui-Yan; Novelli, Giuseppe; Inoko, Hidetoshi; Ryan, Anthony W; Trembath, Richard C; Reis, André; Zhang, Xue-Jun; Elder, James T; Estivill, Xavier

2012-01-01

A multicenter meta-analysis including data from 9389 psoriasis patients and 9477 control subjects was performed to investigate the contribution of the deletion of genes LCE3C and LCE3B, involved in skin barrier defense, to psoriasis susceptibility in different populations. The study confirms that the deletion of LCE3C and LCE3B is a common genetic factor for susceptibility to psoriasis in European populations [OROverall = 1.21 (1.15–1.27)], and for the first time directly demonstrated the deletion's association with psoriasis in [Chinese OR = 1.27 (1.16–1.34); Mongolian OR = 2.08 (1.44–2.99)] populations. The analysis of the HLA-Cw6 locus showed significant differences in the epistatic interaction with the LCE3C and LCE3B deletion in at least some European populations, indicating epistatic effects between these two major genetic contributors to psoriasis. The study highlights the value of examining genetic risk factors in multiple populations to identify genetic interactions, and indicates the need of further studies to understand the interaction of the skin barrier and the immune system in susceptibility to psoriasis. PMID:21107349

Hidden interaction in SBO galaxies

NASA Technical Reports Server (NTRS)

Galletta, G.; Bettoni, D.; Oosterloo, T.; Fasano, G.

1990-01-01

Galaxies, like plants, show a large variety of grafts: an individual of some type connects physically with a neighborhood of same or different type. The effects of these interactions between galaxies have a broad range of morphologies depending, among other quantities, on the distance of the closest approach between systems and the relative size of the two galaxies. A sketch of the possible situations is shown in tabular form. This botanical classification is just indicative, because the effects of interactions can be notable also at relatively large separations, when additional conditions are met, as for example low density of the interacting systems or the presence of intra-cluster gas. In spite of the large variety of encounters and effects, in the literature the same terms are often used to refer to different types of interactions. Analysis indicates that only few of the situations show evident signs of interaction. They appear to be most relevant when the size of the two galaxies is comparable. Bridges and tails, like the well known case of NGC 4038/39, the Antennae, are only observed for a very low percentage of all galaxies (approx. 0.38 percent, Arp and Madore 1977). In most cases of gravitational bond between two galaxies, the effects of interactions are not relevant or evident. For instance, the detection of stellar shells (Malin and Carter 1983), which have been attributed to the accretion of gas stripped from another galaxy or to the capture and disruption of a small stellar system (Quinn 1984), requires particular observing and reduction techniques. Besides these difficulties of detection, time plays an important role in erasing, within a massive galaxy, the effects of interactions with smaller objects. This can happen on a timescale shorter than the Hubble time, so the number of systems now showing signs of interaction suggests lower limits to the true frequency of interactions in the life-time of a stellar system.

Histone modifications influence mediator interactions with chromatin

PubMed Central

Zhu, Xuefeng; Zhang, Yongqiang; Bjornsdottir, Gudrun; Liu, Zhongle; Quan, Amy; Costanzo, Michael; Dávila López, Marcela; Westholm, Jakub Orzechowski; Ronne, Hans; Boone, Charles; Gustafsson, Claes M.; Myers, Lawrence C.

2011-01-01

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. PMID:21742760

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

Design principles and optimal performance for molecular motors under realistic constraints

NASA Astrophysics Data System (ADS)

Tu, Yuhai; Cao, Yuansheng

2018-02-01

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations show that a gating mechanism that restricts forward stepping in a narrow window in configuration space is needed for generating high power at physiologically relevant loads. By deriving general thermodynamics laws for nonequilibrium motors, we find that the maximum torque (force) at stall is less than its theoretical limit for any realistic motor-track interactions due to speed fluctuations. Our study reveals a tradeoff for the motor-track interaction: while a strong interaction generates a high power output for forward steps, it also leads to a higher probability of wasteful spontaneous back steps. Our analysis and simulations show that this tradeoff sets a fundamental limit to the maximum motor efficiency in the presence of spontaneous back steps, i.e., loose-coupling. Balancing this tradeoff leads to an optimal design of the motor-track interaction for achieving a maximum efficiency close to 1 for realistic motors that are not perfectly coupled with the energy source. Comparison with existing data and suggestions for future experiments are discussed.

Gel properties and interactions of Mesona blumes polysaccharide-soy protein isolates mixed gel: The effect of salt addition.

PubMed

Wang, Wenjie; Shen, Mingyue; Liu, Suchen; Jiang, Lian; Song, Qianqian; Xie, Jianhua

2018-07-15

Effect of different salt ions on the gel properties and microstructure of Mesona blumes polysaccharide (MBP)-soy protein isolates (SPI) mixed gels were investigated. Sodium and calcium ions were chosen to explore their effects on the rheological behavior and gel properties of MBP-SPI mixed gels were evaluated by using rheological, X-ray diffraction, protein solubility determination, and microstructure analysis. Results showed that the addition of salt ions change the crystalline state of gels system, the crystal of gel was enhanced at low ion concentrations (0.005-0.01 M). The two peaks of gel characteristic at 8.9° and 19.9° almost disappeared at high salt ions concentrations (0.015-0.02 M), and new crystallization peaks appeared at around 30° and 45°. The elasticity, viscosity, gel strength, water holding capacity, and thermal stability of gel were increased at low ion concentration. Results showed that the main interactions which promoted gel formation and maintain the three-dimensional structure of the gel were electrostatic interactions, hydrophobic interactions, and disulfide interactions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genome-wide interaction study identifies RCBTB1 as a modifier for smoking effect on carotid intima-media thickness.

PubMed

Wang, Liyong; Rundek, Tatjana; Beecham, Ashley; Hudson, Barry; Blanton, Susan H; Zhao, Hongyu; Sacco, Ralph L; Dong, Chuanhui

2014-01-01

Carotid intima-media thickness (cIMT), a marker for atherosclerosis, is affected by smoking and has substantial interindividual variation. We sought to identify the genetic moderators influencing the effect of smoking on cIMT. With a multistage design using 722 379 single nucleotide polymorphisms (SNP), a genome-wide interaction study was performed in a discovery sample of 669 Hispanics, followed by replication in 589 subjects (264 Hispanics, 172 non-Hispanic blacks, 153 non-Hispanic whites). Assuming an additive genetic model, regression analysis was performed to test for smoking-SNP interaction on cIMT while controlling for age, sex, and the top 3 principal components of ancestry. The strongest interaction in Hispanics was found with a synonymous splicing SNP (rs3751383) in exon 9 of RCBTB1 (P=2.5e(-6) in discovery sample; P=0.01 in the Hispanic replication sample; P<8.8e(-9) in the combined Hispanic sample). Stratification analysis in the combined Hispanic sample showed that smoking had no effect on cIMT among rs3751383 G homozygote (P=0.15), a moderate effect among rs3751383 heterozygote (P=0.01), and a strong effect among rs3751383 A homozygote (P=2.1e(-7)). A consistent trend was observed in the non-Hispanic white and black data sets, leading to an interaction effect of P<2.9e(-9) in the meta-analysis of all 1258 subjects. Our study represents the first genome-wide smoking-SNP interaction study of cIMT and identifies RCBTB1 as a modifier of the smoking effect on cIMT. Testing for gene-environment interactions can help uncover genetic factors that contribute to the interindividual variation in response to the same environmental exposure.

MAOA, childhood maltreatment and antisocial behavior: Meta-analysis of a gene-environment interaction

PubMed Central

Byrd, Amy L.; Manuck, Stephen B.

2013-01-01

Background In a seminal study of gene-environment interaction, childhood maltreatment predicted antisocial behavior more strongly in males carrying an MAOA promoter variant of lesser, compared to higher, transcriptional efficiency. Many further investigations have been reported, including studies of other early environmental exposures and females. Here we report a meta-analysis of studies testing the interaction of MAOA genotype and childhood adversities on antisocial outcomes in predominantly non-clinical samples. Method Included were 27 peer-reviewed, English-language studies published through August, 2012, that contained indicators of maltreatment or “other” family (e.g., parenting, sociodemographic) hardships; MAOA genotype; indices of aggressive and antisocial behavior; and statistical test of genotype-environment interaction. Studies of forensic and exclusively clinical samples, clinical cohorts lacking proportionally matched controls, or outcomes non-specific for antisocial behavior were excluded. The Liptak-Stouffer weighted Z-test for meta-analysis was implemented to maximize study inclusion and calculated separately for male and female cohorts. Results Across 20 male cohorts, early adversity presaged antisocial outcomes more strongly for low, relative to high, activity MAOA genotype (P=.0044). Stratified analyses showed the interaction specific to maltreatment (P=.0000008) and robust to several sensitivity analyses. Across 11 female cohorts, MAOA did not interact with combined early life adversities, whereas maltreatment alone predicted antisocial behaviors preferentially, but weakly, in females of high activity MAOA genotype (P=.02). Conclusions We found common regulatory variation in MAOA to moderate effects of childhood maltreatment on male antisocial behaviors, confirming a sentinel finding in research on gene-environment interaction. An analogous, but less consistent, finding in females warrants further investigation. PMID:23786983

MAOA, childhood maltreatment, and antisocial behavior: meta-analysis of a gene-environment interaction.

PubMed

Byrd, Amy L; Manuck, Stephen B

2014-01-01

In a seminal study of gene-environment interaction, childhood maltreatment predicted antisocial behavior more strongly in male subjects carrying an MAOA promoter variant of lesser, compared with higher, transcriptional efficiency. Many further investigations have been reported, including studies of other early environmental exposures and female subjects. Here, we report a meta-analysis of studies testing the interaction of MAOA genotype and childhood adversities on antisocial outcomes in predominantly nonclinical samples. Included were 27 peer-reviewed, English-language studies published through August, 2012, that contained indicators of maltreatment or other family (e.g., parenting, sociodemographic) hardships; MAOA genotype; indices of aggressive and antisocial behavior; and statistical test of genotype-environment interaction. Studies of forensic and exclusively clinical samples, clinical cohorts lacking proportionally matched control subjects, or outcomes nonspecific for antisocial behavior were excluded. The Liptak-Stouffer weighted Z-test for meta-analysis was implemented to maximize study inclusion and calculated separately for male and female cohorts. Across 20 male cohorts, early adversity presaged antisocial outcomes more strongly for low-activity, relative to high- activity, MAOA genotype (p = .0044). Stratified analyses showed the interaction specific to maltreatment (p = .00000082) and robust to several sensitivity analyses. Across 11 female cohorts, MAOA did not interact with combined early life adversities, whereas maltreatment alone predicted antisocial behaviors preferentially, but weakly, in female subjects of high-activity MAOA genotype (p = .02). We found common regulatory variation in MAOA to moderate effects of childhood maltreatment on male antisocial behaviors, confirming a sentinel finding in research on gene-environment interaction. An analogous, but less consistent, finding in female subjects warrants further investigation. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Predicting PDZ domain mediated protein interactions from structure

PubMed Central

2013-01-01

Background PDZ domains are structural protein domains that recognize simple linear amino acid motifs, often at protein C-termini, and mediate protein-protein interactions (PPIs) in important biological processes, such as ion channel regulation, cell polarity and neural development. PDZ domain-peptide interaction predictors have been developed based on domain and peptide sequence information. Since domain structure is known to influence binding specificity, we hypothesized that structural information could be used to predict new interactions compared to sequence-based predictors. Results We developed a novel computational predictor of PDZ domain and C-terminal peptide interactions using a support vector machine trained with PDZ domain structure and peptide sequence information. Performance was estimated using extensive cross validation testing. We used the structure-based predictor to scan the human proteome for ligands of 218 PDZ domains and show that the predictions correspond to known PDZ domain-peptide interactions and PPIs in curated databases. The structure-based predictor is complementary to the sequence-based predictor, finding unique known and novel PPIs, and is less dependent on training–testing domain sequence similarity. We used a functional enrichment analysis of our hits to create a predicted map of PDZ domain biology. This map highlights PDZ domain involvement in diverse biological processes, some only found by the structure-based predictor. Based on this analysis, we predict novel PDZ domain involvement in xenobiotic metabolism and suggest new interactions for other processes including wound healing and Wnt signalling. Conclusions We built a structure-based predictor of PDZ domain-peptide interactions, which can be used to scan C-terminal proteomes for PDZ interactions. We also show that the structure-based predictor finds many known PDZ mediated PPIs in human that were not found by our previous sequence-based predictor and is less dependent on training–testing domain sequence similarity. Using both predictors, we defined a functional map of human PDZ domain biology and predict novel PDZ domain function. Users may access our structure-based and previous sequence-based predictors at http://webservice.baderlab.org/domains/POW. PMID:23336252

Insights into positive and negative requirements for protein-protein interactions by crystallographic analysis of the beta-lactamase inhibitory proteins BLIP, BLIP-I, and BLP.

PubMed

Gretes, Michael; Lim, Daniel C; de Castro, Liza; Jensen, Susan E; Kang, Sung Gyun; Lee, Kye Joon; Strynadka, Natalie C J

2009-06-05

Beta-lactamase inhibitory protein (BLIP) binds a variety of beta-lactamase enzymes with wide-ranging specificity. Its binding mechanism and interface interactions are a well-established model system for the characterization of protein-protein interactions. Published studies have examined the binding of BLIP to diverse target beta-lactamases (e.g., TEM-1, SME-1, and SHV-1). However, apart from point mutations of amino acid residues, variability on the inhibitor side of this enzyme-inhibitor interface has remained unexplored. Thus, we present crystal structures of two likely BLIP relatives: (1) BLIP-I (solved alone and in complex with TEM-1), which has beta-lactamase inhibitory activity very similar to that of BLIP; and (2) beta-lactamase-inhibitory-protein-like protein (BLP) (in two apo forms, including an ultra-high-resolution structure), which is unable to inhibit any tested beta-lactamase. Despite categorical differences in species of origin and function, BLIP-I and BLP share nearly identical backbone conformations, even at loop regions differing in BLIP. We describe interacting residues and provide a comparative structural analysis of the interactions formed at the interface of BLIP-I.TEM-1 versus those formed at the interface of BLIP.TEM-1. Along with initial attempts to functionally characterize BLP, we examine its amino acid residues that structurally correspond to BLIP/BLIP-I binding hotspots to explain its inability to bind and inhibit TEM-1. We conclude that the BLIP family fold is a robust and flexible scaffold that permits the formation of high-affinity protein-protein interactions while remaining highly selective. Comparison of the two naturally occurring, distinct binding interfaces built upon this scaffold (BLIP and BLIP-I) shows that there is substantial variation possible in the subnanomolar binding interaction with TEM-1. The corresponding (non-TEM-1-binding) BLP surface shows that numerous favorable backbone-backbone/backbone-side-chain interactions with a protein partner can be negated by the presence of a few, strongly unfavorable interactions, especially electrostatic repulsions.

Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

PubMed

Varadwaj, Pradeep Risikrishna

2010-05-01

Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond formation. It is found from the analysis of the electron density rho ( c ), the Laplacian of electron charge density nabla(2)rho(c), and the total energy density (H ( c )) at the critical points between the interatomic regions that the interaction N...H is indeed electrostatic in origin (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) < 0) and HX ((rho(c) > 0, nabla(2)rho(c) < 0 and H(c) < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering, E((2)), caused by charge transfer mechanism shows that the interaction N...H is n(N) --> BD*(HX) delocalization.

Protein interactions during flour mixing using wheat flour with altered starch.

PubMed

Wang, Xiaolong; Appels, Rudi; Zhang, Xiaoke; Diepeveen, Dean; Torok, Kitti; Tomoskozi, Sandor; Bekes, Ferenc; Ma, Wujun; Sharp, Peter; Islam, Shahidul

2017-09-15

Wheat grain proteins responses to mixing and thermal treatment were investigated using Mixolab-dough analysis systems with flour from two cultivars, Ventura-26 (normal amylose content) and Ventura-19 (reduced amylose content). Size exclusion high performance liquid chromatography (SE-HPLC) and two-dimensional gel electrophoresis (2-DGE) analysis revealed that, stress associated and metabolic proteins largely interacted with dough matrix of Ventura-26 after 26min (56°C); gliadins, avenin-like b proteins, LMW-GSs, and partial globulins showed stronger interactions within the dough matrix of Ventura-26 at 32min/C3 (80°C), thereafter, however, stronger protein interactions were observed within the dough matrix of Ventura-19 at 38min/C4 (85°C) and 43min (80°C). Thirty-seven proteins associated with changes in dough matrix due to reduced amylose content were identified by mass spectrometry and mainly annotated to the chromosome group 1, 4, and 6. The findings provide new entry points for modifying final product attributes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interactions of zinc octacarboxyphthalocyanine with selected amino acids and with albumin

NASA Astrophysics Data System (ADS)

Kliber, Marta; Broda, Małgorzata A.; Nackiewicz, Joanna

2016-02-01

Effect of selected amino acids (glycine, L-histidine, L-cysteine, L-serine, L-tryptophan) and albumin on the spectroscopic properties and photostability of zinc octacarboxyphthalocyanine (ZnPcOC) was explored in the phosphate buffer at a pH of 7.0. The photodegradation of ZnPcOC alone and in the presence of amino acids or albumin has been investigated in aqueous phase using UV-366 nm and daylight irradiation. Kinetic analysis showed that the interaction with amino acids or albumin enhances the photostability of ZnPcOC. To answer the question of how zinc phthalocyanine interacts with amino acids extensive DFT calculations were performed. Analysis of the optimized geometry features of ZnPcOC: amino acids complexes in the gas phase and in water environment as well as the BSSE corrected interaction energies indicates that the more likely is the formation of equatorial complexes in which H-bonds are formed between the COOH groups of the phthalocyanine and carboxyl or amino groups of amino acids. UV-Vis spectra calculated by employing time dependent density functional theory (TD-DFT) are also consistent with this conclusion.

Interaction entropy for protein-protein binding.

PubMed

Sun, Zhaoxi; Yan, Yu N; Yang, Maoyou; Zhang, John Z H

2017-03-28

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interactionentropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interactionentropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

Visualization of metabolic interaction networks in microbial communities using VisANT 5.0

DOE PAGES

Granger, Brian R.; Chang, Yi -Chien; Wang, Yan; ...

2016-04-15

Here, the complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique meta-graph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction networkmore » between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues.« less

Microstructural characterization of annealed U-12Zr-4Pd and U-12Zr-4Pd-5Ln: Investigating Pd as a metallic fuel additive

NASA Astrophysics Data System (ADS)

Benson, Michael T.; He, Lingfeng; King, James A.; Mariani, Robert D.

2018-04-01

Palladium is being investigated as a potential additive to metallic fuel to control fuel-cladding chemical interaction (FCCI). A primary cause of FCCI is the lanthanide fission products moving to the fuel periphery and interacting with the cladding. This interaction will lead to wastage of the cladding and, given enough time or burn-up, eventually to a cladding breach. The current study is a scanning electron microscopy (SEM) and transmission electron microscopy (TEM) characterization of annealed U-12Zr-4Pd and U-12Zr-4Pd-5Ln, where Ln = 53Nd-25Ce-16Pr-6La. The present study shows that Pd preferentially binds the lanthanides over other fuel constituents, which may prevent lanthanide migration and interaction with the cladding during irradiation. The SEM analysis indicates the 1:1 Pd-Ln compound is being formed, while the TEM analysis, due to higher resolution, found the 1:1 compound, as well as Pd-rich compounds Pd2Ln and Pd3Ln2.

webPIPSA: a web server for the comparison of protein interaction properties

PubMed Central

Richter, Stefan; Wenzel, Anne; Stein, Matthias; Gabdoulline, Razif R.; Wade, Rebecca C.

2008-01-01

Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org. PMID:18420653

Intuitive Cognition and Models of Human-Automation Interaction.

PubMed

Patterson, Robert Earl

2017-02-01

The aim of this study was to provide an analysis of the implications of the dominance of intuitive cognition in human reasoning and decision making for conceptualizing models and taxonomies of human-automation interaction, focusing on the Parasuraman et al. model and taxonomy. Knowledge about how humans reason and make decisions, which has been shown to be largely intuitive, has implications for the design of future human-machine systems. One hundred twenty articles and books cited in other works as well as those obtained from an Internet search were reviewed. Works were deemed eligible if they were published within the past 50 years and common to a given literature. Analysis shows that intuitive cognition dominates human reasoning and decision making in all situations examined. The implications of the dominance of intuitive cognition for the Parasuraman et al. model and taxonomy are discussed. A taxonomy of human-automation interaction that incorporates intuitive cognition is suggested. Understanding the ways in which human reasoning and decision making is intuitive can provide insight for future models and taxonomies of human-automation interaction.

Immobilization of flavan-3-ols onto sensor chips to study their interactions with proteins and pectins by SPR

NASA Astrophysics Data System (ADS)

Watrelot, Aude A.; Tran, Dong Tien; Buffeteau, Thierry; Deffieux, Denis; Le Bourvellec, Carine; Quideau, Stéphane; Renard, Catherine M. G. C.

2016-05-01

Interactions between plant polyphenols and biomacromolecules such as proteins and pectins have been studied by several methods in solution (e.g. isothermal titration calorimetry, dynamic light scattering, nuclear magnetic resonance and spectrophotometry). Herein, these interactions were investigated in real time by Surface Plasmon Resonance (SPR) analysis after immobilization of flavan-3-ols onto a sensor chip surface. (-)-epicatechin, (+)-catechin and flavan-3-ol oligomers with an average degree of polymerization of 2 and 8 were chemically modified using N-(2-(tritylthio)ethyl)propiolamide in order to introduce a spacer unit onto the catecholic B ring. Modified flavan-3-ols were then immobilized onto a carboxymethylated dextran surface (CM5). Immobilization was validated and further verified by evaluating flavan-3-ol interaction with bovine serum albumin (BSA), poly-L-proline or commercial pectins. BSA was found to have a stronger association with monomeric flavan-3-ols than oligomers. SPR analysis of selected flavan-3-ols immobilized onto CM5 sensor chips showed a stronger association for citrus pectins than apple pectins, regardless of flavan-3-ol degree of polymerization.

Sequence co-evolution gives 3D contacts and structures of protein complexes

PubMed Central

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

Information-theoretic metric as a tool to investigate nonclassical correlations

NASA Astrophysics Data System (ADS)

Rudolph, Alexander L.; Lamine, Brahim; Joyce, Michael; Vignolles, Hélène; Consiglio, David

2014-06-01

We report on a project to introduce interactive learning strategies (ILS) to physics classes at the Université Pierre et Marie Curie, one of the leading science universities in France. In Spring 2012, instructors in two large introductory classes, first-year, second-semester mechanics, and second-year introductory electricity and magnetism, enrolling approximately 500 and 250 students, respectively, introduced ILS into some, but not all, of the sections of each class. The specific ILS utilized were think-pair-share questions and Peer Instruction in the main lecture classrooms, and University of Washington Tutorials for Introductory Physics in recitation sections. Pre- and postinstruction assessments [Force Concept Inventory (FCI) and Conceptual Survey of Electricity and Magnetism (CSEM), respectively] were given, along with a series of demographic questions. Since not all lecture or recitation sections in these classes used ILS, we were able to compare the results of the FCI and CSEM between interactive and noninteractive classes taught simultaneously with the same curriculum. We also analyzed final exam results, as well as the results of student and instructor attitude surveys between classes. In our analysis, we argue that multiple linear regression modeling is superior to other common analysis tools, including normalized gain. Our results show that ILS are effective at improving student learning by all measures used: research-validated concept inventories and final exam scores, on both conceptual and traditional problem-solving questions. Multiple linear regression analysis reveals that interactivity in the classroom is a significant predictor of student learning, showing a similar or stronger relationship with student learning than such ascribed characteristics as parents’ education, and achieved characteristics such as grade point average and hours studied per week. Analysis of student and instructor attitudes shows that both groups believe that ILS improve student learning in the physics classroom and increase student engagement and motivation. All of the instructors who used ILS in this study plan to continue their use.

Impact of live interactive teledermatology on diagnosis, disease management, and clinical outcomes.

PubMed

Lamel, Sonia; Chambers, Cindy J; Ratnarathorn, Mondhipa; Armstrong, April W

2012-01-01

To assess the impact of live interactive teledermatology consultations on changes in diagnosis, disease management, and clinical outcomes. We conducted a retrospective analysis of 1500 patients evaluated via live interactive teledermatology between 2003 and 2005 at the University of California, Davis. We compared diagnoses and treatment plans between the referring physicians and the teledermatologists. Patients with 2 or more teledermatology visits within a 1-year period were assessed for changes in clinical outcomes. Academic medical center with an established teledermatology program since 1996. Medical records were evaluated for 1500 patients who underwent live interactive teledermatology consultation. Patients seen for more than 1 teledermatology visit were included in the clinical outcome assessment. Live interactive teledermatology consultation. Changes in diagnosis, disease management, and clinical outcome. Compared with diagnoses and treatment plans from referring physicians, the 1500 live interactive teledermatology consultations resulted in changes in diagnosis in 69.9% of patients and changes in disease management in 97.7% of patients. Among 313 patients with at least 2 teledermatology visits within 1 year, clinical improvement was observed in 68.7% of patients. Multivariate analysis showed that changes in diagnosis (P = .01), changes in disease management (P < .001), and the number of teledermatology visits (P < .001) were significantly associated with improved clinical outcomes. Live interactive teledermatology consultations result in changes in diagnosis and disease management in most consultations. The numbers of live interactive teledermatology visits and changes in diagnosis and disease management are significantly associated with improved clinical outcomes.

Shared polymorphisms and modifiable behavior factors for myocardial infarction and high cholesterol in a retrospective population study

PubMed Central

Liang, Yulan; Kelemen, Arpad

2017-01-01

Abstract Genetic and environmental (behavior, clinical, and demographic) factors are associated with increased risks of both myocardial infarction (MI) and high cholesterol (HC). It is known that HC is major risk factor that may cause MI. However, whether there are common single nucleotide polymorphism (SNPs) associated with both MI and HC is not firmly established, and whether there are modulate and modified effects (interactions of genetic and known environmental factors) on either HC or MI, and whether these joint effects improve the predictions of MI, is understudied. The purpose of this study is to identify novel shared SNPs and modifiable environmental factors on MI and HC. We assess whether SNPs from a metabolic pathway related to MI may relate to HC; whether there are moderate effects among SNPs, lifestyle (smoke and drinking), HC, and MI after controlling other factors [gender, body mass index (BMI), and hypertension (HTN)]; and evaluate prediction power of the joint and modulate genetic and environmental factors influencing the MI and HC. This is a retrospective study with residents of Erie and Niagara counties in New York with a history of MI or with no history of MI. The data set includes environmental variables (demographic, clinical, lifestyle). Thirty-one tagSNPs from a metabolic pathway related to MI are genotyped. Generalized linear models (GLMs) with imputation-based analysis are conducted for examining the common effects of tagSNPs and environmental exposures and their interactions on having a history of HC or MI. MI, BMI, and HTN are significant risk factors for HC. HC shows the strongest effect on risk of MI in addition to HTN; gender and smoking status while drinking status shows protective effect on MI. rs16944 (gene IL-1β) and rs17222772 (gene ALOX) increase the risks of HC, while rs17231896 (gene CETP) has protective effects on HC either with or without the clinical, behavioral, demographic factors with different effect sizes that may indicate the existence of moderate or modifiable effects. Further analysis with the inclusions of gene–gene and gene–environmental interactions shows interactions between rs17231896 (CETP) and rs17222772 (ALOX); rs17231896 (CETP) and gender. rs17237890 (CETP) and rs2070744 (NOS3) are found to be significantly associated with risks of MI adjusted by both SNPs and environmental factors. After multiple testing adjustments, these effects diminished as expected. In addition, an interaction between drinking and smoking status is significant. Overall, the prediction power in successfully classifying MI status is increased to 80% with inclusions of all significant tagSNPs and environmental factors and their interactions compared with environmental factors only (72%). Having a history of either HC or MI has significant effects on each other in both directions, in addition to HTN and gender. Genes/SNPs identified from this analysis that are associated with HC may be potentially linked to MI, which could be further examined and validated through haplotype-pairs analysis with appropriate population stratification corrections, and function/pathway regulation analysis to eliminate the limitations of the current analysis. PMID:28906356

Shared polymorphisms and modifiable behavior factors for myocardial infarction and high cholesterol in a retrospective population study.

PubMed

Liang, Yulan; Kelemen, Arpad

2017-09-01

Genetic and environmental (behavior, clinical, and demographic) factors are associated with increased risks of both myocardial infarction (MI) and high cholesterol (HC). It is known that HC is major risk factor that may cause MI. However, whether there are common single nucleotide polymorphism (SNPs) associated with both MI and HC is not firmly established, and whether there are modulate and modified effects (interactions of genetic and known environmental factors) on either HC or MI, and whether these joint effects improve the predictions of MI, is understudied.The purpose of this study is to identify novel shared SNPs and modifiable environmental factors on MI and HC. We assess whether SNPs from a metabolic pathway related to MI may relate to HC; whether there are moderate effects among SNPs, lifestyle (smoke and drinking), HC, and MI after controlling other factors [gender, body mass index (BMI), and hypertension (HTN)]; and evaluate prediction power of the joint and modulate genetic and environmental factors influencing the MI and HC.This is a retrospective study with residents of Erie and Niagara counties in New York with a history of MI or with no history of MI. The data set includes environmental variables (demographic, clinical, lifestyle). Thirty-one tagSNPs from a metabolic pathway related to MI are genotyped. Generalized linear models (GLMs) with imputation-based analysis are conducted for examining the common effects of tagSNPs and environmental exposures and their interactions on having a history of HC or MI.MI, BMI, and HTN are significant risk factors for HC. HC shows the strongest effect on risk of MI in addition to HTN; gender and smoking status while drinking status shows protective effect on MI. rs16944 (gene IL-1β) and rs17222772 (gene ALOX) increase the risks of HC, while rs17231896 (gene CETP) has protective effects on HC either with or without the clinical, behavioral, demographic factors with different effect sizes that may indicate the existence of moderate or modifiable effects. Further analysis with the inclusions of gene-gene and gene-environmental interactions shows interactions between rs17231896 (CETP) and rs17222772 (ALOX); rs17231896 (CETP) and gender. rs17237890 (CETP) and rs2070744 (NOS3) are found to be significantly associated with risks of MI adjusted by both SNPs and environmental factors. After multiple testing adjustments, these effects diminished as expected. In addition, an interaction between drinking and smoking status is significant. Overall, the prediction power in successfully classifying MI status is increased to 80% with inclusions of all significant tagSNPs and environmental factors and their interactions compared with environmental factors only (72%).Having a history of either HC or MI has significant effects on each other in both directions, in addition to HTN and gender. Genes/SNPs identified from this analysis that are associated with HC may be potentially linked to MI, which could be further examined and validated through haplotype-pairs analysis with appropriate population stratification corrections, and function/pathway regulation analysis to eliminate the limitations of the current analysis.

Analysis of protein interactions within the cytokinin-signaling pathway of Arabidopsis thaliana.

PubMed

Dortay, Hakan; Mehnert, Nijuscha; Bürkle, Lukas; Schmülling, Thomas; Heyl, Alexander

2006-10-01

The signal of the plant hormone cytokinin is perceived by membrane-located sensor histidine kinases and transduced by other members of the plant two-component system. In Arabidopsis thaliana, 28 two-component system proteins (phosphotransmitters and response regulators) act downstream of three receptors, transmitting the signal from the membrane to the nucleus and modulating the cellular response. Although the principal signaling mechanism has been elucidated, redundancy in the system has made it difficult to understand which of the many components interact to control the downstream biological processes. Here, we present a large-scale interaction study comprising most members of the Arabidopsis cytokinin signaling pathway. Using the yeast two-hybrid system, we detected 42 new interactions, of which more than 90% were confirmed by in vitro coaffinity purification. There are distinct patterns of interaction between protein families, but only a few interactions between proteins of the same family. An interaction map of this signaling pathway shows the Arabidopsis histidine phosphotransfer proteins as hubs, which interact with members from all other protein families, mostly in a redundant fashion. Domain-mapping experiments revealed the interaction domains of the proteins of this pathway. Analyses of Arabidopsis histidine phosphotransfer protein 5 mutant proteins showed that the presence of the canonical phospho-accepting histidine residue is not required for the interactions. Interaction of A-type response regulators with Arabidopsis histidine phosphotransfer proteins but not with B-type response regulators suggests that their known activity in feedback regulation may be realized by interfering at the level of Arabidopsis histidine phosphotransfer protein-mediated signaling. This study contributes to our understanding of the protein interactions of the cytokinin-signaling system and provides a framework for further functional studies in planta.

Student’s social interaction in mathematics learning

NASA Astrophysics Data System (ADS)

Apriliyanto, B.; Saputro, D. R. S.; Riyadi

2018-03-01

Mathematics learning achievement is influenced by the internal and external factor of the students. One of the influencing external factors is social interaction with friends in learning activities. In modern learning, the learning is student-centered, so the student interaction is needed to learn about certain basic competence. Potential and motivation of students in learning are expected to develop with good social interaction in order to get maximum results. Social interaction is an important aspect of learning Mathematics because students get the opportunity to express their own thoughts in order to encourage a reflection on the knowledge they have. This research uses the correlational descriptive method involving 36 students for the tenth grade, eleventh grade, and twelfth grade of SMA Negeri 1 Wuryantoro and data collecting technique using questionnaire for social interaction and documentation for learning outcome. The result of this research shows that learning achievement and social interaction of students are not good. Based on the result of data analysis, it is shown that the social interaction and Mathematics learning achievement are still in the low level. This research concludes that students’ social interaction influences student learning achievement in Mathematics subjects.