Identification of Inhibitors of Biological Interactions Involving Intrinsically Disordered Proteins

Directory of Open Access Journals (Sweden)

Daniela Marasco

2015-04-01

Full Text Available Protein–protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few “hot spots”, thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs.

Lexical Cues of Interaction Involvement in Dyadic Instant Messaging Conversations

Science.gov (United States)

Nguyen, Duyen T.; Fussell, Susan R.

2014-01-01

We explore how people express and interpret lexical cues of interaction involvement in dyadic conversations via instant messaging (IM) in two studies. In Study 1, an experiment with 60 participants, we manipulated level of involvement in a conversation with a distraction task. We examined how participants' uses of verbal cues such as pronouns…

Communicative interactions involving plants: information, evolution, and ecology.

Science.gov (United States)

Mescher, Mark C; Pearse, Ian S

2016-08-01

The role of information obtained via sensory cues and signals in mediating the interactions of organisms with their biotic and abiotic environments has been a major focus of work on sensory and behavioral ecology. Information-mediated interactions also have important implications for broader ecological patterns emerging at the community and ecosystem levels that are only now beginning to be explored. Given the extent to which plants dominate the sensory landscapes of terrestrial ecosystems, information-mediated interactions involving plants should be a major focus of efforts to elucidate these broader patterns. Here we explore how such efforts might be enhanced by a clear understanding of information itself-a central and potentially unifying concept in biology that has nevertheless been the subject of considerable confusion-and of its relationship to adaptive evolution and ecology. We suggest that information-mediated interactions should be a key focus of efforts to more fully integrate evolutionary biology and ecology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of safety analysis and constraint detection techniques for process interaction errors

Energy Technology Data Exchange (ETDEWEB)

Fan, Chin-Feng, E-mail: csfanc@saturn.yzu.edu.tw [Computer Science and Engineering Dept., Yuan-Ze University, Taiwan (China); Tsai, Shang-Lin; Tseng, Wan-Hui [Computer Science and Engineering Dept., Yuan-Ze University, Taiwan (China)

2011-02-15

Among the new failure modes introduced by computer into safety systems, the process interaction error is the most unpredictable and complicated failure mode, which may cause disastrous consequences. This paper presents safety analysis and constraint detection techniques for process interaction errors among hardware, software, and human processes. Among interaction errors, the most dreadful ones are those that involve run-time misinterpretation from a logic process. We call them the 'semantic interaction errors'. Such abnormal interaction is not adequately emphasized in current research. In our static analysis, we provide a fault tree template focusing on semantic interaction errors by checking conflicting pre-conditions and post-conditions among interacting processes. Thus, far-fetched, but highly risky, interaction scenarios involve interpretation errors can be identified. For run-time monitoring, a range of constraint types is proposed for checking abnormal signs at run time. We extend current constraints to a broader relational level and a global level, considering process/device dependencies and physical conservation rules in order to detect process interaction errors. The proposed techniques can reduce abnormal interactions; they can also be used to assist in safety-case construction.

Development of safety analysis and constraint detection techniques for process interaction errors

International Nuclear Information System (INIS)

Fan, Chin-Feng; Tsai, Shang-Lin; Tseng, Wan-Hui

2011-01-01

Among the new failure modes introduced by computer into safety systems, the process interaction error is the most unpredictable and complicated failure mode, which may cause disastrous consequences. This paper presents safety analysis and constraint detection techniques for process interaction errors among hardware, software, and human processes. Among interaction errors, the most dreadful ones are those that involve run-time misinterpretation from a logic process. We call them the 'semantic interaction errors'. Such abnormal interaction is not adequately emphasized in current research. In our static analysis, we provide a fault tree template focusing on semantic interaction errors by checking conflicting pre-conditions and post-conditions among interacting processes. Thus, far-fetched, but highly risky, interaction scenarios involve interpretation errors can be identified. For run-time monitoring, a range of constraint types is proposed for checking abnormal signs at run time. We extend current constraints to a broader relational level and a global level, considering process/device dependencies and physical conservation rules in order to detect process interaction errors. The proposed techniques can reduce abnormal interactions; they can also be used to assist in safety-case construction.

THERMODYNAMICS OF PROTEIN-LIGAND INTERACTIONS AND THEIR ANALYSIS

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Rummi Devi Saini

2017-11-01

Full Text Available Physiological processes are controlled mainly by intermolecular recognition mechanisms which involve protein–protein and protein–ligand interactions with a high specificity and affinity to form a specific complex. Proteins being an important class of macromolecules in biological systems, it is important to understand their actions through binding to other molecules of proteins or ligands. In fact, the binding of low molecular weight ligands to proteins plays a significant role in regulating biological processes such as cellular metabolism and signal transmission. Therefore knowledge of the protein–ligand interactions and the knowledge of the mechanisms involved in the protein-ligand recognition and binding are key in understanding biology at molecular level which will facilitate the discovery, design, and development of drugs. In this review, the mechanisms involved in protein–ligand binding, the binding kinetics, thermodynamic concepts and binding driving forces are discussed. Thermodynamic mechanisms involved in a few important protein-ligand binding are described. Various spectroscopic, non-spectroscopic and computational method for analysis of protein–ligand binding are also discussed.

Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate.

Science.gov (United States)

Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2013-08-01

Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.

Analytic Provenance Datasets: A Data Repository of Human Analysis Activity and Interaction Logs

OpenAIRE

Mohseni, Sina; Pachuilo, Andrew; Nirjhar, Ehsanul Haque; Linder, Rhema; Pena, Alyssa; Ragan, Eric D.

2018-01-01

We present an analytic provenance data repository that can be used to study human analysis activity, thought processes, and software interaction with visual analysis tools during exploratory data analysis. We conducted a series of user studies involving exploratory data analysis scenario with textual and cyber security data. Interactions logs, think-alouds, videos and all coded data in this study are available online for research purposes. Analysis sessions are segmented in multiple sub-task ...

Analysis of DNA interactions using single-molecule force spectroscopy.

Science.gov (United States)

Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

2013-06-01

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

Asp30 of Aspergillus oryzae cutinase CutL1 is involved in the ionic interaction with fungal hydrophobin RolA.

Science.gov (United States)

Terauchi, Yuki; Kim, Yoon-Kyung; Tanaka, Takumi; Nanatani, Kei; Takahashi, Toru; Abe, Keietsu

2017-07-01

Aspergillus oryzae hydrophobin RolA adheres to the biodegradable polyester polybutylene succinate-co-adipate (PBSA) and promotes PBSA degradation by interacting with A. oryzae polyesterase CutL1 and recruiting it to the PBSA surface. In our previous studies, we found that positively charged amino acid residues (H32, K34) of RolA and negatively charged residues (E31, D142, D171) of CutL1 are important for the cooperative ionic interaction between RolA and CutL1, but some other charged residues in the triple mutant CutL1-E31S/D142S/D171S are also involved. In the present study, on the basis of the 3D-structure of CutL1, we hypothesized that D30 is also involved in the CutL1-RolA interaction. We substituted D30 with serine and performed kinetic analysis of the interaction between wild-type RolA and the single mutant CutL1-D30S or quadruple mutant CutL1-D30S/E31S/D142S/D171S by using quartz crystal microbalance. Our results indicate that D30 is a novel residue involved in the ionic interaction between RolA and CutL1.

Analysis of large scale UO2 Na interactions performed in Europe

International Nuclear Information System (INIS)

Berthoud, G.; Jacobs, H.; Knowles, B.

1994-01-01

Analysis of the European out of pile Fuel Sodium Interaction Experiments involving kilogram masses of molten oxide is reported i.e. CORECT 2 (CEA), SUS and MFTF-B (AEA), THINA (KfK). Then common conclusions are drawn. (author)

Genes related to antioxidant metabolism are involved in Methylobacterium mesophilicum-soybean interaction.

Science.gov (United States)

Araújo, Welington Luiz; Santos, Daiene Souza; Dini-Andreote, Francisco; Salgueiro-Londoño, Jennifer Katherine; Camargo-Neves, Aline Aparecida; Andreote, Fernando Dini; Dourado, Manuella Nóbrega

2015-10-01

The genus Methylobacterium is composed of pink-pigmented methylotrophic bacterial species that are widespread in natural environments, such as soils, stream water and plants. When in association with plants, this genus colonizes the host plant epiphytically and/or endophytically. This association is known to promote plant growth, induce plant systemic resistance and inhibit plant infection by phytopathogens. In the present study, we focused on evaluating the colonization of soybean seedling-roots by Methylobacterium mesophilicum strain SR1.6/6. We focused on the identification of the key genes involved in the initial step of soybean colonization by methylotrophic bacteria, which includes the plant exudate recognition and adaptation by planktonic bacteria. Visualization by scanning electron microscopy revealed that M. mesophilicum SR1.6/6 colonizes soybean roots surface effectively at 48 h after inoculation, suggesting a mechanism for root recognition and adaptation before this period. The colonization proceeds by the development of a mature biofilm on roots at 96 h after inoculation. Transcriptomic analysis of the planktonic bacteria (with plant) revealed the expression of several genes involved in membrane transport, thus confirming an initial metabolic activation of bacterial responses when in the presence of plant root exudates. Moreover, antioxidant genes were mostly expressed during the interaction with the plant exudates. Further evaluation of stress- and methylotrophic-related genes expression by qPCR showed that glutathione peroxidase and glutathione synthetase genes were up-regulated during the Methylobacterium-soybean interaction. These findings support that glutathione (GSH) is potentially a key molecule involved in cellular detoxification during plant root colonization. In addition to methylotrophic metabolism, antioxidant genes, mainly glutathione-related genes, play a key role during soybean exudate recognition and adaptation, the first step in

A decision analysis framework for stakeholder involvement and learning in groundwater management

Science.gov (United States)

Karjalainen, T. P.; Rossi, P. M.; Ala-aho, P.; Eskelinen, R.; Reinikainen, K.; Kløve, B.; Pulido-Velazquez, M.; Yang, H.

2013-12-01

Multi-criteria decision analysis (MCDA) methods are increasingly used to facilitate both rigorous analysis and stakeholder involvement in natural and water resource planning. Decision-making in that context is often complex and multi-faceted with numerous trade-offs between social, environmental and economic impacts. However, practical applications of decision-support methods are often too technically oriented and hard to use, understand or interpret for all participants. The learning of participants in these processes is seldom examined, even though successful deliberation depends on learning. This paper analyzes the potential of an interactive MCDA framework, the decision analysis interview (DAI) approach, for facilitating stakeholder involvement and learning in groundwater management. It evaluates the results of the MCDA process in assessing land-use management alternatives in a Finnish esker aquifer area where conflicting land uses affect the groundwater body and dependent ecosystems. In the assessment process, emphasis was placed on the interactive role of the MCDA tool in facilitating stakeholder participation and learning. The results confirmed that the structured decision analysis framework can foster learning and collaboration in a process where disputes and diverse interests are represented. Computer-aided interviews helped the participants to see how their preferences affected the desirability and ranking of alternatives. During the process, the participants' knowledge and preferences evolved as they assessed their initial knowledge with the help of fresh scientific information. The decision analysis process led to the opening of a dialogue, showing the overall picture of the problem context and the critical issues for the further process.

The interactive alphabet with augmented reality as a form of involving children in educational process

Directory of Open Access Journals (Sweden)

Vladimir D. Sekerin

2017-01-01

Full Text Available Research objective: to prove the expediency of using technologies with augmented reality in educational process of children in order to increase the level of their involvement and to improve the efficiency of educational process. Materials and methods. The information base of the research was made by scientific publications, information and analytical reviews, periodicals, monographs, information placed in the Internet network, concerning practical application of technologies with augmented reality in educational process, descriptive and comparative methods of analysis form the methodical basis of this research. Results. It is shown that in educational process of children it is expedient to use the modern technological achievements allowing organizing productive interactions and relationship of the students among themselves and with teachers, lecturers. Educational, business, role-playing games, discussions promoting acceleration of acquiring  a new experience and receiving new knowledge are the perspective formats of realizing the educational process. The world of augmented reality has the following properties: combines the real and virtual, interacts in real time mode, and functions in three-dimensional space. The advantages of the Interactive alphabet on the basis of the augmented reality technology are as follows: 1 security of strong emotional responses; 2 the involvement and interactivity promoting steady memorizing; 3 possibilities of interaction with the artificial world by means of gadgets; 4 Digital and offline communication; 5 possibility of carrying out virtual lessons. One of the main features of virtual reality is the feeling of participation and the opportunity to observe everything from the first person. It makes expedient to carry out lessons entirely in the virtual reality. Achievement of full involvement in educational process promotes increase of motivation and progress in knowledge acquisition.  The use of the augmented

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

Science.gov (United States)

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.

Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting.

Science.gov (United States)

Han, Seungsu; Shin, Donghyuk; Choi, Hoon; Lee, Sangho

2014-03-28

Yeast Doa1/Ufd3 is an adaptor protein for Cdc48 (p97 in mammal), an AAA type ATPase associated with endoplasmic reticulum-associated protein degradation pathway and endosomal sorting into multivesicular bodies. Doa1 functions in the endosomal sorting by its association with Hse1, a component of endosomal sorting complex required for transport (ESCRT) system. The association of Doa1 with Hse1 was previously reported to be mediated between PFU domain of Doa1 and SH3 of Hse1. However, it remains unclear which residues are specifically involved in the interaction. Here we report that Doa1/PFU interacts with Hse1/SH3 with a moderate affinity of 5 μM. Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are found to be critical in the interaction while Phe-434, implicated in ubiquitin binding via a hydrophobic interaction, is not. Small-angle X-ray scattering measurements combined with molecular docking and biochemical analysis yield the solution structure of the Doa1/PFU:Hse1/SH3 complex. Taken together, our results suggest that hydrogen bonding is a major determinant in the interaction of Doa1/PFU with Hse1/SH3. Copyright © 2014 Elsevier Inc. All rights reserved.

Nutrient analysis explained for non-chemists by using interactive e-learning material

NARCIS (Netherlands)

Busstra, M.C.; Hulshof, P.J.M.; Houwen, J.; Elburg, L.; Hollman, P.C.H.

2012-01-01

The diverse educational and professional background of individuals involved in food composition data work presents challenges in their training. In particular, it is difficult to explain chemical analysis of nutrients to individuals lacking a background in chemistry. Therefore an interactive

Banana ethylene response factors are involved in fruit ripening through their interactions with ethylene biosynthesis genes.

Science.gov (United States)

Xiao, Yun-yi; Chen, Jian-ye; Kuang, Jiang-fei; Shan, Wei; Xie, Hui; Jiang, Yue-ming; Lu, Wang-jin

2013-05-01

The involvement of ethylene response factor (ERF) transcription factor (TF) in the transcriptional regulation of ethylene biosynthesis genes during fruit ripening remains largely unclear. In this study, 15 ERF genes, designated as MaERF1-MaERF15, were isolated and characterized from banana fruit. These MaERFs were classified into seven of the 12 known ERF families. Subcellular localization showed that MaERF proteins of five different subfamilies preferentially localized to the nucleus. The 15 MaERF genes displayed differential expression patterns and levels in peel and pulp of banana fruit, in association with four different ripening treatments caused by natural, ethylene-induced, 1-methylcyclopropene (1-MCP)-delayed, and combined 1-MCP and ethylene treatments. MaERF9 was upregulated while MaERF11 was downregulated in peel and pulp of banana fruit during ripening or after treatment with ethylene. Furthermore, yeast-one hybrid (Y1H) and transient expression assays showed that the potential repressor MaERF11 bound to MaACS1 and MaACO1 promoters to suppress their activities and that MaERF9 activated MaACO1 promoter activity. Interestingly, protein-protein interaction analysis revealed that MaERF9 and -11 physically interacted with MaACO1. Taken together, these results suggest that MaERFs are involved in banana fruit ripening via transcriptional regulation of or interaction with ethylene biosynthesis genes.

Interaction Analysis and Supervision.

Science.gov (United States)

Amidon, Edmund

This paper describes a model that uses interaction analysis as a tool to provide feedback to a teacher in a microteaching situation. The author explains how interaction analysis can be used for teacher improvement, describes the category system used in the model, the data collection methods used, and the feedback techniques found in the model. (JF)

Digraph matrix analysis applications to systems interactions

International Nuclear Information System (INIS)

Alesso, H.P.; Altenbach, T.; Lappa, D.; Kimura, C.; Sacks, I.J.; Ashmore, B.C.; Fromme, D.; Smith, C.F.; Williams, W.

1984-01-01

Complex events such as Three Mile Island-2, Brown's Ferry-3 and Crystal River-3 have demonstrated that previously unidentified system interdependencies can be important to safety. A major aspect of these events was dependent faults (common cause/mode failures). The term systems interactions has been introduced by the Nuclear Regulatory Commission (NRC) to identify the concepts of spatial and functional coupling of systems which can lead to system interdependencies. Spatial coupling refers to dependencies resulting from a shared environmental condition; functional coupling refers to both dependencies resulting from components shared between safety and/or support systems, and to dependencies involving human actions. The NRC is currently developing guidelines to search for and evaluate adverse systems interactions at light water reactors. One approach utilizes graph theoretical methods and is called digraph matrix analysis (DMA). This methodology has been specifically tuned to the systems interaction problem. The objective of this paper is to present results from two DMA applications and to contrast them with the results from more traditional fault tree approaches

Neural mirroring and social interaction: Motor system involvement during action observation relates to early peer cooperation.

Science.gov (United States)

Endedijk, H M; Meyer, M; Bekkering, H; Cillessen, A H N; Hunnius, S

2017-04-01

Whether we hand over objects to someone, play a team sport, or make music together, social interaction often involves interpersonal action coordination, both during instances of cooperation and entrainment. Neural mirroring is thought to play a crucial role in processing other's actions and is therefore considered important for social interaction. Still, to date, it is unknown whether interindividual differences in neural mirroring play a role in interpersonal coordination during different instances of social interaction. A relation between neural mirroring and interpersonal coordination has particularly relevant implications for early childhood, since successful early interaction with peers is predictive of a more favorable social development. We examined the relation between neural mirroring and children's interpersonal coordination during peer interaction using EEG and longitudinal behavioral data. Results showed that 4-year-old children with higher levels of motor system involvement during action observation (as indicated by lower beta-power) were more successful in early peer cooperation. This is the first evidence for a relation between motor system involvement during action observation and interpersonal coordination during other instances of social interaction. The findings suggest that interindividual differences in neural mirroring are related to interpersonal coordination and thus successful social interaction. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Pyoverdine and PQS Mediated Subpopulation Interactions Involved in Pseudomonas aeruginosa Biofilm Formation

DEFF Research Database (Denmark)

Yang, Liang; Nilsson, Martin; Gjermansen, Morten

2009-01-01

Using flow chamber-grown Pseudomonas aeruginosa biofilms as model system, we show in the present study that formation of heterogeneous biofilms may occur through mechanisms that involve complex subpopulation interactions. One example of this phenomenon is expression of the iron...

DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction.

Directory of Open Access Journals (Sweden)

Muhammed Jamsheer K

Full Text Available Zinc fingers are a ubiquitous class of protein domain with considerable variation in structure and function. Zf-FCS is a highly diverged group of C2-C2 zinc finger which is present in animals, prokaryotes and viruses, but not in plants. In this study we identified that a plant specific domain of unknown function, DUF581 is a zf-FCS type zinc finger. Based on HMM-HMM comparison and signature motif similarity we named this domain as FCS-Like Zinc finger (FLZ domain. A genome wide survey identified that FLZ domain containing genes are bryophytic in origin and this gene family is expanded in spermatophytes. Expression analysis of selected FLZ gene family members of A. thaliana identified an overlapping expression pattern suggesting a possible redundancy in their function. Unlike the zf-FCS domain, the FLZ domain found to be highly conserved in sequence and structure. Using a combination of bioinformatic and protein-protein interaction tools, we identified that FLZ domain is involved in protein-protein interaction.

Evaluation of Lagrangian, Eulerian, and arbitrary Lagrangian-Eulerian methods for fluid-structure interaction problems in HCDA analysis

International Nuclear Information System (INIS)

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

1979-01-01

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

Involvement of Grandmothers in Caring for Children with Autism in the Philippines: An Interpretative Phenomenological Analysis

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Arvin Kim A. Arnilla

2017-05-01

Full Text Available This study looked into the lived experiences of Filipino grandmothers rearing children with autism (CWA focusing particularly on the extent of their involvement. The study used Interpretative P henomenological Analysis (IPA through interview and storytelling of eight (8 Filipino grandmothers. Analysis of data generated three themes such as “I watch him every time his parents are out” (physical involvement, “I hope one day he‟ll be okey” (emoti onal involvement and “Financially, I gave whatever I have” (financial involvement. The study attempts to explain the extent of involvement of grandmothers in rearing children with autism across these dimensions. Physical involvement is bounded by physica l strength, emotional involvement is bounded by self - restraint and financial involvement is bounded by financial capability. The caring and nurturing nature of Filipino grandmothers is translated to their physical, emotional and financial involvement in re aring their grandchildren from conception to adulthood. Filipino children with autism as described in this study had issues covering the broad categories of deficits in social communication and social interaction and restricted, repetitive patterns of beha vior and interests. Given the atypicalities and the inherent impediments experienced by those in the lower socio - economic status, intervention programs can be created and implemented to address them.

Conversation Analysis and Classroom Interaction

Institute of Scientific and Technical Information of China (English)

DING A-ning; LI Fan; CUI Jing

2015-01-01

Conversation Analysis shows the evidence of the social nature of people’s action including talk-in-interaction from a micro-level perspective. The method for basing its analysis on the authentic data rather than the retrospective interviews for gain⁃ing the participants’perception makes it unique in discovering the emic perspective of the social interaction. CA, often called as a“micro”methodology, provides theoretical insights and useful analytical tool for exploring the interaction in classrooms.

Network theory-based analysis of risk interactions in large engineering projects

International Nuclear Information System (INIS)

Fang, Chao; Marle, Franck; Zio, Enrico; Bocquet, Jean-Claude

2012-01-01

This paper presents an approach based on network theory to deal with risk interactions in large engineering projects. Indeed, such projects are exposed to numerous and interdependent risks of various nature, which makes their management more difficult. In this paper, a topological analysis based on network theory is presented, which aims at identifying key elements in the structure of interrelated risks potentially affecting a large engineering project. This analysis serves as a powerful complement to classical project risk analysis. Its originality lies in the application of some network theory indicators to the project risk management field. The construction of the risk network requires the involvement of the project manager and other team members assigned to the risk management process. Its interpretation improves their understanding of risks and their potential interactions. The outcomes of the analysis provide a support for decision-making regarding project risk management. An example of application to a real large engineering project is presented. The conclusion is that some new insights can be found about risks, about their interactions and about the global potential behavior of the project. - Highlights: ► The method addresses the modeling of complexity in project risk analysis. ► Network theory indicators enable other risks than classical criticality analysis to be highlighted. ► This topological analysis improves project manager's understanding of risks and risk interactions. ► This helps project manager to make decisions considering the position in the risk network. ► An application to a real tramway implementation project in a city is provided.

Bioinformatics Analysis Reveals Genes Involved in the Pathogenesis of Ameloblastoma and Keratocystic Odontogenic Tumor.

Science.gov (United States)

Santos, Eliane Macedo Sobrinho; Santos, Hércules Otacílio; Dos Santos Dias, Ivoneth; Santos, Sérgio Henrique; Batista de Paula, Alfredo Maurício; Feltenberger, John David; Sena Guimarães, André Luiz; Farias, Lucyana Conceição

2016-01-01

Pathogenesis of odontogenic tumors is not well known. It is important to identify genetic deregulations and molecular alterations. This study aimed to investigate, through bioinformatic analysis, the possible genes involved in the pathogenesis of ameloblastoma (AM) and keratocystic odontogenic tumor (KCOT). Genes involved in the pathogenesis of AM and KCOT were identified in GeneCards. Gene list was expanded, and the gene interactions network was mapped using the STRING software. "Weighted number of links" (WNL) was calculated to identify "leader genes" (highest WNL). Genes were ranked by K-means method and Kruskal-Wallis test was used (Preview data was used to corroborate the bioinformatics data. CDK1 was identified as leader gene for AM. In KCOT group, results show PCNA and TP53 . Both tumors exhibit a power law behavior. Our topological analysis suggested leader genes possibly important in the pathogenesis of AM and KCOT, by clustering coefficient calculated for both odontogenic tumors (0.028 for AM, zero for KCOT). The results obtained in the scatter diagram suggest an important relationship of these genes with the molecular processes involved in AM and KCOT. Ontological analysis for both AM and KCOT demonstrated different mechanisms. Bioinformatics analyzes were confirmed through literature review. These results may suggest the involvement of promising genes for a better understanding of the pathogenesis of AM and KCOT.

Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy.

Directory of Open Access Journals (Sweden)

Tejaswini Narayanan

Full Text Available Duchenne Muscular Dystrophy (DMD is an important pathology associated with the human skeletal muscle and has been studied extensively. Gene expression measurements on skeletal muscle of patients afflicted with DMD provides the opportunity to understand the underlying mechanisms that lead to the pathology. Community structure analysis is a useful computational technique for understanding and modeling genetic interaction networks. In this paper, we leverage this technique in combination with gene expression measurements from normal and DMD patient skeletal muscle tissue to study the structure of genetic interactions in the context of DMD. We define a novel framework for transforming a raw dataset of gene expression measurements into an interaction network, and subsequently apply algorithms for community structure analysis for the extraction of topological communities. The emergent communities are analyzed from a biological standpoint in terms of their constituent biological pathways, and an interpretation that draws correlations between functional and structural organization of the genetic interactions is presented. We also compare these communities and associated functions in pathology against those in normal human skeletal muscle. In particular, differential enhancements are observed in the following pathways between pathological and normal cases: Metabolic, Focal adhesion, Regulation of actin cytoskeleton and Cell adhesion, and implication of these mechanisms are supported by prior work. Furthermore, our study also includes a gene-level analysis to identify genes that are involved in the coupling between the pathways of interest. We believe that our results serve to highlight important distinguishing features in the structural/functional organization of constituent biological pathways, as it relates to normal and DMD cases, and provide the mechanistic basis for further biological investigations into specific pathways differently regulated

A Scoping Analysis Of The Impact Of SiC Cladding On Late-Phase Accident Progression Involving Core–Concrete Interaction

Energy Technology Data Exchange (ETDEWEB)

Farmer, M. T. [Argonne National Lab. (ANL), Argonne, IL (United States)

2015-11-01

The overall objective of the current work is to carry out a scoping analysis to determine the impact of ATF on late phase accident progression; in particular, the molten core-concrete interaction portion of the sequence that occurs after the core debris fails the reactor vessel and relocates into containment. This additional study augments previous work by including kinetic effects that govern chemical reaction rates during core-concrete interaction. The specific ATF considered as part of this study is SiC-clad UO₂.

Investigation of Fanconi anemia protein interactions by yeast two-hybrid analysis.

Science.gov (United States)

Huber, P A; Medhurst, A L; Youssoufian, H; Mathew, C G

2000-02-05

Fanconi anemia is a chromosomal breakage disorder with eight complementation groups (A-H), and three genes (FANCA, FANCC, and FANCG) have been identified. Initial investigations of the interaction between FANCA and FANCC, principally by co-immunoprecipitation, have proved controversial. We used the yeast two-hybrid assay to test for interactions of the FANCA, FANCC, and FANCG proteins. No activation of the reporter gene was observed in yeast co-expressing FANCA and FANCC as hybrid proteins, suggesting that FANCA does not directly interact with FANCC. However, a high level of activation was found when FANCA was co-expressed with FANCG, indicating strong, direct interaction between these proteins. Both FANCA and FANCG show weak but consistent interaction with themselves, suggesting that their function may involve dimerisation. The site of interaction of FANCG with FANCA was investigated by analysis of 12 mutant fragments of FANCG. Although both N- and C-terminal fragments did interact, binding to FANCA was drastically reduced, suggesting that more than one region of the FANCG protein is required for proper interaction with FANCA. Copyright 2000 Academic Press.

Interaction Analysis for Supporting Students' Self-Regulation during Blog-Based CSCL Activities

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Michailidis, Nikolaos; Kapravelos, Efstathios; Tsiatsos, Thrasyvoulos

2018-01-01

Self-regulated learning is an important means of supporting students' self-awareness and self-regulation level so as to enhance their motivation and engagement. Interaction Analysis (IA) contributes to this end, and its use in studying learning dynamics involved in asynchronous Computer-Supported Collaborative Learning (CSCL) activities has…

Soil-structure interaction analysis by finite element methods - state-of-the-art

International Nuclear Information System (INIS)

Seed, H.B.; Lysmer, J.

1977-01-01

Analyses of soil-structure interaction effects during earthquakes for nuclear power plant structures are usually made by one of two methods-either by means of an idealized complete interaction analysis involving consideration of a compatible variation of motion in the structure and the adjacent soil, or by means of an inertial interaction analysis in which the motions in the adjacent soil are assumed to be the same at all points above the foundation depth. For embedded structures, consideration of the variation of motions with depth is essential if adequate evaluations of soil and structural response are to be obtained without undue conservatism. The finite element analysis procedure is particularly well suited for evaluating the response of embedded structures since it can readily provide consideration of the variation of soil characteristics with depth, the different non-linear deformation and energy absorbing capacities of the various soil strata, the variation of motions with depth in accordance with the general principles of engineering mechanics, the three-dimensional nature of the problem and the effects of adjacent structures on each other. (Auth.)

Analysis of the interaction between experimental and applied behavior analysis.

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Virues-Ortega, Javier; Hurtado-Parrado, Camilo; Cox, Alison D; Pear, Joseph J

2014-01-01

To study the influences between basic and applied research in behavior analysis, we analyzed the coauthorship interactions of authors who published in JABA and JEAB from 1980 to 2010. We paid particular attention to authors who published in both JABA and JEAB (dual authors) as potential agents of cross-field interactions. We present a comprehensive analysis of dual authors' coauthorship interactions using social networks methodology and key word analysis. The number of dual authors more than doubled (26 to 67) and their productivity tripled (7% to 26% of JABA and JEAB articles) between 1980 and 2010. Dual authors stood out in terms of number of collaborators, number of publications, and ability to interact with multiple groups within the field. The steady increase in JEAB and JABA interactions through coauthors and the increasing range of topics covered by dual authors provide a basis for optimism regarding the progressive integration of basic and applied behavior analysis. © Society for the Experimental Analysis of Behavior.

Interactivity in Educational Apps for Young children: A Multimodal Analysis

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Alexandra H. Blitz-Raith

2017-11-01

Full Text Available Interactivity is an important indicator of an educational app's reception. Since most educational apps are multimodal, it justifies a methodological initiative to understand meaningful involvement of multimodality in enacting and even amplifying interactivity in an educational app. Yet research so far has largely concentrated on algorithm construct and user feedback rather than on multimodal interactions, especially from a social semiotics perspective. Drawing from social semiotics approaches, this article proposes a multimodal analytic framework to examine three layers of mode in engendering interaction; namely, multiplicity, function, and relationship. Using the analytic framework in an analysis of The Farm Adventure for Kids, a popular educational app for pre-school children, we found that still images are dominant proportionally and are central in the interactive process. We also found that tapping still images of animals on screen is the main action, with other screen actions deliberately excluded. Such findings suggest that aligning children’s cognitive and physical capabilities to the use of mode become the primary consideration in educational app design and that consistent attendance to this alignment in mobilizing modes significantly affect an educational app’s interactivity, and consequently its reception by young children

Father-child and mother-child interaction in families with a child feeding disorder: The role of paternal involvement.

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Atzaba-Poria, Naama; Meiri, Gal; Millikovsky, Maaian; Barkai, Anat; Dunaevsky-Idan, Maayan; Yerushalmi, Baruch

2010-11-01

To date, research about feeding disorder (FD) has focused almost exclusively on the mother-child dyad, ignoring fathers' roles. The current study investigated father-child interactions with children having FD. The sample consisted of 67 children (1-3 years old) and their mothers and fathers. Thirty-four children, diagnosed with a nonorganic-based FD (FD group) and 33 children without an FD (control group) were matched for age, gender, birth order, and maternal education. Data were collected during home visits. Mothers were interviewed about their and the father's involvement in childcare. In addition, mother-child and father-child interactions were videotaped during play and feeding. Both mothers and fathers from the FD group experienced less positive parent-child interactions than did parents in the control group. Furthermore, mothers in the FD group reported greater maternal versus paternal childcare involvement than did control group mothers. Finally, FD group mothers exhibited more parental sensitivity than did fathers during feeing interactions; however, this difference was observed only when coupled with low paternal involvement. In families where fathers were highly involved, no difference was evident in paternal and maternal sensitivity. These findings highlight the importance of fathers' involvement, especially in families with children exhibiting an FD. Copyright © 2010 Michigan Association for Infant Mental Health.

Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

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Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

2018-02-05

Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of thermoluminescence kinetics of Mg2SiO4:Tb compounds employing an interactive model

International Nuclear Information System (INIS)

Marcazzo, J.; Prokic, M.; Santiago, M.; Molina, P.; Caselli, E.

2009-01-01

The kinetics involved in the thermoluminescence (TL) of Mg 2 SiO 4 :Tb compounds has been investigated by unfolding glow curves employing both the General Order model and a model that takes into account interactions among traps. The dependence of the glow curve shape on dose is only correctly described if interaction among traps is included in the analysis.

Screening key candidate genes and pathways involved in insulinoma by microarray analysis.

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Zhou, Wuhua; Gong, Li; Li, Xuefeng; Wan, Yunyan; Wang, Xiangfei; Li, Huili; Jiang, Bin

2018-06-01

Insulinoma is a rare type tumor and its genetic features remain largely unknown. This study aimed to search for potential key genes and relevant enriched pathways of insulinoma.The gene expression data from GSE73338 were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified between insulinoma tissues and normal pancreas tissues, followed by pathway enrichment analysis, protein-protein interaction (PPI) network construction, and module analysis. The expressions of candidate key genes were validated by quantitative real-time polymerase chain reaction (RT-PCR) in insulinoma tissues.A total of 1632 DEGs were obtained, including 1117 upregulated genes and 514 downregulated genes. Pathway enrichment results showed that upregulated DEGs were significantly implicated in insulin secretion, and downregulated DEGs were mainly enriched in pancreatic secretion. PPI network analysis revealed 7 hub genes with degrees more than 10, including GCG (glucagon), GCGR (glucagon receptor), PLCB1 (phospholipase C, beta 1), CASR (calcium sensing receptor), F2R (coagulation factor II thrombin receptor), GRM1 (glutamate metabotropic receptor 1), and GRM5 (glutamate metabotropic receptor 5). DEGs involved in the significant modules were enriched in calcium signaling pathway, protein ubiquitination, and platelet degranulation. Quantitative RT-PCR data confirmed that the expression trends of these hub genes were similar to the results of bioinformatic analysis.The present study demonstrated that candidate DEGs and enriched pathways were the potential critical molecule events involved in the development of insulinoma, and these findings were useful for better understanding of insulinoma genesis.

Seasonal phenology of interactions involving short-lived annual plants, a multivoltine herbivore and its endoparasitoid wasp

NARCIS (Netherlands)

Fei, Minghui; Gols, R.; Harvey, J.A.

2014-01-01

Spatial-temporal realism is often missing in many studies of multitrophic interactions, which are conducted at a single time frame and/or involving interactions between insects with a single species of plant. In this scenario, an underlying assumption is that the host-plant species is ubiquitous

Involvement of apoptosis in host-parasite interactions in the zebra mussel.

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Laëtitia Minguez

Full Text Available The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro- and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp can be induced. In this protein family, Hsp70 are known to be apoptosis inhibitors. Mussels were diagnosed for their respective infections by standard histological methods; apoptosis was detected using the TUNEL methods on paraffin sections and Hsp70 by immunohistochemistry on cryosections. Circulating hemocytes were the main cells observed in apoptosis whereas infected tissues displayed no or few apoptotic cells. Parasitism by intracellular bacteria Rickettsiales-like and the trematode Bucephalus polymorphus were associated with the inhibition of apoptosis whereas ciliates Ophryoglena spp. or the trematode Phyllodistomum folium did not involve significant differences in apoptosis. Even if some parasites were able to modulate apoptosis in zebra mussels, we did not see evidence of any involvement of Hsp70 on this mechanism.

Involvement of Apoptosis in Host-Parasite Interactions in the Zebra Mussel

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Minguez, Laëtitia; Brulé, Nelly; Sohm, Bénédicte; Devin, Simon; Giambérini, Laure

2013-01-01

The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro- and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp) can be induced. In this protein family, Hsp70 are known to be apoptosis inhibitors. Mussels were diagnosed for their respective infections by standard histological methods; apoptosis was detected using the TUNEL methods on paraffin sections and Hsp70 by immunohistochemistry on cryosections. Circulating hemocytes were the main cells observed in apoptosis whereas infected tissues displayed no or few apoptotic cells. Parasitism by intracellular bacteria Rickettsiales-like and the trematode Bucephalus polymorphus were associated with the inhibition of apoptosis whereas ciliates Ophryoglena spp. or the trematode Phyllodistomum folium did not involve significant differences in apoptosis. Even if some parasites were able to modulate apoptosis in zebra mussels, we did not see evidence of any involvement of Hsp70 on this mechanism. PMID:23785455

Predictive Mechanisms Are Not Involved the Same Way during Human-Human vs. Human-Machine Interactions: A Review

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Aïsha Sahaï

2017-10-01

Full Text Available Nowadays, interactions with others do not only involve human peers but also automated systems. Many studies suggest that the motor predictive systems that are engaged during action execution are also involved during joint actions with peers and during other human generated action observation. Indeed, the comparator model hypothesis suggests that the comparison between a predicted state and an estimated real state enables motor control, and by a similar functioning, understanding and anticipating observed actions. Such a mechanism allows making predictions about an ongoing action, and is essential to action regulation, especially during joint actions with peers. Interestingly, the same comparison process has been shown to be involved in the construction of an individual's sense of agency, both for self-generated and observed other human generated actions. However, the implication of such predictive mechanisms during interactions with machines is not consensual, probably due to the high heterogeneousness of the automata used in the experimentations, from very simplistic devices to full humanoid robots. The discrepancies that are observed during human/machine interactions could arise from the absence of action/observation matching abilities when interacting with traditional low-level automata. Consistently, the difficulties to build a joint agency with this kind of machines could stem from the same problem. In this context, we aim to review the studies investigating predictive mechanisms during social interactions with humans and with automated artificial systems. We will start by presenting human data that show the involvement of predictions in action control and in the sense of agency during social interactions. Thereafter, we will confront this literature with data from the robotic field. Finally, we will address the upcoming issues in the field of robotics related to automated systems aimed at acting as collaborative agents.

Analysis of Patterns of Interaction and Knowledge Construction in On-Line Learning Environments: A Methodological Strategy

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Benilde García Cabrero

2008-05-01

Full Text Available A model of analysis of interaction and construction of knowledge in educational environments based on computer-mediated communication (CMC is proposed. This proposal considers: 1 the contextual factors that constitute the input and the scenario of interaction, 2 the interaction processes: types of interaction and its contents (Garrison, Anderson and Archer, 2000 as well as the discursive strategies (Lemke, 1997, and 3 learning results that involve the quality of the knowledge constructed by the participants (Gunawardena, Lowe and Anderson, 1997. This model was applied to the analysis of the interaction among a group of participants in two web forums (with or without the presence of a teacher, during the teaching of a PhD in Psychology program. The results show evidence of the model’s viability to describe the patterns of interaction and the levels of construction of knowledge in web forums.

Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma.

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Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

2017-01-01

Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

Involvement of lipid-protein complexes in plant-microorganism interactions

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Blein Jean-Pierre

2002-01-01

Full Text Available Increasing concerns about the environmental impact of modern agricultural have prompted research for alternate practices to pesticide treatments, notably using plant defense mechanisms. Thus, isolation and characterization of plant defense elicitors have been the main step of studies in many groups. Moreover, in the global concept of interactions between organisms and their environment, a major concern is to discriminate recognition between exogenous and endogenous signals, notably during pathogenic or allergenic interactions involving small proteins, such as elicitins or lipid transfer proteins (LTPs. Elicitins and lipid transfer proteins (LTP are both able to load and transfer lipidic molecules and share some structural and functional properties. While elicitins are known as elicitors of plant defense mechanisms, the biological function of LTPs is still an enigma. They are ubiquitous plant proteins able to load and transfer hydrophobic molecules such as fatty acids or phospholipids. Among them, LTPs1 (type 1 lipid transfer proteins constitute a multigenic family of secreted plant lipid binding proteins that are constitutively expressed in specific tissues and/or induced in response to biotic and abiotic stress (for reviews [1-4]. Their biological function is still unknown, even if some data provide arguments for a role of these proteins in the assembly of extracellular hydrophobic polymers (i.e., cutin and suberin [2, 4] and/or in plant defense against fungal pathogens [1, 3]. Beside their involvement in plant defense, LTPs1 are also known to be pan-allergens of plant-derived foods [5]. Finally, the discovery of the sterol carrier-properties of elicitins has opened new perspectives dealing with the relationship between this function and the elicitor activity of these small cystein-rich proteins. Nevertheless, this elicitor activity is restrained to few plant species, and thus does not appear in accordance with a universal lipid transfer

Topological and functional analysis of nonalcoholic steatohepatitis through protein interaction mapping

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Asadzadeh-Aghdaee, Hamid; Mansouri, Vahid; Peyvandi, Ali Asghar; Moztarzadeh, Fathollah; Okhovatian, Farshad; Lahmi, Farhad; Vafaee, Reza; Zali, Mohammad Reza

2016-01-01

Aim: The corresponding proteins are important for network mapping since the interaction analysis can provide a new interpretation about disease underlying mechanisms as the aim of this study. Backgroud: Nonalcoholic steatohepatitis (NASH) is one of the main causes of liver disease in the world. It has been known with many susceptible proteins that play essential role in its pathogenesis. Methods: In this paper, protein-protein interaction (PPI) network analysis of fatty liver disease retrieved from STRING db by the application of Cytoscape Software. ClueGO analyzed the associated pathways for the selected top proteins. Results: INS, PPARA, LEP, SREBF1, and ALB are the introduced biomarker panel for fatty liver disease. Conclusion: It seems that pathways related to insulin have a prominent role in fatty liver disease. Therefore, investigation in this case is required to confirm the possible linkage of introduced panel and involvement of insulin pathway in the disease. PMID:28224024

A novel mechanism of hippocampal LTD involving muscarinic receptor-triggered interactions between AMPARs, GRIP and liprin-α

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Dickinson Bryony A

2009-06-01

Full Text Available Abstract Background Long-term depression (LTD in the hippocampus can be induced by activation of different types of G-protein coupled receptors, in particular metabotropic glutamate receptors (mGluRs and muscarinic acethycholine receptors (mAChRs. Since mGluRs and mAChRs activate the same G-proteins and isoforms of phospholipase C (PLC, it would be expected that these two forms of LTD utilise the same molecular mechanisms. However, we find a distinct mechanism of LTD involving GRIP and liprin-α. Results Whilst both forms of LTD require activation of tyrosine phosphatases and involve internalisation of AMPARs, they use different molecular interactions. Specifically, mAChR-LTD, but not mGluR-LTD, is blocked by peptides that inhibit the binding of GRIP to the AMPA receptor subunit GluA2 and the binding of GRIP to liprin-α. Thus, different receptors that utilise the same G-proteins can regulate AMPAR trafficking and synaptic efficacy via distinct molecular mechanisms. Conclusion Our results suggest that mAChR-LTD selectively involves interactions between GRIP and liprin-α. These data indicate a novel mechanism of synaptic plasticity in which activation of M1 receptors results in AMPAR endocytosis, via a mechanism involving interactions between GluA2, GRIP and liprin-α.

A novel statistic for genome-wide interaction analysis.

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Xuesen Wu

2010-09-01

Full Text Available Although great progress in genome-wide association studies (GWAS has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked. The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001interacting pairs of SNPs in genes LST1/NCR3, CXCR5/BCL9L, and GLS2, some of which were located in the target sites of miR-324-3p, miR-433, and miR-382, as well as 15 pairs of interacting SNPs that had nonsynonymous substitutions. Our results demonstrated that genome-wide interaction analysis is a valuable tool for finding remaining missing heritability unexplained by the current GWAS, and the developed novel statistic is able to search significant interaction between SNPs across the genome. Real data analysis showed that the results of genome-wide interaction analysis can be replicated in two independent studies.

Bioinformatic analysis of Msx1 and Msx2 involved in craniofacial development.

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Dai, Jiewen; Mou, Zhifang; Shen, Shunyao; Dong, Yuefu; Yang, Tong; Shen, Steve Guofang

2014-01-01

Msx1 and Msx2 were revealed to be candidate genes for some craniofacial deformities, such as cleft lip with/without cleft palate (CL/P) and craniosynostosis. Many other genes were demonstrated to have a cross-talk with MSX genes in causing these defects. However, there is no systematic evaluation for these MSX gene-related factors. In this study, we performed systematic bioinformatic analysis for MSX genes by combining using GeneDecks, DAVID, and STRING database, and the results showed that there were numerous genes related to MSX genes, such as Irf6, TP63, Dlx2, Dlx5, Pax3, Pax9, Bmp4, Tgf-beta2, and Tgf-beta3 that have been demonstrated to be involved in CL/P, and Fgfr2, Fgfr1, Fgfr3, and Twist1 that were involved in craniosynostosis. Many of these genes could be enriched into different gene groups involved in different signaling ways, different craniofacial deformities, and different biological process. These findings could make us analyze the function of MSX gens in a gene network. In addition, our findings showed that Sumo, a novel gene whose polymorphisms were demonstrated to be associated with nonsyndromic CL/P by genome-wide association study, has protein-protein interaction with MSX1, which may offer us an alternative method to perform bioinformatic analysis for genes found by genome-wide association study and can make us predict the disrupted protein function due to the mutation in a gene DNA sequence. These findings may guide us to perform further functional studies in the future.

Participant Interaction in Asynchronous Learning Environments: Evaluating Interaction Analysis Methods

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Blanchette, Judith

2012-01-01

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

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

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Ueki Masao

2012-05-01

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

Dynamical analysis of yeast protein interaction network during the sake brewing process.

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Mirzarezaee, Mitra; Sadeghi, Mehdi; Araabi, Babak N

2011-12-01

Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.

In silico analysis suggests interaction between Ebola virus and the extracellular matrix

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Veljko eVeljkovic

2015-02-01

Full Text Available The worst Ebola virus (EV outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trendlines in this crisis are grave, and now represents global public health threat concern. Limited therapeutic and/or prophylactic options which are available for humans suffering from Ebola virus disease (EVD further complicate situation. Previous studies suggested that the EV glycoprotein (GP is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM, a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs are involved in interaction between GP and ECM. This finding could contribute to better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.

Realtime Interaction Analysis of Social Interplay in a Multimodal Musical-Sonic Interaction Context

DEFF Research Database (Denmark)

Hansen, Anne-Marie

2010-01-01

This paper presents an approach to the analysis of social interplay among users in a multimodal interaction and musical performance situation. The approach consists of a combined method of realtime sensor data analysis for the description and interpretation of player gestures and video micro......-analysis methods used to describe the interaction situation and the context in which the social interplay takes place. This combined method is used in an iterative process, where the design of interactive games with musical-sonic feedback is improved according to newly discovered understandings and interpretations...

Human U87 astrocytoma cell invasion induced by interaction of βig-h3 with integrin α5β1 involves calpain-2.

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Jie Ma

Full Text Available It is known that βig-h3 is involved in the invasive process of many types of tumors, but its mechanism in glioma cells has not been fully clarified. Using immunofluorescent double-staining and confocal imaging analysis, and co-immunoprecipitation assays, we found that βig-h3 co-localized with integrin α5β1 in U87 cells. We sought to elucidate the function of this interaction by performing cell invasion assays and gelatin zymography experiments. We found that siRNA knockdowns of βig-h3 and calpain-2 impaired cell invasion and MMP secretion. Moreover, βig-h3, integrins and calpain-2 are known to be regulated by Ca(2+, and they are also involved in tumor cell invasion. Therefore, we further investigated if calpain-2 was relevant to βig-h3-integrin α5β1 interaction to affect U87 cell invasion. Our data showed that βig-h3 co-localized with integrin α5β1 to enhance the invasion of U87 cells, and that calpain-2, is involved in this process, acting as a downstream molecule.

THE EVOLUTION OF THE FILM ANALYSIS OF INTERACTION RECORD (FAIR) FROM THE AMIDON-FLANDERS INTERACTION ANALYSIS. APPENDIX G.

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BALDWIN, PATRICIA

A DETAILED LISTING IS GIVEN OF THE REVISIONS THAT WERE MADE TO THE AMIDON-FLANDERS INTERACTION ANALYSIS SCALE WHILE THE FILM ANALYSIS OF INTERACTION RECORD (FAIR) SCALE WAS BEING DEVELOPED. COMMENTS ARE GIVEN FOR GUIDANCE IN THE USE OF SOME OF THE RATINGS ALONG WITH SOME GROUND RULES AND GUIDELINES FOR MAKING A FILM RATING. RELATED REPORTS ARE AA…

Digraph Matrix Analysis: A new approach to systems interaction analysis

International Nuclear Information System (INIS)

Sacks, I.J.; Alesso, H.P.; Ashmore, B.C.

1985-01-01

The term Systems Interaction was introduced by the Nuclear Regulatory Commission to identify interdependency of safety and support systems. Digraph Matrix Analysis was developed to allow the determination of these interdependencies. The main features of DMA are: the reliability model is traced directly from system schematics, all components of front line and support systems are included in a single integrated model, and the model is processed automatically with no heuristic culling applied. The recent application of DMA to the Indian Point-3 systems interaction analysis resulted in the discovery of several significant deeply hidden systems interactions

Interactions involving ozone, Botrytis cinerea, and B. squamosa on onion leaves

Energy Technology Data Exchange (ETDEWEB)

Rist, D.L.

1983-01-01

Interactions involving Botrytis cinerea Pers., B. squamosa Walker, and ozone on onion (alium cepae L.) were investigated. Initially, threshold dosages of ozone required to predispose onion leaves to greater infection by B. cinerea and B. squamosa were determined under controlled conditions in an ozone-exposure chamber. Subsequent experiments supported the hypothesis that nutrients leaking out of ozone-injured cells stimulated lesion production by B. cinerea. The electrical conductivity of, and carbohydrate concentration in, dew collected from leaves of onion plants which had been exposed to ozone were greater than the electrical conductivity of, and carbohydrate concentration in, dew collected from leaves of other, non-exposed onion plants. When conidia of B. cinerea were suspended in dew collected from leaves of plants which had been exposed to ozone and the resulting suspension atomized onto leaves of non-exposed plants, more lesions were induced than on leaves of other non-exposed plants inoculated with conidia suspended in dew collected from plants which had not been exposed to ozone. EDU protected onion leaves from ozone-induced predisposition to these fungi under controlled conditions. Experiments designed to detect interaction between B. cinerea and B. squamosa in onion leaf blighting indicated that such interaction did not occur. Leaves were blighted rapidly when inoculated with B. squamosa whether B. cinerea was present or absent.

Clinically significant drug–drug interactions involving opioid analgesics used for pain treatment in patients with cancer: a systematic review

Directory of Open Access Journals (Sweden)

Kotlinska-Lemieszek A

2015-09-01

Full Text Available Aleksandra Kotlinska-Lemieszek,1 Pål Klepstad,2,3,6 Dagny Faksvåg Haugen2,4,5 1Palliative Medicine Chair and Department, University Hospital of the Lord’s Transfiguration, Karol Marcinkowski University of Medical Sciences, Poznan, Poland; 2European Palliative Care Research Centre, Faculty of Medicine, Norwegian University of Science and Technology,Trondheim, Norway; 3Department of Anaesthesiology and Intensive Care Medicine, St Olavs Hospital, Trondheim, Norway; 4Regional Centre of Excellence for Palliative Care, Haukeland University Hospital, Bergen, Norway; 5Department of Clinical Medicine K1, University of Bergen, Bergen, Norway; 6Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway Background: Opioids are the most frequently used drugs to treat pain in cancer patients. In some patients, however, opioids can cause adverse effects and drug–drug interactions. No advice concerning the combination of opioids and other drugs is given in the current European guidelines. Objective: To identify studies that report clinically significant drug–drug interactions involving opioids used for pain treatment in adult cancer patients. Design and data sources: Systematic review with searches in Embase, MEDLINE, and Cochrane Central Register of Controlled Trials from the start of the databases (Embase from 1980 through January 2014. In addition, reference lists of relevant full-text papers were hand-searched. Results: Of 901 retrieved papers, 112 were considered as potentially eligible. After full-text reading, 17 were included in the final analysis, together with 15 papers identified through hand-searching of reference lists. All of the 32 included publications were case reports or case series. Clinical manifestations of drug–drug interactions involving opioids were grouped as follows: 1 sedation and respiratory depression, 2 other central nervous system symptoms, 3 impairment of pain

Service Interaction Flow Analysis Technique for Service Personalization

DEFF Research Database (Denmark)

Korhonen, Olli; Kinnula, Marianne; Syrjanen, Anna-Liisa

2017-01-01

Service interaction flows are difficult to capture, analyze, outline, and represent for research and design purposes. We examine how variation of personalized service flows in technology-mediated service interaction can be modeled and analyzed to provide information on how service personalization...... could support interaction. We have analyzed service interaction cases in a context of technology-mediated car rental service. With the analysis technique we propose, inspired by Interaction Analysis method, we were able to capture and model the situational service interaction. Our contribution regarding...... technology-mediated service interaction design is twofold: First, with the increased understanding on the role of personalization in managing variation in technology-mediated service interaction, our study contributes to designing service management information systems and human-computer interfaces...

Soil-structure interaction analysis by finite element methods state-of-the-art

International Nuclear Information System (INIS)

Seed, H.B.; Lysmer, J.

1977-01-01

Analyses of soil-structure interaction effects during earthquakes for nuclear power plant structures are usually made by one of two methods - either by means of an idealized complete interaction analysis involving consideration of a compatible variation of motions in the structure and the adjacent soil, or by means of an inertial interaction analysis in which the motions in the adjacent soil are assumed to be the same at all points above the foundation depth. For surface structures, the distribution of free-field motions with depth in the underlying soils has no influence on the structural response and thus, provided the analyses are made in accordance with good practice, good results may be obtained by either method of approach. For embedded structures, however, consideration of the variation of motions with depth is essential if adequate evaluations of soil and structural response are to be obtained without undue conservatism. The finite element analysis procedure is particularly well suited for evaluating the response of embedded structures since it can readily provide consideration of the variation of soil characteristics with depth, the different non-linear deformation and energy absorbing capacities of the various soil strata, the variation of motions with depth in accordance with the general principles of engineering mechanics, the three-dimensional nature of the problem and the effects of adjacent structures on each other

Interaction Involvement in Cross-Culture Computer-Mediated Communication: Examination of a Communication Process in Dyadic Instant Messaging Conversations

Science.gov (United States)

Nguyen, Thi Thao Duyen

2013-01-01

This dissertation explores how participants express and interpret verbal cues of interaction involvement in dyadic conversations via text-based Instant Messaging (IM). Moreover, it seeks to discover differences in the way American participants and Chinese participants use verbal cues when they are highly, or lowly involved. Based on previous…

The Data Party: Involving Stakeholders in Meaningful Data Analysis

Science.gov (United States)

Franz, Nancy K.

2013-01-01

A hallmark of Extension includes the involvement of stakeholders in research and program needs assessment, design, implementation, evaluation, and reporting. A data party can be used to enhance this stakeholder involvement specifically in data analysis. This type of event can not only increase client participation in Extension programming and…

Accelerator physics analysis with interactive tools

International Nuclear Information System (INIS)

Holt, J.A.; Michelotti, L.

1993-05-01

Work is in progress on interactive tools for linear and nonlinear accelerator design, analysis, and simulation using X-based graphics. The BEAMLINE and MXYZPTLK class libraries, were used with an X Windows graphics library to build a program for interactively editing lattices and studying their properties

The paradox of caffeine-zolpidem interaction: a network analysis.

Science.gov (United States)

Myslobodsky, Michael

2009-10-01

A widely prescribed and potent short-acting hypnotic, zolpidem has become the mainstay for the treatment of middle-of-the-night sleeplessness. It is expected to be antagonized by caffeine. Paradoxically, in some cases caffeine appears to slightly enhance zolpidem sedation. The pharmacokinetic and pharmacodynamic nature of this odd effect remains unexplored. The purpose of this study is to reproduce a hypothetical molecular network recruited by caffeine when co-administered with zolpidem using Ingenuity Pathway Analysis. Thus generated, network drew attention to several possible contributors to caffeine sedation, such as tachykinin precursor 1, cannabinoid, and GABA receptors. The present overview is centered on the possibility that caffeine potentiation of zolpidem sedation does not involve a centralized interaction of specific neurotransmitters, but rather is contributed by its antioxidant capacity. It is proposed that by modifying the cellular redox state, caffeine ultimately reduces the pool of reactive oxygen species, thereby increasing the bioavailability of endogenous melatonin for interaction with zolpidem. This side effect of caffeine encourages further studies of multiple antioxidants as an attractive way to potentially increasing somnolence.

DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA.

Science.gov (United States)

Keyamura, Kenji; Katayama, Tsutomu

2011-08-19

Chromosomal replication is initiated from the replication origin oriC in Escherichia coli by the active ATP-bound form of DnaA protein. The regulatory inactivation of DnaA (RIDA) system, a complex of the ADP-bound Hda and the DNA-loaded replicase clamp, represses extra initiations by facilitating DnaA-bound ATP hydrolysis, yielding the inactive ADP-bound form of DnaA. However, the mechanisms involved in promoting the DnaA-Hda interaction have not been determined except for the involvement of an interaction between the AAA+ domains of the two. This study revealed that DnaA Leu-422 and Pro-423 residues within DnaA domain IV, including a typical DNA-binding HTH motif, are specifically required for RIDA-dependent ATP hydrolysis in vitro and that these residues support efficient interaction with the DNA-loaded clamp·Hda complex and with Hda in vitro. Consistently, substitutions of these residues caused accumulation of ATP-bound DnaA in vivo and oriC-dependent inhibition of cell growth. Leu-422 plays a more important role in these activities than Pro-423. By contrast, neither of these residues is crucial for DNA replication from oriC, although they are highly conserved in DnaA orthologues. Structural analysis of a DnaA·Hda complex model suggested that these residues make contact with residues in the vicinity of the Hda AAA+ sensor I that participates in formation of a nucleotide-interacting surface. Together, the results show that functional DnaA-Hda interactions require a second interaction site within DnaA domain IV in addition to the AAA+ domain and suggest that these interactions are crucial for the formation of RIDA complexes that are active for DnaA-ATP hydrolysis.

DnaA Protein DNA-binding Domain Binds to Hda Protein to Promote Inter-AAA+ Domain Interaction Involved in Regulatory Inactivation of DnaA*

Science.gov (United States)

Keyamura, Kenji; Katayama, Tsutomu

2011-01-01

Chromosomal replication is initiated from the replication origin oriC in Escherichia coli by the active ATP-bound form of DnaA protein. The regulatory inactivation of DnaA (RIDA) system, a complex of the ADP-bound Hda and the DNA-loaded replicase clamp, represses extra initiations by facilitating DnaA-bound ATP hydrolysis, yielding the inactive ADP-bound form of DnaA. However, the mechanisms involved in promoting the DnaA-Hda interaction have not been determined except for the involvement of an interaction between the AAA+ domains of the two. This study revealed that DnaA Leu-422 and Pro-423 residues within DnaA domain IV, including a typical DNA-binding HTH motif, are specifically required for RIDA-dependent ATP hydrolysis in vitro and that these residues support efficient interaction with the DNA-loaded clamp·Hda complex and with Hda in vitro. Consistently, substitutions of these residues caused accumulation of ATP-bound DnaA in vivo and oriC-dependent inhibition of cell growth. Leu-422 plays a more important role in these activities than Pro-423. By contrast, neither of these residues is crucial for DNA replication from oriC, although they are highly conserved in DnaA orthologues. Structural analysis of a DnaA·Hda complex model suggested that these residues make contact with residues in the vicinity of the Hda AAA+ sensor I that participates in formation of a nucleotide-interacting surface. Together, the results show that functional DnaA-Hda interactions require a second interaction site within DnaA domain IV in addition to the AAA+ domain and suggest that these interactions are crucial for the formation of RIDA complexes that are active for DnaA-ATP hydrolysis. PMID:21708944

Transportation dose analysis using an interactive menu-driven computer program

International Nuclear Information System (INIS)

Strenge, D.L.; Peloquin, R.A.

1984-10-01

An easy-to-use software package is described for performing radiological consequence analyses for transportation scenarios involving truck or rail transport of spent fuel, HLW and other radioactive waste forms. The consequence analysis is based on the unit radiological factors (person-rem/km) developed by the Transportation Technology Center (Sandia National Laboratories). These generic unit radiological factors are combined with user-supplied information describing transporation distances, routes and waste types to estimate total exposure of the population. The software was developed for use in preparing the Environmental Assessment for the Monitored Retrievable Storage Program and is suitable for such analyses as siting waste repositories. The key feature of the software is the user-oriented, menu-driven interactive input mode available as an alternative to formatted input. The interactive input option allows the user to supply all input data, edit the data and run the program. Output reports can be diverted to a high-speed printer

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population

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Alencar Xavier

2018-02-01

Full Text Available Genetic improvement toward optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs. In this study, the genetic basis of soybean grain yield responsiveness to environmental factors was examined in a large soybean nested association population. For this, a genome-wide association to performance stability estimates generated from a Finlay-Wilkinson analysis and the inclusion of the interaction between marker genotypes and environmental factors was implemented. Genomic footprints were investigated by analysis and meta-analysis using a recently published multiparent model. Results indicated that specific soybean genomic regions were associated with stability, and that multiplicative interactions were present between environments and genetic background. Seven genomic regions in six chromosomes were identified as being associated with genotype-by-environment interactions. This study provides insight into genomic assisted breeding aimed at achieving a more stable agronomic performance of soybean, and documented opportunities to exploit genomic regions that were specifically associated with interactions involving environments and subpopulations.

ANALYSIS OF THE INTERACTIONS BETWEEN IMMIGRANT/FOREIGN CHARACTERS AND NATIONAL/AUTOCHTHONOUS CHARACTERS IN SPANISH TELEVISION FICTION

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María Marcos Ramos

2014-10-01

Full Text Available In this paper we present the results of an empirical research in which it were analysed the interactions between immigrants and national characters in a sample of Spanish television fictional programs broadcasted on prime time. This study is a content analysis of 282 interactions between immigrant/foreign and national characters. Thus, it was found that the largest number of relationships between the characters involved was produced in a working context. Moreover, there was a higher proportion of the use of aggressive humour from the national characters to the immigrant/foreigners than in the reverse way. It was also observed that the immigrant/foreigner characters hardly spoke about their feelings, nor were heard by the nationals when they did it, although there were a high number of interactions in which immigrant characters were expressing their opinions and these were attended by national characters. The analysis of the interactions between immigrant and national characters in television fiction is a very important research issue, because it has been proposed that the parasocial interactions are complementary of the interpersonal interactions taking place in daily life (Müller, 2009; Park, 2012.

Accelerating Robot Development through Integral Analysis of Human-Robot Interaction

NARCIS (Netherlands)

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

2007-01-01

The development of interactive robots is a complicated process, involving a plethora of psychological, technical, and contextual influences. To design a robot capable of operating "intelligently" in everyday situations, one needs a profound understanding of human-robot interaction (HRI). We propose

Anaplasma phagocytophilum MSP4 and HSP70 Proteins Are Involved in Interactions with Host Cells during Pathogen Infection

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Marinela Contreras

2017-07-01

Full Text Available Anaplasma phagocytophilum transmembrane and surface proteins play a role during infection and multiplication in host neutrophils and tick vector cells. Recently, A. phagocytophilum Major surface protein 4 (MSP4 and Heat shock protein 70 (HSP70 were shown to be localized on the bacterial membrane, with a possible role during pathogen infection in ticks. In this study, we hypothesized that A. phagocytophilum MSP4 and HSP70 have similar functions in tick-pathogen and host-pathogen interactions. To address this hypothesis, herein we characterized the role of these bacterial proteins in interaction and infection of vertebrate host cells. The results showed that A. phagocytophilum MSP4 and HSP70 are involved in host-pathogen interactions, with a role for HSP70 during pathogen infection. The analysis of the potential protective capacity of MSP4 and MSP4-HSP70 antigens in immunized sheep showed that MSP4-HSP70 was only partially protective against pathogen infection. This limited protection may be associated with several factors, including the recognition of non-protective epitopes by IgG in immunized lambs. Nevertheless, these antigens may be combined with other candidate protective antigens for the development of vaccines for the control of human and animal granulocytic anaplasmosis. Focusing on the characterization of host protective immune mechanisms and protein-protein interactions at the host-pathogen interface may lead to the discovery and design of new effective protective antigens.

INTERACTION ANALYSIS--RECENT DEVELOPMENTS.

Science.gov (United States)

AMIDON, EDMUND

MODIFICATION OF FLANDERS' INTERACTION ANALYSIS IS PROPOSED TO ENCOMPASS SOME FEATURES OF RELATED SYSTEMS AND TO PROVIDE A SPECIFIC FEEDBACK TOOL FOR ANALYZING ONE'S OWN TEACHING, FORMULATING QUESTIONS, OBSERVING TEACHING PATTERNS, DIAGNOSING TEACHING PROBLEMS, AND FOR ROLE-PLAYING IN THE COLLEGE CLASSROOM. FLANDERS' 10 CATEGORIES ARE DIVIDED INTO…

Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat

DEFF Research Database (Denmark)

Yang, Fen; Jensen, Jens D.; Svensson, Birte

2012-01-01

Fusarium graminearum is a phytopathogenic fungus primarily infecting small grain cereals, including barley and wheat. Secreted enzymes play important roles in the pathogenicity of many fungi. In order to access the secretome of F. graminearum, the fungus was grown in liquid culture with barley...... or wheat flour as the sole nutrient source to mimic the host–pathogen interaction. A gel‐based proteomics approach was employed to identify the proteins secreted into the culture medium. Sixty‐nine unique fungal proteins were identified in 154 protein spots, including enzymes involved in the degradation...... between wheat and barley flour medium were mainly involved in fungal cell wall remodelling and the degradation of plant cell walls, starch and proteins. The in planta expression of corresponding F. graminearum genes was confirmed by quantitative reverse transcriptase‐polymerase chain reaction in barley...

Dyadic Interracial Interactions: A Meta-Analysis

Science.gov (United States)

Toosi, Negin R.; Babbitt, Laura G.; Ambady, Nalini; Sommers, Samuel R.

2012-01-01

This meta-analysis examined over 40 years of research on interracial interactions by exploring 4 types of outcomes: explicit attitudes toward interaction partners, participants' self-reports of their own emotional state, nonverbal or observed behavior, and objective measures of performance. Data were collected from 108 samples (N = 12,463)…

Positioning Theory and Discourse Analysis: Some Tools for Social Interaction Analysis

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Francisco Tirado

2007-05-01

Full Text Available This article outlines positioning theory as a discursive analysis of interaction, focusing on the topic of conflict. Moreover, said theory is applied to a new work environment for the social sciences: virtual spaces. The analysis is organized in the following way. First, the major key psychosocial issues which define the topic of conflict are reviewed. Then, virtual environments are presented as a new work space for the social sciences. Thirdly, a synthesis of positioning theory and its FOUCAULTian legacy is conducted, while appreciating its particular appropriateness for analyzing conflictive interaction in virtual environments. An empiric case is then presented. This consists of an analysis of interactive sequences within a specific virtual environment: the Universitat Oberta de Catalunya (UOC Humanitats i Filologia Catalana studies forum. Through positioning theory, the production and effects that a conflictive interaction sequence has on the community in which it is produced are understood and explained. URN: urn:nbn:de:0114-fqs0702317

The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network.

Science.gov (United States)

Ding, Fangrui; Tan, Aidi; Ju, Wenjun; Li, Xuejuan; Li, Shao; Ding, Jie

2016-01-01

Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet), which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN) induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN) transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and prediction, GCNet

Mass spectrometric analysis of protein interactions

DEFF Research Database (Denmark)

Borch, Jonas; Jørgensen, Thomas J. D.; Roepstorff, Peter

2005-01-01

Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now...... available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope...... labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably....

Evolution of the interaction between Runx2 and VDR, two transcription factors involved in osteoblastogenesis

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Barriga Elias H

2010-03-01

Full Text Available Abstract Background The mineralized skeleton is a major evolutionary novelty that has contributed to the impressive morphological diversifications of the vertebrates. Essential to bone biology is the solidified extracellular matrix secreted by highly specialized cells, the osteoblasts. We now have a rather complete view of the events underlying osteogenesis, from a cellular, molecular, genetic, and epigenetic perspective. Because this knowledge is still largely restricted to mammals, it is difficult, if not impossible, to deduce the evolutionary history of the regulatory network involved in osteoblasts specification and differentiation. In this study, we focused on the transcriptional regulators Runx2 and VDR (the Vitamin D Receptor that, in mammals, directly interact together and stabilize complexes of co-activators and chromatin remodellers, thereby allowing the transcriptional activation of target genes involved in extracellular matrix mineralization. Using a combination of functional, biochemical, and histological approaches, we have asked if the interaction observed between Runx2 and VDR represents a recent mammalian innovation, or if it results from more ancient changes that have occurred deep in the vertebrate lineage. Results Using immunohistochemistry and in situ hybridization in developing embryos of chick, frog and teleost fishes, we have revealed that the co-expression of Runx2 and VDR in skeletal elements has been particularly strengthened in the lineage leading to amniotes. We show that the teleost Runx2 orthologue as well as the three mammalian Runx1, Runx2 and Runx3 paralogues are able to co-immunoprecipitate with the VDR protein present in nuclear extracts of rat osteoblasts stimulated with 1α,25-dihydroxyvitamin D3. In addition, the teleost Runx2 can activate the transcription of the mammalian osteocalcin promoter in transfection experiments, and this response can be further enhanced by 1α,25-dihydroxyvitamin D3. Finally

User involvement in the design of human-computer interactions: some similarities and differences between design approaches

NARCIS (Netherlands)

Bekker, M.M.; Long, J.B.

1998-01-01

This paper presents a general review of user involvement in the design of human-computer interactions, as advocated by a selection of different approaches to design. The selection comprises User-Centred Design, Participatory Design, Socio-Technical Design, Soft Systems Methodology, and Joint

University Physics Students' Use of Models in Explanations of Phenomena Involving Interaction between Metals and Electromagnetic Radiation.

Science.gov (United States)

Redfors, Andreas; Ryder, Jim

2001-01-01

Examines third year university physics students' use of models when explaining familiar phenomena involving interaction between metals and electromagnetic radiation. Concludes that few students use a single model consistently. (Contains 27 references.) (DDR)

Involvement of the carboxyl-terminal region of the yeast peroxisomal half ABC transporter Pxa2p in its interaction with Pxa1p and in transporter function.

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Cheng-Yi Chuang

Full Text Available The peroxisome is a single membrane-bound organelle in eukaryotic cells involved in lipid metabolism, including β-oxidation of fatty acids. The human genetic disorder X-linked adrenoleukodystrophy (X-ALD is caused by mutations in the ABCD1 gene (encoding ALDP, a peroxisomal half ATP-binding cassette [ABC] transporter. This disease is characterized by defective peroxisomal β-oxidation and a large accumulation of very long-chain fatty acids in brain white matter, adrenal cortex, and testis. ALDP forms a homodimer proposed to be the functional transporter, whereas the peroxisomal transporter in yeast is a heterodimer comprising two half ABC transporters, Pxa1p and Pxa2p, both orthologs of human ALDP. While the carboxyl-terminal domain of ALDP is engaged in dimerization, it remains unknown whether the same region is involved in the interaction between Pxa1p and Pxa2p.Using a yeast two-hybrid assay, we found that the carboxyl-terminal region (CT of Pxa2p, but not of Pxa1p, is required for their interaction. Further analysis indicated that the central part of the CT (designated CT2 of Pxa2p was indispensable for its interaction with the carboxyl terminally truncated Pxa1_NBD. An interaction between the CT of Pxa2p and Pxa1_NBD was not detected, but could be identified in the presence of Pxa2_NBD-CT1. A single mutation of two conserved residues (aligned with X-ALD-associated mutations at the same positions in ALDP in the CT2 of the Pxa2_NBD-CT protein impaired its interaction with Pxa1_NBD or Pxa1_NBD-CT, resulting in a mutant protein that exhibited a proteinase K digestion profile different from that of the wild-type protein. Functional analysis of these mutant proteins on oleate plates indicated that they were defective in transporter function.The CT of Pxa2p is involved in its interaction with Pxa1p and in transporter function. This concept may be applied to human ALDP studies, helping to establish the pathological mechanism for CT-related X

Interactivity in Educational Apps for Young Children: A Multimodal Analysis

Science.gov (United States)

Blitz-Raith, Alexandra H.; Liu, Jianxin

2017-01-01

Interactivity is an important indicator of an educational app's reception. Since most educational apps are multimodal, it justifies a methodological initiative to understand meaningful involvement of multimodality in enacting and even amplifying interactivity in an educational app. Yet research so far has largely concentrated on algorithm…

Interactive system design using the complementarity of axiomatic design and fault tree analysis

International Nuclear Information System (INIS)

Heo, Gyun Young; Do, Sung Hee; Lee, Tae Sik

2007-01-01

To efficiently design safety-critical systems such as nuclear power plants, with requirement of high reliability, methodologies allowing for rigorous interactions between the synthesis and analysis processes have been proposed. This paper attempts to develop a reliability-centered design framework through an interactive process between Axiomatic Design (AD) and Fault Tree Analysis (FTA). Integrating AD and FTA into a single framework appears to be a viable solution, as they compliment each other with their unique advantages. AD provides a systematic synthesis tool while FTA is commonly used as a safety analysis tool. These methodologies build a design process that is less subjective, and they enable designers to develop insights that lead to solutions with improved reliability. Due to the nature of the two methodologies, the information involved in each process is complementary: a success tree versus a fault tree. Thus, at each step a system using AD is synthesized, and its reliability is then quantified using the FT derived from the AD synthesis process. The converted FT provides an opportunity to examine the completeness of the outcome from the synthesis process. This study presents an example of the design of a Containment Heat Removal System (CHRS). A case study illustrates the process of designing the CHRS with an interactive design framework focusing on the conversion of the AD process to FTA

Mouse Social Interaction Test (MoST): a quantitative computer automated analysis of behavior.

Science.gov (United States)

Thanos, Panayotis K; Restif, Christophe; O'Rourke, Joseph R; Lam, Chiu Yin; Metaxas, Dimitris

2017-01-01

Rodents are the most commonly used preclinical model of human disease assessing the mechanism(s) involved as well as the role of genetics, epigenetics, and pharmacotherapy on this disease as well as identifying vulnerability factors and risk assessment for disease critical in the development of improved treatment strategies. Unfortunately, the majority of rodent preclinical studies utilize single housed approaches where animals are either entirely housed and tested in solitary environments or group housed but tested in solitary environments. This approach, however, ignores the important contribution of social interaction and social behavior. Social interaction in rodents is found to be a major criterion for the ethological validity of rodent species-specific behavioral characteristics (Zurn et al. 2007; Analysis 2011). It is also well established that there is significant and growing number of reports, which illustrates the important role of social environment and social interaction in all diseases, with particularly significance in all neuropsychiatric diseases. Thus, it is imperative that research studies be able to add large-scale evaluations of social interaction and behavior in mice and benefit from automated tracking of behaviors and measurements by removing user bias and by quantifying aspects of behaviors that cannot be assessed by a human observer. Single mouse setups have been used routinely, but cannot be easily extended to multiple-animal studies where social behavior is key, e.g., autism, depression, anxiety, substance and non-substance addictive disorders, aggression, sexual behavior, or parenting. While recent efforts are focusing on multiple-animal tracking alone, a significant limitation remains the lack of insightful measures of social interactions. We present a novel, non-invasive single camera-based automated tracking method described as Mouse Social Test (MoST) and set of measures designed for estimating the interactions of multiple mice at the

Generation and comprehensive analysis of an influenza virus polymerase cellular interaction network.

Science.gov (United States)

Tafforeau, Lionel; Chantier, Thibault; Pradezynski, Fabrine; Pellet, Johann; Mangeot, Philippe E; Vidalain, Pierre-Olivier; Andre, Patrice; Rabourdin-Combe, Chantal; Lotteau, Vincent

2011-12-01

The influenza virus transcribes and replicates its genome inside the nucleus of infected cells. Both activities are performed by the viral RNA-dependent RNA polymerase that is composed of the three subunits PA, PB1, and PB2, and recent studies have shown that it requires host cell factors to transcribe and replicate the viral genome. To identify these cellular partners, we generated a comprehensive physical interaction map between each polymerase subunit and the host cellular proteome. A total of 109 human interactors were identified by yeast two-hybrid screens, whereas 90 were retrieved by literature mining. We built the FluPol interactome network composed of the influenza virus polymerase (PA, PB1, and PB2) and the nucleoprotein NP and 234 human proteins that are connected through 279 viral-cellular protein interactions. Analysis of this interactome map revealed enriched cellular functions associated with the influenza virus polymerase, including host factors involved in RNA polymerase II-dependent transcription and mRNA processing. We confirmed that eight influenza virus polymerase-interacting proteins are required for virus replication and transcriptional activity of the viral polymerase. These are involved in cellular transcription (C14orf166, COPS5, MNAT1, NMI, and POLR2A), translation (EIF3S6IP), nuclear transport (NUP54), and DNA repair (FANCG). Conversely, we identified PRKRA, which acts as an inhibitor of the viral polymerase transcriptional activity and thus is required for the cellular antiviral response.

An Atomic Force Microscopy Study of the Interactions Involving Polymers and Silane Networks

Directory of Open Access Journals (Sweden)

Rodrigo L. Oréfice

1998-12-01

Full Text Available ABSTRACT: Silane coupling agents have been frequently used as interfacial agents in polymer composites to improve interfacial strength and resistance to fluid migration. Although the capability of these agents in improving properties and performance of composites has been reported, there are still many uncertainties regarding the processing-structure-property relationships and the mechanisms of coupling developed by silane agents. In this work, an Atomic Force Microscope (AFM was used to measure interactions between polymers and silica substrates, where silane networks with a series of different structures were processed. The influence of the structure of silane networks on the interactions with polymers was studied and used to determine the mechanisms involved in the coupling phenomenon. The AFM results showed that phenomena such as chain penetration, entanglements, intersegment bonding, chain conformation in the vicinities of rigid surfaces were identified as being relevant for the overall processes of adhesion and adsorption of polymeric chains within a silane network. AFM adhesion curves showed that penetration of polymeric chains through a more open silane network can lead to higher levels of interactions between polymer and silane agents.

Skill versus luck: A motivational analysis of gambling involvement.

Science.gov (United States)

Chantal, Y; Vallerand, R J

1996-12-01

The purpose of the present investigation was to test the skill/luck distinction among gambling games by comparing the motivations underlying participation in a skill (horse racing) and a luck (lottery) betting activity. Predictions were made using Self-Determination Theory (Deci & Ryan, 1985, 1991). It was predicted that self-determined motivations (intrinsic motivation and identified regulation) would be more prominent for the skill game because it is conducive to optimal challenges, fun, and self-involvement. Conversely, the non self-determined forms of motivation (especially external regulation) should be more important for the game of luck because the luck dimension precludes true involvement of the self and orients the individual towards material gains. Results from a hierarchical discriminant function analysis, with 120 gamblers predominantly involved in one of the two betting activities, supported these hypotheses. These results highlight the relevance of a motivational analysis for a better understanding of the inherent properties of gambling games.

Involvement of two classes of binding sites in the interactions of cyclophilin B with peripheral blood T-lymphocytes.

Science.gov (United States)

Denys, A; Allain, F; Carpentier, M; Spik, G

1998-12-15

Cyclophilin B (CyPB) is a cyclosporin A (CsA)-binding protein, mainly associated with the secretory pathway, and is released in biological fluids. We recently reported that CyPB specifically binds to T-lymphocytes and promotes enhanced incorporation of CsA. The interactions with cellular binding sites involved, at least in part, the specific N-terminal extension of the protein. In this study, we intended to specify further the nature of the CyPB-binding sites on peripheral blood T-lymphocytes. We first provide evidence that the CyPB binding to heparin-Sepharose is prevented by soluble sulphated glycosaminoglycans (GAG), raising the interesting possibility that such interactions may occur on the T-cell surface. We then characterized CyPB binding to T-cell surface GAG and found that these interactions involved the N-terminal extension of CyPB, but not its conserved CsA-binding domain. In addition, we determined the presence of a second CyPB binding site, which we termed a type I site, in contrast with type II for GAG interactions. The two binding sites exhibit a similar affinity but the expression of the type I site was 3-fold lower. The conclusion that CyPB binding to the type I site is distinct from the interactions with GAG was based on the findings that it was (1) resistant to NaCl wash and GAG-degrading enzyme treatments, (2) reduced in the presence of CsA or cyclophilin C, and (3) unmodified in the presence of either the N-terminal peptide of CyPB or protamine. Finally, we showed that the type I binding sites were involved in an endocytosis process, supporting the hypothesis that they may correspond to a functional receptor for CyPB.

A Hybrid Artificial Reputation Model Involving Interaction Trust, Witness Information and the Trust Model to Calculate the Trust Value of Service Providers

Directory of Open Access Journals (Sweden)

Gurdeep Singh Ransi

2014-02-01

Full Text Available Agent interaction in a community, such as the online buyer-seller scenario, is often uncertain, as when an agent comes in contact with other agents they initially know nothing about each other. Currently, many reputation models are developed that help service consumers select better service providers. Reputation models also help agents to make a decision on who they should trust and transact with in the future. These reputation models are either built on interaction trust that involves direct experience as a source of information or they are built upon witness information also known as word-of-mouth that involves the reports provided by others. Neither the interaction trust nor the witness information models alone succeed in such uncertain interactions. In this paper we propose a hybrid reputation model involving both interaction trust and witness information to address the shortcomings of existing reputation models when taken separately. A sample simulation is built to setup buyer-seller services and uncertain interactions. Experiments reveal that the hybrid approach leads to better selection of trustworthy agents where consumers select more reputable service providers, eventually helping consumers obtain more gains. Furthermore, the trust model developed is used in calculating trust values of service providers.

Spacecraft Interactions Modeling and Post-Mission Data Analysis

National Research Council Canada - National Science Library

Bonito, N

1996-01-01

Software systems were designed and developed for data management, data acquisition, interactive visualization and analysis of solar arrays, tethered objects, and large object space plasma interactions...

Analysis of interactions among barriers in project risk management

Science.gov (United States)

Dandage, Rahul V.; Mantha, Shankar S.; Rane, Santosh B.; Bhoola, Vanita

2018-03-01

In the context of the scope, time, cost, and quality constraints, failure is not uncommon in project management. While small projects have 70% chances of success, large projects virtually have no chance of meeting the quadruple constraints. While there is no dearth of research on project risk management, the manifestation of barriers to project risk management is a less dwelt topic. The success of project management is oftentimes based on the understanding of barriers to effective risk management, application of appropriate risk management methodology, proactive leadership to avoid barriers, workers' attitude, adequate resources, organizational culture, and involvement of top management. This paper represents various risk categories and barriers to risk management in domestic and international projects through literature survey and feedback from project professionals. After analysing the various modelling methods used in project risk management literature, interpretive structural modelling (ISM) and MICMAC analysis have been used to analyse interactions among the barriers and prioritize them. The analysis indicates that lack of top management support, lack of formal training, and lack of addressing cultural differences are the high priority barriers, among many others.

Interactive Visual Analysis within Dynamic Ocean Models

Science.gov (United States)

Butkiewicz, T.

2012-12-01

The many observation and simulation based ocean models available today can provide crucial insights for all fields of marine research and can serve as valuable references when planning data collection missions. However, the increasing size and complexity of these models makes leveraging their contents difficult for end users. Through a combination of data visualization techniques, interactive analysis tools, and new hardware technologies, the data within these models can be made more accessible to domain scientists. We present an interactive system that supports exploratory visual analysis within large-scale ocean flow models. The currents and eddies within the models are illustrated using effective, particle-based flow visualization techniques. Stereoscopic displays and rendering methods are employed to ensure that the user can correctly perceive the complex 3D structures of depth-dependent flow patterns. Interactive analysis tools are provided which allow the user to experiment through the introduction of their customizable virtual dye particles into the models to explore regions of interest. A multi-touch interface provides natural, efficient interaction, with custom multi-touch gestures simplifying the otherwise challenging tasks of navigating and positioning tools within a 3D environment. We demonstrate the potential applications of our visual analysis environment with two examples of real-world significance: Firstly, an example of using customized particles with physics-based behaviors to simulate pollutant release scenarios, including predicting the oil plume path for the 2010 Deepwater Horizon oil spill disaster. Secondly, an interactive tool for plotting and revising proposed autonomous underwater vehicle mission pathlines with respect to the surrounding flow patterns predicted by the model; as these survey vessels have extremely limited energy budgets, designing more efficient paths allows for greater survey areas.

Comparing physically abusive, neglectful, and non-maltreating parents during interactions with their children: a meta-analysis of observational studies.

Science.gov (United States)

Wilson, Steven R; Rack, Jessica J; Shi, Xiaowei; Norris, Alda M

2008-09-01

To clarify the nature and extent of differences in the ways that physically abusive, neglectful, and non-maltreating parents communicate during interactions with their children. A meta-analysis was conducted of 33 observational studies comparing parent-child interactions in families where parents have a documented history of physical abuse or neglect vs. where parents have no history of child maltreatment. Parental behaviors were grouped into three clusters (positivity, aversiveness, and involvement) for comparison across studies. When comparing maltreating (physically abusive or neglectful) vs. non-maltreating parents, mean weighted effect sizes for the three behavioral clusters range from d=.46 to .62. Physically abusive parents are distinguished from non-maltreating parents more so than neglectful parents in terms of aversive behavior, whereas the reverse is true for involvement. Publication date, parent and child age, and task structure moderate the magnitude, though not direction, of differences. Parents with a documented history of child physical abuse or child neglect also are distinguished from non-maltreating parents by the levels of aversiveness, positivity, and involvement they display during interactions that constitute the parent-child relationship. Researchers and practitioners need to carefully consider sample size, length and setting of observation, and interaction tasks when using observational methods.

GIS - Based data presentation and interactive communication system for public involvement in EIA

International Nuclear Information System (INIS)

Oprea, I.; Oprea, M.; Guta, V.; Pirvu, V.

2001-01-01

The data presentation and interactive communication system has as main task to integrate technical and administrative information, as well as to ensure an efficient public participation. The system can achieve desired inter-operability between specialists, government and public in decision-making and environmental impact assessment (EIA). It incorporates different modules relative to specific types of parameters and authorities involved. The GIS-based system provides mapping, database, automatic information collection and advanced presentation techniques. It includes a graphically oriented executive support, which has the ability to present information by geographical representation of the zones on the map. The public opinion is taking into account by consideration of alternatives and providing access to the monitoring of environmental effects. The system offers an effective way to avoid negative reactions by interactive communication based on real-time information exchange. The system can be integrated into national or international management systems, being a useful tool for an efficient communication, handling and exchanging a vast amount of information. (authors)

Functional Interaction Network Construction and Analysis for Disease Discovery.

Science.gov (United States)

Wu, Guanming; Haw, Robin

2017-01-01

Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform. In this chapter, we describe the detailed procedures on how this functional interaction network is constructed by integrating multiple external data sources, extracting functional interactions from human curated pathway databases, building a machine learning classifier called a Naïve Bayesian Classifier, predicting interactions based on the trained Naïve Bayesian Classifier, and finally constructing the functional interaction database. We also provide an example on how to use ReactomeFIViz for performing network-based data analysis for a list of genes.

Energy analysis of crack-damage interaction

Science.gov (United States)

Chudnovsky, A.; Wu, Shaofu

1989-01-01

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

Gene-environment interactions involving functional variants

DEFF Research Database (Denmark)

Barrdahl, Myrto; Rudolph, Anja; Hopper, John L

2017-01-01

.36, 95% CI: 1.16-1.59, pint  = 1.9 × 10(-5) ) in relation to ER- disease risk. The remaining two gene-environment interactions were also identified in relation to ER- breast cancer risk and were found between 3p21-rs6796502 and age at menarche (ORint  = 1.26, 95% CI: 1.12-1.43, pint =1.8 × 10...... epidemiological breast cancer risk factors in relation to breast cancer. Analyses were conducted on up to 58,573 subjects (26,968 cases and 31,605 controls) from the Breast Cancer Association Consortium, in one of the largest studies of its kind. Analyses were carried out separately for estrogen receptor (ER......) positive (ER+) and ER negative (ER-) disease. The Bayesian False Discovery Probability (BFDP) was computed to assess the noteworthiness of the results. Four potential gene-environment interactions were identified as noteworthy (BFDP 

MCT expression and lactate influx/efflux in tanycytes involved in glia-neuron metabolic interaction.

Directory of Open Access Journals (Sweden)

Christian Cortés-Campos

Full Text Available Metabolic interaction via lactate between glial cells and neurons has been proposed as one of the mechanisms involved in hypothalamic glucosensing. We have postulated that hypothalamic glial cells, also known as tanycytes, produce lactate by glycolytic metabolism of glucose. Transfer of lactate to neighboring neurons stimulates ATP synthesis and thus contributes to their activation. Because destruction of third ventricle (III-V tanycytes is sufficient to alter blood glucose levels and food intake in rats, it is hypothesized that tanycytes are involved in the hypothalamic glucose sensing mechanism. Here, we demonstrate the presence and function of monocarboxylate transporters (MCTs in tanycytes. Specifically, MCT1 and MCT4 expression as well as their distribution were analyzed in Sprague Dawley rat brain, and we demonstrate that both transporters are expressed in tanycytes. Using primary tanycyte cultures, kinetic analyses and sensitivity to inhibitors were undertaken to confirm that MCT1 and MCT4 were functional for lactate influx. Additionally, physiological concentrations of glucose induced lactate efflux in cultured tanycytes, which was inhibited by classical MCT inhibitors. Because the expression of both MCT1 and MCT4 has been linked to lactate efflux, we propose that tanycytes participate in glucose sensing based on a metabolic interaction with neurons of the arcuate nucleus, which are stimulated by lactate released from MCT1 and MCT4-expressing tanycytes.

Interaction of translationally controlled tumor protein with Apaf-1 is involved in the development of chemoresistance in HeLa cells

International Nuclear Information System (INIS)

Jung, Jaehoon; Kim, Hyo Young; Maeng, Jeehye; Kim, Moonhee; Shin, Dong Hae; Lee, Kyunglim

2014-01-01

Translationally controlled tumor protein (TCTP), alternatively called fortilin, is believed to be involved in the development of the chemoresistance of tumor cells against anticancer drugs such as etoposide, taxol, and oxaliplatin, the underlying mechanisms of which still remain elusive. Cell death analysis of TCTP-overexpressing HeLa cells was performed following etoposide treatment to assess the mitochondria-dependent apoptosis. Apoptotic pathway was analyzed through measuring the cleavage of epidermal growth factor receptor (EGFR) and phospholipase C-γ (PLC-γ), caspase activation, mitochondrial membrane perturbation, and cytochrome c release by flow cytometry and western blotting. To clarify the role of TCTP in the inhibition of apoptosome, in vitro apoptosome reconstitution and immunoprecipitation was used. Pull-down assay and silver staining using the variants of Apaf-1 protein was applied to identify the domain that is responsible for its interaction with TCTP. In the present study, we confirmed that adenoviral overexpression of TCTP protects HeLa cells from cell death induced by cytotoxic drugs such as taxol and etoposide. TCTP antagonized the mitochondria-dependent apoptotic pathway following etoposide treatment, including mitochondrial membrane damage and resultant cytochrome c release, activation of caspase-9, and -3, and eventually, the cleavage of EGFR and PLC-γ. More importantly, TCTP interacts with the caspase recruitment domain (CARD) of Apaf-1 and is incorporated into the heptameric Apaf-1 complex, and that C-terminal cleaved TCTP specifically associates with Apaf-1 of apoptosome in apoptosome-forming condition thereby inhibiting the amplification of caspase cascade. TCTP protects the cancer cells from etoposide-induced cell death by inhibiting the mitochondria-mediated apoptotic pathway. Interaction of TCTP with Apaf-1 in apoptosome is involved in the molecular mechanism of TCTP-induced chemoresistance. These findings suggest that TCTP may serve

Salmonella biofilm formation on Aspergillus niger involves cellulose--chitin interactions.

Directory of Open Access Journals (Sweden)

Maria T Brandl

Full Text Available Salmonella cycles between host and nonhost environments, where it can become an active member of complex microbial communities. The role of fungi in the environmental adaptation of enteric pathogens remains relatively unexplored. We have discovered that S. enterica Typhimurium rapidly attaches to and forms biofilms on the hyphae of the common fungus, Aspergillus niger. Several Salmonella enterica serovars displayed a similar interaction, whereas other bacterial species were unable to bind to the fungus. Bacterial attachment to chitin, a major constituent of fungal cell walls, mirrored this specificity. Pre-incubation of S. Typhimurium with N-acetylglucosamine, the monomeric component of chitin, reduced binding to chitin beads by as much as 727-fold and inhibited attachment to A. niger hyphae considerably. A cellulose-deficient mutant of S. Typhimurium failed to attach to chitin beads and to the fungus. Complementation of this mutant with the cellulose operon restored binding to chitin beads to 79% of that of the parental strain and allowed for attachment and biofilm formation on A. niger, indicating that cellulose is involved in bacterial attachment to the fungus via the chitin component of its cell wall. In contrast to cellulose, S. Typhimurium curli fimbriae were not required for attachment and biofilm development on the hyphae but were critical for its stability. Our results suggest that cellulose-chitin interactions are required for the production of mixed Salmonella-A. niger biofilms, and support the hypothesis that encounters with chitinaceous alternate hosts may contribute to the ecological success of human pathogens.

The required interactions among institutions involved with Research and Development in the power sector

Energy Technology Data Exchange (ETDEWEB)

Vieira Filho, X; Medeiros, J C; Szechtman, M [Centro de Pesquisas de Energia Eletrica (CEPEL), Rio de Janeiro, RJ (Brazil)

1994-12-31

This paper presents the form which CEPEL (Brazilian Federal Research Center in Electric Energy) works for the Brazilian electric system, the interaction with associates, especially with ELETROBRAS (the Federal holding company in Brazil), the modern way of CEPEL operation and interactions with clients, the partnership in Research and Development, the CEPEL philosophy of transferring technology to its clients, and the cost-benefit analysis of Research and Development activities. (author) 2 refs., 4 figs., 1 tab.

Interactive analysis of systems biology molecular expression data

Directory of Open Access Journals (Sweden)

Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Analysis of Metabolites in Stem Parasitic Plant Interactions: Interaction of Cuscuta–Momordica versus Cassytha–Ipomoea

Science.gov (United States)

Furuhashi, Takeshi; Nakamura, Takemichi; Iwase, Koji

2016-01-01

Cuscuta and Cassytha are two well-known stem parasitic plant genera with reduced leaves and roots, inducing haustoria in their stems. Their similar appearance in the field has been recognized, but few comparative studies on their respective plant interactions are available. To compare their interactions, we conducted a metabolite analysis of both the Cassytha–Ipomoea and the Cuscuta–Momordica interaction. We investigated the energy charge of the metabolites by UFLC (ultra-high performance liquid chromatography), and conducted GC-MS (gas chromatography-mass spectrometry) analysis for polar metabolites (e.g., saccharides, polyols) and steroids. The energy charge after parasitization changed considerably in Cassytha but not in Cusucta. Cuscuta changed its steroid pattern during the plant interaction, whereas Cassytha did not. In the polar metabolite analysis, the laminaribiose increase after parasitization was conspicuous in Cuscuta, but not in Cassytha. This metabolite profile difference points to different lifestyles and parasitic strategies. PMID:27941603

Analysis of Metabolites in Stem Parasitic Plant Interactions: Interaction of Cuscuta–Momordica versus Cassytha–Ipomoea

Directory of Open Access Journals (Sweden)

Takeshi Furuhashi

2016-12-01

Full Text Available Cuscuta and Cassytha are two well-known stem parasitic plant genera with reduced leaves and roots, inducing haustoria in their stems. Their similar appearance in the field has been recognized, but few comparative studies on their respective plant interactions are available. To compare their interactions, we conducted a metabolite analysis of both the Cassytha–Ipomoea and the Cuscuta–Momordica interaction. We investigated the energy charge of the metabolites by UFLC (ultra-high performance liquid chromatography, and conducted GC-MS (gas chromatography-mass spectrometry analysis for polar metabolites (e.g., saccharides, polyols and steroids. The energy charge after parasitization changed considerably in Cassytha but not in Cusucta. Cuscuta changed its steroid pattern during the plant interaction, whereas Cassytha did not. In the polar metabolite analysis, the laminaribiose increase after parasitization was conspicuous in Cuscuta, but not in Cassytha. This metabolite profile difference points to different lifestyles and parasitic strategies.

Analysis of Metabolites in Stem Parasitic Plant Interactions: Interaction of Cuscuta-Momordica versus Cassytha-Ipomoea.

Science.gov (United States)

Furuhashi, Takeshi; Nakamura, Takemichi; Iwase, Koji

2016-12-07

Cuscuta and Cassytha are two well-known stem parasitic plant genera with reduced leaves and roots, inducing haustoria in their stems. Their similar appearance in the field has been recognized, but few comparative studies on their respective plant interactions are available. To compare their interactions, we conducted a metabolite analysis of both the Cassytha-Ipomoea and the Cuscuta-Momordica interaction. We investigated the energy charge of the metabolites by UFLC (ultra-high performance liquid chromatography), and conducted GC-MS (gas chromatography-mass spectrometry) analysis for polar metabolites (e.g., saccharides, polyols) and steroids. The energy charge after parasitization changed considerably in Cassytha but not in Cusucta . Cuscuta changed its steroid pattern during the plant interaction, whereas Cassytha did not. In the polar metabolite analysis, the laminaribiose increase after parasitization was conspicuous in Cuscuta , but not in Cassytha . This metabolite profile difference points to different lifestyles and parasitic strategies.

Using Social Media Sentiment Analysis for Interaction Design Choices

DEFF Research Database (Denmark)

McGuire, Mark; Kampf, Constance Elizabeth

2015-01-01

Social media analytics is an emerging skill for organizations. Currently, developers are exploring ways to create tools for simplifying social media analysis. These tools tend to focus on gathering data, and using systems to make it meaningful. However, we contend that making social media data...... meaningful is by nature a human-computer interaction problem. We examine this problem around the emerging field of sentiment analysis, exploring criteria for designing sentiment analysis systems based in Human Computer interaction, HCI. We contend that effective sentiment analysis affects audience analysis...

Soil-structure interaction analysis of ZPR6 reactor facility

International Nuclear Information System (INIS)

Ma, D.C.; Ahmed, H.U.

1981-01-01

Due to the computer storage limitation and economic concern, the current practice of soil-structure interaction analysis is limited to two dimensional analysis. The 2-D plane strain finite element program, FLUSH, is one often most used program in the analysis. Seismic response of soil and basement can be determined very well by FLUSH. The response of the structure above ground level, however, is often underestimated. This is mainly due to the three dimensional characteristics of the structures. This paper describes a detailed soil-structure interaction analysis of a rectangular embedded structure in conjunction with FLUSH program. The objective of the analysis is to derive the mean interaction motions at the structure base and the soil dynamic forces exerted on the basement lateral walls. The base motions and lateral soil dynamic forces are the specified boundary conditions for the later 3-D building response analysis. (orig./RW)

Molecular interactions involved in proton-dependent gating in KcsA potassium channels

Science.gov (United States)

Posson, David J.; Thompson, Ameer N.; McCoy, Jason G.

2013-01-01

The bacterial potassium channel KcsA is gated open by the binding of protons to amino acids on the intracellular side of the channel. We have identified, via channel mutagenesis and x-ray crystallography, two pH-sensing amino acids and a set of nearby residues involved in molecular interactions that influence gating. We found that the minimal mutation of one histidine (H25) and one glutamate (E118) near the cytoplasmic gate completely abolished pH-dependent gating. Mutation of nearby residues either alone or in pairs altered the channel’s response to pH. In addition, mutations of certain pairs of residues dramatically increased the energy barriers between the closed and open states. We proposed a Monod–Wyman–Changeux model for proton binding and pH-dependent gating in KcsA, where H25 is a “strong” sensor displaying a large shift in pKa between closed and open states, and E118 is a “weak” pH sensor. Modifying model parameters that are involved in either the intrinsic gating equilibrium or the pKa values of the pH-sensing residues was sufficient to capture the effects of all mutations. PMID:24218397

Modelization of nanospace interaction involving a ferromagnetic atom: a spin polarization effect study by thermogravimetric analysis.

Science.gov (United States)

Santhanam, K S V; Chen, Xu; Gupta, S

2014-04-01

Ab initio studies of ferromagnetic atom interacting with carbon nanotubes have been reported in the literature that predict when the interaction is strong, a higher hybridization with confinement effect will result in spin polarization in the ferromagnetic atom. The spin polarization effect on the thermal oxidation to form its oxide is modeled here for the ferromagnetic atom and its alloy, as the above studies predict the 4s electrons are polarized in the atom. The four models developed here provide a pathway for distinguishing the type of interaction that exists in the real system. The extent of spin polarization in the ferromagnetic atom has been examined by varying the amount of carbon nanotubes in the composites in the thermogravimetric experiments. In this study we report the experimental results on the CoNi alloy which appears to show selective spin polarization. The products of the thermal oxidation has been analyzed by Fourier Transform Infrared Spectroscopy.

Development of soil-structure interaction analysis method (II) - Volume 1

International Nuclear Information System (INIS)

Chang, S. P.; Ko, H. M.; Park, H. K. and others

1994-02-01

This project includes following six items : free field analysis for the determination of site input motions, impedance analysis which simplifies the effects of soil-structure interaction by using lumped parameters, soil-structure interaction analysis including the material nonlinearity of soil depending on the level of strains, strong geometric nonlinearity due to the uplifting of the base, seismic analysis of underground structure such as varied pipes, seismic analysis of liquid storage tanks. Each item contains following contents respectively : state-of-the-art review on each item and data base construction on the past researches, theoretical review on the technology of soil-structure interaction analysis, proposing preferable technology and estimating the domestic applicability, proposing guidelines for evaluation of safety and analysis scheme

PHIDIAS- Pathogen Host Interaction Data Integration and Analysis

Indian Academy of Sciences (India)

PHIDIAS- Pathogen Host Interaction Data Integration and Analysis- allows searching of integrated genome sequences, conserved domains and gene expressions data related to pathogen host interactions in high priority agents for public health and security ...

Molecular Analysis of Rice CIPKs Involved in Both Biotic and Abiotic Stress Responses

Institute of Scientific and Technical Information of China (English)

CHEN Xi-feng; Gu Zhi-min; LIU Feng; MA Bo-jun; ZHANG Hong-sheng

2011-01-01

Plant calcineurin B-like (CBL) proteins have been proposed as important Ca2+ sensors and specifically interact with CBL-interacting protein kinases (CIPKs) in plant-specific calcium signaling.Here,we identified and isolated 15 CIPK genes in a japonica rice variety Nipponbare based on the predicted sequences of rice CIPK gene family.Gene structure analysis showed that these 15 genes were divided into intron-less and intron-rich groups,and OsCIPK3 and OsCIPK24 exhibited alternative splicing in their mature process.The phylogenetic analyses indicated that rice CIPKs shared an ancestor with Arabidopsis and poplar CIPKs.Analyses of gene expression showed that these OsCIPK genes were differentially induced by biotic stresses such as bacterial blight and abiotic stresses (heavy metal such as Hg2+,high salinity,cold and ABA).Interestingly,five OsCIPK genes,OsCIPK1,2,10,11 and 12,were transcriptionally up-regulated after bacterial blight infection whereas four OsCIPK genes,OsCIPK2,10,11 and 14,were induced by all treatments,indicating that some of OsCIPK genes are involved in multiple stress response pathways in plants.Our finding suggests that CIPKs play a key role in both biotic and abiotic stress responses.

Comparative Analysis of the Interaction between Different Flavonoids and PDIA3

Directory of Open Access Journals (Sweden)

Flavia Giamogante

2016-01-01

Full Text Available Flavonoids, plant secondary metabolites present in fruits, vegetables, and products such as tea and red wine, show antioxidant, anti-inflammatory, antithrombotic, antiviral, and antitumor activity. PDIA3 is a member of the protein disulfide isomerase family mainly involved in the correct folding of newly synthetized glycoproteins. PDIA3 is associated with different human pathologies such as cancer, prion disorders, Alzheimer’s disease, and Parkinson’s diseases and it has the potential to be a pharmacological target. The interaction of different flavonoids with PDIA3 was investigated by quenching fluorescence analysis and the effects on protein activity were evaluated. A higher affinity was observed for eupatorin-5-methyl ether and eupatorin which also inhibit reductase activity of PDIA3 but do not significantly affect its DNA binding activity. The use of several flavonoids differing in chemical structure and functional groups allows us to make some consideration about the relationship between ligand structure and the affinity for PDIA3. The specific flavone backbone conformation and the degree of polarity seem to play an important role for the interaction with PDIA3. The binding site is probably similar but not equivalent to that of green tea catechins, which, as previously demonstrated, can bind to PDIA3 and prevent its interaction with DNA.

Comparative Analysis of the Interaction between Different Flavonoids and PDIA3

Science.gov (United States)

Giamogante, Flavia; Marrocco, Ilaria; Romaniello, Donatella; Eufemi, Margherita; Chichiarelli, Silvia

2016-01-01

Flavonoids, plant secondary metabolites present in fruits, vegetables, and products such as tea and red wine, show antioxidant, anti-inflammatory, antithrombotic, antiviral, and antitumor activity. PDIA3 is a member of the protein disulfide isomerase family mainly involved in the correct folding of newly synthetized glycoproteins. PDIA3 is associated with different human pathologies such as cancer, prion disorders, Alzheimer's disease, and Parkinson's diseases and it has the potential to be a pharmacological target. The interaction of different flavonoids with PDIA3 was investigated by quenching fluorescence analysis and the effects on protein activity were evaluated. A higher affinity was observed for eupatorin-5-methyl ether and eupatorin which also inhibit reductase activity of PDIA3 but do not significantly affect its DNA binding activity. The use of several flavonoids differing in chemical structure and functional groups allows us to make some consideration about the relationship between ligand structure and the affinity for PDIA3. The specific flavone backbone conformation and the degree of polarity seem to play an important role for the interaction with PDIA3. The binding site is probably similar but not equivalent to that of green tea catechins, which, as previously demonstrated, can bind to PDIA3 and prevent its interaction with DNA. PMID:28044092

Fast, Interactive Worst-Case Execution Time Analysis With Back-Annotation

DEFF Research Database (Denmark)

Harmon, Trevor; Schoeberl, Martin; Kirner, Raimund

2012-01-01

into the development cycle, requiring WCET analysis to be postponed until a final verification phase. In this paper, we propose interactive WCET analysis as a new method to provide near-instantaneous WCET feedback to the developer during software programming. We show that interactive WCET analysis is feasible using...

Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

Directory of Open Access Journals (Sweden)

Ji'an Pan

Full Text Available Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12 provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.

INTERACTION ANALYSIS AS A FEEDBACK SYSTEM IN TEACHER PREPARATION.

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AMIDON, EDMUND; POWELL, EVAN

FOUR GROUPS OF 15 STUDENT TEACHERS EACH WERE USED TO TEST THE HYPOTHESIS THAT (A) THOSE TAUGHT INTERACTION ANALYSIS WOULD BE MORE INDIRECT (ACCEPTING OF PUPIL FEELINGS AND IDEAS, ENCOURAGING, QUESTIONING) AT THE END OF STUDENT TEACHING THAN THOSE TAUGHT LEARNING THEORY, AND (B) AMONG THOSE TAUGHT INTERACTION ANALYSIS, THOSE SUPERVISED BY…

A transmembrane polar interaction is involved in the functional regulation of integrin alpha L beta 2.

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Vararattanavech, Ardcharaporn; Chng, Choon-Peng; Parthasarathy, Krupakar; Tang, Xiao-Yan; Torres, Jaume; Tan, Suet-Mien

2010-05-14

Integrins are heterodimeric transmembrane (TM) receptors formed by noncovalent associations of alpha and beta subunits. Each subunit contains a single alpha-helical TM domain. Inside-out activation of an integrin involves the separation of its cytoplasmic tails, leading to disruption of alphabeta TM packing. The leukocyte integrin alpha L beta 2 is required for leukocyte adhesion, migration, proliferation, cytotoxic function, and antigen presentation. In this study, we show by mutagenesis experiments that the packing of alpha L beta 2 TMs is consistent with that of the integrin alpha IIb beta 3 TMs. However, molecular dynamics simulations of alpha L beta 2 TMs in lipids predicted a polar interaction involving the side chains of alpha L Ser1071 and beta2 Thr686 in the outer-membrane association clasp (OMC). This is supported by carbonyl vibrational shifts observed in isotope-labeled alpha L beta 2 TM peptides that were incorporated into lipid bilayers. Molecular dynamics studies simulating the separation of alpha L beta 2 tails showed the presence of polar interaction during the initial perturbation of the inner-membrane association clasp. When the TMs underwent further separation, the polar interaction was disrupted. OMC polar interaction is important in regulating the functions of beta2 integrins because mutations that disrupt the OMC polar interaction generated constitutively activated alpha L beta 2, alpha M beta 2, and alpha X beta 2 in 293T transfectants. We also show that the expression of mutant beta2 Thr686Gly in beta2-deficient T cells rescued cell adhesion to intercellular adhesion molecule 1, but the cells showed overt elongated morphologies in response to chemokine stromal-cell-derived factor 1 alpha treatment as compared to wild-type beta2-expressing cells. These two TM polar residues are totally conserved in other members of the beta2 integrins in humans and across different species. Our results provide an example of the stabilizing effect of polar

Lay involvement in the analysis of qualitative data in health services research: a descriptive study.

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Garfield, S; Jheeta, S; Husson, F; Jacklin, A; Bischler, A; Norton, C; Franklin, B D

2016-01-01

There is a consensus that patients and the public should be involved in research in a meaningful way. However, to date, lay people have been mostly involved in developing research ideas and commenting on patient information.We previously published a paper describing our experience with lay partners conducting observations in a study of how patients in hospital are involved with their medicines. In a later part of the same study, lay partners were also involved in analysing interviews that a researcher had conducted with patients, carers and healthcare professionals about patient and carer involvement with medicines in hospital. We therefore wanted to build on our previous paper and report on our experiences with lay partners helping to conduct data analysis. We therefore interviewed the lay members and researchers involved in the analysis to find out their views.Both lay members and researchers reported that lay partners added value to the study by bringing their own perspectives and identifying further areas for the researcher to look for in the interviews. In this way researchers and lay partners were able to work together to produce a richer analysis than would have been possible from either alone. Background It is recognised that involving lay people in research in a meaningful rather than tokenistic way is both important and challenging. In this paper, we contribute to this debate by describing our experiences of lay involvement in data analysis. Methods We conducted semi-structured interviews with the lay partners and researchers involved in qualitative data analysis in a wider study of inpatient involvement in medication safety. The interviews were transcribed verbatim and coded using open thematic analysis. Results We interviewed three lay partners and the three researchers involved. These interviews demonstrated that the lay members added value to the analysis by bringing their own perspectives; these were systematically integrated into the analysis by the

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

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Venkatesha R. Hathwar

2015-09-01

Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

Proteomic analysis of Fasciola hepatica excretory and secretory products (FhESPs) involved in interacting with host PBMCs and cytokines by shotgun LC-MS/MS.

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Liu, Qing; Huang, Si-Yang; Yue, Dong-Mei; Wang, Jin-Lei; Wang, Yujian; Li, Xiangrui; Zhu, Xing-Quan

2017-02-01

Fasciola hepatica is a helminth parasite with a worldwide distribution, which can cause chronic liver disease, fasciolosis, leading to economic losses in the livestock and public health in many countries. Control is mostly reliant on the use of drugs, and as a result, drug resistance has now emerged. The identification of F. hepatica genes involved in interaction between the parasite and host immune system is utmost important to elucidate the evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, we aimed to identify molecules in F. hepatica excretory and secretory products (FhESPs) interacting with the host peripheral blood mononuclear cells (PBMCs), Th1-like cytokines (IL2 and IFN-γ), and Th17-like cytokines (IL17) by Co-IP combined with tandem mass spectrometry. The results showed that 14, 16, and 9 proteins in FhESPs could bind with IL2, IL17, and IFN-γ, respectively, which indicated that adult F. hepatica may evade the host immune responses through directly interplaying with cytokines. In addition, nine proteins in FhESPs could adhere to PBMCs. Our findings provided potential targets as immuno-regulators, and will be helpful to elucidate the molecular basis of host-parasite interactions and search for new potential proteins as vaccine and drug target candidates.

Involvement of the N-terminal part of cyclophilin B in the interaction with specific Jurkat T-cell binding sites.

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Mariller, C; Haendler, B; Allain, F; Denys, A; Spik, G

1996-07-15

Cyclophilin B (CyPB) is secreted in biological fluids such as blood or milk and binds to a specific receptor present on the human lymphoblastic cell line Jurkat and on human peripheral blood lymphocytes. This study was intended to specify the areas of CyPB that are involved in the interaction with the receptor. A synthetic peptide corresponding to the first 24 N-terminal amino acid residues of CyPB was shown to specifically recognize the receptor. Moreover, modification of Arg18 of CyPB by p-hydroxyphenlglyoxal led to a dramatic loss of affinity for the receptor. However, when this residue was replaced by an alanine residue using site-directed mutagenesis, no modification of the binding properties was found, suggesting that Arg18 is not directly involved but is sufficiently close to the interaction site to interfere with the binding when modified. Competitive binding experiments using a chimaeric protein made up of the 24 N-terminal amino acid residues of CyPB fused to the cyclophilin A core sequence confirmed the involvement of this region of CyPB in receptor binding.

Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

Energy Technology Data Exchange (ETDEWEB)

Neff, Michael M.

2011-06-23

This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

Investigation of scattering processes in quantum few-body systems involving long-range interaction by the complex-rotation method

International Nuclear Information System (INIS)

Volkov, M. V.; Elander, N.; Yakovlev, S. L.; Yarevsky, E. A.

2013-01-01

The complex-rotation method adapted to solving the multichannel scattering problem in the two-body system where the interaction potential contains the long-range Coulomb components is described. The scattering problem is reformulated as the problem of solving a nonhomogeneous Schrödinger equation in which the nonhomogeneous term involves a Coulomb potential cut off at large distances. The incident wave appearing in the nonhomogeneous term is a solution of the Schrödinger equation with longrange Coulomb interaction. This formulation is free from approximations associated with a direct cutoff of Coulomb interaction at large distances. The efficiency of this formalism is demonstrated by considering the example of solving scattering problems in the α-α and p-p systems.

A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process

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El Sawaf Gamal

2009-07-01

Full Text Available Abstract Background The E1 protein of Hepatitis C Virus (HCV can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP, and a C-terminal domain (CT comprising two segments, a pre-anchor and a trans-membrane (TM region. In the currently accepted model of the viral fusion process, the FP and the TM regions are considered to be closely juxtaposed in the post-fusion structure and their physical interaction cannot be excluded. In the present study, we took advantage of the natural sequence variability present among HCV strains to test, by purely sequence-based computational tools, the hypothesis that in this virus the fusion process involves the physical interaction of the FP and CT regions of E1. Results Two computational approaches were applied. The first one is based on the co-evolution paradigm of interacting peptides and consequently on the correlation between the distance matrices generated by the sequence alignment method applied to FP and CT primary structures, respectively. In spite of the relatively low random genetic drift between genotypes, co-evolution analysis of sequences from five HCV genotypes revealed a greater correlation between the FP and CT domains than respect to a control HCV sequence from Core protein, so giving a clear, albeit still inconclusive, support to the physical interaction hypothesis. The second approach relies upon a non-linear signal analysis method widely used in protein science called Recurrence Quantification Analysis (RQA. This method allows for a direct comparison of domains for the presence of common hydrophobicity patterns, on which the physical interaction is based upon. RQA greatly strengthened the reliability of the hypothesis by the scoring of a lot of cross-recurrences between FP and CT peptides hydrophobicity patterning largely outnumbering chance expectations and pointing to putative interaction sites. Intriguingly, mutations in the CT

Interactive Relationship between Job Involvement, Job Satisfaction, Organisational Citizenship Behaviour, and Organizational Commitment in Nigerian Universities

OpenAIRE

B.M. Nwibere

2014-01-01

The study examined the interactive relationship between job involvement, job satisfaction, organisational commitment citizenship behaviour (OCB) and organisational commitment among employees of Nigerian universities. The sample for the study consisted of two hundred and ten academic members of staff (210) from five (5) Federal Government owned universities in the Niger Delta Region of Nigeria. The study utilized both quantitative data (questionnaire) and qualitative data (interview). The Mult...

A meta-analysis of perceptual and cognitive functions involved in useful-field-of-view test performance.

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Woutersen, Karlijn; Guadron, Leslie; van den Berg, Albert V; Boonstra, F Nienke; Theelen, Thomas; Goossens, Jeroen

2017-12-01

The useful-field-of-view (UFOV) test measures the amount of information someone can extract from a visual scene in one glance. Its scores show relatively strong relationships with everyday activities. The UFOV test consists of three computer tests, suggested to measure processing speed and central vision, divided attention, and selective attention. However, other functions seem to be involved as well. In order to investigate the contribution of these suggested and other perceptual and cognitive functions, we performed a meta-analysis of 116 Pearson's correlation coefficients between UFOV scores and other test scores reported in 18 peer-reviewed articles. We divided these correlations into nine domains: attention, executive functioning, general cognition, memory, spatial ability, visual closure, contrast sensitivity, visual processing speed, and visual acuity. A multivariate mixed-effects model analysis revealed that each domain correlated significantly with each of the UFOV subtest scores. These correlations were stronger for Subtests 2 and 3 than for Subtest 1. Furthermore, some domains were more strongly correlated to the UFOV than others across subtests. We did not find interaction effects between subtest and domain, indicating that none of the UFOV subtests is more selectively sensitive to a particular domain than the others. Thus, none of the three UFOV subtests seem to measure one clear construct. Instead, a range of visual and cognitive functions is involved. Perhaps this is the reason for the UFOV's high ecological validity, as it involves many functions at once, making it harder to compensate if one of them fails.

VALIDATION OF CRACK INTERACTION LIMIT MODEL FOR PARALLEL EDGE CRACKS USING TWO-DIMENSIONAL FINITE ELEMENT ANALYSIS

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R. Daud

2013-06-01

Full Text Available Shielding interaction effects of two parallel edge cracks in finite thickness plates subjected to remote tension load is analyzed using a developed finite element analysis program. In the present study, the crack interaction limit is evaluated based on the fitness of service (FFS code, and focus is given to the weak crack interaction region as the crack interval exceeds the length of cracks (b > a. Crack interaction factors are evaluated based on stress intensity factors (SIFs for Mode I SIFs using a displacement extrapolation technique. Parametric studies involved a wide range of crack-to-width (0.05 ≤ a/W ≤ 0.5 and crack interval ratios (b/a > 1. For validation, crack interaction factors are compared with single edge crack SIFs as a state of zero interaction. Within the considered range of parameters, the proposed numerical evaluation used to predict the crack interaction factor reduces the error of existing analytical solution from 1.92% to 0.97% at higher a/W. In reference to FFS codes, the small discrepancy in the prediction of the crack interaction factor validates the reliability of the numerical model to predict crack interaction limits under shielding interaction effects. In conclusion, the numerical model gave a successful prediction in estimating the crack interaction limit, which can be used as a reference for the shielding orientation of other cracks.

Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration

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Tsvetkova, Milena; García-Gavilanes, Ruth; Yasseri, Taha

2016-11-01

Disagreement and conflict are a fact of social life. However, negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. In an attempt to understand the structural and temporal features of negative interactions in the community, we use complex network methods to analyze patterns in the timing and configuration of reverts of article edits to Wikipedia. We investigate how often and how fast pairs of reverts occur compared to a null model in order to control for patterns that are natural to the content production or are due to the internal rules of Wikipedia. Our results suggest that Wikipedia editors systematically revert the same person, revert back their reverter, and come to defend a reverted editor. We further relate these interactions to the status of the involved editors. Even though the individual reverts might not necessarily be negative social interactions, our analysis points to the existence of certain patterns of negative social dynamics within the community of editors. Some of these patterns have not been previously explored and carry implications for the knowledge collection practice conducted on Wikipedia. Our method can be applied to other large-scale temporal collaboration networks to identify the existence of negative social interactions and other social processes.

Generation and Comprehensive Analysis of an Influenza Virus Polymerase Cellular Interaction Network▿†§

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Tafforeau, Lionel; Chantier, Thibault; Pradezynski, Fabrine; Pellet, Johann; Mangeot, Philippe E.; Vidalain, Pierre-Olivier; Andre, Patrice; Rabourdin-Combe, Chantal; Lotteau, Vincent

2011-01-01

The influenza virus transcribes and replicates its genome inside the nucleus of infected cells. Both activities are performed by the viral RNA-dependent RNA polymerase that is composed of the three subunits PA, PB1, and PB2, and recent studies have shown that it requires host cell factors to transcribe and replicate the viral genome. To identify these cellular partners, we generated a comprehensive physical interaction map between each polymerase subunit and the host cellular proteome. A total of 109 human interactors were identified by yeast two-hybrid screens, whereas 90 were retrieved by literature mining. We built the FluPol interactome network composed of the influenza virus polymerase (PA, PB1, and PB2) and the nucleoprotein NP and 234 human proteins that are connected through 279 viral-cellular protein interactions. Analysis of this interactome map revealed enriched cellular functions associated with the influenza virus polymerase, including host factors involved in RNA polymerase II-dependent transcription and mRNA processing. We confirmed that eight influenza virus polymerase-interacting proteins are required for virus replication and transcriptional activity of the viral polymerase. These are involved in cellular transcription (C14orf166, COPS5, MNAT1, NMI, and POLR2A), translation (EIF3S6IP), nuclear transport (NUP54), and DNA repair (FANCG). Conversely, we identified PRKRA, which acts as an inhibitor of the viral polymerase transcriptional activity and thus is required for the cellular antiviral response. PMID:21994455

Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.

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Susan Khor

Full Text Available Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains.

Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

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Khor, Susan

2014-01-01

Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

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Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

2016-05-01

Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

Direct methods of soil-structure interaction analysis for earthquake loadings

International Nuclear Information System (INIS)

Yun, J. B.; Kim, J. M.; Kim, Y. S. and others

1993-07-01

The objectives of this study are to review the methods of soil- structure interaction system analysis, particularly the direct method, and to carry out the blind prediction analysis of the Forced Vibration Test(FVT) before backfill in the course of Hualien LSST project. The scope and contents of this study are as follows : theoretical review on soil-structure interaction analysis methods, free-field response analysis methods, modelling methods of unbounded exterior region, hualien LSST FVT blind prediction analysis before backfill. The analysis results are found to be very well compared with the field test results

Interactions involved in pH protection of the alphavirus fusion protein

Energy Technology Data Exchange (ETDEWEB)

Fields, Whitney; Kielian, Margaret, E-mail: margaret.kielian@einstein.yu.edu

2015-12-15

The alphavirus membrane protein E1 mediates low pH-triggered fusion of the viral and endosome membranes during virus entry. During virus biogenesis E1 associates as a heterodimer with the transmembrane protein p62. Late in the secretory pathway, cellular furin cleaves p62 to the mature E2 protein and a peripheral protein E3. E3 remains bound to E2 at low pH, stabilizing the heterodimer and thus protecting E1 from the acidic pH of the secretory pathway. Release of E3 at neutral pH then primes the virus for fusion during entry. Here we used site-directed mutagenesis and revertant analysis to define residues important for the interactions at the E3–E2 interface. Our data identified a key residue, E2 W235, which was required for E1 pH protection and alphavirus production. Our data also suggest additional residues on E3 and E2 that affect their interacting surfaces and thus influence the pH protection of E1 during alphavirus exit.

Long-range regulatory interactions at the 4q25 atrial fibrillation risk locus involve PITX2c and ENPEP.

Science.gov (United States)

Aguirre, Luis A; Alonso, M Eva; Badía-Careaga, Claudio; Rollán, Isabel; Arias, Cristina; Fernández-Miñán, Ana; López-Jiménez, Elena; Aránega, Amelia; Gómez-Skarmeta, José Luis; Franco, Diego; Manzanares, Miguel

2015-04-17

Recent genome-wide association studies have uncovered genomic loci that underlie an increased risk for atrial fibrillation, the major cardiac arrhythmia in humans. The most significant locus is located in a gene desert at 4q25, approximately 170 kilobases upstream of PITX2, which codes for a transcription factor involved in embryonic left-right asymmetry and cardiac development. However, how this genomic region functionally and structurally relates to PITX2 and atrial fibrillation is unknown. To characterise its function, we tested genomic fragments from 4q25 for transcriptional activity in a mouse atrial cardiomyocyte cell line and in transgenic mouse embryos, identifying a non-tissue-specific potentiator regulatory element. Chromosome conformation capture revealed that this region physically interacts with the promoter of the cardiac specific isoform of Pitx2. Surprisingly, this regulatory region also interacts with the promoter of the next neighbouring gene, Enpep, which we show to be expressed in regions of the developing mouse heart essential for cardiac electrical activity. Our data suggest that de-regulation of both PITX2 and ENPEP could contribute to an increased risk of atrial fibrillation in carriers of disease-associated variants, and show the challenges that we face in the functional analysis of genome-wide disease associations.

Using Interactive Graphics to Teach Multivariate Data Analysis to Psychology Students

Science.gov (United States)

Valero-Mora, Pedro M.; Ledesma, Ruben D.

2011-01-01

This paper discusses the use of interactive graphics to teach multivariate data analysis to Psychology students. Three techniques are explored through separate activities: parallel coordinates/boxplots; principal components/exploratory factor analysis; and cluster analysis. With interactive graphics, students may perform important parts of the…

Analysis of miRNAs Involved in Mouse Brain Damage upon Enterovirus 71 Infection.

Science.gov (United States)

Yang, Xiaoxia; Xie, Jing; Jia, Leili; Liu, Nan; Liang, Yuan; Wu, Fuli; Liang, Beibei; Li, Yongrui; Wang, Jinyan; Sheng, Chunyu; Li, Hao; Liu, Hongbo; Ma, Qiuxia; Yang, Chaojie; Du, Xinying; Qiu, Shaofu; Song, Hongbin

2017-01-01

Enterovirus 71 (EV71) infects the central nervous system (CNS) and causes brainstem encephalitis in children. MiRNAs have been found to play various functions in EV71 infection in human cell lines. To identify potential miRNAs involved in the inflammatory injury in CNS, our study, for the first time, performed a miRNA microarray assay in vivo using EV71 infected mice brains. Twenty differentially expressed miRNAs were identified (four up- and 16 down-regulated) and confirmed by qRT-PCR. The target genes of these miRNAs were analyzed using KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, revealing that the miRNAs were mainly involved in the regulation of inflammation and neural system function. MiR-150-5p, -3082-5p, -3473a, -468-3p, -669n, -721, -709, and -5107-5p that regulate MAPK and chemokine signaling were all down-regulated, which might result in increased cytokine production. In addition, miR-3473a could also regulate focal adhesion and leukocyte trans-endothelial migration, suggesting a role in virus-induced blood-brain barrier disruption. The miRNAs and pathways identified in this study could help to understand the intricate interactions between EV71 and the brain injury, offering new insight for the future research of the molecular mechanism of EV71 induced brainstem encephalitis.

Mapping Haplotype-haplotype Interactions with Adaptive LASSO

Directory of Open Access Journals (Sweden)

Li Ming

2010-08-01

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

Fluid-structure interaction analysis for pressurizer surge line subjected to thermal stratification

International Nuclear Information System (INIS)

Kang, Dong Gu; Jhung, Myung Jo; Chang, Soon Heung

2011-01-01

Research highlights: → Temperature of surge line due to stratified flow is defined using CFD analysis. → Fluid-structure interaction analysis is performed to investigate the response characteristics due to thermal stress. → Fatigue usage factors due to thermal stratification are relatively low. → Simplifying temperature distribution in surge line is not always conservative. - Abstract: Serious mechanical damages such as cracks and plastic deformations due to excessive thermal stress caused by thermal stratification have been experienced in several nuclear power plants. In particular, the thermal stratification in the pressurizer surge line has been addressed as one of the significant safety and technical issues. In this study, a detailed unsteady computational fluid dynamics (CFD) analysis involving conjugate heat transfer analysis is performed to obtain the transient temperature distributions in the wall of the pressurizer surge line subjected to stratified internal flows either during out-surge or in-surge operation. The thermal loads from CFD calculations are transferred to the structural analysis code which is employed for the thermal stress analysis to investigate the response characteristics, and the fatigue analysis is ultimately performed. In addition, the thermal stress and fatigue analysis results obtained by applying the realistic temperature distributions from CFD calculations are compared with those by assuming the simplified temperature distributions to identify some requirements for a realistic and conservative thermal stress analysis from a safety point of view.

Framework for Interactive Parallel Dataset Analysis on the Grid

Energy Technology Data Exchange (ETDEWEB)

Alexander, David A.; Ananthan, Balamurali; /Tech-X Corp.; Johnson, Tony; Serbo, Victor; /SLAC

2007-01-10

We present a framework for use at a typical Grid site to facilitate custom interactive parallel dataset analysis targeting terabyte-scale datasets of the type typically produced by large multi-institutional science experiments. We summarize the needs for interactive analysis and show a prototype solution that satisfies those needs. The solution consists of desktop client tool and a set of Web Services that allow scientists to sign onto a Grid site, compose analysis script code to carry out physics analysis on datasets, distribute the code and datasets to worker nodes, collect the results back to the client, and to construct professional-quality visualizations of the results.

Assessment of pharmacy students' communication competence using the Roter Interaction Analysis System during objective structured clinical examinations.

Science.gov (United States)

Kubota, Yoshie; Yano, Yoshitaka; Seki, Susumu; Takada, Kaori; Sakuma, Mio; Morimoto, Takeshi; Akaike, Akinori; Hiraide, Atsushi

2011-04-11

To determine the value of using the Roter Interaction Analysis System during objective structured clinical examinations (OSCEs) to assess pharmacy students' communication competence. As pharmacy students completed a clinical OSCE involving an interview with a simulated patient, 3 experts used a global rating scale to assess students' overall performance in the interview, and both the student's and patient's languages were coded using the Roter Interaction Analysis System (RIAS). The coders recorded the number of utterances (ie, units of spoken language) in each RIAS category. Correlations between the raters' scores and the number and types of utterances were examined. There was a significant correlation between students' global rating scores on the OSCE and the number of utterances in the RIAS socio-emotional category but not the RIAS business category. The RIAS proved to be a useful tool for assessing the socio-emotional aspect of students' interview skills.

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

Directory of Open Access Journals (Sweden)

Angeline S Andrew

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

Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications.

Science.gov (United States)

Hage, David S

2017-06-01

The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically related binding agent, are 2 methods that can be used to study these interactions. This review presents various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples. © 2016 American Association for Clinical Chemistry.

Glimpses into the blind spot: Social interaction and autism.

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Bottema-Beutel, Kristen

2017-07-01

A primary feature of autism spectrum disorder (ASD) is marked difficulty in social interactions. Despite the centrality of social interaction differences to the clinical presentation of ASD, only a small portion of research in this field characterizes interaction in everyday social contexts. This theoretical paper reviews the growing corpus of interactional research on ASD, including discourse analysis (DA) and conversation analysis (CA) approaches. DA and CA are micro-analytic methods aimed at understanding the organizational structure of, and actions pursued within, social encounters. These methods are aligned with enactive theories of social interaction. The bulk of current ASD research construes social interaction as involving isolated individuals who represent and/or theorize about the minds of an interlocutor. Enactive approaches posit that achieving intersubjectivity does not require theories of other minds, but instead a propensity for coordinating social actions with others. Through the complementary lenses of enactivism and interactional research, I offer an account of autistic social interaction as involving differences in interactional coordination, interactional priorities, and the enactment of meaning across conversational turns. This characterization challenges the explanatory role of cognitive processes such as Theory of Mind, and points to new avenues for conceptualizing, measuring, and supporting social interaction. Copyright © 2017 Elsevier Inc. All rights reserved.

Mother-child and father-child interaction with their 24-month-old children during feeding, considering paternal involvement and the child's temperament in a community sample.

Science.gov (United States)

Cerniglia, Luca; Cimino, Silvia; Ballarotto, Giulia

2014-01-01

The article aims to study mother-child and father-child interactions with 24-month-old children during feeding, considering the possible influence of time spent by the parent with the child, the infantile temperament, and the parental psychological profile. The families were recruited from 12 preschools in Italy (N = 77 families). Through an observation of the feeding [Scala di Valutazione dell'Interazione Alimentare (SVIA - Feeding Scale; I. Chatoor et al., ; L. Lucarelli et al., )], self-reporting [Symptom Checklist-90-Revised (SCL-90-R; L.R. Derogatis, ), and report-form questionnaires [Italian Questionnaires on Temperament (QUIT; G. Axia, )], and information provided by the parents about the amount of time spent with their children, results showed that the overall quality of father-child interactions during feeding is lower than that of mother-child interactions. Fathers showed higher psychological symptoms than did mothers. No associations were found between the fathers' psychopathological risk and the quality of interactions with their children during feeding. Mothers' psychopathological risks predicted less contingent exchanges interactions with their children during feeding. Children's temperaments significantly influence mother-child interactions, but no association exists between maternal involvement and the quality of interactions with their children. Paternal involvement predicts a better quality of father-infant interactions when associated with a child's higher scores on Social Orientation. The quality of parents' interactions with their children during feeding are impacted by different issues originating from the parent's psychological profile, the degree of involvement, and from the child's temperament. © 2014 Michigan Association for Infant Mental Health.

Complex Virus-Host Interactions Involved in the Regulation of Classical Swine Fever Virus Replication: A Minireview.

Science.gov (United States)

Li, Su; Wang, Jinghan; Yang, Qian; Naveed Anwar, Muhammad; Yu, Shaoxiong; Qiu, Hua-Ji

2017-07-05

Classical swine fever (CSF), caused by classical swine fever virus (CSFV), is one of the most devastating epizootic diseases of pigs in many countries. Viruses are small intracellular parasites and thus rely on the cellular factors for replication. Fundamental aspects of CSFV-host interactions have been well described, such as factors contributing to viral attachment, modulation of genomic replication and translation, antagonism of innate immunity, and inhibition of cell apoptosis. However, those host factors that participate in the viral entry, assembly, and release largely remain to be elucidated. In this review, we summarize recent progress in the virus-host interactions involved in the life cycle of CSFV and analyze the potential mechanisms of viral entry, assembly, and release. We conclude with future perspectives and highlight areas that require further understanding.

A typology of affordances: untangling sociomaterial interactions through video analysis

NARCIS (Netherlands)

van Osch, W.; Mendelson, O.

2011-01-01

In this study we untangle the sociomaterial interactions between developers, users, and artifacts by analyzing what types of affordances occur in the interactions between actors and artifacts in the context of group generativity. Hereto, we conducted an in-depth ethnographic and interaction analysis

Some considerations on the dynamic structure-soil-structure interactions analysis

International Nuclear Information System (INIS)

Matthees, W.

1979-01-01

A mixed method has been developed for the approximate analysis of soil-structure or structure-soil-structure interaction problems due to earthquakes. In order to produce comparable results of interaction problems as well as for shallow and for deep soils due to the same earthquake excitation (accelerogram) situated always at the lower bedrock boundary, the analysis is performed in two steps: 1) Calculation of the complex transfer function and the response of the upper interior boundary of a layered soil-system which is connected at its top to a soil-structure-system, using the one-dimensional deconvolution. 2) By making a complete interaction analysis of the surface soil-structure-system using the interior boundary excitation of the calculated response from step 1. The depth of the soil-structure-system must be chosen large enough to exclude interaction effects down to the layered soil-system's interior boundary. (orig.)

Kindergarten Children's Interactions with Touchscreen Mathematics Virtual Manipulatives: An Innovative Mixed Methods Analysis

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Tucker, Stephen I.; Lommatsch, Christina W.; Moyer-Packenham, Patricia S.; Anderson-Pence, Katie L.; Symanzik, Jürgen

2017-01-01

The purpose of this study was to examine patterns of mathematical practices evident during children's interactions with touchscreen mathematics virtual manipulatives. Researchers analyzed 33 Kindergarten children's interactions during activities involving apps featuring mathematical content of early number sense or quantity in base ten, recorded…

Interaction Analysis: Theory, Research and Application.

Science.gov (United States)

Amidon, Edmund J., Ed.; Hough, John J., Ed.

This volume of selected readings developed for students and practitioners at various levels of sophistication is intended to be representative of work done to date on interaction analysis. The contents include journal articles, papers read at professional meetings, abstracts of doctoral dissertations, and selections from larger monographs, plus 12…

Analyzing Social Interactions: Promises and Challenges of Cross Recurrence Quantification Analysis

DEFF Research Database (Denmark)

Fusaroli, Riccardo; Konvalinka, Ivana; Wallot, Sebastian

2014-01-01

The scientific investigation of social interactions presents substantial challenges: interacting agents engage each other at many different levels and timescales (motor and physiological coordination, joint attention, linguistic exchanges, etc.), often making their behaviors interdependent in non......-linear ways. In this paper we review the current use of Cross Recurrence Quantification Analysis (CRQA) in the analysis of social interactions, and assess its potential and challenges. We argue that the method can sensitively grasp the dynamics of human interactions, and that it has started producing valuable...

Integrating R and Java for Enhancing Interactivity of Algorithmic Data Analysis Software Solutions

Directory of Open Access Journals (Sweden)

Titus Felix FURTUNĂ

2016-06-01

Full Text Available Conceiving software solutions for statistical processing and algorithmic data analysis involves handling diverse data, fetched from various sources and in different formats, and presenting the results in a suggestive, tailorable manner. Our ongoing research aims to design programming technics for integrating R developing environment with Java programming language for interoperability at a source code level. The goal is to combine the intensive data processing capabilities of R programing language, along with the multitude of statistical function libraries, with the flexibility offered by Java programming language and platform, in terms of graphical user interface and mathematical function libraries. Both developing environments are multiplatform oriented, and can complement each other through interoperability. R is a comprehensive and concise programming language, benefiting from a continuously expanding and evolving set of packages for statistical analysis, developed by the open source community. While is a very efficient environment for statistical data processing, R platform lacks support for developing user friendly, interactive, graphical user interfaces (GUIs. Java on the other hand, is a high level object oriented programming language, which supports designing and developing performant and interactive frameworks for general purpose software solutions, through Java Foundation Classes, JavaFX and various graphical libraries. In this paper we treat both aspects of integration and interoperability that refer to integrating Java code into R applications, and bringing R processing sequences into Java driven software solutions. Our research has been conducted focusing on case studies concerning pattern recognition and cluster analysis.

Hot-spot analysis for drug discovery targeting protein-protein interactions.

Science.gov (United States)

Rosell, Mireia; Fernández-Recio, Juan

2018-04-01

Protein-protein interactions are important for biological processes and pathological situations, and are attractive targets for drug discovery. However, rational drug design targeting protein-protein interactions is still highly challenging. Hot-spot residues are seen as the best option to target such interactions, but their identification requires detailed structural and energetic characterization, which is only available for a tiny fraction of protein interactions. Areas covered: In this review, the authors cover a variety of computational methods that have been reported for the energetic analysis of protein-protein interfaces in search of hot-spots, and the structural modeling of protein-protein complexes by docking. This can help to rationalize the discovery of small-molecule inhibitors of protein-protein interfaces of therapeutic interest. Computational analysis and docking can help to locate the interface, molecular dynamics can be used to find suitable cavities, and hot-spot predictions can focus the search for inhibitors of protein-protein interactions. Expert opinion: A major difficulty for applying rational drug design methods to protein-protein interactions is that in the majority of cases the complex structure is not available. Fortunately, computational docking can complement experimental data. An interesting aspect to explore in the future is the integration of these strategies for targeting PPIs with large-scale mutational analysis.

Conceptual design of pipe whip restraints using interactive computer analysis

International Nuclear Information System (INIS)

Rigamonti, G.; Dainora, J.

1975-01-01

Protection against pipe break effects necessitates a complex interaction between failure mode analysis, piping layout, and structural design. Many iterations are required to finalize structural designs and equipment arrangements. The magnitude of the pipe break loads transmitted by the pipe whip restraints to structural embedments precludes the application of conservative design margins. A simplified analytical formulation of the nonlinear dynamic problems associated with pipe whip has been developed and applied using interactive computer analysis techniques. In the dynamic analysis, the restraint and the associated portion of the piping system, are modeled using the finite element lumped mass approach to properly reflect the dynamic characteristics of the piping/restraint system. The analysis is performed as a series of piecewise linear increments. Each of these linear increments is terminated by either formation of plastic conditions or closing/opening of gaps. The stiffness matrix is modified to reflect the changed stiffness characteristics of the system and re-started using the previous boundary conditions. The formation of yield hinges are related to the plastic moment of the section and unloading paths are automatically considered. The conceptual design of the piping/restraint system is performed using interactive computer analysis. The application of the simplified analytical approach with interactive computer analysis results in an order of magnitude reduction in engineering time and computer cost. (Auth.)

Types of parental involvement in CBT with anxious youth: a preliminary meta-analysis.

Science.gov (United States)

Manassis, Katharina; Lee, Trevor Changgun; Bennett, Kathryn; Zhao, Xiu Yan; Mendlowitz, Sandra; Duda, Stephanie; Saini, Michael; Wilansky, Pamela; Baer, Susan; Barrett, Paula; Bodden, Denise; Cobham, Vanessa E; Dadds, Mark R; Flannery-Schroeder, Ellen; Ginsburg, Golda; Heyne, David; Hudson, Jennifer L; Kendall, Philip C; Liber, Juliette; Masia-Warner, Carrie; Nauta, Maaike H; Rapee, Ronald M; Silverman, Wendy; Siqueland, Lynne; Spence, Susan H; Utens, Elisabeth; Wood, Jeffrey J

2014-12-01

Meta-analytic studies have not confirmed that involving parents in cognitive behavior therapy (CBT) for anxious children is therapeutically beneficial. There is also great heterogeneity in the type of parental involvement included. We investigated parental involvement focused on contingency management (CM) and transfer of control (TC) as a potential outcome moderator using a meta-analysis with individual patient data. Investigators of randomized controlled trials (RCTs) of CBT for anxious children, identified systematically, were invited to submit their data. Conditions in each RCT were coded based on type of parental involvement in CBT (i.e., low involvement, active involvement without emphasis on CM or TC, active involvement with emphasis on CM or TC). Treatment outcomes were compared using a 1-stage meta-analysis. All cases involved in active treatment (894 of 1,618) were included for subgroup analyses. Across all CBT groups, means of clinical severity, anxiety, and internalizing symptoms significantly decreased posttreatment and were comparable across groups. The group without emphasis on CM or TC showed a higher proportion with posttreatment anxiety diagnoses than the low-involvement group. Between posttreatment and 1-year follow-up, the proportion with anxiety diagnoses significantly decreased in CBT with active parental involvement with emphasis on CM or TC, whereas treatment gains were merely maintained in the other 2 groups. CBT for anxious children is an effective treatment with or without active parental involvement. However, CBT with active parental involvement emphasizing CM or TC may support long-term maintenance of treatment gains. RESULTS should be replicated as additional RCTs are published.

Using a specific RNA-protein interaction to quench the fluorescent RNA Spinach

NARCIS (Netherlands)

Roszyk, Laura; Kollenda, Sebastian; Hennig, Sven

2017-01-01

RNAs are involved in interaction networks with other biomolecules and are crucial for proper cell function. Yet, their biochemical analysis remains challenging. For Förster Resonance Energy Transfer (FRET), a common tool to study such interaction networks, two interacting molecules have to be

Network Graph Analysis of Gene-Gene Interactions in Genome-Wide Association Study Data

Directory of Open Access Journals (Sweden)

Sungyoung Lee

2012-12-01

Full Text Available Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs. For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR is one of the powerful and efficient methods for detecting high-order gene-gene (GxG interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI. Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.

Network graph analysis of gene-gene interactions in genome-wide association study data.

Science.gov (United States)

Lee, Sungyoung; Kwon, Min-Seok; Park, Taesung

2012-12-01

Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR) is one of the powerful and efficient methods for detecting high-order gene-gene (GxG) interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE) data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI). Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.

Pathogenesis of helicobacter pylori infection involves interaction ...

African Journals Online (AJOL)

It is now clear that both bacterial virulence factors and host susceptibility play key roles in disease pathogenesis. The nature and levels of these interactions between these major factors has been found to determine the spectrum of clinical outcomes of the infection with this important bacterium. Virulence factors include the ...

Proteome analysis of interaction between rootstocks and scions in ...

African Journals Online (AJOL)

The main propagation method of rubber tree (Hevea brasiliensis Muell. Arg.) is by grafting. However, the molecular mechanism underlying rootstock-scion interactions remains poorly understood. Identification and analysis of proteins related to rootstock-scion interactions are the bases of clarifying the molecular mechanism ...

Relational interaction in occupational therapy: Conversation analysis of positive feedback.

Science.gov (United States)

Weiste, Elina

2018-01-01

The therapeutic relationship is an important factor for good therapy outcomes. The primary mediator of a beneficial therapy relationship is clinician-client interaction. However, few studies identify the observable interactional attributes of good quality relational interactions, e.g. offering the client positive feedback. The present paper aims to expand current understanding of relational interaction by analyzing the real-time interactional practices therapists use for offering positive feedback, an important value in occupational therapy. The analysis is based on the conversation analysis of 15 video-recorded occupational therapy encounters in psychiatric outpatient clinics. Two types of positive feedback were identified. In aligning feedback, therapists encouraged and complimented clients' positive perspectives on their own achievements in adopting certain behaviour, encouraging and supporting their progress. In redirecting feedback, therapists shifted the perspective from clients' negative experiences to their positive experiences. This shift was interactionally successful if they laid the foundation for the shift in perspective and attuned their expressions to the clients' emotional states. Occupational therapists routinely provide their clients with positive feedback. Awareness of the interactional attributes related to positive feedback is critically important for successful relational interaction.

Informational analysis involving application of complex information system

Science.gov (United States)

Ciupak, Clébia; Vanti, Adolfo Alberto; Balloni, Antonio José; Espin, Rafael

The aim of the present research is performing an informal analysis for internal audit involving the application of complex information system based on fuzzy logic. The same has been applied in internal audit involving the integration of the accounting field into the information systems field. The technological advancements can provide improvements to the work performed by the internal audit. Thus we aim to find, in the complex information systems, priorities for the work of internal audit of a high importance Private Institution of Higher Education. The applied method is quali-quantitative, as from the definition of strategic linguistic variables it was possible to transform them into quantitative with the matrix intersection. By means of a case study, where data were collected via interview with the Administrative Pro-Rector, who takes part at the elaboration of the strategic planning of the institution, it was possible to infer analysis concerning points which must be prioritized at the internal audit work. We emphasize that the priorities were identified when processed in a system (of academic use). From the study we can conclude that, starting from these information systems, audit can identify priorities on its work program. Along with plans and strategic objectives of the enterprise, the internal auditor can define operational procedures to work in favor of the attainment of the objectives of the organization.

The interaction of NDE and failure analysis

International Nuclear Information System (INIS)

Nichols, R.W.

1988-01-01

This paper deals with the use of Non-Destructive Examination (NDE) and failure analysis for the assessment of the structural integrity. It appears that failure analysis enables to know whether NDE is required or not, and can help to direct NDE into the most useful directions by identifying the areas where it is most important that defects are absent. It also appears that failure analysis can help the operator to decide which NDE method is best suited to the component studied and provides detailed specifications for this NDE method. The interaction between failure analysis and NDE is then described. (TEC)

The interaction of NDE and failure analysis

Energy Technology Data Exchange (ETDEWEB)

Nichols, R W

1988-12-31

This paper deals with the use of Non-Destructive Examination (NDE) and failure analysis for the assessment of the structural integrity. It appears that failure analysis enables to know whether NDE is required or not, and can help to direct NDE into the most useful directions by identifying the areas where it is most important that defects are absent. It also appears that failure analysis can help the operator to decide which NDE method is best suited to the component studied and provides detailed specifications for this NDE method. The interaction between failure analysis and NDE is then described. (TEC).

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

Science.gov (United States)

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.

A Meta-analysis of the Effectiveness of Interactive Middle School Cannabis Prevention Programs.

Science.gov (United States)

Lize, Steven E; Iachini, Aidyn L; Tang, Weizhou; Tucker, Joshua; Seay, Kristen D; Clone, Stephanie; DeHart, Dana; Browne, Teri

2017-01-01

This meta-analysis examines the effectiveness of interactive middle school-based drug prevention programs on adolescent cannabis use in North America, as well as program characteristics that could moderate these effects. Interactive programs, compared to more didactic, lecture style programs, involve participants in skill-building activities and focus on interaction among participants. A systematic literature search was conducted for English-language studies from January 1998 to March 2014. Studies included evaluations using random assignment or a quasi-experimental design of interactive school-based substance use prevention programs delivered to adolescents (aged 12-14) in North American middle schools (grades 6-8). Data were extracted using a coding protocol. The outcomes of interest were post-treatment cannabis use, intent to use, and refusal skills compared across intervention and control groups. Effect sizes (Cohen's d) were calculated from continuous measures, and dichotomous measures were converted to the d index. A total of 30 studies yielding 23 independent samples were included. The random effects pooled effect size for cannabis use (k = 21) was small ([Formula: see text]= -0.07, p prevention programs. The pooled effect sizes for intention to use (k = 3) and refusal skills (k = 3) were not significant. Moderator analyses indicated significant differences in program effectiveness between instructor types, with teachers found to be most effective ([Formula: see text]= -0.08, p = 0.02). The findings provide further support for the use of interactive school-based programs to prevent cannabis use among middle school students in North America.

Descriptive analysis of the verbal behavior of a therapist: a known-group validity analysis of the putative behavioral functions involved in clinical interaction.

Science.gov (United States)

Virues-Ortega, Javier; Montaño-Fidalgo, Montserrat; Froján-Parga, María Xesús; Calero-Elvira, Ana

2011-12-01

This study analyzes the interobserver agreement and hypothesis-based known-group validity of the Therapist's Verbal Behavior Category System (SISC-INTER). The SISC-INTER is a behavioral observation protocol comprised of a set of verbal categories representing putative behavioral functions of the in-session verbal behavior of a therapist (e.g., discriminative, reinforcing, punishing, and motivational operations). The complete therapeutic process of a clinical case of an individual with marital problems was recorded (10 sessions, 8 hours), and data were arranged in a temporal sequence using 10-min periods. Hypotheses based on the expected performance of the putative behavioral functions portrayed by the SISC-INTER codes across prevalent clinical activities (i.e., assessing, explaining, Socratic method, providing clinical guidance) were tested using autoregressive integrated moving average (ARIMA) models. Known-group validity analyses provided support to all hypotheses. The SISC-INTER may be a useful tool to describe therapist-client interaction in operant terms. The utility of reliable and valid protocols for the descriptive analysis of clinical practice in terms of verbal behavior is discussed. Copyright © 2011. Published by Elsevier Ltd.

Time-domain soil-structure interaction analysis of nuclear facilities

International Nuclear Information System (INIS)

Coleman, Justin L.; Bolisetti, Chandrakanth; Whittaker, Andrew S.

2016-01-01

The Nuclear Regulatory Commission (NRC) regulation 10 CFR Part 50 Appendix S requires consideration of soil-structure interaction (SSI) in nuclear power plant (NPP) analysis and design. Soil-structure interaction analysis for NPPs is routinely carried out using guidance provided in the ASCE Standard 4-98 titled “Seismic Analysis of Safety-Related Nuclear Structures and Commentary”. This Standard, which is currently under revision, provides guidance on linear seismic soil-structure-interaction (SSI) analysis of nuclear facilities using deterministic and probabilistic methods. A new appendix has been added to the forthcoming edition of ASCE Standard 4 to provide guidance for time-domain, nonlinear SSI (NLSSI) analysis. Nonlinear SSI analysis will be needed to simulate material nonlinearity in soil and/or structure, static and dynamic soil pressure effects on deeply embedded structures, local soil failure at the foundation-soil interface, nonlinear coupling of soil and pore fluid, uplift or sliding of the foundation, nonlinear effects of gaps between the surrounding soil and the embedded structure and seismic isolation systems, none of which can be addressed explicitly at present. Appendix B of ASCE Standard 4 provides general guidance for NLSSI analysis but will not provide a methodology for performing the analysis. This paper provides a description of an NLSSI methodology developed for application to nuclear facilities, including NPPs. This methodology is described as series of sequential steps to produce reasonable results using any time-domain numerical code. These steps require some numerical capabilities, such as nonlinear soil constitutive models, which are also described in the paper.

Customer involvement in greening the supply chain: an interpretive structural modeling methodology

Science.gov (United States)

Kumar, Sanjay; Luthra, Sunil; Haleem, Abid

2013-04-01

The role of customers in green supply chain management needs to be identified and recognized as an important research area. This paper is an attempt to explore the involvement aspect of customers towards greening of the supply chain (SC). An empirical research approach has been used to collect primary data to rank different variables for effective customer involvement in green concept implementation in SC. An interpretive structural-based model has been presented, and variables have been classified using matrice d' impacts croises- multiplication appliqué a un classement analysis. Contextual relationships among variables have been established using experts' opinions. The research may help practicing managers to understand the interaction among variables affecting customer involvement. Further, this understanding may be helpful in framing the policies and strategies to green SC. Analyzing interaction among variables for effective customer involvement in greening SC to develop the structural model in the Indian perspective is an effort towards promoting environment consciousness.

An analysis pipeline for the inference of protein-protein interaction networks

Energy Technology Data Exchange (ETDEWEB)

Taylor, Ronald C.; Singhal, Mudita; Daly, Don S.; Gilmore, Jason M.; Cannon, William R.; Domico, Kelly O.; White, Amanda M.; Auberry, Deanna L.; Auberry, Kenneth J.; Hooker, Brian S.; Hurst, G. B.; McDermott, Jason E.; McDonald, W. H.; Pelletier, Dale A.; Schmoyer, Denise A.; Wiley, H. S.

2009-12-01

An analysis pipeline has been created for deployment of a novel algorithm, the Bayesian Estimator of Protein-Protein Association Probabilities (BEPro), for use in the reconstruction of protein-protein interaction networks. We have combined the Software Environment for BIological Network Inference (SEBINI), an interactive environment for the deployment and testing of network inference algorithms that use high-throughput data, and the Collective Analysis of Biological Interaction Networks (CABIN), software that allows integration and analysis of protein-protein interaction and gene-to-gene regulatory evidence obtained from multiple sources, to allow interactions computed by BEPro to be stored, visualized, and further analyzed. Incorporating BEPro into SEBINI and automatically feeding the resulting inferred network into CABIN, we have created a structured workflow for protein-protein network inference and supplemental analysis from sets of mass spectrometry bait-prey experiment data. SEBINI demo site: https://www.emsl.pnl.gov /SEBINI/ Contact: ronald.taylor@pnl.gov. BEPro is available at http://www.pnl.gov/statistics/BEPro3/index.htm. Contact: ds.daly@pnl.gov. CABIN is available at http://www.sysbio.org/dataresources/cabin.stm. Contact: mudita.singhal@pnl.gov.

Quantitative Analysis of Tau-Microtubule Interaction Using FRET

Directory of Open Access Journals (Sweden)

Isabelle L. Di Maïo

2014-08-01

Full Text Available The interaction between the microtubule associated protein, tau and the microtubules is investigated. A fluorescence resonance energy transfer (FRET assay was used to determine the distance separating tau to the microtubule wall, as well as the binding parameters of the interaction. By using microtubules stabilized with Flutax-2 as donor and tau labeled with rhodamine as acceptor, a donor-to-acceptor distance of 54 ± 1 Å was found. A molecular model is proposed in which Flutax-2 is directly accessible to tau-rhodamine molecules for energy transfer. By titration, we calculated the stoichiometric dissociation constant to be equal to 1.0 ± 0.5 µM. The influence of the C-terminal tails of αβ-tubulin on the tau-microtubule interaction is presented once a procedure to form homogeneous solution of cleaved tubulin has been determined. The results indicate that the C-terminal tails of α- and β-tubulin by electrostatic effects and of recruitment seem to be involved in the binding mechanism of tau.

Vehicle systems: coupled and interactive dynamics analysis

Science.gov (United States)

Vantsevich, Vladimir V.

2014-11-01

This article formulates a new direction in vehicle dynamics, described as coupled and interactive vehicle system dynamics. Formalised procedures and analysis of case studies are presented. An analytical consideration, which explains the physics of coupled system dynamics and its consequences for dynamics of a vehicle, is given for several sets of systems including: (i) driveline and suspension of a 6×6 truck, (ii) a brake mechanism and a limited slip differential of a drive axle and (iii) a 4×4 vehicle steering system and driveline system. The article introduces a formal procedure to turn coupled system dynamics into interactive dynamics of systems. A new research direction in interactive dynamics of an active steering and a hybrid-electric power transmitting unit is presented and analysed to control power distribution between the drive axles of a 4×4 vehicle. A control strategy integrates energy efficiency and lateral dynamics by decoupling dynamics of the two systems thus forming their interactive dynamics.

Substructure method of soil-structure interaction analysis for earthquake loadings

Energy Technology Data Exchange (ETDEWEB)

Park, H. G.; Joe, Y. H. [Industrial Development Research Center, Univ. of Incheon, Incheon (Korea, Republic of)

1997-07-15

Substructure method has been preferably adopted for soil-structure interaction analysis because of its simplicity and economy in practical application. However, substructure method has some limitation in application and does not always give reliable results especially for embedded structures or layered soil conditions. The objective of this study to validate the reliability of the soil-structure interaction analysis results by the proposed substructure method using lumped-parameter model and suggest a method of seismic design of nuclear power plant structures with specific design conditions. In this study, theoretic background and modeling technique of soil-structure interaction phenomenon have been reviewed and an analysis technique based on substructure method using lumped-parameter model has been suggested. The practicality and reliability of the proposed method have been validated through the application of the method to the seismic analysis of the large-scale seismic test models. A technical guide for practical application and evaluation of the proposed method have been also provided through the various type parametric.

Diffraction stress analysis of thin films; investigating elastic grain interaction

International Nuclear Information System (INIS)

Kumar, A.

2005-12-01

This work is dedicated to the investigation of specimens exhibiting anisotropic microstructures (and thus macroscopic elastic anisotropy) and/or inhomogeneous microstructures, as met near surfaces and in textured materials. The following aspects are covered: (i) Analysis of specimens with direction-dependent (anisotropic) elastic grain-interaction. Elastic grain-interaction determines the distribution of stresses and strains over the (crystallographically) differently oriented grains of a mechanically stressed polycrystal and the mechanical and diffraction (X-ray) elastic constants (relating (diffraction) lattice strains to mechanical stresses). Grain interaction models that allow for anisotropic, direction-dependent grain interaction have been developed very recently. The notion 'direction-dependent' grain-interaction signifies that different grain-interaction constraints prevail along different directions in a specimen. Practical examples of direction-dependent grain interaction are the occurrence of surface anisotropy in thin films and the surface regions of bulk polycrystals and the occurrence of grain-shape (morphological) texture. In this work, for the first time, stress analyses of thin films have been performed on the basis of these newly developed grain-interaction models. It has also been demonstrated that the identification of the (dominant) source of direction-dependent grain interaction is possible. The results for the grain interaction have been discussed in the light of microstructural investigations of the specimens by microscopic techniques. (ii) Analysis of specimens with depth gradients: Diffraction stress analysis can be hindered if gradients of the stress state, the composition or the microstructure occur in the specimen under investigation, as the so-called information depth varies in the course of a traditional stress measurement: Ambiguous results are thus generally obtained. In this work, a strategy for stress measurements at fixed

Seasonal phenology of interactions involving short-lived annual plants, a multivoltine herbivore and its endoparasitoid wasp.

Science.gov (United States)

Fei, Minghui; Gols, Rieta; Harvey, Jeffrey A

2014-01-01

Spatial-temporal realism is often missing in many studies of multitrophic interactions, which are conducted at a single time frame and/or involving interactions between insects with a single species of plant. In this scenario, an underlying assumption is that the host-plant species is ubiquitous throughout the season and that the insects always interact with it. We studied interactions involving three naturally occurring wild species of cruciferous plants, Brassica rapa, Sinapis arvensis and Brassica nigra, that exhibit different seasonal phenologies, and a multivoltine herbivore, the large cabbage white butterfly, Pieris brassicae, and its gregarious endoparasitoid wasp, Cotesia glomerata. The three plants have very short life cycles. In central Europe, B. rapa grows in early spring, S. arvensis in late spring and early summer, and B. nigra in mid to late summer. P. brassicae generally has three generations per year, and C. glomerata at least two. This means that different generations of the insects must find and exploit different plant species that may differ in quality and which may be found some distance from one another. Insects were either reared on each of the three plant species for three successive generations or shifted between generations from B. rapa to S. arvensis to B. nigra. Development time from neonate to pupation and pupal fresh mass were determined in P. brassicae and egg-to-adult development time and body mass in C. glomerata. Overall, herbivores performed marginally better on S. arvensis and B. nigra plants than on B. rapa plants. Parasitoids performance was closely tailored with that of the host. Irrespective as to whether the insects were shifted to a new plant in successive generations or not, development time of P. brassicae and C. glomerata decreased dramatically over time. Our results show that there were some differences in insect development on different plant species and when transferred from one species to another. However, all three

PHIDIAS: a pathogen-host interaction data integration and analysis system

OpenAIRE

Xiang, Zuoshuang; Tian, Yuying; He, Yongqun

2007-01-01

The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database system that serves as a centralized source to search, compare, and analyze integrated genome sequences, conserved domains, and gene expression data related to pathogen-host interactions (PHIs) for pathogen species designated as high priority agents for public health and biological security. In addition, PHIDIAS allows submission, search and analysis of PHI genes and molecular networks curated ...

User involvement competence for radical innovation

DEFF Research Database (Denmark)

Lettl, Christopher

2007-01-01

-assisted navigation systems. The case study analysis reveals that firms who closely interact with specific users benefit significantly for their radical innovation work. These users have a high motivation toward new solutions, are open to new technologies, possess diverse competencies, and are embedded into a very......One important market related capability for firms which seek to develop radical innovations is the competence to involve the 'right' users at the 'right' time in the 'right' form. While former studies have identified a rather passive role of users in the radical innovation process, this paper...

User involvement competence for radical innovation

DEFF Research Database (Denmark)

Lettl, Christopher

2007-01-01

One important market related capability for firms which seek to develop radical innovations is the competence to involve the 'right' users at the 'right' time in the 'right' form. While former studies have identified a rather passive role of users in the radical innovation process, this paper......-assisted navigation systems. The case study analysis reveals that firms who closely interact with specific users benefit significantly for their radical innovation work. These users have a high motivation toward new solutions, are open to new technologies, possess diverse competencies, and are embedded into a very...

Elevated level of human RPA interacting protein α (hRIPα) in cervical tumor cells is involved in cell proliferation through regulating RPA transport.

Science.gov (United States)

Namkoong, Sim; Lee, Eun-Ju; Jang, Ik-Soon; Park, Junsoo

2012-10-19

Replication protein A (RPA) is a eukaryotic single-stranded DNA binding protein that is essential for DNA replication, repair, and recombination, and human RPA interacting protein α (hRIPα) is the nuclear transporter of RPA. Here, we report the regulatory role of hRIPα protein in cell proliferation. Western blot analysis revealed that the level of hRIPα was frequently elevated in cervical tumors tissues and hRIPα knockdown by siRNA inhibited cellular proliferation through deregulation of the cell cycle. In addition, overexpression of hRIPα resulted in increased clonogenicity. These results indicate that hRIPα is involved in cell proliferation through regulation of RPA transport. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Integrated analysis of core debris interactions and their effects on containment integrity using the CONTAIN computer code

International Nuclear Information System (INIS)

Carroll, D.E.; Bergeron, K.D.; Williams, D.C.; Tills, J.L.; Valdez, G.D.

1987-01-01

The CONTAIN computer code includes a versatile system of phenomenological models for analyzing the physical, chemical and radiological conditions inside the containment building during severe reactor accidents. Important contributors to these conditions are the interactions which may occur between released corium and cavity concrete. The phenomena associated with interactions between ejected corium debris and the containment atmosphere (Direct Containment Heating or DCH) also pose a potential threat to containment integrity. In this paper, we describe recent enhancements of the CONTAIN code which allow an integrated analysis of these effects in the presence of other mitigating or aggravating physical processes. In particular, the recent inclusion of the CORCON and VANESA models is described and a calculation example presented. With this capability CONTAIN can model core-concrete interactions occurring simultaneously in multiple compartments and can couple the aerosols thereby generated to the mechanistic description of all atmospheric aerosol components. Also discussed are some recent results of modeling the phenomena involved in Direct Containment Heating. (orig.)

Enhancing the discussion of alternatives in EIA using principle component analysis leads to improved public involvement

International Nuclear Information System (INIS)

Kamijo, Tetsuya; Huang, Guangwei

2017-01-01

The purpose of this study is to show the effectiveness of principle component analysis (PCA) as a method of alternatives analysis useful for improving the discussion of alternatives and public involvement. This study examined public consultations by applying quantitative text analysis (QTA) to the minutes of meetings and showed a positive correlation between the discussion of alternatives and the sense of public involvement. The discussion of alternatives may improve public involvement. A table of multiple criteria analysis for alternatives with detailed scores may exclude the public from involvement due to the general public's limited capacity to understand the mathematical algorithm and to process too much information. PCA allowed for the reduction of multiple criteria down to a small number of uncorrelated variables (principle components), a display of the merits and demerits of the alternatives, and potentially made the identification of preferable alternatives by the stakeholders easier. PCA is likely to enhance the discussion of alternatives and as a result, lead to improved public involvement.

Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

Science.gov (United States)

Goel, Parul; Bhuria, Monika; Kaushal, Mamta

2016-01-01

In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C) and Nitrogen (N) are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source) on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N), C source alone (+Suc-N), with N and C source (+Suc+N) or without N and C source (-Suc-N). Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8) in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2) in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen. PMID:27637072

Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

Directory of Open Access Journals (Sweden)

Parul Goel

Full Text Available In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C and Nitrogen (N are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N, C source alone (+Suc-N, with N and C source (+Suc+N or without N and C source (-Suc-N. Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8 in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2 in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen.

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

Directory of Open Access Journals (Sweden)

Wang Kai

2011-05-01

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

Service user involvement in mental health care: an evolutionary concept analysis.

Science.gov (United States)

Millar, Samantha L; Chambers, Mary; Giles, Melanie

2016-04-01

The concept of service user involvement is an evolving concept in the mental health-care literature. This study sought to explore and analyse the concept of service user involvement as used in within the field of mental health care. An evolutionary concept analysis was conducted using a literature-based sample extracted from an electronic database search. One hundred and thirty-four papers met the inclusion criteria and were analysed to discover key attributes, antecedents and consequences of service user involvement and to produce a definition of the concept. Five key attributes of service user involvement within the context of mental health care were identified: a person-centred approach, informed decision making, advocacy, obtaining service user views and feedback and working in partnership. Clarity of the attributes and definition of the concept of service user involvement aims to promote understanding of the concept among key stakeholders including mental health professionals, service users and community and voluntary organizations. The findings of the research have utility in the areas of theory and policy development, research on service user involvement in mental health care and service user involvement in mental health practice. Directions for further research regarding the concept are identified. © 2015 John Wiley & Sons Ltd.

DyNet: visualization and analysis of dynamic molecular interaction networks.

Science.gov (United States)

Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J

2016-09-01

: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Low-dimensional analysis, using POD, for two mixing layer-wake interactions

International Nuclear Information System (INIS)

Braud, Caroline; Heitz, Dominique; Arroyo, Georges; Perret, Laurent; Delville, Joeel; Bonnet, Jean-Paul

2004-01-01

The mixing layer-wake interaction is studied experimentally in the framework of two flow configurations. For the first one, the initial conditions of the mixing layer are modified by using a thick trailing edge, a wake effect is therefore superimposed to the mixing layer from its beginning (blunt trailing edge). In the second flow configuration, a canonical mixing layer is perturbed in its asymptotic region by the wake of a cylinder arranged perpendicular to the plane of the mixing layer. These interactions are analyzed mainly by using two-point velocity correlations and the proper orthogonal decomposition (POD). These two flow configurations differ by the degree of complexity they involve: the former is mainly 2D while the latter is highly 3D. The blunt trailing edge configuration is analyzed by using rakes of hot wire probes. This flow configuration is found to be considerably different when compared to a conventional mixing layer. It appears in particular that the scale of the large structures depends only on the trailing edge thickness and does not grow in its downstream evolution. A criterion, based on POD, is proposed in order to separate wake-mixing layer dominant areas of the downstream evolution of the flow. The complex 3D dynamical behaviour resulting from the interaction between the canonical plane mixing layer and the wake of a cylinder is investigated using data arising from particle image velocimetry measurements. An analysis of the velocity correlations shows different length scales in the regions dominated by wake like structures and shear layer type structures. In order to characterize the particular organization in the plane of symmetry, a POD-Galerkin projection of the Navier-Stokes equations is performed in this plane. This leads to a low-dimensional dynamical system that allows the analysis of the relationship between the dominant frequencies to be performed. A reconstruction of the dominant periodic motion suspected from previous studies is

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

Science.gov (United States)

Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

2014-12-12

Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.

Directory of Open Access Journals (Sweden)

Joyce E Loper

2012-07-01

Full Text Available We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring

Sensitivity analysis: Interaction of DOE SNF and packaging materials

International Nuclear Information System (INIS)

Anderson, P.A.; Kirkham, R.J.; Shaber, E.L.

1999-01-01

A sensitivity analysis was conducted to evaluate the technical issues pertaining to possible destructive interactions between spent nuclear fuels (SNFs) and the stainless steel canisters. When issues are identified through such an analysis, they provide the technical basis for answering what if questions and, if needed, for conducting additional analyses, testing, or other efforts to resolve them in order to base the licensing on solid technical grounds. The analysis reported herein systematically assessed the chemical and physical properties and the potential interactions of the materials that comprise typical US Department of Energy (DOE) SNFs and the stainless steel canisters in which they will be stored, transported, and placed in a geologic repository for final disposition. The primary focus in each step of the analysis was to identify any possible phenomena that could potentially compromise the structural integrity of the canisters and to assess their thermodynamic feasibility

CLASSROOM INTERACTION ANALYSIS IN INDONESIAN EFL SPEAKING CLASS

OpenAIRE

Sinta Hoerun Nisa

2014-01-01

This study entitles “Classroom Interaction Analysis in the EFL Speaking Class” aimed at analyzing the categories of teacher talk, student talk and classroom interaction types used during EFL speaking class. The research employed a qualitative design and applied a case study. Subjects of the research were an English teacher and 25 students at the second semester of English Education Department of the University of Kuningan. The data were gained through naturalistic observation and document ana...

A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

Directory of Open Access Journals (Sweden)

Rajani Rai

2015-11-01

Full Text Available Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR and Classification and Regression Tree Analysis (CRT to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634; FAS (rs2234767; FASL (rs763110; DCC (rs2229080, rs4078288, rs7504990, rs714; PSCA (rs2294008, rs2978974; ADRA2A (rs1801253; ADRB1 (rs1800544; ADRB3 (rs4994; CYP17 (rs2486758 involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634, DCC (rs714, rs2229080, rs4078288 and ADRB3 (rs4994 polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994 to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10 or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10. Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

Analysis of brand personality to involve event involvement and loyalty: A case study of Jakarta Fashion Week 2017

Science.gov (United States)

Nasution, A. H.; Rachmawan, Y. A.

2018-04-01

Fashion trend in the world changed extremely fast. Fashion has become the one of people’s lifestyle in the world. Fashion week events in several areas can be a measurement of fahion trend nowadays. There was a fashion week event in Indonesia called Jakarta Fashion Week (JFW) aims to show fashion trend to people who want to improve their fashion style. People will join some events if the event has involvement to them, hence they will come to that event again and again. Annually and continuously event is really important to create loyalty among people who are involved in it, in order to increase positive development towards the organizer in organizing the next event. Saving a huge amount from the marketing budget, and creating a higher quality event. This study aims to know the effect of 5 brand personality dimension to event involvement and loyalty in Jakarta Fashion Week (JFW). This study use quantitative confirmative method with Structural Equation Model (SEM) analysis technique. The sample of this study is 150 respondents who became a participant of Jakarta Fashion Week 2017. Result show that there was significant effect of 5 brand personality dimension to 3 dimension of event involvement and loyalty. Meanwhile, there was one dimension of event involvement called personal self-expression that has not effect to loyalty.

Quantitative analysis of protein-ligand interactions by NMR.

Science.gov (United States)

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

Musical Imagery Involves Wernicke's Area in Bilateral and Anti-Correlated Network Interactions in Musicians.

Science.gov (United States)

Zhang, Yizhen; Chen, Gang; Wen, Haiguang; Lu, Kun-Han; Liu, Zhongming

2017-12-06

Musical imagery is the human experience of imagining music without actually hearing it. The neural basis of this mental ability is unclear, especially for musicians capable of engaging in accurate and vivid musical imagery. Here, we created a visualization of an 8-minute symphony as a silent movie and used it as real-time cue for musicians to continuously imagine the music for repeated and synchronized sessions during functional magnetic resonance imaging (fMRI). The activations and networks evoked by musical imagery were compared with those elicited by the subjects directly listening to the same music. Musical imagery and musical perception resulted in overlapping activations at the anterolateral belt and Wernicke's area, where the responses were correlated with the auditory features of the music. Whereas Wernicke's area interacted within the intrinsic auditory network during musical perception, it was involved in much more complex networks during musical imagery, showing positive correlations with the dorsal attention network and the motor-control network and negative correlations with the default-mode network. Our results highlight the important role of Wernicke's area in forming vivid musical imagery through bilateral and anti-correlated network interactions, challenging the conventional view of segregated and lateralized processing of music versus language.

Taylor Dispersion Analysis as a promising tool for assessment of peptide-peptide interactions.

Science.gov (United States)

Høgstedt, Ulrich B; Schwach, Grégoire; van de Weert, Marco; Østergaard, Jesper

2016-10-10

Protein-protein and peptide-peptide (self-)interactions are of key importance in understanding the physiochemical behavior of proteins and peptides in solution. However, due to the small size of peptide molecules, characterization of these interactions is more challenging than for proteins. In this work, we show that protein-protein and peptide-peptide interactions can advantageously be investigated by measurement of the diffusion coefficient using Taylor Dispersion Analysis. Through comparison to Dynamic Light Scattering it was shown that Taylor Dispersion Analysis is well suited for the characterization of protein-protein interactions of solutions of α-lactalbumin and human serum albumin. The peptide-peptide interactions of three selected peptides were then investigated in a concentration range spanning from 0.5mg/ml up to 80mg/ml using Taylor Dispersion Analysis. The peptide-peptide interactions determination indicated that multibody interactions significantly affect the PPIs at concentration levels above 25mg/ml for the two charged peptides. Relative viscosity measurements, performed using the capillary based setup applied for Taylor Dispersion Analysis, showed that the viscosity of the peptide solutions increased with concentration. Our results indicate that a viscosity difference between run buffer and sample in Taylor Dispersion Analysis may result in overestimation of the measured diffusion coefficient. Thus, Taylor Dispersion Analysis provides a practical, but as yet primarily qualitative, approach to assessment of the colloidal stability of both peptide and protein formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Conversation analysis as a method for investigating interaction in care home environments.

Science.gov (United States)

Chatwin, John

2014-11-01

This article gives an outline of how the socio-linguistic approach of conversation analysis can be applied to the analysis of carer-patient interaction in care homes. A single case study from a routine encounter in a residential care home is presented. This is used to show how the conversation analysis method works, the kinds of interactional and communication features it can expose, and what specific contribution this kind of micro-interactional approach may make to improving quality of care in these environments. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Acetylome analysis reveals the involvement of lysine acetylation in photosynthesis and carbon metabolism in the model cyanobacterium Synechocystis sp. PCC 6803.

Science.gov (United States)

Mo, Ran; Yang, Mingkun; Chen, Zhuo; Cheng, Zhongyi; Yi, Xingling; Li, Chongyang; He, Chenliu; Xiong, Qian; Chen, Hui; Wang, Qiang; Ge, Feng

2015-02-06

Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC-MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.

Direct methods of soil-structure interaction analysis for earthquake loadings(II)

Energy Technology Data Exchange (ETDEWEB)

Yun, Chung Bang; Lee, S R; Kim, J M; Park, K L; Oh, S B; Choi, J S; Kim, Y S [Korea Advanced Institute of Science Technology, Daejeon (Korea, Republic of)

1994-07-15

In this study, methods for 3-D soil-structure interaction analysis have been studied. They are 3-D axisymmetric analysis method, 3-D axisymmetric finite element method incorporating infinite elements, and 3-D boundary element methods. The computer code, named as 'KIESSI - PF', has been developed which is based on the 3-D axisymmetric finite element method coupled with infinite element method. It is able to simulate forced vibration test results of a soil-structure interaction system. The Hualien FVT post-correlation analysis before backfill and the blind prediction analysis after backfill have been carried out using the developed computer code 'KIESSI - PF'.

Direct methods of soil-structure interaction analysis for earthquake loadings(II)

International Nuclear Information System (INIS)

Yun, Chung Bang; Lee, S. R.; Kim, J. M.; Park, K. L.; Oh, S. B.; Choi, J. S.; Kim, Y. S.

1994-07-01

In this study, methods for 3-D soil-structure interaction analysis have been studied. They are 3-D axisymmetric analysis method, 3-D axisymmetric finite element method incorporating infinite elements, and 3-D boundary element methods. The computer code, named as 'KIESSI - PF', has been developed which is based on the 3-D axisymmetric finite element method coupled with infinite element method. It is able to simulate forced vibration test results of a soil-structure interaction system. The Hualien FVT post-correlation analysis before backfill and the blind prediction analysis after backfill have been carried out using the developed computer code 'KIESSI - PF'

Differential phytosociological interactions involving male and female atriplex bonnevillensis

Science.gov (United States)

Sinclair, J.; Emlen, J.M.; Rinella, M.; Snelgrove, J.; Freeman, D.C.

2009-01-01

Wind-pollinated dioecious plants often exhibit spatial segregation of the sexes. This partial niche separation has most often been explored using abiotic niche axes. However, if the sexes are truly separated in space, then they are apt to encounter different plant species that may heavily affect growth and reproduction. Also, to the extent that their niches differ, the sexes may respond differently to the same co-occurring species. Here we examine interspecific interactions that influence male and female reproductive potential in Atriplex bonnevillensis. Using Emlen's interaction assessment, a technique which assesses species interactions based on cover classes, we show that Salsola species compete significantly with females but not males, while Halogeton glomeratus competes with males but not females. The effect of competition only became apparent when we corrected for site-specific fertility. These results imply that differential competition must be considered when studying dioecious plants that display spatial segregation of the sexes.

Computer-Based Interaction Analysis with DEGREE Revisited

Science.gov (United States)

Barros, B.; Verdejo, M. F.

2016-01-01

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

Associations between Methylated Metabolites of Arsenic and Selenium in Urine of Pregnant Bangladeshi Women and Interactions between the Main Genes Involved.

Science.gov (United States)

Skröder, Helena; Engström, Karin; Kuehnelt, Doris; Kippler, Maria; Francesconi, Kevin; Nermell, Barbro; Tofail, Fahmida; Broberg, Karin; Vahter, Marie

2018-02-01

It has been proposed that interactions between selenium and arsenic in the body may affect their kinetics and toxicity. However, it is unknown how the elements influence each other in humans. We aimed to investigate potential interactions in the methylation of selenium and arsenic. Urinary selenium (U-Se) and arsenic (U-As) were measured using inductively coupled plasma mass spectrometry (ICPMS) in samples collected from pregnant women ( n =226) in rural Bangladesh at gestational weeks (GW) 8, 14, 19, and 30. Urinary concentrations of trimethyl selenonium ion (TMSe) were measured by HPLC-vapor generation-ICPMS, as were inorganic arsenic (iAs), methylarsonic acid (MMA), and dimethylarsinic acid (DMA). Methylation efficiency was assessed based on relative amounts (%) of arsenic and selenium metabolites in urine. Genotyping for the main arsenite and selenium methyltransferases, AS3MT and INMT, was performed using TaqMan probes or Sequenom. Multivariable-adjusted linear regression analyses indicated that %TMSe (at GW8) was positively associated with %MMA (β=1.3, 95% CI: 0.56, 2.0) and U-As, and inversely associated with %DMA and U-Se in producers of TMSe ( INMT rs6970396 AG+AA, n =74), who had a wide range of urinary TMSe (12-42%). Also, %TMSe decreased in parallel to %MMA during pregnancy, especially in the first trimester (-0.58 %TMSe per gestational week). We found a gene-gene interaction for %MMA ( p -interaction=0.076 for haplotype 1). In analysis stratified by INMT genotype, the association between %MMA and both AS3MT haplotypes 1 and 3 was stronger in women with the INMT GG (TMSe nonproducers, 5th-95th percentile: 0.2-2%TMSe) vs. AG+AA genotype. Our findings for Bangladeshi women suggest a positive association between urinary %MMA and %TMSe. Genes involved in the methylation of selenium and arsenic may interact on associations with urinary %MMA. https://doi.org/10.1289/EHP1912.

A two-level solvable model involving competing pairing interactions

International Nuclear Information System (INIS)

Dussel, G.G.; Maqueda, E.E.; Perazzo, R.P.J.; Evans, J.A.

1986-01-01

A model is considered consisting of nucleons moving in two non-degenerate l-shells and interacting through two pairing residual interactions with (S, T) = (1, 0) and (0, 1). These, together with the single particle hamiltonian induce mutually destructive correlations, giving rise to various collective pictures that can be discussed as representing a two-dimensional space of phases. The model is solved exactly using an O(8)xO(8) group theoretical classification scheme. The transfer of correlated pairs and quartets is also discussed. (orig.)

Discovery of proteins involved in the interaction between prebiotics carbohydrates and probiotics & whole proteome analysis of the probiotic strain Bifidobacterium animalis susp. lactis BB-12

DEFF Research Database (Denmark)

Gilad, Ofir

Probiotic bacteria, which primarily belong to the genera Lactobascillus and Bifidobacterium, are live microorganisms that have been related to a variety of health-promoting effects. Prebiotics are indigestible food components that specifically stimulate the growth of probiotic organisms...... in the human gastrointestinal tract. Despite an increased scientific focus within this field, the mechanisms behind the beneficial effects exerted by pre- and probiotics are still far from fully understood. The purpose of the present industrial-PhD project was to identify proteins involved in interactions...... between the widely-used, extensively-studied probiotic strain Bifidobacterium animalis subsp. lactis BB-12 and potentially-prebiotic carbohydrates. The project was initiated with a screening phase in which more than 40 carbohydrates were tested for their ability to promote the growth of the bacterium...

PHIDIAS: a pathogen-host interaction data integration and analysis system.

Science.gov (United States)

Xiang, Zuoshuang; Tian, Yuying; He, Yongqun

2007-01-01

The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database system that serves as a centralized source to search, compare, and analyze integrated genome sequences, conserved domains, and gene expression data related to pathogen-host interactions (PHIs) for pathogen species designated as high priority agents for public health and biological security. In addition, PHIDIAS allows submission, search and analysis of PHI genes and molecular networks curated from peer-reviewed literature. PHIDIAS is publicly available at http://www.phidias.us.

Large gauge invariant nonstandard neutrino interactions

International Nuclear Information System (INIS)

Gavela, M. B.; Hernandez, D.; Ota, T.; Winter, W.

2009-01-01

Theories beyond the standard model must necessarily respect its gauge symmetry. This implies strict constraints on the possible models of nonstandard neutrino interactions, which we analyze. The focus is set on the effective low-energy dimension six and eight operators involving four leptons, decomposing them according to all possible tree-level mediators, as a guide for model building. The new couplings are required to have sizable strength, while processes involving four charged leptons are required to be suppressed. For nonstandard interactions in matter, only diagonal tau-neutrino interactions can escape these requirements and can be allowed to result from dimension six operators. Large nonstandard neutrino interactions from dimension eight operators alone are phenomenologically allowed in all flavor channels and are shown to require at least two new mediator particles. The new couplings must obey general cancellation conditions both at the dimension six and dimension eight levels, which result from expressing the operators obtained from the mediator analysis in terms of a complete basis of operators. We illustrate with one example how to apply this information to model building.

Structural zooming research and development of an interactive computer graphical interface for stress analysis of cracks

Science.gov (United States)

Gerstle, Walter

1989-01-01

Engineering problems sometimes involve the numerical solution of boundary value problems over domains containing geometric feature with widely varying scales. Often, a detailed solution is required at one or more of these features. Small details in large structures may have profound effects upon global performance. Conversely, large-scale conditions may effect local performance. Many man-hours and CPU-hours are currently spent in modeling such problems. With the structural zooming technique, it is now possible to design an integrated program which allows the analyst to interactively focus upon a small region of interest, to modify the local geometry, and then to obtain highly accurate responses in that region which reflect both the properties of the overall structure and the local detail. A boundary integral equation analysis program, called BOAST, was recently developed for the stress analysis of cracks. This program can accurately analyze two-dimensional linear elastic fracture mechanics problems with far less computational effort than existing finite element codes. An interactive computer graphical interface to BOAST was written. The graphical interface would have several requirements: it would be menu-driven, with mouse input; all aspects of input would be entered graphically; the results of a BOAST analysis would be displayed pictorially but also the user would be able to probe interactively to get numerical values of displacement and stress at desired locations within the analysis domain; the entire procedure would be integrated into a single, easy to use package; and it would be written using calls to the graphic package called HOOPS. The program is nearing completion. All of the preprocessing features are working satisfactorily and were debugged. The postprocessing features are under development, and rudimentary postprocessing should be available by the end of the summer. The program was developed and run on a VAX workstation, and must be ported to the SUN

A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility.

Science.gov (United States)

Bush, W S; McCauley, J L; DeJager, P L; Dudek, S M; Hafler, D A; Gibson, R A; Matthews, P M; Kappos, L; Naegelin, Y; Polman, C H; Hauser, S L; Oksenberg, J; Haines, J L; Ritchie, M D

2011-07-01

Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also increases power to detect weak main effects. We conducted a knowledge-driven interaction analysis of a GWAS of 931 multiple sclerosis (MS) trios to discover gene-gene interactions within established biological contexts. We identify heterogeneous signals, including a gene-gene interaction between CHRM3 (muscarinic cholinergic receptor 3) and MYLK (myosin light-chain kinase) (joint P=0.0002), an interaction between two phospholipase C-β isoforms, PLCβ1 and PLCβ4 (joint P=0.0098), and a modest interaction between ACTN1 (actinin alpha 1) and MYH9 (myosin heavy chain 9) (joint P=0.0326), all localized to calcium-signaled cytoskeletal regulation. Furthermore, we discover a main effect (joint P=5.2E-5) previously unidentified by single-locus analysis within another related gene, SCIN (scinderin), a calcium-binding cytoskeleton regulatory protein. This work illustrates that knowledge-driven interaction analysis of GWAS data is a feasible approach to identify new genetic effects. The results of this study are among the first gene-gene interactions and non-immune susceptibility loci for MS. Further, the implicated genes cluster within inter-related biological mechanisms that suggest a neurodegenerative component to MS.

Applicability of soil-structure interaction analysis methods for earthquake loadings (V)

International Nuclear Information System (INIS)

Chang, S. P.; Ko, H. M.; Kim, J. K.; Yoon, J. Y.; Chin, B. M.; Yang, T. S.; Park, J. Y.; Cho, J. R.; Ryu, H.

1997-07-01

The ultimate goals of this research are to cultivate the capability of accurate 551 analysis and to develop the effective soil-structure interaction analysis method and computer program by comparing analysis results obtained in Lotung/Hualien lS5T project. In this research, the scope of this study is to establish the method of soil-structure interaction analysis using hyperlement and to develop a computer program of 551 analysis, to do parametric study for the comprehension of the characteristics and the applicability of hyper elements and to verify the validity and the applicability of this method(or program) through the analysis of seismic response of Hualien lS5T project. In this study, we verified the validity and the efficiency of the soil-structure interaction analysis method using hyper elements and developed computer programs using hyper elements. Based on the I-dimensional wave propagation theory, we developed a computer program of free-field analysis considering the primary non-lineriry of seismic responses. And using this program, we computed the effective ground earthquake motions of soil regions. The computer programs using hyper elements can treat non-homogeneity of soil regions very easily and perform the analysis quickly by the usage of the analytical solutions in horizontal direction. 50 this method would be very efficient and practical method

Tribal and stakeholder involvement in systems analysis

International Nuclear Information System (INIS)

McClure, L.; Swartz, G.; Cooley, C.

1997-01-01

Beginning in early 1995, U.S. Department of Energy began an experiment to link tribal and stakeholder representatives into technology assessment activities related to an Integrated Nonthermal Treatment System (INTS) study. The INTS study moved outside the framework of after-the-fact public involvement by providing the opportunity for technical and non-technical stakeholders alike to work together in the early predecision stages of the criteria development and assessment of options for innovative mixed waste treatment. The stakeholders gained an appreciation of the intense level of effort required to complete such an analysis. The engineers and scientists conducting the systems analyses had the opportunity (some for the first time) to learn more about tribal and stakeholder issues and how they might apply to the technical tasks related to technology assessment and selection

Direct methods of soil-structure interaction analysis for earthquake loadings(II)

Energy Technology Data Exchange (ETDEWEB)

Yun, Chung Bang; Lee, S. R.; Kim, J. M.; Park, K. L.; Oh, S. B.; Choi, J. S.; Kim, Y. S. [Korea Advanced Institute of Science Technology, Daejeon (Korea, Republic of)

1994-07-15

In this study, methods for 3-D soil-structure interaction analysis have been studied. They are 3-D axisymmetric analysis method, 3-D axisymmetric finite element method incorporating infinite elements, and 3-D boundary element methods. The computer code, named as 'KIESSI - PF', has been developed which is based on the 3-D axisymmetric finite element method coupled with infinite element method. It is able to simulate forced vibration test results of a soil-structure interaction system. The Hualien FVT post-correlation analysis before backfill and the blind prediction analysis after backfill have been carried out using the developed computer code 'KIESSI - PF'.

Animated analysis of geoscientific datasets: An interactive graphical application

Science.gov (United States)

Morse, Peter; Reading, Anya; Lueg, Christopher

2017-12-01

Geoscientists are required to analyze and draw conclusions from increasingly large volumes of data. There is a need to recognise and characterise features and changing patterns of Earth observables within such large datasets. It is also necessary to identify significant subsets of the data for more detailed analysis. We present an innovative, interactive software tool and workflow to visualise, characterise, sample and tag large geoscientific datasets from both local and cloud-based repositories. It uses an animated interface and human-computer interaction to utilise the capacity of human expert observers to identify features via enhanced visual analytics. 'Tagger' enables users to analyze datasets that are too large in volume to be drawn legibly on a reasonable number of single static plots. Users interact with the moving graphical display, tagging data ranges of interest for subsequent attention. The tool provides a rapid pre-pass process using fast GPU-based OpenGL graphics and data-handling and is coded in the Quartz Composer visual programing language (VPL) on Mac OSX. It makes use of interoperable data formats, and cloud-based (or local) data storage and compute. In a case study, Tagger was used to characterise a decade (2000-2009) of data recorded by the Cape Sorell Waverider Buoy, located approximately 10 km off the west coast of Tasmania, Australia. These data serve as a proxy for the understanding of Southern Ocean storminess, which has both local and global implications. This example shows use of the tool to identify and characterise 4 different types of storm and non-storm events during this time. Events characterised in this way are compared with conventional analysis, noting advantages and limitations of data analysis using animation and human interaction. Tagger provides a new ability to make use of humans as feature detectors in computer-based analysis of large-volume geosciences and other data.

Interaction analysis method for the Hanford Waste Vitrification Plant

International Nuclear Information System (INIS)

Grant, P.R.; Deshotels, R.L.; Van Katwijk, C.

1993-01-01

In order to anticipate potential problems as early as possible during the design effort, a method for interaction analysis was developed to meet the specific hazards of the Hanford Waste Vitrification Plant (HWVP). The requirement for interaction analysis is given in DOE Order 6430.1B and DOE-STD-1021-92. The purpose of the interaction analysis is to ensure that non-safety class items will not fail in a manner that will adversely affect the ability of any safety class item to perform its safety function. In the HWVP there are few structures, equipment, or controls that are safety class (those with a direct safety function, i.e., confinement of waste). In addition to damage due to failure of non-safety class items as a result of natural phenomena, threats to HWVP safety class items include the following: room flooding from firewater, leakage of chemically reactive liquids, high-pressure gas impingement from leaking piping, rocket-type impact from broken pressurized gas cylinders, loss of control of mobile equipment, cryogenic liquid spill, fire, and smoke. The time needed to perform the interaction analysis is minimized by consolidating safety class items into segregated areas. Each area containing safety class items is evaluated, and any potential threat to the safety functions is noted. After relocation of safety class items is considered, items that pose a threat are generally upgraded to eliminate the threat to the safety class items. Upgraded items are designed to not fail under the conditions being evaluated. Upgrading is the preferred option when relocation is not possible. Other options are to provide barriers, design the safety class item not to be damaged by failed items, or rely on redundancy and isolation from local threats. The upgraded features of non-safety class items are designed to the same quality standards as the safety class items

Analysis of factors associated with injury severity in crashes involving young New Zealand drivers

DEFF Research Database (Denmark)

Weiss, Harold B.; Kaplan, Sigal; Prato, Carlo Giacomo

2014-01-01

measures within youth-oriented road safety programs. The current study estimates discrete choice models of injury severity of crashes involving young drivers conditional on these crashes having occurred. The analysis examined a comprehensive set of single-vehicle and two-vehicle crashes involving at least...

Rapid Blood Pressure Lowering According to Recovery at Different Time Intervals after Acute Intracerebral Hemorrhage: Pooled Analysis of the INTERACT Studies.

Science.gov (United States)

Wang, Xia; Arima, Hisatomi; Al-Shahi Salman, Rustam; Woodward, Mark; Heeley, Emma; Stapf, Christian; Lavados, Pablo M; Robinson, Thompson; Huang, Yining; Wang, Jiguang; Delcourt, Candice; Anderson, Craig S

2015-01-01

Early intensive blood pressure (BP) lowering has been shown to improve functional outcome in acute intracerebral hemorrhage (ICH), but the treatment effect is modest and without a clearly defined underlying explanatory mechanism. We aimed at more reliably quantifying the benefits of this treatment according to different time periods in the recovery of participants in the Intensive Blood Pressure Reduction in Acute Cerebral Hemorrhage Trial (INTERACT) studies. Pooled analysis of the pilot INTERACT1 (n = 404) and main INTERACT2 (n = 2,839) involving patients with spontaneous ICH (patient characteristic subgroups, with trends favoring those randomized early, and with higher SBP and milder neurological severity at baseline. Intensive BP lowering provides beneficial effects on physical functioning that manifests consistently through the early and later phases of recovery from ICH. © 2015 S. Karger AG, Basel.

Interactive analysis of geodata based intelligence

Science.gov (United States)

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

2016-05-01

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

[A Concept Analysis for Mind-Body Interaction].

Science.gov (United States)

Chen, Hsing-Wen; Yeh, Mei-Ling; Rong, Jiin-Ru

2015-08-01

Mind-body interaction (MBI) refers the holistic association and interactive process between wisdom, thinking, belief, and physiological reaction, which critically affects health. The main goal of nursing is to maintain mind and body in a healthy state of well being. Few reports in the literatures have addressed the evaluation and application of MBI. Thus, a conceptual analysis of this subject is worth exploring in depth. This paper analyzes the MBI concept step by step based on the procedures of Walker and Avant. The result defines the characteristics of MBI as (1) being aware of psychosomatic effects, (2) interacting between psychology, neurology, immunology and others, and (3) turning out a bio-psycho-social status. Antecedents include geography, culture, race, gender, age, education, profession, values, personality, experience, and health status. Consequences of MBI include well-being, illness, and death. This paper provides new information on MBI that clarifies its meaning, provides comprehensive cognition, and suggests useful applications.

Monitoring of Students' Interaction in Online Learning Settings by Structural Network Analysis and Indicators.

Science.gov (United States)

Ammenwerth, Elske; Hackl, Werner O

2017-01-01

Learning as a constructive process works best in interaction with other learners. Support of social interaction processes is a particular challenge within online learning settings due to the spatial and temporal distribution of participants. It should thus be carefully monitored. We present structural network analysis and related indicators to analyse and visualize interaction patterns of participants in online learning settings. We validate this approach in two online courses and show how the visualization helps to monitor interaction and to identify activity profiles of learners. Structural network analysis is a feasible approach for an analysis of the intensity and direction of interaction in online learning settings.

Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding

Science.gov (United States)

Verdonk, Marcel L.; Boks, Gertjan J.; Kooijman, Huub; Kanters, Jan A.; Kroon, Jan

1993-04-01

Recently, new evidence was found for the involvement of charged nitrogen-aromatic interactions in ligand-receptor binding. In this study we report two favourable orientations of a phenyl ring with respect to a R-N+(CH3)3 group, based on crystal structure statistics from the Cambridge Structural Database. In the first orientation, the phenyl ring is situated in between the substituents at about 4.5 Å from the nitrogen atom, and the ring is approximately oriented on the sphere around the nitrogen atom. In the second orientation, the phenyl ring is situated in the same direction as one of the N-C bonds at about 6.0 Å from the nitrogen atom, and the ring is tilted with respect to the sphere around the nitrogen atom. The same two orientations were also found in the crystal structures of three ligand-receptor complexes, which implies that these orientations probably play a major role in molecular recognition mechanisms.

Nonactivation interaction techniques in the analysis of environmental samples

International Nuclear Information System (INIS)

Tolgyessy, J.

1986-01-01

Nonactivation interaction analytical methods are based on the interaction processes of nuclear and X-ray radiation with a sample, leading to their absorption and backscattering, to the ionization of gases or excitation of fluorescent X-ray by radiation, but not to the activation of determined elements. From the point of view of environmental analysis, the most useful nonactivation interaction techniques are X-ray fluorescence by photon or charged particle excitation, ionization of gases by nuclear radiation, elastic scattering of charged particles and backscattering of beta radiation. The significant advantage of these methods is that they are nondestructive. (author)

Analysis of Protein-RNA and Protein-Peptide Interactions in Equine Infectious Anemia

Energy Technology Data Exchange (ETDEWEB)

Lee, Jae-Hyung [Iowa State Univ., Ames, IA (United States)

2007-01-01

Macromolecular interactions are essential for virtually all cellular functions including signal transduction processes, metabolic processes, regulation of gene expression and immune responses. This dissertation focuses on the characterization of two important macromolecular interactions involved in the relationship between Equine Infectious Anemia Virus (EIAV) and its host cell in horse: (1) the interaction between the EIAV Rev protein and its binding site, the Rev-responsive element (RRE) and (2) interactions between equine MHC class I molecules and epitope peptides derived from EIAV proteins. EIAV, one of the most divergent members of the lentivirus family, has a single-stranded RNA genome and carries several regulatory and structural proteins within its viral particle. Rev is an essential EIAV regulatory encoded protein that interacts with the viral RRE, a specific binding site in the viral mRNA. Using a combination of experimental and computational methods, the interactions between EIAV Rev and RRE were characterized in detail. EIAV Rev was shown to have a bipartite RNA binding domain contain two arginine rich motifs (ARMs). The RRE secondary structure was determined and specific structural motifs that act as cis-regulatory elements for EIAV Rev-RRE interaction were identified. Interestingly, a structural motif located in the high affinity Rev binding site is well conserved in several diverse lentiviral genoes, including HIV-1. Macromolecular interactions involved in the immune response of the horse to EIAV infection were investigated by analyzing complexes between MHC class I proteins and epitope peptides derived from EIAV Rev, Env and Gag proteins. Computational modeling results provided a mechanistic explanation for the experimental finding that a single amino acid change in the peptide binding domain of the quine MHC class I molecule differentially affectes the recognitino of specific epitopes by EIAV-specific CTL. Together, the findings in this

Phase space analysis of some interacting Chaplygin gas models

Energy Technology Data Exchange (ETDEWEB)

Khurshudyan, M. [Academy of Sciences of Armenia, Institute for Physical Research, Ashtarak (Armenia); Tomsk State University of Control Systems and Radioelectronics, Laboratory for Theoretical Cosmology, Tomsk (Russian Federation); Tomsk State Pedagogical University, Department of Theoretical Physics, Tomsk (Russian Federation); Myrzakulov, R. [Eurasian National University, Eurasian International Center for Theoretical Physics, Astana (Kazakhstan)

2017-02-15

In this paper we discuss a phase space analysis of various interacting Chaplygin gas models in general relativity. Linear and nonlinear sign changeable interactions are considered. For each case appropriate late time attractors of field equations are found. The Chaplygin gas is one of the dark fluids actively considered in modern cosmology due to the fact that it is a joint model of dark energy and dark matter. (orig.)

Who and What Does Involvement Involve?

DEFF Research Database (Denmark)

Hansen, Jeppe Oute; Petersen, Anders; Huniche, Lotte

2015-01-01

This article gives an account of aspects of a multi-sited field study of involvement of relatives in Danish psychiatry. By following metaphors of involvement across three sites of the psychiatric systema family site, a clinical site and a policy sitethe first author (J.O.) investigated how...... theoretical perspective laid out by Ernesto Laclau and Chantal Mouffe, the aim of this study is to show how the dominant discourse about involvement at the political and clinical sites is constituted by understandings of mentally ill individuals and by political objectives of involvement. The analysis...... the responsibility toward the mental health of the ill individual as well as toward the psychological milieu of the family....

Analysis of engagement behavior in children during dyadic interactions using prosodic cues.

Science.gov (United States)

Gupta, Rahul; Bone, Daniel; Lee, Sungbok; Narayanan, Shrikanth

2016-05-01

Child engagement is defined as the interaction of a child with his/her environment in a contextually appropriate manner. Engagement behavior in children is linked to socio-emotional and cognitive state assessment with enhanced engagement identified with improved skills. A vast majority of studies however rely solely, and often implicitly, on subjective perceptual measures of engagement. Access to automatic quantification could assist researchers/clinicians to objectively interpret engagement with respect to a target behavior or condition, and furthermore inform mechanisms for improving engagement in various settings. In this paper, we present an engagement prediction system based exclusively on vocal cues observed during structured interaction between a child and a psychologist involving several tasks. Specifically, we derive prosodic cues that capture engagement levels across the various tasks. Our experiments suggest that a child's engagement is reflected not only in the vocalizations, but also in the speech of the interacting psychologist. Moreover, we show that prosodic cues are informative of the engagement phenomena not only as characterized over the entire task (i.e., global cues), but also in short term patterns (i.e., local cues). We perform a classification experiment assigning the engagement of a child into three discrete levels achieving an unweighted average recall of 55.8% (chance is 33.3%). While the systems using global cues and local level cues are each statistically significant in predicting engagement, we obtain the best results after fusing these two components. We perform further analysis of the cues at local and global levels to achieve insights linking specific prosodic patterns to the engagement phenomenon. We observe that while the performance of our model varies with task setting and interacting psychologist, there exist universal prosodic patterns reflective of engagement.

Analysis of the interaction of participants freight forwarding system

Directory of Open Access Journals (Sweden)

Pavlo Popovych

2016-12-01

Full Text Available Main goal of this work is the analysis of the interaction of participants of freight forwarding activities. Research methods included analysis of scientific literature, theory of systems and systems analysis, methods of induction and deduction. As sources of information used and applied work of fundamental importance known foreign and local scientists and regulatory and legislative documents of Ukraine for the state transport policy. In the article the basic interactions of participants of freight forwarding activities. Classified components freight forwarding services. Assign the concept freight forwarding system and its aim. Established element and forms of cooperation in the freight forwarding system. The main task of forwarding companies are organizing, coordinating and ensuring the delivery from shipper to consignee. Freight forwarding company responsible for the timely delivery of the goods on the condition of preservation of the quantity and quality specified time conditions. Currently used methods are uneffective decision-making, leading to losses. These circumstances require improvement methodology management of freight forwarding companies. This is possible only using modern mathematical methods and information technologies that will improve the operation of freight forwarding companies. The article presents a theoretical exposition of the basic processes of interaction between participants in freight forwarding system. The article may be of interest to specialists of freight forwarding companies.

Interactive Programming and Analysis Aids (IPAA)

Science.gov (United States)

1978-06-01

PAGE 2. GOVT ACCESSION NO.J I JBBIITWj ’"" —— ■ "- INTERACTIVE PROGRAMMING AND ANALYSIS AIDS (IPÄA). 7^ 9. PERFORMING ORGANIZATION ...H fll u u u j o^ o f-« w « » m ^ r>» • ff> o fH CM w * «n >II N ec o^ o »^ ew « isik.f.^iiki>.i«.i^coco<s(Oflos>cocoa> coff >0^ovo«oko^3^a

Soil-structure interaction analysis of NPP containments: substructure and frequency domain methods

International Nuclear Information System (INIS)

Venancio-Filho, F.; Almeida, M.C.F.; Ferreira, W.G.; De Barros, F.C.P.

1997-01-01

Substructure and frequency domain methods for soil-structure interaction are addressed in this paper. After a brief description of mathematical models for the soil and of excitation, the equations for dynamic soil-structure interaction are developed for a rigid surface foundation and for an embedded foundation. The equations for the frequency domain analysis of MDOF systems are provided. An example of soil-structure interaction analysis with frequency-dependent soil properties is given and examples of identification of foundation impedance functions and soil properties are presented. (orig.)

The eClassroom used as a Teacher's Training Laboratory to Measure the Impact of Group Facilitation on Attending, Participation, Interaction, and Involvement

Directory of Open Access Journals (Sweden)

Mia Lobel

2002-10-01

Full Text Available This paper describes and quantifies the role of group facilitation in an experiential, real-time, online, university level credit course entitled eAHSC/ 230 Interpersonal Communications and Relations. A new and unique group interaction pattern called parallel communication, as well as classical elements of group interaction are described and quantified. New measures of online group facilitation attributes with analogous face-to-face (F2F counterparts are presented. Specifically, the impact of effective group facilitation on Attentiveness, on Interaction, on Involvement, and on Participation is explored. The paper also examines the eClassrom’s potential effectiveness as a real time teaching and training laboratory which also functions as a process observation tool that collects and feeds back interaction data, providing teachers and trainers immediate and ongoing measures of facilitation effectiveness.

Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

Directory of Open Access Journals (Sweden)

Zheng Sun

2014-01-01

Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

Analysis of compaction shock interactions during DDT of low density HMX

Science.gov (United States)

Rao, Pratap T.; Gonthier, Keith A.

2017-01-01

Deflagration-to-Detonation Transition (DDT) in confined, low density granular HMX occurs by a complex mechanism that involves compaction shock interactions within the material. Piston driven DDT experiments indicate that detonation is abruptly triggered by the interaction of a strong combustion-supported secondary shock and a piston-supported primary (input) shock, where the nature of the interaction depends on initial packing density and primary shock strength. These interactions influence transition by affecting dissipative heating within the microstructure during pore collapse. Inert meso-scale simulations of successive shock loading of low density HMX are performed to examine how dissipation and hot-spot formation are affected by the initial density, and the primary and secondary shock strengths. This information is used to formulate an ignition and burn model for low density HMX that accounts for the effect of shock densensitization on burn. Preliminary DDT predictions are presented that illustrate how primary shock strength affects the transition mechanism.

Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

KAUST Repository

Chawla, Mohit

2018-04-01

The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

KAUST Repository

Chawla, Mohit

2018-01-01

The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

INFN-Pisa scientific computation environment (GRID, HPC and Interactive Analysis)

International Nuclear Information System (INIS)

Arezzini, S; Carboni, A; Caruso, G; Ciampa, A; Coscetti, S; Mazzoni, E; Piras, S

2014-01-01

The INFN-Pisa Tier2 infrastructure is described, optimized not only for GRID CPU and Storage access, but also for a more interactive use of the resources in order to provide good solutions for the final data analysis step. The Data Center, equipped with about 6700 production cores, permits the use of modern analysis techniques realized via advanced statistical tools (like RooFit and RooStat) implemented in multicore systems. In particular a POSIX file storage access integrated with standard SRM access is provided. Therefore the unified storage infrastructure is described, based on GPFS and Xrootd, used both for SRM data repository and interactive POSIX access. Such a common infrastructure allows a transparent access to the Tier2 data to the users for their interactive analysis. The organization of a specialized many cores CPU facility devoted to interactive analysis is also described along with the login mechanism integrated with the INFN-AAI (National INFN Infrastructure) to extend the site access and use to a geographical distributed community. Such infrastructure is used also for a national computing facility in use to the INFN theoretical community, it enables a synergic use of computing and storage resources. Our Center initially developed for the HEP community is now growing and includes also HPC resources fully integrated. In recent years has been installed and managed a cluster facility (1000 cores, parallel use via InfiniBand connection) and we are now updating this facility that will provide resources for all the intermediate level HPC computing needs of the INFN theoretical national community.

The interaction between theory and experiment in charge density analysis

International Nuclear Information System (INIS)

Coppens, Phillip

2013-01-01

The field of x-ray charge density analysis has gradually morphed into an area benefiting from the strong interactions between theoreticians and experimentalists, leading to new concepts on chemical bonding and of intermolecular interactions in condensed phases. Some highlights of the developments culminating in the 2013 Aminoff Award are described in this paper. (comment)

Control system design and analysis using the INteractive Controls Analysis (INCA) program

Science.gov (United States)

Bauer, Frank H.; Downing, John P.

1987-01-01

The INteractive Controls Analysis (INCA) program was developed at the Goddard Space Flight Center to provide a user friendly efficient environment for the design and analysis of linear control systems. Since its inception, INCA has found extensive use in the design, development, and analysis of control systems for spacecraft, instruments, robotics, and pointing systems. Moreover, the results of the analytic tools imbedded in INCA have been flight proven with at least three currently orbiting spacecraft. This paper describes the INCA program and illustrates, using a flight proven example, how the package can perform complex design analyses with relative ease.

Laser-induced plasmas as an analytical source for quantitative analysis of gaseous and aerosol systems: Fundamentals of plasma-particle interactions

Science.gov (United States)

Diwakar, Prasoon K.

2009-11-01

Laser-induced Breakdown Spectroscopy (LIBS) is a relatively new analytical diagnostic technique which has gained serious attention in recent past due to its simplicity, robustness, and portability and multi-element analysis capabilities. LIBS has been used successfully for analysis of elements in different media including solids, liquids and gases. Since 1963, when the first breakdown study was reported, to 1983, when the first LIBS experiments were reported, the technique has come a long way, but the majority of fundamental understanding of the processes that occur has taken place in last few years, which has propelled LIBS in the direction of being a well established analytical technique. This study, which mostly focuses on LIBS involving aerosols, has been able to unravel some of the mysteries and provide knowledge that will be valuable to LIBS community as a whole. LIBS processes can be broken down to three basic steps, namely, plasma formation, analyte introduction, and plasma-analyte interactions. In this study, these three steps have been investigated in laser-induced plasma, focusing mainly on the plasma-particle interactions. Understanding plasma-particle interactions and the fundamental processes involved is important in advancing laser-induced breakdown spectroscopy as a reliable and accurate analytical technique. Critical understanding of plasma-particle interactions includes study of the plasma evolution, analyte atomization, and the particle dissociation and diffusion. In this dissertation, temporal and spatial studies have been done to understand the fundamentals of the LIBS processes including the breakdown of gases by the laser pulse, plasma inception mechanisms, plasma evolution, analyte introduction and plasma-particle interactions and their influence on LIBS signal. Spectral measurements were performed in a laser-induced plasma and the results reveal localized perturbations in the plasma properties in the vicinity of the analyte species, for

Modeling strategic interaction with application to environmental engineering

Energy Technology Data Exchange (ETDEWEB)

Dagnino, A.

1987-01-01

The main purpose of this thesis is to develop practical decision models for use in the analysis of complex strategic interaction situations. Following the presentation of the different bargain in models that have been developed previously, an algorithm that formally defines, models, and analyzes the cooperation present in strategic interaction is given. In addition to other valuable information, the algorithm predicts the compromise solutions to complex disputes and how a given decision maker can select a strategy to reach a preferable solution. To model misconceptions of decision makers involved in strategic interaction situations, a cooperative hypergame model is developed. Then a computerized algorithm that handles preference information of decision makers involved in strategic interaction is presented. This model allows one to perform exhaustive sensitivity analyses in an efficient and quick manner. Following this, practical decision algorithms useful for mediators seeking for joint solutions are presented. These mediation models allow the study and development of compromise zones among decision makers taking part in a dispute.

Electromagnetic current in weak interactions

International Nuclear Information System (INIS)

Ma, E.

1983-01-01

In gauge models which unify weak and electromagnetic interactions, the weak neutral-current interaction also involves the electromagnetic current. The exact nature of such a component can be explored using e + e - experimental data. In recent years, the existence of a new component of the weak interaction has become firmly established, i.e., the neutral-current interaction. As such, it competes with the electromagnetic interaction whenever the particles involved are also charged, but at a very much lower rate because its effective strength is so small. Hence neutrino processes are best for the detection of the neutral-current interaction. However, in any gauge model which unifies weak and electromagnetic interactions, the weak neutral-current interaction also involves the electromagnetic current

Interactive reliability analysis project. FY 80 progress report

International Nuclear Information System (INIS)

Rasmuson, D.M.; Shepherd, J.C.

1981-03-01

This report summarizes the progress to date in the interactive reliability analysis project. Purpose is to develop and demonstrate a reliability and safety technique that can be incorporated early in the design process. Details are illustrated in a simple example of a reactor safety system

Intergrain exchange interaction estimation from the remanence magnetization analysis

International Nuclear Information System (INIS)

Bolyachkin, Anton S.; Volegov, Aleksey S.; Kudrevatykh, Nikolay V.

2015-01-01

Analysis of δm(H)=[M d (H)−M r (∞)+2M r (H)]/M r (∞) curves constructed from dc demagnetization and isothermal remanent magnetization (M d (H) and M r (H) respectively) is important for characterization of the interactions in ferromagnets. Up to now, it has been mainly used for qualitative deductions about them. In this work, the novel functional relation between the maximum of the δm(H) plot and the microscopic parameters of the weakly coupled Stoner–Wohlfarth ensemble with the isotropic distribution of easy magnetization axes was established using computer modeling. It allows quantitative analysis in the frame of the model to be performed. Finally, a new method of estimating the intergrain exchange interaction constant for nanostructured high anisotropy magnets could be formulated taking into account the results of the modeling. - Highlights: • Computer modelling of the weakly coupled Stoner–Wohlfarth like ensemble was performed. • The novel functional relation for maxima of the Kelly plots is established. • Method of the estimation of intergrain exchange interaction constant is formulated

Involvement of two classes of binding sites in the interactions of cyclophilin B with peripheral blood T-lymphocytes.

OpenAIRE

Denys, A; Allain, F; Carpentier, M; Spik, G

1998-01-01

Cyclophilin B (CyPB) is a cyclosporin A (CsA)-binding protein, mainly associated with the secretory pathway, and is released in biological fluids. We recently reported that CyPB specifically binds to T-lymphocytes and promotes enhanced incorporation of CsA. The interactions with cellular binding sites involved, at least in part, the specific N-terminal extension of the protein. In this study, we intended to specify further the nature of the CyPB-binding sites on peripheral blood T-lymphocytes...

Chemical signaling involved in plant-microbe interactions.

Science.gov (United States)

Chagas, Fernanda Oliveira; Pessotti, Rita de Cassia; Caraballo-Rodríguez, Andrés Mauricio; Pupo, Mônica Tallarico

2018-03-05

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

Qualitative analysis of factors that increase and reduce involvement in gambling

Directory of Open Access Journals (Sweden)

Egidijus

2015-12-01

Full Text Available During the rapid development of gambling business, the number of pathological gamblers is increasing as well. The problem of pathological gambling is just as important as alcoholism or drug addiction. However, there is a lack of information and research of this topicin Lithuania. The aim of work: to investigate and analyse the factors that increase or reduce involvement in gambling. Research questions: 1 What factors increase involvement in gambling? 2 What factors reduce involvement in gambling? Critical case sampling was used for selection of the participants. Subjects were required to a have experience of involvement in gambling for at least one year; b have experience of negative impact of gambling on quality of life; c have at least 6 months of gambling abstinence. Five individuals participated in the research; all of them were males who live in Vilnius. Age of the participants varied from 19 to 45. Semi-structured interviews were used to collect data. Interviews were recorded and transcribed verbatim. The matic analysis of the data led to the identification of four major the matic categories: psychological factors; social relations; material well being; quality of life. There search results show that negatyve childhood experience, gambling friends, escaping from various troubles, disputes in family and high financial needs can increase involvement in gambling. Factors that reduce involvement in gambling are: feeling support of social environment, proper evaluation of financial position, awareness of one‘s own addiction to gambling and desire to change life.

Nonlinear dynamic analysis of framed structures including soil-structure interaction effects

International Nuclear Information System (INIS)

Mahmood, M.N.; Ahmed, S.Y.

2008-01-01

The role of oil-structure interaction on seismic behavior of reinforced concrete structures is investigated in this paper. A finite element approach has been adopted to model the interaction system that consists of the reinforced concrete plane frame, soil deposit and interface which represents the frictional between foundation of the structure and subsoil. The analysis is based on the elasto-plastic behavior of the frame members (beams and columns) that is defined by the ultimate axial force-bending moment interaction curve, while the cap model is adopted to govern the elasto-plastic behavior of the soil material. Mohr-Coulomb failure law is used to determine the initiation of slippage at the interface, while the separation is assumed to determine the initiation of slippage at the interface, while the separation is assumed to occur when the stresses at the interface becomes tension stresses. New-Mark's Predictor-Corrector algorithm is adopted for nonlinear dynamic analysis. The main aim of present work is to evaluate the sensitivity of structures to different behavior of the soil and interface layer when subjected to an earthquake excitation. Predicted results of the dynamic analysis of the interaction system indicate that the soil-structure interaction problem can have beneficial effects on the structural behavior when different soil models (elastic and elasto-plastic) and interface conditions (perfect bond and permitted slip)are considered. (author)

Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

Directory of Open Access Journals (Sweden)

Yonglong Yu

2016-04-01

Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

Changes in cerebro-cerebellar interaction during response inhibition after performance improvement.

Science.gov (United States)

Hirose, Satoshi; Jimura, Koji; Kunimatsu, Akira; Abe, Osamu; Ohtomo, Kuni; Miyashita, Yasushi; Konishi, Seiki

2014-10-01

It has been demonstrated that motor learning is supported by the cerebellum and the cerebro-cerebellar interaction. Response inhibition involves motor responses and the higher-order inhibition that controls the motor responses. In this functional MRI study, we measured the cerebro-cerebellar interaction during response inhibition in two separate days of task performance, and detected the changes in the interaction following performance improvement. Behaviorally, performance improved in the second day, compared to the first day. The psycho-physiological interaction (PPI) analysis revealed the interaction decrease from the right inferior frontal cortex (rIFC) to the cerebellum (lobule VII or VI). It was also revealed that the interaction increased from the same cerebellar region to the primary motor area. These results suggest the involvement of the cerebellum in response inhibition, and raise the possibility that the performance improvement was supported by the changes in the cerebro-cerebellar interaction. Copyright © 2014 Elsevier Inc. All rights reserved.

INTERFACING INTERACTIVE DATA ANALYSIS TOOLS WITH THE GRID: THE PPDG CS-11 ACTIVITY

International Nuclear Information System (INIS)

Perl, Joseph

2003-01-01

For today's physicists, who work in large geographically distributed collaborations, the data grid promises significantly greater capabilities for analysis of experimental data and production of physics results than is possible with today's ''remote access'' technologies. The goal of letting scientists at their home institutions interact with and analyze data as if they were physically present at the major laboratory that houses their detector and computer center has yet to be accomplished. The Particle Physics Data Grid project (www.ppdg.net) has recently embarked on an effort to ''Interface and Integrate Interactive Data Analysis Tools with the grid and identify Common Components and Services''. The initial activities are to collect known and identify new requirements for grid services and analysis tools from a range of current and future experiments to determine if existing plans for tools and services meet these requirements. Follow-on activities will foster the interaction between grid service developers, analysis tool developers, experiment analysis framework developers and end user physicists, and will identify and carry out specific development/integration work so that interactive analysis tools utilizing grid services actually provide the capabilities that users need. This talk will summarize what we know of requirements for analysis tools and grid services, as well as describe the identified areas where more development work is needed

SLXL1, a novel acrosomal protein, interacts with DKKL1 and is involved in fertilization in mice.

Directory of Open Access Journals (Sweden)

Xin-jie Zhuang

Full Text Available BACKGROUND: Spermatogenesis is a complex cellular developmental process which involves diverse families of genes. The Xlr (X-linked, lymphocyte regulated family includes multiple members, only a few of which have reported functions in meiosis, post-meiotic maturation, and fertilization of germ cells. Slx-like1 (Slxl1 is a member of the Xlr family, whose expression and function in spermatogenesis need to be elucidated. METHODOLOGY/PRINCIPAL FINDINGS: The mRNA and protein expression and localization of Slxl1 were investigated by RT-PCR, Western blotting and immunohistochemistry in different tissues and at different stages of spermatogenesis. The interacting partner of SLXL1 was examined by co-immunoprecipitation and co-localization. Assessment of the role of SLXL1 in capacitation, acrosome reaction, zona pellucida binding/penetration, and fertilization was carried out in vitro using blocking antisera. The results showed that Slxl1 mRNA and protein were specifically expressed in the testis. SLXL1 was exclusively located in the acrosome of post-meiotic germ cells and interacts with DKKL1 (Dickkopf-like1, which is an acrosome-associated protein and plays an important role in fertilization. The rates of zona pellucida binding/penetration and fertilization were significantly reduced by the anti-SLXL1 polyclonal antiserum. CONCLUSIONS/SIGNIFICANCE: SLXL1 is the first identified member of the XLR family that is associated with acrosome and is involved in zona pellucid binding/penetration and subsequent fertilization. These results, together with previous studies, suggest that Xlr family members participate in diverse processes from meiosis to fertilization during spermatogenesis.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

Science.gov (United States)

Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

2017-10-01

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

Interactive Actor Analysis for Rural Water Management in The Netherlands : An Application of the Transactional Approach

NARCIS (Netherlands)

J.S. Timmermans (Jos)

2009-01-01

textabstractRecent developments in the policy sciences emphasize the social environment in which decisions are made. The ‘network metaphor’ is often used to describe the key role of interactions between interdependent actors involved in decision making. These interactions take place in a policy

Data analysis through interactive computer animation method (DATICAM)

International Nuclear Information System (INIS)

Curtis, J.N.; Schwieder, D.H.

1983-01-01

DATICAM is an interactive computer animation method designed to aid in the analysis of nuclear research data. DATICAM was developed at the Idaho National Engineering Laboratory (INEL) by EG and G Idaho, Inc. INEL analysts use DATICAM to produce computer codes that are better able to predict the behavior of nuclear power reactors. In addition to increased code accuracy, DATICAM has saved manpower and computer costs. DATICAM has been generalized to assist in the data analysis of virtually any data-producing dynamic process

Supramolecular interactions in the solid state

Directory of Open Access Journals (Sweden)

Giuseppe Resnati

2015-11-01

Full Text Available In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1 an overview and historical review of halogen bonding; (2 exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3 the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4 strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

Mutational analysis of affinity and selectivity of kringle-tetranectin interaction. Grafting novel kringle affinity ontp the trtranectin lectin scaffold

DEFF Research Database (Denmark)

Graversen, Jonas Heilskov; Jacobsen, C; Sigurskjold, B W

2000-01-01

-type lectin-like domain of tetranectin, involving Lys-148, Glu-150, and Asp-165, which mediates calcium-sensitive binding to plasminogen kringle 4. Here, we investigate the effect of conservative substitutions of these and a neighboring amino acid residue. Substitution of Thr-149 in tetranectin...... with a tyrosine residue considerably increases the affinity for plasminogen kringle 4, and, in addition, confers affinity for plasminogen kringle 2. As shown by isothermal titration calorimetry analysis, this new interaction is stronger than the binding of wild-type tetranectin to plasminogen kringle 4...

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.

Science.gov (United States)

Lambrughi, Matteo; De Gioia, Luca; Gervasio, Francesco Luigi; Lindorff-Larsen, Kresten; Nussinov, Ruth; Urani, Chiara; Bruschi, Maurizio; Papaleo, Elena

2016-11-02

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Supporting secure programming in web applications through interactive static analysis.

Science.gov (United States)

Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

2014-07-01

Many security incidents are caused by software developers' failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases.

Coupled dynamics of interacting spin-1 bosons in a double-well potential

Science.gov (United States)

Carvalho, D. W. S.; Foerster, A.; Gusmão, M. A.

2018-03-01

We present a detailed analysis of dynamical processes involving two or three particles in a double-well potential. Motivated by experimental realizations of such a system with optically trapped cold atoms, we focus on spin-1 bosons with special attention on the effects of a spin-dependent interaction in addition to the usual Hubbard-like repulsive one. For a sufficiently weak tunneling amplitude in comparison to the dominant Hubbard coupling, particle motion is strongly correlated, occurring only under fine-tuned relationships between well-depth asymmetry and interactions. We highlight processes involving tunneling of coupled particle pairs and triads, emphasizing the role of the spin-dependent interaction in resonance conditions.

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

Science.gov (United States)

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

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John eMichael

2015-10-01

Full Text Available In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius Syndrome (MS to increase the use of alternative communication strategies (e.g. gestures to compensate for their lack of facial expressiveness. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual nonverbal behavior was assessed via behavioral coders, while verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, while overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact nonverbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment.

Representation of analysis results involving aleatory and epistemic uncertainty.

Energy Technology Data Exchange (ETDEWEB)

Johnson, Jay Dean (ProStat, Mesa, AZ); Helton, Jon Craig (Arizona State University, Tempe, AZ); Oberkampf, William Louis; Sallaberry, Cedric J.

2008-08-01

Procedures are described for the representation of results in analyses that involve both aleatory uncertainty and epistemic uncertainty, with aleatory uncertainty deriving from an inherent randomness in the behavior of the system under study and epistemic uncertainty deriving from a lack of knowledge about the appropriate values to use for quantities that are assumed to have fixed but poorly known values in the context of a specific study. Aleatory uncertainty is usually represented with probability and leads to cumulative distribution functions (CDFs) or complementary cumulative distribution functions (CCDFs) for analysis results of interest. Several mathematical structures are available for the representation of epistemic uncertainty, including interval analysis, possibility theory, evidence theory and probability theory. In the presence of epistemic uncertainty, there is not a single CDF or CCDF for a given analysis result. Rather, there is a family of CDFs and a corresponding family of CCDFs that derive from epistemic uncertainty and have an uncertainty structure that derives from the particular uncertainty structure (i.e., interval analysis, possibility theory, evidence theory, probability theory) used to represent epistemic uncertainty. Graphical formats for the representation of epistemic uncertainty in families of CDFs and CCDFs are investigated and presented for the indicated characterizations of epistemic uncertainty.

Involvement of leucocyte/endothelial cell interactions in anorexia nervosa.

Science.gov (United States)

Víctor, Víctor M; Rovira-Llopis, Susana; Saiz-Alarcón, Vanessa; Sangüesa, Maria C; Rojo-Bofill, Luis; Bañuls, Celia; de Pablo, Carmen; Álvarez, Ángeles; Rojo, Luis; Rocha, Milagros; Hernández-Mijares, Antonio

2015-07-01

Anorexia nervosa is a common psychiatric disorder in adolescence and is related to cardiovascular complications. Our aim was to study the effect of anorexia nervosa on metabolic parameters, leucocyte-endothelium interactions, adhesion molecules and proinflammatory cytokines. This multicentre, cross-sectional, case-control study employed a population of 24 anorexic female patients and 36 controls. We evaluated anthropometric and metabolic parameters, interactions between leucocytes polymorphonuclear neutrophils (PMN) and human umbilical vein endothelial cells (HUVEC), proinflammatory cytokines such as tumour necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) and soluble cellular adhesion molecules (CAMs) including E-selectin, vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1). Anorexia nervosa was related to a decrease in weight, body mass index, waist circumference, systolic blood pressure, glucose, insulin and HOMA-IR, and an increase in HDL cholesterol. These effects disappeared after adjusting for BMI. Anorexia nervosa induced a decrease in PMN rolling velocity and an increase in PMN rolling flux and PMN adhesion. Increases in IL-6 and TNF-α and adhesion molecule VCAM-1 were also observed. This study supports the hypothesis of an association between anorexia nervosa, inflammation and the induction of leucocyte-endothelium interactions. These findings may explain, in part at least, the increased risk of vascular disease among patients with anorexia nervosa. © 2015 Stichting European Society for Clinical Investigation Journal Foundation.

Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome.

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Albrecht von Brunn

2007-05-01

Full Text Available The severe acute respiratory syndrome coronavirus (SARS-CoV genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. The functions of a large number of viral ORFs are poorly understood or unknown. In order to gain more insight into functions and modes of action and interaction of the different proteins, we cloned the viral ORFeome and performed a genome-wide analysis for intraviral protein interactions and for intracellular localization. 900 pairwise interactions were tested by yeast-two-hybrid matrix analysis, and more than 65 positive non-redundant interactions, including six self interactions, were identified. About 38% of interactions were subsequently confirmed by CoIP in mammalian cells. Nsp2, nsp8 and ORF9b showed a wide range of interactions with other viral proteins. Nsp8 interacts with replicase proteins nsp2, nsp5, nsp6, nsp7, nsp8, nsp9, nsp12, nsp13 and nsp14, indicating a crucial role as a major player within the replication complex machinery. It was shown by others that nsp8 is essential for viral replication in vitro, whereas nsp2 is not. We show that also accessory protein ORF9b does not play a pivotal role for viral replication, as it can be deleted from the virus displaying normal plaque sizes and growth characteristics in Vero cells. However, it can be expected to be important for the virus-host interplay and for pathogenicity, due to its large number of interactions, by enhancing the global stability of the SARS proteome network, or play some unrealized role in regulating protein-protein interactions. The interactions identified provide valuable material for future studies.

Continuous atom laser with Bose-Einstein condensates involving three-body interactions

Energy Technology Data Exchange (ETDEWEB)

Carpentier, A V; Michinel, H; Novoa, D [Area de Optica, Facultade de Ciencias de Ourense, Universidade de Vigo, As Lagoas s/n, Ourense, ES-32004 (Spain); Olivieri, D N, E-mail: avcarpentier@uvigo.e [Area de Linguaxes e sistemas informaticos, Escola Superior de EnxenerIa Informatica, Universidade de Vigo, As Lagoas s/n, Ourense, ES-32004 (Spain)

2010-05-28

We demonstrate, through numerical simulations, the emission of a coherent continuous matter wave of constant amplitude from a Bose-Einstein condensate in a shallow optical dipole trap. The process is achieved by spatial control of the variations of the scattering length along the trapping axis, including elastic three-body interactions due to dipole interactions. In our approach, the outcoupling mechanism is atomic interactions, and thus, the trap remains unaltered. We calculate analytically the parameters for the experimental implementation of this continuous wave atom laser.

Social Interaction and Stock Market Participation: Evidence from China

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Zhifeng Liu

2014-01-01

Full Text Available Current research on the impact of social interaction on the stock market participation only involves the traditional way of social interaction, and this paper further investigates the modern social interaction effects on the stock market participation and its activeness. The sample containing 150 Chinese counties is selected, and we apply grouping analysis and linear regression to conclude that social interaction has positive influence on the stock market participation and its activeness. Both traditional and modern social interaction ways affect the stock market participation and its activeness to the similar extent, so modern social interaction is of the same importance. Controlling for the respondents’ age, wealth, and education level, the above conclusion still holds.

Intact long-type DupA protein in Helicobacter pylori is an ATPase involved in multifunctional biological activities.

Science.gov (United States)

Wang, Ming-yi; Chen, Cheng; Shao, Chen; Wang, Shao-bo; Wang, Ai-chu; Yang, Ya-chao; Yuan, Xiao-yan; Shao, Shi-he

2015-04-01

The function of intact long-type DupA protein in Helicobacter pylori was analyzed using immunoblotting and molecular biology techniques in the study. After cloning, expression and purification, ATPase activity of DupA protein was detected. Antibody was produced for localization and interaction proteins analysis. The dupA-deleted mutant was generated for adhesion and CagA protein translocation assay, susceptibility to different pH, IL-8 secretion assay, cytotoxicity to MKN-45 cells and proteins-involved apoptosis analysis. DupA protein exhibited an ATPase activity (129.5±17.8 U/mgprot) and located in bacterial membrane, while it did not involve the adhesion and CagA protein delivery of H. pylori. DupA protein involved the urease secretion as the interaction proteins. The wild type strain had a stronger growth in low pH than the dupA-deleted mutant (p DupA protein located in membrane as ATPase is a true virulence factor associated with duodenal ulcer development involving the IL-8 induction and urease secretion, while it inhibits gastric cancer cell growth in vitro by activating the mitochondria-mediated apoptotic pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

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Gabrielle Stetz

2017-01-01

Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

Analysis of event-mode data with Interactive Data Language

International Nuclear Information System (INIS)

De Young, P.A.; Hilldore, B.B.; Kiessel, L.M.; Peaslee, G.F.

2003-01-01

We have developed an analysis package for event-mode data based on Interactive Data Language (IDL) from Research Systems Inc. This high-level language is high speed, array oriented, object oriented, and has extensive visual (multi-dimensional plotting) and mathematical functions. We have developed a general framework, written in IDL, for the analysis of a variety of experimental data that does not require significant customization for each analysis. Unlike many traditional analysis package, spectra and gates are applied after data are read and are easily changed as analysis proceeds without rereading the data. The events are not sequentially processed into predetermined arrays subject to predetermined gates

Analysis of hepatocellular carcinoma and metastatic hepatic carcinoma via functional modules in a protein-protein interaction network

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Jun Pan

2014-01-01

Full Text Available Introduction: This study aims to identify protein clusters with potential functional relevance in the pathogenesis of hepatocellular carcinoma (HCC and metastatic hepatic carcinoma using network analysis. Materials and Methods: We used human protein interaction data to build a protein-protein interaction network with Cytoscape and then derived functional clusters using MCODE. Combining the gene expression profiles, we calculated the functional scores for the clusters and selected statistically significant clusters. Meanwhile, Gene Ontology was used to assess the functionality of these clusters. Finally, a support vector machine was trained on the gold standard data sets. Results: The differentially expressed genes of HCC were mainly involved in metabolic and signaling processes. We acquired 13 significant modules from the gene expression profiles. The area under the curve value based on the differentially expressed modules were 98.31%, which outweighed the classification with DEGs. Conclusions: Differentially expressed modules are valuable to screen biomarkers combined with functional modules.

Evaluation of conservatism in analysis of fuel-coolant interaction

International Nuclear Information System (INIS)

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

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

Using Online Interactive Physics-based Video Analysis Exercises to Enhance Learning

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Priscilla W. Laws

2017-04-01

Full Text Available As part of our new digital video age, physics students throughout the world can use smart phones, video cameras, computers and tablets to produce and analyze videos of physical phenomena using analysis software such as Logger Pro, Tracker or Coach. For several years, LivePhoto Physics Group members have created short videos of physical phenomena. They have also developed curricular materials that enable students to make predictions and use video analysis software to verify them. In this paper a new LivePhoto Physics project that involves the creation and testing of a series of Interactive Video Vignettes (IVVs will be described. IVVs are short webbased assignments that take less than ten minutes to complete. Each vignette is designed to present a video of a phenomenon, ask for a student’s prediction about it, and then conduct on-line video observations or analyses that allow the user to compare findings with his or her initial prediction. The Vignettes are designed for web delivery as ungraded exercises to supplement textbook reading, or to serve as pre-lecture or pre-laboratory activities that span a number of topics normally introduced in introductory physics courses. A sample Vignette on the topic of Newton’s Third Law will be described, and the outcomes of preliminary research on the impact of Vignettes on student motivation, learning and attitudes will be summarized.

Parallel interactive data analysis with PROOF

International Nuclear Information System (INIS)

Ballintijn, Maarten; Biskup, Marek; Brun, Rene; Canal, Philippe; Feichtinger, Derek; Ganis, Gerardo; Kickinger, Guenter; Peters, Andreas; Rademakers, Fons

2006-01-01

The Parallel ROOT Facility, PROOF, enables the analysis of much larger data sets on a shorter time scale. It exploits the inherent parallelism in data of uncorrelated events via a multi-tier architecture that optimizes I/O and CPU utilization in heterogeneous clusters with distributed storage. The system provides transparent and interactive access to gigabytes today. Being part of the ROOT framework PROOF inherits the benefits of a performant object storage system and a wealth of statistical and visualization tools. This paper describes the data analysis model of ROOT and the latest developments on closer integration of PROOF into that model and the ROOT user environment, e.g. support for PROOF-based browsing of trees stored remotely, and the popular TTree::Draw() interface. We also outline the ongoing developments aimed to improve the flexibility and user-friendliness of the system

Sensitivity analysis of physiochemical interaction model: which pair ...

African Journals Online (AJOL)

... of two model parameters at a time on the solution trajectory of physiochemical interaction over a time interval. Our aim is to use this powerful mathematical technique to select the important pair of parameters of this physical process which is cost-effective. Keywords: Passivation Rate, Sensitivity Analysis, ODE23, ODE45 ...

Interaction Analysis and Microteaching Skill Development in Teaching.

Science.gov (United States)

Amidon, Edmund

This paper presents a training model, Skill Development in Teaching (SKIT), designed for use in improvement programs for inservice teachers and in teacher education programs for preservice trainees. An introductory section notes the early use of Flanders' interaction analysis as a feedback tool for teachers, outlines a 1962 model in which it was…

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.

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Jens Christian Claussen

2017-06-01

Full Text Available The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.

Co-researching with people with learning disabilities: an experience of involvement in qualitative data analysis.

Science.gov (United States)

Tuffrey-Wijne, Irene; Butler, Gary

2010-06-01

People with learning disabilities have been included in research as co-researchers since the 1990s. However, there is limited literature about the processes of involving people with learning disabilities in the more intellectual and analytical stages of the research process. To examine the potential contribution of people with learning disabilities to data analysis in qualitative research. This article is a reflection on one research experience. The two authors include one researcher with and one without learning disabilities. They each describe their experience and understanding of user involvement in analysing the data of an ethnographic study of people with learning disabilities who had cancer. The researcher with learning disabilities was given extensive vignettes and extracts from the research field notes, and was supported to extract themes, which were cross-compared with the analysis of other members of the research team. The researcher with learning disabilities coped well with the emotive content of the data and with the additional support provided, he was able to extract themes that added validity to the overall analysis. His contribution complemented those of the other members of the research team. There were unexpected benefits, in particular, in terms of a more reciprocal and supportive relationship between the two researchers. It is possible and valuable to extend involvement to data analysis, but to avoid tokenism and maintain academic rigour, there must be a clear rationale for such involvement. Extra support, time and costs must be planned for.

Involvement in the professional environment and its significance for lifelong learning

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Litvinova E.Yu.

2017-07-01

Full Text Available The analysis of the existing definitions of a phenomenon of the professional environment and various approaches to understanding of her components is presented in article. The attention is paid to consideration of such social and psychological components of the professional environment as professional culture, professional groups and communities. On the basis of the theoretical analysis the author's understanding of functions of the professional environment is offered, also the model of dynamics of an involvement developed by authors on professional environment is provided, its stages are described. The involvement on professional environment is considered as the steady condition of active interaction of the subject with the professional environment which is shown in behavioral activity both in the environment and beyond its limits as the representative of this professional environment. The multidimensionality and relevance of studying of interference of the professional environment and professional education is accented. Arguments for benefit of rapprochement of the educational and professional environment are adduced. In the article the need of studying of interrelation of the involvement in professional environment and the involvement in lifelong education as conditions of successful adaptation and development of the modern professional is proved for the first time.

Extent of cortical involvement in amyotrophic lateral sclerosis--an analysis based on cortical thickness.

Science.gov (United States)

Thorns, Johannes; Jansma, Henk; Peschel, Thomas; Grosskreutz, Julian; Mohammadi, Bahram; Dengler, Reinhard; Münte, Thomas F

2013-10-18

Besides the defining involvement of upper and lower motor neurons, the involvement of extramotor structures has been increasingly acknowledged in amyotrophic lateral sclerosis (ALS). Here we investigated a group of 14 mildly to moderately affected ALS patients and 14 age-matched healthy control participants using cortical thickness analysis. Cortical thickness was determined from high resolution 3D T1 magnetic resonance images and involved semiautomatic segmentation in grey and white matter, cortical alignment and determination of thickness using the Laplace method. In addition to a whole-cortex analysis a region of interest approach was applied. ALS patients showed regions of significant cortical thinning in the pre- and postcentral gyri bilaterally. Further regions of cortical thinning included superior and inferior parietal lobule, angular and supramarginal gyrus, insula, superior frontal, temporal and occipital regions, thus further substantiating extramotor involvement in ALS. A relationship between cortical thickness of the right superior frontal cortex and clinical severity (assessed by the ALS functional rating scale) was also demonstrated. Cortical thickness is reduced in ALS not only in motor areas but in widespread non-motor cortical areas. Cortical thickness is related to clinical severity.

Effect of crack-microcracks interaction on energy release rates

Science.gov (United States)

Chudnovsky, A.; Wu, Shaofu

1990-01-01

The energy release rates associated with the main crack advancing into its surrounding damage zone, and the damage zone translation relative to the main crack, as well as the energy of interaction between the crack and the damage zone are analyzed. The displacement and stress fields for this crack-damage interaction problem are reconstructed by employing a semi-empirical stress analysis which involves experimental evaluation of the average microcrack density in the damage zone.

Comparative Proteomic Analysis Reveals Proteins Putatively Involved in Toxin Biosynthesis in the Marine Dinoflagellate Alexandrium catenella

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Da-Zhi Wang

2013-01-01

Full Text Available Alexandrium is a neurotoxin-producing dinoflagellate genus resulting in paralytic shellfish poisonings around the world. However, little is known about the toxin biosynthesis mechanism in Alexandrium. This study compared protein profiles of A. catenella collected at different toxin biosynthesis stages (non-toxin synthesis, initial toxin synthesis and toxin synthesizing coupled with the cell cycle, and identified differentially expressed proteins using 2-DE and MALDI-TOF-TOF mass spectrometry. The results showed that toxin biosynthesis of A. catenella occurred within a defined time frame in the G1 phase of the cell cycle. Proteomic analysis indicated that 102 protein spots altered significantly in abundance (P < 0.05, and 53 proteins were identified using database searching. These proteins were involved in a variety of biological processes, i.e., protein modification and biosynthesis, metabolism, cell division, oxidative stress, transport, signal transduction, and translation. Among them, nine proteins with known functions in paralytic shellfish toxin-producing cyanobacteria, i.e., methionine S-adenosyltransferase, chloroplast ferredoxin-NADP+ reductase, S-adenosylhomocysteinase, adenosylhomocysteinase, ornithine carbamoyltransferase, inorganic pyrophosphatase, sulfotransferase (similar to, alcohol dehydrogenase and arginine deiminase, varied significantly at different toxin biosynthesis stages and formed an interaction network, indicating that they might be involved in toxin biosynthesis in A. catenella. This study is the first step in the dissection of the behavior of the A. catenella proteome during different toxin biosynthesis stages and provides new insights into toxin biosynthesis in dinoflagellates.

Surface interactions involved in flashover with high density electronegative gases.

Energy Technology Data Exchange (ETDEWEB)

Hodge, Keith Conquest; Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Wallace, Zachariah Red; Lehr, Jane Marie

2010-01-01

This report examines the interactions involved with flashover along a surface in high density electronegative gases. The focus is on fast ionization processes rather than the later time ionic drift or thermalization of the discharge. A kinetic simulation of the gas and surface is used to examine electron multiplication and includes gas collision, excitation and ionization, and attachment processes, gas photoionization and surface photoemission processes, as well as surface attachment. These rates are then used in a 1.5D fluid ionization wave (streamer) model to study streamer propagation with and without the surface in air and in SF6. The 1.5D model therefore includes rates for all these processes. To get a better estimate for the behavior of the radius we have studied radial expansion of the streamer in air and in SF6. The focus of the modeling is on voltage and field level changes (with and without a surface) rather than secondary effects, such as, velocities or changes in discharge path. An experiment has been set up to carry out measurements of threshold voltages, streamer velocities, and other discharge characteristics. This setup includes both electrical and photographic diagnostics (streak and framing cameras). We have observed little change in critical field levels (where avalanche multiplication sets in) in the gas alone versus with the surface. Comparisons between model calculations and experimental measurements are in agreement with this. We have examined streamer sustaining fields (field which maintains ionization wave propagation) in the gas and on the surface. Agreement of the gas levels with available literature is good and agreement between experiment and calculation is good also. Model calculations do not indicate much difference between the gas alone versus the surface levels. Experiments have identified differences in velocity between streamers on the surface and in the gas alone (the surface values being larger).

Supporting secure programming in web applications through interactive static analysis

Science.gov (United States)

Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

2013-01-01

Many security incidents are caused by software developers’ failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases. PMID:25685513

Supporting secure programming in web applications through interactive static analysis

Directory of Open Access Journals (Sweden)

Jun Zhu

2014-07-01

Full Text Available Many security incidents are caused by software developers’ failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases.

Reexploration of interacting holographic dark energy model. Cases of interaction term excluding the Hubble parameter

Energy Technology Data Exchange (ETDEWEB)

Li, Hai-Li; Zhang, Jing-Fei; Feng, Lu [Northeastern University, Department of Physics, College of Sciences, Shenyang (China); Zhang, Xin [Northeastern University, Department of Physics, College of Sciences, Shenyang (China); Peking University, Center for High Energy Physics, Beijing (China)

2017-12-15

In this paper, we make a deep analysis for the five typical interacting holographic dark energy models with the interaction terms Q = 3βH{sub 0}ρ{sub de}, Q = 3βH{sub 0}ρ{sub c}, Q = 3βH{sub 0}(ρ{sub de} + ρ{sub c}), Q = 3βH{sub 0}√(ρ{sub de}ρ{sub c}), and Q = 3βH{sub 0}(ρ{sub de}ρ{sub c})/(ρ{sub de}+ρ{sub c}), respectively. We obtain observational constraints on these models by using the type Ia supernova data (the Joint Light-Curve Analysis sample), the cosmic microwave background data (Planck 2015 distance priors), the baryon acoustic oscillations data, and the direct measurement of the Hubble constant. We find that the values of χ{sub min}{sup 2} for all the five models are almost equal (around 699), indicating that the current observational data equally favor these IHDE models. In addition, a comparison with the cases of an interaction term involving the Hubble parameter H is also made. (orig.)

Ethanol and Caffeine effects on social interaction and recognition in mice: Involvement of adenosine A2A and A1 receptors

Directory of Open Access Journals (Sweden)

Laura López-Cruz

2016-11-01

Full Text Available Ethanol and caffeine are frequently consumed in combination and have opposite effects on the adenosine system: ethanol metabolism leads to an increase in adenosine levels, while caffeine is a non-selective adenosine A1/A2A receptor antagonist. These receptors are highly expressed in striatum and olfactory tubercle, brain areas involved in exploration and social interaction in rodents. Ethanol modulates social interaction processes, but the role of adenosine in social behavior is still poorly understood. The present work was undertaken to study the impact of ethanol, caffeine and their combination on social behavior, and to explore the involvement of A1 and A2A receptors on those actions. Male CD1 mice were evaluated in a social interaction three-chamber paradigm, for preference of conspecific vs. object, and also for long-term recognition memory of familiar vs. novel conspecific. Ethanol showed a biphasic effect, with low doses (0.25 g/kg increasing social contact and higher doses (1.0-1.5 g/kg reducing social interaction. However, no dose changed social preference; mice always spent more time sniffing the conspecific than the object, independently of the ethanol dose. Ethanol, even at doses that did not change social exploration, produced amnestic effects on social recognition the following day. Caffeine reduced social contact (15.0-60.0 mg/kg, and even blocked social preference at higher doses (30.0-60.0 mg/kg. The A1 antagonist CPT (3-9 mg/kg did not modify social contact or preference on its own, and the A2A antagonist MSX-3 (1.5-6 mg/kg increased social interaction at all doses. Ethanol at intermediate doses (0.5-1.0 g/kg was able to reverse the reduction in social exploration induced by caffeine (15.0-30.0 mg/kg. Although there was no interaction between ethanol and CPT or MSX-3 on social exploration in the first day, MSX-3 blocked the amnestic effects of ethanol observed on the following day. Thus, ethanol impairs the formation of social

Analysis of Interactive Conflict Resolution Tool Usage in a Mixed Equipage Environment

Science.gov (United States)

Homola, Jeffrey; Morey, Susan; Cabrall, Christopher; Martin, Lynne; Mercer, Joey; Prevot, Thomas

2013-01-01

A human-in-the-loop simulation was conducted that examined separation assurance concepts in varying levels of traffic density with mixtures of aircraft equipage and automation. This paper's analysis focuses on one of the experimental conditions in which traffic levels were approximately fifty percent higher than today, and approximately fifty percent of the traffic within the test area were equipped with data communications (data comm) capabilities. The other fifty percent of the aircraft required control by voice much like today. Within this environment, the air traffic controller participants were provided access to tools and automation designed to support the primary task of separation assurance that are currently unavailable. Two tools were selected for analysis in this paper: 1) a pre-probed altitude fly-out menu that provided instant feedback of conflict probe results for a range of altitudes, and 2) an interactive auto resolver that provided on-demand access to an automation-generated conflict resolution trajectory. Although encouraged, use of the support tools was not required; the participants were free to use the tools as they saw fit, and they were also free to accept, reject, or modify the resolutions offered by the automation. This mode of interaction provided a unique opportunity to examine exactly when and how these tools were used, as well as how acceptable the resolutions were. Results showed that the participants used the pre-probed altitude fly-out menu in 14% of conflict cases and preferred to use it in a strategic timeframe on data comm equipped and level flight aircraft. The interactive auto resolver was also used in a primarily strategic timeframe on 22% of conflicts and that their preference was to use it on conflicts involving data comm equipped aircraft as well. Of the 258 resolutions displayed, 46% were implemented and 54% were not. The auto resolver was rated highly by participants in terms of confidence and preference. Factors such as

Nonlinear infragravity–wave interactions on a gently sloping laboratory beach

NARCIS (Netherlands)

De Bakker, A.T.M.; Herbers, T.H.C.; Smit, P.B.; Tissier, M.F.S.; Ruessink, B.G.

2015-01-01

A high-resolution dataset of three irregular wave conditions collected on a gently sloping laboratory beach is analyzed to study nonlinear energy transfers involving infragravity frequencies. This study uses bispectral analysis to identify the dominant, nonlinear interactions and estimate energy

Nonlinear infragravity-wave interactions on a gently sloping laboratory beach

NARCIS (Netherlands)

de Bakker, A. T M; Herbers, T. H C; Smit, P. B.; Tissier, M. F S; Ruessink, B. G.

2015-01-01

A high-resolution dataset of three irregular wave conditions collected on a gently sloping laboratory beach is analyzed to study nonlinear energy transfers involving infragravity frequencies. This study uses bispectral analysis to identify the dominant, nonlinear interactions and estimate energy

Mathematical Analysis for Non-reciprocal-interaction-based Model of Collective Behavior

Science.gov (United States)

Kano, Takeshi; Osuka, Koichi; Kawakatsu, Toshihiro; Ishiguro, Akio

2017-12-01

In many natural and social systems, collective behaviors emerge as a consequence of non-reciprocal interaction between their constituents. As a first step towards understanding the core principle that underlies these phenomena, we previously proposed a minimal model of collective behavior based on non-reciprocal interactions by drawing inspiration from friendship formation in human society, and demonstrated via simulations that various non-trivial patterns emerge by changing parameters. In this study, a mathematical analysis of the proposed model wherein the system size is small is performed. Through the analysis, the mechanism of the transition between several patterns is elucidated.

Identification and expression profiling analysis of TCP family genes involved in growth and development in maize.

Science.gov (United States)

Chai, Wenbo; Jiang, Pengfei; Huang, Guoyu; Jiang, Haiyang; Li, Xiaoyu

2017-10-01

The TCP family is a group of plant-specific transcription factors. TCP genes encode proteins harboring bHLH structure, which is implicated in DNA binding and protein-protein interactions and known as the TCP domain. TCP genes play important roles in plant development and have been evolutionarily and functionally elaborated in various plants, however, no overall phylogenetic analysis or expression profiling of TCP genes in Zea mays has been reported. In the present study, a systematic analysis of molecular evolution and functional prediction of TCP family genes in maize ( Z . mays L.) has been conducted. We performed a genome-wide survey of TCP genes in maize, revealing the gene structure, chromosomal location and phylogenetic relationship of family members. Microsynteny between grass species and tissue-specific expression profiles were also investigated. In total, 29 TCP genes were identified in the maize genome, unevenly distributed on the 10 maize chromosomes. Additionally, ZmTCP genes were categorized into nine classes based on phylogeny and purifying selection may largely be responsible for maintaining the functions of maize TCP genes. What's more, microsynteny analysis suggested that TCP genes have been conserved during evolution. Finally, expression analysis revealed that most TCP genes are expressed in the stem and ear, which suggests that ZmTCP genes influence stem and ear growth. This result is consistent with the previous finding that maize TCP genes represses the growth of axillary organs and enables the formation of female inflorescences. Altogether, this study presents a thorough overview of TCP family in maize and provides a new perspective on the evolution of this gene family. The results also indicate that TCP family genes may be involved in development stage in plant growing conditions. Additionally, our results will be useful for further functional analysis of the TCP gene family in maize.

Applicability of soil-structure interaction analysis methods for earthquake loadings (IV)

International Nuclear Information System (INIS)

Chang, S. P.; Ko, H. M.; Kim, J. K.; Yoon, J. Y.; Chin, B. M.; Yang, T. S.; Park, D. H.; Chung, W.; Park, J. Y.

1996-07-01

The ultimate goals of this research are to cultivate the capability of accurate SSI analysis and to develop the effective soil-structure interaction analysis method and computer program by comparing analysis results obtained in Lotung/Hualien LSST project. In this research, computer analysis program using hyper element was developed to analyze the forced vibration test and seismic test of the on-going Hualien LSST project. Prediction analysis and post-prediction analysis for Hualien LSST forced vibration and seismic response were executed by developed program. Thus this report is mainly composed of two parts. One is the summary of theoretical background of hyper element and the other is prediction analysis and post-prediction analysis results for Hualien LSST forced vibration and seismic response tests executed by developed program. Also, a coupling method of hyper element and generalized three-dimensional finite element or general axisymmetric finite element was presented for the further development of computer analysis program related to three dimensional hybrid soil-structure interaction and for the verification, the dynamic stiffness' of rigid circular /rectangular foundation are calculated. It is confirmed that program using hyper element is efficient and practical because it can consider non-homogeneity easily and execute the analysis in short time by using analytic solution m horizontal direction

Job involvement of primary healthcare employees: does a service provision model play a role?

Science.gov (United States)

Koponen, Anne M; Laamanen, Ritva; Simonsen-Rehn, Nina; Sundell, Jari; Brommels, Mats; Suominen, Sakari

2010-05-01

To investigate whether the development of job involvement of primary healthcare (PHC) employees in Southern Municipality (SM), where PHC services were outsourced to an independent non-profit organisation, differed from that in the three comparison municipalities (M1, M2, M3) with municipal service providers. Also, the associations of job involvement with factors describing the psychosocial work environment were investigated. A panel mail survey 2000-02 in Finland (n=369, response rates 73% and 60%). The data were analysed by descriptive statistics and multivariate linear regression analysis. Despite the favourable development in the psychosocial work environment, job involvement decreased most in SM, which faced the biggest organisational changes. Job involvement decreased also in M3, where the psychosocial work environment deteriorated most. Job involvement in 2002 was best predicted by high baseline level of interactional justice and work control, positive change in interactional justice, and higher age. Also other factors, such as organisational stability, seemed to play a role; after controlling for the effect of the psychosocial work characteristics, job involvement was higher in M3 than in SM. Outsourcing of PHC services may decrease job involvement at least during the first years. A particular service provision model is better than the others only if it is superior in providing a favourable and stable psychosocial work environment.

Analysis of Human-Spacesuit Interaction

Science.gov (United States)

Thomas, Neha

2015-01-01

Astronauts sustain injuries of various natures such as finger delamination, joint pain, and redness due to their interaction with the space suit. The role of the Anthropometry and Biomechanics Facility is to understand the biomechanics, environmental variables, and ergonomics of the suit. This knowledge is then used to make suggestions for improvement in future iterations of the space suit assembly to prevent injuries while allowing astronauts maneuverability, comfort, and tactility. The projects I was involved in were the Extravehicular Mobility Unit (EMU) space suit stiffness study and the glove feasibility study. The EMU project looked at the forces exerted on the shoulder, arm, and wrist when subjects performed kinematic tasks with and without a pressurized suit. The glove study consisted of testing three conditions - the Series 4000 glove, the Phase VI glove, and the no glove condition. With more than forty channels of sensor data total, it was critical to develop programs that could analyze data with basic descriptive statistics and generate relevant graphs to help understand what happens within the space suit and glove. In my project I created a Graphical User Interface (GUI) in MATLAB that would help me visualize what each sensor was doing within a task. The GUI is capable of displaying overlain plots and can be synchronized with video. This was helpful during the stiffness testing to visualize how the forces on the arm acted while the subject performed tasks such as shoulder adduction/abduction and bicep curls. The main project of focus, however, was the glove comparison study. I wrote MATLAB programs which generated movies of the strain vectors during specific tasks. I also generated graphs that summarized the differences between each glove for the strain, shear and FSR sensors. Preliminary results indicate that the Phase VI glove places less strain and shear on the hand. Future work includes continued data analysis of surveys and sensor data. In the end

Variants of SCARB1 and VDR Involved in Complex Genetic Interactions May Be Implicated in the Genetic Susceptibility to Clear Cell Renal Cell Carcinoma

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Ewelina Pośpiech

2015-01-01

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

GxGrare: gene-gene interaction analysis method for rare variants from high-throughput sequencing data.

Science.gov (United States)

Kwon, Minseok; Leem, Sangseob; Yoon, Joon; Park, Taesung

2018-03-19

With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it has been shown that only a small proportion of the genetic etiology of complex diseases could be explained by the genetic factors identified from GWAS. This missing heritability could possibly be explained by gene-gene interaction (epistasis) and rare variants. There has been an exponential growth of gene-gene interaction analysis for common variants in terms of methodological developments and practical applications. Also, the recent advancement of high-throughput sequencing technologies makes it possible to conduct rare variant analysis. However, little progress has been made in gene-gene interaction analysis for rare variants. Here, we propose GxGrare which is a new gene-gene interaction method for the rare variants in the framework of the multifactor dimensionality reduction (MDR) analysis. The proposed method consists of three steps; 1) collapsing the rare variants, 2) MDR analysis for the collapsed rare variants, and 3) detect top candidate interaction pairs. GxGrare can be used for the detection of not only gene-gene interactions, but also interactions within a single gene. The proposed method is illustrated with 1080 whole exome sequencing data of the Korean population in order to identify causal gene-gene interaction for rare variants for type 2 diabetes. The proposed GxGrare performs well for gene-gene interaction detection with collapsing of rare variants. GxGrare is available at http://bibs.snu.ac.kr/software/gxgrare which contains simulation data and documentation. Supported operating systems include Linux and OS X.

Benefits, challenges, and best practices for involving audiences in the development of interactive coastal risk communication tools: Professional communicators' experiences

Science.gov (United States)

Stephens, S. H.; DeLorme, D.

2017-12-01

To make scientific information useful and usable to audiences, communicators must understand audience needs, expectations, and future applications. This presentation synthesizes benefits, challenges, and best practices resulting from a qualitative social science interview study of nine professionals on their experiences developing interactive visualization tools for communicating about coastal environmental risks. Online interactive risk visualization tools, such as flooding maps, are used to provide scientific information about the impacts of coastal hazards. These tools have a wide range of audiences and purposes, including time-sensitive emergency communication, infrastructure and natural resource planning, and simply starting a community conversation about risks. Thus, the science, purposes, and audiences of these tools require a multifaceted communication strategy. In order to make these tools useable and accepted by their audiences, many professional development teams solicit target end-user input or incorporate formal user-centered design into the development process. This presentation will share results of seven interviews with developers of U.S. interactive coastal risk communication tools, ranging from state-level to international in scope. Specific techniques and procedures for audience input that were used in these projects will be discussed, including ad-hoc conversations with users, iterative usability testing with project stakeholder groups, and other participatory mechanisms. The presentation will then focus on benefits, challenges, and recommendations for best practice that the interviewees disclosed about including audiences in their development projects. Presentation attendees will gain an understanding of different procedures and techniques that professionals employ to involve end-users in risk tool development projects, as well as important considerations and recommendations for effectively involving audiences in science communication design.

QTL analysis of citrus tristeza virus-citradia interaction.

Science.gov (United States)

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

2004-02-01

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

A comparative analysis between France and Japan on local governments' involvement in nuclear safety governance

International Nuclear Information System (INIS)

Sugawara, Shin-etsu; Shiroyama, Hideaki

2011-01-01

This paper shows a comparative analysis between France and Japan on the way of the local governments' involvement in nuclear safety governance through some interviews. In France, a law came into force that requires related local governments to establish 'Commision Locale d'Information' (CLI), which means the local governments officially involve in nuclear regulatory activity. Meanwhile, in Japan, related local governments substantially involve in the operation of nuclear facilities through the 'safety agreements' in spite of the lack of legal authority. As a result of comparative analysis, we can point out some institutional input from French cases as follows: to clarify the local governments' roles in the nuclear regulation system, to establish the official channels of communication among nuclear utilities, national regulatory authorities and local governments, and to stipulate explicitly the transparency as a purpose of safety regulation. (author)

Teacher Training in Family Involvement: An Interpersonal Approach.

Science.gov (United States)

Coleman, Mick; Wallinga, Charlotte

2000-01-01

Discusses ways to develop family-school-community involvement, based on an early childhood teacher training course in family involvement. Discusses strategies for using Maslow's Hierarchy of Needs to facilitate family involvement interactions, and using student teachers' experiences for structuring reflective thought about family involvement…

Service user involvement enhanced the research quality in a study using interpretative phenomenological analysis - the power of multiple perspectives.

Science.gov (United States)

Mjøsund, Nina Helen; Eriksson, Monica; Espnes, Geir Arild; Haaland-Øverby, Mette; Jensen, Sven Liang; Norheim, Irene; Kjus, Solveig Helene Høymork; Portaasen, Inger-Lill; Vinje, Hege Forbech

2017-01-01

The aim of this study was to examine how service user involvement can contribute to the development of interpretative phenomenological analysis methodology and enhance research quality. Interpretative phenomenological analysis is a qualitative methodology used in nursing research internationally to understand human experiences that are essential to the participants. Service user involvement is requested in nursing research. We share experiences from 4 years of collaboration (2012-2015) on a mental health promotion project, which involved an advisory team. Five research advisors either with a diagnosis or related to a person with severe mental illness constituted the team. They collaborated with the research fellow throughout the entire research process and have co-authored this article. We examined the joint process of analysing the empirical data from interviews. Our analytical discussions were audiotaped, transcribed and subsequently interpreted following the guidelines for good qualitative analysis in interpretative phenomenological analysis studies. The advisory team became 'the researcher's helping hand'. Multiple perspectives influenced the qualitative analysis, which gave more insightful interpretations of nuances, complexity, richness or ambiguity in the interviewed participants' accounts. The outcome of the service user involvement was increased breadth and depth in findings. Service user involvement improved the research quality in a nursing research project on mental health promotion. The interpretative element of interpretative phenomenological analysis was enhanced by the emergence of multiple perspectives in the qualitative analysis of the empirical data. We argue that service user involvement and interpretative phenomenological analysis methodology can mutually reinforce each other and strengthen qualitative methodology. © 2016 The Authors. Journal of Advanced Nursing Published by John Wiley & Sons Ltd.

Seismic soil structure interaction: analysis and centrifuge model studies

International Nuclear Information System (INIS)

Finn, W.D.L.; Ledbetter, R.H.; Beratan, L.L.

1985-01-01

A method for non-linear dynamic effective stress analysis is introduced which is applicable to soil-structure interaction problems. Full interaction including slip between structure and foundation is taken into account and the major factors are included which must be considered when computing dynamic soil response. An experimental investigation was conducted using simulated earthquake tests on centrifuged geotechnical models in order to obtain prototype response data of foundation soils carrying both surface and embedded structures and to validate the dynamic effective stress analysis. Horizontal and vertical accelerations were measured at various points on structures and in the sand foundation. Seismically-induced pore water pressure changes were also measured at various locations in the foundation. Computer plots of the data were obtained while the centrifuge was in flight and representative samples are presented. The results show clearly the pronounced effect that increasing pore water pressures have on dynamic response. It is demonstrated that a coherent picture of dynamic response of soil-structure systems is provided by dynamic effective stress non-linear analysis. Based on preliminary results, it appears that the pore water pressure effects can be predicted

Seismic soil-structure interaction: Analysis and centrifuge model studies

International Nuclear Information System (INIS)

Finn, W.D.L.; Ledbetter, R.H.; Beratan, L.L.

1986-01-01

A method for nonlinear dynamic effective stress analysis applicable to soil-structure interaction problems is introduced. Full interaction including slip between structure and foundation is taken into account and the major factors that must be considered when computing dynamic soil response are included. An experimental investigation using simulated earthquake tests on centrifuged geotechnical models was conducted to obtain prototype response data of foundation soils carrying both surface and embedded structures and to validate the dynamic effective stress analysis. The centrifuge tests were conducted in the Geotechnical Centrifuge at Cambridge University, England. Horizontal and vertical accelerations were measured at various points on structures and in the sand foundation. Seismically induced pore water pressure changes were also measured at various locations in the foundation. Computer plots of the data were obtained while the centrifuge was in flight and representative samples are presented. The results clearly show the pronounced effect of increasing pore water pressures on dynamic response. It is demonstrated that a coherent picture of dynamic response of soil-structure systems is provided by dynamic effective stress nonlinear analysis. On the basis of preliminary results, it appears that the effects of pore water pressure can be predicted. (orig.)

Interactive Safety Analysis Framework of Autonomous Intelligent Vehicles

Directory of Open Access Journals (Sweden)

Cui You Xiang

2016-01-01

Full Text Available More than 100,000 people were killed and around 2.6 million injured in road accidents in the People’s Republic of China (PRC, that is four to eight times that of developed countries, equivalent to 6.2 mortality per 10 thousand vehicles—the highest rate in the world. There are more than 1,700 fatalities and 840,000 injuries yearly due to vehicle crashes off public highways. In this paper, we proposed a interactive safety situation and threat analysis framework based on driver behaviour and vehicle dynamics risk analysis based on ISO26262…

Interactive visual analysis of nuclear data with ZVView

International Nuclear Information System (INIS)

Zerkin, Viktor

2002-01-01

This paper describes the cross section graphics software package ZVVIEW that was developed for the evaluators to perform efficient interactive visual analysis of experimental and theoretical nuclear data. ZVVIEW is a very powerful and complete package that simplifies the presentation of nuclear cross section data. A CD-ROM version of this computer package is available from the IAEA-NDS on request. (a.n.)

Instrumental biosensors: new perspectives for the analysis of biomolecular interactions.

Science.gov (United States)

Nice, E C; Catimel, B

1999-04-01

The use of instrumental biosensors in basic research to measure biomolecular interactions in real time is increasing exponentially. Applications include protein-protein, protein-peptide, DNA-protein, DNA-DNA, and lipid-protein interactions. Such techniques have been applied to, for example, antibody-antigen, receptor-ligand, signal transduction, and nuclear receptor studies. This review outlines the principles of two of the most commonly used instruments and highlights specific operating parameters that will assist in optimising experimental design, data generation, and analysis.

Extended sequence diagram for human system interaction

International Nuclear Information System (INIS)

Hwang, Jong Rok; Choi, Sun Woo; Ko, Hee Ran; Kim, Jong Hyun

2012-01-01

Unified Modeling Language (UML) is a modeling language in the field of object oriented software engineering. The sequence diagram is a kind of interaction diagram that shows how processes operate with one another and in what order. It is a construct of a message sequence chart. It depicts the objects and classes involved in the scenario and the sequence of messages exchanged between the objects needed to carry out the functionality of the scenario. This paper proposes the Extended Sequence Diagram (ESD), which is capable of depicting human system interaction for nuclear power plants, as well as cognitive process of operators analysis. In the conventional sequence diagram, there is a limit to only identify the activities of human and systems interactions. The ESD is extended to describe operators' cognitive process in more detail. The ESD is expected to be used as a task analysis method for describing human system interaction. The ESD can also present key steps causing abnormal operations or failures and diverse human errors based on cognitive condition

Numerical analysis of interacting cracks in biaxial stress field

International Nuclear Information System (INIS)

Kovac, M.; Cizelj, L.

1999-01-01

The stress corrosion cracks as seen for example in PWR steam generator tubing made of Inconel 600 usually produce highly irregular kinked and branched crack patterns. Crack initialization and propagation depends on stress state underlying the crack pattern. Numerical analysis (such as finite element method) of interacting kinked and branched cracks can provide accurate solutions. This paper discusses the use of general-purpose finite element code ABAQUS for evaluating stress fields at crack tips of interacting complex cracks. The results obtained showed reasonable agreement with the reference solutions and confirmed use of finite elements in such class of problems.(author)

Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

DEFF Research Database (Denmark)

Michael, John; Bogart, Kathleen; Tylén, Kristian

2015-01-01

, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual nonverbal behavior was assessed via behavioral coders, while verbal behavior was automatically extracted from the sound...... files. Alignment was assessed using cross recurrence quantification analysis and mixed effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased...

Preliminary Analysis of the Bundle-Duct Interaction for the fuel of SFR

Energy Technology Data Exchange (ETDEWEB)

Lee, Byoung Oon; Cheon, Jin Sik; Hahn, Do Hee; Lee, Chan Bock [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2008-10-15

BDI (Bundle-Duct Interaction) occurs in the fuel of SFR (Sodium-cooled Fast Reactor) due to the radial expansion and bowing of a fuel pin bundle. Under the BDI condition, excess cladding strain and hot spots would occur. Therefore, BDI, which is the dominant deformation mechanisms in a fuel pin bundle, should be considered to evaluate the FBR fuel integrity. The analysis codes such as ETOILE and BMBOO, have been developed to evaluate the BDI behavior. The bundle duct interaction model is also being developed for SFR in Korea. This model is based on ANSYS. In this paper, the fuel pin configuration model for the BDI calculation was established. The preliminary analysis of the bundle-duct interaction was performed to evaluate the fuel design concept.

Interactive exploratory data analysis tool in Alzheimer’s disease

Directory of Open Access Journals (Sweden)

Diana Furcila

2015-04-01

Thus, MorExAn provide us the possibility to relate histopathological data with neuropsychological and clinical variables. The aid of this interactive visualization tool brings us the possibility to find unexpected conclusions beyond the insight provided by simple statistics analysis, as well as to improve neuroscientists’ productivity.

77 FR 9946 - Draft Guidance for Industry on Drug Interaction Studies-Study Design, Data Analysis, Implications...

Science.gov (United States)

2012-02-21

... industry entitled ``Drug Interaction Studies--Study Design, Data Analysis, Implications for Dosing, and... data analysis in the context of identifying potential drug interactions. The guidance also addresses... Studies--Study Design, Data Analysis, and Implications for Dosing and Labeling.'' Comments were received...

Proteomic analysis of ACTN4-interacting proteins reveals it's a putative involvement in mRNA metabolism

International Nuclear Information System (INIS)

Khotin, Mikhail; Turoverova, Lidia; Aksenova, Vasilisa; Barlev, Nikolai; Borutinskaite, Veronika Viktorija; Vener, Alexander; Bajenova, Olga; Magnusson, Karl-Eric; Pinaev, George P.; Tentler, Dmitri

2010-01-01

Alpha-actinin 4 (ACTN4) is an actin-binding protein. In the cytoplasm, ACTN4 participates in structural organisation of the cytoskeleton via cross-linking of actin filaments. Nuclear localisation of ACTN4 has also been reported, but no clear role in the nucleus has been established. In this report, we describe the identification of proteins associated with ACTN4 in the nucleus. A combination of two-dimensional gel electrophoresis (2D-GE) and MALDI-TOF mass-spectrometry revealed a large number of ACTN4-bound proteins that are involved in various aspects of mRNA processing and transport. The association of ACTN4 with different ribonucleoproteins suggests that a major function of nuclear ACTN4 may be regulation of mRNA metabolism and signaling.

Non-linear soil-structure interaction

International Nuclear Information System (INIS)

Wolf, J.P.

1984-01-01

The basic equation of motion to analyse the interaction of a non-linear structure and an irregular soil with the linear unbounded soil is formulated in the time domain. The contribution of the unbounded soil involves convolution integrals of the dynamic-stiffness coefficients in the time domain and the corresponding motions. As another possibility, a flexibility formulation fot the contribution of the unbounded soil using the dynamic-flexibility coefficients in the time domain, together with the direct-stiffness method for the structure and the irregular soil can be applied. As an example of a non-linear soil-structure-interaction analysis, the partial uplift of the basemat of a structure is examined. (Author) [pt

minepath.org: a free interactive pathway analysis web server.

Science.gov (United States)

Koumakis, Lefteris; Roussos, Panos; Potamias, George

2017-07-03

( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Phthalic Acid Chemical Probes Synthesized for Protein-Protein Interaction Analysis

Directory of Open Access Journals (Sweden)

Chin-Jen Wu

2013-06-01

Full Text Available 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.

Probability and sensitivity analysis of machine foundation and soil interaction

Directory of Open Access Journals (Sweden)

Králik J., jr.

2009-06-01

Full Text Available This paper deals with the possibility of the sensitivity and probabilistic analysis of the reliability of the machine foundation depending on variability of the soil stiffness, structure geometry and compressor operation. The requirements to design of the foundation under rotating machines increased due to development of calculation method and computer tools. During the structural design process, an engineer has to consider problems of the soil-foundation and foundation-machine interaction from the safety, reliability and durability of structure point of view. The advantages and disadvantages of the deterministic and probabilistic analysis of the machine foundation resistance are discussed. The sensitivity of the machine foundation to the uncertainties of the soil properties due to longtime rotating movement of machine is not negligible for design engineers. On the example of compressor foundation and turbine fy. SIEMENS AG the affectivity of the probabilistic design methodology was presented. The Latin Hypercube Sampling (LHS simulation method for the analysis of the compressor foundation reliability was used on program ANSYS. The 200 simulations for five load cases were calculated in the real time on PC. The probabilistic analysis gives us more complex information about the soil-foundation-machine interaction as the deterministic analysis.

On the Importance of Nonbonding Donor-Acceptor Interactions Involving PO2. Radicals: An ab Initio Study.

Science.gov (United States)

Bauzá, Antonio; Frontera, Antonio

2017-08-18

In this study, several σ-type and π-hole bonding complexes between PO 2 . radicals and electron-rich entities have been optimized at the RI-MP2/aug-cc-pVQZ level of theory. We have used Cl - , Br - , I - anions, and ethene, ethyne, HCN, HF, and H 2 O as Lewis bases. In addition, we have performed natural bond orbital (NBO) and Mulliken spin density analyses, highlighting the donor-acceptor nature of the interaction. Moreover, an interesting retro-donation from the single electron lone pair of the PO 2 . radical to the Lewis base also contributes to the stabilization of the complexes studied herein. Finally, the Bader's atoms-in-molecules (AIM) analysis of several complexes has been performed to further characterize the interactions discussed herein. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emotional Processing, Interaction Process, and Outcome in Clarification-Oriented Psychotherapy for Personality Disorders: A Process-Outcome Analysis.

Science.gov (United States)

Kramer, Ueli; Pascual-Leone, Antonio; Rohde, Kristina B; Sachse, Rainer

2016-06-01

It is important to understand the change processes involved in psychotherapies for patients with personality disorders (PDs). One patient process that promises to be useful in relation to the outcome of psychotherapy is emotional processing. In the present process-outcome analysis, we examine this question by using a sequential model of emotional processing and by additionally taking into account a therapist's appropriate responsiveness to a patient's presentation in clarification-oriented psychotherapy (COP), a humanistic-experiential form of therapy. The present study involved 39 patients with a range of PDs undergoing COP. Session 25 was assessed as part of the working phase of each therapy by external raters in terms of emotional processing using the Classification of Affective-Meaning States (CAMS) and in terms of the overall quality of therapist-patient interaction using the Process-Content-Relationship Scale (BIBS). Treatment outcome was assessed pre- and post-therapy using the Global Severity Index (GSI) of the SCL-90-R and the BDI. Results indicate that the good outcome cases showed more self-compassion, more rejecting anger, and a higher quality of therapist-patient interaction compared to poorer outcome cases. For good outcome cases, emotional processing predicted 18% of symptom change at the end of treatment, which was not found for poor outcome cases. These results are discussed within the framework of an integrative understanding of emotional processing as an underlying mechanism of change in COP, and perhaps in other effective therapy approaches for PDs.

Analysis of core-concrete interaction event with flooding for the Advanced Neutron Source reactor

International Nuclear Information System (INIS)

Kim, S.H.; Taleyarkhan, R.P.; Georgevich, V.; Navarro-Valenti, S.

1993-01-01

This paper discusses salient aspects of the methodology, assumptions, and modeling of various features related to estimation of source terms from an accident involving a molten core-concrete interaction event (with and without flooding) in the Advanced Neutron Source (ANS) reactor at the Oak Ridge National Laboratory. Various containment configurations are considered for this postulated severe accident. Several design features (such as rupture disks) are examined to study containment response during this severe accident. Also, thermal-hydraulic response of the containment and radionuclide transport and retention in the containment are studied. The results are described as transient variations of source terms, which are then used for studying off-site radiological consequences and health effects for the support of the Conceptual Safety Analysis Report for ANS. The results are also to be used to examine the effectiveness of subpile room flooding during this type of severe accident

Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells

DEFF Research Database (Denmark)

Vandamme, Julien; Völkel, Pamela; Rosnoblet, Claire

2011-01-01

Polycomb group (PcG) proteins maintain transcriptional repression of hundreds of genes involved in development, signaling or cancer using chromatin-based epigenetic mechanisms. Biochemical studies in Drosophila have revealed that PcG proteins associate in at least two classes of protein complexes...... known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Drosophila core PRC1 is composed of four subunits, Polycomb (Pc), Sex combs extra (Sce), Polyhomeotic (Ph), and Posterior sex combs (Psc). Each of these proteins has multiple orthologs in vertebrates classified respectively as the CBX, RING...... in order to identify interacting partners of CBX family proteins under the same experimental conditions. Our analysis identified with high confidence about 20 proteins co-eluted with CBX2 and CBX7 tagged proteins, about 40 with CBX4, and around 60 with CBX6 and CBX8. We provide evidences that the CBX...

Association analysis of schizophrenia on 18 genes involved in neuronal migration

DEFF Research Database (Denmark)

Kähler, Anna K; Djurovic, Srdjan; Kulle, Bettina

2008-01-01

neuronal function, morphology, and formation of synaptic connections. We have investigated the putative association between SZ and gene variants engaged in the neuronal migration process, by performing an association study on 839 cases and 1,473 controls of Scandinavian origin. Using a gene-wide approach......Several lines of evidence support the theory of schizophrenia (SZ) being a neurodevelopmental disorder. The structural, cytoarchitectural and functional brain abnormalities reported in patients with SZ, might be due to aberrant neuronal migration, since the final position of neurons affects......, tagSNPs in 18 candidate genes have been genotyped, with gene products involved in the neuron-to-glial cell adhesion, interactions with the DISC1 protein and/or rearrangements of the cytoskeleton. Of the 289 markers tested, 19 markers located in genes MDGA1, RELN, ITGA3, DLX1, SPARCL1, and ASTN1...

Reflections on Practical Approaches to Involving Children and Young People in the Data Analysis Process

Science.gov (United States)

Coad, Jane; Evans, Ruth

2008-01-01

This article reflects on key methodological issues emerging from children and young people's involvement in data analysis processes. We outline a pragmatic framework illustrating different approaches to engaging children, using two case studies of children's experiences of participating in data analysis. The article highlights methods of…

The Effect upon the Behavior and Attitudes of Student Teachers of Training Cooperating Teachers and Student Teachers in the Use of Interaction Analysis as a Classroom Observational Technique.

Science.gov (United States)

Amidon, Edmund

In a 2 1/2-year study of the application of interaction analysis (a method of classroom observation) to preservice teacher education, approximately 40 secondary student teachers were involved in an experiment during each of 3 semesters. A 2 by 2 factorial design made it possible to test the influence of 2 independent variables (student teacher…

Proteomic analysis of the compatible interaction of wheat and powdery mildew (Blumeria graminis f. sp. tritici).

Science.gov (United States)

Li, Jie; Yang, Xiwen; Liu, Xinhao; Yu, Haibo; Du, Congyang; Li, Mengda; He, Dexian

2017-02-01

Proteome characteristics of wheat leaves with the powdery mildew pathogen Blumeria graminis f. sp. tritici (Bgt) infection were investigated by two-dimensional electrophoresis and tandem MALDI-TOF/TOF-MS. We identified 46 unique proteins which were differentially expressed at 24, 48, and 72 h post-inoculation. The functional classification of these proteins showed that most of them were involved in photosynthesis, carbohydrate and nitrogen metabolism, defense responses, and signal transduction. Upregulated proteins included primary metabolism pathways and defense responses, while proteins related to photosynthesis and signal transduction were mostly downregulated. As expected, more antioxidative proteins were activated at the later infection stage than the earlier stage, suggesting that the antioxidative system of host plays a role in maintaining the compatible interaction between wheat and powdery mildew. A high accumulation of 6-phosphogluconate dehydrogenase and isocitrate dehydrogenase in infected leaves indicated the regulation of the TCA cycle and pentose phosphate pathway in parallel to the activation of host defenses. The downregulation of MAPK5 could be facilitated for the compatible interaction of wheat plants and Bgt. qRT-PCR analysis supported the data of protein expression profiles. Our results reveal the relevance of primary plant metabolism and defense responses during compatible interaction, and provide new insights into the biology of susceptible wheat in response to Bgt infection. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Global innovation networks and university-firm interactions: an exploratory survey analysis

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Gustavo Britto

2015-02-01

Full Text Available The literature on Global Innovation Networks has contributed to identify changes in the innovation activities of multinational corporations. Although university-firm interactions are seen as an important factor for the emergence of GINs, their role has received limited attention. This paper aims to fill this gap in two ways. First, it carries out an exploratory analysis of an original survey dataset, of firms in three industrial sectors from nine developed and developing countries. Second, the paper analyses whether the role of universities in global innovation networks is related to national systems of innovation with varying degrees of maturity. Multiple correspondence analysis and a Probit model are used to establish the relevance of key factors in driving GINs. The results identify distinctive profiles constructed mainly according to firm characteristics, but reflecting country specific patterns of association. The Probit model confirms that internationalization processes and the existence of local interactions substantially increase the probability of interactions with international institutions.

Emotion and attention interactions in social cognition: brain regions involved in processing anger prosody.

Science.gov (United States)

Sander, David; Grandjean, Didier; Pourtois, Gilles; Schwartz, Sophie; Seghier, Mohamed L; Scherer, Klaus R; Vuilleumier, Patrik

2005-12-01

Multiple levels of processing are thought to be involved in the appraisal of emotionally relevant events, with some processes being engaged relatively independently of attention, whereas other processes may depend on attention and current task goals or context. We conducted an event-related fMRI experiment to examine how processing angry voice prosody, an affectively and socially salient signal, is modulated by voluntary attention. To manipulate attention orthogonally to emotional prosody, we used a dichotic listening paradigm in which meaningless utterances, pronounced with either angry or neutral prosody, were presented simultaneously to both ears on each trial. In two successive blocks, participants selectively attended to either the left or right ear and performed a gender-decision on the voice heard on the target side. Our results revealed a functional dissociation between different brain areas. Whereas the right amygdala and bilateral superior temporal sulcus responded to anger prosody irrespective of whether it was heard from a to-be-attended or to-be-ignored voice, the orbitofrontal cortex and the cuneus in medial occipital cortex showed greater activation to the same emotional stimuli when the angry voice was to-be-attended rather than to-be-ignored. Furthermore, regression analyses revealed a strong correlation between orbitofrontal regions and sensitivity on a behavioral inhibition scale measuring proneness to anxiety reactions. Our results underscore the importance of emotion and attention interactions in social cognition by demonstrating that multiple levels of processing are involved in the appraisal of emotionally relevant cues in voices, and by showing a modulation of some emotional responses by both the current task-demands and individual differences.

Ethanol and Caffeine Effects on Social Interaction and Recognition in Mice: Involvement of Adenosine A2A and A1 Receptors.

Science.gov (United States)

López-Cruz, Laura; San-Miguel, Noemí; Bayarri, Pilar; Baqi, Younis; Müller, Christa E; Salamone, John D; Correa, Mercé

2016-01-01

Ethanol and caffeine are frequently consumed in combination and have opposite effects on the adenosine system: ethanol metabolism leads to an increase in adenosine levels, while caffeine is a non-selective adenosine A 1 /A 2A receptor antagonist. These receptors are highly expressed in striatum and olfactory tubercle, brain areas involved in exploration and social interaction in rodents. Ethanol modulates social interaction processes, but the role of adenosine in social behavior is still poorly understood. The present work was undertaken to study the impact of ethanol, caffeine and their combination on social behavior, and to explore the involvement of A 1 and A 2A receptors on those actions. Male CD1 mice were evaluated in a social interaction three-chamber paradigm, for preference of conspecific vs. object, and also for long-term recognition memory of familiar vs. novel conspecific. Ethanol showed a biphasic effect, with low doses (0.25 g/kg) increasing social contact and higher doses (1.0-1.5 g/kg) reducing social interaction. However, no dose changed social preference; mice always spent more time sniffing the conspecific than the object, independently of the ethanol dose. Ethanol, even at doses that did not change social exploration, produced amnestic effects on social recognition the following day. Caffeine reduced social contact (15.0-60.0 mg/kg), and even blocked social preference at higher doses (30.0-60.0 mg/kg). The A 1 antagonist Cyclopentyltheophylline (CPT; 3-9 mg/kg) did not modify social contact or preference on its own, and the A 2A antagonist MSX-3 (1.5-6 mg/kg) increased social interaction at all doses. Ethanol at intermediate doses (0.5-1.0 g/kg) was able to reverse the reduction in social exploration induced by caffeine (15.0-30.0 mg/kg). Although there was no interaction between ethanol and CPT or MSX-3 on social exploration in the first day, MSX-3 blocked the amnestic effects of ethanol observed on the following day. Thus, ethanol impairs the

Culture Analysis: The Interaction of Organizational and National Culture

OpenAIRE

Marina Arnoldovna Makarchenko

2015-01-01

The article is devoted to the interaction between organizational culture factors. A comparative analysis of the Russian and Argentine companies culture using different methods shows the impact of the national mentality in organizational culture. The thesis is the need to introduce the term "regional culture" in relation to modern Russia.

Analysis of transient plasmonic interactions using an MOT-PMCHWT integral equation solver

KAUST Repository

Uysal, Ismail Enes

2014-07-01

Device design involving metals and dielectrics at nano-scales and optical frequencies calls for simulation tools capable of analyzing plasmonic interactions. To this end finite difference time domain (FDTD) and finite element methods have been used extensively. Since these methods require volumetric meshes, the discretization size should be very small to accurately resolve fast-decaying fields in the vicinity of metal/dielectric interfaces. This can be avoided using integral equation (IE) techniques that discretize only on the interfaces. Additionally, IE solvers implicitly enforce the radiation condition and consequently do not need (approximate) absorbing boundary conditions. Despite these advantages, IE solvers, especially in time domain, have not been used for analyzing plasmonic interactions.

Biospecific protein immobilization for rapid analysis of weak protein interactions using self-interaction nanoparticle spectroscopy.

Science.gov (United States)

Bengali, Aditya N; Tessier, Peter M

2009-10-01

"Reversible" protein interactions govern diverse biological behavior ranging from intracellular transport and toxic protein aggregation to protein crystallization and inactivation of protein therapeutics. Much less is known about weak protein interactions than their stronger counterparts since they are difficult to characterize, especially in a parallel format (in contrast to a sequential format) necessary for high-throughput screening. We have recently introduced a highly efficient approach of characterizing protein self-association, namely self-interaction nanoparticle spectroscopy (SINS; Tessier et al., 2008; J Am Chem Soc 130:3106-3112). This approach exploits the separation-dependent optical properties of gold nanoparticles to detect weak self-interactions between proteins immobilized on nanoparticles. A limitation of our previous work is that differences in the sequence and structure of proteins can lead to significant differences in their affinity to adsorb to nanoparticle surfaces, which complicates analysis of the corresponding protein self-association behavior. In this work we demonstrate a highly specific approach for coating nanoparticles with proteins using biotin-avidin interactions to generate protein-nanoparticle conjugates that report protein self-interactions through changes in their optical properties. Using lysozyme as a model protein that is refractory to characterization by conventional SINS, we demonstrate that surface Plasmon wavelengths for gold-avidin-lysozyme conjugates over a range of solution conditions (i.e., pH and ionic strength) are well correlated with lysozyme osmotic second virial coefficient measurements. Since SINS requires orders of magnitude less protein and time than conventional methods (e.g., static light scattering), we envision this approach will find application in large screens of protein self-association aimed at either preventing (e.g., protein aggregation) or promoting (e.g., protein crystallization) these

A BDNF sensitive mechanism is involved in the fear memory resulting from the interaction between stress and the retrieval of an established trace.

Science.gov (United States)

Giachero, Marcelo; Bustos, Silvia G; Calfa, Gaston; Molina, Victor A

2013-04-15

The present study investigates the fear memory resulting from the interaction of a stressful experience and the retrieval of an established fear memory trace. Such a combination enhanced both fear expression and fear retention in adult Wistar rats. Likewise, midazolam intra-basolateral amygdala (BLA) infusion prior to stress attenuated the enhancement of fear memory thus suggesting the involvement of a stress-induced reduction of the GABAergic transmission in BLA in the stress-induced enhancing effect. It has been suggested that, unlike the immediate-early gene Zif268 which is related to the reconsolidation process, the expression of hippocampal brain-derived neurotrophic factor (BDNF) is highly correlated with consolidation. We therefore evaluate the relative contribution of these two neurobiological processes to the fear memory resulting from the above-mentioned interaction. Intra-dorsal hippocampus (DH) infusions of either the antisense Zif268 or the inhibitor of the protein degradation (Clasto-Lactacystin β-Lactone), suggested to be involved in the retrieval-dependent destabilization process, did not affect the resulting contextual memory. In contrast, the knockdown of hippocampal BDNF mitigated the stress-induced facilitating influence on fear retention. In addition, the retrieval experience elevated BDNF level in DH at 60 min after recall exclusively in stressed animals. These findings suggest the involvement of a hippocampal BDNF sensitive mechanism in the stress-promoting influence on the fear memory following retrieval.

Exhaustive Genome-Wide Search for SNP-SNP Interactions Across 10 Human Diseases

Directory of Open Access Journals (Sweden)

William Murk

2016-07-01

Full Text Available The identification of statistical SNP-SNP interactions may help explain the genetic etiology of many human diseases, but exhaustive genome-wide searches for these interactions have been difficult, due to a lack of power in most datasets. We aimed to use data from the Resource for Genetic Epidemiology Research on Adult Health and Aging (GERA study to search for SNP-SNP interactions associated with 10 common diseases. FastEpistasis and BOOST were used to evaluate all pairwise interactions among approximately N = 300,000 single nucleotide polymorphisms (SNPs with minor allele frequency (MAF ≥ 0.15, for the dichotomous outcomes of allergic rhinitis, asthma, cardiac disease, depression, dermatophytosis, type 2 diabetes, dyslipidemia, hemorrhoids, hypertensive disease, and osteoarthritis. A total of N = 45,171 subjects were included after quality control steps were applied. These data were divided into discovery and replication subsets; the discovery subset had > 80% power, under selected models, to detect genome-wide significant interactions (P < 10−12. Interactions were also evaluated for enrichment in particular SNP features, including functionality, prior disease relevancy, and marginal effects. No interaction in any disease was significant in both the discovery and replication subsets. Enrichment analysis suggested that, for some outcomes, interactions involving SNPs with marginal effects were more likely to be nominally replicated, compared to interactions without marginal effects. If SNP-SNP interactions play a role in the etiology of the studied conditions, they likely have weak effect sizes, involve lower-frequency variants, and/or involve complex models of interaction that are not captured well by the methods that were utilized.

Vulnerabilities, Influences and Interaction Paths: Failure Data for Integrated System Risk Analysis

Science.gov (United States)

Malin, Jane T.; Fleming, Land

2006-01-01

We describe graph-based analysis methods for identifying and analyzing cross-subsystem interaction risks from subsystem connectivity information. By discovering external and remote influences that would be otherwise unexpected, these methods can support better communication among subsystem designers at points of potential conflict and to support design of more dependable and diagnosable systems. These methods identify hazard causes that can impact vulnerable functions or entities if propagated across interaction paths from the hazard source to the vulnerable target. The analysis can also assess combined impacts of And-Or trees of disabling influences. The analysis can use ratings of hazards and vulnerabilities to calculate cumulative measures of the severity and importance. Identification of cross-subsystem hazard-vulnerability pairs and propagation paths across subsystems will increase coverage of hazard and risk analysis and can indicate risk control and protection strategies.

Interactive emergency communication involving persons in crisis.

Science.gov (United States)

Nordby, Halvor; Nøhr, Øyvind

2009-01-01

We studied the dialogue between telephone operators at medical emergency communication centres in Norway and parents of children later diagnosed with sudden infant death syndrome. The aim was to understand how the parents experienced the communication with the telephone operators. The qualitative method involved semi-structured interviews. We interviewed six respondents from urban areas and five from rural areas. An important finding was that all the parents were satisfied with the resuscitation instructions they received. It was also perceived as important that the emergency operators expressed empathy and care. We believe that it is not merely the quality of the resuscitation attempts that the operators' efforts should be measured against. It is also important that the operators provide good explanations and express emotional support. Our findings indicate that this will be enormously appreciated, even if callers do not feel that they are capable of performing optimum resuscitation.

Analysis of protein interactions at native chloroplast membranes by ellipsometry.

Directory of Open Access Journals (Sweden)

Verena Kriechbaumer

Full Text Available Membrane bound receptors play vital roles in cell signaling, and are the target for many drugs, yet their interactions with ligands are difficult to study by conventional techniques due to the technical difficulty of monitoring these interactions in lipid environments. In particular, the ability to analyse the behaviour of membrane proteins in their native membrane environment is limited. Here, we have developed a quantitative approach to detect specific interactions between low-abundance chaperone receptors within native chloroplast membranes and their soluble chaperone partners. Langmuir-Schaefer film deposition was used to deposit native chloroplasts onto gold-coated glass slides, and interactions between the molecular chaperones Hsp70 and Hsp90 and their receptors in the chloroplast membranes were detected and quantified by total internal reflection ellipsometry (TIRE. We show that native chloroplast membranes deposited on gold-coated glass slides using Langmuir-Schaefer films retain functional receptors capable of binding chaperones with high specificity and affinity. Taking into account the low chaperone receptor abundance in native membranes, these binding properties are consistent with data generated using soluble forms of the chloroplast chaperone receptors, OEP61 and Toc64. Therefore, we conclude that chloroplasts have the capacity to selectively bind chaperones, consistent with the notion that chaperones play an important role in protein targeting to chloroplasts. Importantly, this method of monitoring by TIRE does not require any protein labelling. This novel combination of techniques should be applicable to a wide variety of membranes and membrane protein receptors, thus presenting the opportunity to quantify protein interactions involved in fundamental cellular processes, and to screen for drugs that target membrane proteins.

Complex experimental analysis of rifle-shooter interaction

Directory of Open Access Journals (Sweden)

Michał Taraszewski, M.ScEng, PhD. candidate

2017-10-01

Full Text Available In this study, a complex analysis of a man-weapon interaction based on experimental effort is presented. The attention is focused on how a shooter can influence on a rifle, opposite to generally considered in literature rifle's impact on a shooter. It is shown, based on the kbk AKM weapon, that each support point of the rifle has an substantial impact on the system. It is said that identifying human reactions on weapon may let to describe gun movement and thus may be applied to weapon accuracy determination.

Structural Analysis of DNA Interactions with Magnesium Ion Studied by Raman Spectroscopy

OpenAIRE

S. Ponkumar; P. Duraisamy; N. Iyandurai

2011-01-01

Problem statement: In the present study, FT Raman spectroscopy had been used to extend our knowledge about Magnesium ion - DNA interactions at various volume ratios (1:50, 1:20, 1:10 and 1:5). Approach: The analysis of FT Raman data supported the existence of structural specificities in the interaction and also the stability of DNA secondary structure. Results: Results from the Raman spectra clearly indicate that the interaction of Magnesium ion with DNA is mainly through the phosphate groups...

Interactive Materials In The Teaching Of Astronomy

Science.gov (United States)

Macêdo, J. A.; Voelzke, M. R.

2014-10-01

This study presents results of a survey conducted at the Federal Institution of Education, Science and Technology in the North of Minas Gerais (IFNMG), and aimed to investigate the potentialities of the use of interactive materials in the teaching of astronomy. An advanced training course with involved learning activities about basic concepts of astronomy was offered to thirty-two Licenciate students in Physics, Mathematics and Biological Science. The following steps were to be taken: i) analysis of the pedagogical projects (PPC) of the licenciates at the IFNMG, research locus of its Campus Januária; ii) analysis of students' preconceptions about astronomy and digital technologies, identified by the application of an initial questionnaire; iii) preparation of the course taking into account the students' previous knowledge; iv) application of the education proposal developed under part-time presence modality, using various interactive tools; v) application and analysis of the final questionnaire. The test was conducted with the qualitative and quantitative methodology, combined with a content analysis. The results indicated that in the IFNMG only the licenciate-course in physics includes astronomy content diluted in various subjects of the curriculum; the rates of students prior knowledge in relation to astronomy was low; an evidence of meaningful learning of the concepts related to astronomy, and of viability of resource use involving digital technologies in the Teaching of astronomy, which may contribute to the broadening of methodological options of future teachers and meet their training needs.

Efficient analysis using custom interactive visualization tools at a Superfund site

International Nuclear Information System (INIS)

Williams, G.; Durham, L.

1992-01-01

Custom visualization analysis programs were developed and used to analyze contaminant transport calculations from a three-dimensional numerical groundwater flow model developed for a Department of Energy Superfund site. The site hydrogeology, which is highly heterogenous, includes both fractured limestone and dolomite and alluvium deposits. Three-dimensional interactive visualization techniques were used to understand and analyze the three-dimensional, double-porosity modeling results. A graphical object oriented programming environment was applied to efficiently develop custom visualization programs in a coarse-grained data structure language. Comparisons were made, using the results from the three-dimensional, finite-difference model, between traditional two-dimensional analyses (contour and vector plots) and interactive three-dimensional techniques. Subjective comparison areas include the accuracy of analysis, the ability to understand the results of three-dimensional contaminant transport simulation, and the capability to transmit the results of the analysis to the project management. In addition, a quantitative comparison was made on the time required to develop a thorough analysis of the modeling results. The conclusions from the comparative study showed that the visualization analysis provided an increased awareness of the contaminant transport mechanisms, provided new insights into contaminant migration, and resulted in a significant time savings

Efficient analysis using custom interactive visualization tools at a Superfund site

Energy Technology Data Exchange (ETDEWEB)

Williams, G. [Northwestern Univ., Evanston, IL (United States); Durham, L. [Argonne National Lab., IL (United States)

1992-12-01

Custom visualization analysis programs were developed and used to analyze contaminant transport calculations from a three-dimensional numerical groundwater flow model developed for a Department of Energy Superfund site. The site hydrogeology, which is highly heterogenous, includes both fractured limestone and dolomite and alluvium deposits. Three-dimensional interactive visualization techniques were used to understand and analyze the three-dimensional, double-porosity modeling results. A graphical object oriented programming environment was applied to efficiently develop custom visualization programs in a coarse-grained data structure language. Comparisons were made, using the results from the three-dimensional, finite-difference model, between traditional two-dimensional analyses (contour and vector plots) and interactive three-dimensional techniques. Subjective comparison areas include the accuracy of analysis, the ability to understand the results of three-dimensional contaminant transport simulation, and the capability to transmit the results of the analysis to the project management. In addition, a quantitative comparison was made on the time required to develop a thorough analysis of the modeling results. The conclusions from the comparative study showed that the visualization analysis provided an increased awareness of the contaminant transport mechanisms, provided new insights into contaminant migration, and resulted in a significant time savings.

Grapefruit and drug interactions.

Science.gov (United States)

2012-12-01

Since the late 1980s, grapefruit juice has been known to affect the metabolism of certain drugs. Several serious adverse effects involving drug interactions with grapefruit juice have been published in detail. The components of grapefruit juice vary considerably depending on the variety, maturity and origin of the fruit, local climatic conditions, and the manufacturing process. No single component accounts for all observed interactions. Other grapefruit products are also occasionally implicated, including preserves, lyophylised grapefruit juice, powdered whole grapefruit, grapefruit seed extract, and zest. Clinical reports of drug interactions with grapefruit juice are supported by pharmacokinetic studies, each usually involving about 10 healthy volunteers, in which the probable clinical consequences were extrapolated from the observed plasma concentrations. Grapefruit juice inhibits CYP3A4, the cytochrome P450 isoenzyme most often involved in drug metabolism. This increases plasma concentrations of the drugs concerned, creating a risk of overdose and dose-dependent adverse effects. Grapefruit juice also inhibits several other cytochrome P450 isoenzymes, but they are less frequently implicated in interactions with clinical consequences. Drugs interacting with grapefruit and inducing serious clinical consequences (confirmed or very probable) include: immunosuppressants, some statins, benzodiazepines, most calcium channel blockers, indinavir and carbamazepine. There are large inter-individual differences in enzyme efficiency. Along with the variable composition of grapefruit juice, this makes it difficult to predict the magnitude and clinical consequences of drug interactions with grapefruit juice in a given patient. There is increasing evidence that transporter proteins such as organic anion transporters and P-glycoprotein are involved in interactions between drugs and grapefruit juice. In practice, numerous drugs interact with grapefruit juice. Although only a few

Social Interaction in Adventure Recreation Participation

Science.gov (United States)

Michael A. Schuett

1992-01-01

This study investigated the social interaction of white water kayakers and attempted to predict the level of enduring involvement of participants. It was hypothesized that social interaction would shift from classes and programs to peers of similar interests as level of involvement increased. The results did show that social interaction is a primary reason for...

An Analysis of Interaction Patterns in the Focus Group Interview

Directory of Open Access Journals (Sweden)

Gavora Peter

2015-12-01

Full Text Available This paper is based on the analysis of a focus group interview of a moderator and a group of undergraduate students on the topic of self-regulation of learning. The purpose of the investigation was to identify interaction patterns that appeared in the talk of participants and the moderator. In the stream of communication two rudimentary interaction patterns were recognized. The first pattern was named the Catalogue. It consists of a sequence of turns of participants who respond to a request of the moderator and who provide their answers, one by one, without reacting on the content of the previous partner(s talk. The other interaction pattern was called the Domino. In this pattern participants respond to each other. The Catalogue pattern prevailed in the interview. Alongside with identification of patterns of interaction the study demonstrated the functions of the common ground and its accomplishment in the talk of the moderator and participants.

Identification of interfaces involved in weak interactions with application to F-actin-aldolase rafts.

Science.gov (United States)

Hu, Guiqing; Taylor, Dianne W; Liu, Jun; Taylor, Kenneth A

2018-03-01

Macromolecular interactions occur with widely varying affinities. Strong interactions form well defined interfaces but weak interactions are more dynamic and variable. Weak interactions can collectively lead to large structures such as microvilli via cooperativity and are often the precursors of much stronger interactions, e.g. the initial actin-myosin interaction during muscle contraction. Electron tomography combined with subvolume alignment and classification is an ideal method for the study of weak interactions because a 3-D image is obtained for the individual interactions, which subsequently are characterized collectively. Here we describe a method to characterize heterogeneous F-actin-aldolase interactions in 2-D rafts using electron tomography. By forming separate averages of the two constituents and fitting an atomic structure to each average, together with the alignment information which relates the raw motif to the average, an atomic model of each crosslink is determined and a frequency map of contact residues is computed. The approach should be applicable to any large structure composed of constituents that interact weakly and heterogeneously. Copyright © 2017 Elsevier Inc. All rights reserved.

MOVANAID: An Interactive Aid for Analysis of Movement Capabilities.

Science.gov (United States)

Cooper, George E.; And Others

A computer-drive interactive aid for movement analysis, called MOVANAID, has been developed to be of assistance in the performance of certain Army intelligence processing tasks in a tactical environment. It can compute fastest travel times and paths through road networks for military units of various types, as well as fastest times in which…

Seismic simulation analysis of nuclear reactor building by soil-building interaction model

International Nuclear Information System (INIS)

Muto, K.; Kobayashi, T.; Motohashi, S.; Kusano, N.; Mizuno, N.; Sugiyama, N.

1981-01-01

Seismic simulation analysis were performed for evaluating soil-structure interaction effects by an analytical approach using a 'Lattice Model' developed by the authors. The purpose of this paper is to check the adequacy of this procedure for analyzing soil-structure interaction by means of comparing computed results with recorded ones. The 'Lattice Model' approach employs a lumped mass interactive model, in which not only the structure but also the underlying and/or surrounding soil are modeled as descretized elements. The analytical model used for this study extends about 310 m in the horizontal direction and about 103 m in depth. The reactor building is modeled as three shearing-bending sticks (outer wall, inner wall and shield wall) and the underlying and surrounding soil are divided into four shearing sticks (column directly beneath the reactor building, adjacent, near and distant columns). A corresponding input base motion for the 'Lattice Model' was determined by a deconvolution analysis using a recorded motion at elevation -18.5 m in the free-field. The results of this simulation analysis were shown to be in reasonably good agreement with the recorded ones in the forms of the distribution of ground motions and structural responses, acceleration time histories and related response spectra. These results showed that the 'Lattice Model' approach was an appropriate one to estimate the soil-structure interaction effects. (orig./HP)

Comparative proteomic analysis reveals proteins putatively involved in toxin biosynthesis in the marine dinoflagellate Alexandrium catenella.

Science.gov (United States)

Wang, Da-Zhi; Gao, Yue; Lin, Lin; Hong, Hua-Sheng

2013-01-22

Alexandrium is a neurotoxin-producing dinoflagellate genus resulting in paralytic shellfish poisonings around the world. However, little is known about the toxin biosynthesis mechanism in Alexandrium. This study compared protein profiles of A. catenella collected at different toxin biosynthesis stages (non-toxin synthesis, initial toxin synthesis and toxin synthesizing) coupled with the cell cycle, and identified differentially expressed proteins using 2-DE and MALDI-TOF-TOF mass spectrometry. The results showed that toxin biosynthesis of A. catenella occurred within a defined time frame in the G1 phase of the cell cycle. Proteomic analysis indicated that 102 protein spots altered significantly in abundance (P translation. Among them, nine proteins with known functions in paralytic shellfish toxin-producing cyanobacteria, i.e., methionine S-adenosyltransferase, chloroplast ferredoxin-NADP+ reductase, S-adenosylhomocysteinase, adenosylhomocysteinase, ornithine carbamoyltransferase, inorganic pyrophosphatase, sulfotransferase (similar to), alcohol dehydrogenase and arginine deiminase, varied significantly at different toxin biosynthesis stages and formed an interaction network, indicating that they might be involved in toxin biosynthesis in A. catenella. This study is the first step in the dissection of the behavior of the A. catenella proteome during different toxin biosynthesis stages and provides new insights into toxin biosynthesis in dinoflagellates.

Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host

Science.gov (United States)

Xi, Zhiyong; Gavotte, Laurent; Xie, Yan; Dobson, Stephen L

2008-01-01

Background Intracellular Wolbachia bacteria are obligate, maternally-inherited, endosymbionts found frequently in insects and other invertebrates. The success of Wolbachia can be attributed in part to an ability to alter host reproduction via mechanisms including cytoplasmic incompatibility (CI), parthenogenesis, feminization and male killing. Despite substantial scientific effort, the molecular mechanisms underlying the Wolbachia/host interaction are unknown. Results Here, an in vitro Wolbachia infection was generated in the Drosophila S2 cell line, and transcription profiles of infected and uninfected cells were compared by microarray. Differentially-expressed patterns related to reproduction, immune response and heat stress response are observed, including multiple genes that have been previously reported to be involved in the Wolbachia/host interaction. Subsequent in vivo characterization of differentially-expressed products in gonads demonstrates that Angiotensin Converting Enzyme (Ance) varies between Wolbachia infected and uninfected flies and that the variation occurs in a sex-specific manner. Consistent with expectations for the conserved CI mechanism, the observed Ance expression pattern is repeatable in different Drosophila species and with different Wolbachia types. To examine Ance involvement in the CI phenotype, compatible and incompatible crosses of Ance mutant flies were conducted. Significant differences are observed in the egg hatch rate resulting from incompatible crosses, providing support for additional experiments examining for an interaction of Ance with the CI mechanism. Conclusion Wolbachia infection is shown to affect the expression of multiple host genes, including Ance. Evidence for potential Ance involvement in the CI mechanism is described, including the prior report of Ance in spermatid differentiation, Wolbachia-induced sex-specific effects on Ance expression and an Ance mutation effect on CI levels. The results support the use of

Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host.

Science.gov (United States)

Xi, Zhiyong; Gavotte, Laurent; Xie, Yan; Dobson, Stephen L

2008-01-02

Intracellular Wolbachia bacteria are obligate, maternally-inherited, endosymbionts found frequently in insects and other invertebrates. The success of Wolbachia can be attributed in part to an ability to alter host reproduction via mechanisms including cytoplasmic incompatibility (CI), parthenogenesis, feminization and male killing. Despite substantial scientific effort, the molecular mechanisms underlying the Wolbachia/host interaction are unknown. Here, an in vitro Wolbachia infection was generated in the Drosophila S2 cell line, and transcription profiles of infected and uninfected cells were compared by microarray. Differentially-expressed patterns related to reproduction, immune response and heat stress response are observed, including multiple genes that have been previously reported to be involved in the Wolbachia/host interaction. Subsequent in vivo characterization of differentially-expressed products in gonads demonstrates that Angiotensin Converting Enzyme (Ance) varies between Wolbachia infected and uninfected flies and that the variation occurs in a sex-specific manner. Consistent with expectations for the conserved CI mechanism, the observed Ance expression pattern is repeatable in different Drosophila species and with different Wolbachia types. To examine Ance involvement in the CI phenotype, compatible and incompatible crosses of Ance mutant flies were conducted. Significant differences are observed in the egg hatch rate resulting from incompatible crosses, providing support for additional experiments examining for an interaction of Ance with the CI mechanism. Wolbachia infection is shown to affect the expression of multiple host genes, including Ance. Evidence for potential Ance involvement in the CI mechanism is described, including the prior report of Ance in spermatid differentiation, Wolbachia-induced sex-specific effects on Ance expression and an Ance mutation effect on CI levels. The results support the use of Wolbachia infected cell cultures

Measurement and visualization of face-to-face interaction among community-dwelling older adults using wearable sensors.

Science.gov (United States)

Masumoto, Kouhei; Yaguchi, Takaharu; Matsuda, Hiroshi; Tani, Hideaki; Tozuka, Keisuke; Kondo, Narihiko; Okada, Shuichi

2017-10-01

A number of interventions have been undertaken to develop and promote social networks among community-dwelling older adults. However, it has been difficult to examine the effects of these interventions, because of problems in assessing interactions. The present study was designed to quantitatively measure and visualize face-to-face interactions among elderly participants in an exercise program. We also examined relationships among interactional variables, personality and interest in community involvement, including interactions with the local community. Older adults living in the same community were recruited to participate in an exercise program that consisted of four sessions. We collected data on face-to-face interactions of the participants by using a wearable sensor technology device. Network analysis identified the communication networks of participants in the exercise program, as well as changes in these networks. Additionally, there were significant correlations between the number of people involved in face-to-face interactions and changes in both interest in community involvement and interactions with local community residents, as well as personality traits, including agreeableness. Social networks in the community are essential for solving problems caused by the aging society. We showed the possible applications of face-to-face interactional data for identifying core participants having many interactions, and isolated participants having only a few interactions within the community. Such data would be useful for carrying out efficient interventions for increasing participants' involvement with their community. Geriatr Gerontol Int 2017; 17: 1752-1758. © 2017 Japan Geriatrics Society.

The relationship between online campaigning and political involvement

NARCIS (Netherlands)

Kruikemeier, S.; van Noort, G.; Vliegenthart, R.; de Vreese, C.H.

2016-01-01

Purpose-The purpose of this paper is to examine the causal relationship between interactive and personal campaigning on social media and political involvement, and the mechanisms that explain the effects. Specifically, this study examines whether personal and interactive communication on Twitter

Involvement of Gaucher Disease Mutations in Parkinson Disease.

Science.gov (United States)

Vilageliu, Lluisa; Grinberg, Daniel

2017-01-01

Gaucher disease is an autosomal recessive lysosomal storage disorder, caused by mutations in the GBA gene. The frequency of Gaucher disease patients and heterozygote carriers that developed Parkinson disease has been found to be above that of the control population. This fact suggests that mutations in the GBA gene can be involved in Parkison's etiology. Analysis of large cohorts of patients with Parkinson disease has shown that there are significantly more cases bearing GBA mutations than those found among healthy individuals. Functional studies have proven an interaction between α-synuclein and GBA, the levels of which presented an inverse correlation. Mutant GBA proteins cause increases in α-synuclein levels, while an inhibition of GBA by α-synuclein has been also demonstrated. Saposin C, a coactivator of GBA, has been shown to protect GBA from this inhibition. Among the GBA variants associated with Parkinson disease, E326K seems to be one of the most prevalent. Interestingly, it is involved in Gaucher disease only when it forms part of a double-mutant allele, usually with the L444P mutation. Structural analyses have revealed that both residues (E326 and L444) interact with Saposin C and, probably, also with α-synuclein. This could explain the antagonistic role of these two proteins in relation to GBA. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Taylor Dispersion Analysis as a promising tool for assessment of peptide-peptide interactions

DEFF Research Database (Denmark)

Høgstedt, Ulrich B; Schwach, Grégoire; van de Weert, Marco

2016-01-01

solutions increased with concentration. Our results indicate that a viscosity difference between run buffer and sample in Taylor Dispersion Analysis may result in overestimation of the measured diffusion coefficient. Thus, Taylor Dispersion Analysis provides a practical, but as yet primarily qualitative......Protein-protein and peptide-peptide (self-)interactions are of key importance in understanding the physiochemical behavior of proteins and peptides in solution. However, due to the small size of peptide molecules, characterization of these interactions is more challenging than for proteins...

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

Science.gov (United States)

Braberg, Hannes; Moehle, Erica A.; Shales, Michael; Guthrie, Christine; Krogan, Nevan J.

2014-01-01

We have achieved a residue-level resolution of genetic interaction mapping – a technique that measures how the function of one gene is affected by the alteration of a second gene – by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

"Heart trouble" and religious involvement among older white men and women.

Science.gov (United States)

Thompson, Edward H; Killgore, Leslie; Connors, Heather

2009-09-01

Objective Few studies examine how older adults' health status affects spiritual and religious involvement. This study examined the effects of gender and poor cardiac health on older adults' ends, means, and quest religious motivations and frequency of private devotion. Method Longitudinal data (12 months between the T1 and T2 interviews) with 182 older adults sampled from a Northeast city were used to examine in a multivariate analysis of covariance whether gender and the existence of cardiac health problems at T1 affected older adults' spiritual and religious involvement at T2. Findings A gender and cardiac health condition interaction showed older men with heart trouble had more changes in religious involvement-they engaged in more religious doubt, prayed less, and were not as intrinsically oriented at T2. Discussion The findings strongly suggest that older men with heart trouble may maintain a masculine style and shun seeking divine help.

Spectroscopic analysis of the riboflavin-serum albumins interaction on silver nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Voicescu, Mariana, E-mail: voicescu@icf.ro; Angelescu, Daniel G. [Institute of Physical Chemistry ' Ilie Murgulescu' , Romanian Academy (Romania); Ionescu, Sorana [University of Bucharest, Department of Physical Chemistry (Romania); Teodorescu, Valentin S. [Institute of Atomic Physics, National Institute of Materials Physics (Romania)

2013-04-15

Spectrophotometric behavior of riboflavin (RF) adsorbed on silver nanoparticles as well as its interaction with two serum albumins, BSA and HSA, respectively, has been evidenced. The time evolution of the plasmonic features of the complexes formed by RF/BSA/HSA and Ag(0) nanoparticles having an average diameter of 10.0 {+-} 2.0 nm have been investigated by UV-Vis absorption spectroscopy. Using steady-state and time-resolved fluorescence spectroscopy, the structure, stability, and dynamics of the serum albumins have been studied. The efficiency of energy transfer process between RF and serum albumins on silver nanoparticles has been estimated. A reaction mechanism of RF with silver nanoparticles is also proposed and the results are discussed with relevance to the involvement of the silver nanoparticles to the redox process of RF and to the RF-serum albumins interaction into a silver nanoparticles complex.

Spectroscopic analysis of the riboflavin—serum albumins interaction on silver nanoparticles

Science.gov (United States)

Voicescu, Mariana; Angelescu, Daniel G.; Ionescu, Sorana; Teodorescu, Valentin S.

2013-04-01

Spectrophotometric behavior of riboflavin (RF) adsorbed on silver nanoparticles as well as its interaction with two serum albumins, BSA and HSA, respectively, has been evidenced. The time evolution of the plasmonic features of the complexes formed by RF/BSA/HSA and Ag(0) nanoparticles having an average diameter of 10.0 ± 2.0 nm have been investigated by UV-Vis absorption spectroscopy. Using steady-state and time-resolved fluorescence spectroscopy, the structure, stability, and dynamics of the serum albumins have been studied. The efficiency of energy transfer process between RF and serum albumins on silver nanoparticles has been estimated. A reaction mechanism of RF with silver nanoparticles is also proposed and the results are discussed with relevance to the involvement of the silver nanoparticles to the redox process of RF and to the RF-serum albumins interaction into a silver nanoparticles complex.

Seismic analysis of a large LMFBR with fluid-structure interactions

International Nuclear Information System (INIS)

Ma, D.C.

1985-01-01

The seismic analysis of a large LMFBR with many internal components and structures is presented. Both vertical and horizontal seismic excitations are considered. The important hydrodynamic phenomena such as fluid-structure interaction, sloshing, fluid coupling and fluid inertia effects are included in the analysis. The results of this study are discussed in detail. Information which is useful to the design of future reactions under seismic conditions is also given. 4 refs., 12 figs

Association of COMT and COMT-DRD2 interaction with creative potential

Directory of Open Access Journals (Sweden)

Shun eZhang

2014-04-01

Full Text Available Several lines of evidence suggest that genes involved in dopamine (DA transmission may contribute to creativity. Among these genes, the catechol-O-methyltransferase gene (COMT and the dopamine D2 receptor gene (DRD2 are the most promising candidates. Our previous study has revealed evidence for the involvement of DRD2 in creative potential. The present study extended our previous study by systematically exploring the association of COMT with creative potential as well as the interaction between COMT and DRD2. Twelve single nucleotide polymorphisms (SNPs covering COMT were genotyped in 543 healthy Chinese college students whose creative potentials were assessed by divergent thinking tests. Single SNP analysis showed that rs174697 was nominally associated with verbal originality, two SNPs (rs737865 and rs5993883 were nominally associated with figural fluency, and two SNPs (rs737865 and rs4680 were nominally associated with figural originality. Haplotype analysis showed that, the TCT and CCT haplotype (rs737865-rs174675-rs5993882 were nominally associated with figural originality, and the TATGCAG and CGCGGGA haplotype (rs4646312-rs6269-rs4633-rs6267-rs4818-rs4680-rs769224 were nominally associated with figural originality and verbal flexibility, respectively. However, none of these nominal findings survived correction for multiple testing. Gene-gene interaction analysis identified one significant four-way interaction of rs174675 (COMT, rs174697 (COMT, rs1076560 (DRD2 and rs4436578 (DRD2 on verbal fluency, one significant four-way interaction of rs174675 (COMT, rs4818 (COMT, rs1076560 (DRD2 and rs4648317 (DRD2 on verbal flexibility, and one significant three-way interaction of rs5993883 (COMT, rs4648319 (DRD2 and rs4648317 (DRD2 on figural flexibility. In conclusion, the present study provides nominal evidence for the involvement of COMT in creative potential and suggests that DA related genes may act in coordination to contribute to creativity.

Analysis of pedagogical communication and interaction of lessons with tablet application

Directory of Open Access Journals (Sweden)

Maněnová Martina

2016-01-01

Full Text Available The article describes possibilities of lessons evaluation by means of structured observations. Our study took an interest in the use of information and communication technologies in teaching of mathematics on elementary school. Concrete it was case tablets implementation in standard lessons on elementary school. The aim of the submitted project was to find out if tablets application in lessons would influence pedagogical communication and interaction. We selected structured FIAS (Flanders Interaction Analysis system observation as a basic research method. This method was spread on 16 categories in total, which we used for structured observation of lessons. The results were successively processed to interaction characteristics.

Uncertainty in soil-structure interaction analysis arising from differences in analytical techniques

International Nuclear Information System (INIS)

Maslenikov, O.R.; Chen, J.C.; Johnson, J.J.

1982-07-01

This study addresses uncertainties arising from variations in different modeling approaches to soil-structure interaction of massive structures at a nuclear power plant. To perform a comprehensive systems analysis, it is necessary to quantify, for each phase of the traditional analysis procedure, both the realistic seismic response and the uncertainties associated with them. In this study two linear soil-structure interaction techniques were used to analyze the Zion, Illinois nuclear power plant: a direct method using the FLUSH computer program and a substructure approach using the CLASSI family of computer programs. In-structure response from two earthquakes, one real and one synthetic, was compared. Structure configurations from relatively simple to complicated multi-structure cases were analyzed. The resulting variations help quantify uncertainty in structure response due to analysis procedures

Structure soil structure interaction effects: Seismic analysis of safety related collocated concrete structures

International Nuclear Information System (INIS)

Joshi, J.R.

2000-01-01

The Process, Purification and Stack Buildings are collocated safety related concrete shear wall structures with plan dimensions in excess of 100 feet. An important aspect of their seismic analysis was the determination of structure soil structure interaction (SSSI) effects, if any. The SSSI analysis of the Process Building, with one other building at a time, was performed with the SASSI computer code for up to 50 frequencies. Each combined model had about 1500 interaction nodes. Results of the SSSI analysis were compared with those from soil structure interaction (SSI) analysis of the individual buildings, done with ABAQUS and SASSI codes, for three parameters: peak accelerations, seismic forces and the in-structure floor response spectra (FRS). The results may be of wider interest due to the model size and the potential applicability to other deep soil layered sites. Results obtained from the ABAQUS analysis were consistently higher, as expected, than those from the SSI and SSSI analyses using the SASSI. The SSSI effect between the Process and Purification Buildings was not significant. The Process and Stack Building results demonstrated that under certain conditions a massive structure can have an observable effect on the seismic response of a smaller and less stiff structure

Thematic content analysis of work-family interactions: Retired cosmonauts’ reflections

Science.gov (United States)

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.

A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility

NARCIS (Netherlands)

Bush, W.S.; McCauley, J.L.; DeJager, P.L.; Dudek, S.M.; Hafler, D.A.; Gibson, R.A.; Matthews, P.M.; Kappos, L.; Naegelin, Y.; Polman, C.H.; Hauser, S.L.; Oksenberg, J.; Haines, J.L.; Ritchie, M.D.

2011-01-01

Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also

Play with Me! Gender-Typed Social Play Behavior Analysis in Interactive Tag Games

NARCIS (Netherlands)

Moreno, Alejandro; Poppe, R.W.; Heylen, Dirk K J

2016-01-01

Promoting social behavior is one of the key goals in interactive games. In this paper, we present an experimental study in the Interactive Tag Playground (ITP) to investigate whether social behaviors reported in literature can also be observed through automated analysis. We do this by analyzing

Play with Me! Gender-Typed Social Play Behavior Analysis in Interactive Tag Games

NARCIS (Netherlands)

Moreno Celleri, Alejandro Manuel; Poppe, Ronald Walter; Heylen, Dirk K.J.

Promoting social behavior is one of the key goals in interactive games. In this paper, we present an experimental study in the Interactive Tag Playground (ITP) to investigate whether social behaviors reported in literature can also be observed through automated analysis. We do this by analyzing

Use of microring resonators for biospecific interaction analysis

Science.gov (United States)

Chalyan, Tatevik; Besselink, Geert A. J.; Heideman, Rene G.; Pavesi, Lorenzo

2017-08-01

Integrated optical biosensors based on Mach-Zehnder Interferometers and Microring Resonators are widely used for food/drug monitoring and protein studies thank to their high intrinsic sensitivity, easy integration and miniaturization, and low cost.1, 2 In this study, we present a system to perform antibody interaction analysis using a photonic chip made of an array of six microring resonators (MRRs) based on the TriPleX platform. A compact system is presented where the input light is provided by a Vertical Cavity Surface Emitting Laser (VCSEL) pigtailed to a single mode fiber and operating at a ≍ 850nm wavelength. The output signal is detected by PIN photodetectors placed in the optical signal read-out module (the so-called OSROM) and processed by an easy-to-use Fourier Transform algorithm. Bulk sensitivity (Sb=98+/-2.1 nm/RIU) and Limit of Detection (LOD=(7.5+/- 0.5) x10-6 RIU) are measured and appeared to be very similar for the six MRRs on the same chip,3 which is an important property for multianalyte detection. An analysis of the anti-biotin interaction with immobilized biotin is performed by using different concentrations of anti-biotin antibody. The dependence of the resonance wavelength shift from the antibody concentration, as well as the association and the dissociation rate constants are calculated. For the average dissociation constant (KD) of anti-biotin antibody toward immobilized biotin, a value of (1.9+/-0.5) x10-7M is estimated, which is of the same order of magnitude of other published data.4 Furthermore, the specificity of the interaction is confirmed by using negative control antibodies and by performing competition with free, i.e., dissolved, biotin. In addition, the functional surface of the sensors could be regenerated for repeated measurements up to eight times by using 10 mM glycine/HCl pH 1.5.

Analysis of fluid-structure interaction and structural respones of Chernobyl-4 reactor

International Nuclear Information System (INIS)

Wang, C.Y.; Pizzica, P.A.; Gvildys, J.; Spencer, B.W.

1989-01-01

The accident at Chernobyl-4 occurred during the running of a test to determine the turbogenerator's ability to provide in-house emergency power after shutting off its steam supply. The accident was the result of a large, destructive power excursion. This paper presents an analysis of the energetic events associated with the fuel failures, fuel-coolant thermal interactions, and the fluid-structure interaction

Inflexibility as an interactional phenomenon: Using conversation analysis to re-examine a symptom of autism.

Science.gov (United States)

Muskett, Tom; Perkins, Mick; Clegg, Judy; Body, Richard

2010-01-01

Many accounts of autism spectrum disorder (ASD) imply that the condition's behavioural 'symptoms' are direct reflexes of underlying deficits. In doing so, however, they invariably overlook the social contexts in which symptomatic behaviours occur and are identified as pathological. This study addresses this issue, using conversation analysis (CA) to examine the emergence of inflexibility, a behavioural trait symptomatic of ASD, during play involving an adult and diagnosed child. We argue that 'inflexibility' is the product of the child's strategic attempts to retain control over the unfolding interaction, within a context where such attempts breach normative expectations about adult-child play. Furthermore, it demonstrates that the adult does not resist these attempts, on occasion even explicitly providing opportunity for subsequent inflexibility. This challenges the assumption that ASD's behavioural profile solely represents the endpoint of underlying deficit, and demonstrates how 'non-impaired' speakers can be implicated in the manifestation of symptomatic behaviours.

The Interaction between Personality, Social Network Position and Involvement in Innovation Process

NARCIS (Netherlands)

E. Dolgova (Evgenia); W. van Olffen (Woody); F.A.J. van den Bosch (Frans); H.W. Volberda (Henk)

2010-01-01

textabstractAbstract This dissertation proposal investigates how personality and individuals’ social network position affect individuals’ involvement into the innovation process. It posits that people would feel inclined to become involved into the different phases of the innovation process

Intergenerational Analysis of Social Interaction

OpenAIRE

Brown, Sarah; McHardy, Jolian; Taylor, Karl

2011-01-01

We explore the relationship between the social interaction of parents and their offspring from a theoretical and an empirical perspective. Our theoretical framework establishes possible explanations for the intergenerational transfer of social interaction whereby the social interaction of the parent may influence that of their offspring and vice versa. The empirical evidence, based on four data sets covering Great Britain and the U.S., is supportive of our theoretical priors. We find robust e...

Yeast Interacting Proteins Database: YGR013W, YKL012W [Yeast Interacting Proteins Database

Lifescience Database Archive (English)

Full Text Available tion U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitm... PRP40 U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the form...ation of the second commitment complex Rows with this prey as prey (1) Rows with

Visual exploration and analysis of human-robot interaction rules

Science.gov (United States)

Zhang, Hui; Boyles, Michael J.

2013-01-01

We present a novel interaction paradigm for the visual exploration, manipulation and analysis of human-robot interaction (HRI) rules; our development is implemented using a visual programming interface and exploits key techniques drawn from both information visualization and visual data mining to facilitate the interaction design and knowledge discovery process. HRI is often concerned with manipulations of multi-modal signals, events, and commands that form various kinds of interaction rules. Depicting, manipulating and sharing such design-level information is a compelling challenge. Furthermore, the closed loop between HRI programming and knowledge discovery from empirical data is a relatively long cycle. This, in turn, makes design-level verification nearly impossible to perform in an earlier phase. In our work, we exploit a drag-and-drop user interface and visual languages to support depicting responsive behaviors from social participants when they interact with their partners. For our principal test case of gaze-contingent HRI interfaces, this permits us to program and debug the robots' responsive behaviors through a graphical data-flow chart editor. We exploit additional program manipulation interfaces to provide still further improvement to our programming experience: by simulating the interaction dynamics between a human and a robot behavior model, we allow the researchers to generate, trace and study the perception-action dynamics with a social interaction simulation to verify and refine their designs. Finally, we extend our visual manipulation environment with a visual data-mining tool that allows the user to investigate interesting phenomena such as joint attention and sequential behavioral patterns from multiple multi-modal data streams. We have created instances of HRI interfaces to evaluate and refine our development paradigm. As far as we are aware, this paper reports the first program manipulation paradigm that integrates visual programming

Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.

Science.gov (United States)

Marsh, Lorraine

2015-01-01

Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Directory of Open Access Journals (Sweden)

Alawi Malik

2011-06-01

Full Text Available The mapping of DNA-protein interactions is crucial for a full understanding of transcriptional regulation. Chromatin-immunoprecipitation followed bymassively parallel sequencing (ChIP-seq has become the standard technique for analyzing these interactions on a genome-wide scale. We have developed a software system called CASSys (ChIP-seq data Analysis Software System spanning all steps of ChIP-seq data analysis. It supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping and the detection of enriched regions (peakdetection to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side. To demonstrate CASSys’s functionality we used the system for the complete data analysis of a publicly available Chip-seq study that investigated the role of the transcription factor estrogen receptor-α in breast cancer cells.

Gestalt Interactional Groups

Science.gov (United States)

Harman, Robert L.; Franklin, Richard W.

1975-01-01

Gestalt therapy in groups is not limited to individual work in the presence of an audience. Describes several ways to involve gestalt groups interactionally. Interactions described focus on learning by doing and discovering, and are noninterpretive. (Author/EJT)

Interactive graphics analysis system for nuclear engineering applications

International Nuclear Information System (INIS)

Danchak, M.; Moyer, W.R.; Becker, M.

1973-01-01

From working with continuous slowing down theory, the need was recognized for a system which allowed rapid calculation of the theoretical flux, instant comparison with experiment and a simple means of iterating on the slowing down parameters to force flux agreement and reflect cross section modification. Similar requirements exist in other areas of nuclear work for streamlining and simplifying the data analysis process. As a solution, a unique interactive graphics analysis system (RIGAS) was devised to allow a user to calculate, display, compare, manipulate and modify his data without requiring any programming on his part. This was accomplished by establishing human primacy, through extensive human factor considerations, and designing a man-machine dialogue which responds to the mere push of a button. This system results in an instrument which maximizes man's decision making capability and the computer's speed to improve graphic communication and data analysis. (14 figs) (U.S.)

Inferring species interactions through joint mark–recapture analysis

Science.gov (United States)

Yackulic, Charles B.; Korman, Josh; Yard, Michael D.; Dzul, Maria C.

2018-01-01

Introduced species are frequently implicated in declines of native species. In many cases, however, evidence linking introduced species to native declines is weak. Failure to make strong inferences regarding the role of introduced species can hamper attempts to predict population viability and delay effective management responses. For many species, mark–recapture analysis is the more rigorous form of demographic analysis. However, to our knowledge, there are no mark–recapture models that allow for joint modeling of interacting species. Here, we introduce a two‐species mark–recapture population model in which the vital rates (and capture probabilities) of one species are allowed to vary in response to the abundance of the other species. We use a simulation study to explore bias and choose an approach to model selection. We then use the model to investigate species interactions between endangered humpback chub (Gila cypha) and introduced rainbow trout (Oncorhynchus mykiss) in the Colorado River between 2009 and 2016. In particular, we test hypotheses about how two environmental factors (turbidity and temperature), intraspecific density dependence, and rainbow trout abundance are related to survival, growth, and capture of juvenile humpback chub. We also project the long‐term effects of different rainbow trout abundances on adult humpback chub abundances. Our simulation study suggests this approach has minimal bias under potentially challenging circumstances (i.e., low capture probabilities) that characterized our application and that model selection using indicator variables could reliably identify the true generating model even when process error was high. When the model was applied to rainbow trout and humpback chub, we identified negative relationships between rainbow trout abundance and the survival, growth, and capture probability of juvenile humpback chub. Effects on interspecific interactions on survival and capture probability were strongly

Increasing Reasoning Awareness: Video Analysis of Students' Two-Party Virtual Patient Interactions.

Science.gov (United States)

Edelbring, Samuel; Parodis, Ioannis; Lundberg, Ingrid E

2018-02-27

Collaborative reasoning occurs in clinical practice but is rarely developed during education. The computerized virtual patient (VP) cases allow for a stepwise exploration of cases and thus stimulate active learning. Peer settings during VP sessions are believed to have benefits in terms of reasoning but have received scant attention in the literature. The objective of this study was to thoroughly investigate interactions during medical students' clinical reasoning in two-party VP settings. An in-depth exploration of students' interactions in dyad settings of VP sessions was performed. For this purpose, two prerecorded VP sessions lasting 1 hour each were observed, transcribed in full, and analyzed. The transcriptions were analyzed using thematic analysis, and short clips from the videos were selected for subsequent analysis in relation to clinical reasoning and clinical aspects. Four categories of interactions were identified: (1) task-related dialogue, in which students negotiated a shared understanding of the task and strategies for information gathering; (2) case-related insights and perspectives were gained, and the students consolidated and applied preexisting biomedical knowledge into a clinical setting; (3) clinical reasoning interactions were made explicit. In these, hypotheses were followed up and clinical examples were used. The researchers observed interactions not only between students and the VP but also (4) interactions with other resources, such as textbooks. The interactions are discussed in relation to theories of clinical reasoning and peer learning. The dyad VP setting is conducive to activities that promote analytic clinical reasoning. In this setting, components such as peer interaction, access to different resources, and reduced time constraints provided a productive situation in which the students pursued different lines of reasoning. ©Samuel Edelbring, Ioannis Parodis, Ingrid E Lundberg. Originally published in JMIR Medical Education (http

Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions.

Science.gov (United States)

Yamniuk, Aaron P; Newitt, John A; Doyle, Michael L; Arisaka, Fumio; Giannetti, Anthony M; Hensley, Preston; Myszka, David G; Schwarz, Fred P; Thomson, James A; Eisenstein, Edward

2015-12-01

A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions.

Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

Science.gov (United States)

Brautigam, Chad A; Zhao, Huaying; Vargas, Carolyn; Keller, Sandro; Schuck, Peter

2016-05-01

Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.

How can students contribute? A qualitative study of active student involvement in development of technological learning material for clinical skills training.

Science.gov (United States)

Haraldseid, Cecilie; Friberg, Febe; Aase, Karina

2016-01-01

Policy initiatives and an increasing amount of the literature within higher education both call for students to become more involved in creating their own learning. However, there is a lack of studies in undergraduate nursing education that actively involve students in developing such learning material with descriptions of the students' roles in these interactive processes. Explorative qualitative study, using data from focus group interviews, field notes and student notes. The data has been subjected to qualitative content analysis. Active student involvement through an iterative process identified five different learning needs that are especially important to the students: clarification of learning expectations, help to recognize the bigger picture, stimulation of interaction, creation of structure, and receiving context- specific content. The iterative process involvement of students during the development of new technological learning material will enhance the identification of important learning needs for students. The use of student and teacher knowledge through an adapted co-design process is the most optimal level of that involvement.

Parental and Infant Gender Factors in Parent-Infant Interaction: State-Space Dynamic Analysis.

Science.gov (United States)

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

Parental and Infant Gender Factors in Parent–Infant Interaction: State-Space Dynamic Analysis

Directory of Open Access Journals (Sweden)

M. Angeles Cerezo

2017-10-01

Full Text Available 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

Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H2O system.

Science.gov (United States)

Zhen, Jun-Ping; Wei, Xiao-Chun; Shi, Wen-Jing; Huang, Zhu-Yuan; Jin, Bo; Zhou, Yu-Kun

2017-11-14

In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H 2 O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H 2 O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H 2 O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H 2 O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.

Proteomic analysis of protein interactions between Eimeria maxima sporozoites and chicken jejunal epithelial cells by shotgun LC-MS/MS.

Science.gov (United States)

Huang, Jingwei; Liu, Tingqi; Li, Ke; Song, Xiaokai; Yan, Ruofeng; Xu, Lixin; Li, Xiangrui

2018-04-04

Eimeria maxima initiates infection by invading the jejunal epithelial cells of chicken. However, the proteins involved in invasion remain unknown. The research of the molecules that participate in the interactions between E. maxima sporozoites and host target cells will fill a gap in our understanding of the invasion system of this parasitic pathogen. In the present study, chicken jejunal epithelial cells were isolated and cultured in vitro. Western blot was employed to analyze the soluble proteins of E. maxima sporozoites that bound to chicken jejunal epithelial cells. Co-immunoprecipitation (co-IP) assay was used to separate the E. maxima proteins that bound to chicken jejunal epithelial cells. Shotgun LC-MS/MS technique was used for proteomics identification and Gene Ontology was employed for the bioinformatics analysis. The results of Western blot analysis showed that four proteins bands from jejunal epithelial cells co-cultured with soluble proteins of E. maxima sporozoites were recognized by the positive sera, with molecular weights of 70, 90, 95 and 130 kDa. The co-IP dilutions were analyzed by shotgun LC-MS/MS. A total of 204 proteins were identified in the E. maxima protein database using the MASCOT search engine. Thirty-five proteins including microneme protein 3 and 7 had more than two unique peptide counts and were annotated using Gene Ontology for molecular function, biological process and cellular localization. The results revealed that of the 35 annotated peptides, 22 (62.86%) were associated with binding activity and 15 (42.86%) were involved in catalytic activity. Our findings provide an insight into the interaction between E. maxima and the corresponding host cells and it is important for the understanding of molecular mechanisms underlying E. maxima invasion.

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

Science.gov (United States)

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

Survey of methods for integrated sequence analysis with emphasis on man-machine interaction

Energy Technology Data Exchange (ETDEWEB)

Kahlbom, U; Holmgren, P [RELCON, Stockholm (Sweden)

1995-05-01

This report presents a literature study concerning recently developed monotonic methodologies in the human reliability area. The work was performed by RELCON AB on commission by NKS/RAK-1, subproject 3. The topic of subproject 3 is `Integrated Sequence Analysis with Emphasis on Man-Machine Interaction`. The purpose with the study was to compile recently developed methodologies and to propose some of these methodologies for use in the sequence analysis task. The report describes mainly non-dynamic (monotonic) methodologies. One exception is HITLINE, which is a semi-dynamic method. Reference provides a summary of approaches to dynamic analysis of man-machine-interaction, and explains the differences between monotonic and dynamic methodologies. (au) 21 refs.

Survey of methods for integrated sequence analysis with emphasis on man-machine interaction

International Nuclear Information System (INIS)

Kahlbom, U.; Holmgren, P.

1995-05-01

This report presents a literature study concerning recently developed monotonic methodologies in the human reliability area. The work was performed by RELCON AB on commission by NKS/RAK-1, subproject 3. The topic of subproject 3 is 'Integrated Sequence Analysis with Emphasis on Man-Machine Interaction'. The purpose with the study was to compile recently developed methodologies and to propose some of these methodologies for use in the sequence analysis task. The report describes mainly non-dynamic (monotonic) methodologies. One exception is HITLINE, which is a semi-dynamic method. Reference provides a summary of approaches to dynamic analysis of man-machine-interaction, and explains the differences between monotonic and dynamic methodologies. (au) 21 refs

Student’s social interaction in mathematics learning

Science.gov (United States)

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.

Interactive analysis of human error factors in NPP operation events

International Nuclear Information System (INIS)

Zhang Li; Zou Yanhua; Huang Weigang

2010-01-01

Interactive of human error factors in NPP operation events were introduced, and 645 WANO operation event reports from 1999 to 2008 were analyzed, among which 432 were found relative to human errors. After classifying these errors with the Root Causes or Causal Factors, and then applying SPSS for correlation analysis,we concluded: (1) Personnel work practices are restricted by many factors. Forming a good personnel work practices is a systematic work which need supports in many aspects. (2)Verbal communications,personnel work practices, man-machine interface and written procedures and documents play great roles. They are four interaction factors which often come in bundle. If some improvements need to be made on one of them,synchronous measures are also necessary for the others.(3) Management direction and decision process, which are related to management,have a significant interaction with personnel factors. (authors)

Physical interaction between replication protein A (RPA) and MRN: involvement of RPA2 phosphorylation and the N-terminus of RPA1.

Science.gov (United States)

Oakley, Greg G; Tillison, Kristin; Opiyo, Stephen A; Glanzer, Jason G; Horn, Jeffrey M; Patrick, Steve M

2009-08-11

Replication protein A (RPA) is a heterotrimeric protein consisting of RPA1, RPA2, and RPA3 subunits that binds to single-stranded DNA (ssDNA) with high affinity. The response to replication stress requires the recruitment of RPA and the MRE11-RAD50-NBS1 (MRN) complex. RPA bound to ssDNA stabilizes stalled replication forks by recruiting checkpoint proteins involved in fork stabilization. MRN can bind DNA structures encountered at stalled or collapsed replication forks, such as ssDNA-double-stranded DNA (dsDNA) junctions or breaks, and promote the restart of DNA replication. Here, we demonstrate that RPA2 phosphorylation regulates the assembly of DNA damage-induced RPA and MRN foci. Using purified proteins, we observe a direct interaction between RPA with both NBS1 and MRE11. By utilizing RPA bound to ssDNA, we demonstrate that substituting RPA with phosphorylated RPA or a phosphomimetic weakens the interaction with the MRN complex. Also, the N-terminus of RPA1 is a critical component of the RPA-MRN protein-protein interaction. Deletion of the N-terminal oligonucleotide-oligosaccharide binding fold (OB-fold) of RPA1 abrogates interactions of RPA with MRN and individual proteins of the MRN complex. Further identification of residues critical for MRN binding in the N-terminus of RPA1 shows that substitution of Arg31 and Arg41 with alanines disrupts the RPA-MRN interaction and alters cell cycle progression in response to DNA damage. Thus, the N-terminus of RPA1 and phosphorylation of RPA2 regulate RPA-MRN interactions and are important in the response to DNA damage.

Elucidation of electronic structure by the analysis of hyperfine interactions: The MnH A 7Π-X 7Sigma + (0,0) band

Science.gov (United States)

Varberg, Thomas D.; Field, Robert W.; Merer, Anthony J.

1991-08-01

We present a complete analysis of the hyperfine structure of the MnH A 7Π-X 7Σ+ (0,0) band near 5680 Å, studied with sub-Doppler resolution by intermodulated fluorescence spectroscopy. Magnetic hyperfine interactions involving both the 55Mn (I=5/2) and 1H (I=1/2) nuclear spins are observed as well as 55Mn electric quadrupole effects. The manganese Fermi contact interaction in the X 7Σ+ state is the dominant contributor to the observed hyperfine splittings; the ΔF=0, ΔN=0, ΔJ=±1 matrix elements of this interaction mix the electron spin components of the ground state quite strongly at low N, destroying the ``goodness'' of J as a quantum number and inducing rotationally forbidden, ΔJ=±2 and ±3 transitions. The hyperfine splittings of over 50 rotational transitions covering all 7 spin components of both states were analyzed and fitted by least squares, allowing the accurate determination of 14 different hyperfine parameters. Using single electronic configurations to describe the A 7Π and X 7Σ+ states and Herman-Skillman atomic radial wave functions to represent the molecular orbitals, we calculated a priori values for the 55Mn and 1H hyperfine parameters which agree closely with experiment. We show that the five high-spin coupled Mn 3d electrons do not contribute to the manganese hyperfine structure but are responsible for the observed proton magnetic dipolar couplings. Furthermore, the results suggest that the Mn 3d electrons are not significantly involved in bonding and demonstrate that the molecular hyperfine interactions may be quantitatively understood using simple physical interpretations.

Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

Directory of Open Access Journals (Sweden)

Vicente Martí-Centelles

2012-01-01

competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

Using Psycho-Physiological Interaction Analysis with fMRI-Data in IS Research

DEFF Research Database (Denmark)

Hubert, Marco; Linzmajer, Marc; Riedl, René

2017-01-01

The integration of neuroscientific methods in Information Systems (IS) research to better understand how the brain interacts with IS-relevant context has gained in importance. Many papers that highlight the potential of neuroIS and that discuss methodological issues associated with using functional...... brain imaging already exist. However, neuroIS researchers have to keep in mind that the emergence of complex mental processes such as trust in IS contexts is based on activity in a network of brain regions rather than on activity in one area alone. Accordingly, we introduce psycho......-physiological interaction (PPI) analysis, a technique that one can use to analyze fMRI data. Specifically, we review how one can conduct PPI analysis, provide a concrete research example, and show how this analysis can inform IS trust research. Thus, we introduce neuroIS researchers working in the domain of functional...

Compilation of information on uncertainties involved in deposition modeling

International Nuclear Information System (INIS)

Lewellen, W.S.; Varma, A.K.; Sheng, Y.P.

1985-04-01

The current generation of dispersion models contains very simple parameterizations of deposition processes. The analysis here looks at the physical mechanisms governing these processes in an attempt to see if more valid parameterizations are available and what level of uncertainty is involved in either these simple parameterizations or any more advanced parameterization. The report is composed of three parts. The first, on dry deposition model sensitivity, provides an estimate of the uncertainty existing in current estimates of the deposition velocity due to uncertainties in independent variables such as meteorological stability, particle size, surface chemical reactivity and canopy structure. The range of uncertainty estimated for an appropriate dry deposition velocity for a plume generated by a nuclear power plant accident is three orders of magnitude. The second part discusses the uncertainties involved in precipitation scavenging rates for effluents resulting from a nuclear reactor accident. The conclusion is that major uncertainties are involved both as a result of the natural variability of the atmospheric precipitation process and due to our incomplete understanding of the underlying process. The third part involves a review of the important problems associated with modeling the interaction between the atmosphere and a forest. It gives an indication of the magnitude of the problem involved in modeling dry deposition in such environments. Separate analytics have been done for each section and are contained in the EDB

Analysis of Pumphouse RCC Frame Structure for Soil Structure Interaction

OpenAIRE

Mr A.S. Thombare; Prof. V.P. Kumbhar; Prof. A.H. Kumbhar

2016-01-01

When structure is built on ground some elements of structure are direct contact with soil. When loads are applied on structure internal forces are developed in both the structure as well as in soil. It results in deformation of both the components which are independent to each other. This are called soil structure interaction. The analysis is done by using (Bentley STAAD.Pro V8i Version 2007) software. The analysis carried out been pump house structure R.C.C. frame structure find ...

[Analysis of the question-answer activity of a hospital pharmacy. Example of the handling of drug interactions].

Science.gov (United States)

Jacqueroux, E; Lalande, L; Meddour, N; Papailhau, C; Bernard, E; Charroin, C; Perichou, J; Charpiat, B; Locher, F; Garcia, S

2015-05-01

The medical care of patients generates questions among healthcare professionals. Some will necessitate an advanced research. The hospital pharmacist is at the interface between prescribers, caregivers and the medicines and is requested to answer these requests. Studies conducted in other countries showed that this question-answer activity represents a significant amount of time in daily work. In France, this topic was poorly explored. The objective of our work was to study the volume and the type of questions, the clinical situations, the time required, the medicines implicated and the sources of information used. A prospective study was conducted in the pharmacy of a university hospital. All the requests answered by the pharmaceutical team, which needed a specific research, analysis and writing of an answer were collected. A hundred and one questions were analyzed, originating from doctors or medicals interns. Almost half concerned drug interactions, and among them, almost a fourth were not mentioned in the Summary of Product Characteristics of the medicines involved. A pharmaceutical advice was provided in 91.5% of the cases. Time dedicated to the research varied between less than 30 minutes and more than 8 hours. This study illustrates the question-answer activity of a hospital pharmacy, which is currently not taken into account as an indicator of pharmaceutical activity. A large part concerns analysis and management of drug interactions and requires a significant amount of pharmaceutical time. Copyright © 2014 Elsevier Masson SAS. All rights reserved.