The social roles and functions of emotions

NARCIS (Netherlands)

Frijda, N.H.; Mesquita, B.; Markus, H.R.; Kitayama, S.

1994-01-01

(from the chapter) discuss the ways in which the sociocultural environment can be expected to influence the emotional processes, the roles and functions of these processes in social interaction, and the influences of the sociocultural environment upon those roles and functions / discuss the modes of

BioModels: Content, Features, Functionality, and Use

Science.gov (United States)

Juty, N; Ali, R; Glont, M; Keating, S; Rodriguez, N; Swat, MJ; Wimalaratne, SM; Hermjakob, H; Le Novère, N; Laibe, C; Chelliah, V

2015-01-01

BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources. Most model components are cross-linked with external resources to facilitate interoperability. A large proportion of models are manually curated to ensure reproducibility of simulation results. This tutorial presents BioModels' content, features, functionality, and usage. PMID:26225232

Interactive Explanations: The Functional Role of Gestural and Bodily Action for Explaining and Learning Scientific Concepts in Face-to-Face Arrangements

Science.gov (United States)

Scopelitis, Stephanie A.

As human beings, we live in, live with, and live through our bodies. And because of this it is no wonder that our hands and bodies are in motion as we interact with others in our world. Hands and body move as we give directions to another, anticipate which way to turn the screwdriver, and direct our friend to come sit next to us. Gestures, indeed, fill our everyday lives. The purpose of this study is to investigate the functional role of the body in the parts of our lives where we teach and learn with another. This project is an investigation into, what I call, "interactive explanations". I explore how the hands and body work toward the joint achievement of explanation and learning in face-to-face arrangements. The study aims to uncover how the body participates in teaching and learning in and across events as it slides between the multiple, interdependent roles of (1) a communicative entity, (2) a tool for thinking, and (3) a resource to shape interaction. Understanding gestures functional roles as flexible and diverse better explains how the body participates in teaching and learning interactions. The study further aims to show that these roles and functions are dynamic and changeable based on the interests, goals and contingencies of participants' changing roles and aims in interactions, and within and across events. I employed the methodology of comparative microanalysis of pairs of videotaped conversations in which, first, experts in STEM fields (Science, Technology, Engineering and Mathematics) explained concepts to non-experts, and second, these non-experts re-explained the concept to other non-experts. The principle finding is that people strategically, creatively and collaboratively employ the hands and body as vital and flexible resources for the joint achievement of explanation and understanding. Findings further show that gestures used to explain complex STEM concepts travel across time with the non-expert into re-explanations of the concept. My

New Features about Tau Function and Dysfunction

Directory of Open Access Journals (Sweden)

Miguel Medina

2016-04-01

Full Text Available Tau is a brain microtubule-associated protein that directly binds to a microtubule and dynamically regulates its structure and function. Under pathological conditions, tau self-assembles into filamentous structures that end up forming neurofibrillary tangles. Prominent tau neurofibrillary pathology is a common feature in a number of neurodegenerative disorders, collectively referred to as tauopathies, the most common of which is Alzheimer’s disease (AD. Beyond its classical role as a microtubule-associated protein, recent advances in our understanding of tau cellular functions have revealed novel insights into their important role during pathogenesis and provided potential novel therapeutic targets. Regulation of tau behavior and function under physiological and pathological conditions is mainly achieved through post-translational modifications, including phosphorylation, glycosylation, acetylation, and truncation, among others, indicating the complexity and variability of factors influencing regulation of tau toxicity, all of which have significant implications for the development of novel therapeutic approaches in various neurodegenerative disorders. A more comprehensive understanding of the molecular mechanisms regulating tau function and dysfunction will provide us with a better outline of tau cellular networking and, hopefully, offer new clues for designing more efficient approaches to tackle tauopathies in the near future.

New Features about Tau Function and Dysfunction

Science.gov (United States)

Medina, Miguel; Hernández, Félix; Avila, Jesús

2016-01-01

Tau is a brain microtubule-associated protein that directly binds to a microtubule and dynamically regulates its structure and function. Under pathological conditions, tau self-assembles into filamentous structures that end up forming neurofibrillary tangles. Prominent tau neurofibrillary pathology is a common feature in a number of neurodegenerative disorders, collectively referred to as tauopathies, the most common of which is Alzheimer’s disease (AD). Beyond its classical role as a microtubule-associated protein, recent advances in our understanding of tau cellular functions have revealed novel insights into their important role during pathogenesis and provided potential novel therapeutic targets. Regulation of tau behavior and function under physiological and pathological conditions is mainly achieved through post-translational modifications, including phosphorylation, glycosylation, acetylation, and truncation, among others, indicating the complexity and variability of factors influencing regulation of tau toxicity, all of which have significant implications for the development of novel therapeutic approaches in various neurodegenerative disorders. A more comprehensive understanding of the molecular mechanisms regulating tau function and dysfunction will provide us with a better outline of tau cellular networking and, hopefully, offer new clues for designing more efficient approaches to tackle tauopathies in the near future. PMID:27104579

Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks.

Directory of Open Access Journals (Sweden)

Sumeet Agarwal

2010-06-01

Full Text Available The idea of "date" and "party" hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here, we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. However, we find significant correlations between interaction centrality and the functional similarity of the interacting proteins. We suggest that thinking in terms of a date/party dichotomy for hubs in protein interaction networks is not meaningful, and it might be more useful to conceive of roles for protein-protein interactions rather than for individual proteins.

Interaction of a monopole vortex with an isolated topographic feature in a three-layer geophysical flow

Directory of Open Access Journals (Sweden)

E. A. Ryzhov

2013-02-01

Full Text Available In the frame of a three-layer, quasi-geostrophic analytical model of an f-plane geophysical flow, the Lagrangian advection induced by the interaction of a monopole vortex with an isolated topographic feature is addressed. Two different cases when the monopole is located either within the upper or the middle layer are of our interest. In the bottom layer, there is a delta-function topographic feature, which generates a closed recirculation region in its vicinity due to the background flow. This recirculation region extends to the middle and upper layers, and it plays the role of a topographic vortex. The interaction between the monopole and the topographic vortex causes a complex, including chaotic, advection of fluid particles. We show that the model's parameters, namely the monopole and topographic vortices' strengths and initial positions, and the layers' depths and densities, are responsible for the diverse advection patterns. While the patterns are rather complicated, one can single out two major processes, which mostly govern the fluid particle advection. The first one is the variation in time of the system's phase space structure, so that within the closed region of the topographic vortex, there appear periodically unclosed particle pathways by which the particles leave the topographic vortex. The second one is chaotic advection that arises from the nonstationarity of the monopole–topography interaction.

Proteomic analysis of FUS interacting proteins provides insights into FUS function and its role in ALS.

Science.gov (United States)

Kamelgarn, Marisa; Chen, Jing; Kuang, Lisha; Arenas, Alexandra; Zhai, Jianjun; Zhu, Haining; Gal, Jozsef

2016-10-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Mutations in the Fused in Sarcoma/Translocated in Liposarcoma (FUS/TLS) gene cause a subset of familial ALS cases and are also implicated in sporadic ALS. FUS is typically localized to the nucleus. The ALS-related FUS mutations cause cytoplasmic mis-localization and the formation of stress granule-like structures. Abnormal cytoplasmic FUS localization was also found in a subset of frontotemporal dementia (FTLD) cases without FUS mutations. To better understand the function of FUS, we performed wild-type and mutant FUS pull-downs followed by proteomic identification of the interacting proteins. The FUS interacting partners we identified are involved in multiple pathways, including chromosomal organization, transcription, RNA splicing, RNA transport, localized translation, and stress response. FUS interacted with hnRNPA1 and Matrin-3, RNA binding proteins whose mutations were also reported to cause familial ALS, suggesting that hnRNPA1 and Matrin-3 may play common pathogenic roles with FUS. The FUS interactions displayed varied RNA dependence. Numerous FUS interacting partners that we identified are components of exosomes. We found that FUS itself was present in exosomes, suggesting that the secretion of FUS might contribute to the cell-to-cell spreading of FUS pathology. FUS interacting proteins were sequestered into the cytoplasmic mutant FUS inclusions that could lead to their mis-regulation or loss of function, contributing to ALS pathogenesis. Our results provide insights into the physiological functions of FUS as well as important pathways where mutant FUS can interfere with cellular processes and potentially contribute to the pathogenesis of ALS. Copyright © 2016 Elsevier B.V. All rights reserved.

Relations between Automatically Extracted Motion Features and the Quality of Mother-Infant Interactions at 4 and 13 Months.

Science.gov (United States)

Egmose, Ida; Varni, Giovanna; Cordes, Katharina; Smith-Nielsen, Johanne; Væver, Mette S; Køppe, Simo; Cohen, David; Chetouani, Mohamed

2017-01-01

Bodily movements are an essential component of social interactions. However, the role of movement in early mother-infant interaction has received little attention in the research literature. The aim of the present study was to investigate the relationship between automatically extracted motion features and interaction quality in mother-infant interactions at 4 and 13 months. The sample consisted of 19 mother-infant dyads at 4 months and 33 mother-infant dyads at 13 months. The coding system Coding Interactive Behavior (CIB) was used for rating the quality of the interactions. Kinetic energy of upper-body, arms and head motion was calculated and used as segmentation in order to extract coarse- and fine-grained motion features. Spearman correlations were conducted between the composites derived from the CIB and the coarse- and fine-grained motion features. At both 4 and 13 months, longer durations of maternal arm motion and infant upper-body motion were associated with more aversive interactions, i.e., more parent-led interactions and more infant negativity. Further, at 4 months, the amount of motion silence was related to more adaptive interactions, i.e., more sensitive and child-led interactions. Analyses of the fine-grained motion features showed that if the mother coordinates her head movements with her infant's head movements, the interaction is rated as more adaptive in terms of less infant negativity and less dyadic negative states. We found more and stronger correlations between the motion features and the interaction qualities at 4 compared to 13 months. These results highlight that motion features are related to the quality of mother-infant interactions. Factors such as infant age and interaction set-up are likely to modify the meaning and importance of different motion features.

Automatic discovery of cross-family sequence features associated with protein function

Directory of Open Access Journals (Sweden)

Krings Andrea

2006-01-01

Full Text Available Abstract Background Methods for predicting protein function directly from amino acid sequences are useful tools in the study of uncharacterised protein families and in comparative genomics. Until now, this problem has been approached using machine learning techniques that attempt to predict membership, or otherwise, to predefined functional categories or subcellular locations. A potential drawback of this approach is that the human-designated functional classes may not accurately reflect the underlying biology, and consequently important sequence-to-function relationships may be missed. Results We show that a self-supervised data mining approach is able to find relationships between sequence features and functional annotations. No preconceived ideas about functional categories are required, and the training data is simply a set of protein sequences and their UniProt/Swiss-Prot annotations. The main technical aspect of the approach is the co-evolution of amino acid-based regular expressions and keyword-based logical expressions with genetic programming. Our experiments on a strictly non-redundant set of eukaryotic proteins reveal that the strongest and most easily detected sequence-to-function relationships are concerned with targeting to various cellular compartments, which is an area already well studied both experimentally and computationally. Of more interest are a number of broad functional roles which can also be correlated with sequence features. These include inhibition, biosynthesis, transcription and defence against bacteria. Despite substantial overlaps between these functions and their corresponding cellular compartments, we find clear differences in the sequence motifs used to predict some of these functions. For example, the presence of polyglutamine repeats appears to be linked more strongly to the "transcription" function than to the general "nuclear" function/location. Conclusion We have developed a novel and useful approach for

Model Checking Feature Interactions

DEFF Research Database (Denmark)

Le Guilly, Thibaut; Olsen, Petur; Pedersen, Thomas

2015-01-01

This paper presents an offline approach to analyzing feature interactions in embedded systems. The approach consists of a systematic process to gather the necessary information about system components and their models. The model is first specified in terms of predicates, before being refined to t...... to timed automata. The consistency of the model is verified at different development stages, and the correct linkage between the predicates and their semantic model is checked. The approach is illustrated on a use case from home automation....

Movement dynamics reflect a functional role for weak coupling and role structure in dyadic problem solving.

Science.gov (United States)

Abney, Drew H; Paxton, Alexandra; Dale, Rick; Kello, Christopher T

2015-11-01

Successful interaction requires complex coordination of body movements. Previous research has suggested a functional role for coordination and especially synchronization (i.e., time-locked movement across individuals) in different types of human interaction contexts. Although such coordination has been shown to be nearly ubiquitous in human interaction, less is known about its function. One proposal is that synchrony supports and facilitates communication (Topics Cogn Sci 1:305-319, 2009). However, questions still remain about what the properties of coordination for optimizing communication might look like. In the present study, dyads worked together to construct towers from uncooked spaghetti and marshmallows. Using cross-recurrence quantification analysis, we found that dyads with loosely coupled gross body movements performed better, supporting recent work suggesting that simple synchrony may not be the key to effective performance (Riley et al. 2011). We also found evidence that leader-follower dynamics-when sensitive to the specific role structure of the interaction-impact task performance. We discuss our results with respect to the functional role of coordination in human interaction.

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

Science.gov (United States)

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

2009-05-01

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

A feature-based approach to modeling protein–protein interaction hot spots

Science.gov (United States)

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

2009-01-01

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

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae

Directory of Open Access Journals (Sweden)

Araabi Babak N

2010-12-01

Full Text Available Abstract Background It has been understood that biological networks have modular organizations which are the sources of their observed complexity. Analysis of networks and motifs has shown that two types of hubs, party hubs and date hubs, are responsible for this complexity. Party hubs are local coordinators because of their high co-expressions with their partners, whereas date hubs display low co-expressions and are assumed as global connectors. However there is no mutual agreement on these concepts in related literature with different studies reporting their results on different data sets. We investigated whether there is a relation between the biological features of Saccharomyces Cerevisiae's proteins and their roles as non-hubs, intermediately connected, party hubs, and date hubs. We propose a classifier that separates these four classes. Results We extracted different biological characteristics including amino acid sequences, domain contents, repeated domains, functional categories, biological processes, cellular compartments, disordered regions, and position specific scoring matrix from various sources. Several classifiers are examined and the best feature-sets based on average correct classification rate and correlation coefficients of the results are selected. We show that fusion of five feature-sets including domains, Position Specific Scoring Matrix-400, cellular compartments level one, and composition pairs with two and one gaps provide the best discrimination with an average correct classification rate of 77%. Conclusions We study a variety of known biological feature-sets of the proteins and show that there is a relation between domains, Position Specific Scoring Matrix-400, cellular compartments level one, composition pairs with two and one gaps of Saccharomyces Cerevisiae's proteins, and their roles in the protein interaction network as non-hubs, intermediately connected, party hubs and date hubs. This study also confirms the

Inkjet Printing of Functional and Structural Materials: Fluid Property Requirements, Feature Stability, and Resolution

Science.gov (United States)

Derby, Brian

2010-08-01

Inkjet printing is viewed as a versatile manufacturing tool for applications in materials fabrication in addition to its traditional role in graphics output and marking. The unifying feature in all these applications is the dispensing and precise positioning of very small volumes of fluid (1-100 picoliters) on a substrate before transformation to a solid. The application of inkjet printing to the fabrication of structures for structural or functional materials applications requires an understanding as to how the physical processes that operate during inkjet printing interact with the properties of the fluid precursors used. Here we review the current state of understanding of the mechanisms of drop formation and how this defines the fluid properties that are required for a given liquid to be printable. The interactions between individual drops and the substrate as well as between adjacent drops are important in defining the resolution and accuracy of printed objects. Pattern resolution is limited by the extent to which a liquid drop spreads on a substrate and how spreading changes with the overlap of adjacent drops to form continuous features. There are clearly defined upper and lower bounds to the width of a printed continuous line, which can be defined in terms of materials and process variables. Finer-resolution features can be achieved through appropriate patterning and structuring of the substrate prior to printing, which is essential if polymeric semiconducting devices are to be fabricated. Low advancing and receding contact angles promote printed line stability but are also more prone to solute segregation or “coffee staining” on drying.

Evidence that a functional fertilin-like ADAM plays a role in human sperm-oolemmal interactions.

Science.gov (United States)

Bronson, R A; Fusi, F M; Calzi, F; Doldi, N; Ferrari, A

1999-05-01

Fertilin is a protein initially identified in guinea pig spermatozoa; it is the prototype of a larger family of conserved, proteins designated as a disintegrin and a metalloproteinase (ADAM). These heterodimers which consist of alpha and beta subunits, containing metalloproteinase-like and disintegrin-like domains, appear to play a role in mammalian fertilization. Peptides derived from the disintegrin domains of two ADAMs, fertilin and cyritestin, interfere with gamete adhesion and sperm-egg membrane fusion in non-human species. It has been suggested that fertilin-beta binds to an oolemmal integrin, and it is proposed that the tripeptide FEE (Phe-Glu-Glu) is the integrin recognition sequence in human fertilin-beta. We evaluated whether fertilin beta plays a role in human fertilization by studying the effects of a linear octapeptide containing the FEE sequence, SFEECDLP, and a scrambled octapeptide with the same amino acids, SFPCEDEL, on the incorporation of human spermatozoa by human zona-free eggs. The effects of G4120, a potent RGD-containing (Arg-Gly-Asp) thioether-bridged cyclic peptide which blocks both fibronectin and vitronectin receptors, and the relationship between FEE- and RGD-receptor interactions on sperm-egg interactions were also studied. The FEE-containing peptide, but not the scrampled peptide, inhibited sperm adhesion to oocytes and their penetration, over the range 1-5 microM. The inhibition induced by SFEECDLP was reversible and occurred only in the presence of peptide itself. The G4120 peptide exhibited 10-fold less inhibitory effects on sperm adhesion and penetration than did SFEECDLP. When combined, SFEECDLP and G4120 exhibited strong inhibition of both adhesion and penetration at concentrations that individually had been ineffective, suggesting co-operation between the two receptor-ligand interactions during fertilization. We propose that a fertilin-like molecule is functionally active on human spermatozoa and that its interaction with an

Mental exercising through simple socializing: social interaction promotes general cognitive functioning.

Science.gov (United States)

Ybarra, Oscar; Burnstein, Eugene; Winkielman, Piotr; Keller, Matthew C; Manis, Melvin; Chan, Emily; Rodriguez, Joel

2008-02-01

Social interaction is a central feature of people's life and engages a variety of cognitive resources. Thus, social interaction should facilitate general cognitive functioning. Previous studies suggest such a link, but they used special populations (e.g., elderly with cognitive impairment), measured social interaction indirectly (e.g., via marital status), and only assessed effects of extended interaction in correlational designs. Here the relation between mental functioning and direct indicators of social interaction was examined in a younger and healthier population. Study 1 using survey methodology found a positive relationship between social interaction, assessed via amount of actual social contact, and cognitive functioning in people from three age groups including younger adults. Study 2 using an experimental design found that a small amount of social interaction (10 min) can facilitate cognitive performance. The findings are discussed in the context of the benefits social relationships have for so many aspects of people's lives.

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

Science.gov (United States)

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

2016-10-07

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

Density functional study of molecular interactions in secondary structures of proteins.

Science.gov (United States)

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

A Method for Model Checking Feature Interactions

DEFF Research Database (Denmark)

Pedersen, Thomas; Le Guilly, Thibaut; Ravn, Anders Peter

2015-01-01

This paper presents a method to check for feature interactions in a system assembled from independently developed concurrent processes as found in many reactive systems. The method combines and refines existing definitions and adds a set of activities. The activities describe how to populate the ...... the definitions with models to ensure that all interactions are captured. The method is illustrated on a home automation example with model checking as analysis tool. In particular, the modelling formalism is timed automata and the analysis uses UPPAAL to find interactions....

Schizophrenia classification using functional network features

Science.gov (United States)

Rish, Irina; Cecchi, Guillermo A.; Heuton, Kyle

2012-03-01

This paper focuses on discovering statistical biomarkers (features) that are predictive of schizophrenia, with a particular focus on topological properties of fMRI functional networks. We consider several network properties, such as node (voxel) strength, clustering coefficients, local efficiency, as well as just a subset of pairwise correlations. While all types of features demonstrate highly significant statistical differences in several brain areas, and close to 80% classification accuracy, the most remarkable results of 93% accuracy are achieved by using a small subset of only a dozen of most-informative (lowest p-value) correlation features. Our results suggest that voxel-level correlations and functional network features derived from them are highly informative about schizophrenia and can be used as statistical biomarkers for the disease.

The cognitive impact of interactive design features for learning complex materials in medical education.

Science.gov (United States)

Song, Hyuksoon S; Pusic, Martin; Nick, Michael W; Sarpel, Umut; Plass, Jan L; Kalet, Adina L

2014-02-01

To identify the most effective way for medical students to interact with a browser-based learning module on the symptoms and neurological underpinnings of stroke syndromes, this study manipulated the way in which subjects interacted with a graphical model of the brain and examined the impact of functional changes on learning outcomes. It was hypothesized that behavioral interactions that were behaviorally more engaging and which required deeper consideration of the model would result in heightened cognitive interaction and better learning than those whose manipulation required less deliberate behavioral and cognitive processing. One hundred forty four students were randomly assigned to four conditions whose model controls incorporated features that required different levels of behavioral and cognitive interaction: Movie (low behavioral/low cognitive, n = 40), Slider (high behavioral/low cognitive, n = 36), Click (low behavioral/high cognitive, n = 30), and Drag (high behavioral/high cognitive, n = 38). Analysis of Covariates (ANCOVA) showed that students who received the treatments associated with lower cognitive interactivity (Movie and Slider) performed better on a transfer task than those receiving the module associated with high cognitive interactivity (Click and Drag, partial eta squared = .03). In addition, the students in the high cognitive interactivity conditions spent significantly more time on the stroke locator activity than other conditions (partial eta squared = .36). The results suggest that interaction with controls that were tightly coupled with the model and whose manipulation required deliberate consideration of the model's features may have overtaxed subjects' cognitive resources. Cognitive effort that facilitated manipulation of content, though directed at the model, may have resulted in extraneous cognitive load, impeding subjects in recognizing the deeper, global relationships in the materials. Instructional designers must, therefore, keep in

Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection.

Science.gov (United States)

Chen, Yifei; Sun, Yuxing; Han, Bing-Qing

2015-01-01

Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the F1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification.

Appearance-based human gesture recognition using multimodal features for human computer interaction

Science.gov (United States)

Luo, Dan; Gao, Hua; Ekenel, Hazim Kemal; Ohya, Jun

2011-03-01

The use of gesture as a natural interface plays an utmost important role for achieving intelligent Human Computer Interaction (HCI). Human gestures include different components of visual actions such as motion of hands, facial expression, and torso, to convey meaning. So far, in the field of gesture recognition, most previous works have focused on the manual component of gestures. In this paper, we present an appearance-based multimodal gesture recognition framework, which combines the different groups of features such as facial expression features and hand motion features which are extracted from image frames captured by a single web camera. We refer 12 classes of human gestures with facial expression including neutral, negative and positive meanings from American Sign Languages (ASL). We combine the features in two levels by employing two fusion strategies. At the feature level, an early feature combination can be performed by concatenating and weighting different feature groups, and LDA is used to choose the most discriminative elements by projecting the feature on a discriminative expression space. The second strategy is applied on decision level. Weighted decisions from single modalities are fused in a later stage. A condensation-based algorithm is adopted for classification. We collected a data set with three to seven recording sessions and conducted experiments with the combination techniques. Experimental results showed that facial analysis improve hand gesture recognition, decision level fusion performs better than feature level fusion.

Interactive Effects of Dopamine Baseline Levels and Cycle Phase on Executive Functions: The Role of Progesterone

Directory of Open Access Journals (Sweden)

Esmeralda Hidalgo-Lopez

2017-07-01

Full Text Available Estradiol and progesterone levels vary along the menstrual cycle and have multiple neuroactive effects, including on the dopaminergic system. Dopamine relates to executive functions in an “inverted U-shaped” manner and its levels are increased by estradiol. Accordingly, dopamine dependent changes in executive functions along the menstrual cycle have been previously studied in the pre-ovulatory phase, when estradiol levels peak. Specifically it has been demonstrated that working memory is enhanced during the pre-ovulatory phase in women with low dopamine baseline levels, but impaired in women with high dopamine baseline levels. However, the role of progesterone, which peaks in the luteal cycle phase, has not been taken into account previously. Therefore, the main goals of the present study were to extend these findings (i to the luteal cycle phase and (ii to other executive functions. Furthermore, the usefulness of the eye blink rate (EBR as an indicator of dopamine baseline levels in menstrual cycle research was explored. 36 naturally cycling women were tested during three cycle phases (menses–low sex hormones; pre-ovulatory–high estradiol; luteal–high progesterone and estradiol. During each session, women performed a verbal N-back task, as measure of working memory, and a single trial version of the Stroop task, as measure of response inhibition and cognitive flexibility. Hormone levels were assessed from saliva samples and spontaneous eye blink rate was recorded during menses. In the N-back task, women were faster during the luteal phase the higher their progesterone levels, irrespective of their dopamine baseline levels. In the Stroop task, we found a dopamine-cycle interaction, which was also driven by the luteal phase and progesterone levels. For women with higher EBR performance decreased during the luteal phase, whereas for women with lower EBR performance improved during the luteal phase. These findings suggest an important

Determination of morphological features and molecular interactions ...

African Journals Online (AJOL)

This research focused on identifying the morphological features and molecular interactions of the Nigerian Bentonitic clays using Scanning Electron Microscope (SEM) characterisation technique. The SEM microstructure images indicated that the bentonite samples are generally moderately dispersive to dispersive with ...

The role of COBRA-LIKE 2 function, as part of the complex network of interacting pathways regulating Arabidopsis seed mucilage polysaccharide matrix organization.

Science.gov (United States)

Ben-Tov, Daniela; Idan-Molakandov, Anat; Hugger, Anat; Ben-Shlush, Ilan; Günl, Markus; Yang, Bo; Usadel, Björn; Harpaz-Saad, Smadar

2018-05-01

The production of hydrophilic mucilage along the course of seed coat epidermal cell differentiation is a common adaptation in angiosperms. Previous studies have identified COBRA-LIKE 2 (COBL2), a member of the COBRA-LIKE gene family, as a novel component required for crystalline cellulose deposition in seed coat epidermal cells. In recent years, Arabidopsis seed coat epidermal cells (SCEs), also called mucilage secretory cells, have emerged as a powerful model system for the study of plant cell wall components biosynthesis, secretion, assembly and de muro modification. Despite accumulating data, the molecular mechanism of COBL function remains largely unknown. In the current research, we utilized genetic interactions to study the role of COBL2 as part of the protein network required for seed mucilage production. Using correlative phenotyping of structural and biochemical characteristics, unique features of the cobl2 extruded mucilage are revealed, including: 'unraveled' ray morphology, loss of primary cell wall 'pyramidal' organization, reduced Ruthenium red staining intensity of the adherent mucilage layer, and increased levels of the monosaccharides arabinose and galactose. Examination of the cobl2cesa5 double mutant provides insight into the interface between COBL function and cellulose deposition. Additionally, genetic interactions between cobl2 and fei1fei2 as well as between each of these mutants to mucilage-modified 2 (mum2) suggest that COBL2 functions independently of the FEI-SOS pathway. Altogether, the presented data place COBL2 within the complex protein network required for cell wall deposition in the context of seed mucilage and introduce new methodology expending the seed mucilage phenotyping toolbox. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

MRIVIEW: An interactive computational tool for investigation of brain structure and function

International Nuclear Information System (INIS)

Ranken, D.; George, J.

1993-01-01

MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities

Configuration interaction wave functions: A seniority number approach

International Nuclear Information System (INIS)

Alcoba, Diego R.; Torre, Alicia; Lain, Luis; Massaccesi, Gustavo E.; Oña, Ofelia B.

2014-01-01

This work deals with the configuration interaction method when an N-electron Hamiltonian is projected on Slater determinants which are classified according to their seniority number values. We study the spin features of the wave functions and the size of the matrices required to formulate states of any spin symmetry within this treatment. Correlation energies associated with the wave functions arising from the seniority-based configuration interaction procedure are determined for three types of molecular orbital basis: canonical molecular orbitals, natural orbitals, and the orbitals resulting from minimizing the expectation value of the N-electron seniority number operator. The performance of these bases is analyzed by means of numerical results obtained from selected N-electron systems of several spin symmetries. The comparison of the results highlights the efficiency of the molecular orbital basis which minimizes the mean value of the seniority number for a state, yielding energy values closer to those provided by the full configuration interaction procedure

Configuration interaction wave functions: A seniority number approach

Energy Technology Data Exchange (ETDEWEB)

Alcoba, Diego R. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Torre, Alicia; Lain, Luis, E-mail: qfplapel@lg.ehu.es [Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080 Bilbao (Spain); Massaccesi, Gustavo E. [Departamento de Ciencias Exactas, Ciclo Básico Común, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Oña, Ofelia B. [Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de La Plata, CCT La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (S/N), Sucursal 4, CC 16, 1900 La Plata (Argentina)

2014-06-21

This work deals with the configuration interaction method when an N-electron Hamiltonian is projected on Slater determinants which are classified according to their seniority number values. We study the spin features of the wave functions and the size of the matrices required to formulate states of any spin symmetry within this treatment. Correlation energies associated with the wave functions arising from the seniority-based configuration interaction procedure are determined for three types of molecular orbital basis: canonical molecular orbitals, natural orbitals, and the orbitals resulting from minimizing the expectation value of the N-electron seniority number operator. The performance of these bases is analyzed by means of numerical results obtained from selected N-electron systems of several spin symmetries. The comparison of the results highlights the efficiency of the molecular orbital basis which minimizes the mean value of the seniority number for a state, yielding energy values closer to those provided by the full configuration interaction procedure.

Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway.

Science.gov (United States)

Medhurst, A L; Huber, P A; Waisfisz, Q; de Winter , J P; Mathew, C G

2001-02-15

Fanconi anaemia (FA) is an autosomal recessive inherited disorder associated with a progressive aplastic anaemia, diverse congenital abnormalities and cancer. The condition is genetically heterogeneous, with at least seven complementation groups (A-G) described. Cells from individuals who are homozygous for mutations in FA genes are characterized by chromosomal instability and hypersensitivity to DNA interstrand crosslinking agents. These features suggest a possible role for the encoded proteins in the recognition or repair of these lesions, but neither their function nor whether they operate in a concerted or discrete functional pathways is known. The recent cloning of the FANCF and FANCE genes has allowed us to investigate the interaction of the proteins encoded by five of the seven complementation groups of FA. We used the yeast two-hybrid system and co-immunoprecipitation analysis to test the 10 possible pairs of proteins for direct interaction. In addition to the previously described binding of FANCA to FANCG, we now demonstrate direct interaction of FANCF with FANCG, of FANCC with FANCE and a weaker interaction of FANCE with both FANCA and FANCG. These findings show that the newly identified FANCE protein is an integral part of the FA pathway, and support the concept of a functional link between all known proteins encoded by the genes that are mutated in this disorder. These proteins may act either as a multimeric complex or by sequential recruitment of subsets of the proteins in a common pathway that protects the genomic integrity of mammalian cells.

Second feature of the matter two-point function

Science.gov (United States)

Tansella, Vittorio

2018-05-01

We point out the existence of a second feature in the matter two-point function, besides the acoustic peak, due to the baryon-baryon correlation in the early Universe and positioned at twice the distance of the peak. We discuss how the existence of this feature is implied by the well-known heuristic argument that explains the baryon bump in the correlation function. A standard χ2 analysis to estimate the detection significance of the second feature is mimicked. We conclude that, for realistic values of the baryon density, a SKA-like galaxy survey will not be able to detect this feature with standard correlation function analysis.

Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules

Directory of Open Access Journals (Sweden)

Nikhil Sangith

2014-01-01

Full Text Available PSMD9 (Proteasome Macropain non-ATPase subunit 9, a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a proteins with conserved C-termini may share common functions and (b PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein, S14 (a ribosomal protein, CSH1 (a growth hormone, E12 (a transcription factor and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.

Functional connectivity supporting the selective maintenance of feature-location binding in visual working memory

Directory of Open Access Journals (Sweden)

Sachiko eTakahama

2014-06-01

Full Text Available Information on an object’s features bound to its location is very important for maintaining object representations in visual working memory. Interactions with dynamic multi-dimensional objects in an external environment require complex cognitive control, including the selective maintenance of feature-location binding. Here, we used event-related functional magnetic resonance imaging to investigate brain activity and functional connectivity related to the maintenance of complex feature-location binding. Participants were required to detect task-relevant changes in feature-location binding between objects defined by color, orientation, and location. We compared a complex binding task requiring complex feature-location binding (color-orientation-location with a simple binding task in which simple feature-location binding, such as color-location, was task-relevant and the other feature was task-irrelevant. Univariate analyses showed that the dorsolateral prefrontal cortex (DLPFC, hippocampus, and frontoparietal network were activated during the maintenance of complex feature-location binding. Functional connectivity analyses indicated cooperation between the inferior precentral sulcus (infPreCS, DLPFC, and hippocampus during the maintenance of complex feature-location binding. In contrast, the connectivity for the spatial updating of simple feature-location binding determined by reanalyzing the data from Takahama et al. (2010 demonstrated that the superior parietal lobule (SPL cooperated with the DLPFC and hippocampus. These results suggest that the connectivity for complex feature-location binding does not simply reflect general memory load and that the DLPFC and hippocampus flexibly modulate the dorsal frontoparietal network, depending on the task requirements, with the infPreCS involved in the maintenance of complex feature-location binding and the SPL involved in the spatial updating of simple feature-location binding.

Genetic, functional and molecular features of glucocorticoid receptor binding.

Directory of Open Access Journals (Sweden)

Francesca Luca

Full Text Available Glucocorticoids (GCs are key mediators of stress response and are widely used as pharmacological agents to treat immune diseases, such as asthma and inflammatory bowel disease, and certain types of cancer. GCs act mainly by activating the GC receptor (GR, which interacts with other transcription factors to regulate gene expression. Here, we combined different functional genomics approaches to gain molecular insights into the mechanisms of action of GC. By profiling the transcriptional response to GC over time in 4 Yoruba (YRI and 4 Tuscans (TSI lymphoblastoid cell lines (LCLs, we suggest that the transcriptional response to GC is variable not only in time, but also in direction (positive or negative depending on the presence of specific interacting transcription factors. Accordingly, when we performed ChIP-seq for GR and NF-κB in two YRI LCLs treated with GC or with vehicle control, we observed that features of GR binding sites differ for up- and down-regulated genes. Finally, we show that eQTLs that affect expression patterns only in the presence of GC are 1.9-fold more likely to occur in GR binding sites, compared to eQTLs that affect expression only in its absence. Our results indicate that genetic variation at GR and interacting transcription factors binding sites influences variability in gene expression, and attest to the power of combining different functional genomic approaches.

Functionality of system components: Conservation of protein function in protein feature space

DEFF Research Database (Denmark)

Jensen, Lars Juhl; Ussery, David; Brunak, Søren

2003-01-01

well on organisms other than the one on which it was trained. We evaluate the performance of such a method, ProtFun, which relies on protein features as its sole input, and show that the method gives similar performance for most eukaryotes and performs much better than anticipated on archaea......Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties. We show here that such protein features are more conserved among orthologs than paralogs, indicating...... they are crucial for protein function and thus subject to selective pressure. This means that a function prediction method based on sequence-derived features may be able to discriminate between proteins with different function even when they have highly similar structure. Also, such a method is likely to perform...

Protein functional features are reflected in the patterns of mRNA translation speed.

Science.gov (United States)

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

The mental representation of living and nonliving things: differential weighting and interactivity of sensorial and non-sensorial features.

Science.gov (United States)

Ventura, Paulo; Morais, José; Brito-Mendes, Carlos; Kolinsky, Régine

2005-02-01

Warrington and colleagues (Warrington & McCarthy, 1983, 1987; Warrington & Shallice, 1984) claimed that sensorial and functional-associative (FA) features are differentially important in determining the meaning of living things (LT) and nonliving things (NLT). The first aim of the present study was to evaluate this hypothesis through two different access tasks: feature generation (Experiment 1) and cued recall (Experiment 2). The results of both experiments provided consistent empirical support for Warrington and colleagues' assumption. The second aim of the present study was to test a new differential interactivity hypothesis that combines Warrington and colleagueS' assumption with the notion of a higher number of intercorrelations and hence of a stronger connectivity between sensorial and non-sensorial features for LTs than for NLTs. This hypothesis was motivated by previoUs reports of an uncrossed interaction between domain (LTs vs NLTs) and attribute type (sensorial vs FA) in, for example, a feature verification task (Laws, Humber, Ramsey, & McCarthy, 1995): while FA attributes are verified faster than sensorial attributes for NLTs, no difference is observed for LTs. We replicated and generalised this finding using several feature verification tasks on both written words and pictures (Experiment 3), including in conditions aimed at minimising the intervention of priming biases and strategic or mnemonic processes (Experiment 4). The whole set of results suggests that both privileged relations between features and categories, and the differential importance of intercorrelations between features as a function of category, modulate access to semantic features.

Features of Interaction of Business and Government in the Form of Public-private partnership

Directory of Open Access Journals (Sweden)

Oksana N. Taranenko

2016-12-01

Full Text Available Today modernization of relations between the government and the business sector is an important issue particularly relevant in the context of financial globalization in the transition to a market economy. The paper discusses the theoretical concept of public-private partnership, as a form of business organization, combining the functional features of an independent firm or companies and the government, which implementation is caused by the need to ensure the production of the most important benefits in various areas, as well as the features of the interaction of business and government. It is proposed to highlight the definition of public-private partnerships in the form of a special system of relations of economic agents, as well to determine the required features that separate this form of interaction as a partnership from other forms of interaction. Also the authors consider a system of public-private partnership in terms of coordination of joint relations between the government and business, try to identify the basic principles of interaction between the participants, identify their main advantages that each of the participants in the partnership seeks to contribute to the joint project, and identifiess areas to support sustainable development the country's economy. The paper describes the problems associated with the implementation of projects in the public-private partnership system and suggests ways to improve them, discusses the main advantages and disadvantages of such members, as the government and business.

Feature generation and representations for protein-protein interaction classification.

Science.gov (United States)

Lan, Man; Tan, Chew Lim; Su, Jian

2009-10-01

Automatic detecting protein-protein interaction (PPI) relevant articles is a crucial step for large-scale biological database curation. The previous work adopted POS tagging, shallow parsing and sentence splitting techniques, but they achieved worse performance than the simple bag-of-words representation. In this paper, we generated and investigated multiple types of feature representations in order to further improve the performance of PPI text classification task. Besides the traditional domain-independent bag-of-words approach and the term weighting methods, we also explored other domain-dependent features, i.e. protein-protein interaction trigger keywords, protein named entities and the advanced ways of incorporating Natural Language Processing (NLP) output. The integration of these multiple features has been evaluated on the BioCreAtIvE II corpus. The experimental results showed that both the advanced way of using NLP output and the integration of bag-of-words and NLP output improved the performance of text classification. Specifically, in comparison with the best performance achieved in the BioCreAtIvE II IAS, the feature-level and classifier-level integration of multiple features improved the performance of classification 2.71% and 3.95%, respectively.

Proscene: A feature-rich framework for interactive environments

Directory of Open Access Journals (Sweden)

Jean Pierre Charalambos

2017-01-01

Full Text Available We introduce Proscene, a feature-rich, open-source framework for interactive environments. The design of Proscene comprises a three-layered onion-like software architecture, promoting different possible development scenarios. The framework innermost layer decouples user gesture parsing from user-defined actions. The in-between layer implements a feature-rich set of widely-used motion actions allowing the selection and manipulation of objects, including the scene viewpoint. The outermost layer exposes those features as a Processing library. The results have shown the feasibility of our approach together with the simplicity and flexibility of the Proscene framework API.

Protein function prediction using neighbor relativity in protein-protein interaction network.

Science.gov (United States)

Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

2013-04-01

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

FUNCTIONING FEATURES OF COMPUTER TECHNOLOGY WHILE FORMING PRIMARY SCHOOLCHILDREN’S COMMUNICATIVE COMPETENCE

Directory of Open Access Journals (Sweden)

Olena Beskorsa

2017-04-01

Full Text Available The article reveals the problem of functioning features of computer technology while forming primary schoolchildren’s communicative competence whose relevance is proved by the increasing role of a foreign language as a means of communication and modernization of foreign language education. There is a great deal of publications devoted to the issue of foreign language learning at primary school by N. Biriukevych, O. Kolominova, O. Metolkina, O. Petrenko, V. Redko, S. Roman. Implementing of innovative technology as well as computer one is to intensify the language learning process and to improve young learners’ communicative skills. The aim of the article is to identify computer technology functioning features while forming primary schoolchildren communicative competence. In this study we follow the definition of the computer technology as an information technology whose implementation may be accompanied with a computer as one of the tools, excluding the use of audio and video equipment, projectors and other technical tools. Using computer technologies is realized due to a number of tools which are divided into two main groups: electronic learning materials; computer testing software. The analysis of current textbooks and learning and methodological complexes shows that teachers prefer authentic electronic materials to the national ones. The most available English learning materials are on the Internet and they are free. The author of the article discloses several on-line English learning tools and depict the opportunities to use them while forming primary schoolchildren’s communicative competence. Special attention is also paid to multimedia technology, its functioning features and multimedia lesson structure. Computer testing software provides tools for current and control assessing results of mastering language material, communicative skills, and self-assessing in an interactive way. For making tests for assessing English skill

Integrative approaches to the prediction of protein functions based on the feature selection

Directory of Open Access Journals (Sweden)

Lee Hyunju

2009-12-01

Full Text Available Abstract Background Protein function prediction has been one of the most important issues in functional genomics. With the current availability of various genomic data sets, many researchers have attempted to develop integration models that combine all available genomic data for protein function prediction. These efforts have resulted in the improvement of prediction quality and the extension of prediction coverage. However, it has also been observed that integrating more data sources does not always increase the prediction quality. Therefore, selecting data sources that highly contribute to the protein function prediction has become an important issue. Results We present systematic feature selection methods that assess the contribution of genome-wide data sets to predict protein functions and then investigate the relationship between genomic data sources and protein functions. In this study, we use ten different genomic data sources in Mus musculus, including: protein-domains, protein-protein interactions, gene expressions, phenotype ontology, phylogenetic profiles and disease data sources to predict protein functions that are labelled with Gene Ontology (GO terms. We then apply two approaches to feature selection: exhaustive search feature selection using a kernel based logistic regression (KLR, and a kernel based L1-norm regularized logistic regression (KL1LR. In the first approach, we exhaustively measure the contribution of each data set for each function based on its prediction quality. In the second approach, we use the estimated coefficients of features as measures of contribution of data sources. Our results show that the proposed methods improve the prediction quality compared to the full integration of all data sources and other filter-based feature selection methods. We also show that contributing data sources can differ depending on the protein function. Furthermore, we observe that highly contributing data sets can be similar among

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

Directory of Open Access Journals (Sweden)

Eilon Sharon

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

Role of amygdala central nucleus in feature negative discriminations

Science.gov (United States)

Holland, Peter C.

2012-01-01

Consistent with a popular theory of associative learning, the Pearce-Hall (1980) model, the surprising omission of expected events enhances cue associability (the ease with which a cue may enter into new associations), across a wide variety of behavioral training procedures. Furthermore, previous experiments from this laboratory showed that these enhancements are absent in rats with impaired function of the amygdala central nucleus (CeA). A notable exception to these assertions is found in feature negative (FN) discrimination learning, in which a “target” stimulus is reinforced when it is presented alone but nonreinforced when it is presented in compound with another, “feature” stimulus. According to the Pearce-Hall model, reinforcer omission on compound trials should enhance the associability of the feature relative to control training conditions. However, prior experiments have shown no evidence that CeA lesions affect FN discrimination learning. Here we explored this apparent contradiction by evaluating the hypothesis that the surprising omission of an event confers enhanced associability on a cue only if that cue itself generates the disconfirmed prediction. Thus, in a FN discrimination, the surprising omission of the reinforcer on compound trials would enhance the associability of the target stimulus but not that of the feature. Our data confirmed this hypothesis, and showed this enhancement to depend on intact CeA function, as in other procedures. The results are consistent with modern reformulations of both cue and reward processing theories that assign roles for both individual and aggregate error terms in associative learning. PMID:22889308

Feature Interactions Enable Decoding of Sensorimotor Transformations for Goal-Directed Movement

Science.gov (United States)

Barany, Deborah A.; Della-Maggiore, Valeria; Viswanathan, Shivakumar; Cieslak, Matthew

2014-01-01

Neurophysiology and neuroimaging evidence shows that the brain represents multiple environmental and body-related features to compute transformations from sensory input to motor output. However, it is unclear how these features interact during goal-directed movement. To investigate this issue, we examined the representations of sensory and motor features of human hand movements within the left-hemisphere motor network. In a rapid event-related fMRI design, we measured cortical activity as participants performed right-handed movements at the wrist, with either of two postures and two amplitudes, to move a cursor to targets at different locations. Using a multivoxel analysis technique with rigorous generalization tests, we reliably distinguished representations of task-related features (primarily target location, movement direction, and posture) in multiple regions. In particular, we identified an interaction between target location and movement direction in the superior parietal lobule, which may underlie a transformation from the location of the target in space to a movement vector. In addition, we found an influence of posture on primary motor, premotor, and parietal regions. Together, these results reveal the complex interactions between different sensory and motor features that drive the computation of sensorimotor transformations. PMID:24828640

Role of the transmembrane domain of FXYD7 in structural and functional interactions with Na,K-ATPase.

Science.gov (United States)

Li, Ciming; Crambert, Gilles; Thuillard, Delphine; Roy, Sophie; Schaer, Danièle; Geering, Käthi

2005-12-30

Members of the FXYD family are tissue-specific regulators of the Na,K-ATPase. Here, we have investigated the contribution of amino acids in the transmembrane (TM) domain of FXYD7 to the interaction with Na,K-ATPase. Twenty amino acids of the TM domain were replaced individually by tryptophan, and combined mutations and alanine insertion mutants were constructed. Wild type and mutant FXYD7 were expressed in Xenopus oocytes with Na,K-ATPase. Mutational effects on the stable association with Na,K-ATPase and on the functional regulation of Na,K-ATPase were determined by co-immunoprecipitation and two-electrode voltage clamp techniques, respectively. Most residues important for the structural and functional interaction of FXYD7 are clustered in a face of the TM helix containing the two conserved glycine residues, but others are scattered over two-thirds of the FXYD TM helix. Ile-35, Ile-43, and Ile-44 are only involved in the stable association with Na,K-ATPase. Glu-26, Met-30, and Ile-44 are important for the functional effect and/or the efficient association of FXYD7 with Na,K-ATPase, consistent with the prediction that these amino acids contact TM domain 9 of the alpha subunit (Li, C., Grosdidier, A., Crambert, G., Horisberger, J.-D., Michielin, O., and Geering, K. (2004) J. Biol. Chem. 279, 38895-38902). Several amino acids that are not implicated in the efficient association of FXYD7 with the Na,K-ATPase are specifically involved in the functional effect of FXYD7. Leu-32 and Phe-37 influence the apparent affinity for external K+, whereas Val-28 and Ile-42 are implicated in the apparent affinity for both external K+ and external Na+. These amino acids act in a synergistic way. These results highlight the important structural and functional role of the TM domain of FXYD7 and delineate the determinants that mediate the complex interactions of FXYD7 with Na,K-ATPase.

Combining many interaction networks to predict gene function and analyze gene lists.

Science.gov (United States)

Mostafavi, Sara; Morris, Quaid

2012-05-01

In this article, we review how interaction networks can be used alone or in combination in an automated fashion to provide insight into gene and protein function. We describe the concept of a "gene-recommender system" that can be applied to any large collection of interaction networks to make predictions about gene or protein function based on a query list of proteins that share a function of interest. We discuss these systems in general and focus on one specific system, GeneMANIA, that has unique features and uses different algorithms from the majority of other systems. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

Directory of Open Access Journals (Sweden)

Promponas Vasilis J

2003-10-01

Full Text Available Abstract Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating

Machine learning methods enable predictive modeling of antibody feature:function relationships in RV144 vaccinees.

Science.gov (United States)

Choi, Ickwon; Chung, Amy W; Suscovich, Todd J; Rerks-Ngarm, Supachai; Pitisuttithum, Punnee; Nitayaphan, Sorachai; Kaewkungwal, Jaranit; O'Connell, Robert J; Francis, Donald; Robb, Merlin L; Michael, Nelson L; Kim, Jerome H; Alter, Galit; Ackerman, Margaret E; Bailey-Kellogg, Chris

2015-04-01

The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help. The non-neutralizing role of antibodies in stimulating effector cell responses may have been a key mechanism of the protection observed in the RV144 HIV vaccine trial. In an extensive investigation of a rich set of data collected from RV144 vaccine recipients, we here employ machine learning methods to identify and model associations between antibody features (IgG subclass and antigen specificity) and effector function activities (antibody dependent cellular phagocytosis, cellular cytotoxicity, and cytokine release). We demonstrate via cross-validation that classification and regression approaches can effectively use the antibody features to robustly predict qualitative and quantitative functional outcomes. This integration of antibody feature and function data within a machine learning framework provides a new, objective approach to discovering and assessing multivariate immune correlates.

Machine learning methods enable predictive modeling of antibody feature:function relationships in RV144 vaccinees.

Directory of Open Access Journals (Sweden)

Ickwon Choi

2015-04-01

Full Text Available The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help. The non-neutralizing role of antibodies in stimulating effector cell responses may have been a key mechanism of the protection observed in the RV144 HIV vaccine trial. In an extensive investigation of a rich set of data collected from RV144 vaccine recipients, we here employ machine learning methods to identify and model associations between antibody features (IgG subclass and antigen specificity and effector function activities (antibody dependent cellular phagocytosis, cellular cytotoxicity, and cytokine release. We demonstrate via cross-validation that classification and regression approaches can effectively use the antibody features to robustly predict qualitative and quantitative functional outcomes. This integration of antibody feature and function data within a machine learning framework provides a new, objective approach to discovering and assessing multivariate immune correlates.

The Role of Auditory Features Within Slot-Themed Social Casino Games and Online Slot Machine Games.

Science.gov (United States)

Bramley, Stephanie; Gainsbury, Sally M

2015-12-01

Over the last few years playing social casino games has become a popular entertainment activity. Social casino games are offered via social media platforms and mobile apps and resemble gambling activities. However, social casino games are not classified as gambling as they can be played for free, outcomes may not be determined by chance, and players receive no monetary payouts. Social casino games appear to be somewhat similar to online gambling activities in terms of their visual and auditory features, but to date little research has investigated the cross over between these games. This study examines the auditory features of slot-themed social casino games and online slot machine games using a case study design. An example of each game type was played on three separate occasions during which, the auditory features (i.e., music, speech, sound effects, and the absence of sound) within the games were logged. The online slot-themed game was played in demo mode. This is the first study to provide a qualitative account of the role of auditory features within a slot-themed social casino game and an online slot machine game. Our results found many similarities between how sound is utilised within the two games. Therefore the sounds within these games may serve functions including: setting the scene for gaming, creating an image, demarcating space, interacting with visual features, prompting players to act, communicating achievements to players, providing reinforcement, heightening player emotions and the gaming experience. As a result this may reduce the ability of players to make a clear distinction between these two activities, which may facilitate migration between games.

Diversity-interaction modeling: estimating contributions of species identities and interactions to ecosystem function

DEFF Research Database (Denmark)

Kirwan, L; Connolly, J; Finn, J A

2009-01-01

to the roles of evenness, functional groups, and functional redundancy. These more parsimonious descriptions can be especially useful in identifying general diversity-function relationships in communities with large numbers of species. We provide an example of the application of the modeling framework......We develop a modeling framework that estimates the effects of species identity and diversity on ecosystem function and permits prediction of the diversity-function relationship across different types of community composition. Rather than just measure an overall effect of diversity, we separately....... These models describe community-level performance and thus do not require separate measurement of the performance of individual species. This flexible modeling approach can be tailored to test many hypotheses in biodiversity research and can suggest the interaction mechanisms that may be acting....

Conformational transitions and interactions underlying the function of membrane embedded receptor protein kinases.

Science.gov (United States)

Bocharov, Eduard V; Sharonov, Georgy V; Bocharova, Olga V; Pavlov, Konstantin V

2017-09-01

Among membrane receptors, the single-span receptor protein kinases occupy a broad but specific functional niche determined by distinctive features of the underlying transmembrane signaling mechanisms that are briefly overviewed on the basis of some of the most representative examples, followed by a more detailed discussion of several hierarchical levels of organization and interactions involved. All these levels, including single-molecule interactions (e.g., dimerization, liganding, chemical modifications), local processes (e.g. lipid membrane perturbations, cytoskeletal interactions), and larger scale phenomena (e.g., effects of membrane surface shape or electrochemical potential gradients) appear to be closely integrated to achieve the observed diversity of the receptor functioning. Different species of receptor protein kinases meet their specific functional demands through different structural features defining their responses to stimulation, but certain common patterns exist. Signaling by receptor protein kinases is typically associated with the receptor dimerization and clustering, ligand-induced rearrangements of receptor domains through allosteric conformational transitions with involvement of lipids, release of the sequestered lipids, restriction of receptor diffusion, cytoskeleton and membrane shape remodeling. Understanding of complexity and continuity of the signaling processes can help identifying currently neglected opportunities for influencing the receptor signaling with potential therapeutic implications. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova. Copyright © 2017 Elsevier B.V. All rights reserved.

A 2D suspension of active agents: the role of fluid mediated interactions

International Nuclear Information System (INIS)

Behmadi, Hojjat; Najafi, Ali; Fazli, Zahra

2017-01-01

Taking into account both the Vicsek short-range ordering and the far-field hydrodynamic interactions mediated by the ambient fluid, we investigate the role of long-range interactions in the ordering phenomena in a quasi 2-dimensional active suspension. By studying the number fluctuations, the velocity correlation functions and cluster size distribution function, we show that depending on the number density of swimmers and the strength of noise, the hydrodynamic interactions can have significant effects in a suspension. For a fixed value of noise, at larger density of particles, long-range interactions enhance the particle pairing and cluster formation in the system. (paper)

Learner interaction in a massively multiplayer online role playing game (MMORPG): A sociocultural discourse analysis

OpenAIRE

Peterson, Mark

2012-01-01

This exploratory study investigates the linguistic and social interaction of four intermediate EFL learners during game play in a massively multiplayer online role playing game (MMORPG). Twelve illustrative episodes drawn from the participants’ text chat, collected in four 70-minute sessions held over a one-month period, are analyzed from a sociocultural perspective. Qualitative analysis reveals the presence of interactional features associated with the development of sociocultural competence...

Nitrilase enzymes and their role in plant–microbe interactions

Science.gov (United States)

Howden, Andrew J. M.; Preston, Gail M.

2009-01-01

Summary Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant–microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth‐promoting microorganisms, and their activities may have a significant impact on the outcome of plant–microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant‐associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture. PMID:21255276

Scoring functions for protein-protein interactions.

Science.gov (United States)

Moal, Iain H; Moretti, Rocco; Baker, David; Fernández-Recio, Juan

2013-12-01

The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been developed to quantify the structural and energetic properties of interacting proteins, finding use in interrelated challenges revolving around the relationship between sequence, structure and binding free energy. These include loop modelling, side-chain refinement, docking, multimer assembly, affinity prediction, affinity change upon mutation, hotspots location and interface design. Information derived from models optimised for one of these challenges can be used to benefit the others, and can be unified within the theoretical frameworks of multi-task learning and Pareto-optimal multi-objective learning. Copyright © 2013 Elsevier Ltd. All rights reserved.

Role of ligand-ligand vs. core-core interactions in gold nanoclusters.

Science.gov (United States)

Milowska, Karolina Z; Stolarczyk, Jacek K

2016-05-14

The controlled assembly of ligand-coated gold nanoclusters (NCs) into larger structures paves the way for new applications ranging from electronics to nanomedicine. Here, we demonstrate through rigorous density functional theory (DFT) calculations employing novel functionals accounting for van der Waals forces that the ligand-ligand interactions determine whether stable assemblies can be formed. The study of NCs with different core sizes, symmetry forms, ligand lengths, mutual crystal orientations, and in the presence of a solvent suggests that core-to-core van der Waals interactions play a lesser role in the assembly. The dominant interactions originate from combination of steric effects, augmented by ligand bundling on NC facets, and related to them changes in electronic properties induced by neighbouring NCs. We also show that, in contrast to standard colloidal theory approach, DFT correctly reproduces the surprising experimental trends in the strength of the inter-particle interaction observed when varying the length of the ligands. The results underpin the importance of understanding NC interactions in designing gold NCs for a specific function.

The interactive effects of negative symptoms and social role functioning on suicide ideation in individuals with schizophrenia.

Science.gov (United States)

Jahn, Danielle R; Bennett, Melanie E; Park, Stephanie G; Gur, Raquel E; Horan, William P; Kring, Ann M; Blanchard, Jack J

2016-02-01

Findings regarding the protective effect of social role functioning on suicide ideation in individuals with schizophrenia have been mixed. One reason for such inconsistencies in the literature may be that individuals with prominent negative symptoms of schizophrenia may not experience a desire for social closeness, and therefore social role functioning may not influence suicide risk in these individuals. The aim of this study was to examine the moderating effects of self-reported desire for social closeness and interviewer-rated negative symptoms on the relationship between social role functioning and suicide ideation. Our sample consisted of 162 individuals who had been diagnosed with schizophrenia-spectrum disorders; all participants completed self-report questionnaires and clinician-administered interviews, and moderation hypotheses were tested with a non-parametric procedure. The results indicated that motivation and pleasure-related negative symptoms moderated the relationship between social role functioning and suicide ideation; self-reported desire for social closeness and negative symptoms related to expression did not have such a moderating effect. Specifically, better social role functioning was associated with less suicide ideation only in those individuals who had low motivation and pleasure-related negative symptoms; no significant relationship was observed between social role functioning and suicide ideation among those with elevated motivation and pleasure-related negative symptoms. These findings suggest that assessing for negative symptoms and social role functioning may inform suicide risk assessments in individuals with schizophrenia, and improving social role functioning may reduce suicide ideation among those with few motivation and pleasure-related negative symptoms. Copyright © 2015 Elsevier B.V. All rights reserved.

Structural Features Reminiscent of ATP-Driven Protein Translocases Are Essential for the Function of a Type III Secretion-Associated ATPase.

Science.gov (United States)

Kato, Junya; Lefebre, Matthew; Galán, Jorge E

2015-09-01

Many bacterial pathogens and symbionts utilize type III secretion systems to interact with their hosts. These machines have evolved to deliver bacterial effector proteins into eukaryotic target cells to modulate a variety of cellular functions. One of the most conserved components of these systems is an ATPase, which plays an essential role in the recognition and unfolding of proteins destined for secretion by the type III pathway. Here we show that structural features reminiscent of other ATP-driven protein translocases are essential for the function of InvC, the ATPase associated with a Salmonella enterica serovar Typhimurium type III secretion system. Mutational and functional analyses showed that a two-helix-finger motif and a conserved loop located at the entrance of and within the predicted pore formed by the hexameric ATPase are essential for InvC function. These findings provide mechanistic insight into the function of this highly conserved component of type III secretion machines. Type III secretion machines are essential for the virulence or symbiotic relationships of many bacteria. These machines have evolved to deliver bacterial effector proteins into host cells to modulate cellular functions, thus facilitating bacterial colonization and replication. An essential component of these machines is a highly conserved ATPase, which is necessary for the recognition and secretion of proteins destined to be delivered by the type III secretion pathway. Using modeling and structure and function analyses, we have identified structural features of one of these ATPases from Salmonella enterica serovar Typhimurium that help to explain important aspects of its function. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

Directory of Open Access Journals (Sweden)

Donald Adjeroh

2018-03-01

Full Text Available In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI. In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences, and structure information (protein and RNA secondary structures. This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.

Modeling and Detecting Feature Interactions among Integrated Services of Home Network Systems

Science.gov (United States)

Igaki, Hiroshi; Nakamura, Masahide

This paper presents a framework for formalizing and detecting feature interactions (FIs) in the emerging smart home domain. We first establish a model of home network system (HNS), where every networked appliance (or the HNS environment) is characterized as an object consisting of properties and methods. Then, every HNS service is defined as a sequence of method invocations of the appliances. Within the model, we next formalize two kinds of FIs: (a) appliance interactions and (b) environment interactions. An appliance interaction occurs when two method invocations conflict on the same appliance, whereas an environment interaction arises when two method invocations conflict indirectly via the environment. Finally, we propose offline and online methods that detect FIs before service deployment and during execution, respectively. Through a case study with seven practical services, it is shown that the proposed framework is generic enough to capture feature interactions in HNS integrated services. We also discuss several FI resolution schemes within the proposed framework.

Nitrilase enzymes and their role in plant-microbe interactions.

Science.gov (United States)

Howden, Andrew J M; Preston, Gail M

2009-07-01

Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture. © 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Observations and models of star formation in the tidal features of interacting galaxies

International Nuclear Information System (INIS)

Wallin, J.F.; Schombert, J.M.; Struck-Marcell, C.

1990-01-01

Multi-color surface photometry (BVri) is presented for the tidal features in a sample of interacting galaxies. Large color variations are found between the morphological components and within the individual components. The blue colors in the primary and the tidal features are most dramatic in B-V, and not in V-i, indicating that star formation instead of metallicity or age dominates the colors. Color variations between components is larger in systems shortly after interaction begins and diminishes to a very low level in systems which are merged. Photometric models for interacting systems are presented which suggest that a weak burst of star formation in the tidal features could cause the observed color distributions. Dynamical models indicate that compression occurs during the development of tidal features causing an increase in the local density by a factor of between 1.5 and 5. Assuming this density increase can be related to the star formation rate by a Schmidt law, the density increases observed in the dynamical models may be responsible for the variations in color seen in some of the interacting systems. Limitations of the dynamical models are also discussed

Student Interests and Attitude Change toward Drug Educators as a Function of Sex and Role Interaction.

Science.gov (United States)

Cotten-Huston, Annie L.

1982-01-01

Focused on recorded tapes and sex-role interaction of 12 sessions on drug abuse. Subjects were 247 seventh-grade males and females. Communicators (males and females) made two presentations with roles rotated according to ex-addict/learned specialist. Results indicated female and male students were influenced most by female specialist…

Competing role of Interactions in Synchronization of Exciton-Polariton condensates

Science.gov (United States)

Khan, Saeed; Tureci, Hakan E.

We present a theoretical study of synchronization dynamics in incoherently pumped exciton-polariton condensates in coupled traps. Our analysis is based on an expansion in non-Hermitian modes that take into account the trapping potential and the pump-induced complex-valued potential. We find that polariton-polariton and reservoir-polariton interactions play competing roles in the emergence of a synchronized phase as pumping power is increased, leading to qualitatively different synchronized phases. Crucially, these interactions can also act against each other to hinder synchronization. We present a phase diagram and explain the general characteristics of these phases using a generalized Adler equation. Our work sheds light on dynamics strongly influenced by competing interactions particular to incoherently pumped exciton-polariton condensates, which can lead to interesting features in recently engineered polariton lattices. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering.

Structure/functional aspects of the human riboflavin transporter-3 (SLC52A3): role of the predicted glycosylation and substrate-interacting sites.

Science.gov (United States)

Subramanian, Veedamali S; Sabui, Subrata; Teafatiller, Trevor; Bohl, Jennifer A; Said, Hamid M

2017-08-01

The human riboflavin (RF) transporter-3 (hRFVT-3; product of the SLC52A3 gene) plays an essential role in the intestinal RF absorption process and is expressed exclusively at the apical membrane domain of polarized enterocytes. Previous studies have characterized different physiological/biological aspects of this transporter, but nothing is known about the glycosylation status of the hRFVT-3 protein and role of this modification in its physiology/biology. Additionally, little is known about the residues in the hRFVT-3 protein that interact with the ligand, RF. We addressed these issues using appropriate biochemical/molecular approaches, a protein-docking model, and established intestinal/renal epithelial cells. Our results showed that the hRFVT-3 protein is glycosylated and that glycosylation is important for its function. Mutating the predicted N -glycosylation sites at Asn 94 and Asn 168 led to a significant decrease in RF uptake; it also led to a marked intracellular (in the endoplasmic reticulum, ER) retention of the mutated proteins as shown by live-cell confocal imaging studies. The protein-docking model used in this study has identified a number of putative substrate-interacting sites: Ser 16 , Ile 20 , Trp 24 , Phe 142 , Thr 314 , and Asn 315 Mutating these potential interacting sites was indeed found to lead to a significant inhibition in RF uptake and to intracellular (ER) retention of the mutated proteins (except for the Phe 142 mutant). These results demonstrate that the hRFVT-3 protein is glycosylated and this glycosylation is important for its function and cell surface expression. This study also identified a number of residues in the hRFVT-3 polypeptide that are important for its function/cell surface expression.

A multicolor photometric study of the tidal features in interacting galaxies

International Nuclear Information System (INIS)

Schombert, J.M.; Wallin, J.F.; Struck-Marcell, C.

1990-01-01

Four-color surface photometry (BVri) is presented for low-surface-brightness tidal features in interacting galaxies. Objects were selected on the basis of visual morphology including a cross section of tails, bridges, plumes, shells, and extended envelopes. Intensity cross sections and surface brightness suggests that plumes are face-on or near face-on sheets; tails and bridges are more nearly one-dimensional, linear figures. In many cases the colors of tidal features are similar to the outer regions of the primary galaxies, confirming the stripping origin hypothesis. However, large color variations are found among the morphological components within most systems, and within individual components. Blue colors in primaries and tidal features are most dramatic in B-V, not V-1, indicating that star formation, not metallicity or age, is the dominant component. There is clear evidence in the sample of a correlation between the magnitude of the color variation and the time. The color variations are largest a short time after the beginning of the interaction, and they diminish to a very low level in merged systems. This correlation provides an alternate estimator of interaction age in systems with ambiguous morphologies. 49 refs

[Noncovalent cation-π interactions--their role in nature].

Science.gov (United States)

Fink, Krzysztof; Boratyński, Janusz

2014-11-07

Non-covalent interactions play an extremely important role in organisms. The main non-covalent interactions in nature are: ion-ion interactions, dipole-dipole interactions, hydrogen bonds, and van der Waals interactions. A new kind of intermolecular interactions--cation-π interactions--is gaining increasing attention. These interactions occur between a cation and a π system. The main contributors to cation-π interactions are electrostatic, polarization and, to a lesser extent, dispersion interactions. At first, cation-π interactions were studied in a gas phase, with metal cation-aromatic system complexes. The characteristics of these complexes are as follows: an increase of cation atomic number leads to a decrease of interaction energy, and an increase of cation charge leads to an increase of interaction energy. Aromatic amino acids bind with metal cations mainly through interactions with their main chain. Nevertheless, cation-π interaction with a hydrophobic side chain significantly enhances binding energy. In water solutions most cations preferentially interact with water molecules rather than aromatic systems. Cation-π interactions occur in environments with lower accessibility to a polar solvent. Cation-π interactions can have a stabilizing role on the secondary, tertiary and quaternary structure of proteins. These interactions play an important role in substrate or ligand binding sites in many proteins, which should be taken into consideration when the screening of effective inhibitors for these proteins is carried out. Cation-π interactions are abundant and play an important role in many biological processes.

Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks

Directory of Open Access Journals (Sweden)

He Weiming

2010-07-01

Full Text Available Abstract Background Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. Results Here, we weighted edges of a human protein interaction network and a transcriptional regulatory network to construct an integrated network, and introduce a probabilistic model and a bipartite graph framework to exploit human co-regulated modules and uncover their specific features in packaging different biological entities (genes, protein complexes or metabolic pathways. Finally, we identified 96 human co-regulated modules based on this method, and evaluate its effectiveness by comparing it with four other methods. Conclusions Dysfunctions in co-regulated interactions often occur in the development of cancer. Therefore, we focussed on an example co-regulated module and found that it could integrate a number of cancer-related genes. This was extended to causal dysfunctions of some complexes maintained by several physically interacting proteins, thus coordinating several metabolic pathways that directly underlie cancer.

Filtering high-throughput protein-protein interaction data using a combination of genomic features

Directory of Open Access Journals (Sweden)

Patil Ashwini

2005-04-01

Full Text Available Abstract Background Protein-protein interaction data used in the creation or prediction of molecular networks is usually obtained from large scale or high-throughput experiments. This experimental data is liable to contain a large number of spurious interactions. Hence, there is a need to validate the interactions and filter out the incorrect data before using them in prediction studies. Results In this study, we use a combination of 3 genomic features – structurally known interacting Pfam domains, Gene Ontology annotations and sequence homology – as a means to assign reliability to the protein-protein interactions in Saccharomyces cerevisiae determined by high-throughput experiments. Using Bayesian network approaches, we show that protein-protein interactions from high-throughput data supported by one or more genomic features have a higher likelihood ratio and hence are more likely to be real interactions. Our method has a high sensitivity (90% and good specificity (63%. We show that 56% of the interactions from high-throughput experiments in Saccharomyces cerevisiae have high reliability. We use the method to estimate the number of true interactions in the high-throughput protein-protein interaction data sets in Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens to be 27%, 18% and 68% respectively. Our results are available for searching and downloading at http://helix.protein.osaka-u.ac.jp/htp/. Conclusion A combination of genomic features that include sequence, structure and annotation information is a good predictor of true interactions in large and noisy high-throughput data sets. The method has a very high sensitivity and good specificity and can be used to assign a likelihood ratio, corresponding to the reliability, to each interaction.

Structural and functional analysis of VQ motif-containing proteins in Arabidopsis as interacting proteins of WRKY transcription factors.

Science.gov (United States)

Cheng, Yuan; Zhou, Yuan; Yang, Yan; Chi, Ying-Jun; Zhou, Jie; Chen, Jian-Ye; Wang, Fei; Fan, Baofang; Shi, Kai; Zhou, Yan-Hong; Yu, Jing-Quan; Chen, Zhixiang

2012-06-01

WRKY transcription factors are encoded by a large gene superfamily with a broad range of roles in plants. Recently, several groups have reported that proteins containing a short VQ (FxxxVQxLTG) motif interact with WRKY proteins. We have recently discovered that two VQ proteins from Arabidopsis (Arabidopsis thaliana), SIGMA FACTOR-INTERACTING PROTEIN1 and SIGMA FACTOR-INTERACTING PROTEIN2, act as coactivators of WRKY33 in plant defense by specifically recognizing the C-terminal WRKY domain and stimulating the DNA-binding activity of WRKY33. In this study, we have analyzed the entire family of 34 structurally divergent VQ proteins from Arabidopsis. Yeast (Saccharomyces cerevisiae) two-hybrid assays showed that Arabidopsis VQ proteins interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY proteins. Using site-directed mutagenesis, we identified structural features of these two closely related groups of WRKY domains that are critical for interaction with VQ proteins. Quantitative reverse transcription polymerase chain reaction revealed that expression of a majority of Arabidopsis VQ genes was responsive to pathogen infection and salicylic acid treatment. Functional analysis using both knockout mutants and overexpression lines revealed strong phenotypes in growth, development, and susceptibility to pathogen infection. Altered phenotypes were substantially enhanced through cooverexpression of genes encoding interacting VQ and WRKY proteins. These findings indicate that VQ proteins play an important role in plant growth, development, and response to environmental conditions, most likely by acting as cofactors of group I and IIc WRKY transcription factors.

Audio feature extraction using probability distribution function

Science.gov (United States)

Suhaib, A.; Wan, Khairunizam; Aziz, Azri A.; Hazry, D.; Razlan, Zuradzman M.; Shahriman A., B.

2015-05-01

Voice recognition has been one of the popular applications in robotic field. It is also known to be recently used for biometric and multimedia information retrieval system. This technology is attained from successive research on audio feature extraction analysis. Probability Distribution Function (PDF) is a statistical method which is usually used as one of the processes in complex feature extraction methods such as GMM and PCA. In this paper, a new method for audio feature extraction is proposed which is by using only PDF as a feature extraction method itself for speech analysis purpose. Certain pre-processing techniques are performed in prior to the proposed feature extraction method. Subsequently, the PDF result values for each frame of sampled voice signals obtained from certain numbers of individuals are plotted. From the experimental results obtained, it can be seen visually from the plotted data that each individuals' voice has comparable PDF values and shapes.

Coding of visual object features and feature conjunctions in the human brain.

Science.gov (United States)

Martinovic, Jasna; Gruber, Thomas; Müller, Matthias M

2008-01-01

Object recognition is achieved through neural mechanisms reliant on the activity of distributed coordinated neural assemblies. In the initial steps of this process, an object's features are thought to be coded very rapidly in distinct neural assemblies. These features play different functional roles in the recognition process--while colour facilitates recognition, additional contours and edges delay it. Here, we selectively varied the amount and role of object features in an entry-level categorization paradigm and related them to the electrical activity of the human brain. We found that early synchronizations (approx. 100 ms) increased quantitatively when more image features had to be coded, without reflecting their qualitative contribution to the recognition process. Later activity (approx. 200-400 ms) was modulated by the representational role of object features. These findings demonstrate that although early synchronizations may be sufficient for relatively crude discrimination of objects in visual scenes, they cannot support entry-level categorization. This was subserved by later processes of object model selection, which utilized the representational value of object features such as colour or edges to select the appropriate model and achieve identification.

The Role of Public Interaction with the Juno Mission: Documentation, Discussion, Selection and Processing of JunoCam Images of Jovian Cloud Features

Science.gov (United States)

Orton, Glenn; Hansen, Candice; Momary, Thomas; Bolton, Scott

2017-04-01

Among the many "firsts" of the Juno mission is the open enlistment of the public in the operation of its visible camera, JunoCam. Although the scientific thrust of the Juno mission is largely focused on innovative approaches to understanding the structure and composition of Jupiter's interior, JunoCam was added to the payload largely to function in the role of education and public outreach (E/PO). For the first time, the public was able to engage in the discussion and choice of targets for a major NASA mission. The discussion about which features to image is enabled by a continuously updated map of Jupiter's cloud system while Jupiter is far enough from the sun to be observable by non-professional astronomers. Contributors range from very devoted astrophotographers to telescope and video 'hobbyists'. Juno therefore engages the world-wide amateur-astronomy community as a vast network of co-investigators, whose products stimulate conversation and global public awareness of Jupiter and Juno's investigative role. Contributed images also provide a temporal context to inform the Juno atmospheric investigation team of the state and evolution of the atmosphere. The contributed images are used to create s global map on a bi-weekly basis. These bi-weekly maps provide the focus for ongoing discussion about various planetary features over a long time frame. Approximately two weeks before Juno's closest approach to Jupiter on each orbit ("perijove" or PJ), starting in mid-November of 2016 in preparation for PJ3 on December 11, the atmospheric features that have been under discussion and available to JunoCam on that perijove were nominated for voting, and the public at large voted on where to point JunoCam's "elective" features. In addition, JunoCam provides the first close-up images of Jupiter's polar regions from a non-oblique viewpoint for the first time in over 40 years since the passage of Pioneer 11 over Jupiter's north pole. The Juno mission science team also provides

Benefits and Pitfalls of Multimedia and Interactive Features in Technology-Enhanced Storybooks

Science.gov (United States)

Takacs, Zsofia K.; Swart, Elise K.; Bus, Adriana G.

2015-01-01

A meta-analysis was conducted on the effects of technology-enhanced stories for young children’s literacy development when compared to listening to stories in more traditional settings like storybook reading. A small but significant additional benefit of technology was found for story comprehension (g+ = 0.17) and expressive vocabulary (g+ = 0.20), based on data from 2,147 children in 43 studies. When investigating the different characteristics of technology-enhanced stories, multimedia features like animated pictures, music, and sound effects were found beneficial. In contrast, interactive elements like hotspots, games, and dictionaries were found to be distracting. Especially for children disadvantaged because of less stimulating family environments, multimedia features were helpful and interactive features were detrimental. Findings are discussed from the perspective of cognitive processing theories. PMID:26640299

Cell–material interactions on biphasic polyurethane matrix

Science.gov (United States)

Dicesare, Patrick; Fox, Wade M.; Hill, Michael J.; Krishnan, G. Rajesh; Yang, Shuying; Sarkar, Debanjan

2013-01-01

Cell–matrix interaction is a key regulator for controlling stem cell fate in regenerative tissue engineering. These interactions are induced and controlled by the nanoscale features of extracellular matrix and are mimicked on synthetic matrices to control cell structure and functions. Recent studies have shown that nanostructured matrices can modulate stem cell behavior and exert specific role in tissue regeneration. In this study, we have demonstrated that nanostructured phase morphology of synthetic matrix can control adhesion, proliferation, organization and migration of human mesenchymal stem cells (MSCs). Nanostructured biodegradable polyurethanes (PU) with segmental composition exhibit biphasic morphology at nanoscale dimensions and can control cellular features of MSCs. Biodegradable PU with polyester soft segment and hard segment composed of aliphatic diisocyanates and dipeptide chain extender were designed to examine the effect polyurethane phase morphology. By altering the polyurethane composition, morphological architecture of PU was modulated and its effect was examined on MSC. Results show that MSCs can sense the nanoscale morphology of biphasic polyurethane matrix to exhibit distinct cellular features and, thus, signifies the relevance of matrix phase morphology. The role of nanostructured phases of a synthetic matrix in controlling cell–matrix interaction provides important insights for regulation of cell behavior on synthetic matrix and, therefore, is an important tool for engineering tissue regeneration. PMID:23255285

Structures and Functions of Oligosaccharins: The Role of Endoglycanases

Energy Technology Data Exchange (ETDEWEB)

Bergmann, Carl W. [University of Georgia

2008-12-05

The research proposed will investigate two projects that involve studies of the chemistry and biology of protein/protein and protein/carbohydrate interactions involved in host/pathogen interactions. Specifically, the projects involve (i) the interactions between fungal endopolygalacturonases and plant polygalacturonase-inhibiting proteins and (ii) the interactions between fungal endoxylanases and plant arabinoxylans. During pathogenesis fungi secrete families of endoglycanases that fragment the cell wall polysaccharides of the plant host. The result of endoglycanase action on cell wall polysaccharides can include weakening of the wall, penetration of host cells by the pathogen, solubilization of carbohydrate nutrients, and formation of oligosaccharins (oligosaccharides with regulatory function) that can stimulate plant defenses. We have made significant advances during the last funding period to support the hypothesis that the outcome of attempted pathogenesis can be influenced by protein/protein and protein/carbohydrate interactions in the extracellular matrices of the host and pathogen. We plan to expand on those successes by further exploring the mechanism of action of the endoglycanases and their plant-derived inhibitors, the expression of the various members of the endoglycanase families at various stages of infection and their role in the release of oligosaccharins and in pathogenicity, as well as the role played by the polysaccharide substrates in both pathogenicity and endoglycanase-inhibitor interactions.

CD147 Immunoglobulin Superfamily Receptor Function and Role in Pathology

OpenAIRE

Iacono, Kathryn T.; Brown, Amy L.; Greene, Mark I.; Saouaf, Sandra J.

2007-01-01

The immunoglobulin superfamily member CD147 plays an important role in fetal, neuronal, lymphocyte and extracellular matrix development. Here we review the current understanding of CD147 expression and protein interactions with regard to CD147 function and its role in pathologic conditions including heart disease, Alzheimer’s disease, stroke and cancer. A model linking hypoxic conditions found within the tumor microenvironment to up-regulation of CD147 expression and tumor progression is intr...

Structural insights into the interaction of human IgG1 with FcγRI: no direct role of glycans in binding

Energy Technology Data Exchange (ETDEWEB)

Oganesyan, Vaheh, E-mail: oganesyanv@medimmune.com; Mazor, Yariv; Yang, Chunning; Cook, Kimberly E.; Woods, Robert M. [MedImmune LLC, 1 MedImmune Way, Gaithersburg, MD 20878 (United States); Ferguson, Andrew [AstraZeneca Pharmaceuticals, 35 Gatehouse Drive, Mailstop E3, Waltham, MA 02451 (United States); Bowen, Michael A.; Martin, Tom; Zhu, Jie; Wu, Herren; Dall’Acqua, William F., E-mail: oganesyanv@medimmune.com [MedImmune LLC, 1 MedImmune Way, Gaithersburg, MD 20878 (United States)

2015-10-31

In an effort to identify the critical structural features responsible for the high-affinity interaction of IgG1 Fc with FcγRI, the structure of the corresponding complex was solved at a resolution of 2.4 Å. The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Å using molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. This study highlights the critical structural and functional role played by the second extracellular subdomain of FcγRI. It also explains the long-known major energetic contribution of the Fc ‘LLGG’ motif at positions 234–237, and particularly of Leu235, via a ‘lock-and-key’ mechanism. Finally, a previously held belief is corrected and a differing view is offered on the recently proposed direct role of Fc carbohydrates in the corresponding interaction. Structural evidence is provided that such glycan-related effects are strictly indirect.

The interactive roles of parenting, emotion regulation and executive functioning in moral reasoning during middle childhood.

Science.gov (United States)

Hinnant, J Benjamin; Nelson, Jackie A; O'Brien, Marion; Keane, Susan P; Calkins, Susan D

2013-01-01

We examined mother-child co-operative behaviour, children's emotion regulation and executive function, as well as combinations of these factors, as predictors of moral reasoning in 89 10-year-old children. Dyadic co-operation was coded from videotaped observations of laboratory puzzle and speech tasks. Emotion regulation was derived from maternal report, and executive functioning was assessed with the Tower of London task. Moral reasoning was coded during mother-child conversations about morally ambiguous, peer-conflict situations. Two significant interactions indicated that children from more co-operative dyads who also had higher executive function skills had higher moral reasoning scores than other children, and children lower in both emotion regulation and executive function had lower moral reasoning scores than other children. The results contribute to the literature on the multiple and interactive levels of influence on moral reasoning in childhood.

The Interactive Roles of Parenting, Emotion Regulation and Executive Functioning in Moral Reasoning during Middle Childhood

Science.gov (United States)

Hinnant, J. Benjamin; Nelson, Jackie A.; O’Brien, Marion; Keane, Susan P.; Calkins, Susan D.

2013-01-01

We examined mother-child cooperative behavior, children’s emotion regulation and executive function, as well as combinations of these factors, as predictors of moral reasoning in 89 10-year-old children. Dyadic cooperation was coded from videotaped observations of laboratory puzzle and speech tasks. Emotion regulation was derived from maternal report, and executive functioning was assessed with the Tower of London task. Moral reasoning was coded during mother-child conversations about morally ambiguous, peer-conflict situations. Two significant interactions indicated that children from more cooperative dyads who also had higher executive function skills had higher moral reasoning scores than other children, and children lower in both emotion regulation and executive function had lower moral reasoning scores than other children. The results contribute to the literature on the multiple and interactive levels of influence on moral reasoning in childhood. PMID:23650955

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

Directory of Open Access Journals (Sweden)

Oyang Yen-Jen

2010-10-01

Full Text Available Abstract Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.

Infants' Developing Sensitivity to Object Function: Attention to Features and Feature Correlations

Science.gov (United States)

Baumgartner, Heidi A.; Oakes, Lisa M.

2011-01-01

When learning object function, infants must detect relations among features--for example, that squeezing is associated with squeaking or that objects with wheels roll. Previously, Perone and Oakes (2006) found 10-month-old infants were sensitive to relations between object appearances and actions, but not to relations between appearances and…

Expectations and outcome: The role of Proposer features in the Ultimatum Game

NARCIS (Netherlands)

Marchetti, A.; Castelli, I.; Harlé, K.M.; Sanfey, A.G.

2011-01-01

In social decision-making individuals make choices in an interactive context and their decisions may therefore be influenced by information they receive about features of the other player. These features may 'frame' the other player in particular ways and generate expectations about the outcome.

Hedonic Benefits of Close and Distant Interaction Partners: The Mediating Roles of Social Approval and Authenticity.

Science.gov (United States)

Venaglia, Rachel B; Lemay, Edward P

2017-09-01

The current research utilized ecological momentary assessment methodology to examine affective responses to interacting with close versus distant interaction partners during naturally occurring social interactions, and to test predictions regarding the mediating roles of perceived social approval and authenticity. Analysis of 4,602 social interactions reported by 176 participants suggested that, relative to interactions with distant partners, interactions with close partners were characterized by more positive affect. This effect was mediated by perceived social approval and authenticity. These findings suggest that social interactions with close others confer greater hedonic benefits relative to interactions with distant partners due to greater confidence in social approval and feelings of authenticity. Exploratory analyses suggested that interactions with close partners featured warmer and less shy behavior, and that participants who placed more importance on close relationships (as measured by high relational-interdependent self-construal) experienced more approval and authenticity in their interactions, particularly with distant partners.

Mapping genomic features to functional traits through microbial whole genome sequences.

Science.gov (United States)

Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

2014-01-01

Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.

IgG-Fc-mediated effector functions: molecular definition of interaction sites for effector ligands and the role of glycosylation.

Science.gov (United States)

Jefferis, R; Lund, J; Pound, J D

1998-06-01

The Fc region of human IgG expresses interaction sites for many effector ligands. In this review the topographical distributions of ten of these sites are discussed in relation to functional requirement. It is apparent that interaction sites localised to the inter-CH2-CH3 domain region of the Fc allow for functional divalency, whereas sites localised to the hinge proximal region of the CH2 domain are functionally monovalent, with expression of the latter sites being particularly dependent on glycosylation. All x-ray crystal structures for Fc and Fc-ligand complexes report that the protein structure of the hinge proximal region of the CH2 domain is "disordered", suggesting "internal mobility". We propose a model in which such "internal mobility" results in the generation of a dynamic equilibrium between multiple conformers, certain of which express interaction sites specific to individual ligands. The emerging understanding of the influence of oligosaccharide/protein interactions on protein conformation and biological function of IgG antibodies suggests a potential to generate novel glycoforms of antibody molecules having unique profiles of effector functions.

Functional Characterization of the Maize Phytochrome-Interacting Factors PIF4 and PIF5

Directory of Open Access Journals (Sweden)

Qingbiao Shi

2018-01-01

Full Text Available Phytochrome-interacting factors (PIFs play important roles in photomorphogenesis, the shade avoidance response, and other aspects of plant growth and development. PIF family proteins have been well-studied in Arabidopsis thaliana, but little is known about their physiological functions and molecular mechanisms in maize (Zea mays. In this study, we investigated the physiological functions of ZmPIF4 and ZmPIF5, two highly conserved members of the PIF gene family. RT-qPCR and western blot analyses revealed that ZmPIF4 and ZmPIF5 expression and ZmPIF4 and ZmPIF5 levels peak at night and remain low during the day. Overexpression of ZmPIF4 and ZmPIF5 in Arabidopsis partially rescued the reduced hypocotyl elongation and defective response to gravity in pif1 pif3 pif4 pif5 quadruple mutants (pifq. In addition, under high red: far-red light conditions, Arabidopsis lines overexpressing ZmPIF4 exhibited a constitutive shade avoidance response, including early flowering, slender leaves and inflorescences, plant lodging and precocious leaf senescence. Furthermore, ZmPIF4 physically interacted with the Arabidopsis DELLA protein REPRESSOR OF GA1-3 (RGA, indicating a potential interaction between ZmPIF4 and gibberellin signaling pathway on plant growth. Taken together, our results revealed that ZmPIF4 and ZmPIF5 are functionally conserved proteins that may play conserved roles in the response to phytochrome signaling in plants.Highlights:In this study, the functions of ZmPIF4 and ZmPIF5 were characterized by expression in Arabidopsis, revealing conserved roles of PIF family proteins in photomorphogenesis and the shade avoidance response in land plants.

The role of neurexins and neuroligins in the formation, maturation, and function of vertebrate synapses.

Science.gov (United States)

Krueger, Dilja D; Tuffy, Liam P; Papadopoulos, Theofilos; Brose, Nils

2012-06-01

Neurexins (NXs) and neuroligins (NLs) are transsynaptically interacting cell adhesion proteins that play a key role in the formation, maturation, activity-dependent validation, and maintenance of synapses. As complex alternative splicing processes in nerve cells generate a large number of NX and NLs variants, it has been proposed that a combinatorial interaction code generated by these variants may determine synapse identity and network connectivity during brain development. The functional importance of NXs and NLs is exemplified by the fact that mutations in NX and NL genes are associated with several neuropsychiatric disorders, most notably with autism. Accordingly, major research efforts have focused on the molecular mechanisms by which NXs and NLs operate at synapses. In this review, we summarize recent progress in this field and discuss emerging topics, such as the role of alternative interaction partners of NXs and NLs in synapse formation and function, and their relevance for synaptic plasticity in the mature brain. The novel findings highlight the fundamental importance of NX-NL interactions in a wide range of synaptic functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

The role of reaction pathways and support interactions in the development of high activity hydrotreating catalysts

DEFF Research Database (Denmark)

Topsøe, Henrik; Hinnemann, Berit; Nørskov, Jens Kehlet

2005-01-01

structures may be present as single sulfide sheets. Thus, stacking is not an essential feature of Type II catalysts. The article illustrates how the new scientific insight has aided the introduction of the new high activity BRIM (TM) type catalysts for FCC pre-treatment and production of ultra low sulfur...... exhibiting a metallic character are observed to be involved in adsorption, hydrogenation and C-S bond cleavage. The insight is seen to provide a new framework for understanding the DDS and HYD pathways and the role of steric hindrance and poisons. Density functional theory (DFT) calculations have illustrated...... how support interactions may influence the activity of sulfided catalysts. The brim sites and the tendency to form vacancies are seen to differ in types I and II Co-Mo-S. High-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) studies show that the high activity Type II...

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study.

Science.gov (United States)

A Santos, Jose C; Nassif, Houssam; Page, David; Muggleton, Stephen H; E Sternberg, Michael J

2012-07-11

There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. In addition to confirming literature results, ProGolem's model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

Drawing a dog: The role of working memory and executive function.

Science.gov (United States)

Panesi, Sabrina; Morra, Sergio

2016-12-01

Previous research suggests that young children draw animals by adapting their scheme for the human figure. This can be considered an early form of drawing flexibility. This study investigated preschoolers' ability to draw a dog that is different from the human figure. The role of working memory capacity and executive function was examined. The participants were 123 children (36-73 months old) who were required to draw both a person and a dog. The dog figure was scored on a list of features that could render it different from the human figure. Regression analyses showed that both working memory capacity and executive function predicted development in the dog drawing; the dog drawing score correlated with working memory capacity and executive function, even partialling out age, motor coordination, and drawing ability (measured with Goodenough's Draw-a-Man test). These results suggest that both working memory capacity and executive function play an important role in the early development of drawing flexibility. The implications regarding executive functions and working memory are also discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

The clinical features of EDNOS: relationship to mood, health status and general functioning.

Science.gov (United States)

Turner, Hannah; Bryant-Waugh, Rachel; Peveler, Robert

2010-04-01

Eating disorder not otherwise specified (EDNOS) remains poorly evaluated in terms of eating disorder features and relationship to mood, health status and general functioning. This study investigated the clinical profiles of a sample of EDNOS patients, and how they compared to patients with anorexia nervosa (AN) and bulimia nervosa (BN). The sample consisted of 178 patients. All completed the Eating Disorder Examination, Beck Depression Inventory, Work and Social Adjustment Scale and Sf-36. ANOVAs were conducted to explore group differences. No differences were found for depression. No differences were found between BN and EDNOS on measures of health status and general functioning. AN patients reported greater role limitations due to physical health and experienced greater physical pain compared with BN or EDNOS patients, and reported poorer social functioning, lower vitality and higher functional impairment compared with EDNOS patients. EDNOS patients are generally no less clinically impaired than those with BN. However AN patients may be more impaired in some aspects of general functioning compared with BN or EDNOS patients. Copyright 2009 Elsevier Ltd. All rights reserved.

SPECIAL FEATURES OF VIRTUAL PRACTICE INTERACTIVE MEDIA DISCIPLINES FOR DISTANCE LEARNING

Directory of Open Access Journals (Sweden)

M.P. Mazur

2010-08-01

Full Text Available The features of the development of interactive virtual practical training courses for distance learning are examined in the article. The authors propose their own methods of development tools such disciplines as virtual simulation or video-on labs.

The phospholipase PNPLA7 functions as a lysophosphatidylcholine hydrolase and interacts with lipid droplets through its catalytic domain.

Science.gov (United States)

Heier, Christoph; Kien, Benedikt; Huang, Feifei; Eichmann, Thomas O; Xie, Hao; Zechner, Rudolf; Chang, Ping-An

2017-11-17

Mammalian patatin-like phospholipase domain-containing proteins (PNPLAs) are lipid-metabolizing enzymes with essential roles in energy metabolism, skin barrier development, and brain function. A detailed annotation of enzymatic activities and structure-function relationships remains an important prerequisite to understand PNPLA functions in (patho-)physiology, for example, in disorders such as neutral lipid storage disease, non-alcoholic fatty liver disease, and neurodegenerative syndromes. In this study, we characterized the structural features controlling the subcellular localization and enzymatic activity of PNPLA7, a poorly annotated phospholipase linked to insulin signaling and energy metabolism. We show that PNPLA7 is an endoplasmic reticulum (ER) transmembrane protein that specifically promotes hydrolysis of lysophosphatidylcholine in mammalian cells. We found that transmembrane and regulatory domains in the PNPLA7 N-terminal region cooperate to regulate ER targeting but are dispensable for substrate hydrolysis. Enzymatic activity is instead mediated by the C-terminal domain, which maintains full catalytic competence even in the absence of N-terminal regions. Upon elevated fatty acid flux, the catalytic domain targets cellular lipid droplets and promotes interactions of PNPLA7 with these organelles in response to increased cAMP levels. We conclude that PNPLA7 acts as an ER-anchored lysophosphatidylcholine hydrolase that is composed of specific functional domains mediating catalytic activity, subcellular positioning, and interactions with cellular organelles. Our study provides critical structural insights into an evolutionarily conserved class of phospholipid-metabolizing enzymes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The role of fluid-wall interactions on confined liquid diffusion using Mori theory

International Nuclear Information System (INIS)

Devi, Reena; Srivastava, Sunita; Tankeshwar, K.

2015-01-01

The dynamics of fluid confined in a nano-channel with smooth walls have been studied through velocity autocorrelation function within the memory function approach by incorporating the atomic level interactions of fluid with the confining wall. Expressions for the second and fourth sum rules of velocity autocorrelation have been derived for nano-channel which involves fluid-fluid and fluid-wall interactions. These expressions, in addition, involve pair correlation function and density profiles. The numerical contributions of fluid-wall interaction to sum rules are found to play a very significant role, specifically at smaller channel width. Results obtained for velocity autocorrelation and self-diffusion coefficient of a fluid confined to different widths of the nanochannel have been compared with the computer simulation results. The comparison shows a good agreement except when the width of the channel is of the order of two atomic diameters, where it becomes difficult to estimate sum rules involving the triplet correlation’s contribution

Beyond common features: The role of roles in determining similarity1

Science.gov (United States)

Jones, Matt; Love, Bradley C.

2007-01-01

Historically, accounts of object representation and perceived similarity have focused on intrinsic features. Although more recent accounts have explored how objects, scenes, and situations containing common relational structures come to be perceived as similar, less is known about how the perceived similarity of parts or objects embedded within these relational systems is affected. The current studies test the hypothesis that objects situated in common relational systems come to be perceived as more similar. Similarity increases most for objects playing the same role within a relation (e.g., predator), but also increases for objects playing different roles within the same relation (e.g., the predator or prey role in the hunts relation) regardless of whether the objects participate in the same instance of the relation. This pattern of results can be captured by extending existing models that extract meaning from text corpora so that they are sensitive to the verb-specific thematic roles that objects fill. Alternative explanations based on analogical and inferential processes are also considered, as well as the implications of the current findings to research in language processing, personality and person perception, decision making, and category learning. PMID:17094958

Interaction of Myosin Phosphatase Target Subunit (MYPT1) with Myosin Phosphatase-RhoA Interacting Protein (MRIP): A Role of Glutamic Acids in the Interaction.

Science.gov (United States)

Lee, Eunhee; Stafford, Walter F

2015-01-01

Scaffold proteins bind to and functionally link protein members of signaling pathways. Interaction of the scaffold proteins, myosin phosphatase target subunit (MYPT1) and myosin phosphatase-RhoA interacting protein (MRIP), causes co-localization of myosin phosphatase and RhoA to actomyosin. To examine biophysical properties of interaction of MYPT1 with MRIP, we employed analytical ultracentrifugation and surface plasmon resonance. In regard to MRIP, its residues 724-837 are sufficient for the MYPT1/MRIP interaction. Moreover, MRIP binds to MYPT1 as either a monomer or a dimer. With respect to MYPT1, its leucine repeat region, LR (residues 991-1030) is sufficient to account for the MYPT1/MRIP interaction. Furthermore, point mutations that replace glutamic acids 998-1000 within LR reduced the binding affinity toward MRIP. This suggests that the glutamic acids of MYPT1 play an important role in the interaction.

The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.

Directory of Open Access Journals (Sweden)

M Qaiser Fatmi

Full Text Available The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS. TRPS uses a set of α/β-dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand-bound conformations. Our simulations also revealed that the α/β-dimeric unit stabilizes the substrate-protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function.

Home Features and Assistive Technology for the Home-Bound Elderly in a Thai Suburban Community by Applying the International Classification of Functioning, Disability, and Health

Directory of Open Access Journals (Sweden)

Supawadee Putthinoi

2017-01-01

Full Text Available The ageing population is having an impact worldwide and has created a serious challenge in Thailand’s healthcare systems, whereby healthcare practitioners play a major role in promoting independent interaction of their client’s abilities, as well as environmental factors. The purpose of this study was to survey features of the home and assistive technology (AT for the home-bound elderly in the community of Chiang Mai, Thailand. Home evaluation included features inside and outside the home, and AT was based on the International Classification of Functioning, Disability, and Health (ICF concept. Methods included observation and an interview that were used by the researcher for evaluation. The study found that every home had at least one hazardous home feature such as inappropriate width of the door, high door threshold, tall stair steps, no bedside rail, and inappropriate height of the toilet pan. AT was found in houses as general products and technology for personal use in daily living and for personal indoor and outdoor mobility as well as transportation. Therefore, home features and AT can afford the home-bound elderly independent living within the community. Perspective AT according to the ICF concept could provide a common language for ageing in place benefits.

Prediction and Dissection of Protein-RNA Interactions by Molecular Descriptors.

Science.gov (United States)

Liu, Zhi-Ping; Chen, Luonan

2016-01-01

Protein-RNA interactions play crucial roles in numerous biological processes. However, detecting the interactions and binding sites between protein and RNA by traditional experiments is still time consuming and labor costing. Thus, it is of importance to develop bioinformatics methods for predicting protein-RNA interactions and binding sites. Accurate prediction of protein-RNA interactions and recognitions will highly benefit to decipher the interaction mechanisms between protein and RNA, as well as to improve the RNA-related protein engineering and drug design. In this work, we summarize the current bioinformatics strategies of predicting protein-RNA interactions and dissecting protein-RNA interaction mechanisms from local structure binding motifs. In particular, we focus on the feature-based machine learning methods, in which the molecular descriptors of protein and RNA are extracted and integrated as feature vectors of representing the interaction events and recognition residues. In addition, the available methods are classified and compared comprehensively. The molecular descriptors are expected to elucidate the binding mechanisms of protein-RNA interaction and reveal the functional implications from structural complementary perspective.

Technical Evaluation Report 51: Text-based Conferencing: Features vs. functionality

Directory of Open Access Journals (Sweden)

Lynn Anderson

2005-11-01

Full Text Available This report examines three text-based conferencing products: WowBB, Invision Power Board, and vBulletin. Their selection was prompted by a feature-by-feature comparison of the same products on the WowBB website. The comparison chart painted a misleading impression of WowBB’s features in relation to the other two products; so the evaluation team undertook a more comprehensive and impartial comparison using the categories and criteria for online software evaluation developed by the American Society for Training and Development (ASTD. The findings are summarised in terms of the softwares’ pricing, common features/ functions, and differentiating features.

Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors1[W][OA

Science.gov (United States)

Cheng, Yuan; Zhou, Yuan; Yang, Yan; Chi, Ying-Jun; Zhou, Jie; Chen, Jian-Ye; Wang, Fei; Fan, Baofang; Shi, Kai; Zhou, Yan-Hong; Yu, Jing-Quan; Chen, Zhixiang

2012-01-01

WRKY transcription factors are encoded by a large gene superfamily with a broad range of roles in plants. Recently, several groups have reported that proteins containing a short VQ (FxxxVQxLTG) motif interact with WRKY proteins. We have recently discovered that two VQ proteins from Arabidopsis (Arabidopsis thaliana), SIGMA FACTOR-INTERACTING PROTEIN1 and SIGMA FACTOR-INTERACTING PROTEIN2, act as coactivators of WRKY33 in plant defense by specifically recognizing the C-terminal WRKY domain and stimulating the DNA-binding activity of WRKY33. In this study, we have analyzed the entire family of 34 structurally divergent VQ proteins from Arabidopsis. Yeast (Saccharomyces cerevisiae) two-hybrid assays showed that Arabidopsis VQ proteins interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY proteins. Using site-directed mutagenesis, we identified structural features of these two closely related groups of WRKY domains that are critical for interaction with VQ proteins. Quantitative reverse transcription polymerase chain reaction revealed that expression of a majority of Arabidopsis VQ genes was responsive to pathogen infection and salicylic acid treatment. Functional analysis using both knockout mutants and overexpression lines revealed strong phenotypes in growth, development, and susceptibility to pathogen infection. Altered phenotypes were substantially enhanced through cooverexpression of genes encoding interacting VQ and WRKY proteins. These findings indicate that VQ proteins play an important role in plant growth, development, and response to environmental conditions, most likely by acting as cofactors of group I and IIc WRKY transcription factors. PMID:22535423

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

Directory of Open Access Journals (Sweden)

A Santos Jose C

2012-07-01

Full Text Available Abstract Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP, which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners.

INTERACTIVE VISUALIZATION OF PROBABILITY AND CUMULATIVE DENSITY FUNCTIONS

KAUST Repository

Potter, Kristin; Kirby, Robert Michael; Xiu, Dongbin; Johnson, Chris R.

2012-01-01

The probability density function (PDF), and its corresponding cumulative density function (CDF), provide direct statistical insight into the characterization of a random process or field. Typically displayed as a histogram, one can infer probabilities of the occurrence of particular events. When examining a field over some two-dimensional domain in which at each point a PDF of the function values is available, it is challenging to assess the global (stochastic) features present within the field. In this paper, we present a visualization system that allows the user to examine two-dimensional data sets in which PDF (or CDF) information is available at any position within the domain. The tool provides a contour display showing the normed difference between the PDFs and an ansatz PDF selected by the user and, furthermore, allows the user to interactively examine the PDF at any particular position. Canonical examples of the tool are provided to help guide the reader into the mapping of stochastic information to visual cues along with a description of the use of the tool for examining data generated from an uncertainty quantification exercise accomplished within the field of electrophysiology.

Membrane trafficking pathways and their roles in plant-microbe interactions.

Science.gov (United States)

Inada, Noriko; Ueda, Takashi

2014-04-01

Membrane trafficking functions in the delivery of proteins that are newly synthesized in the endoplasmic reticulum (ER) to their final destinations, such as the plasma membrane (PM) and the vacuole, and in the internalization of extracellular components or PM-associated proteins for recycling or degradative regulation. These trafficking pathways play pivotal roles in the rapid responses to environmental stimuli such as challenges by microorganisms. In this review, we provide an overview of the current knowledge of plant membrane trafficking and its roles in plant-microbe interactions. Although there is little information regarding the mechanism of pathogenic modulation of plant membrane trafficking thus far, recent research has identified many membrane trafficking factors as possible targets of microbial modulation.

Modeling nuclear weak-interaction processes with relativistic energy density functionals

International Nuclear Information System (INIS)

Paar, N.; Marketin, T.; Vale, D.; Vretenar, D.

2015-01-01

Relativistic energy density functionals have become a standard framework for nuclear structure studies of ground state properties and collective excitations over the entire nuclide chart. In this paper, we review recent developments in modeling nuclear weak-interaction processes: Charge-exchange excitations and the role of isoscalar proton–neutron pairing, charged-current neutrino–nucleus reactions relevant for supernova evolution and neutrino detectors and calculation of β-decay rates for r-process nucleosynthesis. (author)

Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses

Directory of Open Access Journals (Sweden)

Murilo S. Alves

2014-03-01

Full Text Available Responses to biotic stress in plants lead to dramatic reprogramming of gene expression, favoring stress responses at the expense of normal cellular functions. Transcription factors are master regulators of gene expression at the transcriptional level, and controlling the activity of these factors alters the transcriptome of the plant, leading to metabolic and phenotypic changes in response to stress. The functional analysis of interactions between transcription factors and other proteins is very important for elucidating the role of these transcriptional regulators in different signaling cascades. In this review, we present an overview of protein-protein interactions for the six major families of transcription factors involved in plant defense: basic leucine zipper containing domain proteins (bZIP, amino-acid sequence WRKYGQK (WRKY, myelocytomatosis related proteins (MYC, myeloblastosis related proteins (MYB, APETALA2/ ETHYLENE-RESPONSIVE ELEMENT BINDING FACTORS (AP2/EREBP and no apical meristem (NAM, Arabidopsis transcription activation factor (ATAF, and cup-shaped cotyledon (CUC (NAC. We describe the interaction partners of these transcription factors as molecular responses during pathogen attack and the key components of signal transduction pathways that take place during plant defense responses. These interactions determine the activation or repression of response pathways and are crucial to understanding the regulatory networks that modulate plant defense responses.

The function of communities in protein interaction networks at multiple scales

Directory of Open Access Journals (Sweden)

Jones Nick S

2010-07-01

Full Text Available Abstract Background If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological modules and network communities in yeast and its relationship to the scale at which we probe the network. Results Our results demonstrate that the functional homogeneity of communities depends on the scale selected, and that almost all proteins lie in a functionally homogeneous community at some scale. We judge functional homogeneity using a novel test and three independent characterizations of protein function, and find a high degree of overlap between these measures. We show that a high mean clustering coefficient of a community can be used to identify those that are functionally homogeneous. By tracing the community membership of a protein through multiple scales we demonstrate how our approach could be useful to biologists focusing on a particular protein. Conclusions We show that there is no one scale of interest in the community structure of the yeast protein interaction network, but we can identify the range of resolution parameters that yield the most functionally coherent communities, and predict which communities are most likely to be functionally homogeneous.

A Novel Interaction of Ecdysoneless (ECD) Protein with R2TP Complex Component RUVBL1 Is Required for the Functional Role of ECD in Cell Cycle Progression.

Science.gov (United States)

Mir, Riyaz A; Bele, Aditya; Mirza, Sameer; Srivastava, Shashank; Olou, Appolinaire A; Ammons, Shalis A; Kim, Jun Hyun; Gurumurthy, Channabasavaiah B; Qiu, Fang; Band, Hamid; Band, Vimla

2015-12-28

Ecdysoneless (ECD) is an evolutionarily conserved protein whose germ line deletion is embryonic lethal. Deletion of Ecd in cells causes cell cycle arrest, which is rescued by exogenous ECD, demonstrating a requirement of ECD for normal mammalian cell cycle progression. However, the exact mechanism by which ECD regulates cell cycle is unknown. Here, we demonstrate that ECD protein levels and subcellular localization are invariant during cell cycle progression, suggesting a potential role of posttranslational modifications or protein-protein interactions. Since phosphorylated ECD was recently shown to interact with the PIH1D1 adaptor component of the R2TP cochaperone complex, we examined the requirement of ECD phosphorylation in cell cycle progression. Notably, phosphorylation-deficient ECD mutants that failed to bind to PIH1D1 in vitro fully retained the ability to interact with the R2TP complex and yet exhibited a reduced ability to rescue Ecd-deficient cells from cell cycle arrest. Biochemical analyses demonstrated an additional phosphorylation-independent interaction of ECD with the RUVBL1 component of the R2TP complex, and this interaction is essential for ECD's cell cycle progression function. These studies demonstrate that interaction of ECD with RUVBL1, and its CK2-mediated phosphorylation, independent of its interaction with PIH1D1, are important for its cell cycle regulatory function. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Do all roads lead to Rome? The role of neuro-immune interactions before birth in the programming of offspring obesity

Directory of Open Access Journals (Sweden)

Christine eJasoni

2015-02-01

Full Text Available The functions of the nervous system can be powerfully modulated by the immune system. Although traditionally considered to be quite separate, neuro-immune interactions are increasingly recognized as critical for both normal and pathological nervous system function in the adult. However, a growing body of information supports a critical role for neuro-immune interactions before birth, particularly in the prenatal programming of later-life neurobehavioral disease risk. This review will focus on maternal obesity, as it represents an environment of pathological immune system function during pregnancy that elevates offspring neurobehavioral disease risk. We will first delineate the normal role of the immune system during pregnancy, including the role of the placenta as both a barrier and relayer of inflammatory information between the maternal and fetal environments. This will be followed by the current exciting findings of how immuno-modulatory molecules may elevate offspring risk of neurobehavioral disease by altering brain development and, consequently, later life function. Finally, by drawing parallels with pregnancy complications other than obesity, we will suggest that aberrant immune activation, irrespective of its origin, may lead to neuro-immune interactions that otherwise would not exist in the developing brain. These interactions could conceivably derail normal brain development and/or later life function, and thereby elevate risk for obesity and other neurobehavioral disorders later in the offspring’s life.

Human Sirtuin 2 Localization, Transient Interactions, and Impact on the Proteome Point to Its Role in Intracellular Trafficking.

Science.gov (United States)

Budayeva, Hanna G; Cristea, Ileana M

2016-10-01

Human sirtuin 2 (SIRT2) is an NAD + -dependent deacetylase that primarily functions in the cytoplasm, where it can regulate α-tubulin acetylation levels. SIRT2 is linked to cancer progression, neurodegeneration, and infection with bacteria or viruses. However, the current knowledge about its interactions and the means through which it exerts its functions has remained limited. Here, we aimed to gain a better understanding of its cellular functions by characterizing SIRT2 subcellular localization, the identity and relative stability of its protein interactions, and its impact on the proteome of primary human fibroblasts. To assess the relative stability of SIRT2 interactions, we used immunoaffinity purification in conjunction with both label-free and metabolic labeling quantitative mass spectrometry. In addition to the expected associations with cytoskeleton proteins, including its known substrate TUBA1A, our results reveal that SIRT2 specifically interacts with proteins functioning in membrane trafficking, secretory processes, and transcriptional regulation. By quantifying their relative stability, we found most interactions to be transient, indicating a dynamic SIRT2 environment. We discover that SIRT2 localizes to the ER-Golgi intermediate compartment (ERGIC), and that this recruitment requires an intact ER-Golgi trafficking pathway. Further expanding these findings, we used microscopy and interaction assays to establish the interaction and coregulation of SIRT2 with liprin-β1 scaffolding protein (PPFiBP1), a protein with roles in focal adhesions disassembly. As SIRT2 functions may be accomplished via interactions, enzymatic activity, and transcriptional regulation, we next assessed the impact of SIRT2 levels on the cellular proteome. SIRT2 knockdown led to changes in the levels of proteins functioning in membrane trafficking, including some of its interaction partners. Altogether, our study expands the knowledge of SIRT2 cytoplasmic functions to define a

The Role of RNA Interference (RNAi in Arbovirus-Vector Interactions

Directory of Open Access Journals (Sweden)

Carol D. Blair

2015-02-01

Full Text Available RNA interference (RNAi was shown over 18 years ago to be a mechanism by which arbovirus replication and transmission could be controlled in arthropod vectors. During the intervening period, research on RNAi has defined many of the components and mechanisms of this antiviral pathway in arthropods, yet a number of unexplored questions remain. RNAi refers to RNA-mediated regulation of gene expression. Originally, the term described silencing of endogenous genes by introduction of exogenous double-stranded (dsRNA with the same sequence as the gene to be silenced. Further research has shown that RNAi comprises three gene regulation pathways that are mediated by small RNAs: the small interfering (siRNA, micro (miRNA, and Piwi-interacting (piRNA pathways. The exogenous (exo-siRNA pathway is now recognized as a major antiviral innate immune response of arthropods. More recent studies suggest that the piRNA and miRNA pathways might also have important roles in arbovirus-vector interactions. This review will focus on current knowledge of the role of the exo-siRNA pathway as an arthropod vector antiviral response and on emerging research into vector piRNA and miRNA pathway modulation of arbovirus-vector interactions. Although it is assumed that arboviruses must evade the vector’s antiviral RNAi response in order to maintain their natural transmission cycles, the strategies by which this is accomplished are not well defined. RNAi is also an important tool for arthropod gene knock-down in functional genomics studies and in development of arbovirus-resistant mosquito populations. Possible arbovirus strategies for evasion of RNAi and applications of RNAi in functional genomics analysis and arbovirus transmission control will also be reviewed.

Hippocampal sleep features: relations to human memory function

Directory of Open Access Journals (Sweden)

Michele eFerrara

2012-04-01

Full Text Available The recent spread of intracranial EEG recordings techniques for presurgical evaluation of drug-resistant epileptic patients is providing new information on the activity of different brain structures during both wakefulness and sleep. The interest has been mainly focused on the medial temporal lobe, and in particular the hippocampal formation, whose peculiar local sleep features have been recently described, providing support to the idea that sleep is not a spatially global phenomenon. The study of the hippocampal sleep electrophysiology is particularly interesting because of its central role in the declarative memory formation. Recent data indicate that sleep contributes to memory formation. Therefore, it is relevant to understand whether specific pattern of activity taking place during sleep are related to memory consolidation processes. Fascinating similarities between different states of consciousness (wakefulness, REM sleep, NREM sleep in some electrophysiological mechanisms underlying cognitive processes have been reported. For instance, large-scale synchrony in gamma activity is important for waking memory and perception processes, and its changes during sleep may be the neurophysiological substrate of sleep-related deficits of declarative memory. Hippocampal activity seems to specifically support memory consolidation during sleep, through specific coordinated neurophysiological events (slow waves, spindles, ripples that would facilitate the integration of new information into the pre-existing cortical networks. A few studies indeed provided direct evidence that rhinal ripples as well as slow hippocampal oscillations are correlated with memory consolidation in humans. More detailed electrophysiological investigations assessing the specific relations between different types of memory consolidation and hippocampal EEG features are in order. These studies will add an important piece of knowledge to the elucidation of the ultimate sleep

Hippocampal Sleep Features: Relations to Human Memory Function

Science.gov (United States)

Ferrara, Michele; Moroni, Fabio; De Gennaro, Luigi; Nobili, Lino

2012-01-01

The recent spread of intracranial electroencephalographic (EEG) recording techniques for presurgical evaluation of drug-resistant epileptic patients is providing new information on the activity of different brain structures during both wakefulness and sleep. The interest has been mainly focused on the medial temporal lobe, and in particular the hippocampal formation, whose peculiar local sleep features have been recently described, providing support to the idea that sleep is not a spatially global phenomenon. The study of the hippocampal sleep electrophysiology is particularly interesting because of its central role in the declarative memory formation. Recent data indicate that sleep contributes to memory formation. Therefore, it is relevant to understand whether specific patterns of activity taking place during sleep are related to memory consolidation processes. Fascinating similarities between different states of consciousness (wakefulness, REM sleep, non-REM sleep) in some electrophysiological mechanisms underlying cognitive processes have been reported. For instance, large-scale synchrony in gamma activity is important for waking memory and perception processes, and its changes during sleep may be the neurophysiological substrate of sleep-related deficits of declarative memory. Hippocampal activity seems to specifically support memory consolidation during sleep, through specific coordinated neurophysiological events (slow waves, spindles, ripples) that would facilitate the integration of new information into the pre-existing cortical networks. A few studies indeed provided direct evidence that rhinal ripples as well as slow hippocampal oscillations are correlated with memory consolidation in humans. More detailed electrophysiological investigations assessing the specific relations between different types of memory consolidation and hippocampal EEG features are in order. These studies will add an important piece of knowledge to the elucidation of the ultimate

Massive Multiplayer Online Role Playing Games and Interaction: A Measurable Model of Interaction for Online Learning

Science.gov (United States)

Anderson, Bodi

2014-01-01

This current study examines the need for operational definitions of the concept of interaction in distance education studies. It is proposed that a discourse analysis of linguistic features conversation noted as being representative of interaction can be used to operationalize interaction in synchronous CMC. This study goes on compare two…

Prediction of human protein function from post-translational modifications and localization features

DEFF Research Database (Denmark)

Jensen, Lars Juhl; Gupta, Ramneek; Blom, Nikolaj

2002-01-01

a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier to predict, than protein structure. These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects......We have developed an entirely sequence-based method that identifies and integrates relevant features that can be used to assign proteins of unknown function to functional classes, and enzyme categories for enzymes. We show that strategies for the elucidation of protein function may benefit from...

Specific interaction with cardiolipin triggers functional activation of Dynamin-Related Protein 1.

Directory of Open Access Journals (Sweden)

Itsasne Bustillo-Zabalbeitia

Full Text Available Dynamin-Related Protein 1 (Drp1, a large GTPase of the dynamin superfamily, is required for mitochondrial fission in healthy and apoptotic cells. Drp1 activation is a complex process that involves translocation from the cytosol to the mitochondrial outer membrane (MOM and assembly into rings/spirals at the MOM, leading to membrane constriction/division. Similar to dynamins, Drp1 contains GTPase (G, bundle signaling element (BSE and stalk domains. However, instead of the lipid-interacting Pleckstrin Homology (PH domain present in the dynamins, Drp1 contains the so-called B insert or variable domain that has been suggested to play an important role in Drp1 regulation. Different proteins have been implicated in Drp1 recruitment to the MOM, although how MOM-localized Drp1 acquires its fully functional status remains poorly understood. We found that Drp1 can interact with pure lipid bilayers enriched in the mitochondrion-specific phospholipid cardiolipin (CL. Building on our previous study, we now explore the specificity and functional consequences of this interaction. We show that a four lysine module located within the B insert of Drp1 interacts preferentially with CL over other anionic lipids. This interaction dramatically enhances Drp1 oligomerization and assembly-stimulated GTP hydrolysis. Our results add significantly to a growing body of evidence indicating that CL is an important regulator of many essential mitochondrial functions.

Host Epithelial Interactions with Helicobacter Pylori: A Role for Disrupted Gastric Barrier Function in the Clinical Outcome of Infection?

Directory of Open Access Journals (Sweden)

Andre G Buret

2005-01-01

Full Text Available Infection of the human stomach with Helicobacter pylori may develop into gastritis, ulceration, adenocarcinoma and mucosal lymphomas. The pathogenic mechanisms that determine the clinical outcome from this microbial-epithelial interaction remain poorly understood. An increasing number of reports suggests that disruptions of epithelial barrier function may contribute to pathology and postinfectious complications in a variety of gastrointestinal infections. The aim of this review is to critically discuss the implications of H pylori persistence on gastric disease, with emphasis on the role of myosin light chain kinase, claudins and matrix metalloproteinases in gastric permeability defects, and their contribution to the development of cancer. These mechanisms and the associated signalling events may represent novel therapeutic targets to control disease processes induced by H pylori, a microbial pathogen that colonizes the stomach of over 50% of the human population.

Functional Modeling of Neural-Glia Interaction

DEFF Research Database (Denmark)

Postnov, D.E.; Brazhe, N.A.; Sosnovtseva, Olga

2012-01-01

Functional modeling is an approach that focuses on the representation of the qualitative dynamics of the individual components (e.g. cells) of a system and on the structure of the interaction network.......Functional modeling is an approach that focuses on the representation of the qualitative dynamics of the individual components (e.g. cells) of a system and on the structure of the interaction network....

Role of early visual cortex in trans-saccadic memory of object features.

Science.gov (United States)

Malik, Pankhuri; Dessing, Joost C; Crawford, J Douglas

2015-08-01

Early visual cortex (EVC) participates in visual feature memory and the updating of remembered locations across saccades, but its role in the trans-saccadic integration of object features is unknown. We hypothesized that if EVC is involved in updating object features relative to gaze, feature memory should be disrupted when saccades remap an object representation into a simultaneously perturbed EVC site. To test this, we applied transcranial magnetic stimulation (TMS) over functional magnetic resonance imaging-localized EVC clusters corresponding to the bottom left/right visual quadrants (VQs). During experiments, these VQs were probed psychophysically by briefly presenting a central object (Gabor patch) while subjects fixated gaze to the right or left (and above). After a short memory interval, participants were required to detect the relative change in orientation of a re-presented test object at the same spatial location. Participants either sustained fixation during the memory interval (fixation task) or made a horizontal saccade that either maintained or reversed the VQ of the object (saccade task). Three TMS pulses (coinciding with the pre-, peri-, and postsaccade intervals) were applied to the left or right EVC. This had no effect when (a) fixation was maintained, (b) saccades kept the object in the same VQ, or (c) the EVC quadrant corresponding to the first object was stimulated. However, as predicted, TMS reduced performance when saccades (especially larger saccades) crossed the remembered object location and brought it into the VQ corresponding to the TMS site. This suppression effect was statistically significant for leftward saccades and followed a weaker trend for rightward saccades. These causal results are consistent with the idea that EVC is involved in the gaze-centered updating of object features for trans-saccadic memory and perception.

Circular RNAs: Biogenesis, Function and Role in Human Diseases

Directory of Open Access Journals (Sweden)

John Greene

2017-06-01

Full Text Available Circular RNAs (circRNAs are currently classed as non-coding RNA (ncRNA that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3′ and 5′ ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization. Interestingly, they have been found to be abundant, evolutionally conserved and relatively stable in the cytoplasm. These features confer numerous potential functions to circRNAs, such as acting as miRNA sponges, or binding to RNA-associated proteins to form RNA-protein complexes that regulate gene transcription. It has been proposed that circRNA regulate gene expression at the transcriptional or post-transcriptional level by interacting with miRNAs and that circRNAs may have a role in regulating miRNA function in cancer initiation and progression. circRNAs appear to be more often downregulated in tumor tissue compared to normal tissue and this may be due to (i errors in the back-splice machinery in malignant tissues, (ii degradation of circRNAs by deregulated miRNAs in tumor tissue, or (iii increasing cell proliferation leading to a reduction of circRNAs. circRNAs have been identified in exosomes and more recently, chromosomal translocations in cancer have been shown to generate aberrant fusion-circRNAs associated with resistance to drug treatments. In addition, though originally thought to be non-coding, there is now increasing evidence to suggest that select circRNAs can be translated into functional proteins. Although much remains to be elucidated about circRNA biology and mechanisms of gene regulation, these ncRNAs are quickly emerging as

Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1.

Science.gov (United States)

Yu, Hyun Young; Ziegelhoffer, Thomas; Osipiuk, Jerzy; Ciesielski, Szymon J; Baranowski, Maciej; Zhou, Min; Joachimiak, Andrzej; Craig, Elizabeth A

2015-04-10

Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at their C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways, Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activity with Hsp70∆EEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interactions between the J-domain and glycine-rich region control co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. However, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD binding adaptor proteins. These interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Interactive prostate segmentation using atlas-guided semi-supervised learning and adaptive feature selection.

Science.gov (United States)

Park, Sang Hyun; Gao, Yaozong; Shi, Yinghuan; Shen, Dinggang

2014-11-01

Accurate prostate segmentation is necessary for maximizing the effectiveness of radiation therapy of prostate cancer. However, manual segmentation from 3D CT images is very time-consuming and often causes large intra- and interobserver variations across clinicians. Many segmentation methods have been proposed to automate this labor-intensive process, but tedious manual editing is still required due to the limited performance. In this paper, the authors propose a new interactive segmentation method that can (1) flexibly generate the editing result with a few scribbles or dots provided by a clinician, (2) fast deliver intermediate results to the clinician, and (3) sequentially correct the segmentations from any type of automatic or interactive segmentation methods. The authors formulate the editing problem as a semisupervised learning problem which can utilize a priori knowledge of training data and also the valuable information from user interactions. Specifically, from a region of interest near the given user interactions, the appropriate training labels, which are well matched with the user interactions, can be locally searched from a training set. With voting from the selected training labels, both confident prostate and background voxels, as well as unconfident voxels can be estimated. To reflect informative relationship between voxels, location-adaptive features are selected from the confident voxels by using regression forest and Fisher separation criterion. Then, the manifold configuration computed in the derived feature space is enforced into the semisupervised learning algorithm. The labels of unconfident voxels are then predicted by regularizing semisupervised learning algorithm. The proposed interactive segmentation method was applied to correct automatic segmentation results of 30 challenging CT images. The correction was conducted three times with different user interactions performed at different time periods, in order to evaluate both the efficiency

Interaction features for prediction of perceptual segmentation

DEFF Research Database (Denmark)

Hartmann, Martin; Lartillot, Olivier; Toiviainen, Petri

2017-01-01

As music unfolds in time, structure is recognised and understood by listeners, regardless of their level of musical expertise. A number of studies have found spectral and tonal changes to quite successfully model boundaries between structural sections. However, the effects of musical expertise...... and experimental task on computational modelling of structure are not yet well understood. These issues need to be addressed to better understand how listeners perceive the structure of music and to improve automatic segmentation algorithms. In this study, computational prediction of segmentation by listeners...... was investigated for six musical stimuli via a real-time task and an annotation (non real-time) task. The proposed approach involved computation of novelty curve interaction features and a prediction model of perceptual segmentation boundary density. We found that, compared to non-musicians’, musicians...

Significance of Joint Features Derived from the Modified Group Delay Function in Speech Processing

Directory of Open Access Journals (Sweden)

Murthy Hema A

2007-01-01

Full Text Available This paper investigates the significance of combining cepstral features derived from the modified group delay function and from the short-time spectral magnitude like the MFCC. The conventional group delay function fails to capture the resonant structure and the dynamic range of the speech spectrum primarily due to pitch periodicity effects. The group delay function is modified to suppress these spikes and to restore the dynamic range of the speech spectrum. Cepstral features are derived from the modified group delay function, which are called the modified group delay feature (MODGDF. The complementarity and robustness of the MODGDF when compared to the MFCC are also analyzed using spectral reconstruction techniques. Combination of several spectral magnitude-based features and the MODGDF using feature fusion and likelihood combination is described. These features are then used for three speech processing tasks, namely, syllable, speaker, and language recognition. Results indicate that combining MODGDF with MFCC at the feature level gives significant improvements for speech recognition tasks in noise. Combining the MODGDF and the spectral magnitude-based features gives a significant increase in recognition performance of 11% at best, while combining any two features derived from the spectral magnitude does not give any significant improvement.

Spectrofluorometric and thermal gravimetric study on binding interaction of thiabendazole with hemoglobin on epoxy-functionalized magnetic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Maltas, Esra, E-mail: maltasesra@gmail.com; Ozmen, Mustafa

2015-09-01

The interaction of thiabendazole (Tbz) with hemoglobin (Hb) on epoxy-functionalized iron oxide nanoparticles was presented in this study. The binding capacity of Tbz was determined by measuring at an excitation wavelength of 299 nm using fluorescence spectroscopy. The thermodynamic parameters of the Hb–Tbz interaction were calculated from Stern–Volmer and van't Hoff equations. The values of enthalpy change, ∆H, and entropy change, ∆S, were found to be 0.20 kJ mol{sup −1} and 0.70 J mol{sup −1} K{sup −1}, respectively, which indicates that the hydrophilic interaction plays a main role in the binding process. The interaction ability was confirmed by Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). Also, the thermal behavior of the Hb–Tbz interaction on functionalized iron oxide nanoparticles was studied by using the thermogravimetric analysis (TGA) technique in the temperature range of 25–950 °C, and then the kinetic parameters for the thermal decomposition were determined using the Horowitz–Metzger method. - Highlights: • Hb was immobilized by covalent attachment on GPTS–SPIONs. • Interaction of Tbz with Hb–GPTS–SPIONs was studied. • Thermodynamic parameters for interaction were calculated. • Hydrophilic interaction plays a main role in the binding process.

Interaction function of coupled bursting neurons

International Nuclear Information System (INIS)

Shi Xia; Zhang Jiadong

2016-01-01

The interaction functions of electrically coupled Hindmarsh–Rose (HR) neurons for different firing patterns are investigated in this paper. By applying the phase reduction technique, the phase response curve (PRC) of the spiking neuron and burst phase response curve (BPRC) of the bursting neuron are derived. Then the interaction function of two coupled neurons can be calculated numerically according to the PRC (or BPRC) and the voltage time course of the neurons. Results show that the BPRC is more and more complicated with the increase of the spike number within a burst, and the curve of the interaction function oscillates more and more frequently with it. However, two certain things are unchanged: ϕ = 0, which corresponds to the in-phase synchronization state, is always the stable equilibrium, while the anti-phase synchronization state with ϕ = 0.5 is an unstable equilibrium. (paper)

Coupling functions: Universal insights into dynamical interaction mechanisms

Science.gov (United States)

Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E.; Stefanovska, Aneta

2017-10-01

The dynamical systems found in nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. A coherent and comprehensive review is presented encompassing the rapid progress made recently in the analysis, understanding, and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics, and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

Possible role of neuroimmunoendocrine interactions in the development of postirradiation pathology

International Nuclear Information System (INIS)

Malyzhev, V.A.; Gubrij, I.B.; Sergeeva, T.A.

1992-01-01

On the basis of the literature a postulate was proposed that the immune system contributed to regulating the intensity and direction of ednocrine and nervous system functions in normal conditions and after the effect of ionizing radiation. The role of neuroimmunoendocrine interactions and their impairment in the realization of stochastic and nonstochastic sequeles of irradiation at various levels of radiation affecting the organism under normal conditions and in a combination with other unfavourable factors was studied

Benefits and Pitfalls of Multimedia and Interactive Features in Technology-Enhanced Storybooks: A Meta-Analysis.

Science.gov (United States)

Takacs, Zsofia K; Swart, Elise K; Bus, Adriana G

2015-12-01

A meta-analysis was conducted on the effects of technology-enhanced stories for young children's literacy development when compared to listening to stories in more traditional settings like storybook reading. A small but significant additional benefit of technology was found for story comprehension (g+ = 0.17) and expressive vocabulary (g+ = 0.20), based on data from 2,147 children in 43 studies. When investigating the different characteristics of technology-enhanced stories, multimedia features like animated pictures, music, and sound effects were found beneficial. In contrast, interactive elements like hotspots, games, and dictionaries were found to be distracting. Especially for children disadvantaged because of less stimulating family environments, multimedia features were helpful and interactive features were detrimental. Findings are discussed from the perspective of cognitive processing theories.

An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction

Directory of Open Access Journals (Sweden)

Thahir Mohamed

2012-11-01

Full Text Available Abstract Background Machine learning approaches for classification learn the pattern of the feature space of different classes, or learn a boundary that separates the feature space into different classes. The features of the data instances are usually available, and it is only the class-labels of the instances that are unavailable. For example, to classify text documents into different topic categories, the words in the documents are features and they are readily available, whereas the topic is what is predicted. However, in some domains obtaining features may be resource-intensive because of which not all features may be available. An example is that of protein-protein interaction prediction, where not only are the labels ('interacting' or 'non-interacting' unavailable, but so are some of the features. It may be possible to obtain at least some of the missing features by carrying out a few experiments as permitted by the available resources. If only a few experiments can be carried out to acquire missing features, which proteins should be studied and which features of those proteins should be determined? From the perspective of machine learning for PPI prediction, it would be desirable that those features be acquired which when used in training the classifier, the accuracy of the classifier is improved the most. That is, the utility of the feature-acquisition is measured in terms of how much acquired features contribute to improving the accuracy of the classifier. Active feature acquisition (AFA is a strategy to preselect such instance-feature combinations (i.e. protein and experiment combinations for maximum utility. The goal of AFA is the creation of optimal training set that would result in the best classifier, and not in determining the best classification model itself. Results We present a heuristic method for active feature acquisition to calculate the utility of acquiring a missing feature. This heuristic takes into account the change in

Multimodal Discrimination of Schizophrenia Using Hybrid Weighted Feature Concatenation of Brain Functional Connectivity and Anatomical Features with an Extreme Learning Machine

Directory of Open Access Journals (Sweden)

Muhammad Naveed Iqbal Qureshi

2017-09-01

Full Text Available Multimodal features of structural and functional magnetic resonance imaging (MRI of the human brain can assist in the diagnosis of schizophrenia. We performed a classification study on age, sex, and handedness-matched subjects. The dataset we used is publicly available from the Center for Biomedical Research Excellence (COBRE and it consists of two groups: patients with schizophrenia and healthy controls. We performed an independent component analysis and calculated global averaged functional connectivity-based features from the resting-state functional MRI data for all the cortical and subcortical anatomical parcellation. Cortical thickness along with standard deviation, surface area, volume, curvature, white matter volume, and intensity measures from the cortical parcellation, as well as volume and intensity from sub-cortical parcellation and overall volume of cortex features were extracted from the structural MRI data. A novel hybrid weighted feature concatenation method was used to acquire maximal 99.29% (P < 0.0001 accuracy which preserves high discriminatory power through the weight of the individual feature type. The classification was performed by an extreme learning machine, and its efficiency was compared to linear and non-linear (radial basis function support vector machines, linear discriminant analysis, and random forest bagged tree ensemble algorithms. This article reports the predictive accuracy of both unimodal and multimodal features after 10-by-10-fold nested cross-validation. A permutation test followed the classification experiment to assess the statistical significance of the classification results. It was concluded that, from a clinical perspective, this feature concatenation approach may assist the clinicians in schizophrenia diagnosis.

The role of species functional traits for distribuitional patterns in lowland stream vegetation

DEFF Research Database (Denmark)

Cavalli, Giulia; Baattrup-Pedersen, Annette; Riis, Tenna

Freshwater ecosystems provide goods and service to human society and invasion is a major threat to them. Plant invasion affect community dynamics, threatens biodiversity and promote biological homogenization. In this study we explore functional traits in three groups of species e.g. invasive...... species, disturbance-tolerant species and rare species in lowland streams. In order to investigate the role of functional traits for species distributional patterns we investigate relationships between a range of species features and species abundance in app. 1,200 stream sites in Denmark covering...

Self-interaction corrections in density functional theory

International Nuclear Information System (INIS)

Tsuneda, Takao; Hirao, Kimihiko

2014-01-01

Self-interaction corrections for Kohn-Sham density functional theory are reviewed for their physical meanings, formulations, and applications. The self-interaction corrections get rid of the self-interaction error, which is the sum of the Coulomb and exchange self-interactions that remains because of the use of an approximate exchange functional. The most frequently used self-interaction correction is the Perdew-Zunger correction. However, this correction leads to instabilities in the electronic state calculations of molecules. To avoid these instabilities, several self-interaction corrections have been developed on the basis of the characteristic behaviors of self-interacting electrons, which have no two-electron interactions. These include the von Weizsäcker kinetic energy and long-range (far-from-nucleus) asymptotic correction. Applications of self-interaction corrections have shown that the self-interaction error has a serious effect on the states of core electrons, but it has a smaller than expected effect on valence electrons. This finding is supported by the fact that the distribution of self-interacting electrons indicates that they are near atomic nuclei rather than in chemical bonds

The role of experiential avoidance, psychopathology, and borderline personality features in experiencing positive emotions: a path analysis.

Science.gov (United States)

Jacob, Gitta A; Ower, Nicole; Buchholz, Angela

2013-03-01

Experiential avoidance (EA) is an important factor in maintaining different forms of psychopathology including borderline personality pathology (BPD). So far little is known about the functions of EA, BPD features and general psychopathology for positive emotions. In this study we investigated three different anticipated pathways of their influence on positive emotions. A total of 334 subjects varying in general psychopathology &/or BPD features completed an online survey including self-ratings of BPD features, psychopathology, negative and positive emotions, and EA. Measures of positive emotions included both a general self-rating (PANAS) and emotional changes induced by two positive movie clips. Data were analyzed by means of path analysis. In comparing the three path models, one model was found clearly superior: In this model, EA acts as a mediator of the influence of psychopathology, BPD features, and negative emotions in the prediction of both measures of positive emotions. EA plays a central role in maintaining lack of positive emotions. Therapeutic implications and study limitations are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

The nature and role of the gold-krypton interactions in small neutral gold clusters.

Science.gov (United States)

Mancera, Luis A; Benoit, David M

2015-03-26

We investigate the nature and role of krypton embedding in small neutral gold clusters. For some of these clusters, we observe a particular site-dependent character of the Kr binding that does not completely follow the criterion of binding at low-coordinated sites, widely accepted for interaction of a noble gas with closed-shell metal systems such as metal surfaces. We aim at understanding the effect of low dimensionality and open-shell electronic structure of the odd-numbered clusters on the noble gas-metal cluster interaction. First, we investigate the role of attractive and repulsive forces, and the frontier molecular orbitals. Second, we investigate the Au-Kr interaction in terms of reactivity and bonding character. We use a reactivity index derived from Fukui formalism, and criteria provided by the electron localization function (ELF), in order to classify the type of bonding. We carry out this study on the minimum energy structures of neutral gold clusters, as obtained using pseudo potential plane-wave density functional theory (DFT). A model is proposed that includes the effect of attractive electrostatic, van der Waals and repulsive forces, together with effects originating from orbital overlap. This satisfactorily explains minimum configurations of the noble gas-gold cluster systems, the site preference of the noble gas atoms, and changes in electronic properties.

Stochastic nanoroughness modulates neuron-astrocyte interactions and function via mechanosensing cation channels.

Science.gov (United States)

Blumenthal, Nils R; Hermanson, Ola; Heimrich, Bernd; Shastri, V Prasad

2014-11-11

Extracellular soluble signals are known to play a critical role in maintaining neuronal function and homeostasis in the CNS. However, the CNS is also composed of extracellular matrix macromolecules and glia support cells, and the contribution of the physical attributes of these components in maintenance and regulation of neuronal function is not well understood. Because these components possess well-defined topography, we theorize a role for topography in neuronal development and we demonstrate that survival and function of hippocampal neurons and differentiation of telencephalic neural stem cells is modulated by nanoroughness. At roughnesses corresponding to that of healthy astrocytes, hippocampal neurons dissociated and survived independent from astrocytes and showed superior functional traits (increased polarity and calcium flux). Furthermore, telencephalic neural stem cells differentiated into neurons even under exogenous signals that favor astrocytic differentiation. The decoupling of neurons from astrocytes seemed to be triggered by changes to astrocyte apical-surface topography in response to nanoroughness. Blocking signaling through mechanosensing cation channels using GsMTx4 negated the ability of neurons to sense the nanoroughness and promoted decoupling of neurons from astrocytes, thus providing direct evidence for the role of nanotopography in neuron-astrocyte interactions. We extrapolate the role of topography to neurodegenerative conditions and show that regions of amyloid plaque buildup in brain tissue of Alzheimer's patients are accompanied by detrimental changes in tissue roughness. These findings suggest a role for astrocyte and ECM-induced topographical changes in neuronal pathologies and provide new insights for developing therapeutic targets and engineering of neural biomaterials.

Interactive prostate segmentation using atlas-guided semi-supervised learning and adaptive feature selection

Energy Technology Data Exchange (ETDEWEB)

Park, Sang Hyun [Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 (United States); Gao, Yaozong, E-mail: yzgao@cs.unc.edu [Department of Computer Science, Department of Radiology, and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 (United States); Shi, Yinghuan, E-mail: syh@nju.edu.cn [State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210023 (China); Shen, Dinggang, E-mail: dgshen@med.unc.edu [Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and Department of Brain and Cognitive Engineering, Korea University, Seoul 136-713 (Korea, Republic of)

2014-11-01

Purpose: Accurate prostate segmentation is necessary for maximizing the effectiveness of radiation therapy of prostate cancer. However, manual segmentation from 3D CT images is very time-consuming and often causes large intra- and interobserver variations across clinicians. Many segmentation methods have been proposed to automate this labor-intensive process, but tedious manual editing is still required due to the limited performance. In this paper, the authors propose a new interactive segmentation method that can (1) flexibly generate the editing result with a few scribbles or dots provided by a clinician, (2) fast deliver intermediate results to the clinician, and (3) sequentially correct the segmentations from any type of automatic or interactive segmentation methods. Methods: The authors formulate the editing problem as a semisupervised learning problem which can utilize a priori knowledge of training data and also the valuable information from user interactions. Specifically, from a region of interest near the given user interactions, the appropriate training labels, which are well matched with the user interactions, can be locally searched from a training set. With voting from the selected training labels, both confident prostate and background voxels, as well as unconfident voxels can be estimated. To reflect informative relationship between voxels, location-adaptive features are selected from the confident voxels by using regression forest and Fisher separation criterion. Then, the manifold configuration computed in the derived feature space is enforced into the semisupervised learning algorithm. The labels of unconfident voxels are then predicted by regularizing semisupervised learning algorithm. Results: The proposed interactive segmentation method was applied to correct automatic segmentation results of 30 challenging CT images. The correction was conducted three times with different user interactions performed at different time periods, in order to

Interactive prostate segmentation using atlas-guided semi-supervised learning and adaptive feature selection

International Nuclear Information System (INIS)

Park, Sang Hyun; Gao, Yaozong; Shi, Yinghuan; Shen, Dinggang

2014-01-01

Purpose: Accurate prostate segmentation is necessary for maximizing the effectiveness of radiation therapy of prostate cancer. However, manual segmentation from 3D CT images is very time-consuming and often causes large intra- and interobserver variations across clinicians. Many segmentation methods have been proposed to automate this labor-intensive process, but tedious manual editing is still required due to the limited performance. In this paper, the authors propose a new interactive segmentation method that can (1) flexibly generate the editing result with a few scribbles or dots provided by a clinician, (2) fast deliver intermediate results to the clinician, and (3) sequentially correct the segmentations from any type of automatic or interactive segmentation methods. Methods: The authors formulate the editing problem as a semisupervised learning problem which can utilize a priori knowledge of training data and also the valuable information from user interactions. Specifically, from a region of interest near the given user interactions, the appropriate training labels, which are well matched with the user interactions, can be locally searched from a training set. With voting from the selected training labels, both confident prostate and background voxels, as well as unconfident voxels can be estimated. To reflect informative relationship between voxels, location-adaptive features are selected from the confident voxels by using regression forest and Fisher separation criterion. Then, the manifold configuration computed in the derived feature space is enforced into the semisupervised learning algorithm. The labels of unconfident voxels are then predicted by regularizing semisupervised learning algorithm. Results: The proposed interactive segmentation method was applied to correct automatic segmentation results of 30 challenging CT images. The correction was conducted three times with different user interactions performed at different time periods, in order to

A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network

Directory of Open Access Journals (Sweden)

Han Kyungsook

2010-06-01

Full Text Available Abstract Background Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship between double concurrent perturbation and various higher level phenotypic changes, e.g. those in cells, tissues or organs. Modifier screens, such as synthetic genetic arrays (SGA can help us to understand the phenotype caused by combined gene mutations. Unfortunately, exhaustive tests on all possible combined mutations in any genome are vulnerable to combinatorial explosion and are infeasible either technically or financially. Therefore, an accurate computational approach to predict genetic interaction is highly desirable, and such methods have the potential of alleviating the bottleneck on experiment design. Results In this work, we introduce a computational systems biology approach for the accurate prediction of pairwise synthetic genetic interactions (SGI. First, a high-coverage and high-precision functional gene network (FGN is constructed by integrating protein-protein interaction (PPI, protein complex and gene expression data; then, a graph-based semi-supervised learning (SSL classifier is utilized to identify SGI, where the topological properties of protein pairs in weighted FGN is used as input features of the classifier. We compare the proposed SSL method with the state-of-the-art supervised classifier, the support vector machines (SVM, on a benchmark dataset in S. cerevisiae to validate our method's ability to distinguish synthetic genetic interactions from non-interaction gene pairs. Experimental results show that the proposed method can accurately predict genetic interactions in S. cerevisiae (with a sensitivity of 92% and specificity of 91%. Noticeably, the SSL method is more efficient than SVM, especially for

Design Features for Linguistically-Mediated Meaning Construction: The Relative Roles of the Linguistic and Conceptual Systems in Subserving the Ideational Function of Language.

Science.gov (United States)

Evans, Vyvyan

2016-01-01

Recent research in language and cognitive science proposes that the linguistic system evolved to provide an "executive" control system on the evolutionarily more ancient conceptual system (e.g., Barsalou et al., 2008; Evans, 2009, 2015a,b; Bergen, 2012). In short, the claim is that embodied representations in the linguistic system interface with non-linguistic representations in the conceptual system, facilitating rich meanings, or simulations, enabling linguistically mediated communication. In this paper I build on these proposals by examining the nature of what I identify as design features for this control system. In particular, I address how the ideational function of language-our ability to deploy linguistic symbols to convey meanings of great complexity-is facilitated. The central proposal of this paper is as follows. The linguistic system of any given language user, of any given linguistic system-spoken or signed-facilitates access to knowledge representation-concepts-in the conceptual system, which subserves this ideational function. In the most general terms, the human meaning-making capacity is underpinned by two distinct, although tightly coupled representational systems: the conceptual system and the linguistic system. Each system contributes to meaning construction in qualitatively distinct ways. This leads to the first design feature: given that the two systems are representational-they are populated by semantic representations-the nature and function of the representations are qualitatively different. This proposed design feature I term the bifurcation in semantic representation. After all, it stands to reason that if a linguistic system has a different function, vis-à-vis the conceptual system, which is of far greater evolutionary antiquity, then the semantic representations will be complementary, and as such, qualitatively different, reflecting the functional distinctions of the two systems, in collectively giving rise to meaning. I consider the

Family roles as family functioning regulators

OpenAIRE

STEPANYAN ARMINE

2015-01-01

The author examines the problems of formation and functioning of family roles. Having social roots, family roles appear on individual level by performing the social function of the formation of family as a social institute.

The Role of Attention in the Maintenance of Feature Bindings in Visual Short-term Memory

Science.gov (United States)

Johnson, Jeffrey S.; Hollingworth, Andrew; Luck, Steven J.

2008-01-01

This study examined the role of attention in maintaining feature bindings in visual short-term memory. In a change-detection paradigm, participants attempted to detect changes in the colors and orientations of multiple objects; the changes consisted of new feature values in a feature-memory condition and changes in how existing feature values were…

The three isoforms of the light-harvesting complex II Spectroscopic features, trimer formation, and functional roles

CERN Document Server

Standfuss, Jorg

2004-01-01

The major light-harvesting complex (LHC-II) of higher plants plays a crucial role in capturing light energy for photosynthesis and in regulating the flow of energy within the photosynthetic apparatus. Native LHC-II isolated from plant tissue consists of three isoforms, Lhcb1, Lhcb2, and Lhcb3, which form homo- and heterotrimers. All three isoforms are highly conserved among different species, suggesting distinct functional roles. We produced the three LHC-II isoforms by heterologous expression of the polypeptide in Escherichia coli and in vitro refolding with purified pigments. Although Lhcb1 and Lhcb2 are very similar in polypeptide sequence and pigment content, Lhcb3 is clearly different because it lacks an N-terminal phosphorylation site and has a higher chlorophyll a/b ratio, suggesting the absence of one chlorophyll b. Low temperature absorption and fluorescence emission spectra of the pure isoforms revealed small but significant differences in pigment organization. The oligomeric state of the pure isofo...

Diverse role of CBL-interacting protein kinases in plant

Indian Academy of Sciences (India)

admin

Diverse role of CBL-interacting protein kinases in plant. Most of the extracellular and ... to their role in stress signalling. Their role in transport of plant hormone auxin and mechanism of action in stress response shed new light on diverse role of.

Role of the MAGUK protein family in synapse formation and function.

Science.gov (United States)

Oliva, Carlos; Escobedo, Pía; Astorga, César; Molina, Claudia; Sierralta, Jimena

2012-01-01

Synaptic function is crucially dependent on the spatial organization of the presynaptic and postsynaptic apparatuses and the juxtaposition of both membrane compartments. This precise arrangement is achieved by a protein network at the submembrane region of each cell that is built around scaffold proteins. The membrane-associated guanylate kinase (MAGUK) family of proteins is a widely expressed and well-conserved group of proteins that plays an essential role in the formation and regulation of this scaffolding. Here, we review general features of this protein family, focusing on the discs large and calcium/calmodulin-dependent serine protein kinase subfamilies of MAGUKs in the formation, function, and plasticity of synapses. Copyright © 2011 Wiley Periodicals, Inc.

Functional, interactive and critical health literacy: Varying relationships with control over care and number of GP visits.

Science.gov (United States)

van der Heide, Iris; Heijmans, Monique; Schuit, A Jantine; Uiters, Ellen; Rademakers, Jany

2015-08-01

The aim of this study is to examine the extent to which functional, interactive and critical health literacy are associated with patients' perceived control over care and frequency of GP visits. Data from the Dutch 'National Panel of People with Chronic Illness or Disability' was used (N=2508). Health literacy was assessed by the Functional, Communicative and Critical Health Literacy measure. Perceived control over care was indicated by perceived ability to organize care, interact with providers and to perform self-care. By multivariate linear and logistic regression analyses, associations between health literacy and perceived control over care and subsequently frequency of GP visits were studied. Mainly interactive health literacy was associated with patients' perceived ability to organize care, interact with healthcare providers and perform self-care, whereas only functional health literacy was associated with number of GP visits. The results imply that some patients' may be less able to exert control over their care because of lower health literacy. Functional, interactive and critical health literacy vary in their relevance for patients' ability to exert control. Initiatives for strengthening patients' role in healthcare may be improved by paying attention to patients' health literacy, specifically functional and interactive health literacy. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Biomaterials that promote cell-cell interactions enhance the paracrine function of MSCs.

Science.gov (United States)

Qazi, Taimoor H; Mooney, David J; Duda, Georg N; Geissler, Sven

2017-09-01

Mesenchymal stromal cells (MSCs) secrete paracrine factors that play crucial roles during tissue regeneration. Whether this paracrine function is influenced by the properties of biomaterials in general, and those used for cell delivery in particular, largely remains unexplored. Here, we investigated if three-dimensional culture in distinct microenvironments - nanoporous hydrogels (mean pore size ∼5 nm) and macroporous scaffolds (mean pore size ∼120 μm) - affects the secretion pattern of MSCs, and consequently leads to differential paracrine effects on target progenitor cells such as myoblasts. We report that compared to MSCs encapsulated in hydrogels, scaffold seeded MSCs show an enhanced secretion profile and exert beneficial paracrine effects on various myoblast functions including migration and proliferation. Additionally, we show that the heightened paracrine effects of scaffold seeded cells can in part be attributed to N-cadherin mediated cell-cell interactions during culture. In hydrogels, this physical interaction between cells is prevented by the encapsulating matrix. Functionally blocking N-cadherin negatively affected the secretion profile and paracrine effects of MSCs on myoblasts, with stronger effects observed for scaffold seeded compared to hydrogel encapsulated cells. Together, these findings demonstrate that the therapeutic potency of MSCs can be enhanced by biomaterials that promote cell-cell interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Brain Gut Microbiome Interactions and Functional Bowel Disorders

Science.gov (United States)

Mayer, Emeran A.; Savidge, Tor; Shulman, Robert J.

2014-01-01

Alterations in the bidirectional interactions between the gut and the nervous system play an important role in IBS pathophysiology and symptom generation. A body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. Characterizations of alterations of gut microbiota in unselected IBS patients, and assessment of changes in subjective symptoms associated with manipulations of the gut microbiota with prebiotics, probiotics and antibiotics support a small, but poorly defined role of dybiosis in overall IBS symptoms. It remains to be determined if the observed abnormalities are a consequence of altered top down signaling from the brain to the gut and microbiota, if they are secondary to a primary perturbation of the microbiota, and if they play a role in the development of altered brain gut interactions early in life. Different mechanisms may play role in subsets of patients. Characterization of gut microbiome alterations in large cohorts of well phenotyped patients as well as evidence correlating gut metabolites with specific abnormalities in the gut brain axis are required to answer these questions. PMID:24583088

Effect of carbon nanotube functionalization on mechanical and thermal properties of cross-linked epoxy-carbon nanotube nanocomposites: role of strengthening the interfacial interactions.

Science.gov (United States)

Khare, Ketan S; Khabaz, Fardin; Khare, Rajesh

2014-05-14

We have used amido-amine functionalized carbon nanotubes (CNTs) that form covalent bonds with cross-linked epoxy matrices to elucidate the role of the matrix-filler interphase in the enhancement of mechanical and thermal properties in these nanocomposites. For the base case of nanocomposites of cross-linked epoxy and pristine single-walled CNTs, our previous work (Khare, K. S.; Khare, R. J. Phys. Chem. B 2013, 117, 7444-7454) has shown that weak matrix-filler interactions cause the interphase region in the nanocomposite to be more compressible. Furthermore, because of the weak matrix-filler interactions, the nanocomposite containing dispersed pristine CNTs has a glass transition temperature (Tg) that is ∼66 K lower than the neat polymer. In this work, we demonstrate that in spite of the presence of stiff CNTs in the nanocomposite, the Young's modulus of the nanocomposite containing dispersed pristine CNTs is virtually unchanged compared to the neat cross-linked epoxy. This observation suggests that the compressibility of the matrix-filler interphase interferes with the ability of the CNTs to reinforce the matrix. Furthermore, when the compressibility of the interphase is reduced by the use of amido-amine functionalized CNTs, the mechanical reinforcement due to the filler is more effective, resulting in a ∼50% increase in the Young's modulus compared to the neat cross-linked epoxy. Correspondingly, the functionalization of the CNTs also led to a recovery in the Tg making it effectively the same as the neat polymer and also resulted in a ∼12% increase in the thermal conductivity of the nanocomposite containing functionalized CNTs compared to that containing pristine CNTs. These results demonstrate that the functionalization of the CNTs facilitates the transfer of both mechanical load and thermal energy across the matrix-filler interface.

The role of lipids in host microbe interactions.

Science.gov (United States)

Lang, Roland; Mattner, Jochen

2017-06-01

Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

Calculation of deuteron wave functions with relativistic interactions

International Nuclear Information System (INIS)

Buck, W.W. III.

1976-01-01

Deuteron wave functions with a repulsive core are obtained numerically from a fully relativistic wave equation introduced by Gross. The numerical technique enables analytic solutions for classes of interactions composed of the relativistic exchanges of a single pion and a single phenomenological meson, sigma. The pion is chosen to interact as a mixture of pseudoscalar and pseudovector. The amount of mixture is determined by a free mixing parameter, lambda, ranging between 1 (pure pseudoscalar) and (pure pseudovector). Each value of lambda corresponds, then, to a different interaction. Solutions are found for lambda = 1, .9, .8, .6, and 0. The wave functions for each interaction come in a group of four. Of the four wave functions, two are the usual S and D state wave functions, while the remaining two, arising out of the relativistic prescription, are identified as 3 P 1 and 1 P 1 wave functions (P state wave functions). For the interactions solved for, the D state probabilities ranged between 5.1 percent and 6.3 percent, while the total P state probabilities ranged between 0.7 percent and 2.7 percent. The method of obtaining solutions was to adjust the sigma meson parameters to give the correct binding energy and a good quadrupole moment. All wave functions obtained are applied to relativistic N-d scattering in the backward direction where the effect of the P states is quite measurable

Direct interaction with the public: making it a "serious game" with role playing

Science.gov (United States)

Vercelli, Samuela; Lombardi, Salvatore; Jones, David; Pearce, Jonathan; Persoglia, Sergio; De Vittor, Cinzia; Gemeni, Vassiliki; Svendsen Skriung, Camilla; Bigi, Sabina; Franzese, Carmela; Riley, Nick; McConnell, Brian; Volpi, Valentina; Donda, Federica

2014-05-01

Researchers have an important role in the societal process of understanding and evaluating new technologies, but their role is often undermined by the lack of appropriate contexts where a constructive dialogue can take place, thus leading to awareness of issues and correct perception of scientific data. In the case of geoscience the problem can be even harsher, due to the often limited education on the subject, complexity of the imaginative relationship with the underground, lack of social shared representations of key geological features. This contribution reports about an interactive session organised during the 2012 ESOF - European Science Open Forum http://esof2012.org/ for the FP7 project RISCS - 'Research into Impacts and Safety in CO2 Storage' http://www.riscs-co2.eu/ and in collaboration with the FP7 project CGS Europe http://www.cgseurope.net/ . The session saw the participation of about 100 people. The RISCS project is a European project which has explored the potential environmental impacts of the geological storage of CO2, as a technology for abating CO2 emissions. The session was meant to introduce the participants to the information produced within the RISCS project on possible impacts of CO2 on onshore and offshore ecosystems and human population. The objective was to experiment a process for facilitating, through dialogue and self-discovery, an understanding of the particular issues that need to be considered when evaluating the potential impacts of CO2 storage. It was also an opportunity to test an innovative and original format for science communication, aimed at involving a large group of participants in interactive activities with experts, based on the Role Playing Game pattern. The structure of the workshop included an exploration of participants' questions on and interest in CCS impacts, small group interaction with researchers and a final feed-back from each group to the plenary. Each group of about 10 participants was provided the

Special features of high-speed interaction of supercavitating solids in water

Energy Technology Data Exchange (ETDEWEB)

Ishchenko, Aleksandr, E-mail: ichan@niipmm.tsu.ru; Afanas’eva, Svetlana, E-mail: s.a.afanasyeva@mail.ru; Burkin, Viktor, E-mail: v.v.burkin@mail.ru; Diachkovskii, Aleksei, E-mail: lex-okha@mail.ru; Korolkov, Leonid, E-mail: dmm1@sibmail.com; Moiseev, Dmitrii; Khabibullin, Marat, E-mail: lenmar07@rambler.ru [National Research Tomsk State University, 36, Lenin Ave., Tomsk, 634050 (Russian Federation); Akinshin, Ruslan, E-mail: rakinshin@yandex.ru; Borisenkov, Igor, E-mail: rakinshin@yandex.ru [Subdivision of applied problems under the RAS presidium 3, Gubkin St, Moscow, 117971 (Russian Federation)

2016-01-15

Special features of material behavior of a supercavitating projectile are investigated at various initial velocities of entering water on the basis of the developed stress-strain state model with possibility of destruction of solids when moving in water and interacting with various underwater barriers with the use of consistent methodological approach of mechanics of continuous media. The calculation-experimental method was used to study the modes of motion of supercavitating projectiles at sub- and supersonic velocities in water medium after acceleration in the barrelled accelerator, as well as their interaction with barriers. Issues of stabilization of the supercavitating projectile on the initial flight path in water were studied. Microphotographs of state of solids made of various materials, before and after interaction with water, at subsonic and supersonic velocities were presented. Supersonic velocity of the supercavitating projectile motion in water of 1590 m/s was recorded.

Special features of high-speed interaction of supercavitating solids in water

International Nuclear Information System (INIS)

Ishchenko, Aleksandr; Afanas’eva, Svetlana; Burkin, Viktor; Diachkovskii, Aleksei; Korolkov, Leonid; Moiseev, Dmitrii; Khabibullin, Marat; Akinshin, Ruslan; Borisenkov, Igor

2016-01-01

Special features of material behavior of a supercavitating projectile are investigated at various initial velocities of entering water on the basis of the developed stress-strain state model with possibility of destruction of solids when moving in water and interacting with various underwater barriers with the use of consistent methodological approach of mechanics of continuous media. The calculation-experimental method was used to study the modes of motion of supercavitating projectiles at sub- and supersonic velocities in water medium after acceleration in the barrelled accelerator, as well as their interaction with barriers. Issues of stabilization of the supercavitating projectile on the initial flight path in water were studied. Microphotographs of state of solids made of various materials, before and after interaction with water, at subsonic and supersonic velocities were presented. Supersonic velocity of the supercavitating projectile motion in water of 1590 m/s was recorded

Unveiling network-based functional features through integration of gene expression into protein networks.

Science.gov (United States)

Jalili, Mahdi; Gebhardt, Tom; Wolkenhauer, Olaf; Salehzadeh-Yazdi, Ali

2018-06-01

Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype-phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies. In this work, we highlight and review the progress, challenges and advantages associated with emerging approaches, integrating gene expression and protein-protein interaction networks to unravel network-based functional features. This includes identifying disease related genes, gene prioritization, clustering protein interactions, developing the modules, extract active subnetworks and static protein complexes or dynamic/temporal protein complexes. We also discuss how these approaches contribute to our understanding of the biology of complex traits and diseases. This article is part of a Special Issue entitled: Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Feature confirmation in object perception: Feature integration theory 26 years on from the Treisman Bartlett lecture.

Science.gov (United States)

Humphreys, Glyn W

2016-10-01

The Treisman Bartlett lecture, reported in the Quarterly Journal of Experimental Psychology in 1988, provided a major overview of the feature integration theory of attention. This has continued to be a dominant account of human visual attention to this day. The current paper provides a summary of the work reported in the lecture and an update on critical aspects of the theory as applied to visual object perception. The paper highlights the emergence of findings that pose significant challenges to the theory and which suggest that revisions are required that allow for (a) several rather than a single form of feature integration, (b) some forms of feature integration to operate preattentively, (c) stored knowledge about single objects and interactions between objects to modulate perceptual integration, (d) the application of feature-based inhibition to object files where visual features are specified, which generates feature-based spreading suppression and scene segmentation, and (e) a role for attention in feature confirmation rather than feature integration in visual selection. A feature confirmation account of attention in object perception is outlined.

Three-Dimensional Reconstructions Come to Life – Interactive 3D PDF Animations in Functional Morphology

Science.gov (United States)

van de Kamp, Thomas; dos Santos Rolo, Tomy; Vagovič, Patrik; Baumbach, Tilo; Riedel, Alexander

2014-01-01

Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering. PMID:25029366

Predictability of Genetic Interactions from Functional Gene Modules

Directory of Open Access Journals (Sweden)

Jonathan H. Young

2017-02-01

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

The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

Energy Technology Data Exchange (ETDEWEB)

Chen, Fang; Venugopal, Vandavasi; Murray, Beverly; Rudenko, Gabby (Michigan)

2014-10-02

{alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha} carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

Unveiling protein functions through the dynamics of the interaction network.

Directory of Open Access Journals (Sweden)

Irene Sendiña-Nadal

Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

Centrality of Social Interaction in Human Brain Function.

Science.gov (United States)

Hari, Riitta; Henriksson, Linda; Malinen, Sanna; Parkkonen, Lauri

2015-10-07

People are embedded in social interaction that shapes their brains throughout lifetime. Instead of emerging from lower-level cognitive functions, social interaction could be the default mode via which humans communicate with their environment. Should this hypothesis be true, it would have profound implications on how we think about brain functions and how we dissect and simulate them. We suggest that the research on the brain basis of social cognition and interaction should move from passive spectator science to studies including engaged participants and simultaneous recordings from the brains of the interacting persons. Copyright © 2015 Elsevier Inc. All rights reserved.

Interface, information, interaction: a narrative review of design and functional requirements for clinical decision support.

Science.gov (United States)

Miller, Kristen; Mosby, Danielle; Capan, Muge; Kowalski, Rebecca; Ratwani, Raj; Noaiseh, Yaman; Kraft, Rachel; Schwartz, Sanford; Weintraub, William S; Arnold, Ryan

2018-05-01

Provider acceptance and associated patient outcomes are widely discussed in the evaluation of clinical decision support systems (CDSSs), but critical design criteria for tools have generally been overlooked. The objective of this work is to inform electronic health record alert optimization and clinical practice workflow by identifying, compiling, and reporting design recommendations for CDSS to support the efficient, effective, and timely delivery of high-quality care. A narrative review was conducted from 2000 to 2016 in PubMed and The Journal of Human Factors and Ergonomics Society to identify papers that discussed/recommended design features of CDSSs that are associated with the success of these systems. Fourteen papers were included as meeting the criteria and were found to have a total of 42 unique recommendations; 11 were classified as interface features, 10 as information features, and 21 as interaction features. Features are defined and described, providing actionable guidance that can be applied to CDSS development and policy. To our knowledge, no reviews have been completed that discuss/recommend design features of CDSS at this scale, and thus we found that this was important for the body of literature. The recommendations identified in this narrative review will help to optimize design, organization, management, presentation, and utilization of information through presentation, content, and function. The designation of 3 categories (interface, information, and interaction) should be further evaluated to determine the critical importance of the categories. Future work will determine how to prioritize them with limited resources for designers and developers in order to maximize the clinical utility of CDSS. This review will expand the field of knowledge and provide a novel organization structure to identify key recommendations for CDSS.

Fungal endophytes: diversity and functional roles

Science.gov (United States)

Rodriguez, R.J.; White, J.F.; Arnold, A.E.; Redman, R.S.

2009-01-01

All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.

The roles of amensalistic and commensalistic interactions in large ecological network stability.

Science.gov (United States)

Mougi, Akihiko

2016-07-13

Ecological communities comprise diverse species and their interactions. Notably, ecological and evolutionary studies have revealed that reciprocal interactions such as predator-prey, competition, and mutualism, are key drivers of community dynamics. However, there is an argument that many species interactions are asymmetric, where one species unilaterally affects another species (amensalism or commensalism). This raises the unanswered question of what is the role of unilateral interactions in community dynamics. Here I use a theoretical approach to demonstrate that unilateral interactions greatly enhance community stability. The results suggested that amensalism and commensalism were more stabilizing than symmetrical interactions, such as competition and mutualism, but they were less stabilizing than an asymmetric antagonistic interaction. A mix of unilateral interactions increased stability. Furthermore, in communities with all interaction types, unilateral interactions tended to increase stability. This study suggests that unilateral interactions play a major role in maintaining communities, underlining the need to further investigate their roles in ecosystem dynamics.

Caspase-2 associates with FAN through direct interaction and overlapping functionality.

Science.gov (United States)

Forsberg, Jeremy; Li, Xinge; Zamaraev, Aleksey V; Panaretakis, Theocharis; Zhivotovsky, Boris; Olsson, Magnus

2018-05-23

Caspase-2 has been implicated in diverse cellular processes, and the identification of factors with which it interacts has steadily increased. In the present study, we report a direct interaction between caspase-2 and factor associated with neutral sphingomyelinase activation (FAN) using yeast two-hybrid screening and co-immunoprecipitation. Further, stable suppression of caspase-2 expression in HEK293T and HeLa cells enabled a systematic investigation of putative novel enzyme functionalities, especially with respect to ceramide production, cell migration, IL-6 production and vesicular homeostasis, all of which have been previously reported to be associated with FAN. Lipidomics excluded the involvement of caspase-2 in the generation of ceramide species, but caspase-2-dependent deregulation of IL-6 release, vesicular size and delayed cell relocation supported an association between caspase-2 and FAN. Collectively, these data identify a novel caspase-2-interacting factor, FAN, and expand the role for the enzyme in seemingly non-apoptotic cellular mechanisms. Copyright © 2018 Elsevier Inc. All rights reserved.

GA Based Optimal Feature Extraction Method for Functional Data Classification

OpenAIRE

Jun Wan; Zehua Chen; Yingwu Chen; Zhidong Bai

2010-01-01

Classification is an interesting problem in functional data analysis (FDA), because many science and application problems end up with classification problems, such as recognition, prediction, control, decision making, management, etc. As the high dimension and high correlation in functional data (FD), it is a key problem to extract features from FD whereas keeping its global characters, which relates to the classification efficiency and precision to heavens. In this paper...

LINGUISTIC FEATURES ANALYSIS OF THE ENGLISH ELECTRONIC COMMERCE WEBSITES

Directory of Open Access Journals (Sweden)

Siti Nurani

2014-06-01

Full Text Available This research aims at identifying linguistic features used in the English electronic commerce websites used in correlation with the field, tenor and mode of discourse as parts of Systemic Functional Linguistics (SFL approach. Findings have shown that in the field of discourse, the linguistic features are largely appeared in the experiential domain analysis which shows that all terms of registers function as technical terms, of which the two major forms of nouns and verbs were the most frequent categories among other kinds of technical terms. The goal orientation is considered to be as a long term and the social activity is exchange. In the tenor of discourse, the linguistic features are highly appeared in the social distance analysis which shows that the social distance between participants is considered minimal. The agentive role is said to be equal and the social role is considered as non-hierarchic. In the mode of discourse, the linguistic features are excessively occurred in the language role analysis which exists equally of both constitutive and ancillary. The channel is in graphic mode. The medium is in written with a visual contact as its device.

A novel functional role of collagen glycosylation

DEFF Research Database (Denmark)

Jürgensen, Henrik J; Madsen, Daniel H; Ingvarsen, Signe

2011-01-01

Collagens make up the most abundant component of interstitial extracellular matrices and basement membranes. Collagen remodeling is a crucial process in many normal physiological events and in several pathological conditions. Some collagen subtypes contain specific carbohydrate side chains......, the function of which is poorly known. The endocytic collagen receptor urokinase plasminogen activator receptor-associated protein (uPARAP)/Endo180 plays an important role in matrix remodeling through its ability to internalize collagen for lysosomal degradation. uPARAP/Endo180 is a member of the mannose...... receptor protein family. These proteins all include a fibronectin type II domain and a series of C-type lectin-like domains, of which only a minor part possess carbohydrate recognition activity. At least two of the family members, uPARAP/Endo180 and the mannose receptor, interact with collagens...

Brain gut microbiome interactions and functional bowel disorders

Science.gov (United States)

Alterations in the bidirectional interactions between the intestine and the nervous system have important roles in the pathogenesis of irritable bowel syndrome (IBS). A body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. A small and poorly defined r...

Enhancing Web Service Selection by User Preferences of Non-Functional Features

OpenAIRE

Badr , Youakim; Abraham , Ajith; Biennier , Frédérique; Grosan , Crina

2008-01-01

International audience; Selection of an appropriate Web service for a particular task has become a difficult challenge due to the increasing number of Web services offering similar functionalities. The functional properties describe what the service can do and the nonfunctional properties depict how the service can do it. Non-functional properties involving qualitative or quantitative features have become essential criteria to enhance the selection process of services making the selection pro...

Study of the pair-interaction function in some normal metals; Etude de l'interaction de paire dans quelques metaux normaux

Energy Technology Data Exchange (ETDEWEB)

Pick, R [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1965-06-01

The pair interaction function has been derived for the following metals: Li, Na, K, Al. It is obtained via a second order perturbation expansion of the wave functions of the conduction electrons using a self-consistent pseudo-potential. Exchange and correlations between those electrons have been ignored. Such an interaction is only valid at constant volume and depends on a single experimental parameter, namely the ionic volume. Its main features are a pronounced minimum in the vicinity of the nearest neighbours, especially marked in alkaline metals, and an asymptotic decrease of the form cos(2k{sub F}r)/r{sup 3}. This interaction gives the correct crystalline structure of these metals at 0 K as well as a good approximation of the phonon spectrum of an alkaline. The validity of the perturbation technique is discussed. We prove that the pair interaction function is correctly given to second order in the pseudo-potential despite the various approximations and errors involved by such a method. (author) [French] L'interaction de paire effective entre ions a ete calculee dans les metaux Li, Na, K et Al. Elle est obtenue par un developpement en serie de perturbation des fonctions d'onde des electrons de conduction. Le developpement est pousse au deuxieme ordre et utilise un pseudo-potentiel self-consistant. Les phenomenes d'echange et de correlations entre ces electrons ont ete negliges. L'interaction calculee n'a de sens qu'a volume constant. Elle depend d'un seul parametre experimental, le volume ionique. Elle se caracterise par un minimum prononce de l'energie de paire pour les proches voisins, surtout marque chez les alcalins. Elle decroit asymptotiquement en cos(2k{sub F}r)/r{sup 3}. Elle permet de predire la structure cristalline la plus stable a 0 K; elle donne le spectre de phonons des alcalins avec une assez bonne precision. Par ailleurs, la validite de la methode de perturbation du deuxieme ordre est discutee. On montre qu'elle donne correctement l'interaction

Features of the magnetic field of a rectangular combined function bending magnet

International Nuclear Information System (INIS)

Hwang, C.S.; National Chiao Tung Univ., Hsinchu; Chang, C.H.; Hwang, G.J.; Uen, T.M.; Tseng, P.K.; National Taiwan Univ., Taipei

1996-01-01

Magnetic field features of the combined function bending magnet with dipole and quadrupole field components are essential for the successful operation of the electron beam trajectory. These fields also dominate the photon beam quality. The vertical magnetic field B y (x,y) calculation is performed by a computer code MAGNET at the magnet center (s = 0). Those results are compared with the 2-D field measurement by the Hall probe mapping system. Also detailed survey has been made of the harmonic field strength and the main features of the fundamental integrated strength, effective length, magnetic symmetry, tilt of the pole face, offset of the field center and the fringe field. The end shims that compensate for the strong end negative sextupole field to increase the good field region for the entire integrated strength are discussed. An important physical feature of this combined function bending magnet is the constant ratio of dipole and quadrupole strength ∫Bds/∫Gds which is expressed as a function of excitation current in the energy range 0.6 to 1.5 GeV

The Extended Role of the Communication Partner in AAC interaction

DEFF Research Database (Denmark)

Pilesjö, Maja Sigurd

in the field.FindingsThe findings demonstrate that the speaking co-participant is sensitive to the actions of the person with impairments’ display of attention and actions within the local ‘contextual configuration’ (Goodwin, 2000). Due to differing resources, the relevant options for the next move......The Extended Role of the Communication Partner in AAC interactionIntroductionThe speaking communication partner in AAC interaction has a unique role (Blackstone et al., 2007). Interactional research in the field of AAC has, for instance, found that the interaction is characterized by a great deal......-analyses on naturally occurring social interaction, this session will demonstrate tasks that the speaking communication partner can undertake in AAC- interaction.Method and dataThe method of Conversation analysis (CA) is used in the current study (Higginbotham & Engelke, 2013). The general aim of CA is at getting...

The Essence and Meaning of Cross-Functional Teams in the System of Interaction of Personnel of Enterprises

Directory of Open Access Journals (Sweden)

Krasnostup Vladimir M.

2017-12-01

Full Text Available The article analyzes preconditions of formation and development of the «cross-functional teams» in the system of interaction of personnel of enterprises. The business philosophy of kaizen which precedes introduction of the cross-functional interaction of personnel was researched. The role and value of the studied category of «cross-functional team» have been defined, the existing interpretations of the definition of its essence have been considered, the obligatory achievement of synergistic effect has been emphasized. The main objectives of formation together with boundaries of functioning of a cross-functional team in the context of using different business technologies have been characterized. Conditions of creation and obstacles of functioning of a cross-functional command have been allocated. It has been determined that companies that aspire to sustainable innovation development should form cross-functional teams to increase their efficiency level and create stable competitive advantages in the market.

Disrupting functional interactions between platelet chemokines inhibits atherosclerosis in hyperlipidemic mice

DEFF Research Database (Denmark)

Koenen, RR; Hundelshausen, P; Nesmelova, IV

2009-01-01

Atherosclerosis is characterized by chronic inflammation of the arterial wall due to chemokine-driven mononuclear cell recruitment. Activated platelets can synergize with chemokines to exacerbate atherogenesis; for example, by deposition of the chemokines platelet factor-4 (PF4, also known as CXC...... monocyte recruitment and reducing atherosclerosis without the aforementioned side effects. These results establish the in vivo relevance of chemokine heteromers and show the potential of targeting heteromer formation to achieve therapeutic effects......) and RANTES (CCL5), triggering monocyte arrest on inflamed endothelium. Homo-oligomerization is required for the recruitment functions of CCL5, and chemokine heteromerization has more recently emerged as an additional regulatory mechanism, as evidenced by a mutual modulation of CXCL8 and CXCL4 activities...... compromise systemic immune responses, delay macrophage-mediated viral clearance and impair normal T cell functions. Here we determined structural features of CCL5-CXCL4 heteromers and designed stable peptide inhibitors that specifically disrupt proinflammatory CCL5-CXCL4 interactions, thereby attenuating...

Role amplification of the coulomb interaction in nuclear reactions

Energy Technology Data Exchange (ETDEWEB)

Kumar, Ashok; Soni, S K; Pancholi, S K; Gupta, S L [AN SSSR, Moscow. Radiotekhnicheskij Inst.

1976-10-01

The genarally adopted estimate of coulomb interaction in nuclear reactions based on the comparison of relative energies of real particles participating in the reaction with the coulomb barrier has been shown to provide wrong presentation of the role of coulomb interaction in the reaction mechanism. The relative energy of particles participating in virtual processes forming the reaction mechanism and its relation to the coulomb barrier turn out to be tens of per cent less than for the particles in an inlet channel. This is the main reason of increasing the role of coulomb interaction in the reaction mechanism. This increase is particularly significant for nuclei with large charges, in particular, in heavy ion reaction.

Decoding the different states of visual attention using functional and effective connectivity features in fMRI data.

Science.gov (United States)

Parhizi, Behdad; Daliri, Mohammad Reza; Behroozi, Mehdi

2018-04-01

The present paper concentrates on the impact of visual attention task on structure of the brain functional and effective connectivity networks using coherence and Granger causality methods. Since most studies used correlation method and resting-state functional connectivity, the task-based approach was selected for this experiment to boost our knowledge of spatial and feature-based attention. In the present study, the whole brain was divided into 82 sub-regions based on Brodmann areas. The coherence and Granger causality were applied to construct functional and effective connectivity matrices. These matrices were converted into graphs using a threshold, and the graph theory measures were calculated from it including degree and characteristic path length. Visual attention was found to reveal more information during the spatial-based task. The degree was higher while performing a spatial-based task, whereas characteristic path length was lower in the spatial-based task in both functional and effective connectivity. Primary and secondary visual cortex (17 and 18 Brodmann areas) were highly connected to parietal and prefrontal cortex while doing visual attention task. Whole brain connectivity was also calculated in both functional and effective connectivity. Our results reveal that Brodmann areas of 17, 18, 19, 46, 3 and 4 had a significant role proving that somatosensory, parietal and prefrontal regions along with visual cortex were highly connected to other parts of the cortex during the visual attention task. Characteristic path length results indicated an increase in functional connectivity and more functional integration in spatial-based attention compared with feature-based attention. The results of this work can provide useful information about the mechanism of visual attention at the network level.

Evaluating the Role of Drone-Produced Chemical Signals in Mediating Social Interactions in Honey Bees (Apis mellifera).

Science.gov (United States)

Villar, Gabriel; Wolfson, Megan D; Hefetz, Abraham; Grozinger, Christina M

2018-01-01

Pheromones play a critical role in shaping societies of social insects, including honey bees, Apis mellifera. While diverse functions have been ascribed to queen- and worker-produced compounds, few studies have explored the identity and function of male-produced (drone) compounds. However, several lines of evidence suggest that drones engage in a variety of social interactions inside and outside of the colony. Here we elucidate the chemical composition of extracts of the drone mandibular gland, and test the hypothesis that compounds produced in these glands, or a synthetic blend consisting of the six main compounds, mediate drone social interactions in and out of the colony. Drone mandibular glands primarily produce a blend of saturated, unsaturated and methyl branched fatty acids ranging in chain length from nonanoic to docosanoic acids, and both gland extracts and synthetic blends of these chemicals serve to attract drones outside of the hive, but do not attract workers inside the hive. These studies shed light on the role drones and drone-produced chemicals have on mediating social interactions with other drones and highlight their potential importance in communicating with other castes.

The functional role of the periphery in emotional language comprehension

Directory of Open Access Journals (Sweden)

David A. Havas

2013-05-01

Full Text Available Language can impact emotion, even when it makes no reference to emotion states. For example, reading sentences with positive meanings (The water park is refreshing on the hot summer day induces patterns of facial feedback congruent with the sentence emotionality (smiling, whereas sentences with negative meanings induce a frown. Moreover, blocking facial afference with botox selectively slows comprehension of emotional sentences. Therefore, theories of cognition should account for emotion-language interactions above the level of explicit emotion words, and the role of peripheral feedback in comprehension. For this special issue exploring frontiers in the role of the body and environment in cognition, we propose a theory in which facial feedback provides a context-sensitive constraint on the simulation of actions described in language. Paralleling the role of emotions in real-world behavior, our account proposes that 1 facial expressions accompany sudden shifts in well-being as described in language; 2 facial expressions modulate emotion states during reading; and 3 emotion states prepare the reader for an effective simulation of the ensuing language content. To inform the theory and guide future research, we outline a framework based on internal models for motor control. To support the theory, we assemble evidence from diverse areas of research. Taking a functional view of emotion, we tie the theory to behavioral and neural evidence for a role of facial feedback in cognition. Our theoretical framework provides a detailed account that can guide future research on the role of emotional feedback in language processing, and on interactions of language and emotion. It also highlights the bodily periphery as relevant to theories of embodied cognition.

"Prey Play": Learning about Predators and Prey through an Interactive, Role-Play Game

Science.gov (United States)

Deaton, Cynthia C. M.; Dodd, Kristen; Drennon, Katherine; Nagle, Jack

2012-01-01

"Prey Play" is an interactive role-play activity that provides fifth-grade students with opportunities to examine predator-prey interactions. This four-part, role-play activity allows students to take on the role of a predator and prey as they reflect on the behaviors animals exhibit as they collect food and interact with one another, as well as…

Annexin-Phospholipid Interactions. Functional Implications

Directory of Open Access Journals (Sweden)

Javier Turnay

2013-01-01

Full Text Available Annexins constitute an evolutionary conserved multigene protein superfamily characterized by their ability to interact with biological membranes in a calcium dependent manner. They are expressed by all living organisms with the exception of certain unicellular organisms. The vertebrate annexin core is composed of four (eight in annexin A6 homologous domains of around 70 amino acids, with the overall shape of a slightly bent ring surrounding a central hydrophilic pore. Calcium- and phospholipid-binding sites are located on the convex side while the N-terminus links domains I and IV on the concave side. The N-terminus region shows great variability in length and amino acid sequence and it greatly influences protein stability and specific functions of annexins. These proteins interact mainly with acidic phospholipids, such as phosphatidylserine, but differences are found regarding their affinity for lipids and calcium requirements for the interaction. Annexins are involved in a wide range of intra- and extracellular biological processes in vitro, most of them directly related with the conserved ability to bind to phospholipid bilayers: membrane trafficking, membrane-cytoskeleton anchorage, ion channel activity and regulation, as well as antiinflammatory and anticoagulant activities. However, the in vivo physiological functions of annexins are just beginning to be established.

Early Contact Stage of Apoptosis: Its Morphological Features and Function

Directory of Open Access Journals (Sweden)

Etheri Mikadze

2006-01-01

Full Text Available Apoptosis has been a biological phenomenon of intense interest for 20 years, but the earlier morphological features of apoptosis have not been determined hitherto. Using the methods of semi- and ultrathin sections, the livers of intact embryos and young rats have been studied under the effect of cycloheximide to determine morphological features of an early stage of apoptosis. It is discovered that both in hepatoblasts and hepatocytes, apoptosis, besides the well-known stages, also includes an early contact stage, distinguishing features of which are agglutination of bound ribosomes (breaking of translation, elimination of the nucleolus, reduction of free polysomes (and in hepatocytes, reduction of cisterns of rough endoplasmic reticulum, formation of cytoplasmic excrescences, and cell shape changes. The early stage of apoptosis is characterized by close contact with neighboring cells. At a certain phase of the contact stage of apoptosis, the nucleolus reappears in the nucleus and the number of free polysomes in the cytoplasm increases, which suggests the renewal of synthesis of new RNA and proteins. Close contact of differentiating and mitotic hepatoblasts with apoptotic cells indicates a certain functional relationship between these cells that is realized not only by micropinocytosis, but through gap junctions as well. We assume that the apoptotic cell, besides proteolytic products, can contain newly synthesized, low-molecular substances, the relocation of which from apoptotic to neighboring cells may contribute to both functional activity and proliferation of adjacent hepatoblasts and, therefore, the function of apoptosis may not be limited only to the elimination of harmful, damaged, and unwanted cells.

Roles of water in protein structure and function studied by molecular liquid theory.

Science.gov (United States)

Imai, Takashi

2009-01-01

The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

Superconductivity in a Fermi liquid from repulsive interactions: The role of electron–phonon interaction

International Nuclear Information System (INIS)

Fan, J.D.; Malozovsky, Y.M.

2013-01-01

Highlights: • The sign reversal of pair interaction in momentum space is proved. • It is also shown that electron-phonon interaction in fact leads to the pairing-break effect. • Transition temperature into superconductivity depends on competition between electron-phonon and Coulomb interactions. • Calculated exponent α of the isotope effect shows the possibility equal to, greater or less than 0.5, and even negative. -- Abstract: Based on our previously proven theorem that the interaction between a pair of quasiparticles in the normal Fermi liquid has an opposite sign to the interaction between particles, we consider pair correlation between a pair of quasiparticles when the interaction between particles is repulsive. For the convenience of statements, we have presented in this article once again the proof of the theorem in terms of an exact equation for the thermodynamic potential due to interaction between particles and based on the Green’s function method. Further, we have derived the Landau expansion of the thermodynamic potentials in terms of the variation of the quasiparticle distribution function. We have also derived the expansion of the thermodynamic potential in terms of the variation of an exact single particle (not quasiparticles), these derivations lead to the relationship between the interaction function for two quasiparticles and the interaction energy between two particles as shown. According to the proven theorem the interaction between a pair of quasiparticles is attractive in this case, the pairing – Cooper’s pairing between a pair of quasiparticles is possible. We solve the Bethe–Salpeter type equation for paring of two quasiparticles when both interactions – the Coulomb repulsive and electron–phonon interaction are present. We show that the electron–phonon interaction, in fact, leads to the pair breaking effect, in contrast to the common belief that electron–phonon interaction is the main mechanism for Cooper’s pair

Specificity of molecular interactions in transient protein-protein interaction interfaces.

Science.gov (United States)

Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

2006-11-15

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of

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.

CD54-Mediated Interaction with Pro-inflammatory Macrophages Increases the Immunosuppressive Function of Human Mesenchymal Stromal Cells

OpenAIRE

Espagnolle, Nicolas; Balguerie, Ad?lie; Arnaud, Emmanuelle; Senseb?, Luc; Varin, Audrey

2017-01-01

Summary: Mesenchymal stromal cells (MSCs) sense and modulate inflammation and represent potential clinical treatment for immune disorders. However, many details of the bidirectional interaction of MSCs and the innate immune compartment are still unsolved. Here we describe an unconventional but functional interaction between pro-inflammatory classically activated macrophages (M1MΦ) and MSCs, with CD54 playing a central role. CD54 was upregulated and enriched specifically at the contact area be...

A global interaction network maps a wiring diagram of cellular function

Science.gov (United States)

Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N.; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D.; Pelechano, Vicent; Styles, Erin B.; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S.; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F.; Li, Sheena C.; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; Luis, Bryan-Joseph San; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W.; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G.; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M.; Moore, Claire L.; Rosebrock, Adam P.; Caudy, Amy A.; Myers, Chad L.; Andrews, Brenda; Boone, Charles

2017-01-01

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing over 23 million double mutants, identifying ~550,000 negative and ~350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell. PMID:27708008

RISM theory distribution functions for Lennard--Jones interaction site fluids

International Nuclear Information System (INIS)

Johnson, E.; Hazoume, R.P.

1978-01-01

Reference interaction site model (RISM) theory distribution functions for Lennard-Jones interaction site fluids are discussed. The comparison with computer simulation results suggests that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

Interactive Spacecraft Trajectory Design Strategies Featuring Poincare Map Topology

Science.gov (United States)

Schlei, Wayne R.

Space exploration efforts are shifting towards inexpensive and more agile vehicles. Versatility regarding spacecraft trajectories refers to the agility to correct deviations from an intended path or even the ability to adapt the future path to a new destination--all with limited spaceflight resources (i.e., small DeltaV budgets). Trajectory design methods for such nimble vehicles incorporate equally versatile procedures that allow for rapid and interactive decision making while attempting to reduce Delta V budgets, leading to a versatile trajectory design platform. A versatile design paradigm requires the exploitation of Poincare map topology , or the interconnected web of dynamical structures, existing within the chaotic dynamics of multi-body gravitational models to outline low-Delta V transfer options residing nearby to a current path. This investigation details an autonomous procedure to extract the periodic orbits (topology nodes) and correlated asymptotic flow structures (or the invariant manifolds representing topology links). The autonomous process summarized in this investigation (termed PMATE) overcomes discontinuities on the Poincare section that arise in the applied multi-body model (the planar circular restricted three-body problem) and detects a wide variety of novel periodic orbits. New interactive capabilities deliver a visual analytics foundation for versatile spaceflight design, especially for initial guess generation and manipulation. Such interactive strategies include the selection of states and arcs from Poincare section visualizations and the capabilities to draw and drag trajectories to remove dependency on initial state input. Furthermore, immersive selection is expanded to cull invariant manifold structures, yielding low-DeltaV or even DeltaV-free transfers between periodic orbits. The application of interactive design strategies featuring a dense extraction of Poincare map topology is demonstrated for agile spaceflight with a simple

CD44 plays a functional role in Helicobacter pylori-induced epithelial cell proliferation.

Directory of Open Access Journals (Sweden)

Nina Bertaux-Skeirik

2015-02-01

Full Text Available The cytotoxin-associated gene (Cag pathogenicity island is a strain-specific constituent of Helicobacter pylori (H. pylori that augments cancer risk. CagA translocates into the cytoplasm where it stimulates cell signaling through the interaction with tyrosine kinase c-Met receptor, leading cellular proliferation. Identified as a potential gastric stem cell marker, cluster-of-differentiation (CD CD44 also acts as a co-receptor for c-Met, but whether it plays a functional role in H. pylori-induced epithelial proliferation is unknown. We tested the hypothesis that CD44 plays a functional role in H. pylori-induced epithelial cell proliferation. To assay changes in gastric epithelial cell proliferation in relation to the direct interaction with H. pylori, human- and mouse-derived gastric organoids were infected with the G27 H. pylori strain or a mutant G27 strain bearing cagA deletion (∆CagA::cat. Epithelial proliferation was quantified by EdU immunostaining. Phosphorylation of c-Met was analyzed by immunoprecipitation followed by Western blot analysis for expression of CD44 and CagA. H. pylori infection of both mouse- and human-derived gastric organoids induced epithelial proliferation that correlated with c-Met phosphorylation. CagA and CD44 co-immunoprecipitated with phosphorylated c-Met. The formation of this complex did not occur in organoids infected with ∆CagA::cat. Epithelial proliferation in response to H. pylori infection was lost in infected organoids derived from CD44-deficient mouse stomachs. Human-derived fundic gastric organoids exhibited an induction in proliferation when infected with H. pylori that was not seen in organoids pre-treated with a peptide inhibitor specific to CD44. In the well-established Mongolian gerbil model of gastric cancer, animals treated with CD44 peptide inhibitor Pep1, resulted in the inhibition of H. pylori-induced proliferation and associated atrophic gastritis. The current study reports a unique

Multi-function robots with speech interaction and emotion feedback

Science.gov (United States)

Wang, Hongyu; Lou, Guanting; Ma, Mengchao

2018-03-01

Nowadays, the service robots have been applied in many public circumstances; however, most of them still don’t have the function of speech interaction, especially the function of speech-emotion interaction feedback. To make the robot more humanoid, Arduino microcontroller was used in this study for the speech recognition module and servo motor control module to achieve the functions of the robot’s speech interaction and emotion feedback. In addition, W5100 was adopted for network connection to achieve information transmission via Internet, providing broad application prospects for the robot in the area of Internet of Things (IoT).

CD54-Mediated Interaction with Pro-inflammatory Macrophages Increases the Immunosuppressive Function of Human Mesenchymal Stromal Cells

Directory of Open Access Journals (Sweden)

Nicolas Espagnolle

2017-04-01

Full Text Available Summary: Mesenchymal stromal cells (MSCs sense and modulate inflammation and represent potential clinical treatment for immune disorders. However, many details of the bidirectional interaction of MSCs and the innate immune compartment are still unsolved. Here we describe an unconventional but functional interaction between pro-inflammatory classically activated macrophages (M1MΦ and MSCs, with CD54 playing a central role. CD54 was upregulated and enriched specifically at the contact area between M1MФ and MSCs. Moreover, the specific interaction induced calcium signaling and increased the immunosuppressive capacities of MSCs dependent on CD54 mediation. Our data demonstrate that MSCs can detect an inflammatory microenvironment via a direct and physical interaction with innate immune cells. This finding opens different perspectives for MSC-based cell therapy. : Mesenchymal stromal cells (MSCs are promising for cell-based therapy in inflammatory disorders by switching off the immune response. Varin and colleagues demonstrate that MSCs and inflammatory macrophages communicate via an unconventional but functional interaction that strongly increases the immunosuppressive capacities of MSCs. This new communication between the innate immune system and MSCs opens new perspectives for MSC-based cell therapy. Keywords: macrophages, bone marrow mesenchymal stromal cells, functional interaction, CD54, immunosuppression, indoleamine 2,3-dioxygenase, cell therapy

Eco-nomics: Are the Planet-Unfriendly Features of Capitalism Barriers to Sustainability?

OpenAIRE

Merrill Singer

2010-01-01

This paper argues that there are essential features of capitalist modes of production, consumption, and waste dispersal in interaction with the environment and its built-in systemic features that contradict long-term sustainable development. These features include: (a) contradictions in the origin and meaning of sustainability; (b) the central role of the productivity ethic in capitalism and its reproduction in emergent green capitalism; (c) the commodification of nature and the continued pro...

Functional Interaction Map of Lyssavirus Phosphoprotein: Identification of the Minimal Transcription Domains

Science.gov (United States)

Jacob, Yves; Real, Eléonore; Tordo, Noël

2001-01-01

Lyssaviruses, the causative agents of rabies encephalitis, are distributed in seven genotypes. The phylogenetically distant rabies virus (PV strain, genotype 1) and Mokola virus (genotype 3) were used to develop a strategy to identify functional homologous interactive domains from two proteins (P and N) which participate in the viral ribonucleoprotein (RNP) transcription-replication complex. This strategy combined two-hybrid and green fluorescent protein–reverse two-hybrid assays in Saccharomyces cerevisiae to analyze protein-protein interactions and a reverse genetic assay in mammalian cells to study the transcriptional activity of the reconstituted RNP complex. Lyssavirus P proteins contain two N-binding domains (N-BDs), a strong one encompassing amino acid (aa) 176 to the C terminus and a weak one in the 189 N-terminal aa. The N-terminal portion of P (aa 52 to 189) also contains a homomultimerization site. Here we demonstrate that N-P interactions, although weaker, are maintained between proteins of the different genotypes. A minimal transcriptional module of the P protein was obtained by fusing the first 60 N-terminal aa containing the L protein binding site to the C-terminal strong N-BD. Random mutation of the strong N-BD on P protein identified three highly conserved K residues crucial for N-P interaction. Their mutagenesis in full-length P induced a transcriptionally defective RNP. The analysis of homologous interactive domains presented here and previously reported dissections of the P protein allowed us to propose a model of the functional interaction network of the lyssavirus P protein. This model underscores the central role of P at the interface between L protein and N-RNA template. PMID:11559793

Extracting intrinsic functional networks with feature-based group independent component analysis.

Science.gov (United States)

Calhoun, Vince D; Allen, Elena

2013-04-01

There is increasing use of functional imaging data to understand the macro-connectome of the human brain. Of particular interest is the structure and function of intrinsic networks (regions exhibiting temporally coherent activity both at rest and while a task is being performed), which account for a significant portion of the variance in functional MRI data. While networks are typically estimated based on the temporal similarity between regions (based on temporal correlation, clustering methods, or independent component analysis [ICA]), some recent work has suggested that these intrinsic networks can be extracted from the inter-subject covariation among highly distilled features, such as amplitude maps reflecting regions modulated by a task or even coordinates extracted from large meta analytic studies. In this paper our goal was to explicitly compare the networks obtained from a first-level ICA (ICA on the spatio-temporal functional magnetic resonance imaging (fMRI) data) to those from a second-level ICA (i.e., ICA on computed features rather than on the first-level fMRI data). Convergent results from simulations, task-fMRI data, and rest-fMRI data show that the second-level analysis is slightly noisier than the first-level analysis but yields strikingly similar patterns of intrinsic networks (spatial correlations as high as 0.85 for task data and 0.65 for rest data, well above the empirical null) and also preserves the relationship of these networks with other variables such as age (for example, default mode network regions tended to show decreased low frequency power for first-level analyses and decreased loading parameters for second-level analyses). In addition, the best-estimated second-level results are those which are the most strongly reflected in the input feature. In summary, the use of feature-based ICA appears to be a valid tool for extracting intrinsic networks. We believe it will become a useful and important approach in the study of the macro

Depressive and conduct disorder symptoms in youth living with HIV: the independent and interactive roles of coping and neuropsychological functioning.

Science.gov (United States)

Salama, Christina; Morris, Mary; Armistead, Lisa; Koenig, Linda J; Demas, Penelope; Ferdon, Corinne; Bachanas, Pamela

2013-01-01

Emerging research suggests the importance of psychosocial characteristics (e.g., coping and social support) for positive adaptation among youth with behaviorally acquired HIV. However, little is known about how these traits interact with cognitive abilities to impact emotional and behavioral adjustment. This study examined whether coping skills and executive functioning interact in their association with psychological adjustment in HIV-positive youth. Data from Project Adolescents Living with HIV/AIDS (ALPHA), a study to examine psychosocial, behavioral and neuropsychological functioning of youth with behaviorally acquired HIV, were used. Fifty-nine participants, aged 14-23, diagnosed with HIV prior to age 20 and receiving care in one of two HIV clinics in Atlanta or New York City, were recruited, consented and enrolled. Participants completed measures of depressive symptoms (Beck Depression Inventory), conduct disorder (Adolescent Symptom Index), and use of positive and negative coping strategies (Kidcope). The Wisconsin Card Sorting Test (WCST) assessed abstract reasoning (categories completed) and cognitive inflexibility (perseverative errors). In this sample of HIV-positive youth, depressive symptoms were best predicted by an interactive combination of negative coping skills and poor neuropsychological functioning. Neuropsychological functioning (cognitive inflexibility) and negative coping skills were directly associated with conduct disorder symptoms. Results highlight the importance of including neuropsychological assessment in the evaluation of HIV-positive youth, particularly those with emotional or behavioral problems.

Semantic integration to identify overlapping functional modules in protein interaction networks

Directory of Open Access Journals (Sweden)

Ramanathan Murali

2007-07-01

Full Text Available Abstract Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification.

Monocular channels have a functional role in endogenous orienting.

Science.gov (United States)

Saban, William; Sekely, Liora; Klein, Raymond M; Gabay, Shai

2018-03-01

The literature has long emphasized the role of higher cortical structures in endogenous orienting. Based on evolutionary explanation and previous data, we explored the possibility that lower monocular channels may also have a functional role in endogenous orienting of attention. Sensitive behavioral manipulation was used to probe the contribution of monocularly segregated regions in a simple cue - target detection task. A central spatially informative cue, and its ensuing target, were presented to the same or different eyes at varying cue-target intervals. Results indicated that the onset of endogenous orienting was apparent earlier when the cue and target were presented to the same eye. The data provides converging evidence for the notion that endogenous facilitation is modulated by monocular portions of the visual stream. This, in turn, suggests that higher cortical mechanisms are not exclusively responsible for endogenous orienting, and that a dynamic interaction between higher and lower neural levels, might be involved. Copyright © 2018 Elsevier Ltd. All rights reserved.

Association between PTGS1 polymorphisms and functional outcomes in Chinese patients with stroke during aspirin therapy: Interaction with smoking.

Science.gov (United States)

Cai, Huan; Cai, Biyang; Sun, Lingli; Zhang, Hao; Zhou, Shuyu; Cao, Liping; Guo, Hongquan; Sun, Wen; Yan, Bernard; Davis, Stephen M; Zhang, Zhizhong; Liu, Xinfeng

2017-05-15

Prostaglandin-Endoperoxide Synthase 1 (PTGS1) and smoking may play important roles in aspirin nonresponsiveness, but the effect of their interaction on stroke outcomes remains largely unknown. We examined the effects of PTGS1 polymorphisms, smoking status, and their interaction on functional outcomes in a cohort of Chinese Han patients with stroke during aspirin therapy. A total of 617 ischemic stroke patients taking aspirin were enrolled. Three single nucleotide polymorphisms (SNPs) rs1330344, rs3842788, and rs5788 in PTGS1 were determined for genotyping. Poor functional outcomes were defined as a modified Rankin Scale (mRS) of 3-6 at 90-day follow-up. The influence of PTGS1 gene-smoking interaction on functional outcomes was examined. Poor functional outcomes occurred in 145 (23.5%) patients. When adjusting multiple factors by logistic regression, CC genotype of rs1330344 was associated with poor functional outcomes (risk ratio [RR]=1.73; 95% confidence interval [CI]: 1.17-2.37). A similar connection was found in the CGC haplotype (RR=1.40; 95% CI: 1.08-1.77). Furthermore, we found a significant interaction between rs1330344 and smoking status (P interaction =0.018); the interaction effect between the PTGS1 haplotype and smoking also showed statistical significance (P interaction =0.040). In Chinese Han stroke patients with aspirin therapy, the adverse effect of PTGS1 polymorphisms on functional outcomes may be modulated by the smoking status. PTGS1 gene-smoking interaction might in part reflect the heterogeneity in the prognosis of patients treated with aspirin. Copyright © 2017 Elsevier B.V. All rights reserved.

Jaw1/LRMP has a role in maintaining nuclear shape via interaction with SUN proteins.

Science.gov (United States)

Kozono, Takuma; Tadahira, Kazuko; Okumura, Wataru; Itai, Nao; Tamura-Nakano, Miwa; Dohi, Taeko; Tonozuka, Takashi; Nishikawa, Atsushi

2018-06-06

Jaw1/LRMP is characterized as a type II integral membrane protein that is localized to endoplasmic reticulum (ER), however, its physiological functions have been poorly understood. An alignment of amino acid sequence of Jaw1 with KASH proteins, outer nuclear membrane proteins, revealed that Jaw1 has a partial homology to the KASH domain. Here, we show that the function of Jaw1 is to maintain nuclear shape in mouse melanoma cell line. The siRNA-mediated knockdown of Jaw1 caused a severe defect in nuclear shape, and the defect was rescued by ectopic expression of siRNA-resistant Jaw1. Since co-immunoprecipitation assay indicates that Jaw1 interacts with SUN proteins that are inner nuclear proteins and microtubules, this study suggests that Jaw1 has a role in maintaining nuclear shape via interactions with SUN proteins and microtubules.

Top-Down Control of Visual Attention by the Prefrontal Cortex. Functional Specialization and Long-Range Interactions

Science.gov (United States)

Paneri, Sofia; Gregoriou, Georgia G.

2017-01-01

The ability to select information that is relevant to current behavioral goals is the hallmark of voluntary attention and an essential part of our cognition. Attention tasks are a prime example to study at the neuronal level, how task related information can be selectively processed in the brain while irrelevant information is filtered out. Whereas, numerous studies have focused on elucidating the mechanisms of visual attention at the single neuron and population level in the visual cortices, considerably less work has been devoted to deciphering the distinct contribution of higher-order brain areas, which are known to be critical for the employment of attention. Among these areas, the prefrontal cortex (PFC) has long been considered a source of top-down signals that bias selection in early visual areas in favor of the attended features. Here, we review recent experimental data that support the role of PFC in attention. We examine the existing evidence for functional specialization within PFC and we discuss how long-range interactions between PFC subregions and posterior visual areas may be implemented in the brain and contribute to the attentional modulation of different measures of neural activity in visual cortices. PMID:29033784

Top-Down Control of Visual Attention by the Prefrontal Cortex. Functional Specialization and Long-Range Interactions

Directory of Open Access Journals (Sweden)

Sofia Paneri

2017-09-01

Full Text Available The ability to select information that is relevant to current behavioral goals is the hallmark of voluntary attention and an essential part of our cognition. Attention tasks are a prime example to study at the neuronal level, how task related information can be selectively processed in the brain while irrelevant information is filtered out. Whereas, numerous studies have focused on elucidating the mechanisms of visual attention at the single neuron and population level in the visual cortices, considerably less work has been devoted to deciphering the distinct contribution of higher-order brain areas, which are known to be critical for the employment of attention. Among these areas, the prefrontal cortex (PFC has long been considered a source of top-down signals that bias selection in early visual areas in favor of the attended features. Here, we review recent experimental data that support the role of PFC in attention. We examine the existing evidence for functional specialization within PFC and we discuss how long-range interactions between PFC subregions and posterior visual areas may be implemented in the brain and contribute to the attentional modulation of different measures of neural activity in visual cortices.

The Role of Book Features in Young Children's Transfer of Information from Picture Books to Real-World Contexts.

Science.gov (United States)

Strouse, Gabrielle A; Nyhout, Angela; Ganea, Patricia A

2018-01-01

Picture books are an important source of new language, concepts, and lessons for young children. A large body of research has documented the nature of parent-child interactions during shared book reading. A new body of research has begun to investigate the features of picture books that support children's learning and transfer of that information to the real world. In this paper, we discuss how children's symbolic development, analogical reasoning, and reasoning about fantasy may constrain their ability to take away content information from picture books. We then review the nascent body of findings that has focused on the impact of picture book features on children's learning and transfer of words and letters, science concepts, problem solutions, and morals from picture books. In each domain of learning we discuss how children's development may interact with book features to impact their learning. We conclude that children's ability to learn and transfer content from picture books can be disrupted by some book features and research should directly examine the interaction between children's developing abilities and book characteristics on children's learning.

The Role of Book Features in Young Children's Transfer of Information from Picture Books to Real-World Contexts

Science.gov (United States)

Strouse, Gabrielle A.; Nyhout, Angela; Ganea, Patricia A.

2018-01-01

Picture books are an important source of new language, concepts, and lessons for young children. A large body of research has documented the nature of parent-child interactions during shared book reading. A new body of research has begun to investigate the features of picture books that support children's learning and transfer of that information to the real world. In this paper, we discuss how children's symbolic development, analogical reasoning, and reasoning about fantasy may constrain their ability to take away content information from picture books. We then review the nascent body of findings that has focused on the impact of picture book features on children's learning and transfer of words and letters, science concepts, problem solutions, and morals from picture books. In each domain of learning we discuss how children's development may interact with book features to impact their learning. We conclude that children's ability to learn and transfer content from picture books can be disrupted by some book features and research should directly examine the interaction between children's developing abilities and book characteristics on children's learning. PMID:29467690

The Role of Book Features in Young Children's Transfer of Information from Picture Books to Real-World Contexts

Directory of Open Access Journals (Sweden)

Gabrielle A. Strouse

2018-02-01

Full Text Available Picture books are an important source of new language, concepts, and lessons for young children. A large body of research has documented the nature of parent-child interactions during shared book reading. A new body of research has begun to investigate the features of picture books that support children's learning and transfer of that information to the real world. In this paper, we discuss how children's symbolic development, analogical reasoning, and reasoning about fantasy may constrain their ability to take away content information from picture books. We then review the nascent body of findings that has focused on the impact of picture book features on children's learning and transfer of words and letters, science concepts, problem solutions, and morals from picture books. In each domain of learning we discuss how children's development may interact with book features to impact their learning. We conclude that children's ability to learn and transfer content from picture books can be disrupted by some book features and research should directly examine the interaction between children's developing abilities and book characteristics on children's learning.

Specialized functional diversity and interactions of the Na,K-ATPase

Directory of Open Access Journals (Sweden)

Igor I. Krivoi

2016-05-01

Full Text Available Na,K-ATPase is a protein ubiquitously expressed in the plasma membrane of all animal cells and vitally essential for their functions. A specialized functional diversity of the Na,K-ATPase isozymes is provided by molecular heterogeneity, distinct subcellular localizations and functional interactions with molecular environment. Studies over the last decades clearly demonstrated complex and isoform-specific reciprocal functional interactions between the Na,K-ATPase and neighboring proteins and lipids. These interactions are enabled by a spatially restricted ion homeostasis, direct protein-protein/lipid interactions and protein kinase signaling pathways. In addition to its ‘classical’ function in ion translocation, the Na,K-ATPase is now considered as one of the most important signaling molecules in neuronal, epithelial, skeletal, cardiac and vascular tissues. Accordingly, the Na,K-ATPase forms specialized sub-cellular multimolecular microdomains which act as receptors to circulating endogenous cardiotonic steroids triggering a number of signaling pathways. Changes in these endogenous cardiotonic steroid levels and initiated signaling responses have significant adaptive values for tissues and whole organisms under numerous physiological and pathophysiological conditions. This review discusses recent progress in the studies of functional interactions between the Na,K-ATPase and molecular microenvironment, the Na,K-ATPase-dependent signaling pathways and their significance for diversity of cell function.

Features of polycystic ovary syndrome (PCOS) in women with functional hypothalamic amenorrhea (FHA) may be reversible with recovery of menstrual function.

Science.gov (United States)

Carmina, Enrico; Fruzzetti, Franca; Lobo, Roger A

2018-04-01

Since features of polycystic ovary syndrome (PCOS) have been found to be prevalent in women with functional hypothalamic amenorrhea (FHA), we wished to determine what happens to these features after recovery of menstrual function in FHA Design: Prospective cohort study. Twenty-eight women with FHA and 30 age-matched ovulatory controls were studied. Twenty-eight women with FHA and 30 age-matched ovulatory controls were studied. We measured serum estradiol, LH, FSH, testosterone, DHEAS, anti-Mullerian hormone (AMH), body mass index, and ovarian morphology on transvaginal ultrasound. At baseline, 12 of the 28 women (43%) had increased AMH (>4.7 ng/mL), and higher testosterone and larger ovaries compared to the other 16 women with normal AMH. One year after recovery of menstrual function, in the 12 women with increased AMH, serum AMH, testosterone and ovarian size decreased, while LH and estradiol increased. At one year, only one of the 12 women in the high AMH group developed clinical features of PCOS. In the majority of women with FHA who have PCOS-like features, these features may be due to the hypothalamic state and appear to be reversible. Few women may develop clinical PCOS after recovery.

Canonical partition functions: ideal quantum gases, interacting classical gases, and interacting quantum gases

Science.gov (United States)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-02-01

In statistical mechanics, for a system with a fixed number of particles, e.g. a finite-size system, strictly speaking, the thermodynamic quantity needs to be calculated in the canonical ensemble. Nevertheless, the calculation of the canonical partition function is difficult. In this paper, based on the mathematical theory of the symmetric function, we suggest a method for the calculation of the canonical partition function of ideal quantum gases, including ideal Bose, Fermi, and Gentile gases. Moreover, we express the canonical partition functions of interacting classical and quantum gases given by the classical and quantum cluster expansion methods in terms of the Bell polynomial in mathematics. The virial coefficients of ideal Bose, Fermi, and Gentile gases are calculated from the exact canonical partition function. The virial coefficients of interacting classical and quantum gases are calculated from the canonical partition function by using the expansion of the Bell polynomial, rather than calculated from the grand canonical potential.

Analysis of Conserved Structural Features of Selenoprotein K | Al ...

African Journals Online (AJOL)

Selenium plays important roles in human health and these roles may be exerted through its presence in selenoproteins. Among the 25 selenoproteins in human is selenoprotein K (SelK) whose exact function is still unclear. Here, we investigated the conserved structural features of SelK using bioinformatics as an approach ...

Managerial Roles and Functions in Negotiation Process

Directory of Open Access Journals (Sweden)

Andrzej Kozina

2014-06-01

Full Text Available The paper is focused on negotiation processes performed in a company and presents author’s concept of the description of the roles and functions accomplished by managers within those processes and being of significant importance from the point of view of negotiations’ outcomes. Such a concept aims at providing the analysis and conducting of business negotiations with effective support. Firstly (following introduction, the concept, types, and comprehensive model of such negotiations is presented as a useful methodological framework for specifying managerial roles and functions. Secondly, some classic concepts of those roles are reviewed, drawing special attention to the ones that concern negotiation process. Thirdly, general managerial functions within that process are described. Fourthly, those functions are precised by relating them to typical hierarchical levels. Fifthly, peculiar managerial functions within negotiating team are discussed. Finally, specific issue of the role of manager as a mediator is addressed. Summing up the paper, the crucial areas for subsequent research were pointed out. In order to elaborate the presented concept the author carried out the comparative study of negotiation literature as well as developed his original ideas.

Functional features of travel magazines: retrospective view

Directory of Open Access Journals (Sweden)

Gromova Lyudmila Petrovna

2015-09-01

Full Text Available The article considers the features of the functional purpose of travel magazines (travelogue, their genesis, evolution, traits, depending on the socio-political context and, accordingly, requests from the readership. The progenitor of the travel magazines in Russia was journey literature that took root in the genre of travel notes. The forerunner of today’s travelogues can be considered «Nikita Akinfievich Demidov’s travel magazine» (1786, presenting daily travel notes, mostly laconic, sometimes deployed to fascinating travel notes Magazines at different times performed cultural and educational, didactic, aesthetic and ideological functions, immersing the reader in the living conditions of the countries and continents, showing the diversity of the world. Today, traveling is seen as a multifaceted activity that is due to the result of freedom of movement, numerous hiking trails, access to information in the network space takes new character. Accordingly, the media market is a process of qualitative and quantitative changes. There is a growing number of distribution channels, many of which are convergent evolution. The transformation of the old forms is determined by market demand. These processes are inevitably reflected in the dominance of certain functions of the travelogue. However, their essential purpose remains the same: to inform, educate and entertain.

Pedagogical Interaction in High School, the Structural and Functional Model of Pedagogical Interaction

Science.gov (United States)

Semenova, Larissa A.; Kazantseva, Anastassiya I.; Sergeyeva, Valeriya V.; Raklova, Yekaterina M.; Baiseitova, Zhanar B.

2016-01-01

The study covers the problems of pedagogical technologies and their experimental implementation in the learning process. The theoretical aspects of the "student-teacher" interaction are investigated. A structural and functional model of pedagogical interaction is offered, which determines the conditions for improving pedagogical…

GeoQuest an Interactive Role Playing game

Science.gov (United States)

Maraffi, Sabina; Sacerdoti, Francesco; Scamardella, Alessandra

2015-04-01

The acquisition of knowledge and enhancing skills at actual time requires different approaches, involving students as much as possible, taking advantage of informal learning strengths and opportunities of formal learning. In this perspective, the game seems to be a perfect vehicle, not a single student's playing but a cooperative one. The GeoQuest project consists of an interactive role-playing game which involves all students using a patented system: the "teaching projector". This system allows the interaction of the class group through the use of smartphones and tablets, and it shows in real-time the game progress to the whole class. Our role-playing game is based on three routes at different degrees. The students, divided into several categories (physicist, chemists, disseminators, technicians, historians) have to follow a geological trail in order to discover the present and the past of the Earth. During the path, students have to pass some doors in teamwork; they allow assessment and represent the main sharing/disclosure moment. The doors allow to modulate the activities according to single lesson, teaching unit, module. Main Objectives: Working on PC by themselves, students could be even more alone: it needs a best fitting between ICT and cooperative learning. Role-playing helps students to reach their goals easily through cooperation; this in order to avoid the risk of loneliness of Inquiry Based Science Education, preserving entirely the educational value. Science Research now is based on field expert interaction: the role-playing game categories reflect the necessary team to get their goal. The several roles allow everyone to enhance their own skills. the "teaching projector" allows students to comment and to evaluate the groups activities and route them, providing real-time corrections to everybody. The playing categories represent all the aspects of the research areas: from scientists (physicists, chemists), to technicians, to disseminators and

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency.

Science.gov (United States)

Chen, Yuhan; Wang, Shengjun; Hilgetag, Claus C; Zhou, Changsong

2017-09-01

The primate connectome, possessing a characteristic global topology and specific regional connectivity profiles, is well organized to support both segregated and integrated brain function. However, the organization mechanisms shaping the characteristic connectivity and its relationship to functional requirements remain unclear. The primate brain connectome is shaped by metabolic economy as well as functional values. Here, we explored the influence of two competing factors and additional advanced functional requirements on the primate connectome employing an optimal trade-off model between neural wiring cost and the representative functional requirement of processing efficiency. Moreover, we compared this model with a generative model combining spatial distance and topological similarity, with the objective of statistically reproducing multiple topological features of the network. The primate connectome indeed displays a cost-efficiency trade-off and that up to 67% of the connections were recovered by optimal combination of the two basic factors of wiring economy and processing efficiency, clearly higher than the proportion of connections (56%) explained by the generative model. While not explicitly aimed for, the trade-off model captured several key topological features of the real connectome as the generative model, yet better explained the connectivity of most regions. The majority of the remaining 33% of connections unexplained by the best trade-off model were long-distance links, which are concentrated on few cortical areas, termed long-distance connectors (LDCs). The LDCs are mainly non-hubs, but form a densely connected group overlapping on spatially segregated functional modalities. LDCs are crucial for both functional segregation and integration across different scales. These organization features revealed by the optimization analysis provide evidence that the demands of advanced functional segregation and integration among spatially distributed regions may

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier

KAUST Repository

Kulmanov, Maxat

2017-09-27

Motivation A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often only done rigorously for few selected model organisms. Computational function prediction approaches have been suggested to fill this gap. The functions of proteins are classified using the Gene Ontology (GO), which contains over 40 000 classes. Additionally, proteins have multiple functions, making function prediction a large-scale, multi-class, multi-label problem. Results We have developed a novel method to predict protein function from sequence. We use deep learning to learn features from protein sequences as well as a cross-species protein–protein interaction network. Our approach specifically outputs information in the structure of the GO and utilizes the dependencies between GO classes as background information to construct a deep learning model. We evaluate our method using the standards established by the Computational Assessment of Function Annotation (CAFA) and demonstrate a significant improvement over baseline methods such as BLAST, in particular for predicting cellular locations.

Indicators of causal agency in physical interactions: the role of the prior context.

Science.gov (United States)

Mayrhofer, Ralf; Waldmann, Michael R

2014-09-01

The question how agent and patient roles are assigned to causal participants has largely been neglected in the psychological literature on force dynamics. Inspired by the linguistic theory of Dowty (1991), we propose that agency attributions are based on a prototype concept of human intervention. We predicted that the number of criteria a participant in a causal interaction shares with this prototype determines the strength of agency intuitions. We showed in two experiments using versions of Michotte's (1963) launching scenarios that agency intuitions were moderated by manipulations of the context prior to the launching event. Altering features, such as relative movement, sequence of visibility, and self-propelled motion, tended to increase agency attributions to the participant that is normally viewed as patient in the standard scenario. Copyright © 2014 Elsevier B.V. All rights reserved.

Image features dependant correlation-weighting function for efficient PRNU based source camera identification.

Science.gov (United States)

Tiwari, Mayank; Gupta, Bhupendra

2018-04-01

For source camera identification (SCI), photo response non-uniformity (PRNU) has been widely used as the fingerprint of the camera. The PRNU is extracted from the image by applying a de-noising filter then taking the difference between the original image and the de-noised image. However, it is observed that intensity-based features and high-frequency details (edges and texture) of the image, effect quality of the extracted PRNU. This effects correlation calculation and creates problems in SCI. For solving this problem, we propose a weighting function based on image features. We have experimentally identified image features (intensity and high-frequency contents) effect on the estimated PRNU, and then develop a weighting function which gives higher weights to image regions which give reliable PRNU and at the same point it gives comparatively less weights to the image regions which do not give reliable PRNU. Experimental results show that the proposed weighting function is able to improve the accuracy of SCI up to a great extent. Copyright © 2018 Elsevier B.V. All rights reserved.

A fuzzy method for improving the functionality of search engines based on user's web interactions

Directory of Open Access Journals (Sweden)

Farzaneh Kabirbeyk

2015-04-01

Full Text Available Web mining has been widely used to discover knowledge from various sources in the web. One of the important tools in web mining is mining of web user’s behavior that is considered as a way to discover the potential knowledge of web user’s interaction. Nowadays, Website personalization is regarded as a popular phenomenon among web users and it plays an important role in facilitating user access and provides information of users’ requirements based on their own interests. Extracting important features about web user behavior plays a significant role in web usage mining. Such features are page visit frequency in each session, visit duration, and dates of visiting a certain pages. This paper presents a method to predict user’s interest and to propose a list of pages based on their interests by identifying user’s behavior based on fuzzy techniques called fuzzy clustering method. Due to the user’s different interests and use of one or more interest at a time, user’s interest may belong to several clusters and fuzzy clustering provide a possible overlap. Using the resulted cluster helps extract fuzzy rules. This helps detecting user’s movement pattern and using neural network a list of suggested pages to the users is provided.

Syndecans as cell surface receptors: Unique structure equates with functional diversity

DEFF Research Database (Denmark)

Choi, Youngsil; Chung, Heesung; Jung, Heyjung

2011-01-01

An increasing number of functions for syndecan cell surface heparan sulfate proteoglycans have been proposed over the last decade. Moreover, aberrant syndecan regulation has been found to play a critical role in multiple pathologies, including cancers, as well as wound healing and inflammation....... As receptors, they have much in common with other molecules on the cell surface. Syndecans are type I transmembrane molecules with cytoplasmic domains that link to the actin cytoskeleton and can interact with a number of regulators. However, they are also highly complex by virtue of their external...... glycosaminoglycan chains, especially heparan sulfate. This heterodisperse polysaccharide has the potential to interact with many ligands from diverse protein families. Here, we relate the structural features of syndecans to some of their known functions....

The physical and functional interaction of NDRG2 with MSP58 in cells

International Nuclear Information System (INIS)

Zhang Jing; Liu Junye; Li Xia; Li Fuyang; Wang Lifeng; Zhang Jian; Liu Xinping; Shen Lan; Liu Na; Deng Yanchun; Yang Angang; Han Hua; Zhao Mujun; Yao Libo

2007-01-01

NDRG2, a member of N-Myc downstream regulated gene family, exerts the important functions in cell differentiation and tumor suppression. Although the ectopic expressed Ndrg2 inhibits the proliferation of tumor cells, its intracellular signal transduction pathway is hardly known. Here, we identified MSP58, a 58-kDa microspherule protein, as an interacting partner of human Ndrg2 by using yeast two-hybrid screening. The interaction was confirmed by glutathione S-transferase pull-down assay in vitro and by co-immune-precipitation assay in vivo. The forkhead associated domain of MSP58 is essential for its interaction with Ndrg2. Ndrg2 could co-localize with MSP58 in nuclear of HeLa cell during cell stress. Furthermore, the modulation of Ndrg2 level influences the cell cycle process together with MSP58. In conclusion, the findings offered a novel insight into the physiological roles of Ndrg2

Functional roles for Rad9 in prostate cancer

International Nuclear Information System (INIS)

Lieberman, H.B.; Broustas, C.G.

2012-01-01

The goal of this work is to understand the mechanistic relationship between high levels of Rad9 protein and prostate cancer. The study is based on several findings suggesting a role for Rad9 in this disease. Rad9 has all the hallmark features of an oncogene or tumor suppressor. It regulates genomic stability, multiple cell cycle checkpoints, apoptosis and DNA repair. In addition, it can transactivate downstream target genes via direct interaction with promoter DNA sequences. We found Rad9 protein levels were very high in prostate cancer cell lines. Furthermore, we examined 52 primary normal prostate and 339 prostate cancer specimens for Rad9 protein by immunohistochemical staining. Statistical significance for Rad9 positive staining versus cancer, and stain intensity versus Stage were tested. We get a p-value of <0.001 when comparing percentage positive by cancer Stage, or stain intensity by cancer Stage. Based on these data, we sought to define the nature of the relationship between Rad9 and prostate cancer. We demonstrate that Rad9 acts as an oncogene in prostate cancer by playing a critical role in tumor formation in a mouse xenograph model. We also show that Rad9 is important for cellular phenotypes essential for metastasis, including tumor cell migration, invasion and resistance to programmed cell death after detachment from extracellular matrix. Therefore, Rad9 is critical for several aspects of prostate tumor progression, and could serve as a novel target for anti-cancer therapy

Using tactile features to help functionally blind individuals denominate banknotes.

Science.gov (United States)

Lederman, Susan J; Hamilton, Cheryl

2002-01-01

This study, which was conducted for the Bank of Canada, assessed the feasibility of presenting a raised texture feature together with a tactile denomination code on the next Canadian banknote series ($5, $10, $20, $50, and $100). Adding information accessible by hand would permit functionally blind individuals to independently denominate banknotes. In Experiment 1, 20 blindfolded, sighted university students denominated a set of 8 alternate tactile feature designs. Across the 8 design series, the proportion of correct responses never fell below .97; the mean response time per banknote ranged from 11.4 to 13.1 s. In Experiment 2, 27 functionally blind participants denominated 4 of the previous 8 candidate sets of banknotes. The proportion of correct responses never fell below .92; the corresponding mean response time per banknote ranged from 11.7 to 13.0 s. The Bank of Canada selected one of the four raised-texture designs for inclusion on its new banknote series. Other potential applications include designing haptic displays for teleoperation and virtual environment systems.

Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: unique roles for Hda AAA Box VI and VII motifs.

Science.gov (United States)

Nakamura, Kenta; Katayama, Tsutomu

2010-04-01

Escherichia coli ATP-DnaA initiates chromosomal replication. For preventing extra-initiations, a complex of ADP-Hda and the DNA-loaded replicase clamp promotes DnaA-ATP hydrolysis, yielding inactive ADP-DnaA. However, the Hda-DnaA interaction mode remains unclear except that the Hda Box VII Arg finger (Arg-153) and DnaA sensor II Arg-334 within each AAA(+) domain are crucial for the DnaA-ATP hydrolysis. Here, we demonstrate that direct and functional interaction of ADP-Hda with DnaA requires the Hda residues Ser-152, Phe-118 and Asn-122 as well as Hda Arg-153 and DnaA Arg-334. Structural analyses suggest intermolecular interactions between Hda Ser-152 and DnaA Arg-334 and between Hda Phe-118 and the DnaA Walker B motif region, in addition to an intramolecular interaction between Hda Asn-122 and Arg-153. These interactions likely sustain a specific association of ADP-Hda and DnaA, promoting DnaA-ATP hydrolysis. Consistently, ATP-DnaA and ADP-DnaA interact with the ADP-Hda-DNA-clamp complex with similar affinities. Hda Phe-118 and Asn-122 are contained in the Box VI region, and their hydrophobic and electrostatic features are basically conserved in the corresponding residues of other AAA(+) proteins, suggesting a conserved role for Box VI. These findings indicate novel interaction mechanisms for Hda-DnaA as well as a potentially fundamental mechanism in AAA(+) protein interactions.

Biological adaptations for functional features of language in the face of cultural evolution.

Science.gov (United States)

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

Interacting with women can impair men's cognitive functioning

NARCIS (Netherlands)

Karremans, J.C.T.M.; Verwijmeren, T.; Pronk, T.M.; Reitsma, M.

2009-01-01

The present research tested the prediction that mixed-sex interactions may temporarily impair cognitive functioning. Two studies, in which participants interacted either with a same-sex or opposite-sex other, demonstrated that men's (but not women's) cognitive performance declined following a

ESL students learning biology: The role of language and social interactions

Science.gov (United States)

Jaipal, Kamini

This study explored three aspects related to ESL students in a mainstream grade 11 biology classroom: (1) the nature of students' participation in classroom activities, (2) the factors that enhanced or constrained ESL students' engagement in social interactions, and (3) the role of language in the learning of science. Ten ESL students were observed over an eight-month period in this biology classroom. Data were collected using qualitative research methods such as participant observation, audio-recordings of lessons, field notes, semi-structured interviews, short lesson recall interviews and students' written work. The study was framed within sociocultural perspectives, particularly the social constructivist perspectives of Vygotsky (1962, 1978) and Wertsch (1991). Data were analysed with respect to the three research aspects. Firstly, the findings showed that ESL students' preferred and exhibited a variety of participation practices that ranged from personal-individual to socio-interactive in nature. Both personal-individual and socio-interactive practices appeared to support science and language learning. Secondly, the findings indicated that ESL students' engagement in classroom social interactions was most likely influenced by the complex interactions between a number of competing factors at the individual, interpersonal and community/cultural levels (Rogoff, Radziszewska, & Masiello, 1995). In this study, six factors that appeared to enhance or constrain ESL students' engagement in classroom social interactions were identified. These factors were socio-cultural factors, prior classroom practice, teaching practices, affective factors, English language proficiency, and participation in the research project. Thirdly, the findings indicated that language played a significant mediational role in ESL students' learning of science. The data revealed that the learning of science terms and concepts can be explained by a functional model of language that includes: (1

Interactive definition of transfer functions in volume rendering based on image markers

International Nuclear Information System (INIS)

Teistler, Michael; Nowinski, Wieslaw L.; Breiman, Richard S.; Liong, Sauw Ming; Ho, Liang Yoong; Shahab, Atif

2007-01-01

Objectives A user interface for transfer function (TF) definition in volume rendering (VR) was developed that allows the user to intuitively assign color and opacity to the original image intensities. This software may surpass solutions currently deployed in clinical practice by simplifying the use of TFs beyond predefined settings that are not always applicable. Materials and methods The TF definition is usually a cumbersome task that requires the user to manipulate graphical representations of the TF (e.g. trapezoids). A new method that allows the user to place markers at points of interest directly on CT and MRI images or orthogonal reformations was developed based on two-dimensional region growing and a few user-definable marker-related parameters. For each user defined image marker, a segment of the transfer function is computed. The resulting TF can also be applied to the slice image views. Results were judged subjectively. Results Each individualized TF can be defined interactively in a few simple steps. For every user interaction, immediate visual feedback is given. Clinicians who tested the application appreciated being able to directly work on familiar slice images to generate the desired 3D views. Conclusion Interactive TF definition can increase the actual utility of VR, help to understand the role of the TF with its variations, and increase the acceptance of VR as a clinical tool. (orig.)

In or Out of the Pumpkin Shell? Sex Role Differentiation in Classroom Interaction.

Science.gov (United States)

Cooper, Pamela J.

A review of research on sex role differentiation in classroom interaction reveals that women are marginalized from education by its content and by the classroom interactional processes. Sex-role stereotyping exists in curriculum materials at all educational levels, with textbooks more likely to portray boys in active roles and girls in passive…

Role of theory of mind and executive function in explaining social intelligence: a structural equation modeling approach.

Science.gov (United States)

Yeh, Zai-Ting

2013-01-01

Social intelligence is the ability to understand others and the social context effectively and thus to interact with people successfully. Research has suggested that the theory of mind (ToM) and executive function may play important roles in explaining social intelligence. The specific aim of the present study was to test with structural equation modeling (SEM) the hypothesis that performance on ToM tasks is more associated with social intelligence in the elderly than is performance on executive functions. One hundred and seventy-seven participants (age 56-96) completed ToM, executive function, and other basic cognition tasks, and were rated with social intelligence scales. The SEM results showed that ToM and executive function were strongly correlated (0.54); however, only the path coefficient from ToM to social intelligence, and not from executive function, was significant (0.37). ToM performance, but not executive function, was strongly correlated with social intelligence among elderly individuals. ToM and executive function might play different roles in social behavior during normal aging; however, based on the present results, it is possible that ToM might play an important role in social intelligence.

The molecular understanding of interfacial interactions of functionalized graphene and chitosan

International Nuclear Information System (INIS)

Zhang, Hong-ping; Luo, Xue-gang; Lin, Xiao-yan; Lu, Xiong; Tang, Youhong

2016-01-01

Graphical abstract: The type of the functional groups can be used to modulating interactions between graphene sheet and chitosan. - Highlights: • Investigate interfacial interactions between chitosan and functionalized graphene by DFT. • Observe covalent linkages between COOH-modified graphene and chitosan units. • Multi-functionalized graphene regulates the interfacial interactions with chitosan. • It is useful for guiding the preparation of graphene/chitosan composites. - Abstract: Graphene-reinforced chitosan scaffolds have been extensively studied for several years as promising hard tissue replacements. However, the interfacial interactions between graphene and chitosan are strongly related to the solubility, processability, and mechanical properties of graphene-reinforced chitosan (G–C) composites. The functionalization of graphene is regarded as the most effective way to improve the abovementioned properties of the G–C composite. In this study, the interfacial interactions between chitosan and functionalized graphene sheets with carboxylization (COOH-), amination (NH 2 -), and hydroxylation (OH-) groups were systematically studied at the electronic level using the method of ab initio simulations based on quantum mechanics theory and the observations were compared with reported experimental results. The covalent linkages between COOH-modified graphene and the chitosan units were demonstrated and the combination of multi-functionalization on graphene could regulate the interfacial interactions between graphene and the chitosan. The interfacial interactions between chitosan and properly functionalized graphene are critical for the preparation of G–C-based composites for tissue engineering scaffolds and other applications.

Lateral hypothalamus, nucleus accumbens, and ventral pallidum roles in eating and hunger: interactions between homeostatic and reward circuitry

Directory of Open Access Journals (Sweden)

Daniel Charles Castro

2015-06-01

Full Text Available The study of the neural bases of eating behavior, hunger, and reward has consistently implicated the lateral hypothalamus (LH and its interactions with mesocorticolimbic circuitry, such as mesolimbic dopamine projections to nucleus accumbens (NAc and ventral pallidum (VP, in controlling motivation to eat. The NAc and VP play special roles in mediating the hedonic impact (‘liking’ and motivational incentive salience (‘wanting’ of food rewards, and their interactions with LH help permit regulatory hunger/satiety modulation of food motivation and reward. Here, we review some progress that has been made regarding this circuitry and its functions: the identification of localized anatomical hedonic hotspots within NAc and VP for enhancing hedonic impact; interactions of NAc/VP hedonic hotspots with specific LH signals such as orexin; an anterior-posterior gradient of sites in NAc shell for producing intense appetitive eating versus intense fearful reactions; and anatomically distributed appetitive functions of dopamine and mu opioid signals in NAc shell and related structures. Such findings help improve our understanding of NAc, VP, and LH interactions in mediating affective and motivation functions, including ‘liking’ and ‘wanting’ for food rewards.

Eco-nomics: Are the Planet-Unfriendly Features of Capitalism Barriers to Sustainability?

Directory of Open Access Journals (Sweden)

Merrill Singer

2010-01-01

Full Text Available This paper argues that there are essential features of capitalist modes of production, consumption, and waste dispersal in interaction with the environment and its built-in systemic features that contradict long-term sustainable development. These features include: (a contradictions in the origin and meaning of sustainability; (b the central role of the productivity ethic in capitalism and its reproduction in emergent green capitalism; (c the commodification of nature and the continued promotion of expanding consumption; (d globalism and the contradictions of continued Western-style development; and (e the emergence of anthropogenic ecocrises and crises interaction. In light of these barriers to capitalist sustainability, an alternative social narrative is needed, one that embraces values, understandings, and relationships that promote ecological stability and justice.

Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains

Directory of Open Access Journals (Sweden)

Branislava Gemovic

2013-01-01

Full Text Available There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM, a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.

Science.gov (United States)

Funk, Christopher S; Kahanda, Indika; Ben-Hur, Asa; Verspoor, Karin M

2015-01-01

Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In this work we evaluate both ontology term co-mention and bag-of-words features mined from the biomedical literature and analyze their impact in the context of a structured output support vector machine model, GOstruct. We find that even simple literature based features are useful for predicting human protein function (F-max: Molecular Function =0.408, Biological Process =0.461, Cellular Component =0.608). One advantage of using literature features is their ability to offer easy verification of automated predictions. We find through manual inspection of misclassifications that some false positive predictions could be biologically valid predictions based upon support extracted from the literature. Additionally, we present a "medium-throughput" pipeline that was used to annotate a large subset of co-mentions; we suggest that this strategy could help to speed up the rate at which proteins are curated.

Interaction between organophosphate pesticide exposure and PON1 activity on thyroid function

International Nuclear Information System (INIS)

Lacasana, Marina; Lopez-Flores, Inmaculada; Rodriguez-Barranco, Miguel; Aguilar-Garduno, Clemente; Blanco-Munoz, Julia; Perez-Mendez, Oscar; Gamboa, Ricardo; Gonzalez-Alzaga, Beatriz; Bassol, Susana; Cebrian, Mariano E.

2010-01-01

Organophosphate pesticides are widely used in agricultural purposes. Recently, a few studies have demonstrated the ability of these chemicals to alter the function of the thyroid gland in human. Moreover, the paraoxonase-1 enzyme (PON1) plays an important role in the toxicity of some organophosphate pesticides, with low PON1 activity being associated with higher pesticide sensitivity. This study evaluates the interaction between exposure to organophosphate compounds and PON1 enzyme activity on serum levels of TSH and thyroid hormones in a population of workers occupationally exposed to pesticides. A longitudinal study was conducted on a population of floriculture workers from Mexico, during two periods of high and low-intensity levels of pesticide application. A structured questionnaire was completed by workers containing questions on sociodemographic characteristics and other variables of interest. Urine and blood samples were taken, and biomarkers of exposure (dialkylphosphates), susceptibility (PON1 polymorphisms and activity) and effect (thyroid hormone levels) were determined. Interaction between dialkylphosphates and PON1 polymorphisms or PON1 activity on hormone levels was evaluated by generalized estimating equation (GEE) models. A significant interaction was found between serum diazoxonase activity and total dialkylphosphates (ΣDAP) on TSH levels. Thus, when PON1 activity was increased we observed a decrease in the percentage of variation of TSH level for each increment in one logarithmic unit of the ΣDAP levels. This interaction was also observed with the PON1 192 RR genotype. These results suggest a stronger association between organophosphate pesticides and thyroid function in individuals with lower PON1 activity.

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…

Density-functional theory in one dimension for contact-interacting fermions

International Nuclear Information System (INIS)

Magyar, R.J.; Burke, K.

2004-01-01

A density-functional theory is developed for fermions in one dimension, interacting via a δ function. Such systems provide a natural testing ground for questions of principle, as the local-density approximation should be highly accurate since for this interaction type the exchange contribution to the local-density approximation is intrinsically self-interaction-free. The exact-exchange contribution to the total energy is a local functional of the density. A local-density approximation for correlation is obtained using perturbation theory and Bethe ansatz results for the one-dimensional contact-interacting uniform Fermi gas. The ground-state energies are calculated for two finite systems, the analogs of helium and of Hooke's atom. The local-density approximation is shown to be excellent as expected

A global genetic interaction network maps a wiring diagram of cellular function.

Science.gov (United States)

Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D; Pelechano, Vicent; Styles, Erin B; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F; Li, Sheena C; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; San Luis, Bryan-Joseph; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M; Moore, Claire L; Rosebrock, Adam P; Caudy, Amy A; Myers, Chad L; Andrews, Brenda; Boone, Charles

2016-09-23

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell. Copyright © 2016, American Association for the Advancement of Science.

Role of medial cortical, hippocampal and striatal interactions during cognitive set-shifting.

Science.gov (United States)

Graham, Steven; Phua, Elaine; Soon, Chun Siong; Oh, Tomasina; Au, Chris; Shuter, Borys; Wang, Shih-Chang; Yeh, Ing Berne

2009-05-01

To date, few studies have examined the functional connectivity of brain regions involved in complex executive function tasks, such as cognitive set-shifting. In this study, eighteen healthy volunteers performed a cognitive set-shifting task modified from the Wisconsin card sort test while undergoing functional magnetic resonance imaging. These modifications allowed better disambiguation between cognitive processes and revealed several novel findings: 1) peak activation in the caudate nuclei in the first instance of negative feedback signaling a shift in rule, 2) lowest caudate activation once the rule had been identified, 3) peak hippocampal activation once the identity of the rule had been established, and 4) decreased hippocampal activation during the generation of new rule candidates. This pattern of activation across cognitive set-shifting events suggests that the caudate nuclei play a role in response generation when the identity of the new rule is unknown. In contrast, the reciprocal pattern of hippocampal activation suggests that the hippocampi help consolidate knowledge about the correct stimulus-stimulus associations, associations that become inappropriate once the rule has changed. Functional connectivity analysis using Granger Causality Mapping revealed that caudate and hippocampal regions interacted indirectly via a circuit involving the medial orbitofrontal and posterior cingulate regions, which are known to bias attention towards stimuli based on expectations built up from task-related feedback. Taken together, the evidence suggests that these medial regions may mediate striato-hippocampal interactions and hence affect goal-directed attentional transitions from a response strategy based on stimulus-reward heuristics (caudate-dependent) to one based on stimulus-stimulus associations (hippocampus-dependent).

Response functions for infinite fermion systems with velocity dependent interactions

International Nuclear Information System (INIS)

Garcia-Recio, C.; Salcedo, L.L.; Navarro, J.; Nguyen Van Giai

1991-01-01

Response functions of infinite Fermi systems are studied in the framework of the self-consistent Random Phase Approximation. Starting from an effective interaction with velocity and density dependence, or equivalently from a local energy density functional, algebraic expressions for the RPA response function are derived. Simple formulae for the energy-weighted and polarizability sum rules are obtained. The method is illustrated by applications to nuclear matter and liquid 3 He. In nuclear matter, it is shown that existing Skyrme interactions give spin-isospin response functions close to those calculated with finite range interactions. The different renormalization of longitudinal and transverse Coulomb sum rules in nuclear matter is discussed. In 3 He, the low-lying collective spin oscillation can be well described in a wide range of momenta with a Skyrme-type interaction if the relevant Landau parameters are fitted. For the high-lying density oscillation, the introduction of a finite range term in the energy functional improves considerably the agreement with the data. (author) 54 refs., 19 figs., 4 tabs

Candida albicans Agglutinin-Like Sequence (Als) Family Vignettes: A Review of Als Protein Structure and Function

Science.gov (United States)

Hoyer, Lois L.; Cota, Ernesto

2016-01-01

Approximately two decades have passed since the description of the first gene in the Candida albicans ALS (agglutinin-like sequence) family. Since that time, much has been learned about the composition of the family and the function of its encoded cell-surface glycoproteins. Solution of the structure of the Als adhesive domain provides the opportunity to evaluate the molecular basis for protein function. This review article is formatted as a series of fundamental questions and explores the diversity of the Als proteins, as well as their role in ligand binding, aggregative effects, and attachment to abiotic surfaces. Interaction of Als proteins with each other, their functional equivalence, and the effects of protein abundance on phenotypic conclusions are also examined. Structural features of Als proteins that may facilitate invasive function are considered. Conclusions that are firmly supported by the literature are presented while highlighting areas that require additional investigation to reveal basic features of the Als proteins, their relatedness to each other, and their roles in C. albicans biology. PMID:27014205

Plant functional diversity affects climate-vegetation interaction

Science.gov (United States)

Groner, Vivienne P.; Raddatz, Thomas; Reick, Christian H.; Claussen, Martin

2018-04-01

We present how variations in plant functional diversity affect climate-vegetation interaction towards the end of the African Humid Period (AHP) in coupled land-atmosphere simulations using the Max Planck Institute Earth system model (MPI-ESM). In experiments with AHP boundary conditions, the extent of the green Sahara varies considerably with changes in plant functional diversity. Differences in vegetation cover extent and plant functional type (PFT) composition translate into significantly different land surface parameters, water cycling, and surface energy budgets. These changes have not only regional consequences but considerably alter large-scale atmospheric circulation patterns and the position of the tropical rain belt. Towards the end of the AHP, simulations with the standard PFT set in MPI-ESM depict a gradual decrease of precipitation and vegetation cover over time, while simulations with modified PFT composition show either a sharp decline of both variables or an even slower retreat. Thus, not the quantitative but the qualitative PFT composition determines climate-vegetation interaction and the climate-vegetation system response to external forcing. The sensitivity of simulated system states to changes in PFT composition raises the question how realistically Earth system models can actually represent climate-vegetation interaction, considering the poor representation of plant diversity in the current generation of land surface models.

The operator's role and safety functions

International Nuclear Information System (INIS)

Corcoran, W.R.; Finnicum, D.J.; Hubbard, F.R.; Musick, C.R.; Walzer, R.F.

1980-01-01

A nuclear power plant can be thought of as a single system with two major subsystems: equipment and people. Both play important roles in nuclear safety. Whereas, in the past, the role of equipment had been emphasized in nuclear safety, the accident at Three Mile Island and its subsequent investigations point out the vital role of the operator. This paper outlines the operator's roles in nuclear safety and suggests how the concept of safety functions can be used to reduce economic losses and increase safety margins. (auth)

The Role of Couples’ Interactions in Application of Communication Skills

Directory of Open Access Journals (Sweden)

منصوره‌السادات صادقی

2014-02-01

Full Text Available The aim of this research was to predict the role of couples’ interactions in application of communication skills based on observing their positive and negative interactions. A sample of 31 couples [adapted (15 and maladapted (16] who were living in Tehran, were selected via accessible sampling. The couples’ interactions were videotaped through a designed scenario including problem solving, decision making, and reviewing conversation about a shared pleasure event. Participants also completed the Marital Adjustment Test (MAT. The couple’s interactions were coded using the Iranian Couples Interaction Coding System (ICICS. Results revealed that the more increase in positive interactions between couples, the more use of “problem solving” and “negotiation” skills observed, whereas increase in the couples’ negative interactions was associated with less application of this skills. It was also revealed that while the couples’ negative interactions were significantly predictive of using the “decision making” skill, couples with more positive interactions were located in the group who was able to have a review conversation about a shared positive event. In addition, results indicated that couples who were more able to apply problem solving, negotiation, decision making and review conversation about a shared event skills, had also higher scores on marital adjustment. Destructive role of the couples’ negative interactions and intensifying the negative emotions between them has been discussed, as if it seems that couples are not willing to help each other for resolving conflicts. As interactions getting more negative, by creating a negative filtering, memory becomes biased towards negative events at the expense of shared positive events.

Cognitive control and motivation in children with ADHD: How reinforcement interacts with the assessment and training of executive functioning

NARCIS (Netherlands)

Dovis, S.

2014-01-01

This dissertation focuses on the interaction between two neuropsychological processes that are proposed to play a pivotal role in explaining the problems of children with ADHD: executive functioning (EF) and motivation. We examined the effects of reinforcement on assessment and training of EF in

Physical, metabolic and developmental functions of the seed coat

Science.gov (United States)

Radchuk, Volodymyr; Borisjuk, Ljudmilla

2014-01-01

The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction. PMID:25346737

Interactions of Kraft lignin and wheat gluten during biomaterial processing: evidence for the role of phenolic groups.

Science.gov (United States)

Kaewtatip, Kaewta; Menut, Paul; Auvergne, Remi; Tanrattanakul, Varaporn; Morel, Marie-Helene; Guilbert, Stephane

2010-04-14

The chemical interactions between Kraft lignin and wheat gluten under processing conditions were investigated by determining the extent of the protein network formation. To clarify the role of different chemical functions found in lignin, the effect of Kraft lignin was compared with that of an esterified lignin, in which hydroxyl groups had been suppressed by esterification, and with a series of simple aromatics and phenolic structures with different functionalities (conjugated double bonds, hydroxyl, carboxylic acid, and aldehyde). The protein solubility was determined by using the Kjeldahl method. The role of the hydroxyl function was assessed by the significantly lower effect of esterified lignin. The importance of the phenolic radical scavenging structure is evidenced by the effect of guaiacol, which results in a behavior similar to that of the Kraft lignin. In addition, the significant effect of conjugated double bonds on gluten reactivity, through nucleophilic addition, was demonstrated.

Local Area Network Material Accounting System (LANMAS) Functions and Features Overview

International Nuclear Information System (INIS)

Robichaux, J.J.

1998-07-01

The Local Area Network Material Accounting System (LANMAS) application is a standardized approach to comply with the DOE Order 5633.3B, control and Accountability of Nuclear Material, material accounting requirements. This paper provides a general overview of the functions and features included in the LANMAS application

Deep Visual Attributes vs. Hand-Crafted Audio Features on Multidomain Speech Emotion Recognition

Directory of Open Access Journals (Sweden)

Michalis Papakostas

2017-06-01

Full Text Available Emotion recognition from speech may play a crucial role in many applications related to human–computer interaction or understanding the affective state of users in certain tasks, where other modalities such as video or physiological parameters are unavailable. In general, a human’s emotions may be recognized using several modalities such as analyzing facial expressions, speech, physiological parameters (e.g., electroencephalograms, electrocardiograms etc. However, measuring of these modalities may be difficult, obtrusive or require expensive hardware. In that context, speech may be the best alternative modality in many practical applications. In this work we present an approach that uses a Convolutional Neural Network (CNN functioning as a visual feature extractor and trained using raw speech information. In contrast to traditional machine learning approaches, CNNs are responsible for identifying the important features of the input thus, making the need of hand-crafted feature engineering optional in many tasks. In this paper no extra features are required other than the spectrogram representations and hand-crafted features were only extracted for validation purposes of our method. Moreover, it does not require any linguistic model and is not specific to any particular language. We compare the proposed approach using cross-language datasets and demonstrate that it is able to provide superior results vs. traditional ones that use hand-crafted features.

Stress assessment based on EEG univariate features and functional connectivity measures.

Science.gov (United States)

Alonso, J F; Romero, S; Ballester, M R; Antonijoan, R M; Mañanas, M A

2015-07-01

The biological response to stress originates in the brain but involves different biochemical and physiological effects. Many common clinical methods to assess stress are based on the presence of specific hormones and on features extracted from different signals, including electrocardiogram, blood pressure, skin temperature, or galvanic skin response. The aim of this paper was to assess stress using EEG-based variables obtained from univariate analysis and functional connectivity evaluation. Two different stressors, the Stroop test and sleep deprivation, were applied to 30 volunteers to find common EEG patterns related to stress effects. Results showed a decrease of the high alpha power (11 to 12 Hz), an increase in the high beta band (23 to 36 Hz, considered a busy brain indicator), and a decrease in the approximate entropy. Moreover, connectivity showed that the high beta coherence and the interhemispheric nonlinear couplings, measured by the cross mutual information function, increased significantly for both stressors, suggesting that useful stress indexes may be obtained from EEG-based features.

Specific Features of Functioning of the Corporate Tax Management

Directory of Open Access Journals (Sweden)

Tkachyk Lesya P.

2013-12-01

Full Text Available The article identifies and reveals the essence of functional elements of corporate tax management, which are tax planning, tax analysis, tax accounting and reporting, tax control and tax monitoring. The article builds a functional model of corporate tax management that reflects interaction of its functional elements in the process of realisation of tax activity of economic subjects. Pursuant to this model, the corporate tax management is conducted in several stages, namely: development of alternative variants of tax activity, analysis of alternative variants of tax activity, selection of the optimal variant of tax activity, realisation of tax activity, control over realisation of tax activity and development of measures of increase of efficiency of tax management. Application of the functional model of corporate tax management, which envisages use of all instruments, allows optimisation of tax payments of economic subjects.

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Profiles of Teacher-Child Interaction Quality in Preschool Classrooms and Teachers' Professional Competence Features

Science.gov (United States)

Hu, Bi Ying; Chen, Liang; Fan, Xitao

2018-01-01

This paper investigates early childhood education (ECE) teachers' self-reported and observed teacher-child interaction quality (TIQ) and the associated teachers' professional competence features using a latent profile analysis (LPA) approach to identify the variations in the quality of classroom experiences in Chinese preschools. A total of 164…

Introduction to the feature section on functional imaging of the pelvic floor.

Science.gov (United States)

Maccioni, Francesca

2013-10-01

This is the introduction to the feature section of functional imaging of the pelvic floor, which includes 6 articles, two focused on clinical issues, while four on radiological aspects, mostly on dynamic pelvic floor MRI.

Multiscale wavelet representations for mammographic feature analysis

Science.gov (United States)

Laine, Andrew F.; Song, Shuwu

1992-12-01

This paper introduces a novel approach for accomplishing mammographic feature analysis through multiresolution representations. We show that efficient (nonredundant) representations may be identified from digital mammography and used to enhance specific mammographic features within a continuum of scale space. The multiresolution decomposition of wavelet transforms provides a natural hierarchy in which to embed an interactive paradigm for accomplishing scale space feature analysis. Choosing wavelets (or analyzing functions) that are simultaneously localized in both space and frequency, results in a powerful methodology for image analysis. Multiresolution and orientation selectivity, known biological mechanisms in primate vision, are ingrained in wavelet representations and inspire the techniques presented in this paper. Our approach includes local analysis of complete multiscale representations. Mammograms are reconstructed from wavelet coefficients, enhanced by linear, exponential and constant weight functions localized in scale space. By improving the visualization of breast pathology we can improve the changes of early detection of breast cancers (improve quality) while requiring less time to evaluate mammograms for most patients (lower costs).

Aluminium distribution in ZSM-5 revisited: The role of Al–Al interactions

International Nuclear Information System (INIS)

Ruiz-Salvador, A. Rabdel; Grau-Crespo, Ricardo; Gray, Aileen E.; Lewis, Dewi W.

2013-01-01

We present a theoretical study of the distribution of Al atoms in zeolite ZSM-5 with Si/Al=47, where we focus on the role of Al–Al interactions rather than on the energetics of Al/Si substitutions at individual sites. Using interatomic potential methods, we evaluate the energies of the full set of symmetrically independent configurations of Al siting in a Si 94 Al 2 O 192 cell. The equilibrium Al distribution is determined by the interplay of two factors: the energetics of the Al/Si substitution at an individual site, which tends to populate particular T sites (e.g., the T14 site), and the Al–Al interaction, which at this Si/Al maximises Al–Al distances in general agreement with Dempsey’s rule. However, it is found that the interaction energy changes approximately as the inverse of the square of the distance between the two Al atoms, rather than the inverse of the distance expected if this were merely charge repulsion. Moreover, we find that the anisotropic nature of the framework density plays an important role in determining the magnitude of the interactions, which are not simply dependent on Al–Al distances. - Graphical abstract: Role of Al–Al interactions in high silica ZSM-5 is shown to be anisotropic in nature and not dependent solely on Coulombic interactions. Highlights: ► Si–Al distribution in ZSM-5 is revisited, stressing the role of the Al–Al interaction. ► Coulomb interactions are not the key factors controlling the Al siting. ► Anisotropy of the framework is identified as a source of departure from Dempsey’s rule.

Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.

Science.gov (United States)

Yan, Yumeng; Wen, Zeyu; Zhang, Di; Huang, Sheng-You

2018-05-18

RNA-RNA interactions play fundamental roles in gene and cell regulation. Therefore, accurate prediction of RNA-RNA interactions is critical to determine their complex structures and understand the molecular mechanism of the interactions. Here, we have developed a physics-based double-iterative strategy to determine the effective potentials for RNA-RNA interactions based on a training set of 97 diverse RNA-RNA complexes. The double-iterative strategy circumvented the reference state problem in knowledge-based scoring functions by updating the potentials through iteration and also overcame the decoy-dependent limitation in previous iterative methods by constructing the decoys iteratively. The derived scoring function, which is referred to as DITScoreRR, was evaluated on an RNA-RNA docking benchmark of 60 test cases and compared with three other scoring functions. It was shown that for bound docking, our scoring function DITScoreRR obtained the excellent success rates of 90% and 98.3% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 63.3% and 71.7% for van der Waals interactions, 45.0% and 65.0% for ITScorePP, and 11.7% and 26.7% for ZDOCK 2.1, respectively. For unbound docking, DITScoreRR achieved the good success rates of 53.3% and 71.7% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 13.3% and 28.3% for van der Waals interactions, 11.7% and 26.7% for our ITScorePP, and 3.3% and 6.7% for ZDOCK 2.1, respectively. DITScoreRR also performed significantly better in ranking decoys and obtained significantly higher score-RMSD correlations than the other three scoring functions. DITScoreRR will be of great value for the prediction and design of RNA structures and RNA-RNA complexes.

The Role of Couples’ Interactions in Application of Communication Skills

OpenAIRE

منصوره‌السادات صادقی; محمدعلی مظاهری; فرشته موتابی

2014-01-01

The aim of this research was to predict the role of couples’ interactions in application of communication skills based on observing their positive and negative interactions. A sample of 31 couples [adapted (15) and maladapted (16)] who were living in Tehran, were selected via accessible sampling. The couples’ interactions were videotaped through a designed scenario including problem solving, decision making, and reviewing conversation about a shared pleasure event. Participants also completed...

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

Directory of Open Access Journals (Sweden)

M. Kim

2017-12-01

Full Text Available Biological soil crusts (biocrusts are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

Science.gov (United States)

Kim, Minsu; Or, Dani

2017-12-01

Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

Improved features of MARS 1.4 and verification

Energy Technology Data Exchange (ETDEWEB)

Lee, Won Jae; Chung, Bub Don; Jeong, Jae Jun; Ha, Kwi Seok [Korea Atomic Energy Research Institute, Taejon (Korea)

1999-09-01

MARS 1.4 code has been developed as a basic code frame for multi-dimensional thermal-hydraulic analysis of light water reactor transients. This report describes the newly improved features of MARS 1.4 and their verification results. The new features of MARS 1.4 include the implementation of point kinetics model in the 3D module, the coupled heat structure model, the extension of control functions and input check functions in the 3D module, the implementation of new features of RELAP5/MOD3.2.2 -version, the addition of automatic initialization function for fuel 3-D analysis and the unification of material properties and forcing functions, etc. These features have been implemented in the code in order to extend the code modeling capability and to enhance the user friendliness. Among these features, this report describes the implementation of new features of RELAP5/MOD3.3.3-version such as reflood model and critical heat flux models, etc., the automatic initialization function, the unification of material properties and forcing functions and the other code improvements and error corrections, which were not reported in the previous report. Through the verification calculations, the new features of MARS 1.4 have been verified well implemented in the code. In conclusion, MARS 1.4 code has been developed and verified as implemented in the code. In conclusion, MARS 1.4 code has been developed and verified as a multi-dimensional system thermal-hydraulic analysis tool. And, it can play its role as a basic code frame for the future development of a multi-purpose consolidated code, MARS 2.x, for coupled analysis of multi-dimensional system thermal hydraulics, 3D core kinetics, core CHF and containment as well as for further improvement of thermal-hydraulic and numerical models. 4 refs., 10 figs. (Author)

Feature selection in classification of eye movements using electrooculography for activity recognition.

Science.gov (United States)

Mala, S; Latha, K

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition.

On-line Social Interactions and Executive Functions

Directory of Open Access Journals (Sweden)

Oscar eYbarra

2012-04-01

Full Text Available A successful social interaction requires fast, on-line, and active construction of an ever-changing mental-model of another’s person beliefs, expectations, emotions, and desires. It also requires the ability to inhibit inappropriate behaviors, problem-solve, take-turns, and pursue goals in a distraction-rich environment. All these tasks rely on executive functions (EF—working memory, attention/cognitive control, and inhibition. Executive functioning has long been viewed as relatively static. However, starting with recent reports of successful cognitive interventions, this view is changing and now EFs are seen as much more open to both short and long term training, warm-up, and exhaustion effects. Some of the most intriguing evidence comes from research showing how social interaction enhances performance on standard EF tests. Interestingly, the latest research indicates these EF benefits are selectively conferred by certain on-line, dynamic social interactions, which require participants to engage with another person and actively construct the model of their mind. We review this literature and highlight its connection with evolutionary and cultural theories emphasizing links between intelligence and social life.

Long-range functional interactions of anterior insula and medial frontal cortex are differently modulated by visuospatial and inductive reasoning tasks.

Science.gov (United States)

Ebisch, Sjoerd J H; Mantini, Dante; Romanelli, Roberta; Tommasi, Marco; Perrucci, Mauro G; Romani, Gian Luca; Colom, Roberto; Saggino, Aristide

2013-09-01

The brain is organized into functionally specific networks as characterized by intrinsic functional relationships within discrete sets of brain regions. However, it is poorly understood whether such functional networks are dynamically organized according to specific task-states. The anterior insular cortex (aIC)-dorsal anterior cingulate cortex (dACC)/medial frontal cortex (mFC) network has been proposed to play a central role in human cognitive abilities. The present functional magnetic resonance imaging (fMRI) study aimed at testing whether functional interactions of the aIC-dACC/mFC network in terms of temporally correlated patterns of neural activity across brain regions are dynamically modulated by transitory, ongoing task demands. For this purpose, functional interactions of the aIC-dACC/mFC network are compared during two distinguishable fluid reasoning tasks, Visualization and Induction. The results show an increased functional coupling of bilateral aIC with visual cortices in the occipital lobe during the Visualization task, whereas coupling of mFC with right anterior frontal cortex was enhanced during the Induction task. These task-specific modulations of functional interactions likely reflect ability related neural processing. Furthermore, functional connectivity strength between right aIC and right dACC/mFC reliably predicts general task performance. The findings suggest that the analysis of long-range functional interactions may provide complementary information about brain-behavior relationships. On the basis of our results, it is proposed that the aIC-dACC/mFC network contributes to the integration of task-common and task-specific information based on its within-network as well as its between-network dynamic functional interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Features of Functioning the Integrated Building Thermal Model

Directory of Open Access Journals (Sweden)

Morozov Maxim N.

2017-01-01

Full Text Available A model of the building heating system, consisting of energy source, a distributed automatic control system, elements of individual heating unit and heating system is designed. Application Simulink of mathematical package Matlab is selected as a platform for the model. There are the specialized application Simscape libraries in aggregate with a wide range of Matlab mathematical tools allow to apply the “acausal” modeling concept. Implementation the “physical” representation of the object model gave improving the accuracy of the models. Principle of operation and features of the functioning of the thermal model is described. The investigations of building cooling dynamics were carried out.

Reconstitution of proapoptotic BAK function in liposomes reveals a dual role for mitochondrial lipids in the BAK-driven membrane permeabilization process.

Science.gov (United States)

Landeta, Olatz; Landajuela, Ane; Gil, David; Taneva, Stefka; Di Primo, Carmelo; Sot, Begoña; Valle, Mikel; Frolov, Vadim A; Basañez, Gorka

2011-03-11

BAK is a key effector of mitochondrial outer membrane permeabilization (MOMP) whose molecular mechanism of action remains to be fully dissected in intact cells, mainly due to the inherent complexity of the intracellular apoptotic machinery. Here we show that the core features of the BAK-driven MOMP pathway can be reproduced in a highly simplified in vitro system consisting of recombinant human BAK lacking the carboxyl-terminal 21 residues (BAKΔC) and tBID in combination with liposomes bearing an appropriate lipid environment. Using this minimalist reconstituted system we established that tBID suffices to trigger BAKΔC membrane insertion, oligomerization, and pore formation. Furthermore, we demonstrate that tBID-activated BAKΔC permeabilizes the membrane by forming structurally dynamic pores rather than a large proteinaceous channel of fixed size. We also identified two distinct roles played by mitochondrial lipids along the molecular pathway of BAKΔC-induced membrane permeabilization. First, using several independent approaches, we showed that cardiolipin directly interacts with BAKΔC, leading to a localized structural rearrangement in the protein that "primes" BAKΔC for interaction with tBID. Second, we provide evidence that selected curvature-inducing lipids present in mitochondrial membranes specifically modulate the energetic expenditure required to create the BAKΔC pore. Collectively, our results support the notion that BAK functions as a direct effector of MOMP akin to BAX and also adds significantly to the growing evidence indicating that mitochondrial membrane lipids are actively implicated in BCL-2 protein family function.

Multiple structure-intrinsic disorder interactions regulate and coordinate Hox protein function

Science.gov (United States)

Bondos, Sarah

During animal development, Hox transcription factors determine fate of developing tissues to generate diverse organs and appendages. Hox proteins are famous for their bizarre mutant phenotypes, such as replacing antennae with legs. Clearly, the functions of individual Hox proteins must be distinct and reliable in vivo, or the organism risks malformation or death. However, within the Hox protein family, the DNA-binding homeodomains are highly conserved and the amino acids that contact DNA are nearly invariant. These observations raise the question: How do different Hox proteins correctly identify their distinct target genes using a common DNA binding domain? One possible means to modulate DNA binding is through the influence of the non-homeodomain protein regions, which differ significantly among Hox proteins. However genetic approaches never detected intra-protein interactions, and early biochemical attempts were hindered because the special features of ``intrinsically disordered'' sequences were not appreciated. We propose the first-ever structural model of a Hox protein to explain how specific contacts between distant, intrinsically disordered regions of the protein and the homeodomain regulate DNA binding and coordinate this activity with other Hox molecular functions.

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency.

Directory of Open Access Journals (Sweden)

Yuhan Chen

2017-09-01

Full Text Available The primate connectome, possessing a characteristic global topology and specific regional connectivity profiles, is well organized to support both segregated and integrated brain function. However, the organization mechanisms shaping the characteristic connectivity and its relationship to functional requirements remain unclear. The primate brain connectome is shaped by metabolic economy as well as functional values. Here, we explored the influence of two competing factors and additional advanced functional requirements on the primate connectome employing an optimal trade-off model between neural wiring cost and the representative functional requirement of processing efficiency. Moreover, we compared this model with a generative model combining spatial distance and topological similarity, with the objective of statistically reproducing multiple topological features of the network. The primate connectome indeed displays a cost-efficiency trade-off and that up to 67% of the connections were recovered by optimal combination of the two basic factors of wiring economy and processing efficiency, clearly higher than the proportion of connections (56% explained by the generative model. While not explicitly aimed for, the trade-off model captured several key topological features of the real connectome as the generative model, yet better explained the connectivity of most regions. The majority of the remaining 33% of connections unexplained by the best trade-off model were long-distance links, which are concentrated on few cortical areas, termed long-distance connectors (LDCs. The LDCs are mainly non-hubs, but form a densely connected group overlapping on spatially segregated functional modalities. LDCs are crucial for both functional segregation and integration across different scales. These organization features revealed by the optimization analysis provide evidence that the demands of advanced functional segregation and integration among spatially

Interactions between genetic background, insulin resistance and β-cell function.

Science.gov (United States)

Kahn, S E; Suvag, S; Wright, L A; Utzschneider, K M

2012-10-01

An interaction between genes and the environment is a critical component underlying the pathogenesis of the hyperglycaemia of type 2 diabetes. The development of more sophisticated techniques for studying gene variants and for analysing genetic data has led to the discovery of some 40 genes associated with type 2 diabetes. Most of these genes are related to changes in β-cell function, with a few associated with decreased insulin sensitivity and obesity. Interestingly, using quantitative traits based on continuous measures rather than dichotomous ones, it has become evident that not all genes associated with changes in fasting or post-prandial glucose are also associated with a diagnosis of type 2 diabetes. Identification of these gene variants has provided novel insights into the physiology and pathophysiology of the β-cell, including the identification of molecules involved in β-cell function that were not previously recognized as playing a role in this critical cell. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

On the role of temporary storage in interactive evolution

DEFF Research Database (Denmark)

Dahlstedt, Palle

2009-01-01

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

Serpin functions in host-pathogen interactions

Directory of Open Access Journals (Sweden)

Jialing Bao

2018-04-01

Full Text Available Serpins are a broadly distributed superfamily of protease inhibitors that are present in all kingdoms of life. The acronym, serpin, is derived from their function as potent serine proteases inhibitors. Early studies of serpins focused on their functions in haemostasis since modulating serine proteases activities are essential for coagulation. Additional research has revealed that serpins function in infection and inflammation, by modulating serine and cysteine proteases activities. The aim of this review is to summarize the accumulating findings and current understanding of the functions of serpins in host-pathogen interactions, serving as host defense proteins as well as pathogenic factors. We also discuss the potential crosstalk between host and pathogen serpins. We anticipate that future research will elucidate the therapeutic value of this novel target.

Hemichannels: new roles in astroglial function

Directory of Open Access Journals (Sweden)

Jimmy eStehberg

2014-06-01

Full Text Available The role of astrocytes in brain function has evolved over the last decade, from support cells to active participants in the neuronal synapse through the release of gliotransmitters. Astrocytes express receptors for most neurotransmitters and respond to them through Ca2+ intracellular oscillations and propagation of intercellular Ca2+ waves. While such waves are able to propagate among neighboring astrocytes through gap junctions, thereby activating several astrocytes simultaneously, they can also trigger the release of gliotransmitters, including glutamate, d-serine, glycine, ATP, adenosine or GABA. There are several mechanisms by which gliotransmitter release occurs, including functional hemichannels. These gliotransmitters can activate neighboring astrocytes and participate in the propagation of intercellular Ca2+ waves, or activate pre- and post-synaptic receptors, including NMDA, AMPA and purinergic receptors. In consequence, hemichannels could play a pivotal role in astrocyte-to-astrocyte communication and astrocyte-to-neuron cross-talk. Recent evidence suggests that astroglial hemichannels are involved in higher brain functions including memory and glucose sensing. The present review will focus on the role of hemichannels in astrocyte-to-astrocyte and astrocyte-to neuron communication and in brain physiology.

Use cases and DEMO: aligning functional features of ICT-infrastructure to business processes.

Science.gov (United States)

Maij, E; Toussaint, P J; Kalshoven, M; Poerschke, M; Zwetsloot-Schonk, J H M

2002-11-12

The proper alignment of functional features of the ICT-infrastructure to business processes is a major challenge in health care organisations. This alignment takes into account that the organisational structure not only shapes the ICT-infrastructure, but that the inverse also holds. To solve the alignment problem, relevant features of the ICT-infrastructure should be derived from the organisational structure and the influence of this envisaged ICT to the work practices should be pointed out. The objective of our study was to develop a method to solve this alignment problem. In a previous study we demonstrated the appropriateness of the business process modelling methodology Dynamic Essential Modelling of Organizations (DEMO). A proven and widely used modelling language for expressing functional features is Unified Modelling Language (UML). In the context of a specific case study at the University Medical Centre Utrecht in the Netherlands we investigated if the combined use of DEMO and UML could solve the alignment problem. The study demonstrated that the DEMO models were suited as a starting point in deriving system functionality by using the use case concept of UML. Further, the case study demonstrated that in using this approach for the alignment problem, insight is gained into the mutual influence of ICT-infrastructure and organisation structure: (a) specification of independent, re-usable components-as a set of related functionalities-is realised, and (b) a helpful representation of the current and future work practice is provided for in relation to the envisaged ICT support.

Testing odorant-receptor interaction theories in humans through discrimination of isotopomers

Directory of Open Access Journals (Sweden)

Mara Andrione

2017-12-01

Full Text Available Odour reception takes place on the olfactory receptor neuron membrane, where molecular receptors interact with volatile odorant molecules. This interaction is classically thought to rely on chemical and structural features of the odorant, e.g. size, shape, functional groups. However, this model does not allow formulating a correct prediction for the smell of an odorant, suggesting that other molecular properties may play a role in the odour transduction process. An alternative model of olfaction maintains that odorant receptors can probe not only the structural and chemical features, but also the molecular vibration spectrum of the odorants. This constitutes the so-called vibration model of olfaction. According to this model, two isotopomers of the same molecule, i.e. two forms of the same molecule, one unaltered and one in which one or more hydrogen atoms are substituted with deuterium – which are therefore structurally and chemically identical, but with different molecular vibration spectra – would interact differently with an olfactory receptor, producing different olfactory perceptions in the brain. Here, we report on a duo-trio discrimination experiment conducted on human subjects, testing isotopomer pairs that have recently been shown to be differentially encoded in the honeybee brain.

Grazer Functional Roles, Induced Defenses, and Indirect Interactions: Implications for Eelgrass Restoration in San Francisco Bay

Directory of Open Access Journals (Sweden)

Jeffrey T. Lewis

2014-11-01

Full Text Available Understanding the individual and interactive roles of consumer species is more than academic when the host plant is a subject of intense conservation interest. In a mesocosm experiment, we compared effects of common invertebrate grazers in San Francisco Bay seagrass (Zostera marina, eelgrass beds, finding that some species (a native opisthobranch, Phyllaplysia taylori; a native isopod, Idotea resecata; and an introduced gastropod, Ilyanassa obsoleta enhanced eelgrass growth through removal of epiphytic algae, as is often predicted for small invertebrate grazers on seagrasses, while one (an introduced caprellid amphipod, Caprella cf. drepanochir had neutral effects. In contrast, the putatively-introduced gammaridean amphipod, Ampithoe valida, had strong negative effects on eelgrass (in addition to epiphytes through consumption, as we had previously observed in the field during restoration programs. We tested whether other common grazer species could influence the effects of the eelgrass-grazing Ampithoe, and found that Idotea induced production of phenolic compounds and limited eelgrass damage by Ampithoe, without affecting Ampithoe abundance. These results have implications for restoration strategies, and contribute to a growing awareness of the importance of trait-mediated indirect grazer interactions through grazer-induced changes in plant traits, providing the first example in a seagrass system.

Stacking of purines in water: the role of dipolar interactions in caffeine.

Science.gov (United States)

Tavagnacco, L; Di Fonzo, S; D'Amico, F; Masciovecchio, C; Brady, J W; Cesàro, A

2016-05-11

During the last few decades it has been ascertained that base stacking is one of the major contributions stabilizing nucleic acid conformations. However, the understanding of the nature of the interactions involved in the stacking process remains under debate and it is a subject of theoretical and experimental studies. Structural similarity between purine bases (guanine and adenine) in DNA and the caffeine molecule makes caffeine an excellent model for the purine bases. The present study clearly shows that dipolar interactions play a fundamental role in determining stacking of purine molecules in solution. In order to reach this achievement, polarized ultraviolet Raman resonant scattering experiments have been carried out on caffeine aqueous solutions as a function of concentration and temperature. The investigation pointed out at the aggregation and solvation properties, particularly at elevated temperatures. Kubo-Anderson theory was used as a framework to investigate the non-coincidence effect (NCE) occurring in the totally symmetric breathing modes of the purine rings, and in the bending modes of the methyl groups of caffeine. The NCE concentration dependence shows that caffeine aggregation at 80 °C occurs by planar stacking of the hydrophobic faces. The data clearly indicate that dipolar interactions determine the reorientational motion of the molecules in solution and are the driving force for the stacking of caffeine. In parallel, the observed dephasing times imply a change in caffeine interactions as a function of temperature and concentration. A decrease, at low water content, of the dephasing time for the ring breathing vibration mode indicates that self-association alters the solvation structure that is detectable at low concentration. These results are in agreement with simulation predictions and serve as an important validation of the models used in those calculations.

Theories of inter-hemispheric interactions in aphasia: the role of tDCS in rehabilitation of post-stroke aphasia

Directory of Open Access Journals (Sweden)

Roy H Hamilton

2014-04-01

Full Text Available Mounting data from behavioral and neuroimaging studies have shown that the process of recovery from aphasia is largely driven by the reorganization of brain networks related to language. Evidence implicates a variety of potential mechanisms in this reorganization, some of which involve substantive changes in brain functional activity within and between cerebral hemispheres. These changes include intrahemispheric recruitment of perilesional left-hemisphere regions and transcallosal interhemispheric interactions between lesioned left-hemisphere language areas and homologous regions in the right hemisphere. With respect to the role of the right hemisphere, it is debated whether interhemispheric interactions are beneficial or deleterious to recovering language networks. Recent years have also seen the emergence of noninvasive brain stimulation techniques such as transcranial magnetic stimulation (TMS and transcranial direct current stimulation (tDCS as potential novel treatments for post-stroke aphasia. Because these techniques are predicated on either focal excitation or inhibition of brain areas, characterization of the functional roles of the left and right hemispheres and transcallosal interactions in aphasia recovery is of central importance to the development and refinement of stimulation-based therapies. However, most treatment studies involving noninvasive brain stimulation in aphasia have tacitly accepted the interhemispheric inhibition model, in which right hemisphere activity interferes with language recovery that is mediated by left hemisphere perisylvian regions. Based on this account, many studies in aphasia involving TMS and tDCS have adopted one of two approaches consistent with the model: left hemisphere excitation or right hemisphere inhibition. In this presentation, we will review both clinical and cognitive neuroscience evidence that elucidates different hemispheric mechanisms that influence recovery from aphasia after stroke

Functional role of stromal interaction molecule 1 (STIM1) in vascular smooth muscle cells

International Nuclear Information System (INIS)

Takahashi, Yoichiro; Watanabe, Hiroyuki; Murakami, Manabu; Ono, Kyoichi; Munehisa, Yoshiko; Koyama, Takashi; Nobori, Kiyoshi; Iijima, Toshihiko; Ito, Hiroshi

2007-01-01

We investigated the functional role of STIM1, a Ca 2+ sensor in the endoplasmic reticulum (ER) that regulates store-operated Ca 2+ entry (SOCE), in vascular smooth muscle cells (VSMCs). STIM1 was mainly localized at the ER and plasma membrane. The knockdown of STIM1 expression by small interfering (si) RNA drastically decreased SOCE. In contrast, an EF-hand mutant of STIM1, STIM1 E87A , produced a marked increase in SOCE, which was abolished by co-transfection with siRNA to transient receptor potential canonical 1 (TRPC1). In addition, transfection with siRNA against STIM1 suppressed phosphorylation of cAMP-responsive element binding protein (CREB) and cell growth. These results suggest that STIM1 is an essential component of SOCE and that it is involved in VSMC proliferation

Real-time skin feature identification in a time-sequential video stream

Science.gov (United States)

Kramberger, Iztok

2005-04-01

Skin color can be an important feature when tracking skin-colored objects. Particularly this is the case for computer-vision-based human-computer interfaces (HCI). Humans have a highly developed feeling of space and, therefore, it is reasonable to support this within intelligent HCI, where the importance of augmented reality can be foreseen. Joining human-like interaction techniques within multimodal HCI could, or will, gain a feature for modern mobile telecommunication devices. On the other hand, real-time processing plays an important role in achieving more natural and physically intuitive ways of human-machine interaction. The main scope of this work is the development of a stereoscopic computer-vision hardware-accelerated framework for real-time skin feature identification in the sense of a single-pass image segmentation process. The hardware-accelerated preprocessing stage is presented with the purpose of color and spatial filtering, where the skin color model within the hue-saturation-value (HSV) color space is given with a polyhedron of threshold values representing the basis of the filter model. An adaptive filter management unit is suggested to achieve better segmentation results. This enables the adoption of filter parameters to the current scene conditions in an adaptive way. Implementation of the suggested hardware structure is given at the level of filed programmable system level integrated circuit (FPSLIC) devices using an embedded microcontroller as their main feature. A stereoscopic clue is achieved using a time-sequential video stream, but this shows no difference for real-time processing requirements in terms of hardware complexity. The experimental results for the hardware-accelerated preprocessing stage are given by efficiency estimation of the presented hardware structure using a simple motion-detection algorithm based on a binary function.

Investigating the relationship among transformational leadership, interpersonal interaction and mentoring functions.

Science.gov (United States)

Huang, Ching-Yuan; Weng, Rhay-Hung; Chen, Yi-Ting

2016-08-01

This study aims to ascertain the relationship between transformational leadership, interpersonal interaction and mentoring functions among new staff nurses. Mentoring functions could improve the job performance of new nurses, provide them with support and thus reduce their turnover rate. A cross-sectional study was employed. A questionnaire survey was carried out to collect data among a sample of new nurses from three hospitals in Taiwan. After gathering a total of 306 valid surveys, multiple regression analysis was applied to test the hypothesis. Inspirational motivation, idealised influence and individualised consideration had positive correlations with the overall mentoring function, but intellectual stimulation showed a positive association only with career development function. Perceived similarity and interaction frequency also had positive correlations with mentoring functions. When the shift overlap rate exceeded 80%, mentoring function showed a negative result. The transformational leadership of mentors would improve the mentoring functions among new staff nurses. Perceived similarity and interaction frequency between mentees and mentors also had positive correlations with mentoring functions. It is crucial for hospitals to redesign their leadership training and motivation programmes to enhance the transformational leadership of mentors. Furthermore, nursing managers should promote interaction between new staff nurses and their mentors; however, the shift overlap rate should not be too high. © 2016 John Wiley & Sons Ltd.

Arabidopsis thaliana Remorins Interact with SnRK1 and Play a Role in Susceptibility to Beet Curly Top Virus and Beet Severe Curly Top Virus

Directory of Open Access Journals (Sweden)

Seungmin Son

2014-09-01

Full Text Available Remorins, a family of plant-specific proteins containing a variable N-terminal region and conserved C-terminal domain, play a role in various biotic and abiotic stresses, including host-microbe interactions. However, their functions remain to be completely elucidated, especially for the Arabidopsis thaliana remorin group 4 (AtREM4. To elucidate the role of remorins in Arabidopsis, we first showed that AtREM4s have typical molecular characteristics of the remorins, such as induction by various types of biotic and abiotic stresses, localization in plasma membrane and homo- and hetero-oligomeric interaction. Next, we showed that their loss-of-function mutants displayed reduced susceptibility to geminiviruses, Beet Curly Top Virus and Beet Severe Curly Top Virus, while overexpressors enhanced susceptibility. Moreover, we found that they interacted with SnRK1, which phosphorylated AtREM4.1, and were degraded by the 26S proteasome pathway. These results suggest that AtREM4s may be involved in the SnRK1-mediated signaling pathway and play a role as positive regulators of the cell cycle during geminivirus infection.

Prediction of Protein–Protein Interactions by Evidence Combining Methods

Directory of Open Access Journals (Sweden)

Ji-Wei Chang

2016-11-01

Full Text Available Most cellular functions involve proteins’ features based on their physical interactions with other partner proteins. Sketching a map of protein–protein interactions (PPIs is therefore an important inception step towards understanding the basics of cell functions. Several experimental techniques operating in vivo or in vitro have made significant contributions to screening a large number of protein interaction partners, especially high-throughput experimental methods. However, computational approaches for PPI predication supported by rapid accumulation of data generated from experimental techniques, 3D structure definitions, and genome sequencing have boosted the map sketching of PPIs. In this review, we shed light on in silico PPI prediction methods that integrate evidence from multiple sources, including evolutionary relationship, function annotation, sequence/structure features, network topology and text mining. These methods are developed for integration of multi-dimensional evidence, for designing the strategies to predict novel interactions, and for making the results consistent with the increase of prediction coverage and accuracy.

ESSENCE, FEATURES AND FUNCTIONS OF THE LABOUR DIGITAL MARKET

Directory of Open Access Journals (Sweden)

N. Azmuk

2015-06-01

Full Text Available In the article the author has presented the comparative analysis of both digital and traditional segments of the global labour market. The main functions of the digital labour market are social, economic and stimulant ones. The features of the digital labour market are digital employment, globality, high level of flexibility, large competition, dynamic changes of labour force and working places. The main kinds of digital employment are electronic free lance and electronic outsourcing. In the article the advantages and the risks of digital employment using have been determined.

The role of plant-microbiome interactions in weed establishment and control.

Science.gov (United States)

Trognitz, Friederike; Hackl, Evelyn; Widhalm, Siegrid; Sessitsch, Angela

2016-10-01

The soil microbiome plays an important role in the establishment of weeds and invasive plants. They associate with microorganisms supporting their growth and health. Weed management strategies, like tillage and herbicide treatments, to control weeds generally alter soil structure going alongside with changes in the microbial community. Once a weed population establishes in the field, the plants build up a close relationship with the available microorganisms. Seeds or vegetative organs overwinter in soil and select early in the season their own microbiome before crop plants start to vegetate. Weed and crop plants compete for light, nutrition and water, but may differently interact with soil microorganisms. The development of new sequencing technologies for analyzing soil microbiomes has opened up the possibility for in depth analysis of the interaction between 'undesired' plants and crop plants under different management systems. These findings will help us to understand the functions of microorganisms involved in crop productivity and plant health, weed establishment and weed prevention. Exploitation of the knowledge offers the possibility to search for new biocontrol methods against weeds based on soil and plant-associated microorganisms. This review discusses the recent advances in understanding the functions of microbial communities for weed/invasive plant establishment and shows new ways to use plant-associated microorganisms to control weeds and invasive plants in different land management systems. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Three-body interactions in sociophysics and their role in coalition forming

Science.gov (United States)

Naumis, Gerardo G.; Samaniego-Steta, F.; del Castillo-Mussot, M.; Vázquez, G. J.

2007-06-01

An study of the effects of three-body interactions in the process of coalition formation is presented. In particular, we modify a spin glass model of bimodal propensities and also a Potts model in order to include a particular three-body Hamiltonian that reproduces the main features of the required interactions. The model can be used to study conflicts, political struggles, political parties, social networks, wars and organizational structures. As an application, we analyze a simplified model of the Iraq war.

Speech networks at rest and in action: interactions between functional brain networks controlling speech production

Science.gov (United States)

Fuertinger, Stefan

2015-01-01

Speech production is one of the most complex human behaviors. Although brain activation during speaking has been well investigated, our understanding of interactions between the brain regions and neural networks remains scarce. We combined seed-based interregional correlation analysis with graph theoretical analysis of functional MRI data during the resting state and sentence production in healthy subjects to investigate the interface and topology of functional networks originating from the key brain regions controlling speech, i.e., the laryngeal/orofacial motor cortex, inferior frontal and superior temporal gyri, supplementary motor area, cingulate cortex, putamen, and thalamus. During both resting and speaking, the interactions between these networks were bilaterally distributed and centered on the sensorimotor brain regions. However, speech production preferentially recruited the inferior parietal lobule (IPL) and cerebellum into the large-scale network, suggesting the importance of these regions in facilitation of the transition from the resting state to speaking. Furthermore, the cerebellum (lobule VI) was the most prominent region showing functional influences on speech-network integration and segregation. Although networks were bilaterally distributed, interregional connectivity during speaking was stronger in the left vs. right hemisphere, which may have underlined a more homogeneous overlap between the examined networks in the left hemisphere. Among these, the laryngeal motor cortex (LMC) established a core network that fully overlapped with all other speech-related networks, determining the extent of network interactions. Our data demonstrate complex interactions of large-scale brain networks controlling speech production and point to the critical role of the LMC, IPL, and cerebellum in the formation of speech production network. PMID:25673742

Functional interaction of TRPV4 channel protein with annexin A2 in DRG.

Science.gov (United States)

Ning, Liping; Wang, Chuanwei; Ding, Xinli; Zhang, Yang; Wang, Xuping; Yue, Shouwei

2012-09-01

Transient receptor potential vanilloid 4 (TRPV4) is a Ca(2+)-permeable, non-selective cation channel that is involved in the transmission of pain signals mediated by dorsal root ganglion (DRG). Annexin A2 belongs to a class of membrane-binding proteins that plays an important role in the regulation of ion channels. Nevertheless, little is known about the interaction between them in DRG. In this paper, we evaluated the functional interaction of TRPV4 with annexin A2 in DRG. We have used immunocytochemistry and co-immunoprecipitation assays to investigate the interaction between annexin A2 and TRPV4 in DRG. The role of annexin A2 in the regulation of TRPV4 activity in DRG was further verified by measurement of intracellular free calcium concentrations ([Ca(2+)](i)) and substance P (SP) release. First, annexin A2 was showed partial co-localization with TRPV4 in DRG neurons. Then, annexin A2 and TRPV4 were co-precipitated with each other in DRG lysates. Furthermore, the downregulation of annexin A2 using specific small interfering RNA significantly inhibited Ca(2+) influx and SP mediated by TRPV4. Our results provide evidence that annexin A2 is associated with TRPV4 and regulates TRPV4-mediated Ca(2+) influx and SP release in DRG neurons. The objective of this work is to determine the influence of annexin A2 on TRPV4 in DRG neurons, which may be the basis for treatment of pain relief.

Unravelling the Functional Biomechanics of Dental Features and Tooth Wear

OpenAIRE

Benazzi, Stefano; Nguyen, Huynh Nhu; Kullmer, Ottmar; Hublin, Jean-Jacques

2013-01-01

Most of the morphological features recognized in hominin teeth, particularly the topography of the occlusal surface, are generally interpreted as an evolutionary functional adaptation for mechanical food processing. In this respect, we can also expect that the general architecture of a tooth reflects a response to withstand the high stresses produced during masticatory loadings. Here we use an engineering approach, finite element analysis (FEA), with an advanced loading concept derived from i...

Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase

Science.gov (United States)

2016-01-01

Catalase-peroxidases (KatGs) are unique bifunctional heme peroxidases with an additional posttranslationally formed redox-active Met-Tyr-Trp cofactor that is essential for catalase activity. On the basis of studies of bacterial KatGs, controversial mechanisms of hydrogen peroxide oxidation were proposed. The recent discovery of eukaryotic KatGs with differing pH optima of catalase activity now allows us to scrutinize those postulated reaction mechanisms. In our study, secreted KatG from the fungus Magnaporthe grisea (MagKatG2) was used to analyze the role of a remote KatG-typical mobile arginine that was shown to interact with the Met-Tyr-Trp adduct in a pH-dependent manner in bacterial KatGs. Here we present crystal structures of MagKatG2 at pH 3.0, 5.5, and 7.0 and investigate the mobility of Arg461 by molecular dynamics simulation. Data suggest that at pH ≥4.5 Arg461 mostly interacts with the deprotonated adduct Tyr. Elimination of Arg461 by mutation to Ala slightly increases the thermal stability but does not alter the active site architecture or the kinetics of cyanide binding. However, the variant Arg461Ala lost the wild-type-typical optimum of catalase activity at pH 5.25 (kcat = 6450 s–1) but exhibits a broad plateau between pH 4.5 and 7.5 (kcat = 270 s–1 at pH 5.5). Moreover, significant differences in the kinetics of interconversion of redox intermediates of wild-type and mutant protein mixed with either peroxyacetic acid or hydrogen peroxide are observed. These findings together with published data from bacterial KatGs allow us to propose a role of Arg461 in the H2O2 oxidation reaction of KatG. PMID:27293030

featsel: A framework for benchmarking of feature selection algorithms and cost functions

OpenAIRE

Marcelo S. Reis; Gustavo Estrela; Carlos Eduardo Ferreira; Junior Barrera

2017-01-01

In this paper, we introduce featsel, a framework for benchmarking of feature selection algorithms and cost functions. This framework allows the user to deal with the search space as a Boolean lattice and has its core coded in C++ for computational efficiency purposes. Moreover, featsel includes Perl scripts to add new algorithms and/or cost functions, generate random instances, plot graphs and organize results into tables. Besides, this framework already comes with dozens of algorithms and co...

Interaction of boron with graphite: A van der Waals density functional study

International Nuclear Information System (INIS)

Liu, Juan; Wang, Chen; Liang, Tongxiang; Lai, Wensheng

2016-01-01

Highlights: • A van der Waals density-functional approach is applied to study the interaction of boron with graphite. • VdW-DF functionals give fair agreement of crystal parameters with experiments. • The π electron approaches boron while adsorbing on graphite surface. • The hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. • PBE cannot describe the interstitial boron in graphite because of the ignoring binding of graphite sheets. - Abstract: Boron doping has been widely investigated to improve oxidation resistance of graphite. In this work the interaction of boron with graphite is investigated by a van der Waals density-functional approach (vdW-DF). The traditional density-functional theory (DFT) is well accounted for the binding in boron-substituted graphite. However, to investigate the boron atom on graphite surface and the interstitial impurities require use of a description of graphite interlayer binding. Traditional DFT cannot describe the vdW physics, for instance, GGA calculations show no relevant binding between graphite sheets. LDA shows some binding, but they fail to provide an accurate account of vdW forces. In this paper, we compare the calculation results of graphite lattice constant and cohesive energy by several functionals, it shows that vdW-DF such as two optimized functionals optB88-vdW and optB86b-vdW give much improved results than traditional DFT. The vdW-DF approach is then applied to study the interaction of boron with graphite. Boron adsorption, substitution, and intercalation are discussed in terms of structural parameters and electronic structures. When adsorbing on graphite surface, boron behaves as π electron acceptor. The π electron approaches boron atom because of more electropositive of boron than carbon. For substitution situation, the hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. The B-doped graphite system with the hole has less

Interaction of boron with graphite: A van der Waals density functional study

Energy Technology Data Exchange (ETDEWEB)

Liu, Juan; Wang, Chen [Beijing Key Lab of Fine Ceramics, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Liang, Tongxiang, E-mail: txliang@tsinghua.edu.cn [State Key Lab of New Ceramic and Fine Processing, Tsinghua University, Beijing 100084 (China); Lai, Wensheng [Advanced Material Laboratory, School of Materials Science & Engineering, Tsinghua University, Beijing, 100084 (China)

2016-08-30

Highlights: • A van der Waals density-functional approach is applied to study the interaction of boron with graphite. • VdW-DF functionals give fair agreement of crystal parameters with experiments. • The π electron approaches boron while adsorbing on graphite surface. • The hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. • PBE cannot describe the interstitial boron in graphite because of the ignoring binding of graphite sheets. - Abstract: Boron doping has been widely investigated to improve oxidation resistance of graphite. In this work the interaction of boron with graphite is investigated by a van der Waals density-functional approach (vdW-DF). The traditional density-functional theory (DFT) is well accounted for the binding in boron-substituted graphite. However, to investigate the boron atom on graphite surface and the interstitial impurities require use of a description of graphite interlayer binding. Traditional DFT cannot describe the vdW physics, for instance, GGA calculations show no relevant binding between graphite sheets. LDA shows some binding, but they fail to provide an accurate account of vdW forces. In this paper, we compare the calculation results of graphite lattice constant and cohesive energy by several functionals, it shows that vdW-DF such as two optimized functionals optB88-vdW and optB86b-vdW give much improved results than traditional DFT. The vdW-DF approach is then applied to study the interaction of boron with graphite. Boron adsorption, substitution, and intercalation are discussed in terms of structural parameters and electronic structures. When adsorbing on graphite surface, boron behaves as π electron acceptor. The π electron approaches boron atom because of more electropositive of boron than carbon. For substitution situation, the hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. The B-doped graphite system with the hole has less

Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

Science.gov (United States)

Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

2016-07-12

In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

Nongaussian Features from Inflationary Particle Production

International Nuclear Information System (INIS)

Barnaby, Neil

2010-01-01

The inflaton field can be expected to couple to a number of additional fields whose energy density does not play any significant role in driving inflation. Such couplings may lead to isolated bursts of particle production during inflation, for example via parametric resonance or a phase transition, and leave observable imprints in the cosmological fluctuations. I illustrate this effect for a simple prototype interaction g 2 (φ - φ 0 ) 2 χ between the inflaton, φ, and iso-inflaton, χ. Using both classical lattice simulations and analytical quantum field theory computations, I show that this mechanism generates localized bump-like features in the power spectrum and also a completely new type of nongaussianity. Observations are consistent with relatively large features of this type and the nongaussianity from particle production may be observable in future missions.

Nursing roles and functions addressing relatives during in-hospital rehabilitation following stroke. Care needs and involvement

DEFF Research Database (Denmark)

Aadal, Lena; Angel, Sanne; Langhorn, Leanne

2017-01-01

RATIONALE: In the last decades, length of stay of in-hospital rehabilitation of patients with stroke has been significantly reduced. Health authorities expect relatives to be at disposal to convey the knowledge of everyday life and to provide emotional as well as practical support in relation...... and the actual contribution from nurses. AIM: This study describes nurses' experienced roles and functions addressing the relatives of patients with stroke during in-hospital rehabilitation. METHODOLOGICAL DESIGN: A phenomenological hermeneutic approach influenced by Paul Ricoeur. In a secondary analysis focus...... and the relatives and support the interaction between the patient and the relatives. Four themes occurred: the changed lives of relatives; shared life after stroke; noncooperating relatives; time for the relatives. CONCLUSION: Nurses experience their roles and functions addressing relatives after stroke as crucial...

Functional renormalization group approach to interacting three-dimensional Weyl semimetals

Science.gov (United States)

Sharma, Anand; Scammell, Arthur; Krieg, Jan; Kopietz, Peter

2018-03-01

We investigate the effect of long-range Coulomb interaction on the quasiparticle properties and the dielectric function of clean three-dimensional Weyl semimetals at zero temperature using a functional renormalization group (FRG) approach. The Coulomb interaction is represented via a bosonic Hubbard-Stratonovich field which couples to the fermionic density. We derive truncated FRG flow equations for the fermionic and bosonic self-energies and for the three-legged vertices with two fermionic and one bosonic external legs. We consider two different cutoff schemes—cutoff in fermionic or bosonic propagators—in order to calculate the renormalized quasiparticle velocity and the dielectric function for an arbitrary number of Weyl nodes and the interaction strength. If we approximate the dielectric function by its static limit, our results for the velocity and the dielectric function are in good agreement with that of A. A. Abrikosov and S. D. Beneslavskiĭ [Sov. Phys. JETP 32, 699 (1971)] exhibiting slowly varying logarithmic momentum dependence for small momenta. We extend their result for an arbitrary number of Weyl nodes and finite frequency by evaluating the renormalized velocity in the presence of dynamic screening and calculate the wave function renormalization.

Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+.

Directory of Open Access Journals (Sweden)

Yosef Y Kuttner

2013-04-01

Full Text Available Knowledge of the structural basis of protein-protein interactions (PPI is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM, whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+. Calmodulin is a regulatory protein that acts as an intracellular Ca(2+ sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+ and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+ binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.

Functions of NQO1 in Cellular Protection and CoQ10 Metabolism and its Potential Role as a Redox Sensitive Molecular Switch

Directory of Open Access Journals (Sweden)

David Ross

2017-08-01

Full Text Available NQO1 is one of the two major quinone reductases in mammalian systems. It is highly inducible and plays multiple roles in cellular adaptation to stress. A prevalent polymorphic form of NQO1 results in an absence of NQO1 protein and activity so it is important to elucidate the specific cellular functions of NQO1. Established roles of NQO1 include its ability to prevent certain quinones from one electron redox cycling but its role in quinone detoxification is dependent on the redox stability of the hydroquinone generated by two-electron reduction. Other documented roles of NQO1 include its ability to function as a component of the plasma membrane redox system generating antioxidant forms of ubiquinone and vitamin E and at high levels, as a direct superoxide reductase. Emerging roles of NQO1 include its function as an efficient intracellular generator of NAD+ for enzymes including PARP and sirtuins which has gained particular attention with respect to metabolic syndrome. NQO1 interacts with a growing list of proteins, including intrinsically disordered proteins, protecting them from 20S proteasomal degradation. The interactions of NQO1 also extend to mRNA. Recent identification of NQO1 as a mRNA binding protein have been investigated in more detail using SERPIN1A1 (which encodes the serine protease inhibitor α-1-antitrypsin as a target mRNA and indicate a role of NQO1 in control of translation of α-1-antitrypsin, an important modulator of COPD and obesity related metabolic syndrome. NQO1 undergoes structural changes and alterations in its ability to bind other proteins as a result of the cellular reduced/oxidized pyridine nucleotide ratio. This suggests NQO1 may act as a cellular redox switch potentially altering its interactions with other proteins and mRNA as a result of the prevailing redox environment.

A multilevel cross-cultural examination of role overload and organizational commitment: investigating the interactive effects of context.

Science.gov (United States)

Fisher, David M

2014-07-01

Considering the influential nature of context, the current investigation examined whether the relationship between role overload and organizational commitment was affected by various contextual factors. Drawing on the occupational stress literature, structural empowerment and cooperative climate were examined as factors that would mitigate the negative effects of role overload on organizational commitment. In addition, national culture was examined to determine whether empowerment and cooperative climate had consistent moderating effects across cultures. The relationships among these variables were examined using hierarchical linear modeling in a sample of 6,264 employees working at a multinational organization in 337 different work locations across 18 countries. Results suggested that the negative effect of role overload on organizational commitment did not vary as a function of culture in the current sample, but empowerment and cooperative climate had a moderating influence on this relationship. Furthermore, a 3-way interaction was observed between the cultural variable of power distance, empowerment, and role overload in predicting organizational commitment, suggesting that factors that serve to mitigate the negative effects of role overload in one culture may be ineffectual in another. This 3-way interaction was observed regardless of whether Hofstede's (2001) cultural value indices were used or the cultural practice scores from the Global Leadership and Organizational Behavior Effectiveness (GLOBE) project (R. J. House, Hanges, Javidan, Dorfman, & Gupta, 2004).

Interactivity in automatic control: foundations and experiences

OpenAIRE

Dormido Bencomo, Sebastián; Guzmán Sánchez, José Luis; Costa Castelló, Ramon; Berenguel, M

2012-01-01

The first part of this paper presents the concepts of interactivity and visualization and its essential role in learning the fundamentals and techniques of automatic control. More than 10 years experience of the authors in the development and design of interactive tools dedicated to the study of automatic control concepts are also exposed. The second part of the paper summarizes the main features of the “Automatic Control with Interactive Tools” text that has been recently published by Pea...

Increased Global Interaction Across Functional Brain Modules During Cognitive Emotion Regulation.

Science.gov (United States)

Brandl, Felix; Mulej Bratec, Satja; Xie, Xiyao; Wohlschläger, Afra M; Riedl, Valentin; Meng, Chun; Sorg, Christian

2017-07-13

Cognitive emotion regulation (CER) enables humans to flexibly modulate their emotions. While local theories of CER neurobiology suggest interactions between specialized local brain circuits underlying CER, e.g., in subparts of amygdala and medial prefrontal cortices (mPFC), global theories hypothesize global interaction increases among larger functional brain modules comprising local circuits. We tested the global CER hypothesis using graph-based whole-brain network analysis of functional MRI data during aversive emotional processing with and without CER. During CER, global between-module interaction across stable functional network modules increased. Global interaction increase was particularly driven by subregions of amygdala and cuneus-nodes of highest nodal participation-that overlapped with CER-specific local activations, and by mPFC and posterior cingulate as relevant connector hubs. Results provide evidence for the global nature of human CER, complementing functional specialization of embedded local brain circuits during successful CER. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Microscopic nucleon spectral function for finite nuclei featuring two- and three-nucleon short-range correlations: The model versus ab initio calculations for three-nucleon systems

Science.gov (United States)

Ciofi degli Atti, Claudio; Mezzetti, Chiara Benedetta; Morita, Hiko

2017-04-01

Background: Two-nucleon (2 N ) short-range correlations (SRC) in nuclei have been recently thoroughly investigated, both theoretically and experimentally and the study of three-nucleon (3 N ) SRC, which could provide important information on short-range hadronic structure, is underway. Novel theoretical ideas concerning 2 N and 3 N SRC are put forward in the present paper. Purpose: The general features of a microscopic one-nucleon spectral function which includes the effects of both 2 N and 3 N SRC and its comparison with ab initio spectral functions of the three-nucleon systems are illustrated. Methods: A microscopic and parameter-free one-nucleon spectral function expressed in terms of a convolution integral involving ab initio relative and center-of-mass (c.m.) momentum distributions of a 2 N pair and aimed at describing two- and three-nucleon short-range correlations, is obtained by using: (i) the two-nucleon momentum distributions obtained within ab initio approaches based upon nucleon-nucleon interactions of the Argonne family; (ii) the exact relation between one- and two-nucleon momentum distributions; (iii) the fundamental property of factorization of the nuclear wave function at short internucleon ranges. Results: The comparison between the ab initio spectral function of 3He and the one based upon the convolution integral shows that when the latter contains only two-nucleon short-range correlations the removal energy location of the peaks and the region around them exhibited by the ab initio spectral function are correctly predicted, unlike the case of the high and low removal energy tails; the inclusion of the effects of three-nucleon correlations brings the convolution model spectral function in much better agreement with the ab initio one; it is also found that whereas the three-nucleon short-range correlations dominate the high energy removal energy tail of the spectral function, their effects on the one-nucleon momentum distribution are almost one

The persuasive role of ethos in doctor-patient interactions.

Science.gov (United States)

Bigi, Sarah

2011-01-01

In 'expert-to-non-expert' interactions, one of the distinguishing features is that there is no or very little shared knowledge between the subjects. This situation may become particularly challenging when the unshared knowledge is of a very technical kind, as the likeliness of misunderstandings or unsuccessful communication becomes very high. This is particularly true of interactions between patients and physicians. In the course of such interactions, physicians are expected to inform, advise and persuade patients regarding their health problems. It is especially when differences of opinion emerge that physicians need to be persuasive, but it is also then that this may become very difficult, as the patient does not share the medical expertise of the physician. At these moments, one of the most powerful means of persuasion in the hands of physicians is their professional ethos, or authority. The paper presents partial results of an ongoing research project aimed at describing the ways in which physicians construct their professional ethos in interactions with their patients, and how they use it to reconcile patients' diverging opinions with their own. The analysis is carried out on a corpus of video recordings of doctor-patient interactions and it is aimed at identifying different persuasive strategies based on the professional ethos.

Family Functioning in First-Episode and Chronic Psychosis: The Role of Patient's Symptom Severity and Psychosocial Functioning.

Science.gov (United States)

Koutra, Katerina; Triliva, Sofia; Roumeliotaki, Theano; Basta, Maria; Lionis, Christos; Vgontzas, Alexandros N

2016-08-01

The aim of the present study was to assess the relationship between illness-related characteristics, such as symptom severity and psychosocial functioning, and specific aspects of family functioning both in patients experiencing their first episode of psychosis (FEP) and chronically ill patients. A total of 50 FEP and 50 chronic patients diagnosed with schizophrenia or bipolar disorder (most recent episode manic severe with psychotic features) and their family caregivers participated in the study. Family functioning was evaluated in terms of cohesion and flexibility (FACES IV Package), expressed emotion (FQ), family burden (FBS) and caregivers' psychological distress (GHQ-28). Patients' symptom severity (BPRS) and psychosocial functioning (GAS) were assessed by their treating psychiatrist within 2 weeks from the caregivers' assessment. Increased symptom severity was associated with greater dysfunction in terms of family cohesion and flexibility (β coefficient -0.13; 95 % CI -0.23, -0.03), increased caregivers' EE levels on the form of emotional overinvolvement (β coefficient 1.03; 95 % CI 0.02, 2.03), and psychological distress (β coefficient 3.37; 95 % CI 1.29, 5.45). Family burden was found to be significantly related to both symptom severity (β coefficient 3.01; 95 % CI 1.50, 4.51) and patient's functioning (β coefficient -2.04; 95 % CI -3.55, -0.53). No significant interaction effect of chronicity was observed in the afore-mentioned associations. These findings indicate that severe psychopathology and patient's low psychosocial functioning are associated with poor family functioning. It appears that the effect for family function is significant from the early stages of the illness. Thus, early psychoeducational interventions should focus on patients with severe symptomatology and impaired functioning and their families.

Comparison of advanced mid-sized reactors regarding passive features, core damage frequencies and core melt retention features

International Nuclear Information System (INIS)

Wider, H.

2005-01-01

New Light Water Reactors, whose regular safety systems are complemented by passive safety systems, are ready for the market. The special aspect of passive safety features is their actuation and functioning independent of the operator. They add significantly to reduce the core damage frequency (CDF) since the operator continues to play its independent role in actuating the regular safety devices based on modern instrumentation and control (I and C). The latter also has passive features regarding the prevention of accidents. Two reactors with significant passive features that are presently offered on the market are the AP1000 PWR and the SWR 1000 BWR. Their passive features are compared and also their core damage frequencies (CDF). The latter are also compared with those of a VVER-1000. A further discussion about the two passive plants concerns their mitigating features for severe accidents. Regarding core-melt retention both rely on in-vessel cooling of the melt. The new VVER-1000 reactor, on the other hand features a validated ex-vessel concept. (author)

Social interaction in type 2 diabetes computer-mediated environments: How inherent features of the channels influence peer-to-peer interaction.

Science.gov (United States)

Lewinski, Allison A; Fisher, Edwin B

2016-06-01

Interventions via the internet provide support to individuals managing chronic illness. The purpose of this integrative review was to determine how the features of a computer-mediated environment influence social interactions among individuals with type 2 diabetes. A combination of MeSH and keyword terms, based on the cognates of three broad groupings: social interaction, computer-mediated environments, and chronic illness, was used to search the PubMed, PsychInfo, Sociology Research Database, and Cumulative Index to Nursing and Allied Health Literature databases. Eleven articles met the inclusion criteria. Computer-mediated environments enhance an individual's ability to interact with peers while increasing the convenience of obtaining personalized support. A matrix, focused on social interaction among peers, identified themes across all articles, and five characteristics emerged: (1) the presence of synchronous and asynchronous communication, (2) the ability to connect with similar peers, (3) the presence or absence of a moderator, (4) personalization of feedback regarding individual progress and self-management, and (5) the ability of individuals to maintain choice during participation. Individuals interact with peers to obtain relevant, situation-specific information and knowledge about managing their own care. Computer-mediated environments facilitate the ability of individuals to exchange this information despite temporal or geographical barriers that may be present, thus improving T2D self-management. © The Author(s) 2015.

The Role of Platelet and its Interaction with Aspirin

Directory of Open Access Journals (Sweden)

Luisa Fernanda Zúñiga Cerón

2016-04-01

Conclusion. It is recognized the role of platelet in different physiopathological processes and thus its interaction with aspirin, preventing its aggregation and thrombus formation in the spleen and other organs, this way contributing to the prevention of future cardiovascular events.

The role of crossmodal interaction in psychological and brain organization of mathematical abilities

Directory of Open Access Journals (Sweden)

Nikita A. Khokhlov

2016-12-01

Full Text Available The paper analyzes the work of Russian and foreign scholars devoted to the role of cross analyzer cooperation in developing and implementing mathematical abilities.Crossmodal interaction is considered as an additional category of neuropsychological analysis that allows to extend the existing ideas about the psychological structure and brain providing the mathematical ability. There are data that confirm the relevance of studying the interaction of the senses. Many of the research on this issue are carried out using the synesthesia which is considered a rare phenomenon. However, both Russian and foreign works suggest that the interaction of analyzers is not characteristic only to those whose brain is synesthetic. The joint work of the senses is characteristic of every person since his/her childhood, and is an obligatory condition for cognitive processes. Cross analyzer synthesis is assumed to play an important role in producing spatial representations and the ability to intuitively perceive the notion of quantity (evolutionary foundations of mathematical ability. On the brain level, these processes are provided primarily by functioning of parietal and tertiary cortical areas located at the junctionof cortical analyzer areas and also temporal areas that border on the parahippocampal brain area. When dealing with school mathematics the structure of mathematical abilities is changing due to verbal and symbolic representations of numerical coding. Dealing with symbols opens up new opportunities, but it also narrows the spectrum of modalities involved in doing mathematical sums. Thus, the ability to re-encode information from one modality to another after school mathematics is perceived has an impact on the efficacy of mathematical activity. Doing mathematical sums is accompanied by crossmodal interaction that occurs on the unconscious level. Some problem conditions may be efficiently processed in one modality, others may be solved in other modality

Gender Differences in Figural Matrices: The Moderating Role of Item Design Features

Science.gov (United States)

Arendasy, Martin E.; Sommer, Markus

2012-01-01

There is a heated debate on whether observed gender differences in some figural matrices in adults can be attributed to gender differences in inductive reasoning/G[subscript f] or differential item functioning and/or test bias. Based on previous studies we hypothesized that three specific item design features moderate the effect size of the gender…

Influence of contrast morphogenetic features of urban constructed soils on the functioning of Moscow green lawn urban ecosystems: analysis based on the field model experiment

Science.gov (United States)

Epikhina, Anna; Vizirskaya, Mariya; Mazirov, Ilya; Vasenev, Vyacheslav; Vasenev, Ivan; Valentini, Riccardo

2014-05-01

Green lawns are the key element of the urban environment. They occupy a considerable part of the city area and locate in different urban functional zones. Urban constructed soils under green lawns have a unique spatial variability in chemical and morphogenetic features. So far, there is lack of information on the influence of morphogenetic features of urban soils on the functioning of the green lawn ecosystems especially in Moscow - the biggest megalopolis in Europe. Urban lawns perform a number of principal functions including both aesthetic and environmental. The role of the green lawn ecosystems in global carbon cycle is one of their main environmental functions. It is traditionally assessed through carbon stocks and fluxes in the basic ecosystem components. So far, such a data for the urban lawn ecosystems of the Moscow megapolis is lacking. In addition to environmental functions, green lawns perform an important ornamental role, which is also a critical criterion of their optimal functioning. Considering the variability of driving factors, influencing green lawns in urban environment, we carry out the model experiment in order to analyze "pure" effect of soil morphogenetic features. The current study aimed to analyze the influence of contrast morphogenetic features of urban constructed soils on the environmental and aesthetic functions of lawn ecosystems in Moscow megapolis basing in the model experiment. We carry out the model experiment located at the experimental field of the Russian State Agrarian University. Special transparent containers developed for the experiment, provided an option to observe soil morphogenetic features dynamics, including the depth and material of the organic transformation. At the same soil body inside the containers was united with the outside environment through the system of holes in the bottom and walls. The set of urban constructed soils includ four contrast types of the top soil (turf (T), turf-sand (TSa), turf-soil (TSo) and

Ionizing spectra of stars that lose their envelope through interaction with a binary companion: role of metallicity

OpenAIRE

Gotberg, Y.; de Mink, S. E.; Groh, J. H.

2017-01-01

Understanding ionizing fluxes of stellar populations is crucial for various astrophysical problems including the epoch of reionization. Massive short-lived Wolf-Rayet stars are generally considered as the main ionizing sources. We examine the role of less massive stars that lose their envelope through interaction with a companion. We use the evolutionary code MESA and the radiative transfer code CMFGEN to investigate stripped stars as a function of metallicity (Z). We show that typical progen...

The role of emotion in musical improvisation: an analysis of structural features.

Science.gov (United States)

McPherson, Malinda J; Lopez-Gonzalez, Monica; Rankin, Summer K; Limb, Charles J

2014-01-01

One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor) and emotion (happy vs. sad) do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

Role of Polyamines in Immune Cell Functions

Directory of Open Access Journals (Sweden)

Rebecca S. Hesterberg

2018-03-01

Full Text Available The immune system is remarkably responsive to a myriad of invading microorganisms and provides continuous surveillance against tissue damage and developing tumor cells. To achieve these diverse functions, multiple soluble and cellular components must react in an orchestrated cascade of events to control the specificity, magnitude and persistence of the immune response. Numerous catabolic and anabolic processes are involved in this process, and prominent roles for l-arginine and l-glutamine catabolism have been described, as these amino acids serve as precursors of nitric oxide, creatine, agmatine, tricarboxylic acid cycle intermediates, nucleotides and other amino acids, as well as for ornithine, which is used to synthesize putrescine and the polyamines spermidine and spermine. Polyamines have several purported roles and high levels of polyamines are manifest in tumor cells as well in autoreactive B- and T-cells in autoimmune diseases. In the tumor microenvironment, l-arginine catabolism by both tumor cells and suppressive myeloid cells is known to dampen cytotoxic T-cell functions suggesting there might be links between polyamines and T-cell suppression. Here, we review studies suggesting roles of polyamines in normal immune cell function and highlight their connections to autoimmunity and anti-tumor immune cell function.

ICOS:ICOS-ligand interaction is required for type 2 innate lymphoid cell function, homeostasis, and induction of airway hyperreactivity.

Science.gov (United States)

Maazi, Hadi; Patel, Nisheel; Sankaranarayanan, Ishwarya; Suzuki, Yuzo; Rigas, Diamanda; Soroosh, Pejman; Freeman, Gordon J; Sharpe, Arlene H; Akbari, Omid

2015-03-17

Allergic asthma is caused by Th2-cell-type cytokines in response to allergen exposure. Type 2 innate lymphoid cells (ILC2s) are a newly identified subset of immune cells that, along with Th2 cells, contribute to the pathogenesis of asthma by producing copious amounts of IL-5 and IL-13, which cause eosinophilia and airway hyperreactivity (AHR), a cardinal feature of asthma. ILC2s express ICOS, a T cell costimulatory molecule with a currently unknown function. Here we showed that a lack of ICOS on murine ILC2s and blocking the ICOS:ICOS-ligand interaction in human ILC2s reduced AHR and lung inflammation. ILC2s expressed both ICOS and ICOS-ligand, and the ICOS:ICOS-ligand interaction promoted cytokine production and survival in ILC2s through STAT5 signaling. Thus, ICOS:ICOS-ligand signaling pathway is critically involved in ILC2 function and homeostasis. Copyright © 2015 Elsevier Inc. All rights reserved.

Distinct roles of autophagy-dependent and -independent functions of FIP200 revealed by generation and analysis of a mutant knock-in mouse model

Science.gov (United States)

Chen, Song; Wang, Chenran; Yeo, Syn; Liang, Chun-Chi; Okamoto, Takako; Sun, Shaogang; Wen, Jian; Guan, Jun-Lin

2016-01-01

Autophagy is an evolutionarily conserved cellular process controlled through a set of essential autophagy genes (Atgs). However, there is increasing evidence that most, if not all, Atgs also possess functions independent of their requirement in canonical autophagy, making it difficult to distinguish the contributions of autophagy-dependent or -independent functions of a particular Atg to various biological processes. To distinguish these functions for FIP200 (FAK family-interacting protein of 200 kDa), an Atg in autophagy induction, we examined FIP200 interaction with its autophagy partner, Atg13. We found that residues 582–585 (LQFL) in FIP200 are required for interaction with Atg13, and mutation of these residues to AAAA (designated the FIP200-4A mutant) abolished its canonical autophagy function in vitro. Furthermore, we created a FIP200-4A mutant knock-in mouse model and found that specifically blocking FIP200 interaction with Atg13 abolishes autophagy in vivo, providing direct support for the essential role of the ULK1/Atg13/FIP200/Atg101 complex in the process beyond previous studies relying on the complete knockout of individual components. Analysis of the new mouse model showed that nonautophagic functions of FIP200 are sufficient to fully support embryogenesis by maintaining a protective role in TNFα-induced apoptosis. However, FIP200-mediated canonical autophagy is required to support neonatal survival and tumor cell growth. These studies provide the first genetic evidence linking an Atg's autophagy and nonautophagic functions to different biological processes in vivo. PMID:27013233

Mobile personal health records: an evaluation of features and functionality.

Science.gov (United States)

Kharrazi, Hadi; Chisholm, Robin; VanNasdale, Dean; Thompson, Benjamin

2012-09-01

To evaluate stand-alone mobile personal health record (mPHR) applications for the three leading cellular phone platforms (iOS, BlackBerry, and Android), assessing each for content, function, security, and marketing characteristics. Nineteen stand-alone mPHR applications (8 for iOS, 5 for BlackBerry, and 6 for Android) were identified and evaluated. Main criteria used to include mPHRs were: operating standalone on a mobile platform; not requiring external connectivity; and covering a wide range of health topics. Selected mPHRs were analyzed considering product characteristics, data elements, and application features. We also reviewed additional features such as marketing tactics. Within and between the different mobile platforms attributes for the mPHR were highly variable. None of the mPHRs contained all attributes included in our evaluation. The top four mPHRs contained 13 of the 14 features omitting only the in-case-of emergency feature. Surprisingly, seven mPHRs lacked basic security measures as important as password protection. The mPHRs were relatively inexpensive: ranging from no cost to $9.99. The mPHR application cost varied in some instances based on whether it supported single or multiple users. Ten mPHRs supported multiple user profiles. Notably, eight mPHRs used scare tactics as marketing strategy. mPHR is an emerging health care technology. The majority of existing mPHR apps is limited by at least one of the attributes considered for this study; however, as the mobile market continues to expand it is likely that more comprehensive mPHRs will be developed in the near future. New advancements in mobile technology can be utilized to enhance mPHRs by long-term patient empowerment features. Marketing strategies for mPHRs should target specific subpopulations and avoid scare tactics. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

About some distinguishing features of weak interactions

International Nuclear Information System (INIS)

Beshtoev, Kh.M.

1999-01-01

It is shown that, in contrast to strong and electromagnetic theories, additive conserved numbers (such as lepton, aromatic and another numbers) and γ 5 anomaly do not appear in the standard weak interaction theory. It means that in this interaction the additive numbers cannot be conserved. These results are the consequence of specific character of the weak interaction: the right components of spinors do not participate in this interaction. The schemes of violation of the aromatic and lepton numbers were considered

Audio Query by Example Using Similarity Measures between Probability Density Functions of Features

Directory of Open Access Journals (Sweden)

Marko Helén

2010-01-01

Full Text Available This paper proposes a query by example system for generic audio. We estimate the similarity of the example signal and the samples in the queried database by calculating the distance between the probability density functions (pdfs of their frame-wise acoustic features. Since the features are continuous valued, we propose to model them using Gaussian mixture models (GMMs or hidden Markov models (HMMs. The models parametrize each sample efficiently and retain sufficient information for similarity measurement. To measure the distance between the models, we apply a novel Euclidean distance, approximations of Kullback-Leibler divergence, and a cross-likelihood ratio test. The performance of the measures was tested in simulations where audio samples are automatically retrieved from a general audio database, based on the estimated similarity to a user-provided example. The simulations show that the distance between probability density functions is an accurate measure for similarity. Measures based on GMMs or HMMs are shown to produce better results than that of the existing methods based on simpler statistics or histograms of the features. A good performance with low computational cost is obtained with the proposed Euclidean distance.

P2-18: Temporal and Featural Separation of Memory Items Play Little Role for VSTM-Based Change Detection

Directory of Open Access Journals (Sweden)

Dae-Gyu Kim

2012-10-01

Full Text Available Classic studies of visual short-term memory (VSTM found that presenting memory items either sequentially or simultaneously does not affect recognition accuracy of the remembered items. Other studies also suggest that capacity of VSTM benefits from formation of bound object-based representations leading to no cost of remembering multi-feature items. According to these ideas, we aimed to examine the role of temporal and featural separation of memory items in VSTM change detection, (1 if sample items are separated across different temporal moments and (2 if across different feature dimensions. In a series of change detection experiments, we asked participants to report a change between a sample and a test display with a brief delay in between. In experiment 1, the sample items were split into two sets with a different onset time. In experiment 2, the sample items were split across two different feature dimensions (e.g., half color and half orientation. The change detection accuracy in Experiment 1 showed no substantial drop when the memory items were separated into two onset groups compared to simultaneous onset. The accuracy did not drop either when the features of sample items were split across two different feature groups compared to when were not split. The results indicate that temporal and featural separation of VWM items does not play a significant role for VSTM-based change detection.

Functional Complementation Studies Reveal Different Interaction Partners of Escherichia coli IscS and Human NFS1.

Science.gov (United States)

Bühning, Martin; Friemel, Martin; Leimkühler, Silke

2017-08-29

The trafficking and delivery of sulfur to cofactors and nucleosides is a highly regulated and conserved process among all organisms. All sulfur transfer pathways generally have an l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of sulfur-containing biomolecules like iron-sulfur (Fe-S) clusters, thiamine, biotin, lipoic acid, the molybdenum cofactor (Moco), and thiolated nucleosides in tRNA. The human l-cysteine desulfurase NFS1 and the Escherichia coli homologue IscS share a level of amino acid sequence identity of ∼60%. While E. coli IscS has a versatile role in the cell and was shown to have numerous interaction partners, NFS1 is mainly localized in mitochondria with a crucial role in the biosynthesis of Fe-S clusters. Additionally, NFS1 is also located in smaller amounts in the cytosol with a role in Moco biosynthesis and mcm 5 s 2 U34 thio modifications of nucleosides in tRNA. NFS1 and IscS were conclusively shown to have different interaction partners in their respective organisms. Here, we used functional complementation studies of an E. coli iscS deletion strain with human NFS1 to dissect their conserved roles in the transfer of sulfur to a specific target protein. Our results show that human NFS1 and E. coli IscS share conserved binding sites for proteins involved in Fe-S cluster assembly like IscU, but not with proteins for tRNA thio modifications or Moco biosynthesis. In addition, we show that human NFS1 was almost fully able to complement the role of IscS in Moco biosynthesis when its specific interaction partner protein MOCS3 from humans was also present.

Depth-time interpolation of feature trends extracted from mobile microelectrode data with kernel functions.

Science.gov (United States)

Wong, Stephen; Hargreaves, Eric L; Baltuch, Gordon H; Jaggi, Jurg L; Danish, Shabbar F

2012-01-01

Microelectrode recording (MER) is necessary for precision localization of target structures such as the subthalamic nucleus during deep brain stimulation (DBS) surgery. Attempts to automate this process have produced quantitative temporal trends (feature activity vs. time) extracted from mobile MER data. Our goal was to evaluate computational methods of generating spatial profiles (feature activity vs. depth) from temporal trends that would decouple automated MER localization from the clinical procedure and enhance functional localization in DBS surgery. We evaluated two methods of interpolation (standard vs. kernel) that generated spatial profiles from temporal trends. We compared interpolated spatial profiles to true spatial profiles that were calculated with depth windows, using correlation coefficient analysis. Excellent approximation of true spatial profiles is achieved by interpolation. Kernel-interpolated spatial profiles produced superior correlation coefficient values at optimal kernel widths (r = 0.932-0.940) compared to standard interpolation (r = 0.891). The choice of kernel function and kernel width resulted in trade-offs in smoothing and resolution. Interpolation of feature activity to create spatial profiles from temporal trends is accurate and can standardize and facilitate MER functional localization of subcortical structures. The methods are computationally efficient, enhancing localization without imposing additional constraints on the MER clinical procedure during DBS surgery. Copyright © 2012 S. Karger AG, Basel.

Speech networks at rest and in action: interactions between functional brain networks controlling speech production.

Science.gov (United States)

Simonyan, Kristina; Fuertinger, Stefan

2015-04-01

Speech production is one of the most complex human behaviors. Although brain activation during speaking has been well investigated, our understanding of interactions between the brain regions and neural networks remains scarce. We combined seed-based interregional correlation analysis with graph theoretical analysis of functional MRI data during the resting state and sentence production in healthy subjects to investigate the interface and topology of functional networks originating from the key brain regions controlling speech, i.e., the laryngeal/orofacial motor cortex, inferior frontal and superior temporal gyri, supplementary motor area, cingulate cortex, putamen, and thalamus. During both resting and speaking, the interactions between these networks were bilaterally distributed and centered on the sensorimotor brain regions. However, speech production preferentially recruited the inferior parietal lobule (IPL) and cerebellum into the large-scale network, suggesting the importance of these regions in facilitation of the transition from the resting state to speaking. Furthermore, the cerebellum (lobule VI) was the most prominent region showing functional influences on speech-network integration and segregation. Although networks were bilaterally distributed, interregional connectivity during speaking was stronger in the left vs. right hemisphere, which may have underlined a more homogeneous overlap between the examined networks in the left hemisphere. Among these, the laryngeal motor cortex (LMC) established a core network that fully overlapped with all other speech-related networks, determining the extent of network interactions. Our data demonstrate complex interactions of large-scale brain networks controlling speech production and point to the critical role of the LMC, IPL, and cerebellum in the formation of speech production network. Copyright © 2015 the American Physiological Society.

Wide range of interacting partners of pea Gβ subunit of G-proteins suggests its multiple functions in cell signalling.

Science.gov (United States)

Bhardwaj, Deepak; Lakhanpaul, Suman; Tuteja, Narendra

2012-09-01

Climate change is a major concern especially in view of the increasing global population and food security. Plant scientists need to look for genetic tools whose appropriate usage can contribute to sustainable food availability. G-proteins have been identified as some of the potential genetic tools that could be useful for protecting plants from various stresses. Heterotrimeric G-proteins consisting of three subunits Gα, Gβ and Gγ are important components of a number of signalling pathways. Their structure and functions are already well studied in animals but their potential in plants is now gaining attention for their role in stress tolerance. Earlier we have reported that over expressing pea Gβ conferred heat tolerance in tobacco plants. Here we report the interacting partners (proteins) of Gβ subunit of Pisum sativum and their putative role in stress and development. Out of 90 transformants isolated from the yeast-two-hybrid (Y2H) screening, seven were chosen for further investigation due to their recurrence in multiple experiments. These interacting partners were confirmed using β-galactosidase colony filter lift and ONPG (O-nitrophenyl-β-D-galactopyranoside) assays. These partners include thioredoxin H, histidine-containing phosphotransfer protein 5-like, pathogenesis-related protein, glucan endo-beta-1, 3-glucosidase (acidic isoform), glycine rich RNA binding protein, cold and drought-regulated protein (corA gene) and soluble inorganic pyrophosphatase 1. This study suggests the role of pea Gβ subunit in stress signal transduction and development pathways owing to its capability to interact with a wide range of proteins of multiple functions. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Is Early-onset in Major Depression a Predictor of Specific Clinical Features with More Impaired Social Function?

Institute of Scientific and Technical Information of China (English)

Yan-Hong Liu; Lin Chen; Yun-Ai Su; Yi-Ru Fang; Manit Srisurapanont; Jin Pyo Hong; Ahmad Hatim

2015-01-01

Background:Early-onset major depressive disorder (MDD) (EOD) is often particularly malignant due to its special clinical features,accompanying impaired social function,protracted recovery time,and frequent recurrence.This study aimed to observe the effects of age onset on clinical characteristics and social function in MDD patients in Asia.Methods:In total,547 out-patients aged 18-65 years who were from 13 study sites in five Asian countries were included.These patients had MDD diagnose according to the Diagnostic and Statistical Manual of Mental Disorders,4th Edition criteria.Clinical features and social function were assessed using Symptom Checklist-90-revised (SCL-90-R) and Sheehan Disability Scale (SDS).Quality of life was assessed by a 36-item Short-form Health Survey (SF-36).Analyses were performed using a continuous or dichotomous (cut-off:30 years)age-of-onset indicator.Results:Early-onset MDD (EOD,＜30 years) was associated with longer illness (P =0.003),unmarried status (P ＜ 0.001),higher neuroticism (P ≤ 0.002) based on the SCL-90-R,and more limited social function and mental health (P =0.006,P =0.007) based on the SF-36 and SDS.The impairment of social function and clinical severity were more prominent at in-patients with younger onset ages.Special clinical features and more impaired social function and quality of life were associated with EOD,as in western studies.Conclusions:EOD often follows higher levels of neuroticism.Age of onset of MDD may be a predictor of clinical features and impaired social function,allowing earlier diagnosis and treatment.

FIT: Computer Program that Interactively Determines Polynomial Equations for Data which are a Function of Two Independent Variables

Science.gov (United States)

Arbuckle, P. D.; Sliwa, S. M.; Roy, M. L.; Tiffany, S. H.

1985-01-01

A computer program for interactively developing least-squares polynomial equations to fit user-supplied data is described. The program is characterized by the ability to compute the polynomial equations of a surface fit through data that are a function of two independent variables. The program utilizes the Langley Research Center graphics packages to display polynomial equation curves and data points, facilitating a qualitative evaluation of the effectiveness of the fit. An explanation of the fundamental principles and features of the program, as well as sample input and corresponding output, are included.

Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

Science.gov (United States)

Clare, David S; Spencer, Matthew; Robinson, Leonie A; Frid, Christopher L J

2016-01-01

Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions) and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions) but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive) or antagonistic (negative) depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

Directory of Open Access Journals (Sweden)

David S Clare

Full Text Available Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive or antagonistic (negative depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

The Effectiveness of Role Theory Based Group Counseling on Family Function of Families With Slow-Learning Children

Directory of Open Access Journals (Sweden)

فرناز حوله کیان

2015-12-01

Full Text Available The purpose of this study was to examine the effectiveness of group counseling based on the role theory on function of families with slow-learningchildren. The present study is a Quasi - experimental research with pre-test and post - test, and with experimental and control groups. Statistical population in cludes all mothers of slow - learning children in thecity of Hamadan. A sample of 30 subjects selected through available sampling method from high schools with equal numbers of both genders. Based on cloning features were allocated in experimental and control groups. The experimental group received 10 group counseling and control group was placed in the waiting list. Data collection instrument is family function questionnaire. Descriptive statistics, covariance analysis and t-test were applied to analyze data. It was found that there is a significant difference between post-test of experimental and control group (p<0/001. t-test showed significant difference in effectiveness of role theory group counseling for mothers with slow-learning girl and boy (p<0/001. So we can conclude that group counseling based on the role theory is effective on improving the function of families with slow-learning children. In addition, this effectivenessis different for families of slow-learning children based on the gender of child.

Functional Interactions Between Early Biopolymers and Primitive Cells

Science.gov (United States)

Heili, J.; Gaut, N.; Han, Q.; Gomez-Garcia, J.; Szostak, J. W.; Adamala, K. P.; Engelhart, A. E.

2017-07-01

Recently, we have demonstrated that compartmentalized biomolecules exhibit functional behaviors not observed in bulk solution. We suggest that numerous synthetic and regulatory processes might have been enabled by membrane-biomolecule interactions.

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

Science.gov (United States)

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.

Examining the Impact of Maternal Individual Features on Children's Behavioral Problems in Adoptive Families: The Role of Maternal Temperament and Neurobiological Markers.

Science.gov (United States)

Ozturk, Yagmur; Barone, Virginia; Barone, Lavinia

2018-01-24

The first year after adoption constitutes a sensitive period for both strengthening the new emotional bond in the family and checking its appropriate development by adoption services. A key variable for children's catch-up are adoptive parents' socioemotional and individual features. The aim of this study is to investigate links between adoptive mothers' individual features and behavioral problems in their children in the first year after adoption placement, by testing the moderating role of both age at adoption and maternal genetic polymorphisms. Seventy-eight adoptive mothers completed temperament and genetic measures. Mothers showed a specific pattern of interaction between basic temperament traits and genetic markers in their assessment of children's behavioral problems; dopamine D4 receptor gene and children's age at adoption are two moderators in the association in which mothers' temperament was affecting the evaluation of their children's behavioral problems. Findings highlight a still undervalued area of parenting resources in the process of post-institutionalized children's catch-up after adoption placement, by showing how individual features count in the commonly measured variable of children's behavioral and emotional problems. This could help in orienting identification and choice of key variables for family assessment after adoption placement, thus contributing in fostering children's healthy development.

Fractographic features of glass-ceramic and zirconia-based dental restorations fractured during clinical function.

Science.gov (United States)

Oilo, Marit; Hardang, Anne D; Ulsund, Amanda H; Gjerdet, Nils R

2014-06-01

Fractures during clinical function have been reported as the major concern associated with all-ceramic dental restorations. The aim of this study was to analyze the fracture features of glass-ceramic and zirconia-based restorations fractured during clinical use. Twenty-seven crowns and onlays were supplied by dentists and dental technicians with information about type of cement and time in function, if available. Fourteen lithium disilicate glass-ceramic restorations and 13 zirconia-based restorations were retrieved and analyzed. Fractographic features were examined using optical microscopy to determine crack initiation and crack propagation of the restorations. The material comprised fractured restorations from one canine, 10 incisors, four premolars, and 11 molars. One crown was not categorized because of difficulty in orientation of the fragments. The results revealed that all core and veneer fractures initiated in the cervical margin and usually from the approximal area close to the most coronally placed curvature of the margin. Three cases of occlusal chipping were found. The margin of dental all-ceramic single-tooth restorations was the area of fracture origin. The fracture features were similar for zirconia, glass-ceramic, and alumina single-tooth restorations. Design features seem to be of great importance for fracture initiation. © 2014 Eur J Oral Sci.

Direct interaction of beta-amyloid with Na,K-ATPase as a putative regulator of the enzyme function

Science.gov (United States)

Petrushanko, Irina Yu.; Mitkevich, Vladimir A.; Anashkina, Anastasia A.; Adzhubei, Alexei A.; Burnysheva, Ksenia M.; Lakunina, Valentina A.; Kamanina, Yulia V.; Dergousova, Elena A.; Lopina, Olga D.; Ogunshola, Omolara O.; Bogdanova, Anna Yu.; Makarov, Alexander A.

2016-06-01

By maintaining the Na+ and K+ transmembrane gradient mammalian Na,K-ATPase acts as a key regulator of neuronal electrotonic properties. Na,K-ATPase has an important role in synaptic transmission and memory formation. Accumulation of beta-amyloid (Aβ) at the early stages of Alzheimer’s disease is accompanied by reduction of Na,K-ATPase functional activity. The molecular mechanism behind this phenomenon is not known. Here we show that the monomeric Aβ(1-42) forms a tight (Kd of 3 μM), enthalpy-driven equimolar complex with α1β1 Na,K-ATPase. The complex formation results in dose-dependent inhibition of the enzyme hydrolytic activity. The binding site of Aβ(1-42) is localized in the “gap” between the alpha- and beta-subunits of Na,K-ATPase, disrupting the enzyme functionality by preventing the subunits from shifting towards each other. Interaction of Na,K-ATPase with exogenous Aβ(1-42) leads to a pronounced decrease of the enzyme transport and hydrolytic activity and Src-kinase activation in neuroblastoma cells SH-SY5Y. This interaction allows regulation of Na,K-ATPase activity by short-term increase of the Aβ(1-42) level. However prolonged increase of Aβ(1-42) level under pathological conditions could lead to chronical inhibition of Na,K-ATPase and disruption of neuronal function. Taken together, our data suggest the role of beta-amyloid as a novel physiological regulator of Na,K-ATPase.

Collaborative role construction in a conversation with dementia: an application of systemic functional linguistics.

Science.gov (United States)

Müller, Nicole; Wilson, Brent T

2008-01-01

This study applies the tools provided by Systemic Functional Linguistics (SFL) to the description of patterns in a conversation between a person with dementia and a person without. It shows how, in the presence of, on the one hand, considerable communicative and cognitive deficits, and on the other, a collaborative interlocutor, a person with dementia succeeds in leading and sustaining a lengthy conversation, and of constructing for himself a positive role in the interaction, namely that of the elder advising a much younger man.

The role of asymmetric interactions on the effect of habitat destruction in mutualistic networks.

Directory of Open Access Journals (Sweden)

Guillermo Abramson

Full Text Available Plant-pollinator mutualistic networks are asymmetric in their interactions: specialist plants are pollinated by generalist animals, while generalist plants are pollinated by a broad range involving specialists and generalists. It has been suggested that this asymmetric--or disassortative--assemblage could play an important role in determining the observed equal susceptibility of specialist and generalist plants under habitat destruction. At the core of the analysis of the phenomenon lies the observation that specialist plants, otherwise candidates to extinction, could cope with the disruption thanks to their interaction with a few generalist pollinators. We present a theoretical framework that supports this thesis. We analyze a dynamical model of a system of mutualistic plants and pollinators, subject to the destruction of their habitat. We analyze and compare two families of interaction topologies, ranging from highly assortative to highly disassortative ones, as well as real pollination networks. We found that several features observed in natural systems are predicted by the mathematical model. First, there is a tendency to increase the asymmetry of the network as a result of the extinctions. Second, an entropy measure of the differential susceptibility to extinction of specialist and generalist species show that they tend to balance when the network is disassortative. Finally, the disappearance of links in the network, as a result of extinctions, shows that specialist plants preserve more connections than the corresponding plants in an assortative system, enabling them to resist the disruption.

Improving functional modules discovery by enriching interaction networks with gene profiles

KAUST Repository

Salem, Saeed

2013-05-01

Recent advances in proteomic and transcriptomic technologies resulted in the accumulation of vast amount of high-throughput data that span multiple biological processes and characteristics in different organisms. Much of the data come in the form of interaction networks and mRNA expression arrays. An important task in systems biology is functional modules discovery where the goal is to uncover well-connected sub-networks (modules). These discovered modules help to unravel the underlying mechanisms of the observed biological processes. While most of the existing module discovery methods use only the interaction data, in this work we propose, CLARM, which discovers biological modules by incorporating gene profiles data with protein-protein interaction networks. We demonstrate the effectiveness of CLARM on Yeast and Human interaction datasets, and gene expression and molecular function profiles. Experiments on these real datasets show that the CLARM approach is competitive to well established functional module discovery methods.

Pro-recombination role of Srs2 protein requires SUMO (small ubiquitin-like modifier) but is independent of PCNA (proliferating cell nuclear antigen) interaction

DEFF Research Database (Denmark)

Kolesar, Peter; Altmannova, Veronika; Pinela da Silva, Sonia Cristina

2016-01-01

of SIM in asrs2ΔPIMstrain leads to a decrease in recombination, indicating a pro-recombination role of SUMO. Thus SIM has an ambivalent function in Srs2 regulation; it not only mediates interaction with SUMO-PCNA to promote the anti-recombination function but it also plays a PCNA-independent pro......-recombination role, probably by stimulating the formation of recombination complexes. The fact that deletion of PIM suppresses the phenotypes of Srs2 lacking SIM suggests that proper balance between the anti-recombination PCNA-bound and pro-recombination pools of Srs2 is crucial. Notably, sumoylation of Srs2 itself...

Multiple genetic interaction experiments provide complementary information useful for gene function prediction.

Directory of Open Access Journals (Sweden)

Magali Michaut

Full Text Available Genetic interactions help map biological processes and their functional relationships. A genetic interaction is defined as a deviation from the expected phenotype when combining multiple genetic mutations. In Saccharomyces cerevisiae, most genetic interactions are measured under a single phenotype - growth rate in standard laboratory conditions. Recently genetic interactions have been collected under different phenotypic readouts and experimental conditions. How different are these networks and what can we learn from their differences? We conducted a systematic analysis of quantitative genetic interaction networks in yeast performed under different experimental conditions. We find that networks obtained using different phenotypic readouts, in different conditions and from different laboratories overlap less than expected and provide significant unique information. To exploit this information, we develop a novel method to combine individual genetic interaction data sets and show that the resulting network improves gene function prediction performance, demonstrating that individual networks provide complementary information. Our results support the notion that using diverse phenotypic readouts and experimental conditions will substantially increase the amount of gene function information produced by genetic interaction screens.

Reductio ad discrimen: Where features come from

Directory of Open Access Journals (Sweden)

Elizabeth Cowper

2015-04-01

Full Text Available This paper addresses two fundamental questions about the nature of formal features in phonology and morphosyntax: what is their expressive power, and where do they come from? To answer these questions, we begin with the most restrictive possible hypothesis (all features are privative, and are wholly dictated by Universal Grammar, with no room for cross-linguistic variation, and examine the extent to which empirical evidence from a variety of languages compels a retreat from this position. We argue that there is little to be gained by positing a universal set of specific features, and propose instead that the crucial contribution of UG is the language learner's ability to construct features by identifying correlations between contrasts at different levels of linguistic structure. This view resonates with current research on how the interaction between UG and external 'third factors' shapes the structure of language, while at the same time harking back to the Saussurean notion that contrast is the central function of linguistic representations.

On the role of electrostatics on protein-protein interactions

Science.gov (United States)

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-01-01

The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

Protozoa lectins and their role in host-pathogen interactions.

Science.gov (United States)

Singh, Ram Sarup; Walia, Amandeep Kaur; Kanwar, Jagat Rakesh

2016-01-01

Lectins are proteins/glycoproteins of non-immune origin that agglutinate red blood cells, lymphocytes, fibroblasts, etc., and bind reversibly to carbohydrates present on the apposing cells. They have at least two carbohydrate binding sites and their binding can be inhibited by one or more carbohydrates. Owing to carbohydrate binding specificity of lectins, they mediate cell-cell interactions and play role in protozoan adhesion and host cell cytotoxicity, thus are central to the pathogenic property of the parasite. Several parasitic protozoa possess lectins which mediate parasite adherence to host cells based on their carbohydrate specificities. These interactions could be exploited for development of novel therapeutics, targeting the adherence and thus helpful in eradicating wide spread of protozoan diseases. The current review highlights the present state knowledge with regard to protozoal lectins with an emphasis on their haemagglutination activity, carbohydrate specificity, characteristics and also their role in pathogenesis notably as adhesion molecules, thereby aiding the pathogen in disease establishment. Copyright © 2016 Elsevier Inc. All rights reserved.

Measuring functional, interactive and critical health literacy of Chinese secondary school students: reliable, valid and feasible?

Science.gov (United States)

Guo, Shuaijun; Davis, Elise; Yu, Xiaoming; Naccarella, Lucio; Armstrong, Rebecca; Abel, Thomas; Browne, Geoffrey; Shi, Yanqin

2018-04-01

Health literacy is an increasingly important topic in the global context. In mainland China, health literacy measures mainly focus on health knowledge and practices or on the functional domain for adolescents. However, little is known about interactive and critical domains. This study aimed to adopt a skills-based and three-domain (functional, interactive and critical) instrument to measure health literacy in Chinese adolescents and to examine the status and determinants of each domain. Using a systematic review, the eight-item Health Literacy Assessment Tool (HLAT-8) was selected and translated from English to Chinese (c-HLAT-8). Following the translation process, a cross-sectional study was conducted in four secondary schools in Beijing, China. A total of 650 students in Years 7-9 were recruited to complete a self-administered questionnaire that assessed socio-demographics, self-efficacy, social support, school environment, community environment and health literacy. Results showed that the c-HLAT-8 had satisfactory reliability (Cronbach's α = 0.79; intra-class correlation coefficient = 0.72) and strong validity (translation validity index (TVI) ≥0.95; χ 2 / df = 3.388, p students had an average score of 26.37 (±5.89) for the c-HLAT-8. When the determinants of each domain of health literacy were examined, social support was the strongest predictor of interactive and critical health literacy. On the contrary, self-efficacy and school environment played more dominant roles in predicting functional health literacy. The c-HLAT-8 was demonstrated to be a reliable, valid and feasible instrument for measuring functional, interactive and critical health literacy among Chinese students. The current findings indicate that increasing self-efficacy, social support and creating supportive environments are important for promoting health literacy in secondary school settings in China.

Industrial requirements for interactive product configurators

DEFF Research Database (Denmark)

Queva, Matthieu Stéphane Benoit; Probst, Christian W.; Vikkelsøe, Per

2009-01-01

The demand for highly customized products at low cost is driving the industry towards Mass Customization. Interactive product configurators play an essential role in this new trend, and must be able to support more and more complex features. The purpose of this paper is, firstly, to identify...... requirements for modern interactive configurators. Existing modeling and solving technologies for configuration are then reviewed and their limitations discussed. Finally, a proposition for a future product configuration system is described....

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.

Science.gov (United States)

Kulmanov, Maxat; Khan, Mohammed Asif; Hoehndorf, Robert; Wren, Jonathan

2018-02-15

A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often only done rigorously for few selected model organisms. Computational function prediction approaches have been suggested to fill this gap. The functions of proteins are classified using the Gene Ontology (GO), which contains over 40 000 classes. Additionally, proteins have multiple functions, making function prediction a large-scale, multi-class, multi-label problem. We have developed a novel method to predict protein function from sequence. We use deep learning to learn features from protein sequences as well as a cross-species protein-protein interaction network. Our approach specifically outputs information in the structure of the GO and utilizes the dependencies between GO classes as background information to construct a deep learning model. We evaluate our method using the standards established by the Computational Assessment of Function Annotation (CAFA) and demonstrate a significant improvement over baseline methods such as BLAST, in particular for predicting cellular locations. Web server: http://deepgo.bio2vec.net, Source code: https://github.com/bio-ontology-research-group/deepgo. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Reduced TET2 function leads to T-cell lymphoma with follicular helper T-cell-like features in mice

International Nuclear Information System (INIS)

Muto, H; Sakata-Yanagimoto, M; Nagae, G; Shiozawa, Y; Miyake, Y; Yoshida, K; Enami, T; Kamada, Y; Kato, T; Uchida, K; Nanmoku, T; Obara, N; Suzukawa, K; Sanada, M; Nakamura, N; Aburatani, H; Ogawa, S; Chiba, S

2014-01-01

TET2 (Ten Eleven Translocation 2) is a dioxygenase that converts methylcytosine (mC) to hydroxymethylcytosine (hmC). TET2 loss-of-function mutations are highly frequent in subtypes of T-cell lymphoma that harbor follicular helper T (Tfh)-cell-like features, such as angioimmunoblastic T-cell lymphoma (30–83%) or peripheral T-cell lymphoma, not otherwise specified (10–49%), as well as myeloid malignancies. Here, we show that middle-aged Tet2 knockdown (Tet2 gt/gt ) mice exhibit Tfh-like cell overproduction in the spleen compared with control mice. The Tet2 knockdown mice eventually develop T-cell lymphoma with Tfh-like features after a long latency (median 67 weeks). Transcriptome analysis revealed that these lymphoma cells had Tfh-like gene expression patterns when compared with splenic CD4-positive cells of wild-type mice. The lymphoma cells showed lower hmC densities around the transcription start site (TSS) and higher mC densities at the regions of the TSS, gene body and CpG islands. These epigenetic changes, seen in Tet2 insufficiency-triggered lymphoma, possibly contributed to predated outgrowth of Tfh-like cells and subsequent lymphomagenesis. The mouse model described here suggests that TET2 mutations play a major role in the development of T-cell lymphoma with Tfh-like features in humans

Self-esteem as a mediator of the relationship between role functioning and symptoms for individuals with severe mental illness: a prospective analysis of Modified Labeling theory.

Science.gov (United States)

Davis, Lisa; Kurzban, Seth; Brekke, John

2012-05-01

Despite a growing body of evidence supporting the efficacy of psychosocial rehabilitation for individuals with severe mental illness (SMI), a large proportion of these individuals remain unable to maintain basic social roles such as employee, parent, or spouse. This study investigated whether changes in role functioning over time impact symptom severity indirectly through the mechanism of changes in self-esteem as posited by Modified Labeling theory. The study sample was composed of 148 individuals diagnosed with schizophrenia, schizoaffective disorder, bipolar disorder with psychotic features, and major depression with psychotic features who elected to participate in community-based psychosocial rehabilitation services. Measures of role functioning, self-esteem, and psychiatric symptoms were gathered at baseline and six months through a combination of structured clinical interviews and self-report surveys. SEM results at baseline provided support for a model in which self-esteem fully mediated the relationship between role functioning and psychiatric symptoms. The final model explained 20% of the variance in psychiatric symptoms. Analyses at six months post-baseline (time 2) indicate that changes in self-esteem fully mediated the relationship between changes in role functioning and changes in psychiatric symptoms. The final change model explained 23% of the variance in changes in psychiatric symptoms. Results provide empirical support for the principles underlying Modified Labeling theory. Implications include the need for interventions that focus on social participation as a means of improving self-esteem, thereby decreasing symptom exacerbation and future relapse for people with SMI. Copyright © 2012 Elsevier B.V. All rights reserved.

The role of emotion in musical improvisation: an analysis of structural features.

Directory of Open Access Journals (Sweden)

Malinda J McPherson

Full Text Available One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor and emotion (happy vs. sad do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

Is Early-onset in Major Depression a Predictor of Specific Clinical Features with More Impaired Social Function?

Science.gov (United States)

Liu, Yan-Hong; Chen, Lin; Su, Yun-Ai; Fang, Yi-Ru; Srisurapanont, Manit; Hong, Jin Pyo; Hatim, Ahmad; Chua, Hong Choon; Bautista, Dianne; Si, Tian-Mei

2015-01-01

Background: Early-onset major depressive disorder (MDD) (EOD) is often particularly malignant due to its special clinical features, accompanying impaired social function, protracted recovery time, and frequent recurrence. This study aimed to observe the effects of age onset on clinical characteristics and social function in MDD patients in Asia. Methods: In total, 547 out-patients aged 18–65 years who were from 13 study sites in five Asian countries were included. These patients had MDD diagnose according to the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition criteria. Clinical features and social function were assessed using Symptom Checklist-90-revised (SCL-90-R) and Sheehan Disability Scale (SDS). Quality of life was assessed by a 36-item Short-form Health Survey (SF-36). Analyses were performed using a continuous or dichotomous (cut-off: 30 years) age-of-onset indicator. Results: Early-onset MDD (EOD, <30 years) was associated with longer illness (P = 0.003), unmarried status (P < 0.001), higher neuroticism (P ≤ 0.002) based on the SCL-90-R, and more limited social function and mental health (P = 0.006, P = 0.007) based on the SF-36 and SDS. The impairment of social function and clinical severity were more prominent at in-patients with younger onset ages. Special clinical features and more impaired social function and quality of life were associated with EOD, as in western studies. Conclusions: EOD often follows higher levels of neuroticism. Age of onset of MDD may be a predictor of clinical features and impaired social function, allowing earlier diagnosis and treatment. PMID:25758278

HTLV-1 specific CD8+ T cell function augmented by blockade of 2B4/CD48 interaction in HTLV-1 infection.

Directory of Open Access Journals (Sweden)

Chibueze Chioma Ezinne

Full Text Available CD8+ T cell response is important in the response to viral infections; this response though is regulated by inhibitory receptors. Expression of inhibitory receptors has been positively correlated with CD8+ T cell exhaustion; the consequent effect of simultaneous blockade of these inhibitory receptors on CD8+ T cell response in viral infections have been studied, however, the role of individual blockade of receptor-ligand pair is unclear. 2B4/CD48 interaction is involved in CD8+T cell regulation, its signal transducer SAP (signaling lymphocyte activation molecule (SLAM-associated protein is required for stimulatory function of 2B4/CD244 on lymphocytes hence, we analyzed 2B4/CD244 (natural killer cell receptor and SAP (signaling lymphocyte activation molecule(SLAM-associated protein on total CD8+ and HTLV-1 specific CD8+T cells in HTLV-1 infection and the effect of blockade of interaction with ligand CD48 on HTLV-1 specific CD8+ T cell function. We observed a high expression of 2B4/CD244 on CD8+ T cells relative to uninfected and further upregulation on HTLV-1 specific CD8+ T cells. 2B4+ CD8+ T cells exhibited more of an effector and terminally differentiated memory phenotype. Blockade of 2B4/CD48 interaction resulted in improvement in function via perforin expression and degranulation as measured by CD107a surface mobilization on HTLV-1 specific CD8+ T cells. In the light of these findings, we thus propose an inhibitory role for 2B4/CD48 interaction on CD8+T cell function.

Intranasal oxytocin modulates neural functional connectivity during human social interaction.

Science.gov (United States)

Rilling, James K; Chen, Xiangchuan; Chen, Xu; Haroon, Ebrahim

2018-02-10

Oxytocin (OT) modulates social behavior in primates and many other vertebrate species. Studies in non-primate animals have demonstrated that, in addition to influencing activity within individual brain areas, OT influences functional connectivity across networks of areas involved in social behavior. Previously, we used fMRI to image brain function in human subjects during a dyadic social interaction task following administration of either intranasal oxytocin (INOT) or placebo, and analyzed the data with a standard general linear model. Here, we conduct an extensive re-analysis of these data to explore how OT modulates functional connectivity across a neural network that animal studies implicate in social behavior. OT induced widespread increases in functional connectivity in response to positive social interactions among men and widespread decreases in functional connectivity in response to negative social interactions among women. Nucleus basalis of Meynert, an important regulator of selective attention and motivation with a particularly high density of OT receptors, had the largest number of OT-modulated connections. Regions known to receive mesolimbic dopamine projections such as the nucleus accumbens and lateral septum were also hubs for OT effects on functional connectivity. Our results suggest that the neural mechanism by which OT influences primate social cognition may include changes in patterns of activity across neural networks that regulate social behavior in other animals. © 2018 Wiley Periodicals, Inc.

The Association between Belgian Older Adults' Physical Functioning and Physical Activity: What Is the Moderating Role of the Physical Environment?

Science.gov (United States)

Van Holle, Veerle; Van Cauwenberg, Jelle; Gheysen, Freja; Van Dyck, Delfien; Deforche, Benedicte; Van de Weghe, Nico; De Bourdeaudhuij, Ilse

2016-01-01

Better physical functioning in the elderly may be associated with higher physical activity levels. Since older adults spend a substantial part of the day in their residential neighborhood, the neighborhood physical environment may moderate associations between functioning and older adults' physical activity. The present study investigated the moderating role of the objective and perceived physical environment on associations between Belgian older adults' physical functioning and transport walking, recreational walking, and moderate-to-vigorous physical activity. Data from 438 older adults were included. Objective physical functioning was assessed using the Short Physical Performance Battery. Potential moderators included objective neighborhood walkability and perceptions of land use mix diversity, access to recreational facilities, access to services, street connectivity, physical barriers for walking, aesthetics, crime-related safety, traffic speeding-related safety, and walking infrastructure. Transport and recreational walking were self-reported, moderate-to-vigorous physical activity was assessed through accelerometers. Multi-level regression analyses were conducted using MLwiN to examine two-way interactions between functioning and the environment on both walking outcomes. Based on a previous study where environment x neighborhood income associations were found for Belgian older adults' moderate-to-vigorous physical activity, three-way functioning x environment x income interactions were examined for moderate-to-vigorous physical activity. Objectively-measured walkability moderated the association between functioning and transport walking; this positive association was only present in high-walkable neighborhoods. Moreover, a three-way interaction was observed for moderate-to-vigorous physical activity. Only in high-income, high-walkable neighborhoods, there was a positive association between functioning and moderate-to-vigorous physical activity. No

Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

Science.gov (United States)

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter; Salas, Margarita; Redrejo-Rodríguez, Modesto

2017-07-26

Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing the knowledge of the viral proteome, we carried out a comprehensive yeast two-hybrid analysis among all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprises 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggested that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, being the latter also supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving non-structural proteins, such as the DNA binding protein P1 and the genome terminal protein (P4), which was confirmed by co-immunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tail-less viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown

Role of Teacher in Forming Experience of Intercultural Interaction in Students

Directory of Open Access Journals (Sweden)

V I Kazarenkov

2014-12-01

Full Text Available The article considers the role of the teacher in the realization of one of the significant aspects of the problem of forming the experience of intercultural interaction in higher school students. The significance of personal and professional resources of the higher school teacher for the effective development in the future experts the requirement for intercultural interaction, the experience of intercultural interaction is revealed. The separate directions and forms of the activity of the teacher aimed at forming in students the experience of intercultural interaction in socially-educational space of the higher school are presented.

The early development of executive function and its relation to social interaction: A brief review

Directory of Open Access Journals (Sweden)

Yusuke eMoriguchi

2014-04-01

Full Text Available Executive function (EF refers to the ability to execute appropriate actions and to inhibit inappropriate actions for the attainment of a specific goal. Research has shown that this ability develops rapidly during the preschool years. Recently, it has been proposed that research on executive function should consider the importance of social interaction. In this article, recent evidence regarding the early development of executive function and its relation to social interaction has been reviewed. Research consistently showed that social interaction can influence executive function skills in young children. However, the development of executive function may facilitate the cognitive skills that are important for social interaction. Taken together, there might be functional dependency between the development of executive function and social interaction.

How linear features alter predator movement and the functional response.

KAUST Repository

McKenzie, Hannah W

2012-01-18

In areas of oil and gas exploration, seismic lines have been reported to alter the movement patterns of wolves (Canis lupus). We developed a mechanistic first passage time model, based on an anisotropic elliptic partial differential equation, and used this to explore how wolf movement responses to seismic lines influence the encounter rate of the wolves with their prey. The model was parametrized using 5 min GPS location data. These data showed that wolves travelled faster on seismic lines and had a higher probability of staying on a seismic line once they were on it. We simulated wolf movement on a range of seismic line densities and drew implications for the rate of predator-prey interactions as described by the functional response. The functional response exhibited a more than linear increase with respect to prey density (type III) as well as interactions with seismic line density. Encounter rates were significantly higher in landscapes with high seismic line density and were most pronounced at low prey densities. This suggests that prey at low population densities are at higher risk in environments with a high seismic line density unless they learn to avoid them.

How linear features alter predator movement and the functional response.

KAUST Repository

McKenzie, Hannah W; Merrill, Evelyn H; Spiteri, Raymond J; Lewis, Mark A

2012-01-01

In areas of oil and gas exploration, seismic lines have been reported to alter the movement patterns of wolves (Canis lupus). We developed a mechanistic first passage time model, based on an anisotropic elliptic partial differential equation, and used this to explore how wolf movement responses to seismic lines influence the encounter rate of the wolves with their prey. The model was parametrized using 5 min GPS location data. These data showed that wolves travelled faster on seismic lines and had a higher probability of staying on a seismic line once they were on it. We simulated wolf movement on a range of seismic line densities and drew implications for the rate of predator-prey interactions as described by the functional response. The functional response exhibited a more than linear increase with respect to prey density (type III) as well as interactions with seismic line density. Encounter rates were significantly higher in landscapes with high seismic line density and were most pronounced at low prey densities. This suggests that prey at low population densities are at higher risk in environments with a high seismic line density unless they learn to avoid them.

Roles, tasks and educational functions of postgraduate programme directors: a qualitative study.

Science.gov (United States)

Frydén, Hanna; Ponzer, Sari; Heikkilä, Kristiina; Kihlström, Lars; Nordquist, Jonas

2015-10-01

A programme director is often required to organise postgraduate medical education. This leadership role can include educational as well as managerial duties. Only a few published studies have explored programme directors' own perceptions of their role. There is a need to explore the use of theoretical frameworks to improve the understanding of educational roles. To explore programme directors' own perceptions of their role in terms of tasks and functions, and to relate these roles to the theoretical framework developed by Bolman and Deal. Semi-structured interviews were conducted with 17 programme directors between February and August 2013. The data were subjected to content analysis using a deductive approach. The various roles and tasks included by participants in their perceptions of their work could be categorised within the framework of functions described by Bolman and Deal. These included: structuring the education (structural function); supporting individuals and handling relations (human resource function); negotiating between different interests (political function); and influencing the culture at the departmental level (symbolic function). The functions most often emphasised by participants were the structural and human resource functions. Some tasks involved several functions which varied over time. Programme directors' own perceptions of their roles, tasks and functions varied widely. The theoretical framework of Bolman and Deal might be helpful when explaining and developing these roles. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Application of functional analysis methods to assess human-dog interactions.