WorldWideScience

Sample records for transfer interactions mapping

  1. Quantum maps from transfer operators

    International Nuclear Information System (INIS)

    Bogomolny, E.B.; Carioli, M.

    1992-09-01

    The Selberg zeta function ζ S (s) yields an exact relationship between the periodic orbits of a fully chaotic Hamiltonian system (the geodesic flow on surfaces of constant negative curvature) and the corresponding quantum system (the spectrum of the Laplace-Beltrami operator on the same manifold). It was found that for certain manifolds, ζ S (s) can be exactly rewritten as the Fredholm-Grothendieck determinant det(1-T s ), where T s is a generalization of the Ruelle-Perron-Frobenius transfer operator. An alternative derivation of this result is given, yielding a method to find not only the spectrum but also the eigenfunctions of the Laplace-Beltrami operator in terms of eigenfunctions of T s . Various properties of the transfer operator are investigated both analytically and numerically for several systems. (author) 30 refs.; 16 figs.; 2 tabs

  2. Golgi: interactive online brain mapping

    Directory of Open Access Journals (Sweden)

    Ramsay Alexander Brown

    2015-11-01

    Full Text Available Golgi (http://www.usegolgi.com is a prototype interactive brain map of the rat brain that helps researchers intuitively interact with neuroanatomy, connectomics, and cellular and chemical architecture. The flood of '-omic' data urges new ways to help researchers connect discrete findings to the larger context of the nervous system. Here we explore Golgi's underlying reasoning and techniques and how our design decisions balance the constraints of building both a scientifically useful and usable tool. We demonstrate how Golgi can enhance connectomic literature searches with a case study investigating a thalamocortical circuit involving the Nucleus Accumbens and we explore Golgi's potential and future directions for growth in systems neuroscience and connectomics.

  3. Analytic transfer maps for Lie algebraic design codes

    International Nuclear Information System (INIS)

    van Zeijts, J.; Neri, F.; Dragt, A.J.

    1990-01-01

    Lie algebraic methods provide a powerful tool for modeling particle transport through Hamiltonian systems. Briefly summarized, Lie algebraic design codes work as follows: first the time t flow generated by a Hamiltonian system is represented by a Lie algebraic map acting on the initial conditions. Maps are generated for each element in the lattice or beamline under study. Next all these maps are concatenated into a one-turn or one-pass map that represents the complete dynamics of the system. Finally, the resulting map is analyzed and design decisions are made based on the linear and nonlinear entries in the map. The authors give a short description of how to find Lie algebraic transfer maps in analytic form, for inclusion in accelerator design codes. As an example they find the transfer map, through third order, for the combined-function quadrupole magnet, and use such magnets to correct detrimental third-order aberrations in a spot forming system

  4. Contextualising Archaeological Information Through Interactive Maps

    Directory of Open Access Journals (Sweden)

    Ian Johnson

    2002-09-01

    Full Text Available Many web sites use maps delivered as non-interactive images. With the development of web-enabled mapping, new methods of presenting and contextualising archaeological and historical data are becoming available. However, most current examples are static views of contemporary framework data or specific time slices, and do not provide interactivity relating to the time dimension, which is so important to archaeology and related disciplines. In this article I look at some of the advantages of time-enabled interactive mapping and map animation in providing educational experiences to museum visitors and the web-browsing public. These will be illustrated through three example applications of the TimeMap methodology developed at the University of Sydney Archaeological Computing Laboratory: 1. the Sydney TimeMap kiosk at the Museum of Sydney; 2. an embedded Java mapping applet developed for MacquarieNet, a major Australian online educational encyclopaedia; and 3. the metadata clearinghouse mapping applet developed for the Electronic Cultural Atlas Initiative, Berkeley. In each of these examples, a wide range of resources are delivered through a time-enabled map interface which accesses live database data rather than pre-structured curated presentations of data. This flexibility brings its own challenges in providing intuitive pathways and appropriate levels of detail in response to free-ranging user enquiries. The paper outlines some of the approaches I have adopted to resolve these issues.

  5. Mapping Letters through Interaction Design

    NARCIS (Netherlands)

    Iturrioz, T.; Cano, J.; Wachowicz, M.

    2009-01-01

    Many kinds of text documents (e.g. newspapers, reports and letters) provide a potential source of geo-referenced information that is often underutilized. In interaction design, the use of dynamic icons and animation plays an important role in creating a sense of interactivity and feedback with

  6. Interactive Heat Transfer Simulations for Everyone

    Science.gov (United States)

    Xie, Charles

    2012-01-01

    Heat transfer is widely taught in secondary Earth science and physics. Researchers have identified many misconceptions related to heat and temperature. These misconceptions primarily stem from hunches developed in everyday life (though the confusions in terminology often worsen them). Interactive computer simulations that visualize thermal energy,…

  7. DIMA 3.0: Domain Interaction Map.

    Science.gov (United States)

    Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

    2011-01-01

    Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

  8. Interactive map of refugee movement in Europe

    Directory of Open Access Journals (Sweden)

    Calka Beata

    2016-12-01

    Full Text Available Considering the recent mass movement of people fleeing war and oppression, an analysis of changes in migration, in particular an analysis of the final destination refugees choose, seems to be of utmost importance. Many international organisations like UNHCR (the United Nations High Commissioner for Refugees or EuroStat gather and provide information on the number of refugees and the routes they follow. What is also needed to study the state of affairs closely is a visual form presenting the rapidly changing situation. An analysis of the problem together with up-to-date statistical data presented in the visual form of a map is essential. This article describes methods of preparing such interactive maps displaying movement of refugees in European Union countries. Those maps would show changes taking place throughout recent years but also the dynamics of the development of the refugee crisis in Europe. The ArcGIS software was applied to make the map accessible on the Internet. Additionally, online sources and newspaper articles were used to present the movement of migrants. The interactive map makes it possible to watch spatial data with an opportunity to navigate within the map window. Because of that it is a clear and convenient tool to visualise such processes as refugee migration in Europe.

  9. Interactive map of refugee movement in Europe

    Science.gov (United States)

    Calka, Beata; Cahan, Bruce

    2016-12-01

    Considering the recent mass movement of people fleeing war and oppression, an analysis of changes in migration, in particular an analysis of the final destination refugees choose, seems to be of utmost importance. Many international organisations like UNHCR (the United Nations High Commissioner for Refugees) or EuroStat gather and provide information on the number of refugees and the routes they follow. What is also needed to study the state of affairs closely is a visual form presenting the rapidly changing situation. An analysis of the problem together with up-to-date statistical data presented in the visual form of a map is essential. This article describes methods of preparing such interactive maps displaying movement of refugees in European Union countries. Those maps would show changes taking place throughout recent years but also the dynamics of the development of the refugee crisis in Europe. The ArcGIS software was applied to make the map accessible on the Internet. Additionally, online sources and newspaper articles were used to present the movement of migrants. The interactive map makes it possible to watch spatial data with an opportunity to navigate within the map window. Because of that it is a clear and convenient tool to visualise such processes as refugee migration in Europe.

  10. Baryon number transfer in hadronic interactions

    International Nuclear Information System (INIS)

    Arakelyan, G.H.; Capella, A.; Kaidalov, A.B.; Shabelski, Yu.M.

    2002-01-01

    The process of baryon number transfer due to string junction propagation in rapidity space is analyzed. It has a significant effect on the net baryon production in pp collisions at mid-rapidities and an even larger effect in the forward hemisphere in the cases of πp and γp interactions. The results of numerical calculations in the framework of the quark-gluon string model are in reasonable agreement with the data. (orig.)

  11. Detecting mutually exclusive interactions in protein-protein interaction maps.

    KAUST Repository

    Sánchez Claros, Carmen

    2012-06-08

    Comprehensive protein interaction maps can complement genetic and biochemical experiments and allow the formulation of new hypotheses to be tested in the system of interest. The computational analysis of the maps may help to focus on interesting cases and thereby to appropriately prioritize the validation experiments. We show here that, by automatically comparing and analyzing structurally similar regions of proteins of known structure interacting with a common partner, it is possible to identify mutually exclusive interactions present in the maps with a sensitivity of 70% and a specificity higher than 85% and that, in about three fourth of the correctly identified complexes, we also correctly recognize at least one residue (five on average) belonging to the interaction interface. Given the present and continuously increasing number of proteins of known structure, the requirement of the knowledge of the structure of the interacting proteins does not substantially impact on the coverage of our strategy that can be estimated to be around 25%. We also introduce here the Estrella server that embodies this strategy, is designed for users interested in validating specific hypotheses about the functional role of a protein-protein interaction and it also allows access to pre-computed data for seven organisms.

  12. Keratinocyte-melanocyte interactions during melanosome transfer.

    Science.gov (United States)

    Seiberg, M

    2001-08-01

    The epidermal-melanin unit is composed of one melanocyte and approximately 36 neighboring keratinocytes, working in synchrony to produce and distribute melanin. Melanin is synthesized in melanosomes, transferred to the dendrite tips, and translocated into keratinocytes, forming caps over the keratinocyte nuclei. The molecular and cellular mechanisms involved in melanosome transfer and the keratinocyte-melanocyte interactions required for this process are not yet completely understood. Suggested mechanisms of melanosome transfer include melanosome release and endocytosis, direct inoculation ('injection'), keratinocyte-melanocyte membrane fusion, and phagocytosis. Studies of the keratinocyte receptor protease-activated receptor-2 (PAR-2) support the phagocytosis theory. PAR-2 controls melanosome ingestion and phagocytosis by keratinocytes and exerts a regulatory role in skin pigmentation. Modulation of PAR-2 activity can enhance or decrease melanosome transfer and affects pigmentation only when there is keratinocyte-melanocyte contact. Moreover, PAR-2 is induced by UV irradiation and inhibition of PAR-2 activation results in the prevention of UVB-induced tanning. The role of PAR-2 in mediating UV-induced responses remains to be elucidated.

  13. How Concept-Mapping Perception Navigates Student Knowledge Transfer Performance

    Science.gov (United States)

    Tseng, Kuo-Hung; Chang, Chi-Cheng; Lou, Shi-Jer; Tan, Yue; Chiu, Chien-Jung

    2012-01-01

    The purpose of this paper is to investigate students' perception of concept maps as a learning tool where knowledge transfer is the goal. This article includes an evaluation of the learning performance of 42 undergraduate students enrolled in a nanotech course at a university in Taiwan. Canonical correlation and MANOVA analyses were employed to…

  14. An Interactive Map for Showcasing Repository Impacts

    Directory of Open Access Journals (Sweden)

    Hui Zhang

    2017-04-01

    Full Text Available Digital repository managers rely on usage metrics such as the number of downloads to demonstrate research visibility and impacts of the repositories. Increasingly, they find that current tools such as spreadsheets and charts are ineffective for revealing important elements of usage, including reader locations, and for attracting the targeted audiences. This article describes the design and development of a readership map that provides an interactive, near-real-time visualization of actual visits to an institutional repository using data from Google Analytics. The readership map exhibits the global impacts of a repository by displaying the city of every view or download together with the title of the scholarship being read and a hyperlink to its page in the repository. We will discuss project motivation and development issues such as authentication with Google API, metadata integration, performance tuning, and data privacy.

  15. One-Page Multimedia Interactive Map

    Directory of Open Access Journals (Sweden)

    Nicola Maiellaro

    2017-01-01

    Full Text Available The relevance of local knowledge in cultural heritage is by now acknowledged. It helps to determine many community-based projects by identifying the material to be digitally maintained in multimedia collections provided by communities of volunteers, rather than for-profit businesses or government entities. Considering that the search and browsing of texts, images, video, and 3D models related to places is more essential than using a simple text-based search, an interactive multimedia map was implemented in this study. The map, which is loaded on a single HyperText Markup Language (HTML page using AJAX (Asynchronous JavaScript and XML, with a client-side control mechanism utilising jQuery components that are both freely available and ad-hoc developed, is updated according to user interaction. To simplify the publication of geo-referenced information, the application stores all the data in a Geographic JavaScript Object Notation (GeoJSON file rather than in a database. The multimedia contents—associated with the selected Points of Interest (PoIs—can be selected through text search and list browsing as well as by viewing their previews one by one in a sequence all together in a scrolling window (respectively: “Table”, “Folder”, and “Tile” functions. PoIs—visualised on the map with multi-shape markers using a set of unambiguous colours—can be filtered through their categories and types, accessibility status and timeline, thus improving the system usability. The map functions are illustrated using data collected in a Comenius project. Notes on the application software and architecture are also presented in this paper.

  16. 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

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

    CERN Document Server

    Meng, Liqiu; Winter, Stephan; Popovich, Vasily

    2008-01-01

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

  18. Mapping chromatin interactions with 5C technology

    Science.gov (United States)

    Ferraiuolo, Maria A.; Sanyal, Amartya; Naumova, Natalia; Dekker, Job; Dostie, Josée

    2013-01-01

    In eukaryotes, genome organization can be observed on many levels and at different scales. This organization is important not only to reduce chromosome length but also for the proper execution of various biological processes. High-resolution mapping of spatial chromatin structure was made possible by the development of the chromosome conformation capture (3C) technique. 3C uses chemical cross-linking followed by proximity-based ligation of fragmented DNA to capture frequently interacting chromatin segments in cell populations. Several 3C-related methods capable of higher chromosome conformation mapping throughput were reported afterwards. These techniques include the 3C-carbon copy (5C) approach, which offers the advantage of being highly quantitative and reproducible. We provide here a reference protocol for the production of 5C libraries analyzed by next-generation sequencing or onto microarrays. A procedure used to verify that 3C library templates bear the high quality required to produce superior 5C libraries is also described. We believe that this comprehensive detailed protocol will help guide researchers in probing spatial genome organization and its role in various biological processes. PMID:23137922

  19. Interactive Joint Transfer of Energy and Information

    DEFF Research Database (Denmark)

    Popovski, Petar; Fouladgar, A. M.; Simeone, Osvaldo

    2013-01-01

    In some communication networks, such as passive RFID systems, the energy used to transfer information between a sender and a recipient can be reused for successive communication tasks. In fact, from known results in physics, any system that exchanges information via the transfer of given physical...

  20. Energy Transfer and Triadic Interactions in Compressible Turbulence

    Science.gov (United States)

    1997-11-01

    No. 97-62 ANNIVERSARY Energy Transfer and Triadic Interactions in Compressible Turbulence F. Bataille INSA, Centre for Thermique de Lyon, France Ye...19480 November 1997 1997112 ENERGY TRANSFER AND TRIADIC INTERACTIONS IN COMPRESSIBLE TURBULENCE* F. BATAILLE t , YE ZHOU1 , AND JEAN-PIERRE BERTOGLIO...Abstract. Using a two-point closure theory, the Eddy-Damped-Quasi-Normal-Markovian (EDQNM) approximation, we have investigated the energy transfer

  1. The interaction of private intergenerational transfers types

    OpenAIRE

    Albuquerque, Paula C.

    2014-01-01

    The rapid ageing of the population, particularly in the developed world, accentuates the importance of both the family and of private intergenerational transfers, whether this be due to the longer periods of coexistence resulting from longer life expectancy or the threat posed to the very sustainability of the welfare state. While the magnitude of intergenerational transfers is well documented, and the motives underlying them have received broad attention, we focus on a much less studied top...

  2. Interactive Global Illumination Effects Using Deterministically Directed Layered Depth Maps

    DEFF Research Database (Denmark)

    Aalund, F. P.; Frisvad, Jeppe Revall; Bærentzen, Jakob Andreas

    2015-01-01

    A layered depth map is an extension of the well-known depth map used in rasterization. Multiple layered depth maps can be used as a coarse scene representation. We develop two global illumination methods which use said scene representation. The first is an interactive ambient occlusion method....... The second is an interactive singlebounce indirect lighting method based on photon differentials. All of this is implemented in a rasterization-based pipeline....

  3. Effects of dipole—dipole interaction on entanglement transfer

    International Nuclear Information System (INIS)

    Guo Hong; Xiong Hengna

    2008-01-01

    A system consisting of two different atoms interacting with a two-mode vacuum, where each atom is resonant only with one cavity mode, is considered. The effects of dipole—dipole (dd) interaction between two atoms on the atom-atom entanglement and mode-mode entanglement are investigated. For a weak dd interaction, when the atoms are initially separable, the entanglement between them can be induced by the dd interaction, and the entanglement transfer between the atoms and the modes occurs efficiently; when the atoms are initially entangled, the entanglement transfer is almost not influenced by the dd interaction. However, for a strong dd interaction, it is difficult to transfer the entanglement from the atoms to the modes, but the atom-atom entanglement can be maintained when the atoms are initially entangled

  4. Effect of electrostatic interactions on the formation of proton transfer ...

    Indian Academy of Sciences (India)

    WINTEC

    Electrostatic interactions are known to play a crucial role in protein structure and function as evident from a large number of studies, for example, in enzymatic catalysis,1,2 proton transfer,3,4 electron transfer,5,6 ion channels7,8 and ligand binding.9,10 Therefore, quantita- tive estimations of the electrostatic energies and.

  5. R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping

    OpenAIRE

    Broman, Karl W.

    2014-01-01

    Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl?s static graphs, as well as additional interactive graphs for the explor...

  6. Modeling, Designing, and Implementing an Avatar-based Interactive Map

    Directory of Open Access Journals (Sweden)

    Stefan Andrei

    2016-03-01

    Full Text Available Designing interactive maps has always been a challenge due to the geographical complexity of the earth’s landscape and the difficulty of resolving details to a high resolution. In the past decade or so, one of the most impressive map-based software application, the Global Positioning System (GPS, has probably the highest level of interaction with the user. This article describes an innovative technique for designing an avatar-based virtual interactive map for the Lamar University Campus, which will entail the buildings’ exterior as well as their interiors. Many universities provide 2D or 3D maps and even interactive maps. However, these maps do not provide a complete interaction with the user. To the best of our knowledge, this project is the first avatar-based interaction game that allows 100% interaction with the user. This work provides tremendous help to the freshman students and visitors of Lamar University. As an important marketing tool, the main objective is to get better visibility of the campus worldwide and to increase the number of students attending Lamar University.

  7. Quantitative genetic-interaction mapping in mammalian cells

    Science.gov (United States)

    Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

    2013-01-01

    Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

  8. A map of directional genetic interactions in a metazoan cell.

    Science.gov (United States)

    Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

    2015-03-06

    Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

  9. Quantification of Fracture Interaction Using Stress Intensity Factor Variation Maps

    Science.gov (United States)

    Thomas, Robin N.; Paluszny, Adriana; Zimmerman, Robert W.

    2017-10-01

    Accurate and flexible models of fracture interaction are sought after in the fields of mechanics and geology. Stress intensity factors (SIFs) quantify the energy concentrated at the fracture tips and are perturbed from their isolated values when two fractures are close to one another. Using a three-dimensional finite element fracture mechanics code to simulate static fractures in tension and compression, interaction effects are examined. SIF perturbations are characterized by introducing three interaction measures: the circumferential and maximum SIF perturbation provide the "magnitude" of the effect of interaction, and the amplification to shielding ratio quantifies the balance between increased and decreased SIFs along the tip. These measures are used to demonstrate the change in interaction with fracture separation and to find the separation at which interaction becomes negligible. Interaction maps are constructed by plotting the values of the interaction measures for a static fracture as a second fracture is moved around it. These maps are presented for several common fracture orientations in tension. They explore interaction by highlighting regions in which growth is more likely to occur and where fractures will grow into nonplanar geometries. Interaction maps can be applied to fracture networks with multiple discontinuities to analyze the effect of geometric variations on fracture interaction.

  10. Web mapping: tools and solutions for creating interactive maps of forestry interest

    Directory of Open Access Journals (Sweden)

    Notarangelo G

    2011-12-01

    Full Text Available The spread of geobrowsers as tools for displaying geographically referenced information provides insights and opportunities to those who, not being specialists in Geographic Information Systems, want to take advantage from exploration and communication power offered by these software. Through the use of web services such as Google Maps and the use of suitable markup languages, one can create interactive maps starting from highly heterogeneous data and information. These interactive maps can also be easily distributed and shared with Internet users, because they do not need to use proprietary software nor special skills but only a web browser. Unlike the maps created with GIS, whose output usually is a static image, the interactive maps retain all their features to users advantage. This paper describes a web application that, using the Keyhole Markup Language and the free service of Google Maps, produces choropleth maps relating to some forest indicators estimated by the last Italian National Forest Inventory. The creation of a map is done through a simple and intuitive interface. The maps created by users can be downloaded as KML file and can be viewed or modified via the freeware application Google Earth or free and open source GIS software like Quantum GIS. The web application is free and available at www.ricercaforestale.it.

  11. Molecular interaction maps as information organizers and simulation guides.

    Science.gov (United States)

    Kohn, Kurt W.

    2001-03-01

    A graphical method for mapping bioregulatory networks is presented that is suited for the representation of multimolecular complexes, protein modifications, as well as actions at cell membranes and between protein domains. The symbol conventions defined for these molecular interaction maps are designed to accommodate multiprotein assemblies and protein modifications that can generate combinatorially large numbers of molecular species. Diagrams can either be "heuristic," meaning that detailed knowledge of all possible reaction paths is not required, or "explicit," meaning that the diagrams are totally unambiguous and suitable for simulation. Interaction maps are linked to annotation lists and indexes that provide ready access to pertinent data and references, and that allow any molecular species to be easily located. Illustrative interaction maps are included on the domain interactions of Src, transcription control of E2F-regulated genes, and signaling from receptor tyrosine kinase through phosphoinositides to Akt/PKB. A simple method of going from an explicit interaction diagram to an input file for a simulation program is outlined, in which the differential equations need not be written out. The role of interaction maps in selecting and defining systems for modeling is discussed. (c) 2001 American Institute of Physics.

  12. Heat transfer and mechanical interactions in fusion nuclear systems

    International Nuclear Information System (INIS)

    Nygren, R.E.

    1984-01-01

    This general review of design issues in heat transfer and mechanical interactions of the first wall, blanket and shield systems of tokamak and mirror fusion reactors begins with a brief introduction to fusion nuclear systems. The design issues are summarized in tables and the following examples are described to illustrate these concerns: the surface heating of limiters, heat transfer from solid breeders, MHD effects in liquid metal blankets, mechanical loads from electromagnetic transients and remote maintenance

  13. Mapping Social Interactions: The Science of Proxemics.

    Science.gov (United States)

    McCall, Cade

    Interpersonal distance and gaze provide a wealth of information during face-to-face social interactions. These "proxemic" behaviors offer a window into everyday social cognition by revealing interactants' affective states (e.g., interpersonal attitudes) and cognitive responses (e.g., social attention). Here we provide a brief overview of the social psychological literature in this domain. We focus on new techniques for experimentally manipulating and measuring proxemics, including the use of immersive virtual environments and digital motion capture. We also discuss ways in which these approaches can be integrated with psychophysiological and neuroimaging techniques. Throughout, we argue that contemporary proxemics research provides psychology and neuroscience with a means to study social cognition and behavior as they naturally emerge and unfold in vivo.

  14. Drosophila Protein interaction Map (DPiM)

    OpenAIRE

    Guruharsha, K.G.; Obar, Robert A.; Mintseris, Julian; Aishwarya, K.; Krishnan, R.T.; VijayRaghavan, K.; Artavanis-Tsakonas, Spyros

    2012-01-01

    Proteins perform essential cellular functions as part of protein complexes, often in conjunction with RNA, DNA, metabolites and other small molecules. The genome encodes thousands of proteins but not all of them are expressed in every cell type; and expressed proteins are not active at all times. Such diversity of protein expression and function accounts for the level of biological intricacy seen in nature. Defining protein-protein interactions in protein complexes, and establishing the when,...

  15. R/qtlcharts: interactive graphics for quantitative trait locus mapping.

    Science.gov (United States)

    Broman, Karl W

    2015-02-01

    Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl's static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data. Copyright © 2015 by the Genetics Society of America.

  16. Advanced patient transfer assist device with intuitive interaction control.

    Science.gov (United States)

    Humphreys, Heather C; Choi, Young Mi; Book, Wayne J

    2017-10-24

    This research aims to improve patient transfers by developing a new type of advanced robotic assist device. It has multiple actuated degrees of freedom and a powered steerable base to maximize maneuverability around obstacles. An intuitive interface and control strategy allows the caregiver to simply push on the machine in the direction of desired patient motion. The control integrates measurements of both force and proximity to mitigate any potential large collision forces and provides operators information about obstacles with a form of haptic feedback. Electro-hydraulic pump controlled actuation provides high force density for the actuation. Nineteen participants performed tests to compare transfer operations (transferring a 250-lb mannequin between a wheelchair, chair, bed, and floor) and interaction control of a prototype device with a commercially available patient lift. The testing included a time study of the transfer operations and subjective rating of device performance. The results show that operators perform transfer tasks significantly faster and rate performance higher using the prototype patient transfer assist device than with a current market patient lift. With further development, features of the new patient lift can help facilitate patient transfers that are safer, easier, and more efficient for caregivers.

  17. Euglena gracilis chloroplast transfer RNA transcription units. I. Physical map of the transfer RNA gene loci.

    Science.gov (United States)

    Orozco, E M; Hallick, R B

    1982-03-25

    The locations of transfer RNA genes with respect to the restriction endonuclease cleavage map of Euglena gracilis Klebs, strain Z Pringsheim chloroplast DNA have been determined. Purified chloroplast tRNAs were treated with snake venom phosphodiesterase to remove the 3'-CCA terminus, and radioactively labeled by the action of Escherichia coli tRNA nucleotidyltransferase in the presence of [alpha-32P]CTP. Chloroplast DNA was treated individually and with combinations of the enzymes Bal I, Bam HI, Eco RI, Pst I, Pvu II, Sal I, and Xho I. The location of tRNA genes with respect to the cleavage sites for these enzymes was determined by hybridization of the 32P-labeled tRNAs to membrane filter blots of the chloroplast DNA restriction nuclease fragments following gel electrophoresis. The 145-kilobase pair genome was resolved into nine areas of strong tRNA hybridization, separated by areas of weak or no tRNA hybridization. The loci of tRNA genes are within the Eco RI fragments Eco A, B, G, H, I, J', P, Q, and V.

  18. Nuclear Effects in Neutrino Interactions at Low Momentum Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Miltenberger, Ethan Ryan [Univ. of Minnesota, Minneapolis, MN (United States)

    2015-05-01

    This is a study to identify predicted effects of the carbon nucleus environment on neutrino - nucleus interactions with low momentum transfer. A large sample of neutrino interaction data collected by the MINERvA experiment is analyzed to show the distribution of charged hadron energy in a region with low momentum transfer. These distributions reveal a major discrepancy between the data and a popular interaction model with only the simplest Fermi gas nuclear effects. Detailed analysis of systematic uncertainties due to energy scale and resolution can account for only a little of the discrepancy. Two additional nuclear model effects, a suppression/screening effect (RPA), and the addition of a meson exchange current process (MEC), are shown to improve the description of the data.

  19. CONTIG EXPLORER: Interactive marker-content map assembly

    Energy Technology Data Exchange (ETDEWEB)

    Nadkarni, P.M.; Miller, P.; Banks, A. [Yale School of Medicine, New Haven, CT (United States)] [and others

    1996-02-01

    In STS-content mapping of a region, multiple optimal or near-optimal putative orders of markers exist. Determining which of the markers lack sufficient evidence to be placed requires software that facilitates exploratory sensitivity analysis and interactive reassembly with different subsets of the input data and that also assists the evaluation of any arbitrary (user-specified) marker order. We describe CONTIG EXPLORER, a package for interactive assembly of STS-content maps that provides the user with various ways of performing such analysis, thereby facilitating the design of laboratory experiments aimed at reducing ambiguity in STS order. We then compare the output of CONTIG EXPLORER with two other assembly programs, SEGMAP and CONTIGMAKER, for a region of chromosome 12p between 21 and 38 cM on the sex-averaged CEPH/Genethon linkage map. 18 refs., 4 figs.

  20. Energy Transfer and Triadic Interactions in Compressible Turbulence

    Science.gov (United States)

    Bataille, F.; Zhou, Ye; Bertoglio, Jean-Pierre

    1997-01-01

    Using a two-point closure theory, the Eddy-Damped-Quasi-Normal-Markovian (EDQNM) approximation, we have investigated the energy transfer process and triadic interactions of compressible turbulence. In order to analyze the compressible mode directly, the Helmholtz decomposition is used. The following issues were addressed: (1) What is the mechanism of energy exchange between the solenoidal and compressible modes, and (2) Is there an energy cascade in the compressible energy transfer process? It is concluded that the compressible energy is transferred locally from the solenoidal part to the compressible part. It is also found that there is an energy cascade of the compressible mode for high turbulent Mach number (M(sub t) greater than or equal to 0.5). Since we assume that the compressibility is weak, the magnitude of the compressible (radiative or cascade) transfer is much smaller than that of solenoidal cascade. These results are further confirmed by studying the triadic energy transfer function, the most fundamental building block of the energy transfer.

  1. A protein interaction map of the kalimantacin biosynthesis assembly line

    Directory of Open Access Journals (Sweden)

    Birgit Uytterhoeven

    2016-11-01

    Full Text Available The antimicrobial secondary metabolite kalimantacin is produced by a hybrid polyketide/ non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein-protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites.This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.

  2. Heat transfer modelling of pulsed laser-tissue interaction

    Science.gov (United States)

    Urzova, J.; Jelinek, M.

    2018-03-01

    Due to their attributes, the application of medical lasers is on the rise in numerous medical fields. From a biomedical point of view, the most interesting applications are the thermal interactions and the photoablative interactions, which effectively remove tissue without excessive heat damage to the remaining tissue. The objective of this work is to create a theoretical model for heat transfer in the tissue following its interaction with the laser beam to predict heat transfer during medical laser surgery procedures. The dimensions of the ablated crater (shape and ablation depth) were determined by computed tomography imaging. COMSOL Multiphysics software was used for temperature modelling. The parameters of tissue and blood, such as density, specific heat capacity, thermal conductivity and diffusivity, were calculated from the chemical ratio. The parameters of laser-tissue interaction, such as absorption and reflection coefficients, were experimentally determined. The parameters of the laser beam were power density, repetition frequency, pulse length and spot dimensions. Heat spreading after laser interaction with tissue was captured using a Fluke thermal camera. The model was verified for adipose tissue, skeletal muscle tissue and heart muscle tissue.

  3. Probing hydrogen bonding interactions and proton transfer in proteins

    Science.gov (United States)

    Nie, Beining

    Scope and method of study. Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. It is therefore important to probe dynamic changes in hydrogen bonding interactions during protein folding and function. Time-resolved Fourier transform infrared spectroscopy is highly sensitive to hydrogen bonding interactions. However, it lacks quantitative correlation between the vibrational frequencies and the number, type, and strength of hydrogen bonding interactions of ionizable and polar residues. We employ quantum physics theory based ab initio calculations to study the effects of hydrogen bonding interactions on vibrational frequencies of Asp, Glu, and Tyr residues and to develop vibrational spectral markers for probing hydrogen bonding interactions using infrared spectroscopy. In addition, proton transfer process plays a crucial role in a wide range of energy transduction, signal transduction, and enzymatic reactions. We study the structural basis for proton transfer using photoactive yellow protein as an excellent model system. Molecular dynamics simulation is employed to investigate the structures of early intermediate states. Quantum theory based ab initio calculations are used to study the impact of hydrogen bond interactions on proton affinity and proton transfer. Findings and conclusions. Our extensive density function theory based calculations provide rich structural, spectral, and energetic information on hydrogen bonding properties of protonated side chain groups of Asp/Glu and Tyr. We developed vibrational spectral markers and 2D FTIR spectroscopy for structural characterization on the number and the type of hydrogen bonding interactions of the COOH group of Asp/Glu and neutral phenolic group of Tyr. These developments greatly enhance the power of time-resolved FTIR spectroscopy as a major experimental tool for structural characterization of functionally important

  4. Effects of electrostatic interactions on electron transfer reactions

    International Nuclear Information System (INIS)

    Hickel, B.

    1987-01-01

    The fast reactions of electron transfer are studied by pulse radiolysis. This technique allows the creation in about 10 -8 second radicals and radical ions with high redox potentials. For solvated electrons electrostatic interaction on the kinetics of reactions limited by diffusion is described by Debye's equation when ion mobility is known. Deviation from theory can occur in ion pairs formation. This is evidenced experimentally for anions by cation complexation with a cryptate. Relatively slow reactions are more sensitive to electrostatic interactions than limited by diffusion. If ion pairs are not formed kinetics constant depends on dielectric constant of solvent and reaction radius. Experimentally is studied the effect of electrostatic interaction on the rate constants of solvated electrons with anions and cations in water-ethanol mixtures where the dielectric constant change from 80 to 25 at room temperature. 17 refs

  5. Probing the pairing interaction through two-neutron transfer reactions

    Directory of Open Access Journals (Sweden)

    Margueron J.

    2012-12-01

    Full Text Available The treatment of the pairing interaction in mean-field-based models is addressed. In particular, the possibility to use pair transfers as A tool to better constrain this interaction is discussed. First, pairing inter-actions with various density dependencies (surface/volume mixing are used in the microscopic Hartree-Fock-Bogoliubov + quasiparticle random-phase approximation model to generate the form factors to be used in reaction calculations. Cross sections for (p,t two-neutron transfer reactions are calculated in the one-step zero-range distorted-wave Born approximation for some Tin isotopes and for incident proton energies from 15 to 35 MeV. Three different surface/volume mixings of A zero-range density-dependent pairing interaction are employed in the microscopic calculations and the sensitivity of the cross sections to the different mixings is analyzed. Differences among the three different theoretical predictions are found espacially for the nucleus 136Sn and they are more important at the incident proton energy of 15 MeV. We thus indicate (p,t two-neutron transfer reactions with very neutron-rich Sn isotopes and at proton energies around 15 MeV as good experimental cases where the surface/volume mixing of the pairing interaction may be probed. In the second part of the manuscript, ground-state to ground-state transitions are investigated. Approximations made to estimate two-nucleon transfer probabilities in ground-state to ground-state transitions and the physical interpretation of these probabilities are discussed. Probabilities are often calculated by approximating both ground states of the initial nucleus A and of the final nucleus A±2 by the same quasiparticle vacuum. We analyze two improvements of this approach. First, the effect of using two different ground states with average numbers of particles A and A±2 is quantified. Second, by using projection techniques, the role of particle number restoration is analyzed. Our analysis

  6. Asymmetric radiation transfer based on linear light-matter interaction

    Science.gov (United States)

    Jia, Zi-xun; Shuai, Yong; Zhang, Jia-hui; Tan, He-ping

    2017-11-01

    In this paper, asymmetric radiation transfer based on linear light-matter interaction has been proposed. Two naturally different numerical methods, finite difference time domain (FDTD) and rigorous coupled wave analysis (RCWA), are utilized to verify that asymmetric radiation transfer can exist for linear plasmonic meta-material. The overall asymmetry has been introduced to evaluate bifacial transmission. Physics for the asymmetric optical responses have been understood via electromagnetic field distributions. Dispersion relation for surface plasmon polariton (SPP) and temporal coupled mode theory (TCMT) have been employed to verify the physics discussed in the paper. Geometric effects and the disappearing of asymmetric transmission have also been investigated. The results gained herein broaden the cognition of linear optical system, facilitate the design of novel energy harvesting device.

  7. Self-interaction and charge transfer in organic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Koerzdoerfer, Thomas

    2009-12-18

    This work concentrates on the problem of self-interaction, which is one of the most serious problems of commonly used approximative density functionals. As a major result of this work, it is demonstrated that self-interaction plays a decisive role for the performance of different approximative functionals in predicting accurate electronic properties of organic molecular semiconductors. In search for a solution to the self-interaction problem, a new concept for correcting commonly used density functionals for self-interaction is introduced and applied to a variety of systems, spanning small molecules, extended molecular chains, and organic molecular semiconductors. It is further shown that the performance of functionals that are not free from self-interaction can vary strongly for different systems and observables of interest, thus entailing the danger of misinterpretation of the results obtained from those functionals. The underlying reasons for the varying performance of commonly used density functionals are discussed thoroughly in this work. Finally, this thesis provides strategies that allow to analyze the reliability of commonly used approximations to the exchange-correlation functional for particular systems of interest. This cumulative dissertation is divided into three parts. Part I gives a short introduction into DFT and its time-dependent extension (TDDFT). Part II provides further insights into the self-interaction problem, presents a newly developed concept for the correction of self-interaction, gives an introduction into the publications, and discusses their basic results. Finally, the four publications on self-interaction and charge-transfer in extended molecular systems and organic molecular semiconductors are collected in Part III. (orig.)

  8. Mapping side chain interactions at protein helix termini.

    Science.gov (United States)

    Newell, Nicholas E

    2015-07-25

    Interactions that involve one or more amino acid side chains near the ends of protein helices stabilize helix termini and shape the geometry of the adjacent loops, making a substantial contribution to overall protein structure. Previous work has identified key helix-terminal motifs, such as Asx/ST N-caps, the capping box, and hydrophobic and electrostatic interactions, but important questions remain, including: 1) What loop backbone geometries are favoured by each motif? 2) To what extent are multi-amino acid motifs likely to represent genuine cooperative interactions? 3) Can new motifs be identified in a large, recent dataset using the latest bioinformatics tools? Three analytical tools are applied here to answer these questions. First, helix-terminal structures are partitioned by loop backbone geometry using a new 3D clustering algorithm. Next, Cascade Detection, a motif detection algorithm recently published by the author, is applied to each cluster to determine which sequence motifs are overrepresented in each geometry. Finally, the results for each motif are presented in a CapMap, a 3D conformational heatmap that displays the distribution of the motif's overrepresentation across loop geometries, enabling the rapid isolation and characterization of the associated side chain interaction. This work identifies a library of geometry-specific side chain interactions that provides a new, detailed picture of loop structure near the helix terminus. Highlights include determinations of the favoured loop geometries for the Asx/ST N-cap motifs, capping boxes, "big" boxes, and other hydrophobic, electrostatic, H-bond, and pi stacking interactions, many of which have not been described before. This work demonstrates that the combination of structural clustering and motif detection in the sequence space can efficiently identify side chain motifs and map them to the loop geometries which they support. Protein designers should find this study useful, because it identifies side

  9. Effect of electrostatic interactions on electron-transfer reactions

    International Nuclear Information System (INIS)

    Hickel, B.

    1987-01-01

    Fast reactions of electron transfer are studied by pulsed radiolysis. By this technique radicals and ionic radicals with high redox potentials are created homogeneously in the solution in about 10 -8 second. For solvated electron effect of electrostatic interaction on kinetics of reactions limited by diffusion is obtained with a good approximation by the Debye equation when ion mobility is known. Deviation from the theory occurs in ion pair formation, which is evidenced experimentally in reactions between anions when cations are complexed by a cryptate. Slow reactions k 8 M -1 s -1 are more sensitive to electrostatic interactions than reactions limited by diffusion. When there is no ion pair formation the velocity constant depends upon dielectric constant of the solvent and reaction distance. 17 refs

  10. MIMO: an efficient tool for molecular interaction maps overlap

    Science.gov (United States)

    2013-01-01

    Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

  11. Mapping radiation transfer through sea ice using a remotely operated vehicle (ROV

    Directory of Open Access Journals (Sweden)

    M. Nicolaus

    2013-05-01

    Full Text Available Transmission of sunlight into and through sea ice is of critical importance for sea-ice associated organisms and photosynthesis because light is their primary energy source. The amount of visible light transferred through sea ice contributes to the energy budget of the sea ice and the uppermost ocean. However, our current knowledge on the amount and distribution of light under sea ice is still restricted to a few local observations, and our understanding of light-driven processes and interdisciplinary interactions is still sparse. The main reasons are that the under-ice environment is difficult to access and that measurements require large logistical and instrumental efforts. Hence, it has not been possible to map light conditions under sea ice over larger areas and to quantify spatial variability on different scales. Here we present a detailed methodological description for operating spectral radiometers on a remotely operated vehicle (ROV under sea ice. Recent advances in ROV and radiation-sensor technology have allowed us to map under-ice spectral radiance and irradiance on floe scales within a few hours of station time. The ROV was operated directly from the sea ice, allowing for direct relations of optical properties to other sea-ice and surface features. The ROV was flown close to the sea ice in order to capture small-scale variability. Results from the presented data set and similar future studies will allow for better quantification of light conditions under sea ice. The presented experiences will support further developments in order to gather large data sets of under-ice radiation for different ice conditions and during different seasons.

  12. Duchenne Muscular Dystrophy (DMD) Protein-Protein Interaction Mapping.

    Science.gov (United States)

    Rezaei Tavirani, Mostafa; OkHOVATIAN, Farshad; Zamanian Azodi, Mona; Rezaei Tavirani, Majid

    2017-01-01

    Duchenne muscular dystrophy (DMD) is one of the mortal diseases, subjected to study in terms of molecular investigation. In this study, the protein interaction map of this muscle-wasting condition was generated to gain a better knowledge of interactome profile of DMD. Applying Cytoscape and String Database, the protein-protein interaction network was constructed and the gene ontology of the constructed network was analyzed for biological process, molecular function, and cellular component annotations. Among 100 proteins related to DMD, dystrophin, utrophin, caveolin 3, and myogenic differentiation 1 play key roles in DMD network. In addition, the gene ontology analysis showed that regulation processes, kinase activity, and sarcoplasmic reticulum were the highlighted biological processes, molecular function, and cell component enrichments respectively for the proteins related to DMD. The central proteins and the enriched ontologies can be suggested as possible prominent agents in DMD; however, the validation studies may be required.

  13. Spin Orbit Interaction Engineering for beyond Spin Transfer Torque memory

    Science.gov (United States)

    Wang, Kang L.

    Spin transfer torque memory uses electron current to transfer the spin torque of electrons to switch a magnetic free layer. This talk will address an alternative approach to energy efficient non-volatile spintronics through engineering of spin orbit interaction (SOC) and the use of spin orbit torque (SOT) by the use of electric field to improve further the energy efficiency of switching. I will first discuss the engineering of interface SOC, which results in the electric field control of magnetic moment or magneto-electric (ME) effect. Magnetic memory bits based on this ME effect, referred to as magnetoelectric RAM (MeRAM), is shown to have orders of magnitude lower energy dissipation compared with spin transfer torque memory (STTRAM). Likewise, interests in spin Hall as a result of SOC have led to many advances. Recent demonstrations of magnetization switching induced by in-plane current in heavy metal/ferromagnetic heterostructures have been shown to arise from the large SOC. The large SOC is also shown to give rise to the large SOT. Due to the presence of an intrinsic extraordinarily strong SOC and spin-momentum lock, topological insulators (TIs) are expected to be promising candidates for exploring spin-orbit torque (SOT)-related physics. In particular, we will show the magnetization switching in a chromium-doped magnetic TI bilayer heterostructure by charge current. A giant SOT of more than three orders of magnitude larger than those reported in heavy metals is also obtained. This large SOT is shown to come from the spin-momentum locked surface states of TI, which may further lead to innovative low power applications. I will also describe other related physics of SOC at the interface of anti-ferromagnetism/ferromagnetic structure and show the control exchange bias by electric field for high speed memory switching. The work was in part supported by ERFC-SHINES, NSF, ARO, TANMS, and FAME.

  14. Charge transfer interactions in oligomer coated gold nanoclusters

    International Nuclear Information System (INIS)

    Newmai, M. Boazbou; Kumar, Pandian Senthil

    2016-01-01

    Gold nanoclusters were synthesized by a bottom-up synergistic approach of in-situ oligomerization of the monomer, N-vinyl pyrrolidone (NVP) and simultaneous weak reduction of Au-NVP complexes in the absence of any other external energy sources, thereby making these tiny gold clusters as the most elemental building blocks to construct further novel nano/microstructures with application potentials. It is well-known that metal clusters with less than 2 nm size do not show the usual surface plasmon band, because of the presence of a band-gap at the fermi level. Nevertheless, our present oligomer coated gold clusters show a discrete intense band at around 630 nm, which could very well be attributed to the charge transfer between the oligomer chain and the surface Au atoms. Such kind of sacrificial plasmon induced charge transfer interaction, observed for the very first time to the best of our knowledge, were also strongly corroborated through the enhancement / shifting of specific vibrational / rotational peaks as observed from the FTIR and Raman measurements as a function of the metal oxidation states, thus representing a new prototype for an efficient solar energy conversion probe.

  15. Transferability of polarizable models for ion-water electrostatic interaction

    International Nuclear Information System (INIS)

    Masia, Marco

    2009-01-01

    Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li + - water and Cl - -water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

  16. Charge-transfer interactions of Cr species with DNA.

    Science.gov (United States)

    Nowicka, Anna M; Matysiak-Brynda, Edyta; Hepel, Maria

    2017-10-01

    Interactions of Cr species with nucleic acids in living organisms depend strongly on Cr oxidation state and the environmental conditions. As the effects of these interactions range from benign to pre-mutagenic to carcinogenic, careful assessment of the hazard they pose to human health is necessary. We have investigated methods that would enable quantifying the DNA damage caused by Cr species under varying environmental conditions, including UV, O 2 , and redox potential, using simple instrumental techniques which could be in future combined into a field-deployable instrumentation. We have employed electrochemical quartz crystal nanogravimetry (EQCN), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) to evaluate the extent of DNA damage expressed in terms of guanine oxidation yield (η) and changes in specific characteristics provided by these techniques. The effects of the interactions of Cr species with DNA were analyzed using a model calf thymus DNA (ctDNA) film on a gold electrode (Au@ctDNA) in different media, including: (i) Cr(VI), (ii) Cr(VI) reduced at -0.2V, (iii) Cr(III)+UV radiation+O 2 , and Cr(III), obtaining the η values: 7.4±1.4, 1.5±0.4, 1.1±0.31%, and 0%, respectively, thus quantifying the hazard posed. The EIS measurements have enabled utilizing the decrease in charge-transfer resistance (R ct ) for ferri/ferrocyanide redox probe at an Au@ctDNA electrode to assess the oxidative ctDNA damage by Cr(VI) species. In this case, circular dichroism indicates an extensive damage to the ctDNA hydrogen bonding. On the other hand, Cr(III) species have not induced any damage to ctDNA, although the EQCN measurements show an electrostatic binding to DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. A look inside HIV resistance through retroviral protease interaction maps.

    Directory of Open Access Journals (Sweden)

    Aleksejs Kontijevskis

    2007-03-01

    Full Text Available Retroviruses affect a large number of species, from fish and birds to mammals and humans, with global socioeconomic negative impacts. Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral proteases. Using multivariate analysis of the sequence-based physiochemical descriptions of 61 retroviral proteases comprising wild-type proteases, natural mutants, and drug-resistant forms of proteases from nine different viral species in relation to their ability to cleave 299 substrates, the authors mapped the physicochemical properties and cross-dependencies of the amino acids of the proteases and their substrates, which revealed a complex molecular interaction network of substrate recognition and cleavage. The approach allowed a detailed analysis of the molecular-chemical mechanisms involved in substrate cleavage by retroviral proteases.

  18. Interactive maps: What we know and what we need to know

    Directory of Open Access Journals (Sweden)

    Robert E. Roth

    2013-06-01

    Full Text Available This article provides a review of the current state of science regarding cartographic interaction, a complement to the traditional focus within cartography on cartographic representation. Cartographic interaction is defined as the dialog between a human and map, mediated through a computing device, and is essential to the research into interactive cartography, geovisualization, and geovisual analytics. The review is structured around six fundamental questions facing a science of cartographic interaction: (1 what is cartographic interaction (e.g., digital versus analog interactions, interaction versus interfaces, stages of interaction, interactive maps versus mapping systems versus map mash-ups; (2 why provide cartographic interaction (e.g., visual thinking, geographic insight, the stages of science, the cartographic problematic; (3 when should cartographic interaction be provided (e.g., static versus interactive maps, interface complexity, the productivity paradox, flexibility versus constraint, work versus enabling interactions; (4 who should be provided with cartographic interaction (e.g., user-centered design, user ability, expertise, and motivation, adaptive cartography and geocollaboration; (5 where should cartographic interaction be provided (e.g., input capabilities, bandwidth and processing power, display capabilities, mobile mapping and location-based services; and (6 how should cartographic interaction be provided (e.g., interaction primitives, objective-based versus operator-based versus operand-based taxonomies, interface styles, interface design? The article concludes with a summary of research questions facing cartographic interaction and offers an outlook for cartography as a field of study moving forward.

  19. Biomolecular interactions probed by fluorescence resonance energy transfer

    Science.gov (United States)

    Lange, Daniela Charlotte

    2000-09-01

    This thesis describes how a physical phenomenon, Fluorescence Resonance Energy Transfer (FRET), can be exploited for the study of interactions between biomolecules. The physical basis of this phenomenon is discussed and it is described how some of its characteristics can be exploited in measurement. A recently introduced method, photobleaching FRET microscopy, was implemented and its image analysis refined to suit our biological context. Further, a new technique is proposed, which combines FRET with confocal laser scanning microscopy to optimize resolution and to allow for 3D-studies in living cells. The first part of this thesis presents the application of FRET to the study of oligomerization of G-protein coupled receptors (GPCRs), which was performed at the Fraser Laboratories at McGill University in Montreal. It is demonstrated how FRET microscopy allowed us to circumvent problems of traditional biochemical approaches and provided the first direct evidence for GPCR oligomerization in intact cells. We found that somatostatin receptors (SSTRs) functionally interact by forming oligomers with their own kind, with different SSTR isoforms, and even with distantly related GPCRs, such as dopamine receptors, the latter of which is breaking with the dogma that GPCRs would only pair up with their own kind. The high sensitivity of the FRET technique allowed us to characterize these interactions under more physiological conditions, which lead to the observation that oligomerization is induced by receptor agonist. We further studied the differential effects of agonists and antagonists on receptor oligomerization, leading to a model for the molecular mechanism underlying agonist/antagonist function and receptor activation. The second part was carried out at the Neurobiology Laboratory of the VA Medical Center in Newington, CT. The objective was to further our understanding of Niemann- Pick type C disease, which is characterized by a defect in intracellular cholesterol

  20. Mapping glycoconjugate-mediated interactions of marine Bacteroidetes with diatoms.

    Science.gov (United States)

    Bennke, Christin M; Neu, Thomas R; Fuchs, Bernhard M; Amann, Rudolf

    2013-09-01

    The degradation of diatoms is mainly catalyzed by Bacteroidetes and this process is of global relevance for the carbon cycle. In this study, a combination of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) and fluorescent lectin binding analysis (FLBA) was used to identify and map glycoconjugates involved in the specific interactions of Bacteroidetes and diatoms, as well as detritus, at the coastal marine site Helgoland Roads (German Bight, North Sea). The study probed both the presence of lectin-specific extracellular polymeric substances (EPS) of Bacteroidetes for cell attachment and that of glycoconjugates on diatoms with respect to binding sites for Bacteroidetes. Members of the clades Polaribacter and Ulvibacter were shown to form microcolonies within aggregates for which FLBA indicated the presence of galactose containing slime. Polaribacter spp. was shown to bind specifically to the setae of the abundant diatom Chaetoceros spp., and the setae were stained with fucose-specific lectins. In contrast, Ulvibacter spp. attached to diatoms of the genus Asterionella which bound, among others, the mannose-specific lectin PSA. The newly developed CARD-FISH/FLBA protocol was limited to the glycoconjugates that persisted after the initial CARD-FISH procedure. The differential attachment of bacteroidetal clades to diatoms and their discrete staining by FLBA provided evidence for the essential role that formation and recognition of glycoconjugates play in the interaction of bacteria with phytoplankton. Copyright © 2013 Elsevier GmbH. All rights reserved.

  1. Skill Learning and Skill Transfer Mediated by Cooperative Haptic Interaction.

    Science.gov (United States)

    Avila Mireles, Edwin Johnatan; Zenzeri, Jacopo; Squeri, Valentina; Morasso, Pietro; De Santis, Dalia

    2017-07-01

    It is known that physical coupling between two subjects may be advantageous in joint tasks. However, little is known about how two people mutually exchange information to exploit the coupling. Therefore, we adopted a reversed, novel perspective to the standard one that focuses on the ability of physically coupled subjects to adapt to cooperative contexts that require negotiating a common plan: we investigated how training in pairs on a novel task affects the development of motor skills of each of the interacting partners. The task involved reaching movements in an unstable dynamic environment using a bilateral non-linear elastic tool that could be used bimanually or dyadically. The main result is that training with an expert leads to the greatest performance in the joint task. However, the performance in the individual test is strongly affected by the initial skill level of the partner. Moreover, practicing with a peer rather than an expert appears to be more advantageous for a naive; and motor skills can be transferred to a bimanual context, after training with an expert, only if the non-expert subject had prior experience of the dynamics of the novel task.

  2. A Novel Transfer Learning Method Based on Common Space Mapping and Weighted Domain Matching

    KAUST Repository

    Liang, Ru-Ze

    2017-01-17

    In this paper, we propose a novel learning framework for the problem of domain transfer learning. We map the data of two domains to one single common space, and learn a classifier in this common space. Then we adapt the common classifier to the two domains by adding two adaptive functions to it respectively. In the common space, the target domain data points are weighted and matched to the target domain in term of distributions. The weighting terms of source domain data points and the target domain classification responses are also regularized by the local reconstruction coefficients. The novel transfer learning framework is evaluated over some benchmark cross-domain data sets, and it outperforms the existing state-of-the-art transfer learning methods.

  3. Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions.

    Science.gov (United States)

    Guruharsha, K G; Obar, Robert A; Mintseris, Julian; Aishwarya, K; Krishnan, R T; Vijayraghavan, K; Artavanis-Tsakonas, Spyros

    2012-01-01

    Proteins perform essential cellular functions as part of protein complexes, often in conjunction with RNA, DNA, metabolites and other small molecules. The genome encodes thousands of proteins but not all of them are expressed in every cell type; and expressed proteins are not active at all times. Such diversity of protein expression and function accounts for the level of biological intricacy seen in nature. Defining protein-protein interactions in protein complexes, and establishing the when, what and where of potential interactions, is therefore crucial to understanding the cellular function of any protein-especially those that have not been well studied by traditional molecular genetic approaches. We generated a large-scale resource of affinity-tagged expression-ready clones and used co-affinity purification combined with tandem mass-spectrometry to identify protein partners of nearly 5,000 Drosophila melanogaster proteins. The resulting protein complex "map" provided a blueprint of metazoan protein complex organization. Here we describe how the map has provided valuable insights into protein function in addition to generating hundreds of testable hypotheses. We also discuss recent technological advancements that will be critical in addressing the next generation of questions arising from the map.

  4. Reciprocal Trust Mediates Deep Transfer of Learning between Games of Strategic Interaction

    Science.gov (United States)

    Juvina, Ion; Saleem, Muniba; Martin, Jolie M.; Gonzalez, Cleotilde; Lebiere, Christian

    2013-01-01

    We studied transfer of learning across two games of strategic interaction. We found that the interpersonal relation between two players during and across two games influence development of reciprocal trust and transfer of learning from one game to another. We show that two types of similarities between the games affect transfer: (1) deep…

  5. A comprehensive molecular interaction map for rheumatoid arthritis.

    Science.gov (United States)

    Wu, Gang; Zhu, Lisha; Dent, Jennifer E; Nardini, Christine

    2010-04-16

    Computational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine--the scientific approach to medicine in tight relation with basic science--, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Rheumatoid Arthritis (RA). Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA. We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being--at the moment--a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at 'www.picb.ac.cn/ClinicalGenomicNTW/temp.html' and 'www.celldesigner.org'.

  6. A comprehensive molecular interaction map for rheumatoid arthritis.

    Directory of Open Access Journals (Sweden)

    Gang Wu

    2010-04-01

    Full Text Available Computational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine--the scientific approach to medicine in tight relation with basic science--, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Rheumatoid Arthritis (RA.Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA.We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being--at the moment--a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at 'www.picb.ac.cn/ClinicalGenomicNTW/temp.html' and 'www.celldesigner.org'.

  7. Interaction mechanism for energy transfer from Ce to Tb ions in silica

    Energy Technology Data Exchange (ETDEWEB)

    Seed Ahmed, H.A.A. [Department of Physics, University of the Free State, Bloemfontein (South Africa); Department of Physics, University of Khartoum, Khartoum (Sudan); Chae, W.S. [Korea Basic Science Institute (KBSI), Gangneung (Korea, Republic of); Ntwaeaborwa, O.M. [Department of Physics, University of the Free State, Bloemfontein (South Africa); Kroon, R.E., E-mail: KroonRE@ufs.ac.za [Department of Physics, University of the Free State, Bloemfontein (South Africa)

    2016-01-01

    Energy transfer phenomena can play an important role in the development of luminescent materials. In this study, numerical simulations based on theoretical models of non-radiative energy transfer are compared to experimental results for Ce, Tb co-doped silica. Energy transfer from the donor (Ce) to the acceptor (Tb) resulted in a decrease in the Ce luminescence intensity and lifetime. The decrease in intensity corresponded best with the energy transfer models based on the exchange interaction and the dipole-dipole interaction. The critical transfer distance obtained from the fitting using both these models is around 2 nm. Since the exchange interaction requires a distance shorter than 1 nm to occur, the mechanism most likely to account for the energy transfer is concluded to be the dipole–dipole interaction. This is supported by an analysis of the lifetime data.

  8. Evaluating web-based static, animated and interactive maps for injury prevention

    Directory of Open Access Journals (Sweden)

    Jonathan Cinnamon

    2009-11-01

    Full Text Available Public health planning can benefit from visual exploration and analysis of geospatial data. Maps and geovisualization tools must be developed with the user-group in mind. User-needs assessment and usability testing are crucial elements in the iterative process of map design and implementation. This study presents the results of a usability test of static, animated and interactive maps of injury rates and socio-demographic determinants of injury by a sample of potential end-users in Toronto, Canada. The results of the user-testing suggest that different map types are useful for different purposes and for satisfying the varying skill level of the individual user. The static maps were deemed to be easy to use and versatile, while the animated maps could be made more useful if animation controls were provided. The split-screen concept of the interactive maps was highlighted as particularly effective for map comparison. Overall, interactive maps were identified as the preferred map type for comparing patterns of injury and related socio-demographic risk factors. Information collected from the user-tests is being used to expand and refine the injury web maps for Toronto, and could inform other public health-related geo-visualization projects.

  9. Saharasar: An Interactive SAR Image Database for Desert Mapping

    Science.gov (United States)

    Lopez, S.; Paillou, Ph.

    2017-06-01

    We present a dedicated tool for accessing radar images acquired by the ALOS/PALSAR mission over Sahara and Arabia. We developed a dedicated web site, using the Mapserver web mapping server and the Cesium javascript library.

  10. The transfer from survey (map-like to route representations into Virtual Reality Mazes: effect of age and cerebral lesion

    Directory of Open Access Journals (Sweden)

    Stampatori Chiara

    2011-01-01

    Full Text Available Abstract Background To go from one place to another, we routinely generate internal representations of surrounding spaces, which can include egocentric (body-centred and allocentric (world-centred coordinates, combined into route and survey representations. Recent studies have shown how both egocentric and allocentric representations exist in parallel and are joined to support behaviour according to the task. Our study investigated the transfer from survey (map-like to route representations in healthy and brain-damaged subjects. The aim was two-fold: first, to understand how this ability could change with age in a sample of healthy participants, aged from 40 to 71 years old; second, to investigate how it is affected after a brain lesion in a 8 patients' sample, with reference to specific neuropsychological frames. Methods Participants were first required to perform the paper and pencil version of eight mazes, then to translate the map-like paths into egocentric routes, in order to find the right way into equivalent Virtual Reality (VR mazes. Patients also underwent a comprehensive neuropsychological evaluation, including a specific investigation of some topographical orientation components. Results As regards the healthy sample, we found age-related deterioration in VR task performance. While education level and gender were not found to be related to performance, global cognitive level (Mini Mental State Examination, previous experience with computer and fluidity of navigation into the VR appeared to influence VR task results. Considering the clinical sample, there was a difficulty in performing the VR Maze task; executive functions and visuo-spatial abilities deficits appeared to be more relevant for predicting patients' results. Conclusions Our study suggests the importance of developing tools aimed at investigating the survey to route transfer ability in both healthy elderly and clinical samples, since this skill seems high cognitive

  11. The transfer from survey (map-like) to route representations into Virtual Reality Mazes: effect of age and cerebral lesion.

    Science.gov (United States)

    Carelli, Laura; Rusconi, Maria Luisa; Scarabelli, Chiara; Stampatori, Chiara; Mattioli, Flavia; Riva, Giuseppe

    2011-01-31

    To go from one place to another, we routinely generate internal representations of surrounding spaces, which can include egocentric (body-centred) and allocentric (world-centred) coordinates, combined into route and survey representations.Recent studies have shown how both egocentric and allocentric representations exist in parallel and are joined to support behaviour according to the task.Our study investigated the transfer from survey (map-like) to route representations in healthy and brain-damaged subjects. The aim was two-fold: first, to understand how this ability could change with age in a sample of healthy participants, aged from 40 to 71 years old; second, to investigate how it is affected after a brain lesion in a 8 patients' sample, with reference to specific neuropsychological frames. Participants were first required to perform the paper and pencil version of eight mazes, then to translate the map-like paths into egocentric routes, in order to find the right way into equivalent Virtual Reality (VR) mazes.Patients also underwent a comprehensive neuropsychological evaluation, including a specific investigation of some topographical orientation components. As regards the healthy sample, we found age-related deterioration in VR task performance. While education level and gender were not found to be related to performance, global cognitive level (Mini Mental State Examination), previous experience with computer and fluidity of navigation into the VR appeared to influence VR task results.Considering the clinical sample, there was a difficulty in performing the VR Maze task; executive functions and visuo-spatial abilities deficits appeared to be more relevant for predicting patients' results. Our study suggests the importance of developing tools aimed at investigating the survey to route transfer ability in both healthy elderly and clinical samples, since this skill seems high cognitive demanding and sensitive to cognitive decline.Human-computer interaction

  12. A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer

    Science.gov (United States)

    Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini

    2017-12-01

    We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.

  13. Fluorescence energy transfer monitoring of protein-protein interaction in human cells: the Cyclin T1-HIV1 Tat case.

    Science.gov (United States)

    Ferrari, Aldo; Cinelli, Riccardo A. G.; Pellegrini, Vittorio; Beltram, Fabio; Marcello, Alessandro; Tyagi, Mudit; Giacca, Mauro

    2001-03-01

    The human immunodeficiency virus type 1 (HIV-1) Tat protein promotes transcriptional elongation of viral RNAs. Here we show that human Cyclin T1 directly binds Tat in cultured cells. By mapping fluorescence resonance energy transfer (FRET) in different cellular compartments we shall present a quantitative analysis of this interaction. The matched tagging pair consists of two optically matched variants of the green fluorescent protein: the enhanced GFP and the blue fluorescent protein. Strong energy transfer was observed between Cyclin T1 and Tat both in the cytoplasm and in specific subnuclear regions. We shall argue that such high-resolution optical studies can provide significant new insight in molecular processes and demonstrate that, for the specific case-study presented, they lead to a model by which Tat recruits Cyclin T1 out of the nuclear compartments where the protein resides to promote transcriptional activation.

  14. They can interact, but can they learn? Toddlers' transfer learning from touchscreens and television.

    Science.gov (United States)

    Moser, Alecia; Zimmermann, Laura; Dickerson, Kelly; Grenell, Amanda; Barr, Rachel; Gerhardstein, Peter

    2015-09-01

    Despite the ubiquity of touchscreen applications and television programs for young children, developmental research suggests that learning in this context is degraded relative to face-to-face interactions. Most previous research has been limited to transfer of learning from videos, making it difficult to isolate the relative perceptual and social influences for transfer difficulty, and has not examined whether the transfer deficit persists across early childhood when task complexity increases. The current study examined whether the transfer deficit persists in older children using a complex puzzle imitation task constructed to investigate transfer from video demonstrations. The current test adapted this task to permit bidirectional transfer from touchscreens as well. To test for bidirectional transfer deficits, 2.5- and 3-year-olds were shown how to assemble a three-piece puzzle on either a three-dimensional magnetic board or a two-dimensional touchscreen (Experiment 1). Unidirectional transfer from video was also tested (Experiment 2). Results indicate that a bidirectional transfer deficit persists through 3 years, with younger children showing a greater transfer deficit; despite high perceptual similarities and social engagement, children learned less in transfer tasks, supporting the memory flexibility account of the transfer deficit. Implications of these findings for use of screen media (e.g., video, tablets) in early education are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. A bioluminescence resonance energy transfer (BRET) system: Application to interacting circadian clock proteins

    OpenAIRE

    Xu, Yao; Piston, David W.; Johnson, Carl Hirschie

    1999-01-01

    We describe a method for assaying protein interactions that offers some attractive advantages over previous assays. This method, called bioluminescence resonance energy transfer (BRET), uses a bioluminescent luciferase that is genetically fused to one candidate protein, and a green fluorescent protein mutant fused to another protein of interest. Interactions between the two fusion proteins can bring the luciferase and green fluorescent protein close enough for resonance energy transfer to occ...

  16. Shared-Screen Interaction: Engaging Groups in Map-Mediated Nonverbal Communication

    Science.gov (United States)

    Chorianopoulos, Konstantinos; Rieniets, Tim

    This chapter describes the design and development of an interactive video installation that allows participants to explore a map narrative, and engage in group interactions through a shared screen. For this purpose, several layers of cartographic information were employed in a computer application, which was programmed with motion-tracking libraries in the open source tool processing. The interactive video installation has been chosen as a medium to achieve the following aims: (1) The visualization of urban-conflict as an interactive map narrative, and (2) the encouragement of social encounters through a shared screen. The development process begins with the design of interaction between the system and the participants, as well as between the participants themselves. Then we map the interaction design concepts into multimedia and architectural design. Finally, we provide a discussion on the creative process and the collaboration between different disciplines, such as architecture, urban planning, cartography, computer engineering, and media studies.

  17. Dissection of DNA damage responses using multiconditional genetic interaction maps

    NARCIS (Netherlands)

    Guénolé, Aude

    2013-01-01

    To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different

  18. American Samoa: coral reef monitoring interactive map and information layers primarily from 2010 surveys

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This interactive map displays American Samoa data collected by the NOAA Coral Reef Ecosystem Division (CRED) during the Pacific Reef Assessment and Monitoring...

  19. Renormalization of effective interactions in a negative charge transfer insulator

    Science.gov (United States)

    Seth, Priyanka; Peil, Oleg E.; Pourovskii, Leonid; Betzinger, Markus; Friedrich, Christoph; Parcollet, Olivier; Biermann, Silke; Aryasetiawan, Ferdi; Georges, Antoine

    2017-11-01

    We compute from first principles the effective interaction parameters appropriate for a low-energy description of the rare-earth nickelate LuNiO3 involving the partially occupied eg states only. The calculation uses the constrained random-phase approximation and reveals that the effective on-site Coulomb repulsion is strongly reduced by screening effects involving the oxygen-p and nickel-t2 g states. The long-range component of the effective low-energy interaction is also found to be sizable. As a result, the effective on-site interaction between parallel-spin electrons is reduced down to a small negative value. This validates effective low-energy theories of these materials that were proposed earlier. Electronic structure methods combined with dynamical mean-field theory are used to construct and solve an appropriate low-energy model and explore its phase diagram as a function of the on-site repulsion and Hund's coupling. For the calculated values of these effective interactions, we find that in agreement with experiments, LuNiO3 is a metal without disproportionation of the eg occupancy when considered in its orthorhombic structure, while the monoclinic phase is a disproportionated insulator.

  20. Mapping Haplotype-haplotype Interactions with Adaptive LASSO

    Directory of Open Access Journals (Sweden)

    Li Ming

    2010-08-01

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

  1. Toward accelerating landslide mapping with interactive machine learning techniques

    Science.gov (United States)

    Stumpf, André; Lachiche, Nicolas; Malet, Jean-Philippe; Kerle, Norman; Puissant, Anne

    2013-04-01

    Despite important advances in the development of more automated methods for landslide mapping from optical remote sensing images, the elaboration of inventory maps after major triggering events still remains a tedious task. Image classification with expert defined rules typically still requires significant manual labour for the elaboration and adaption of rule sets for each particular case. Machine learning algorithm, on the contrary, have the ability to learn and identify complex image patterns from labelled examples but may require relatively large amounts of training data. In order to reduce the amount of required training data active learning has evolved as key concept to guide the sampling for applications such as document classification, genetics and remote sensing. The general underlying idea of most active learning approaches is to initialize a machine learning model with a small training set, and to subsequently exploit the model state and/or the data structure to iteratively select the most valuable samples that should be labelled by the user and added in the training set. With relatively few queries and labelled samples, an active learning strategy should ideally yield at least the same accuracy than an equivalent classifier trained with many randomly selected samples. Our study was dedicated to the development of an active learning approach for landslide mapping from VHR remote sensing images with special consideration of the spatial distribution of the samples. The developed approach is a region-based query heuristic that enables to guide the user attention towards few compact spatial batches rather than distributed points resulting in time savings of 50% and more compared to standard active learning techniques. The approach was tested with multi-temporal and multi-sensor satellite images capturing recent large scale triggering events in Brazil and China and demonstrated balanced user's and producer's accuracies between 74% and 80%. The assessment also

  2. Mapping Protein-Protein Interactions by Quantitative Proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2010-01-01

    Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions....

  3. Interaction of bullets with intermediate targets: material transfer and damage.

    Science.gov (United States)

    Vermeij, Erwin; Rijnders, Marco; Pieper, Pascal; Hermsen, Rob

    2012-11-30

    In complex shooting incidents, it is not always clear which bullet hit or eventually killed the victim and who fired it. The examination of traces of foreign material embedded in or adhered to bullets provides critical information in the trajectory reconstruction of spent bullets. Such a reconstruction can have considerable legal implications because it can prove that it was not someone's intention to kill. However, the microtraces that remain on spent bullets are often ignored. Microtraces on bullets, around bullet-holes and on ricochet marks were investigated using SEM/EDX for two different types of bullets: a relatively hard, full metal jacket (FMJ) bullet and a relatively soft, lead round-nose (LRN) bullet. A total of 179 bullets were fired into intermediate targets, sheets of 5 different materials (MDF, greenboard, gypsum fibreboard, glass and steel), at approximate incident angles of 90°, 10° and 5°. Of the 144 bullets fired at incident angles of 90°, 130 bullets perforated one of the materials, and 14 bullets perforated two of the materials. The 35 bullets fired at incident angles of 10° and 5° ricocheted off the intermediate targets, producing ricochet marks. In the majority of cases, traces from the target materials were found on the bullet, both after perforation and ricochet. The only exceptions were (1) the perforation of 9-mm sheets of MDF by FMJ bullets and (2) ricochet off glass when the glass did not break. Steel targets transfer small, but still detectable traces of iron to the bullet. The order in which targets are hit was reflected in the traces found on the bullets, i.e., materials from a secondary target were deposited on top of deposits from the primary target. This result implies that it is possible to determine the order of impact from the stratification of the material analysed. Traces from the bullets were found around all the bullet holes. Wipe-off from lead bullets is sometimes visible by the naked eye. Ricocheting bullets produce

  4. User-Centered Design for Interactive Maps: A Case Study in Crime Analysis

    Directory of Open Access Journals (Sweden)

    Robert E. Roth

    2015-02-01

    Full Text Available In this paper, we address the topic of user-centered design (UCD for cartography, GIScience, and visual analytics. Interactive maps are ubiquitous in modern society, yet they often fail to “work” as they could or should. UCD describes the process of ensuring interface success—map-based or otherwise—by gathering input and feedback from target users throughout the design and development of the interface. We contribute to the expanding literature on UCD for interactive maps in two ways. First, we synthesize core concepts on UCD from cartography and related fields, as well as offer new ideas, in order to organize existing frameworks and recommendations regarding the UCD of interactive maps. Second, we report on a case study UCD process for GeoVISTA CrimeViz, an interactive and web-based mapping application supporting visual analytics of criminal activity in space and time. The GeoVISTA CrimeViz concept and interface were improved iteratively by working through a series of user→utility→usability loops in which target users provided input and feedback on needs and designs (user, prompting revisions to the conceptualization and functional requirements of the interface (utility, and ultimately leading to new mockups and prototypes of the interface (usability for additional evaluation by target users (user… and so on. Together, the background review and case study offer guidance for applying UCD to interactive mapping projects, and demonstrate the benefit of including target users throughout design and development.

  5. Metals interaction in the process of torch mass transfer

    International Nuclear Information System (INIS)

    Khaldeev, V.N.; Pashko, O.V.; Belova, V.P.; Sevryugina, N.D.; Vasil'eva, A.I.

    2000-01-01

    The billet material components interaction with the work surface material of the electrode-tool under the action of a torch jet which is formed in the process of electro-erosion treatment is investigated. It is established that metallic film arises on a surface of the electrode-tool under certain conditions in the process of electro-erosion forming is identical with the composition of the worked material. Components of the metal alloy worked diffuse into the tool material with formation of a particular compounds [ru

  6. Heat transfer in reactor cavity during core-concrete interaction

    International Nuclear Information System (INIS)

    Adroguer, B.; Cenerino, G.

    1989-08-01

    In the unlikely event of a severe accident in a nuclear power plant, the core may melt through the vessel and slump into the concrete reactor cavity. The hot mixture of the core material called corium interacts thermally with the concrete basemat. The WECHSL code, developed at K.f.K. Karlsruhe in Germany is used at the Protection and Nuclear Safety Institute (I.P.S.N.) of CEA to compute this molten corium concrete interaction (MCCI). Some uncertainties remain in the partition of heat from the corium between the basemat and the upper surrounding structures in the cavity where the thermal conditions are not computer. The CALTHER code, under development to perform a more mechanistic evaluation of the upward heat flux has been linked to WECHSL-MOD2 code. This new version enables the modelling of the feedback effects from the conditions in the cavity to the MCCI and the computation of the fraction of upward flux directly added to the cavity atmosphere. The present status is given in the paper. Preliminary calculations of the reactor case for silicate and limestone common sand (L.C.S.) concretes are presented. Significant effects are found on concrete erosion, gases release and temperature of the upper part of corium, particularly for L.C.S. concrete

  7. Mapping Cultural Frame Shifting in Interaction Design with Blending Theory

    DEFF Research Database (Denmark)

    Markussen, Thomas; Krogh, Peter Gall

    2008-01-01

    In this paper, we introduce Gilles Fauconnier & Mark Turner's blending theory as a new conceptual framework for explaining ‘cultural frame shifting' in interaction design. Cultural frame shifting is when people, through their explorative use of technology, are required imaginatively to reorganize...... their cultural background knowledge and expectations. In current HCI research it has occasionally been pointed out that a proper understanding of this phenomenon hinges on addressing the relationship between embodied interaction and cultural meaning construction as part of a larger interactive system. However......, the given treatments of this relationship are mostly unbalanced. Thus, there is a research bias towards either leaving the question of meaning construction aside, or trying to answer it exclusively in terms of embodiment - often grounded in phenomenology. As a tool of analysis and interpretation we apply...

  8. Understanding Urban Watersheds through Digital Interactive Maps, San Francisco Bay Area, California

    Science.gov (United States)

    Sowers, J. M.; Ticci, M. G.; Mulvey, P.

    2014-12-01

    Dense urbanization has resulted in the "disappearance" of many local creeks in urbanized areas surrounding the San Francisco Bay. Long reaches of creeks now flow in underground pipes. Municipalities and water agencies trying to reduce non-point-source pollution are faced with a public that cannot see and therefore does not understand the interconnected nature of the drainage system or its ultimate discharge to the bay. Since 1993, we have collaborated with the Oakland Museum, the San Francisco Estuary Institute, public agencies, and municipalities to create creek and watershed maps to address the need for public understanding of watershed concepts. Fifteen paper maps are now published (www.museumca.org/creeks), which have become a standard reference for educators and anyone working on local creek-related issues. We now present digital interactive creek and watershed maps in Google Earth. Four maps are completed covering urbanized areas of Santa Clara and Alameda Counties. The maps provide a 3D visualization of the watersheds, with cartography draped over the landscape in transparent colors. Each mapped area includes both Present and Past (circa 1800s) layers which can be clicked on or off by the user. The Present layers include the modern drainage network, watershed boundaries, and reservoirs. The Past layers include the 1800s-era creek systems, tidal marshes, lagoons, and other habitats. All data are developed in ArcGIS software and converted to Google Earth format. To ensure the maps are interesting and engaging, clickable icons pop-up provide information on places to visit, restoration projects, history, plants, and animals. Maps of Santa Clara Valley are available at http://www.valleywater.org/WOW.aspx. Maps of western Alameda County will soon be available at http://acfloodcontrol.org/. Digital interactive maps provide several advantages over paper maps. They are seamless within each map area, and the user can zoom in or out, and tilt, and fly over to explore

  9. Energy dependence of angular momentum transfer in post-collision interaction. Classical view

    Science.gov (United States)

    Gerchikov, L.; Sheinerman, S.

    2018-03-01

    A classical approach to the description of angular momentum transfer between the Auger electron and photoelectron in post-collision interaction is worked out. The results of the classical approach coincide with the quantum mechanical ones at the photoionization threshold. Besides, the approach developed provides a description of angular momentum transfer beyond the photoionization threshold. In particular, it is suitable in the energy region of comparable velocities of two emitted electrons.

  10. Radiative transfer modeling of MESSENGER VIRS spectra: Detection and mapping of submicroscopic iron and carbon

    Science.gov (United States)

    Trang, David; Lucey, Paul G.; Izenberg, Noam R.

    2017-09-01

    We model the spectral effects of submicroscopic Fe and submicroscopic C particles within a transparent mineral host in order to investigate whether such materials could reproduce the major spectral characteristics of Mercury's reflectance spectra (i.e., low reflectance relative to the Moon, a lack of Fe absorption features in the near infrared, and an increasing continuum slope between visible and near-infrared wavelengths). By using the radiative transfer technique to model the VIRS (Visible and Infrared Spectrograph) spectral dataset obtained from the MESSENGER (MErcury Surface, Space ENvironment, GEochemistry, and Ranging) mission, we found that our spectral models based on nanophase and microphase Fe and C consistently fit the VIRS data (except of regions of Mercury's low-reflectance material). Our models show that the mean global submicroscopic Fe abundance is 2.5 wt%, which exceeds the total Fe abundances obtained from the MESSENGER Gamma-Ray Spectrometer (GRS) and the X-Ray Spectrometer (XRS) and the global average submicroscopic C abundance is 1.9 wt%, which is within the three-standard-deviation level of the MESSENGER GRS C measurements for Mercury's northern hemisphere. We also produced nanophase and microphase Fe and C abundance maps that show: (1) submicroscopic C is present at percent levels across the surface, (2) the spatial variations of submicroscopic particle abundances are correlated to the maximum surface temperature, (3) lower concentrations of nanophase Fe in fresh craters and their ejecta, (4) the submicroscopic Fe abundance is lower in the northern volcanic plains and Caloris basin than the global average, (5) the submicroscopic C and Fe abundances are very low around NE Rachmaninoff, a pyroclastic deposit, and (6) the submicroscopic particle abundances vary between low-reflectance material (LRM) deposits. In correlating these maps to geology and surface temperatures, we concluded that Ostwald ripening is responsible for the longitudinal and

  11. Nano-inspired smart interfaces: fluidic interactivity and its impact on heat transfer

    Science.gov (United States)

    Kim, Beom Seok; Lee, Byoung In; Lee, Namkyu; Choi, Geehong; Gemming, Thomas; Cho, Hyung Hee

    2017-03-01

    Interface-inspired convection is a key heat transfer scheme for hot spot cooling and thermal energy transfer. An unavoidable trade-off of the convective heat transfer is pressure loss caused by fluidic resistance on an interface. To overcome this limitation, we uncover that nano-inspired interfaces can trigger a peculiar fluidic interactivity, which can pursue all the two sides of the coin: heat transfer and fluidic friction. We demonstrate the validity of a quasi-fin effect of Si-based nanostructures based on conductive capability of heat dissipation valid under the interactivity with fluidic viscous sublayer. The exclusive fluid-interface friction is achieved when the height of the nanostructures is much less than the thickness of the viscous sublayers in the turbulent regime. The strategic nanostructures show an enhancement of heat transfer coefficients in the wall jet region by more than 21% without any significant macroscale pressure loss under single-phase impinging jet. Nanostructures guaranteeing fluid access via an equivalent vacancy larger than the diffusive path length of viscid flow lead to local heat transfer enhancement of more than 13% at a stagnation point. Functional nanostructures will give shape to possible breakthroughs in heat transfer and its optimization can be pursued for engineered systems.

  12. A simulation framework for mapping risks in clinical processes: the case of in-patient transfers

    Science.gov (United States)

    Ong, Mei-Sing; Westbrook, Johanna I; Magrabi, Farah; Coiera, Enrico; Wobcke, Wayne

    2011-01-01

    Objective To model how individual violations in routine clinical processes cumulatively contribute to the risk of adverse events in hospital using an agent-based simulation framework. Design An agent-based simulation was designed to model the cascade of common violations that contribute to the risk of adverse events in routine clinical processes. Clinicians and the information systems that support them were represented as a group of interacting agents using data from direct observations. The model was calibrated using data from 101 patient transfers observed in a hospital and results were validated for one of two scenarios (a misidentification scenario and an infection control scenario). Repeated simulations using the calibrated model were undertaken to create a distribution of possible process outcomes. The likelihood of end-of-chain risk is the main outcome measure, reported for each of the two scenarios. Results The simulations demonstrate end-of-chain risks of 8% and 24% for the misidentification and infection control scenarios, respectively. Over 95% of the simulations in both scenarios are unique, indicating that the in-patient transfer process diverges from prescribed work practices in a variety of ways. Conclusions The simulation allowed us to model the risk of adverse events in a clinical process, by generating the variety of possible work subject to violations, a novel prospective risk analysis method. The in-patient transfer process has a high proportion of unique trajectories, implying that risk mitigation may benefit from focusing on reducing complexity rather than augmenting the process with further rule-based protocols. PMID:21486883

  13. A double-mutant collection targeting MAP kinase related genes in Arabidopsis for studying genetic interactions.

    Science.gov (United States)

    Su, Shih-Heng; Krysan, Patrick J

    2016-12-01

    Mitogen-activated protein kinase cascades are conserved in all eukaryotes. In Arabidopsis thaliana there are approximately 80 genes encoding MAP kinase kinase kinases (MAP3K), 10 genes encoding MAP kinase kinases (MAP2K), and 20 genes encoding MAP kinases (MAPK). Reverse genetic analysis has failed to reveal abnormal phenotypes for a majority of these genes. One strategy for uncovering gene function when single-mutant lines do not produce an informative phenotype is to perform a systematic genetic interaction screen whereby double-mutants are created from a large library of single-mutant lines. Here we describe a new collection of 275 double-mutant lines derived from a library of single-mutants targeting genes related to MAP kinase signaling. To facilitate this study, we developed a high-throughput double-mutant generating pipeline using a system for growing Arabidopsis seedlings in 96-well plates. A quantitative root growth assay was used to screen for evidence of genetic interactions in this double-mutant collection. Our screen revealed four genetic interactions, all of which caused synthetic enhancement of the root growth defects observed in a MAP kinase 4 (MPK4) single-mutant line. Seeds for this double-mutant collection are publicly available through the Arabidopsis Biological Resource Center. Scientists interested in diverse biological processes can now screen this double-mutant collection under a wide range of growth conditions in order to search for additional genetic interactions that may provide new insights into MAP kinase signaling. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  14. Accurate transfer maps for realistic beam-line elements: Straight elements

    Directory of Open Access Journals (Sweden)

    Chad E. Mitchell

    2010-06-01

    Full Text Available The behavior of orbits in charged-particle beam transport systems, including both linear and circular accelerators as well as final focus sections and spectrometers, can depend sensitively on nonlinear fringe-field and high-order-multipole effects in the various beam-line elements. The inclusion of these effects requires a detailed and realistic model of the interior and fringe fields, including their high spatial derivatives. A collection of surface fitting methods has been developed for extracting this information accurately from three-dimensional field data on a grid, as provided by various three-dimensional finite-element field codes. Based on these realistic field models, Lie or other methods may be used to compute accurate design orbits and accurate transfer maps about these orbits. Part I of this work presents a treatment of straight-axis magnetic elements, while part II will treat bending dipoles with large sagitta. An exactly soluble but numerically challenging model field is used to provide a rigorous collection of performance benchmarks.

  15. Optimal design method to minimize users' thinking mapping load in human-machine interactions.

    Science.gov (United States)

    Huang, Yanqun; Li, Xu; Zhang, Jie

    2015-01-01

    The discrepancy between human cognition and machine requirements/behaviors usually results in serious mental thinking mapping loads or even disasters in product operating. It is important to help people avoid human-machine interaction confusions and difficulties in today's mental work mastered society. Improving the usability of a product and minimizing user's thinking mapping and interpreting load in human-machine interactions. An optimal human-machine interface design method is introduced, which is based on the purpose of minimizing the mental load in thinking mapping process between users' intentions and affordance of product interface states. By analyzing the users' thinking mapping problem, an operating action model is constructed. According to human natural instincts and acquired knowledge, an expected ideal design with minimized thinking loads is uniquely determined at first. Then, creative alternatives, in terms of the way human obtains operational information, are provided as digital interface states datasets. In the last, using the cluster analysis method, an optimum solution is picked out from alternatives, by calculating the distances between two datasets. Considering multiple factors to minimize users' thinking mapping loads, a solution nearest to the ideal value is found in the human-car interaction design case. The clustering results show its effectiveness in finding an optimum solution to the mental load minimizing problems in human-machine interaction design.

  16. Mapping the material in the LHCb vertex locator using secondary hadronic interactions arXiv

    CERN Document Server

    Alexander, M.; Bay, A.; Bel, L.J.; van Beuzekom, M.; Bogdanova, G.; Borghi, S.; Bowcock, T.J.V.; Buchanan, E.; Buytaert, J.; Carvalho Akiba, K.; Chen, S.; Coco, V.; Collins, P.; Crocombe, A.; Da Cunha Marinho, F.; Dall'Occo, E.; De Capua, S.; Dean, C.T.; Dettori, F.; Dossett, D.; Dreimanis, K.; Dujany, G.; Eklund, L.; Evans, T.; Ferro-Luzzi, M.; Gersabeck, M.; Gershon, T.; Hadavizadeh, T.; Harrison, J.; Hennessy, K.; Hulsbergen, W.; Hutchcroft, D.; Jans, P.Ilten E.; John, M.; Kopciewicz, P.; Koppenburg, P.; Lafferty, G.; Latham, T.; Leflat, A.; Majewski, M.W.; McNulty, R.; Mylroie-Smith, J.; Oblakowska-Mucha, A.; Parkes, C.; Pearce, A.; Poluektov, A.; Pritchard, A.; Qian, W.; Redford, S.; Richards, S.; Rinnert, K.; Rodrigues, E.; Sarpis, G.; Schiller, M.; Schindler, H.; Smith, M.; Smith, N.A.; Szumlak, T.; Velthuis, J.J.; Volkov, V.; Wallace, C.; Wark, H.M.; Webber, A.; Williams, M.R.J.; Williams, M.

    Precise knowledge of the location of the material in the LHCb vertex locator (VELO) is essential to reducing background in searches for long-lived exotic particles, and in identifying jets that originate from beauty and charm quarks. Secondary interactions of hadrons produced in beam-gas collisions are used to map the location of material in the VELO. Using this material map, along with properties of a reconstructed secondary vertex and its constituent tracks, a $p$-value can be assigned to the hypothesis that the secondary vertex originates from a material interaction. A validation of this procedure is presented using photon conversions to dimuons.

  17. A Novel Image Encryption Scheme Based on Clifford Attractor and Noisy Logistic Map for Secure Transferring Images in Navy

    Directory of Open Access Journals (Sweden)

    Mohadeseh Kanafchian

    2017-04-01

    In this paper, we first give a brief introduction into chaotic image encryption and then we investigate some important properties and behaviour of the logistic map. The logistic map, aperiodic trajectory, or random-like fluctuation, could not be obtained with some choice of initial condition. Therefore, a noisy logistic map with an additive system noise is introduced. The proposed scheme is based on the extended map of the Clifford strange attractor, where each dimension has a specific role in the encryption process. Two dimensions are used for pixel permutation and the third dimension is used for pixel diffusion. In order to optimize the Clifford encryption system we increase the space key by using the noisy logistic map and a novel encryption scheme based on the Clifford attractor and the noisy logistic map for secure transfer images is proposed. This algorithm consists of two parts: the noisy logistic map shuffle of the pixel position and the pixel value. We use times for shuffling the pixel position and value then we generate the new pixel position and value by the Clifford system. To illustrate the efficiency of the proposed scheme, various types of security analysis are tested. It can be concluded that the proposed image encryption system is a suitable choice for practical applications.

  18. Decision making based on optical excitation transfer via near-field interactions between quantum dots

    International Nuclear Information System (INIS)

    Naruse, Makoto; Nomura, Wataru; Ohtsu, Motoichi; Aono, Masashi; Sonnefraud, Yannick; Drezet, Aurélien; Huant, Serge; Kim, Song-Ju

    2014-01-01

    Optical near-field interactions between nanostructured matters, such as quantum dots, result in unidirectional optical excitation transfer when energy dissipation is induced. This results in versatile spatiotemporal dynamics of the optical excitation, which can be controlled by engineering the dissipation processes and exploited to realize intelligent capabilities such as solution searching and decision making. Here, we experimentally demonstrate the ability to solve a decision making problem on the basis of optical excitation transfer via near-field interactions by using colloidal quantum dots of different sizes, formed on a geometry-controlled substrate. We characterize the energy transfer behavior due to multiple control light patterns and experimentally demonstrate the ability to solve the multi-armed bandit problem. Our work makes a decisive step towards the practical design of nanophotonic systems capable of efficient decision making, one of the most important intellectual attributes of the human brain.

  19. Facilitating participatory multilevel decision-making by using interactive mental maps

    Directory of Open Access Journals (Sweden)

    Constanze Pfeiffer

    2008-11-01

    Full Text Available Participation of citizens in political, economic or social decisions is increasingly recognized as a precondition to foster sustainable development processes. Since spatial information is often important during planning and decisionmaking, participatory mapping gains in popularity. However, little attention has been paid to the fact that information must be presented in a useful way to reach city planners and policy makers. Above all, the importance of visualisation tools to support collaboration, analytical reasoning, problem solving and decision-making in analysing and planning processes has been underestimated. In this paper, we describe how an interactive mental map tool has been developed in a highly interdisciplinary disaster management project in Chennai, India. We moved from a hand drawn mental maps approach to an interactive mental map tool. This was achieved by merging socio-economic and geospatial data on infrastructure, local perceptions, coping and adaptation strategies with remote sensing data and modern technology of map making. This newly developed interactive mapping tool allowed for insights into different locally-constructed realities and facilitated the communication of results to the wider public and respective policy makers. It proved to be useful in visualising information and promoting participatory decision-making processes. We argue that the tool bears potential also for health research projects. The interactive mental map can be used to spatially and temporally assess key health themes such as availability of, and accessibility to, existing health care services, breeding sites of disease vectors, collection and storage of water, waste disposal, location of public toilets or defecation sites.

  20. Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families.

    Science.gov (United States)

    Voloshanenko, Oksana; Gmach, Philipp; Winter, Jan; Kranz, Dominique; Boutros, Michael

    2017-11-01

    Signaling pathway modules are often encoded by several closely related paralogous genes that can have redundant roles and are therefore difficult to analyze by loss-of-function analysis. A typical example is the Wnt signaling pathway, which in mammals is mediated by 19 Wnt ligands that can bind to 10 Frizzled (FZD) receptors. Although significant progress in understanding Wnt-FZD receptor interactions has been made in recent years, tools to generate systematic interaction maps have been largely lacking. Here we generated cell lines with multiplex mutant alleles of FZD1 , FZD2 , and FZD7 and demonstrate that these cells are unresponsive to canonical Wnt ligands. Subsequently, we performed genetic rescue experiments with combinations of FZDs and canonical Wnts to create a functional ligand-receptor interaction map. These experiments showed that whereas several Wnt ligands, such as Wnt3a, induce signaling through a broad spectrum of FZD receptors, others, such as Wnt8a, act through a restricted set of FZD genes. Together, our results map functional interactions of FZDs and 10 Wnt ligands and demonstrate how multiplex targeting by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 can be used to systematically elucidate the functions of multigene families.-Voloshanenko, O., Gmach, P., Winter, J., Kranz, D., Boutros, M. Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families. © The Author(s).

  1. Local shell-to-shell energy transfer via nonlocal interactions in fluid ...

    Indian Academy of Sciences (India)

    The computation has been done using first-order perturbative field theory. In three dimensions, magnitude of triad interactions is large for nonlocal triads, and small for local triads. However, the shell-to-shell energy transfer rate is found to be local and forward. This result is due to the fact that the nonlocal triads occupy much ...

  2. Local shell-to-shell energy transfer via nonlocal interactions in fluid ...

    Indian Academy of Sciences (India)

    August 2005 physics pp. 297–310. Local shell-to-shell energy transfer via nonlocal interactions in fluid turbulence. MAHENDRA K VERMA1, ARVIND AYYER2, OLIVIER ... MS received 1 October 2004; revised 2 March 2005; accepted 13 April 2005 ...... Kraichnan [23,24] first raised the above objection, and proposed.

  3. Local shell-to-shell energy transfer via nonlocal interactions in fluid ...

    Indian Academy of Sciences (India)

    in a triad, and the energy exchanges between wave-number shells in incompressible fluid turbulence. The computation has been done using first-order perturbative field theory. In three dimensions, magnitude of triad interactions is large for nonlocal triads, and small for local triads. However, the shell-to-shell energy transfer ...

  4. Quantum transfer energy in the framework of time-dependent dipole-dipole interaction

    Science.gov (United States)

    El-Shishtawy, Reda M.; Haddon, Robert C.; Al-Heniti, Saleh H.; Raffah, Bahaaudin M.; Berrada, K.; Abdel-Khalek, S.; Al-Hadeethi, Yas F.

    2018-03-01

    In this work, we examine the process of the quantum transfer of energy considering time-dependent dipole-dipole interaction in a dimer system characterized by two-level atom systems. By taking into account the effect of the acceleration and speed of the atoms in the dimer coupling, we demonstrate that the improvement of the probability for a single-excitation transfer energy extremely benefits from the incorporation of atomic motion effectiveness and the energy detuning. We explore the relevance between the population and entanglement during the time-evolution and show that this kind of nonlocal correlation may be generated during the process of the transfer of energy. Our work may provide optimal conditions to implement realistic experimental scenario in the transfer of the quantum energy.

  5. Nonlocal interaction of inverse magnetic energy transfer in hall magnetohydrodynamic turbulence

    International Nuclear Information System (INIS)

    Araki, Keisuke; Miura, Hideaki

    2011-01-01

    A detailed analysis of forward and inverse energy transfer processes due to the Hall term effect in freely decaying, homogeneous, isotropic Hall magnetohydrodynamics (HMHD) turbulence is performed through Fourier and wavelet analyses. We analyzed three snapshot datasets that were taken from such a period to allow the turbulence to develop sufficiently with a nearly constant magnetic Reynolds number. Because the Fourier energy spectra in these snapshots show remarkable agreement after the normalization in terms of the dissipation rates and the diffusion coefficients, they are considered as a universal equilibrium state. By analyzing the numerical solutions that are generated without any external forcing, it is confirmed that the inverse energy transfer due to the Hall term effect is intrinsic to HMHD dynamics. Orthonormal divergence-free wavelet analysis reveals that nonlinear mode interactions contributing to the inverse energy transfer exhibit a nonlocal feature, while those for the forward transfer are dominated by a local feature. (author)

  6. Construction and Implementation of Teaching Mode for Digital Mapping based on Interactive Micro-course Technology

    Directory of Open Access Journals (Sweden)

    Ning Gao

    2018-02-01

    Full Text Available The era of “Internet + education” has caused reforms in teaching ideas, teaching modes, and learning styles. The emergence of micro-course technology provides new strategies for integrating learning styles. Task-driven digital mapping teaching, known as traditional classroom organization, has poor teaching effect due to single learning style and strategy. A new teaching mode for digital mapping was constructed in this study based on micro-course technology by combining interactive micro-course technology and digital mapping teaching to adapt to the demands of modern teaching. This teaching mode mainly included four modules, namely, micro-courseware, micro-video, micro-exercise, and micro-examination. It realized the hierarchical teaching of knowledge points in digital mapping course, simplification of basic principles, simulation of engineering cases, and self-evaluation of learning outcomes. The teaching mode was applied to 114 students from the Mapping Engineering Department of Henan University of Urban Construction. Results indicate that the proposed teaching mode based on interactive micro-course technology promoting the independent after-class learning of the students, stimulating their learning enthusiasm, enhancing their practical abilities of the students, and improving the effect of teaching. This mode of teaching provides a new concept for the teaching mode reform of other courses in mapping engineering.

  7. Interactive Web-Based Map: Applications to Large Data Sets in the Geosciences. Interactive Web-Based Map: Applications to Large Data Sets in the Geosciences.

    Science.gov (United States)

    Garbow, Z. A.; Olson, N. R.; Yuen, D. A.; Boggs, J. M.

    2001-12-01

    Current advances in computer hardware, information technology and data collection techniques have produced very large data sets, sometimes more than terabytes,in a wide variety of scientific and engineering disciplines. We must harness this opportunity to visualize and extract useful information from geophysical and geological data. We have taken the task of data-mining by using a map-like approach over the web for interrogating the humongous data, using a client-server paradigm. The spatial-data is mapped onto a two-dimensional grid from which the user ( client ) can quiz the data with the map-interface as a user extension . The data is stored on high-end compute server. The computational gateway separating the client and the server can be the front-end of an electronic publication , electronic classroom , a Grid system device or e-business. We have used a combination of JAVA, JAVA-3D and Perl for processing the data and communicating them between the client and the server. The user can interrogate the geospatial data over any particular region with arbitrary length scales and pose relevant statistical questions, such as the histogram plots and local statistics. We have applied this method for the following data sets (1.) distribution of prime numbers (2.) two-dimensional mantle convection (3.) three-dimensional mantle convection (4) high-resolution satellite reflectance data over the Upper Midwest for multiple wavelengths (5) molecular dynamics describing the flow of blood in narrow vessels. Using this map-interface concept, the user can actually interrogate these data over the web. This strategy for dissecting large data-sets can be easily applied to other areas, such as satellite geodesy and earthquake data. This mode of data-query may function in an adequately covered wireless web environment with a transfer rate of around 10 Mbit/sec .

  8. An Interactive Immersive Serious Game Application for Kunyu Quantu World Map

    Science.gov (United States)

    Peng, S.-T.; Hsu, S.-Y.; Hsieh, K.-C.

    2015-08-01

    In recent years, more and more digital technologies and innovative concepts are applied on museum education. One of the concepts applied is "Serious game." Serious game is not designed for entertainment purpose but allows users to learn real world's cultural and educational knowledge in the virtual world through game-experiencing. Technologies applied on serious game are identical to those applied on entertainment game. Nowadays, the interactive technology applications considering users' movement and gestures in physical spaces are developing rapidly, which are extensively used in entertainment games, such as Kinect-based games. The ability to explore space via Kinect-based games can be incorporated into the design of serious game. The ancient world map, Kunyu Quantu, from the collection of the National Palace Museum is therefore applied in serious game development. In general, the ancient world map does not only provide geological information, but also contains museum knowledge. This particular ancient world map is an excellent content applied in games as teaching material. In the 17th century, it was first used by a missionary as a medium to teach the Kangxi Emperor of the latest geologic and scientific spirits from the West. On this map, it also includes written biological knowledge and climate knowledge. Therefore, this research aims to present the design of the interactive and immersive serious game based installation that developed from the rich content of the Kunyu Quantu World Map, and to analyse visitor's experience in terms of real world's cultural knowledge learning and interactive responses.

  9. Optimization of selective inversion recovery magnetization transfer imaging for macromolecular content mapping in the human brain.

    Science.gov (United States)

    Dortch, Richard D; Bagnato, Francesca; Gochberg, Daniel F; Gore, John C; Smith, Seth A

    2018-03-24

    To optimize a selective inversion recovery (SIR) sequence for macromolecular content mapping in the human brain at 3.0T. SIR is a quantitative method for measuring magnetization transfer (qMT) that uses a low-power, on-resonance inversion pulse. This results in a biexponential recovery of free water signal that can be sampled at various inversion/predelay times (t I/ t D ) to estimate a subset of qMT parameters, including the macromolecular-to-free pool-size-ratio (PSR), the R 1 of free water (R 1f ), and the rate of MT exchange (k mf ). The adoption of SIR has been limited by long acquisition times (≈4 min/slice). Here, we use Cramér-Rao lower bound theory and data reduction strategies to select optimal t I /t D combinations to reduce imaging times. The schemes were experimentally validated in phantoms, and tested in healthy volunteers (N = 4) and a multiple sclerosis patient. Two optimal sampling schemes were determined: (i) a 5-point scheme (k mf estimated) and (ii) a 4-point scheme (k mf assumed). In phantoms, the 5/4-point schemes yielded parameter estimates with similar SNRs as our previous 16-point scheme, but with 4.1/6.1-fold shorter scan times. Pair-wise comparisons between schemes did not detect significant differences for any scheme/parameter. In humans, parameter values were consistent with published values, and similar levels of precision were obtained from all schemes. Furthermore, fixing k mf reduced the sensitivity of PSR to partial-volume averaging, yielding more consistent estimates throughout the brain. qMT parameters can be robustly estimated in ≤1 min/slice (without independent measures of ΔB 0 , B1+, and T 1 ) when optimized t I -t D combinations are selected. © 2018 International Society for Magnetic Resonance in Medicine.

  10. Stability maps, unstable periodic orbits and transfers in the Jovian system

    Science.gov (United States)

    Villac, Benjamin; Lara, Martin

    2005-01-01

    Low cost transfers of a spacecraft in a multi-gravitational orbital environment, which are based on connections between unstable periodic orbits, present several trade-offs, such time-of-flight v.s transfer fuel cost.

  11. ODIN: Observational Data Interactive Navigation, an interactive map of all CO-OPS active stations

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The CO-OPS Station Map has many features designed to provide a quick and easy way to find a CO-OPS station, and to view real-time observations as well as plot the...

  12. Global mapping of miRNA-target interactions in cattle (Bos taurus)

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Moore, Michael J; Luna, Joseph M

    2017-01-01

    With roles in development, cell proliferation and disease, micro-RNA (miRNA) biology is of great importance and a potential therapeutic target. Here we used cross-linking immunoprecipitation (CLIP) and ligation of miRNA-target chimeras on the Argonaute (AGO) protein to globally map miRNA interact...

  13. Interactive noise maps for action planning in the framework of the European Noise Directive

    NARCIS (Netherlands)

    Borst, H.C.; Miedema, H.M.E.; Lohman, W.J.A.

    2007-01-01

    The European Noise Directive (END) requires assessment of noise exposures as well as the formulation of Action Plans for the reduction of the number of people harmfully affected by environmental noise. Within the framework of the project ‘Urban Strategy’, TNO has developed an interactive noise map.

  14. Interactive overlays: a new method for generating global journal maps from Web-of-Science data

    NARCIS (Netherlands)

    Leydesdorff, L.; Rafols, I.

    2012-01-01

    Recent advances in methods and techniques enable us to develop interactive overlays to a global map of science based on aggregated citation relations among the 9162 journals contained in the Science Citation Index and Social Science Citation Index 2009. We first discuss the pros and cons of the

  15. Prototype of interactive Web Maps: an approach based on open sources

    Directory of Open Access Journals (Sweden)

    Jürgen Philips

    2004-07-01

    Full Text Available To explore the potentialities available in the World Wide Web (WWW, a prototype with interactive Web map was elaborated using standardized codes and open sources, such as eXtensible Markup Language (XML, Scalable Vector Graphics (SVG, Document Object Model (DOM , script languages ECMAScript/JavaScript and “PHP: Hypertext Preprocessor”, and PostgreSQL and its extension, the PostGIS, to disseminate information related to the urban real estate register. Data from the City Hall of São José - Santa Catarina, were used, referring to Campinas district. Using Client/Server model, a prototype of a Web map with standardized codes and open sources was implemented, allowing a user to visualize Web maps using only the Adobe’s plug-in Viewer 3.0 in his/her browser. Aiming a good cartographic project for the Web, it was obeyed rules of graphical translation and was implemented different functionalities of interaction, like interactive legends, symbolization and dynamic scale. From the results, it can be recommended the use of using standardized codes and open sources in interactive Web mapping projects. It is understood that, with the use of Open Source code, in the public and private administration, the possibility of technological development is amplified, and consequently, a reduction with expenses in the acquisition of computer’s program. Besides, it stimulates the development of computer applications targeting specific demands and requirements.

  16. Role of charge transfer interaction and the chemical physics behind effective fulleropyrrolidine/porphyrin non-covalent interaction in solution.

    Science.gov (United States)

    Mondal, Ashis; Santhosh, Kotni; Bauri, Ajoy; Bhattacharya, Sumanta

    2014-01-01

    The present paper reports the photophysical insights on supramolecular interaction of a monoporphyrin derivative, namely, 1, with C60 pyrrolidine tris-acid ethyl ester (PyC60) in toluene and benzonitrile. The ground state interaction between PyC60 and 1 is facilitated through charge transfer interaction. Both UV-Vis and steady state measurements elicit almost similar magnitude of binding constant for the PyC60/1 complex in toluene and benzonitrile, viz., 6825 and 6540 dm(3 )mol(-1), respectively. Life time measurement evokes that rate of charge separation is fast in benzonitrile. Both hybrid-DFT and DFT calculations provide very good support in favor of electronic charge-separation in PyC60/1 system in vacuo. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Generalized hidden-mapping ridge regression, knowledge-leveraged inductive transfer learning for neural networks, fuzzy systems and kernel methods.

    Science.gov (United States)

    Deng, Zhaohong; Choi, Kup-Sze; Jiang, Yizhang; Wang, Shitong

    2014-12-01

    Inductive transfer learning has attracted increasing attention for the training of effective model in the target domain by leveraging the information in the source domain. However, most transfer learning methods are developed for a specific model, such as the commonly used support vector machine, which makes the methods applicable only to the adopted models. In this regard, the generalized hidden-mapping ridge regression (GHRR) method is introduced in order to train various types of classical intelligence models, including neural networks, fuzzy logical systems and kernel methods. Furthermore, the knowledge-leverage based transfer learning mechanism is integrated with GHRR to realize the inductive transfer learning method called transfer GHRR (TGHRR). Since the information from the induced knowledge is much clearer and more concise than that from the data in the source domain, it is more convenient to control and balance the similarity and difference of data distributions between the source and target domains. The proposed GHRR and TGHRR algorithms have been evaluated experimentally by performing regression and classification on synthetic and real world datasets. The results demonstrate that the performance of TGHRR is competitive with or even superior to existing state-of-the-art inductive transfer learning algorithms.

  18. Journal maps, interactive overlays, and the measurement of interdisciplinarity on the basis of Scopus data (1996-2012)

    NARCIS (Netherlands)

    Leydesdorff, L.; de Moya-Anegón, F.; Guerrero-Bote, V.P.

    2015-01-01

    Using Scopus data, we construct a global map of science based on aggregated journal-journal citations from 1996-2012 (N of journals = 20,554). This base map enables users to overlay downloads from Scopus interactively. Using a single year (e.g., 2012), results can be compared with mappings based on

  19. Web Mapping for Promoting Interaction and Collaboration in Community Land Planning

    Science.gov (United States)

    Veenendaal, B.; Dhliwayo, M.

    2013-10-01

    There is an inherent advantage of geographic information Systems (GIS) and mapping in facilitating dialogue between experts and non-experts during land use plan development. Combining visual mapping information and effective user interaction can result in considerable benefits for developing countries like Botswana. Although the adoption of information and communication technologies has lagged behind that for developed countries, initiatives by the Botswana government in providing suitable information infrastructures, including internet and web based communications, are enabling multiple users to interact and collaborate in community land planning. A web mapping application was developed for the Maun Development Plan (MDP) in the Okavango Delta region in Botswana. It was designed according to requirements of land planners and managers and implemented using ArcGIS Viewer for Flex. Land planners and managers from two organisations in Maun involved in the development of the MDP were asked to evaluate the web mapping tools. This paper describes the results of implementation and some preliminary results of the web mapping evaluation.

  20. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

    Science.gov (United States)

    Newton, Yulia; Novak, Adam M; Swatloski, Teresa; McColl, Duncan C; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S; Baertsch, Robert; Salama, Sofie R; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C; Haussler, David; Morozova, Olena; Stuart, Joshua M

    2017-11-01

    Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111-4. ©2017 AACR . ©2017 American Association for Cancer Research.

  1. GIS-based interactive tool to map the advent of world conquerors

    Science.gov (United States)

    Lakkaraju, Mahesh

    The objective of this thesis is to show the scale and extent of some of the greatest empires the world has ever seen. This is a hybrid project between the GIS based interactive tool and the web-based JavaScript tool. This approach lets the students learn effectively about the emperors themselves while understanding how long and far their empires spread. In the GIS based tool, a map is displayed with various points on it, and when a user clicks on one point, the relevant information of what happened at that particular place is displayed. Apart from this information, users can also select the interactive animation button and can walk through a set of battles in chronological order. As mentioned, this uses Java as the main programming language, and MOJO (Map Objects Java Objects) provided by ESRI. MOJO is very effective as its GIS related features can be included in the application itself. This app. is a simple tool and has been developed for university or high school level students. D3.js is an interactive animation and visualization platform built on the Javascript framework. Though HTML5, CSS3, Javascript and SVG animations can be used to derive custom animations, this tool can help bring out results with less effort and more ease of use. Hence, it has become the most sought after visualization tool for multiple applications. D3.js has provided a map-based visualization feature so that we can easily display text-based data in a map-based interface. To draw the map and the points on it, D3.js uses data rendered in TOPO JSON format. The latitudes and longitudes can be provided, which are interpolated into the Map svg. One of the main advantages of doing it this way is that more information is retained when we use a visual medium.

  2. Ion-ion interaction and energy transfer of 4+ transuranium ions in cerium tetrafluoride

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.K.; Beitz, J.V.

    1990-01-01

    Dynamics of excited 5f electron states of the transuranium ions Cm{sup 4+} and Bk{sup 4+} in CeF{sub 4} are compared. Based on time- and wavelength-resolved laser-induced fluorescence, excitation energy transfer processes have been probed. Depending on concentration and electronic energy level structure of the studied 4+ transuranium ion, the dominant energy transfer mechanisms were identified as cross relaxation, exciton-exciton annihilation, and trapping. Energy transfer rates derived from the fitting of the observed fluorescence decays to theoretical models, based on electric multipolar ion-ion interactions, are contrasted with prior studies of 4f states of 3+ lanthanide and 3d states of transition metal ions. 16 refs., 1 tab.

  3. Determination of heat transfer coefficient for an interaction of sub-cooled gas and metal

    International Nuclear Information System (INIS)

    Sidek, Mohd Zaidi; Kamarudin, Muhammad Syahidan

    2016-01-01

    Heat transfer coefficient (HTC) for a hot metal surface and their surrounding is one of the need be defined parameter in hot forming process. This study has been conducted to determine the HTC for an interaction between sub-cooled gas sprayed on a hot metal surface. Both experiments and finite element have been adopted in this work. Initially, the designated experiment was conducted to obtain temperature history of spray cooling process. Then, an inverse method was adopted to calculate the HTC value before we validate in a finite element simulation model. The result shows that the heat transfer coefficient for interaction of subcooled gas and hot metal surface is 1000 W/m 2 K. (paper)

  4. Initial development of direct interaction for a transfer robotic Arm system for caregivers.

    Science.gov (United States)

    Jeannis, Hervens; Grindle, Garrett G; Kelleher, Annmarie; Wang, Hongwu; Brewer, Bambi; Cooper, Rory

    2013-06-01

    The most common injuries in healthcare are related to transfers. The Strong Arm system assists caregivers in providing fully dependent transfers from an electric power wheelchair to a bed, shower bench, toilet or other surface. However, this system currently controlled by buttons could be more successful with a more intuitive method during use. This paper presents the initial development of direct interaction for a robotic transfer system called Strong Arm. Direct interaction was used to make a transfer system more intuitive to operate using a three-axis load cell. To move Strong Arm, the user must apply intentional force on any of the given axes by surpassing the axis threshold. Unintentional movement could lead to injury. The results indicate that the thresholds for each axis were at least 3.5 N in X, 16.9 N in Y and 5.3N in Z in order to prevent unintentional forces from a human hand that would cause the robot to move.

  5. Trigger - and heat-transfer times measured during experimental molten-fuel-interactions

    OpenAIRE

    Spitznagel, N.; Durig, T.; Zimanowski, B.

    2016-01-01

    A modified setup featuring high speed high resolution data and video recording was developed to obtain detailed information on trigger and heat transfer times during explosive molten fuel-coolant-interaction (MFCI). MFCI occurs predominantly in configurations where water is entrapped by hot melt. The setup was modified to allow direct observation of the trigger and explosion onset. In addition the influences of experimental control and data acquisition can now be more clearly distinguished fr...

  6. The effect of turbulence-radiation interaction on radiative entropy generation and heat transfer

    International Nuclear Information System (INIS)

    Caldas, Miguel; Semiao, Viriato

    2007-01-01

    The analysis under the second law of thermodynamics is the gateway for optimisation in thermal equipments and systems. Through entropy minimisation techniques it is possible to increase the efficiency and overall performance of all kinds of thermal systems. Radiation, being the dominant mechanism of heat transfer in high-temperature systems, plays a determinant role in entropy generation within such equipments. Turbulence is also known to be a major player in the phenomenon of entropy generation. Therefore, turbulence-radiation interaction is expected to have a determinant effect on entropy generation. However, this is a subject that has not been dealt with so far, at least to the extent of the authors' knowledge. The present work attempts to fill that void, by studying the effect of turbulence-radiation interaction on entropy generation. All calculations are approached in such a way as to make them totally compatible with standard engineering methods for radiative heat transfer, namely the discrete ordinates method. It was found that turbulence-radiation interaction does not significantly change the spatial pattern of entropy generation, or heat transfer, but does change significantly their magnitude, in a way approximately proportional to the square of the intensity of turbulence

  7. Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping

    Directory of Open Access Journals (Sweden)

    Yue Peng

    2010-03-01

    Full Text Available Abstract HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language, the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript. This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities.

  8. Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.

    Science.gov (United States)

    Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng

    2010-03-03

    HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities.

  9. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

    Science.gov (United States)

    Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

    2017-07-03

    Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

  10. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

    Directory of Open Access Journals (Sweden)

    Andrews Brenda

    2005-06-01

    Full Text Available Abstract Background Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology, and expression correlation. Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction. Results To study more complex relationships involving multiple biological interaction types, we assembled an integrated Saccharomyces cerevisiae network in which nodes represent genes (or their protein products and differently colored links represent the aforementioned five biological interaction types. We examined three- and four-node interconnection patterns containing multiple interaction types and found many enriched multi-color network motifs. Furthermore, we showed that most of the motifs form 'network themes' – classes of higher-order recurring interconnection patterns that encompass multiple occurrences of network motifs. Network themes can be tied to specific biological phenomena and may represent more fundamental network design principles. Examples of network themes include a pair of protein complexes with many inter-complex genetic interactions – the 'compensatory complexes' theme. Thematic maps – networks rendered in terms of such themes – can simplify an otherwise confusing tangle of biological relationships. We show this by mapping the S. cerevisiae network in terms of two specific network themes. Conclusion Significantly enriched motifs in an integrated S. cerevisiae interaction network are often signatures of network themes, higher-order network structures that correspond to biological phenomena. Representing networks in terms of network themes provides a useful simplification of complex biological relationships.

  11. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

    Science.gov (United States)

    Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

    2016-11-01

    Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

  12. BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy

    OpenAIRE

    Mikula, Shawn; Stone, James M.; Jones, Edward G.

    2008-01-01

    BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegic...

  13. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Science.gov (United States)

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  14. Multiple-embryo transfer for studying very early maternal-embryo interactions in cattle.

    Science.gov (United States)

    Gómez, E; Muñoz, M

    2015-08-01

    In the present paper, we highlight the need to study very early maternal-embryo interactions and discuss how these interactions can be addressed. Bovine species normally carry one or, less frequently, two embryos to term; there are very rare cases of triplets or higher-order multiple pregnancies in which all the offspring are born alive. Multiple-embryo transfer (MET) in cattle allows for the detection of endometrial responses in scenarios where single-embryo transfer would not. Although MET is non-physiological, the present study shows that at the very early embryonic stages, a uterus carrying zona-enclosed embryos does not exhibit non-physiological reactions. On the contrary, MET should be considered the sum of multiple individual effects triggered by developing embryos. We provide arguments to support our hypothesis that describe a rationale for current work with MET, and we discuss alternative hypotheses. Using cattle as a model, we describe how technical approaches to analyzing zona-enclosed early embryo-maternal interactions (i.e., transcriptomics, proteomics, and endometrial cell culture) can help identify molecular changes that may be difficult to observe when only a single embryo is present. We conclude that MET can be used for studying very early maternal-embryo interactions in vivo in monotocous species. Free Spanish abstract: A Spanish translation of this abstract is freely available at http://www.reproduction-online.org/content/150/2/R35/suppl/DC1. © 2015 Society for Reproduction and Fertility.

  15. Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins.

    Directory of Open Access Journals (Sweden)

    Suyu Mei

    Full Text Available Reconstruction of host-pathogen protein interaction networks is of great significance to reveal the underlying microbic pathogenesis. However, the current experimentally-derived networks are generally small and should be augmented by computational methods for less-biased biological inference. From the point of view of computational modelling, data scarcity, data unavailability and negative data sampling are the three major problems for host-pathogen protein interaction networks reconstruction. In this work, we are motivated to address the three concerns and propose a probability weighted ensemble transfer learning model for HIV-human protein interaction prediction (PWEN-TLM, where support vector machine (SVM is adopted as the individual classifier of the ensemble model. In the model, data scarcity and data unavailability are tackled by homolog knowledge transfer. The importance of homolog knowledge is measured by the ROC-AUC metric of the individual classifiers, whose outputs are probability weighted to yield the final decision. In addition, we further validate the assumption that only the homolog knowledge is sufficient to train a satisfactory model for host-pathogen protein interaction prediction. Thus the model is more robust against data unavailability with less demanding data constraint. As regards with negative data construction, experiments show that exclusiveness of subcellular co-localized proteins is unbiased and more reliable than random sampling. Last, we conduct analysis of overlapped predictions between our model and the existing models, and apply the model to novel host-pathogen PPIs recognition for further biological research.

  16. On the interaction of a fan stator and acoustic treatments using the transfer element method

    International Nuclear Information System (INIS)

    Wang Xiaoyu; Sun Xiaofeng

    2010-01-01

    In the present investigation, a theoretical model is suggested to study the interaction of a fan stator and acoustic treatments using the transfer element method. Firstly, the solution of an acoustic field caused by a fan stator in an infinite duct is extended to that in a finite domain with all knowns and unknowns on the interface plane. Secondly, the related numerical results for an annular cascade are compared with the data obtained by directly solving an integral equation based on the blade boundary condition, which have good agreement with each other. Finally, more emphasis is placed on studying how a fan stator interacts with both upstream and downstream acoustic treatments. It is found that the interaction has an important influence on sound attenuation. In addition, optimal sound attenuation will depend on the combined design of both acoustic treatment and the fan stator. (invited paper)

  17. Mapping sensory circuits by anterograde trans-synaptic transfer of recombinant rabies virus

    Science.gov (United States)

    Zampieri, Niccolò; Jessell, Thomas M.; Murray, Andrew J.

    2014-01-01

    Summary Primary sensory neurons convey information from the external world to relay circuits within the central nervous system (CNS), but the identity and organization of the neurons that process incoming sensory information remains sketchy. Within the CNS viral tracing techniques that rely on retrograde trans-synaptic transfer provide a powerful tool for delineating circuit organization. Viral tracing of the circuits engaged by primary sensory neurons has, however, been hampered by the absence of a genetically tractable anterograde transfer system. In this study we demonstrate that rabies virus can infect sensory neurons in the somatosensory system, is subject to anterograde trans-synaptic transfer from primary sensory to spinal target neurons, and can delineate output connectivity with third-order neurons. Anterograde trans-synaptic transfer is a feature shared by other classes of primary sensory neurons, permitting the identification and potentially the manipulation of neural circuits processing sensory feedback within the mammalian CNS. PMID:24486087

  18. Empirical mapping of the convective heat transfer coefficients with local hot spots on highly conductive surfaces

    Directory of Open Access Journals (Sweden)

    Tekelioğlu Murat

    2017-01-01

    Full Text Available An experimental method was proposed to assess the natural and forced convective heat transfer coefficients on highly conductive bodies. Experiments were performed at air velocities of 0m/s, 4.0m/s, and 5.4m/s, and comparisons were made between the current results and available literature. These experiments were extended to arbitrary-shape bodies. External flow conditions were maintained throughout. In the proposed method, in determination of the surface convective heat transfer coefficients, flow condition is immaterial, i.e., either laminar or turbulent. With the present method, it was aimed to acquire the local heat transfer coefficients on any arbitrary conductive shape. This method was intended to be implemented by the heat transfer engineer to identify the local heat transfer rates with local hot spots. Finally, after analyzing the proposed experimental results, appropriate decisions can be made to control the amount of the convective heat transfer off the surface. Limited mass transport was quantified on the cooled plate.

  19. Quantum state transfer in spin chains with q-deformed interaction terms

    International Nuclear Information System (INIS)

    Jafarov, E I; Van der Jeugt, J

    2010-01-01

    We study the time evolution of a single spin excitation state in certain linear spin chains, as a model for quantum communication. Some years ago it was discovered that when the spin chain data (the nearest-neighbour interaction strengths and the magnetic field strengths) are related to the Jacobi matrix entries of Krawtchouk polynomials or dual Hahn polynomials the so-called perfect state transfer takes place. The extension of these ideas to other types of discrete orthogonal polynomials did not lead to new models with perfect state transfer, but did allow more insight in the general computation of the correlation function. In this paper, we extend the study to discrete orthogonal polynomials of q-hypergeometric type. A remarkable result is a new analytic model where perfect state transfer is achieved: this is when the spin chain data are related to the Jacobi matrix of q-Krawtchouk polynomials. The other cases studied here (affine q-Krawtchouk polynomials, quantum q-Krawtchouk polynomials, dual q-Krawtchouk polynomials, q-Hahn polynomials, dual q-Hahn polynomials and q-Racah polynomials) do not give rise to models with perfect state transfer. However, the computation of the correlation function itself is quite interesting, leading to advanced q-series manipulations.

  20. A heat transfer correlation based on a surface renewal model for molten core concrete interaction study

    International Nuclear Information System (INIS)

    Tourniaire, B. . E-mail bruno.tourniaire@cea.fr

    2006-01-01

    The prediction of heat transfer between corium pool and concrete basemat is of particular significance in the framework of the study of PWR's severe accident. Heat transfer directly governs the ablation velocity of concrete in case of molten core concrete interaction (MCCI) and, consequently, the time delay when the reactor cavity may fail. From a restricted hydrodynamic point of view, this issue is related to heat transfer between a heated bubbling pool and a porous wall with gas injection. Several experimental studies have been performed with simulant materials and many correlations have been provided to address this issue. The comparisons of the results of these correlations with the measurements and their extrapolation to reactor materials show that strong discrepancies between the results of these models are obtained which probably means that some phenomena are not well taken into account. The main purpose of this paper is to present an alternative heat transfer model which was originally developed for chemical engineering applications (bubble columns) by Deckwer. A part of this work is devoted to the presentation of this model, which is based on a surface renewal assumption. Comparison of the results of this model with available experimental data in different systems are presented and discussed. These comparisons clearly show that this model can be used to deal with the particular problem of MCCI. The analyses also lead to enrich the original model by taking into account the thermal resistance of the wall: a new formulation of the Deckwer's correlation is finally proposed

  1. Charge transfer dynamics from adsorbates to surfaces with single active electron and configuration interaction based approaches

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Raghunathan, E-mail: r.ramakrishnan@unibas.ch [Institute of Physical Chemistry, National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel (Switzerland); Nest, Mathias [Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching (Germany)

    2015-01-13

    Highlights: • We model electron dynamics across cyano alkanethiolates attached to gold cluster. • We present electron transfer time scales from TD-DFT and TD-CI based simulations. • Both DFT and CI methods qualitatively predict the trend in time scales. • TD-CI predicts the experimental relative time scale very accurately. - Abstract: We employ wavepacket simulations based on many-body time-dependent configuration interaction (TD-CI), and single active electron theories, to predict the ultrafast molecule/metal electron transfer time scales, in cyano alkanethiolates bonded to model gold clusters. The initial states represent two excited states where a valence electron is promoted to one of the two virtual π{sup ∗} molecular orbitals localized on the cyanide fragment. The ratio of the two time scales indicate the efficiency of one charge transfer channel over the other. In both our one-and many-electron simulations, this ratio agree qualitatively with each other as well as with the previously reported experimental time scales (Blobner et al., 2012), measured for a macroscopic metal surface. We study the effect of cluster size and the description of electron correlation on the charge transfer process.

  2. Intramolecular energy transfer at donor-acceptor interactions in model and biological membranes

    International Nuclear Information System (INIS)

    Umarova, Fatima T.

    2011-01-01

    Intramolecular triplet-triplet energy transfer between molecules of sensibilisator and photochrome for registration of protein interactions in the membrane preparation of Na,K-ATPase was investigated. Erythrosinithiocyanate (ERITC) was used as the triplet label of sensibilisator, and 4-acetoamido-4 -isothiocyanatostilbene-2,2 disullfonic acid (SITS) was used as the photochrome label. Na,K-ATPase preparations were covalently bound with ERITC in active centre of enzyme, and SITS molecules were covalently bound by NH2-groups. In model system, in chymotrypsinogene molecule, SITS and ERITC labels were used also. The cis-trans-isomerization of SITS was initiated by triplet-triplet energy transfer from light excited ERITC molecule to photochrome. The kinetics of isomerization was recorded by the SITS fluorescence measurements. The constant of rate of triplet-triplet energy transfer from ERITC to cis-isomers of SITS in Na,K-ATPase was determined as (3-7)x10 3 M -1 s -1 , and in model system it equals 1x 10 7 M 1 s -1 . The value of energy transfer between loos molecules of erythrosine and SITS in buffer solution equaled to 7x10 7 M -1 s -1 . This drop of R m y in the membrane preparation of Na,K-ATPase at 10 4 reflected the decrease in the frequency of label collisions caused by the increase in the media viscosity and steric hindrances. (author)

  3. Mapping receptor-ligand interactions with synthetic peptide arrays: exploring the structure and function of membrane receptors.

    Science.gov (United States)

    Volkmer, Rudolf; Kretzschmar, Ines; Tapia, Victor

    2012-04-01

    Development of synthetic peptide array technology started in the early 1990s. The technique originally developed by Ronald Frank has become a powerful tool for high throughput approaches in biology and chemistry mapping protein interaction sites. In this review we focus on peptide arrays applied to investigate receptor-ligand interactions, such as peroxisomal membrane receptor proteins, the maltose importer machinery and receptor proteins recognizing short linear motifs of their partners. We present several systematic sets of peptide arrays useful for mapping protein-protein- or receptor-ligand binding sites. Besides a more technical description of the peptide array preparation we discuss in detail the reliability and improvement of mapping protein-protein interactions by synthetic peptide arrays. At least proteomic approaches for mapping protein-protein interactions by peptide arrays are shown especially for the case of protein interaction domains. Copyright © 2011 Elsevier GmbH. All rights reserved.

  4. TRANSFER OF TECHNOLOGY FOR CADASTRAL MAPPING IN TAJIKISTAN USING HIGH RESOLUTION SATELLITE DATA

    Directory of Open Access Journals (Sweden)

    R. Kaczynski

    2012-07-01

    Full Text Available European Commission funded project entitled: "Support to the mapping and certification capacity of the Agency of Land Management, Geodesy and Cartography" in Tajikistan was run by FINNMAP FM-International and Human Dynamics from Nov. 2006 to June 2011. The Agency of Land Management, Geodesy and Cartography is the state agency responsible for development, implementation, monitoring and evaluation of state policies on land tenure and land management, including the on-going land reform and registration of land use rights. The specific objective was to support and strengthen the professional capacity of the "Fazo" Institute in the field of satellite geodesy, digital photogrammetry, advanced digital satellite image processing of high resolution satellite data and digital cartography. Lectures and on-the-job trainings for the personnel of "Fazo" and Agency in satellite geodesy, digital photogrammetry, cartography and the use of high resolution satellite data for cadastral mapping have been organized. Standards and Quality control system for all data and products have been elaborated and implemented in the production line. Technical expertise and trainings in geodesy, photogrammetry and satellite image processing to the World Bank project "Land Registration and Cadastre System for Sustainable Agriculture" has also been completed in Tajikistan. The new map projection was chosen and the new unclassified geodetic network has been established for all of the country in which all agricultural parcel boundaries are being mapped. IKONOS, QuickBird and WorldView1 panchromatic data have been used for orthophoto generation. Average accuracy of space triangulation of non-standard (long up to 90km satellite images of QuickBird Pan and IKONOS Pan on ICPs: RMSEx = 0.5m and RMSEy = 0.5m have been achieved. Accuracy of digital orthophoto map is RMSExy = 1.0m. More then two and half thousands of digital orthophoto map sheets in the scale of 1:5000 with pixel size 0.5m

  5. Network structure beyond food webs: mapping non-trophic and trophic interactions on Chilean rocky shores.

    Science.gov (United States)

    Sonia Kéfi; Berlow, Eric L; Wieters, Evie A; Joppa, Lucas N; Wood, Spencer A; Brose, Ulrich; Navarrete, Sergio A

    2015-01-01

    How multiple types of non-trophic interactions map onto trophic networks in real communities remains largely unknown. We present the first effort, to our knowledge, describing a comprehensive ecological network that includes all known trophic and diverse non-trophic links among >100 coexisting species for the marine rocky intertidal community of the central Chilean coast. Our results suggest that non-trophic interactions exhibit highly nonrandom structures both alone and with respect to food web structure. The occurrence of different types of interactions, relative to all possible links, was well predicted by trophic structure and simple traits of the source and target species. In this community, competition for space and positive interactions related to habitat/refuge provisioning by sessile and/or basal species were by far the most abundant non-trophic interactions. If these patterns are orroborated in other ecosystems, they may suggest potentially important dynamic constraints on the combined architecture of trophic and non-trophic interactions. The nonrandom patterning of non-trophic interactions suggests a path forward for developing a more comprehensive ecological network theory to predict the functioning and resilience of ecological communities.

  6. Concept mapping One-Carbon Metabolism to model future ontologies for nutrient-gene-phenotype interactions.

    Science.gov (United States)

    Joslin, A C; Green, R; German, J B; Lange, M C

    2014-09-01

    Advances in the development of bioinformatic tools continue to improve investigators' ability to interrogate, organize, and derive knowledge from large amounts of heterogeneous information. These tools often require advanced technical skills not possessed by life scientists. User-friendly, low-barrier-to-entry methods of visualizing nutrigenomics information are yet to be developed. We utilized concept mapping software from the Institute for Human and Machine Cognition to create a conceptual model of diet and health-related data that provides a foundation for future nutrigenomics ontologies describing published nutrient-gene/polymorphism-phenotype data. In this model, maps containing phenotype, nutrient, gene product, and genetic polymorphism interactions are visualized as triples of two concepts linked together by a linking phrase. These triples, or "knowledge propositions," contextualize aggregated data and information into easy-to-read knowledge maps. Maps of these triples enable visualization of genes spanning the One-Carbon Metabolism (OCM) pathway, their sequence variants, and multiple literature-mined associations including concepts relevant to nutrition, phenotypes, and health. The concept map development process documents the incongruity of information derived from pathway databases versus literature resources. This conceptual model highlights the importance of incorporating information about genes in upstream pathways that provide substrates, as well as downstream pathways that utilize products of the pathway under investigation, in this case OCM. Other genes and their polymorphisms, such as TCN2 and FUT2, although not directly involved in OCM, potentially alter OCM pathway functionality. These upstream gene products regulate substrates such as B12. Constellations of polymorphisms affecting the functionality of genes along OCM, together with substrate and cofactor availability, may impact resultant phenotypes. These conceptual maps provide a foundational

  7. iMAR: An Interactive Web-Based Application for Mapping Herbicide Resistant Weeds.

    Directory of Open Access Journals (Sweden)

    Silvia Panozzo

    Full Text Available Herbicides are the major weed control tool in most cropping systems worldwide. However, the high reliance on herbicides has led to environmental issues as well as to the evolution of herbicide-resistant biotypes. Resistance is a major concern in modern agriculture and early detection of resistant biotypes is therefore crucial for its management and prevention. In this context, a timely update of resistance biotypes distribution is fundamental to devise and implement efficient resistance management strategies. Here we present an innovative web-based application called iMAR (interactive MApping of Resistance for the mapping of herbicide resistant biotypes. It is based on open source software tools and translates into maps the data reported in the GIRE (Italian herbicide resistance working group database of herbicide resistance at national level. iMAR allows an automatic, easy and cost-effective updating of the maps a nd provides two different systems, "static" and "dynamic". In the first one, the user choices are guided by a hierarchical tree menu, whereas the latter is more flexible and includes a multiple choice criteria (type of resistance, weed species, region, cropping systems that permits customized maps to be created. The generated information can be useful to various stakeholders who are involved in weed resistance management: farmers, advisors, national and local decision makers as well as the agrochemical industry. iMAR is freely available, and the system has the potential to handle large datasets and to be used for other purposes with geographical implications, such as the mapping of invasive plants or pests.

  8. iMAR: An Interactive Web-Based Application for Mapping Herbicide Resistant Weeds.

    Science.gov (United States)

    Panozzo, Silvia; Colauzzi, Michele; Scarabel, Laura; Collavo, Alberto; Rosan, Valentina; Sattin, Maurizio

    2015-01-01

    Herbicides are the major weed control tool in most cropping systems worldwide. However, the high reliance on herbicides has led to environmental issues as well as to the evolution of herbicide-resistant biotypes. Resistance is a major concern in modern agriculture and early detection of resistant biotypes is therefore crucial for its management and prevention. In this context, a timely update of resistance biotypes distribution is fundamental to devise and implement efficient resistance management strategies. Here we present an innovative web-based application called iMAR (interactive MApping of Resistance) for the mapping of herbicide resistant biotypes. It is based on open source software tools and translates into maps the data reported in the GIRE (Italian herbicide resistance working group) database of herbicide resistance at national level. iMAR allows an automatic, easy and cost-effective updating of the maps a nd provides two different systems, "static" and "dynamic". In the first one, the user choices are guided by a hierarchical tree menu, whereas the latter is more flexible and includes a multiple choice criteria (type of resistance, weed species, region, cropping systems) that permits customized maps to be created. The generated information can be useful to various stakeholders who are involved in weed resistance management: farmers, advisors, national and local decision makers as well as the agrochemical industry. iMAR is freely available, and the system has the potential to handle large datasets and to be used for other purposes with geographical implications, such as the mapping of invasive plants or pests.

  9. Mapping the Genetic Basis of Symbiotic Variation in Legume-Rhizobium Interactions in Medicago truncatula

    Science.gov (United States)

    Gorton, Amanda J.; Heath, Katy D.; Pilet-Nayel, Marie-Laure; Baranger, Alain

    2012-01-01

    Mutualisms are known to be genetically variable, where the genotypes differ in the fitness benefits they gain from the interaction. To date, little is known about the loci that underlie such genetic variation in fitness or whether the loci influencing fitness are partner specific, and depend on the genotype of the interaction partner. In the legume-rhizobium mutualism, one set of potential candidate genes that may influence the fitness benefits of the symbiosis are the plant genes involved in the initiation of the signaling pathway between the two partners. Here we performed quantitative trait loci (QTL) mapping in Medicago truncatula in two different rhizobium strain treatments to locate regions of the genome influencing plant traits, assess whether such regions are dependent on the genotype of the rhizobial mutualist (QTL × rhizobium strain), and evaluate the contribution of sequence variation at known symbiosis signaling genes. Two of the symbiotic signaling genes, NFP and DMI3, colocalized with two QTL affecting average fruit weight and leaf number, suggesting that natural variation in nodulation genes may potentially influence plant fitness. In both rhizobium strain treatments, there were QTL that influenced multiple traits, indicative of either tight linkage between loci or pleiotropy, including one QTL with opposing effects on growth and reproduction. There was no evidence for QTL × rhizobium strain or genotype × genotype interactions, suggesting either that such interactions are due to small-effect loci or that more genotype-genotype combinations need to be tested in future mapping studies. PMID:23173081

  10. Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions

    Energy Technology Data Exchange (ETDEWEB)

    Schumann, Frank H.; Riepl, Hubert [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany); Maurer, Till [Boehringer Ingelheim Pharma GmbH and Co. KG, Analytical Sciences Department (Germany); Gronwald, Wolfram [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany); Neidig, Klaus-Peter [Bruker BioSpin GmbH, Software Department (Germany); Kalbitzer, Hans Robert [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany)], E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de

    2007-12-15

    Protein-protein interactions are often studied by chemical shift mapping using solution NMR spectroscopy. When heteronuclear data are available the interaction interface is usually predicted by combining the chemical shift changes of different nuclei to a single quantity, the combined chemical shift perturbation {delta}{delta}{sub comb}. In this paper different procedures (published and non-published) to calculate {delta}{delta}{sub comb} are examined that include a variety of different functional forms and weighting factors for each nucleus. The predictive power of all shift mapping methods depends on the magnitude of the overlap of the chemical shift distributions of interacting and non-interacting residues and the cut-off criterion used. In general, the quality of the prediction on the basis of chemical shift changes alone is rather unsatisfactory but the combination of chemical shift changes on the basis of the Hamming or the Euclidian distance can improve the result. The corrected standard deviation to zero of the combined chemical shift changes can provide a reasonable cut-off criterion. As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data.

  11. Adige river in Trento flooding map, 1892: private or public risk transfer?

    Science.gov (United States)

    Ranzi, Roberto

    2016-04-01

    For the determination of the flood risk hydrologist and hydraulic engineers focuse their attention mainly to the estimation of physical factors determining the flood hazard, while economists and experts of social sciences deal mainly with the estimation of vulnerability and exposure. The fact that flood zoning involves both hydrological and socio-economic aspects, however, was clear already in the XIX century when the impact of floods on inundated areas started to appear in flood maps, for instance in the UK and in Italy. A pioneering 'flood risk' map for the Adige river in Trento, Italy, was already published in 1892, taking into account in detail both hazard intensity in terms of velocity and depth, frequency of occurrence, vulnerability and economic costs for flood protection with river embankments. This map is likely to be the reinterpreted certainly as a pioneering, and possibly as the first flood risk map for an Italian river and worldwide. Risk levels were divided in three categories and seven sub-categories, depending on flood water depth, velocity, frequency and damage costs. It is interesting to notice the fact that at that time the map was used to share the cost of levees' reparation and enhancement after the severe September 1882 flood as a function of the estimated level of protection of the respective areas against the flood risk. The sharing of costs between public bodies, the railway company and private owners was debated for about 20 years and at the end the public sustained the major costs. This shows how already at that time the economic assessment of structural flood protections was based on objective and rational cost-benefit criteria, that hydraulic risk mapping was perceived by the society as fundamental for the design of flood protection systems and that a balanced cost sharing between public and private was an accepted approach although some protests arose at that time.

  12. Interactive Maps on War and Peace: A WebGIS Application for Civic Education

    Science.gov (United States)

    Wirkus, Lars; Strunck, Alexander

    2013-04-01

    War and violent conflict are omnipresent-be it war in the Middle East, violent conflicts in failed states or increasing military expenditures and exports/ imports of military goods. To understand certain conflicts or peace processes and their possible interrelation, to conduct a well-founded political discussion and to support or influence decision-making, one matter is of special importance: easily accessible and, in particular, reliable data and information. Against this background, the Bonn International Center for Conversion (BICC) in close cooperation with the German Federal Agency for Civic Education (bpb) has been developing a map-based information portal on war and peace with various thematic modules for the latter's online service (http://sicherheitspolitik.bpb.de). The portal will eventually offer nine of such modules that are intended to give various target groups, such as interested members of the public, teachers and learners, policymakers and representatives of the media access to the required information in form of an interactive and country-based global overview or a comparison of different issues. Five thematic modules have been completed so far: War and conflict, peace and demobilization, military capacities, resources and conflict, conventional weapons. The portal offers a broad spectrum of different data processing and visualization tools. Its central feature is an interactive mapping component based on WebGIS and a relational database. Content and data provided through thematic maps in the form of WebGIS layers are generally supplemented by info graphics, data tables and short articles providing deeper knowledge on the respective issue. All modules and their sub-chapters are introduced by background texts. They put all interactive maps of a module into an appropriate context and help the users to also understand the interrelation between various layers. If a layer is selected, all corresponding texts and graphics are shown automatically below

  13. Interactive web-based mapping: bridging technology and data for health

    Directory of Open Access Journals (Sweden)

    Highfield Linda

    2011-12-01

    Full Text Available Abstract Background The Community Health Information System (CHIS online mapping system was first launched in 1998. Its overarching goal was to provide researchers, residents and organizations access to health related data reflecting the overall health and well-being of their communities within the Greater Houston area. In September 2009, initial planning and development began for the next generation of CHIS. The overarching goal for the new version remained to make health data easily accessible for a wide variety of research audiences. However, in the new version we specifically sought to make the CHIS truly interactive and give the user more control over data selection and reporting. Results In July 2011, a beta version of the next-generation of the application was launched. This next-generation is also a web based interactive mapping tool comprised of two distinct portals: the Breast Health Portal and Project Safety Net. Both are accessed via a Google mapping interface. Geographic coverage for the portals is currently an 8 county region centered on Harris County, Texas. Data accessed by the application include Census 2000, Census 2010 (underway, cancer incidence from the Texas Cancer Registry (TX Dept. of State Health Services, death data from Texas Vital Statistics, clinic locations for free and low-cost health services, along with service lists, hours of operation, payment options and languages spoken, uninsured and poverty data. Conclusions The system features query on the fly technology, which means the data is not generated until the query is provided to the system. This allows users to interact in real-time with the databases and generate customized reports and maps. To the author's knowledge, the Breast Health Portal and Project Safety Net are the first local-scale interactive online mapping interfaces for public health data which allow users to control the data generated. For example, users may generate breast cancer incidence rates

  14. Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

    Science.gov (United States)

    Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Minor, Wladek

    2018-01-01

    Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼90% are an interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric. The possible consequences of basing research on suboptimal models make it imperative to inspect the agreement of a model with its experimental evidence. Molstack, a web-based interactive publishing platform for structural data, allows users to present density maps and structural models by displaying a collection of maps and models, including different interpretation of one's own data, re-refinements, and corrections of existing structures. Molstack organizes the sharing and dissemination of these structural models along with their experimental evidence as an interactive session. Molstack was designed with three groups of users in mind; researchers can present the evidence of their interpretation, reviewers and readers can independently judge the experimental evidence of the authors' conclusions, and other researchers can present or even publish their new hypotheses in the context of prior results. The server is available at http://molstack.bioreproducibility.org. © 2017 The Protein Society.

  15. Mapping texts through dimensionality reduction and visualization techniques for interactive exploration of document collections

    Science.gov (United States)

    de Andrade Lopes, Alneu; Minghim, Rosane; Melo, Vinícius; Paulovich, Fernando V.

    2006-01-01

    The current availability of information many times impair the tasks of searching, browsing and analyzing information pertinent to a topic of interest. This paper presents a methodology to create a meaningful graphical representation of documents corpora targeted at supporting exploration of correlated documents. The purpose of such an approach is to produce a map from a document body on a research topic or field based on the analysis of their contents, and similarities amongst articles. The document map is generated, after text pre-processing, by projecting the data in two dimensions using Latent Semantic Indexing. The projection is followed by hierarchical clustering to support sub-area identification. The map can be interactively explored, helping to narrow down the search for relevant articles. Tests were performed using a collection of documents pre-classified into three research subject classes: Case-Based Reasoning, Information Retrieval, and Inductive Logic Programming. The map produced was capable of separating the main areas and approaching documents by their similarity, revealing possible topics, and identifying boundaries between them. The tool can deal with the exploration of inter-topics and intra-topic relationship and is useful in many contexts that need deciding on relevant articles to read, such as scientific research, education, and training.

  16. Mapping tropical biodiversity using spectroscopic imagery : characterization of structural and chemical diversity with 3-D radiative transfer modeling

    Science.gov (United States)

    Feret, J. B.; Gastellu-Etchegorry, J. P.; Lefèvre-Fonollosa, M. J.; Proisy, C.; Asner, G. P.

    2014-12-01

    The accelerating loss of biodiversity is a major environmental trend. Tropical ecosystems are particularly threatened due to climate change, invasive species, farming and natural resources exploitation. Recent advances in remote sensing of biodiversity confirmed the potential of high spatial resolution spectroscopic imagery for species identification and biodiversity mapping. Such information bridges the scale-gap between small-scale, highly detailed field studies and large-scale, low-resolution satellite observations. In order to produce fine-scale resolution maps of canopy alpha-diversity and beta-diversity of the Peruvian Amazonian forest, we designed, applied and validated a method based on spectral variation hypothesis to CAO AToMS (Carnegie Airborne Observatory Airborne Taxonomic Mapping System) images, acquired from 2011 to 2013. There is a need to understand on a quantitative basis the physical processes leading to this spectral variability. This spectral variability mainly depends on canopy chemistry, structure, and sensor's characteristics. 3D radiative transfer modeling provides a powerful framework for the study of the relative influence of each of these factors in dense and complex canopies. We simulated series of spectroscopic images with the 3D radiative model DART, with variability gradients in terms of leaf chemistry, individual tree structure, spatial and spectral resolution, and applied methods for biodiversity mapping. This sensitivity study allowed us to determine the relative influence of these factors on the radiometric signal acquired by different types of sensors. Such study is particularly important to define the domain of validity of our approach, to refine requirements for the instrumental specifications, and to help preparing hyperspectral spatial missions to be launched at the horizon 2015-2025 (EnMAP, PRISMA, HISUI, SHALOM, HYSPIRI, HYPXIM). Simulations in preparation include topographic variations in order to estimate the robustness

  17. Trigger - and heat-transfer times measured during experimental molten-fuel-interactions

    Directory of Open Access Journals (Sweden)

    N. Spitznagel

    2013-10-01

    Full Text Available A modified setup featuring high speed high resolution data and video recording was developed to obtain detailed information on trigger and heat transfer times during explosive molten fuel-coolant-interaction (MFCI. MFCI occurs predominantly in configurations where water is entrapped by hot melt. The setup was modified to allow direct observation of the trigger and explosion onset. In addition the influences of experimental control and data acquisition can now be more clearly distinguished from the pure phenomena. More precise experimental studies will facilitate the description of MFCI thermodynamics.

  18. Reducing Communication Overhead by Scheduling TCP Transfers on Mobile Devices using Wireless Network Performance Maps

    DEFF Research Database (Denmark)

    Højgaard-Hansen, Kim; Madsen, Tatiana Kozlova; Schwefel, Hans-Peter

    2012-01-01

    The performance of wireless communication networks has been shown to have a strong location dependence. Measuring the performance while having accurate location information available makes it possible to generate performance maps. In this paper we propose a framework for the generation and use of...

  19. Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-06-01

    A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. Rule Set Transferability for Object-Based Feature Extraction: An Example for Cirque Mapping

    NARCIS (Netherlands)

    Anders, N.S.; Seijmonsbergen, A.C.; Bouten, W.

    2015-01-01

    Cirques are complex landforms resulting from glacial erosion and can be used to estimate Equilibrium Line Altitudes and infer climate history. Automated extraction of cirques may help research on glacial geomorphology and climate change. Our objective was to test the transferability of an

  1. Protein-protein interaction map is a key gateway into liver regeneration

    Science.gov (United States)

    Xie, Chao; Gao, Jin; Zhu, Run-Zhi; Yuan, Yun-Sheng; He, Hong-Lin; Huang, Qiu-Shi; Han, Wei; Yu, Yan

    2010-01-01

    Recent studies indicate that the process of liver regeneration involves multiple signaling pathways and a variety of genes, cytokines and growth factors. Protein-protein interactions (PPIs) play a role in nearly all events that take place within the cell and PPI maps should be helpful in further understanding the process of liver regeneration. In this review, we discuss recent progress in understanding the PPIs that occur during liver regeneration especially those in the transforming growth factor β signaling pathways. We believe the use of large-scale PPI maps for integrating the information already known about the liver regeneration is a useful approach in understanding liver regeneration from the standpoint of systems biology. PMID:20653057

  2. CellMap visualizes protein-protein interactions and subcellular localization

    Science.gov (United States)

    Dallago, Christian; Goldberg, Tatyana; Andrade-Navarro, Miguel Angel; Alanis-Lobato, Gregorio; Rost, Burkhard

    2018-01-01

    Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers. PMID:29497493

  3. Charge-transfer interaction mediated organogels from 18β-glycyrrhetinic acid appended pyrene

    Directory of Open Access Journals (Sweden)

    Jun Hu

    2013-12-01

    Full Text Available We describe herein the two-component charge-transfer (CT interaction induced organogel formation with 18β-glycyrrhetinic acid appended pyrene (GA-pyrene, 3 as the donor, and 2,4,7-trinitrofluorenone (TNF, 4 as the acceptor. The use of TNF (4 as a versatile electron acceptor in the formation of CT gels is demonstrated through the formation of gels in a variety of solvents. Thermal stability, stoichiometry, scanning electron microscopy (SEM, optical micrographs, and circular dichroism (CD are performed on these CT gels to investigate their thermal and assembly properties. UV–vis, fluorescence, mass spectrometric as well as variable-temperature 1H NMR experiments on these gels suggest that the CT interaction is one of the major driving forces for the formation of these organogels.

  4. Numerical examination of acousto-optic Bragg interactions for profiled lightwaves using a transfer function formalism

    Science.gov (United States)

    Chatterjee, Monish R.; Almehmadi, Fares S.

    2013-10-01

    Classically, acousto-optic (AO) interactions comprise scattering of photons by energetic phonons into higher and lower orders. Standard weak interaction theory describes diffraction in the Bragg regime as the propagation of a uniform plane wave of light through a uniform plane wave of sound, resulting in the well-known first- and zeroth-order diffraction. Our preliminary investigation of the nature of wave diffraction and photon scattering from a Bragg cell under intensity feedback with profiled light beams indicates that the diffracted (upshifted photon) light continues to maintain the expected (uniform plane wave) behavior versus the optical phase shift in the cell within a small range of the Q-parameter, and at larger Qs, begins to deviate. Additionally, we observe the asymptotic axial shift of the beam center as predicted by the transfer function formalism.

  5. Analyzing Interactions by an IIS-Map-Based Method in Face-to-Face Collaborative Learning: An Empirical Study

    Science.gov (United States)

    Zheng, Lanqin; Yang, Kaicheng; Huang, Ronghuai

    2012-01-01

    This study proposes a new method named the IIS-map-based method for analyzing interactions in face-to-face collaborative learning settings. This analysis method is conducted in three steps: firstly, drawing an initial IIS-map according to collaborative tasks; secondly, coding and segmenting information flows into information items of IIS; thirdly,…

  6. Developing nurses' intercultural/intraprofessional communication skills using the EXCELLence in Cultural Experiential Learning and Leadership Social Interaction Maps.

    Science.gov (United States)

    Henderson, Saras; Barker, Michelle

    2017-09-27

    To examine how the use of Social Interaction Maps, a tool in the EXCELLence in Cultural Experiential Learning and Leadership Program, can enhance the development of nurses' intercultural/intraprofessional communication skills. Nurses face communication challenges when interacting with others from similar background as well as those from a culturally and linguistically diverse background. We used the EXCELLence in Cultural Experiential Learning and Leadership Program's Social Interaction Maps tool to foster intercultural/intraprofessional communication skills in nurses. Social Interaction Maps describe verbal and nonverbal communication behaviours that model ways of communicating in a culturally appropriate manner. The maps include four stages of an interaction, namely Approach, Bridging, Communicating and Departing using the acronym ABCD. Qualitative approach was used with a purposeful sample of nurses enrolled in a postgraduate course. Fifteen participants were recruited. The Social Interaction Map tool was taught to participants in a workshop where they engaged in sociocultural communication activities using scenarios. Participants were asked to apply Social Interaction Maps in their workplaces. Six weeks later, participants completed a semistructured open-ended questionnaire and participated in a discussion forum on their experience of using Social Interaction Maps. Data were content-analysed. Four themes identified in the use of the Social Interaction Maps were (i) enhancing self-awareness of communication skills; (ii) promoting skills in being nonconfrontational during difficult interactions; (iii) highlighting the importance of A (Approach) and B (Bridging) in interaction with others; and (iv) awareness of how others interpret what is said C (Communicating) and discussing to resolve issues before closure D (Departing). Application of the EXCELLence in Cultural Experiential Learning and Leadership Social Interaction Mapping tool was shown to be useful in

  7. Understanding solution-state noncovalent interactions between xenobiotics and natural organic matter using 19F/1H heteronuclear saturation transfer difference nuclear magnetic resonance spectroscopy.

    Science.gov (United States)

    Longstaffe, James G; Simpson, André J

    2011-08-01

    A combination of forward and reverse heteronuclear ((19)F/(1)H) saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopic techniques were applied to characterize the noncovalent interactions between perfluorinated aromatic xenobiotics and dissolved humic acid. These NMR techniques produce detailed molecular-level descriptions of weak noncovalent associations between components in complex environmental mixtures, allowing the mechanisms underlying these interactions to be explored; (19)F observed heteronuclear STD (H-STD) is used to describe the average molecular orientation of the xenobiotics during their interactions with humic acid, whereas (1)H observed reverse-heteronuclear STD (RH-STD) is used to both identify and quantify preferences exhibited by xenobiotics for interactions at different types of humic acid moieties. First, by using H-STD, it is shown that selected aromatic organofluorides orient with their nonfluorine functional groups (OH, NH(2), and COOH) directed away from humic acid during the interactions, suggesting that these functional groups are not specifically involved. Second, the RH-STD experiment is shown to be sensitive to subtle differences in preferred interaction sites in humic acid and is used here to demonstrate preferential interactions at aromatic humic acid sites for selected aromatic xenobiotics, C(10)F(7)OH, and C(6)F(4)X(2), (where X = F, OH, NH(2), NO(2), or COOH), that can be predicted from the electrostatic potential density maps of the xenobiotic. Copyright © 2011 SETAC.

  8. Plant–Agrobacterium interaction mediated by ethylene and super-Agrobacterium conferring efficient gene transfer

    Science.gov (United States)

    Nonaka, Satoko; Ezura, Hiroshi

    2014-01-01

    Agrobacterium tumefaciens has a unique ability to transfer genes into plant genomes. This ability has been utilized for plant genetic engineering. However, the efficiency is not sufficient for all plant species. Several studies have shown that ethylene decreased the Agrobacterium-mediated transformation frequency. Thus, A. tumefaciens with an ability to suppress ethylene evolution would increase the efficiency of Agrobacterium-mediated transformation. Some studies showed that plant growth-promoting rhizobacteria (PGPR) can reduce ethylene levels in plants through 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, which cleaves the ethylene precursor ACC into α-ketobutyrate and ammonia, resulting in reduced ethylene production. The whole genome sequence data showed that A. tumefaciens does not possess an ACC deaminase gene in its genome. Therefore, providing ACC deaminase activity to the bacteria would improve gene transfer. As expected, A. tumefaciens with ACC deaminase activity, designated as super-Agrobacterium, could suppress ethylene evolution and increase the gene transfer efficiency in several plant species. In this review, we summarize plant–Agrobacterium interactions and their applications for improving Agrobacterium-mediated genetic engineering techniques via super-Agrobacterium. PMID:25520733

  9. Multi-Modal, Multi-Touch Interaction with Maps in Disaster Management Applications

    Directory of Open Access Journals (Sweden)

    V. Paelke

    2012-07-01

    Full Text Available Multi-touch interaction has become popular in recent years and impressive advances in technology have been demonstrated, with the presentation of digital maps as a common presentation scenario. However, most existing systems are really technology demonstrators and have not been designed with real applications in mind. A critical factor in the management of disaster situations is the access to current and reliable data. New sensors and data acquisition platforms (e.g. satellites, UAVs, mobile sensor networks have improved the supply of spatial data tremendously. However, in many cases this data is not well integrated into current crisis management systems and the capabilities to analyze and use it lag behind sensor capabilities. Therefore, it is essential to develop techniques that allow the effective organization, use and management of heterogeneous data from a wide variety of data sources. Standard user interfaces are not well suited to provide this information to crisis managers. Especially in dynamic situations conventional cartographic displays and mouse based interaction techniques fail to address the need to review a situation rapidly and act on it as a team. The development of novel interaction techniques like multi-touch and tangible interaction in combination with large displays provides a promising base technology to provide crisis managers with an adequate overview of the situation and to share relevant information with other stakeholders in a collaborative setting. However, design expertise on the use of such techniques in interfaces for real-world applications is still very sparse. In this paper we report on interdisciplinary research with a user and application centric focus to establish real-world requirements, to design new multi-modal mapping interfaces, and to validate them in disaster management applications. Initial results show that tangible and pen-based interaction are well suited to provide an intuitive and visible way to

  10. Female behaviour and the interaction of male and female genital traits mediate sperm transfer during mating.

    Science.gov (United States)

    Friesen, C R; Uhrig, E J; Mason, R T; Brennan, P L R

    2016-05-01

    Natural selection and post-copulatory sexual selection, including sexual conflict, contribute to genital diversification. Fundamental first steps in understanding how these processes shape the evolution of specific genital traits are to determine their function experimentally and to understand the interactions between female and male genitalia during copulation. Our experimental manipulations of male and female genitalia in red-sided garter snakes (Thamnophis sirtalis parietalis) reveal that copulation duration and copulatory plug deposition, as well as total and oviductal/vaginal sperm counts, are influenced by the interaction between male and female genital traits and female behaviour during copulation. By mating females with anesthetized cloacae to males with spine-ablated hemipenes using a fully factorial design, we identified significant female-male copulatory trait interactions and found that females prevent sperm from entering their oviducts by contracting their vaginal pouch. Furthermore, these muscular contractions limit copulatory plug size, whereas the basal spine of the male hemipene aids in sperm and plug transfer. Our results are consistent with a role of sexual conflict in mating interactions and highlight the evolutionary importance of female resistance to reproductive outcomes. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  11. Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM

    DEFF Research Database (Denmark)

    Wierzbicki, Rafal; Købler, Carsten; Jensen, Mikkel Ravn Boye

    2013-01-01

    substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition...... a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map...

  12. Uncertainty of Monetary Valued Ecosystem Services - Value Transfer Functions for Global Mapping.

    Science.gov (United States)

    Schmidt, Stefan; Manceur, Ameur M; Seppelt, Ralf

    2016-01-01

    Growing demand of resources increases pressure on ecosystem services (ES) and biodiversity. Monetary valuation of ES is frequently seen as a decision-support tool by providing explicit values for unconsidered, non-market goods and services. Here we present global value transfer functions by using a meta-analytic framework for the synthesis of 194 case studies capturing 839 monetary values of ES. For 12 ES the variance of monetary values could be explained with a subset of 93 study- and site-specific variables by utilizing boosted regression trees. This provides the first global quantification of uncertainties and transferability of monetary valuations. Models explain from 18% (water provision) to 44% (food provision) of variance and provide statistically reliable extrapolations for 70% (water provision) to 91% (food provision) of the terrestrial earth surface. Although the application of different valuation methods is a source of uncertainty, we found evidence that assuming homogeneity of ecosystems is a major error in value transfer function models. Food provision is positively correlated with better life domains and variables indicating positive conditions for human well-being. Water provision and recreation service show that weak ownerships affect valuation of other common goods negatively (e.g. non-privately owned forests). Furthermore, we found support for the shifting baseline hypothesis in valuing climate regulation. Ecological conditions and societal vulnerability determine valuation of extreme event prevention. Valuation of habitat services is negatively correlated with indicators characterizing less favorable areas. Our analysis represents a stepping stone to establish a standardized integration of and reporting on uncertainties for reliable and valid benefit transfer as an important component for decision support.

  13. Uncertainty of Monetary Valued Ecosystem Services - Value Transfer Functions for Global Mapping.

    Directory of Open Access Journals (Sweden)

    Stefan Schmidt

    Full Text Available Growing demand of resources increases pressure on ecosystem services (ES and biodiversity. Monetary valuation of ES is frequently seen as a decision-support tool by providing explicit values for unconsidered, non-market goods and services. Here we present global value transfer functions by using a meta-analytic framework for the synthesis of 194 case studies capturing 839 monetary values of ES. For 12 ES the variance of monetary values could be explained with a subset of 93 study- and site-specific variables by utilizing boosted regression trees. This provides the first global quantification of uncertainties and transferability of monetary valuations. Models explain from 18% (water provision to 44% (food provision of variance and provide statistically reliable extrapolations for 70% (water provision to 91% (food provision of the terrestrial earth surface. Although the application of different valuation methods is a source of uncertainty, we found evidence that assuming homogeneity of ecosystems is a major error in value transfer function models. Food provision is positively correlated with better life domains and variables indicating positive conditions for human well-being. Water provision and recreation service show that weak ownerships affect valuation of other common goods negatively (e.g. non-privately owned forests. Furthermore, we found support for the shifting baseline hypothesis in valuing climate regulation. Ecological conditions and societal vulnerability determine valuation of extreme event prevention. Valuation of habitat services is negatively correlated with indicators characterizing less favorable areas. Our analysis represents a stepping stone to establish a standardized integration of and reporting on uncertainties for reliable and valid benefit transfer as an important component for decision support.

  14. Mapping Protein-Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry.

    Science.gov (United States)

    Gallagher, Elyssia S; Hudgens, Jeffrey W

    2016-01-01

    Biological processes are the result of noncovalent, protein-ligand interactions, where the ligands range from small organic and inorganic molecules to lipids, nucleic acids, peptides, and proteins. Amide groups within proteins constantly exchange protons with water. When immersed in heavy water (D2O), mass spectrometry (MS) can measure the change of mass associated with the hydrogen to deuterium exchange (HDX). Protein-ligand interactions modify the hydrogen exchange rates of amide protons, and the measurement of the amide exchange rates can provide rich information regarding the dynamical structure of the protein-ligand complex. This chapter describes a protocol for conducting bottom-up, continuous uptake, proteolytic fragmentation HDX-MS experiments that can help identify and map the interacting peptides of a protein-ligand interface. This tutorial outlines the fundamental theory governing hydrogen exchange; provides practical information regarding the preparation of protein samples and solutions; and describes the exchange reaction, reaction quenching, enzymatic digestion, chromatographic separation, and peptide analysis by MS. Tables list representative combinations of fluidic components used by HDX-MS researchers and summarize the available HDX-MS analysis software packages. Additionally, two HDX-MS case studies are used to illustrate protein-ligand interactions involving: (1) a continuous sequence of interacting residues and (2) a set of discontinuously numbered residues, residing spatially near each other. © 2016 Elsevier Inc. All rights reserved.

  15. Vertically arrayed stimuli and responses: transfer of incompatible spatial mapping to Simon task occurs regardless of response-device orientation.

    Science.gov (United States)

    Zhong, Qi; Xiong, Aiping; Vu, Kim-Phuong L; Proctor, Robert W

    2018-01-01

    Conde et al. (Exp Brain Res 233:3313-3321, 2015) found that the Simon effect for vertically arrayed stimuli and responses was reduced after 100 prior practice trials with an incompatible mapping of the stimulus locations and responses. This finding was contrary to Vu's (Mem Cognit 35:1463-1471, 2007) finding of no transfer effect with 72 trials of prior practice. Conde et al. proposed that the different results were due to their responses being coded as top and bottom in the frontal plane, whereas Vu's were coded as far and near in the transverse plane. We conducted four experiments to test this possibility in which participants responded with keypresses using their thumbs on a numeric keypad held vertically (upright in the frontal plane) or horizontally (flat in the transverse plane). Experiment 1 showed that, without any prior practice, a similar sized Simon effect was obtained when the response device was oriented in the transverse plane as when it was oriented in the frontal plane. In Experiments 2 and 3 participants performed with the same device orientation in the incompatible practice and Simon transfer tasks, with orientation manipulated between-subjects in the former and within-subjects in the latter. The Simon effect was reduced in both cases, with no significant difference in transfer effect for transverse and frontal planes. In Experiment 4, the device orientation differed between the incompatible practice and Simon transfer tasks, and the Simon effect was reduced similarly across both response-device orientations. Thus, the differences between Conde et al.'s and Vu's findings cannot be attributed to the response-device orientation. Our results are consistent with the view that people code response locations in the transverse plane as top and bottom, rather than far and near, in agreement with the terminology of "top row" and "bottom row" for computer keyboards.

  16. Topological and functional analysis of nonalcoholic steatohepatitis through protein interaction mapping

    Science.gov (United States)

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

    2016-01-01

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

  17. Transferred hyperfine interaction between the rare-earth ions and the fluorine nuclei in rare-earth trifluorides

    DEFF Research Database (Denmark)

    Hansen, P. E.; Nevald, Rolf; Guggenheim, H. G.

    1978-01-01

    The isotropic and anisotropic transferred hyperfine interactions between F ions in the two chemically inequivalent sites and the rare-earth ions (R) have been derived from 19F NMR measurements in the temperature region 100-300 K on single crystals of TbF3 and DyF3. The isotropic interactions are ...

  18. Web GIS in practice V: 3-D interactive and real-time mapping in Second Life

    Directory of Open Access Journals (Sweden)

    Burden David

    2007-11-01

    Full Text Available Abstract This paper describes technologies from Daden Limited for geographically mapping and accessing live news stories/feeds, as well as other real-time, real-world data feeds (e.g., Google Earth KML feeds and GeoRSS feeds in the 3-D virtual world of Second Life, by plotting and updating the corresponding Earth location points on a globe or some other suitable form (in-world, and further linking those points to relevant information and resources. This approach enables users to visualise, interact with, and even walk or fly through, the plotted data in 3-D. Users can also do the reverse: put pins on a map in the virtual world, and then view the data points on the Web in Google Maps or Google Earth. The technologies presented thus serve as a bridge between mirror worlds like Google Earth and virtual worlds like Second Life. We explore the geo-data display potential of virtual worlds and their likely convergence with mirror worlds in the context of the future 3-D Internet or Metaverse, and reflect on the potential of such technologies and their future possibilities, e.g. their use to develop emergency/public health virtual situation rooms to effectively manage emergencies and disasters in real time. The paper also covers some of the issues associated with these technologies, namely user interface accessibility and individual privacy.

  19. Ternary Interactions and Energy Transfer between Fluorescein Isothiocyanate, Adenosine Triphosphate, and Graphene Oxide Nanocarriers.

    Science.gov (United States)

    Ratajczak, Katarzyna; Stobiecka, Magdalena

    2017-07-20

    The interactions of fluorescent probes and biomolecules with nanocarriers are of key importance to the emerging targeted drug delivery systems. Graphene oxide nanosheets (GONs) as the nanocarriers offer biocompatibility and robust drug binding capacity. The interactions of GONs with fluorophores lead to strong fluorescence quenching, which may interfere with fluorescence bioimaging and biodetection. Herein, we report on the interactions and energy transfers in a model ternary system: GONs-FITC-ATP, where FITC is a model fluorophore (fluorescein isothiocyanate) and ATP is a common biomolecule (adenosine-5'-triphosphate). We have found that FITC fluorescence is considerably quenched by ATP (the quenching constant K SV = 113 ± 22 M -1 ). The temperature coefficient of K SV is positive (α T = 4.15 M -1 deg -1 ). The detailed analysis of a model for internal self-quenching of FITC indicates that the temperature dependence of the net quenching efficiency η for the FITC-ATP pair is dominated by FITC internal self-quenching modes with their contribution estimated at 79%. The quenching of FITC by GONs is much stronger (K SV = 598 ± 29 M -1 ) than that of FITC-ATP and is associated with the formation of supramolecular assemblies bound with hydrogen bonding and π-π stacking interactions. For the analysis of the complex behavior of the ternary system GONs-FITC-ATP, a model of chemisorption of ATP on GONs, with partial blocking of FITC quenching, has been developed. Our results indicate that ATP acts as a moderator for FITC quenching by GONs. The interactions between ATP, FITC, and GONs have been corroborated using molecular dynamics and quantum mechanical calculations.

  20. CH···π interactions do not contribute to hydrogen transfer catalysis by glycerol dehydratase.

    Science.gov (United States)

    Liu, Yuemin; Gallo, August A; Xu, Wu; Bajpai, Rakesh; Florián, Jan

    2011-10-20

    The role of the nonbonded CH···π interaction in the hydrogen abstraction from glycerol by the coenzyme B(12)-independent glycerol dehydratase (GDH) was examined using the QM/MM (ONIOM), MP2, and CCSD(T) methods. The studied CH···π interaction included the hydrogen atom of the -C(2)H(OH)- group of the glycerol substrate and the tyrosine-339 residue of the dehydratase. A contribution of this interaction to the stabilization of the transition state for the transfer of a hydrogen atom from the adjacent terminal C(1)H(2)(OH) group to cysteine 433 was determined by ab initio HF, MP2, and CCSD(T) calculations with the aug-cc-pvDZ basis set for the corresponding methane/benzene, methanol/phenol, and glycerol radical/phenol subsystems. The calculated CH···π distance, defined as the distance between the H atom and the center of the phenol ring, shortened from 2.62 to 2.52 Å upon going from the ground- to the transition-state of the GDH-catalyzed reaction. However, this shortening was not accompanied by the expected lowering of the CH···π interaction free energy. Instead, this interaction remained weak (about -1 kcal/mol) along the entire reaction coordinate. Additionally, the mutual orientation of the CH group and the phenol ring did not change significantly during the reaction. These results suggest that the phenol group of the tyrosine-339 does not contribute to lowering the activation barrier in the enzyme, but do not exclude the possibility that tyrosine 339 facilitates proper orientation of glycerol for the electrostatic catalysis, or inhibits side-reactions of the reactive glycerol radical intermediate.

  1. Mapping defects in a carbon nanotube by momentum transfer dependent electron energy loss spectromicroscopy

    International Nuclear Information System (INIS)

    Najafi, Ebrahim; Hitchcock, Adam P.; Rossouw, David; Botton, Gianluigi A.

    2012-01-01

    Momentum resolved electron energy loss (EELS) spectra of multi-walled carbon nanotubes (MWCNT) have been measured at the C 1s edge in a transmission electron microscope (TEM). We demonstrate that structurally sensitive electron linear dichroic (ELD) signals analogous to X-ray linear dichroic (XLD) signals (Najafi et al., 2008) can be measured by TEM-EELS from individual MWCNT if sample tilt and deflection of the inelastic scattering signal relative to the EELS spectrometer entrance aperture are used. This method is used to map defects in MWCNT at higher spatial resolution than is currently possible with X-ray microscopy. -- Highlights: ► We show how to measure electron linear dichroism using TEM-EELS and sample tilt. ► We measure this electron linear dichroism (ELD) signal for a high quality MWCNT. ► We show the ELD is similar to that of X-ray linear dichroism (XLD). ► We measure ELD for a defective MWCNT. ► We present ELD-derived maps of the defects with 5 nm spatial sampling.

  2. Inverting Steric Effects: Using "Attractive" Noncovalent Interactions To Direct Silver-Catalyzed Nitrene Transfer.

    Science.gov (United States)

    Huang, Minxue; Yang, Tzuhsiung; Paretsky, Jonathan D; Berry, John F; Schomaker, Jennifer M

    2017-12-06

    Nitrene transfer (NT) reactions represent powerful and direct methods to convert C-H bonds into amine groups that are prevalent in many commodity chemicals and pharmaceuticals. The importance of the C-N bond has stimulated the development of numerous transition-metal complexes to effect chemo-, regio-, and diastereoselective NT. An ongoing challenge is to understand how subtle interactions between catalyst and substrate influence the site-selectivity of the C-H amination event. In this work, we explore the underlying reasons why Ag(tpa)OTf (tpa = tris(pyridylmethyl)amine) prefers to activate α-conjugated C-H bonds over 3° alkyl C(sp 3 )-H bonds and apply these insights to reaction optimization and catalyst design. Experimental results suggest possible roles of noncovalent interactions (NCIs) in directing the NT; computational studies support the involvement of π···π and Ag···π interactions between catalyst and substrate, primarily by lowering the energy of the directed transition state and reaction conformers. A simple Hess's law relationship can be employed to predict selectivities for new substrates containing competing NCIs. The insights presented herein are poised to inspire the design of other catalyst-controlled C-H functionalization reactions.

  3. Mapping the interactions between the Alzheimer's Aβ-peptide and human serum albumin beyond domain resolution.

    Science.gov (United States)

    Algamal, Moustafa; Milojevic, Julijana; Jafari, Naeimeh; Zhang, William; Melacini, Giuseppe

    2013-10-01

    Human serum albumin (HSA) is a potent inhibitor of Aβ self-association and this novel, to our knowledge, function of HSA is of potential therapeutic interest for the treatment of Alzheimer's disease. It is known that HSA interacts with Aβ oligomers through binding sites evenly partitioned across the three albumin domains and with comparable affinities. However, as of this writing, no information is available on the HSA-Aβ interactions beyond domain resolution. Here, we map the HSA-Aβ interactions at subdomain and peptide resolution. We show that each separate subdomain of HSA domain 3 inhibits Aβ self-association. We also show that fatty acids (FAs) compete with Aβ oligomers for binding to domain 3, but the determinant of the HSA/Aβ oligomer interactions are markedly distinct from those of FAs. Although salt bridges with the FA carboxylate determine the FA binding affinities, hydrophobic contacts are pivotal for Aβ oligomer recognition. Specifically, we identified a site of Aβ oligomer recognition that spans the HSA (494-515) region and aligns with the central hydrophobic core of Aβ. The HSA (495-515) segment includes residues affected by FA binding and this segment is prone to self-associate into β-amyloids, suggesting that sites involved in fibrilization may provide a lead to develop inhibitors of Aβ self-association. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    Energy Technology Data Exchange (ETDEWEB)

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of

  5. Significance of force transfer in mitral valve-left ventricular interaction: in vivo assessment.

    Science.gov (United States)

    Askov, Jesper B; Honge, Jesper L; Jensen, Morten O; Nygaard, Hans; Hasenkam, J Michael; Nielsen, Sten L

    2013-06-01

    The objective of this study was to assess the combined force transfer from the papillary muscle tips to the mitral valve through the chordae tendineae in vivo, and thereby quantify the force transmitted through the papillary-chordal complex to augment left ventricular ejection. In an acute porcine model (n = 8), force transfer between papillary muscles and the mitral valve was recorded on the anterior and posterior papillary muscle tip using dedicated force transducers. Ultrasound sonomicrometry was utilized to record and calculate left ventricular long-axis shortening and mitral annular geometry. The closing force acting on the mitral valve leaflets was calculated as mitral annular area multiplied by the transmitral pressure difference throughout systole. Mitral valve competence was verified before measurements with color Doppler ultrasound. Peak force in the anterior and posterior papillary muscle was 5.9 ± 0.6 N and 5.8 ± 0.7 N (mean ± standard error of the mean), respectively, and peak closing force was 6.8 ± 0.3 N all at a transmitral pressure of 90 mm Hg. Peak rate of left ventricular contraction coincided with peak papillary muscle force. This study is the first to assess the magnitude and time course of the longitudinal force transmitted through the papillary-chordal complex to the left ventricular wall during ejection. The study also demonstrates a significant force transfer to the closing force acting on the mitral valve leaflets that constitutes an essential component of valvular-ventricular interaction to enhance left ventricular systolic pump performance. The magnitude of the combined papillary muscle force component emphasizes the crucial role of preserving mitral valve-left ventricular continuity in mitral valve surgery. Copyright © 2013 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

  6. TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network.

    Science.gov (United States)

    Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L; Costanzo, Michael; Andrews, Brenda; Boone, Charles

    2017-05-05

    Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. Copyright © 2017 Usaj et al.

  7. Supramolecular fullerene/porphyrin charge transfer interaction studied by absorption spectrophotometric method

    International Nuclear Information System (INIS)

    Mukherjee, Partha; Bhattacharya, Shrabanti; Nayak, Sandip K.; Chattopadhyay, Subrata; Bhattacharya, Sumanta

    2009-01-01

    A detailed UV-Vis spectrometric and thermodynamic studies were done to look insight into the nature of molecular interactions of the electron donor-acceptor complexes of C 60 and C 70 with 5,10,15,20-tetrakis(octadecyloxyphenyl)-21H,23H-porphyrin (1) in chloroform and toluene. Charge transfer (CT) absorption bands were located in the visible region and vertical ionization potential of 1 was determined utilizing CT transition energy. Low values of oscillator and transition dipole strengths suggested that the complexes were almost of neutral character in ground states. The high binding constant value for the C 70 -1 complex indicated high selectivity of 1 molecule towards C 70 . Experimental as well as theoretically determined of enthalpies of formation value substantiated the trend in K values for fullerene-1 complexes.

  8. Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

    Science.gov (United States)

    Lee, Mi Kyung; Coker, David F

    2016-08-18

    An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.

  9. Supramolecular fullerene/porphyrin charge transfer interaction studied by absorption spectrophotometric method

    Science.gov (United States)

    Mukherjee, Partha; Bhattacharya (Banerjee), Shrabanti; Nayak, Sandip K.; Chattopadhyay, Subrata; Bhattacharya, Sumanta

    2009-06-01

    A detailed UV-Vis spectrometric and thermodynamic studies were done to look insight into the nature of molecular interactions of the electron donor-acceptor complexes of C60 and C70 with 5,10,15,20-tetrakis(octadecyloxyphenyl)-21H,23H-porphyrin (1) in chloroform and toluene. Charge transfer (CT) absorption bands were located in the visible region and vertical ionization potential of 1 was determined utilizing CT transition energy. Low values of oscillator and transition dipole strengths suggested that the complexes were almost of neutral character in ground states. The high binding constant value for the C70-1 complex indicated high selectivity of 1 molecule towards C70. Experimental as well as theoretically determined of enthalpies of formation value substantiated the trend in K values for fullerene-1 complexes.

  10. Modeling Radiative Heat Transfer and Turbulence-Radiation Interactions in Engines

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Chandan [Pennsylvania State Univ., University Park, PA (United States); Sircar, Arpan [Pennsylvania State Univ., University Park, PA (United States); Ferreyro-Fernandez, Sebastian [Pennsylvania State Univ., University Park, PA (United States); Imren, Abdurrahman [Pennsylvania State Univ., University Park, PA (United States); Haworth, Daniel C [Pennsylvania State Univ., University Park, PA (United States); Roy, Somesh P [Marquette University (United States); Ge, Wenjun [University of California Merced (United States); Modest, Michael F [University of California Merced (United States)

    2017-04-26

    Detailed radiation modelling in piston engines has received relatively little attention to date. Recently, it is being revisited in light of current trends towards higher operating pressures and higher levels of exhaust-gas recirculation, both of which enhance molecular gas radiation. Advanced high-efficiency engines also are expected to function closer to the limits of stable operation, where even small perturbations to the energy balance can have a large influence on system behavior. Here several different spectral radiation property models and radiative transfer equation (RTE) solvers have been implemented in an OpenFOAM-based engine CFD code, and simulations have been performed for a full-load (peak pressure ~200 bar) heavy-duty diesel engine. Differences in computed temperature fields, NO and soot levels, and wall heat transfer rates are shown for different combinations of spectral models and RTE solvers. The relative importance of molecular gas radiation versus soot radiation is examined. And the influence of turbulence-radiation interactions is determined by comparing results obtained using local mean values of composition and temperature to compute radiative emission and absorption with those obtained using a particle-based transported probability density function method.

  11. Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

    Science.gov (United States)

    Kumar, Rajendra; Sobhy, Haitham; Stenberg, Per; Lizana, Ludvig

    2017-09-29

    Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Identification of residue pairing in interacting β-strands from a predicted residue contact map.

    Science.gov (United States)

    Mao, Wenzhi; Wang, Tong; Zhang, Wenxuan; Gong, Haipeng

    2018-04-19

    Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. Our algorithm RDb 2 C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb 2 C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb 2 C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb 2 C. Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .

  13. Tunable self-assembled spin chains of strongly interacting cold atoms for demonstration of reliable quantum state transfer

    DEFF Research Database (Denmark)

    Loft, N. J. S.; Marchukov, O. V.; Petrosyan, D.

    2016-01-01

    We have developed an efficient computational method to treat long, one-dimensional systems of strongly-interacting atoms forming self-assembled spin chains. Such systems can be used to realize many spin chain model Hamiltonians tunable by the external confining potential. As a concrete...... demonstration, we consider quantum state transfer in a Heisenberg spin chain and we show how to determine the confining potential in order to obtain nearly-perfect state transfer....

  14. Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm.

    Science.gov (United States)

    Yu, Long-Xi; Lorenz, Aaron; Rutkoski, Jessica; Singh, Ravi P; Bhavani, Sridhar; Huerta-Espino, Julio; Sorrells, Mark E

    2011-12-01

    The recent emergence of wheat stem rust Ug99 and evolution of new races within the lineage threatens global wheat production because they overcome widely deployed stem rust resistance (Sr) genes that had been effective for many years. To identify loci conferring adult plant resistance to races of Ug99 in wheat, we employed an association mapping approach for 276 current spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT). Breeding lines were genotyped with Diversity Array Technology (DArT) and microsatellite markers. Phenotypic data was collected on these lines for stem rust race Ug99 resistance at the adult plant stage in the stem rust resistance screening nursery in Njoro, Kenya in seasons 2008, 2009 and 2010. Fifteen marker loci were found to be significantly associated with stem rust resistance. Several markers appeared to be linked to known Sr genes, while other significant markers were located in chromosome regions where no Sr genes have been previously reported. Most of these new loci colocalized with QTLs identified recently in different biparental populations. Using the same data and Q + K covariate matrices, we investigated the interactions among marker loci using linear regression models to calculate P values for pairwise marker interactions. Resistance marker loci including the Sr2 locus on 3BS and the wPt1859 locus on 7DL had significant interaction effects with other loci in the same chromosome arm and with markers on chromosome 6B. Other resistance marker loci had significant pairwise interactions with markers on different chromosomes. Based on these results, we propose that a complex network of gene-gene interactions is, in part, responsible for resistance to Ug99. Further investigation may provide insight for understanding mechanisms that contribute to this resistance gene network.

  15. Interactive segmentation of tongue contours in ultrasound video sequences using quality maps

    Science.gov (United States)

    Ghrenassia, Sarah; Ménard, Lucie; Laporte, Catherine

    2014-03-01

    Ultrasound (US) imaging is an effective and non invasive way of studying the tongue motions involved in normal and pathological speech, and the results of US studies are of interest for the development of new strategies in speech therapy. State-of-the-art tongue shape analysis techniques based on US images depend on semi-automated tongue segmentation and tracking techniques. Recent work has mostly focused on improving the accuracy of the tracking techniques themselves. However, occasional errors remain inevitable, regardless of the technique used, and the tongue tracking process must thus be supervised by a speech scientist who will correct these errors manually or semi-automatically. This paper proposes an interactive framework to facilitate this process. In this framework, the user is guided towards potentially problematic portions of the US image sequence by a segmentation quality map that is based on the normalized energy of an active contour model and automatically produced during tracking. When a problematic segmentation is identified, corrections to the segmented contour can be made on one image and propagated both forward and backward in the problematic subsequence, thereby improving the user experience. The interactive tools were tested in combination with two different tracking algorithms. Preliminary results illustrate the potential of the proposed framework, suggesting that the proposed framework generally improves user interaction time, with little change in segmentation repeatability.

  16. Mapping substrate interactions of the human membrane-associated neuraminidase, NEU3, using STD NMR.

    Science.gov (United States)

    Albohy, Amgad; Richards, Michele R; Cairo, Christopher W

    2015-03-01

    Saturation transfer difference (STD) nuclear magnetic resonance (NMR) is a powerful technique which can be used to investigate interactions between proteins and their substrates. The method identifies specific sites of interaction found on a small molecule ligand when in complex with a protein. The ability of STD NMR to provide specific insight into binding interactions in the absence of other structural data is an attractive feature for its use with membrane proteins. We chose to employ STD NMR in our ongoing investigations of the human membrane-associated neuraminidase NEU3 and its interaction with glycolipid substrates (e.g., GM3). In order to identify critical substrate-enzyme interactions, we performed STD NMR with a catalytically inactive form of the enzyme, NEU3(Y370F), containing an N-terminal maltose-binding protein (MBP)-affinity tag. In the absence of crystallographic data on the enzyme, these data represent a critical experimental test of proposed homology models, as well as valuable new structural data. To aid interpretation of the STD NMR data, we compared the results with molecular dynamics (MD) simulations of the enzyme-substrate complexes. We find that the homology model is able to predict essential features of the experimental data, including close contact of the hydrophobic aglycone and the Neu5Ac residue with the enzyme. Additionally, the model and STD NMR data agree on the facial recognition of the galactose and glucose residues of the GM3-analog studied. We conclude that the homology model of NEU3 can be used to predict substrate recognition, but our data indicate that unstructured portions of the NEU3 model may require further refinement. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Mapping cortical degeneration in ALS with magnetization transfer ratio and voxel-based morphometry.

    Directory of Open Access Journals (Sweden)

    Mirco Cosottini

    Full Text Available Pathological and imaging data indicate that amyotrophic lateral sclerosis (ALS is a multisystem disease involving several cerebral cortical areas. Advanced quantitative magnetic resonance imaging (MRI techniques enable to explore in vivo the volume and microstructure of the cerebral cortex in ALS. We studied with a combined voxel-based morphometry (VBM and magnetization transfer (MT imaging approach the capability of MRI to identify the cortical areas affected by neurodegeneration in ALS patients. Eighteen ALS patients and 18 age-matched healthy controls were examined on a 1.5T scanner using a high-resolution 3D T1 weighted spoiled gradient recalled sequence with and without MT saturation pulse. A voxel-based analysis (VBA was adopted in order to automatically compute the regional atrophy and MT ratio (MTr changes of the entire cerebral cortex. By using a multimodal image analysis MTr was adjusted for local gray matter (GM atrophy to investigate if MTr changes can be independent of atrophy of the cerebral cortex. VBA revealed several clusters of combined GM atrophy and MTr decrease in motor-related areas and extra-motor frontotemporal cortex. The multimodal image analysis identified areas of isolated MTr decrease in premotor and extra-motor frontotemporal areas. VBM and MTr are capable to detect the distribution of neurodegenerative alterations in the cortical GM of ALS patients, supporting the hypothesis of a multi-systemic involvement in ALS. MT imaging changes exist beyond volume loss in frontotemporal cortices.

  18. Impact of flame-wall interaction on premixed flame dynamics and transfer function characteristics

    KAUST Repository

    Kedia, K.S.

    2011-01-01

    In this paper, we numerically investigate the response of a perforated-plate stabilized laminar methane-air premixed flame to imposed inlet velocity perturbations. A flame model using detailed chemical kinetics mechanism is applied and heat exchange between the burner plate and the gas mixture is incorporated. Linear transfer functions, for low mean inlet velocity oscillations, are analyzed for different equivalence ratio, mean inlet velocity, plate thermal conductivity and distance between adjacent holes. The oscillations of the heat exchange rate at the top of the burner surface plays a critical role in driving the growth of the perturbations over a wide range of conditions, including resonance. The flame response to the perturbations at its base takes the form of consumption speed oscillations in this region. Flame stand-off distance increases/decreases when the flame-wall interaction strengthens/weakens, impacting the overall dynamics of the heat release. The convective lag between the perturbations and the flame base response govern the phase of heat release rate oscillations. There is an additional convective lag between the perturbations at the flame base and the flame tip which has a weaker impact on the heat release rate oscillations. At higher frequencies, the flame-wall interaction is weaker and the heat release oscillations are driven by the flame area oscillations. The response of the flame to higher amplitude oscillations are used to gain further insight into the mechanisms. © 2010 Published by Elsevier Inc. on behalf of The Combustion Institute. All rights reserved.

  19. A Hurricane Hits Home: An Interactive Science Museum Exhibit on Ocean Mapping and Marine Debris

    Science.gov (United States)

    Butkiewicz, T.; Vasta, D. J.; Gager, N. C.; Fruth, B. W.; LeClair, J.

    2016-12-01

    As part of the outreach component for a project involving the detection and analysis of marine debris generated by Super Storm Sandy, The Center for Coastal and Ocean Mapping / Joint Hydrographic Center partnered with The Seacoast Science Center to develop an interactive museum exhibit that engages the public with a touchscreen based game revolving around the detection and identification of marine debris. "A Hurricane Hits Home" is a multi-station touchscreen exhibit geared towards children, and integrates a portion of a historical wooden shipwreck into its physical design. The game invites museum guests to examine a number of coastal regions and harbors in Sandy affected areas. It teaches visitors about modern mapping technology by having them control boats with multibeam sonars and airplanes with lidar sensors. They drag these vehicles around maps to reveal the underlying bathymetry below the satellite photos. They learn the applications and limitations of sonar and lidar by where the vehicles can and cannot collect survey data (e.g. lidar doesn't work in deep water, and the boat can't go in shallow areas). As users collect bathymetry data, they occasionally reveal marine debris objects on the seafloor. Once all the debris objects in a level have been located, the game challenges them to identify them based on their appearance in the bathymetry data. They must compare the simulated bathymetry images of the debris targets to photos of possible objects, and choose the correct matches to achieve a high score. The exhibit opened January 2016 at the Seacoast Science Center in Rye, NH.

  20. Building a grid-semantic map for the navigation of service robots through human–robot interaction

    Directory of Open Access Journals (Sweden)

    Cheng Zhao

    2015-11-01

    Full Text Available This paper presents an interactive approach to the construction of a grid-semantic map for the navigation of service robots in an indoor environment. It is based on the Robot Operating System (ROS framework and contains four modules, namely Interactive Module, Control Module, Navigation Module and Mapping Module. Three challenging issues have been focused during its development: (i how human voice and robot visual information could be effectively deployed in the mapping and navigation process; (ii how semantic names could combine with coordinate data in an online Grid-Semantic map; and (iii how a localization–evaluate–relocalization method could be used in global localization based on modified maximum particle weight of the particle swarm. A number of experiments are carried out in both simulated and real environments such as corridors and offices to verify its feasibility and performance.

  1. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2011-11-01

    Full Text Available As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium and prototrophic (minimal medium culture conditions. The differential patterns of genetic interactions detected among > 235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens and an important target.

  2. Phosphatidylcholine transfer protein interacts with thioesterase superfamily member 2 to attenuate insulin signaling.

    Science.gov (United States)

    Ersoy, Baran A; Tarun, Akansha; D'Aquino, Katharine; Hancer, Nancy J; Ukomadu, Chinweike; White, Morris F; Michel, Thomas; Manning, Brendan D; Cohen, David E

    2013-07-30

    Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenced by insulin-independent IRS2 activation after knockdown, genetic ablation, or chemical inhibition of PC-TP. In addition, IRS2 was activated after knockdown of THEM2, providing support for a role for the interaction of PC-TP with THEM2 in suppressing insulin signaling. Additionally, we showed that PC-TP bound to tuberous sclerosis complex 2 (TSC2) and stabilized the components of the TSC1-TSC2 complex, which functions to inhibit mTORC1. Preventing phosphatidylcholine from binding to PC-TP disrupted interactions of PC-TP with THEM2 and TSC2, and disruption of the PC-TP-THEM2 complex was associated with increased activation of both IRS2 and mTORC1. In livers of mice with genetic ablation of PC-TP or that had been treated with a PC-TP inhibitor, steady-state amounts of IRS2 were increased, whereas those of TSC2 were decreased. These findings reveal a phospholipid-dependent mechanism that suppresses insulin signaling downstream of its receptor.

  3. Analysis of genotype × environment interactions for polyphenols and antioxidant capacity of rice by association mapping.

    Science.gov (United States)

    Shao, Yafang; Tang, Fufu; Huang, Yan; Xu, Feifei; Chen, Yaling; Tong, Chuan; Chen, Hao; Bao, Jinsong

    2014-06-11

    Uncovering the genetic basis of polyphenol content and antioxidant activity traits in rice accessions is important to improve the nutritional quality of whole grain rice and to ameliorate the increasing nutrition problem of the rice-eating population. In this study, 20 diverse rice accessions were planted in Hainan province, China, for 2 years to investigate the effects of genotype, environment, and their interactions on total phenolic (TPC), flavonoid (TFC), proanthocyanidins content (TPAC), ABTS, and DPPH radical scavenging activity by association mapping. Analyses of variance (ANOVA) showed that TPC, TFC, TPAC, ABTS, and DPPH were mainly affected by genetic variance, accounting for >94% of the total variance. The interaction between genotype × environment (G × E) was also highly significant (P 0.96; P < 0.001). Twenty-three putative unique loci were identified by association mapping. Five loci were close to previously identified genes or quantitative trait loci (QTLs). Among them, qPAC7-3 identified for TPAC in 2011 was near to the brown pericarp and seed coat (Rc) gene, and the locus at the qPC4/qFC4/qPAC4/qACA4/qACD4 cluster on chromosome 4 detected in two environments was near to a transcriptional activator A (Ra) gene. Some loci were identified in only one environment, indicating that these QTLs were sensitive to environment. This study provides a primary SNP-resource for further identification of genes responsible for polyhenol contents and antioxidant activity in rice whole grains.

  4. Usability Assessment of the Missouri Cancer Registry’s Published Interactive Mapping Reports: Round One

    Science.gov (United States)

    Jackson-Thompson, Jeannette; Schmaltz, Chester Lee

    2017-01-01

    Background  Many users of spatial data have difficulty interpreting information in health-related spatial reports. The Missouri Cancer Registry and Research Center (MCR-ARC) has produced interactive reports for several years. These reports have never been tested for usability. Objective  The aims of this study were to: (1) conduct a multi-approach usability testing study to understand ease of use (user friendliness) and user satisfaction; and (2) evaluate the usability of MCR-ARC’s published InstantAtlas reports. Methods   An institutional review board (IRB) approved mixed methodology usability testing study using a convenience sample of health professionals. A recruiting email was sent to faculty in the Master of Public Health program and to faculty and staff in the Department of Health Management and Informatics at the University of Missouri-Columbia. The study included 7 participants. The test included a pretest questionnaire, a multi-task usability test, and the System Usability Scale (SUS). Also, the researchers collected participants’ comments about the tested maps immediately after every trial. Software was used to record the computer screen during the trial and the participants’ spoken comments. Several performance and usability metrics were measured to evaluate the usability of MCR-ARC’s published mapping reports. Results Of the 10 assigned tasks, 6 reached a 100% completion success rate, and this outcome was relative to the complexity of the tasks. The simple tasks were handled more efficiently than the complicated tasks. The SUS score ranged between 20-100 points, with an average of 62.7 points and a median of 50.5 points. The tested maps’ effectiveness outcomes were better than the efficiency and satisfaction outcomes. There was a statistically significant relationship between the subjects’ performance on the study test and the users’ previous experience with geographic information system (GIS) tools (P=.03). There were no

  5. The use of interactive graphical maps for browsing medical/health Internet information resources

    Directory of Open Access Journals (Sweden)

    Boulos Maged

    2003-01-01

    Full Text Available Abstract As online information portals accumulate metadata descriptions of Web resources, it becomes necessary to develop effective ways for visualising and navigating the resultant huge metadata repositories as well as the different semantic relationships and attributes of described Web resources. Graphical maps provide a good method to visualise, understand and navigate a world that is too large and complex to be seen directly like the Web. Several examples of maps designed as a navigational aid for Web resources are presented in this review with an emphasis on maps of medical and health-related resources. The latter include HealthCyberMap maps http://healthcybermap.semanticweb.org/, which can be classified as conceptual information space maps, and the very abstract and geometric Visual Net maps of PubMed http://map.net (for demos. Information resources can be also organised and navigated based on their geographic attributes. Some of the maps presented in this review use a Kohonen Self-Organising Map algorithm, and only HealthCyberMap uses a Geographic Information System to classify Web resource data and render the maps. Maps based on familiar metaphors taken from users' everyday life are much easier to understand. Associative and pictorial map icons that enable instant recognition and comprehension are preferred to geometric ones and are key to successful maps for browsing medical/health Internet information resources.

  6. Usability Assessment of the Missouri Cancer Registry's Published Interactive Mapping Reports: Round One.

    Science.gov (United States)

    Ben Ramadan, Awatef Ahmed; Jackson-Thompson, Jeannette; Schmaltz, Chester Lee

    2017-08-04

     Many users of spatial data have difficulty interpreting information in health-related spatial reports. The Missouri Cancer Registry and Research Center (MCR-ARC) has produced interactive reports for several years. These reports have never been tested for usability.  The aims of this study were to: (1) conduct a multi-approach usability testing study to understand ease of use (user friendliness) and user satisfaction; and (2) evaluate the usability of MCR-ARC's published InstantAtlas reports.   An institutional review board (IRB) approved mixed methodology usability testing study using a convenience sample of health professionals. A recruiting email was sent to faculty in the Master of Public Health program and to faculty and staff in the Department of Health Management and Informatics at the University of Missouri-Columbia. The study included 7 participants. The test included a pretest questionnaire, a multi-task usability test, and the System Usability Scale (SUS). Also, the researchers collected participants' comments about the tested maps immediately after every trial. Software was used to record the computer screen during the trial and the participants' spoken comments. Several performance and usability metrics were measured to evaluate the usability of MCR-ARC's published mapping reports. Of the 10 assigned tasks, 6 reached a 100% completion success rate, and this outcome was relative to the complexity of the tasks. The simple tasks were handled more efficiently than the complicated tasks. The SUS score ranged between 20-100 points, with an average of 62.7 points and a median of 50.5 points. The tested maps' effectiveness outcomes were better than the efficiency and satisfaction outcomes. There was a statistically significant relationship between the subjects' performance on the study test and the users' previous experience with geographic information system (GIS) tools (P=.03). There were no statistically significant relationships between users

  7. An interactive mapping tool for visualizing lacunarity of laser scanned point clouds

    Science.gov (United States)

    Kania, Adam; Székely, Balázs

    2016-04-01

    Lacunarity, a measure of the spatial distribution of the empty space in a certain model or real space over large spatial scales, is found to be a useful descriptive quantity in many fields using imagery, including, among others, geology, dentistry, neurology. Its application in ecology was suggested more than 20 years ago. The main problem of its application was the lack of appropriate high resolution data. Nowadays, full-waveform laser scanning, also known as FWF LiDAR, provides the tool for mapping the vegetation in unprecedented details and accuracy. Consequently, the lacunarity concept can be revitalized, in order to study the structure of the vegetation in this sense as well. Calculation of lacunarity, even if it is done in two dimensions (2D), is still has its problems: on one hand it is a number-crunching procedure, on the other hand, it produces 4D results: at each 3D point it returns a set of data that are function of scale. These data sets are difficult to visualize, to evaluate, and to compare. In order to solve this problem, an interactive mapping tool has been conceptualized that is designed to manipulate and visualize the data, lets the user set parameters for best visualization or comparison results. The system is able to load large amounts of data, visualize them as lacunarity curves, or map view as horizontal slices or in 3D point clouds coloured according to the user's choice. Lacunarity maps are presented as a series of (usually) horizontal profiles, e.g. rasters, which cells contain color-mapped values of selected lacunarity of the point cloud. As lacunarity is usually analysed in a series of successive windows sizes, the tool can show a series of rasters with sequentially animated lacunarity maps calculated for various window sizes. A very fast switching of colour schemes is possible to facilitate rapid visual feedback to better understand underlying data patterns exposed by lacunarity functions. In the comparison mode, two sites (or two areas

  8. Social interaction facilitates word learning in preverbal infants: Word-object mapping and word segmentation.

    Science.gov (United States)

    Hakuno, Yoko; Omori, Takahide; Yamamoto, Jun-Ichi; Minagawa, Yasuyo

    2017-08-01

    In natural settings, infants learn spoken language with the aid of a caregiver who explicitly provides social signals. Although previous studies have demonstrated that young infants are sensitive to these signals that facilitate language development, the impact of real-life interactions on early word segmentation and word-object mapping remains elusive. We tested whether infants aged 5-6 months and 9-10 months could segment a word from continuous speech and acquire a word-object relation in an ecologically valid setting. In Experiment 1, infants were exposed to a live tutor, while in Experiment 2, another group of infants were exposed to a televised tutor. Results indicate that both younger and older infants were capable of segmenting a word and learning a word-object association only when the stimuli were derived from a live tutor in a natural manner, suggesting that real-life interaction enhances the learning of spoken words in preverbal infants. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions

    Science.gov (United States)

    Borner, Georg H. H.; Hein, Marco Y.; Hirst, Jennifer; Edgar, James R.; Mann, Matthias; Robinson, Margaret S.

    2014-01-01

    We developed “fractionation profiling,” a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps. PMID:25165137

  10. Process maps for plasma spray: Part 1: Plasma-particle interactions

    International Nuclear Information System (INIS)

    Gilmore, Delwyn L.; Neiser, Richard A. Jr.; Wan, Yuepeng; Sampath, Sanjay

    2000-01-01

    This is the first paper of a two part series based on an integrated study carried out at Sandia National Laboratories and the State University of New York at Stony Brook. The aim of the study is to develop a more fundamental understanding of plasma-particle interactions, droplet-substrate interactions, deposit formation dynamics and microstructural development as well as final deposit properties. The purpose is to create models that can be used to link processing to performance. Process maps have been developed for air plasma spray of molybdenum. Experimental work was done to investigate the importance of such spray parameters as gun current, auxiliary gas flow, and powder carrier gas flow. In-flight particle diameters, temperatures, and velocities were measured in various areas of the spray plume. Samples were produced for analysis of microstructures and properties. An empirical model was developed, relating the input parameters to the in-flight particle characteristics. Multi-dimensional numerical simulations of the plasma gas flow field and in-flight particles under different operating conditions were also performed. In addition to the parameters which were experimentally investigated, the effect of particle injection velocity was also considered. The simulation results were found to be in good general agreement with the experimental data

  11. Final report: Mapping Interactions in Hybrid Systems with Active Scanning Probes

    Energy Technology Data Exchange (ETDEWEB)

    Berezovsky, Jesse [Case Western Reserve Univ., Cleveland, OH (United States)

    2017-09-29

    This project aimed to study and map interactions between components of hybrid nanodevices using a novel scanning probe approach. To enable this work, we initially constructed a flexible experimental apparatus allowing for simultaneous scanning probe and confocal optical microscopy measurements. This setup was first used for all-optical measurements of nanostructures, with the focus then shifting to hybrid devices in which single coherent electron spins are coupled to micron-scale ferromagnetic elements, which may prove useful for addressing single spins, enhanced sensing, or spin-wave-mediated coupling of spins for quantum information applications. A significant breakthrough was the realization that it is not necessary to fabricate a magnetic structure on a scanning probe – instead a ferromagnetic vortex core can act as an integrated, solid state, scanning probe. The core of the vortex produces a very strong, localized fringe field which can be used analogously to an MFM tip. Unlike a traditional MFM tip, however, the vortex core is scanned within an integrated device (eliminating drift), and can be moved on vastly faster timescales. This approach allows the detailed investigation of interactions between single spins and complex driven ferromagnetic dynamics.

  12. Collaborative filtering for brain-computer interaction using transfer learning and active class selection.

    Directory of Open Access Journals (Sweden)

    Dongrui Wu

    Full Text Available Brain-computer interaction (BCI and physiological computing are terms that refer to using processed neural or physiological signals to influence human interaction with computers, environment, and each other. A major challenge in developing these systems arises from the large individual differences typically seen in the neural/physiological responses. As a result, many researchers use individually-trained recognition algorithms to process this data. In order to minimize time, cost, and barriers to use, there is a need to minimize the amount of individual training data required, or equivalently, to increase the recognition accuracy without increasing the number of user-specific training samples. One promising method for achieving this is collaborative filtering, which combines training data from the individual subject with additional training data from other, similar subjects. This paper describes a successful application of a collaborative filtering approach intended for a BCI system. This approach is based on transfer learning (TL, active class selection (ACS, and a mean squared difference user-similarity heuristic. The resulting BCI system uses neural and physiological signals for automatic task difficulty recognition. TL improves the learning performance by combining a small number of user-specific training samples with a large number of auxiliary training samples from other similar subjects. ACS optimally selects the classes to generate user-specific training samples. Experimental results on 18 subjects, using both k nearest neighbors and support vector machine classifiers, demonstrate that the proposed approach can significantly reduce the number of user-specific training data samples. This collaborative filtering approach will also be generalizable to handling individual differences in many other applications that involve human neural or physiological data, such as affective computing.

  13. Collaborative filtering for brain-computer interaction using transfer learning and active class selection.

    Science.gov (United States)

    Wu, Dongrui; Lance, Brent J; Parsons, Thomas D

    2013-01-01

    Brain-computer interaction (BCI) and physiological computing are terms that refer to using processed neural or physiological signals to influence human interaction with computers, environment, and each other. A major challenge in developing these systems arises from the large individual differences typically seen in the neural/physiological responses. As a result, many researchers use individually-trained recognition algorithms to process this data. In order to minimize time, cost, and barriers to use, there is a need to minimize the amount of individual training data required, or equivalently, to increase the recognition accuracy without increasing the number of user-specific training samples. One promising method for achieving this is collaborative filtering, which combines training data from the individual subject with additional training data from other, similar subjects. This paper describes a successful application of a collaborative filtering approach intended for a BCI system. This approach is based on transfer learning (TL), active class selection (ACS), and a mean squared difference user-similarity heuristic. The resulting BCI system uses neural and physiological signals for automatic task difficulty recognition. TL improves the learning performance by combining a small number of user-specific training samples with a large number of auxiliary training samples from other similar subjects. ACS optimally selects the classes to generate user-specific training samples. Experimental results on 18 subjects, using both k nearest neighbors and support vector machine classifiers, demonstrate that the proposed approach can significantly reduce the number of user-specific training data samples. This collaborative filtering approach will also be generalizable to handling individual differences in many other applications that involve human neural or physiological data, such as affective computing.

  14. Collaborative Filtering for Brain-Computer Interaction Using Transfer Learning and Active Class Selection

    Science.gov (United States)

    Wu, Dongrui; Lance, Brent J.; Parsons, Thomas D.

    2013-01-01

    Brain-computer interaction (BCI) and physiological computing are terms that refer to using processed neural or physiological signals to influence human interaction with computers, environment, and each other. A major challenge in developing these systems arises from the large individual differences typically seen in the neural/physiological responses. As a result, many researchers use individually-trained recognition algorithms to process this data. In order to minimize time, cost, and barriers to use, there is a need to minimize the amount of individual training data required, or equivalently, to increase the recognition accuracy without increasing the number of user-specific training samples. One promising method for achieving this is collaborative filtering, which combines training data from the individual subject with additional training data from other, similar subjects. This paper describes a successful application of a collaborative filtering approach intended for a BCI system. This approach is based on transfer learning (TL), active class selection (ACS), and a mean squared difference user-similarity heuristic. The resulting BCI system uses neural and physiological signals for automatic task difficulty recognition. TL improves the learning performance by combining a small number of user-specific training samples with a large number of auxiliary training samples from other similar subjects. ACS optimally selects the classes to generate user-specific training samples. Experimental results on 18 subjects, using both nearest neighbors and support vector machine classifiers, demonstrate that the proposed approach can significantly reduce the number of user-specific training data samples. This collaborative filtering approach will also be generalizable to handling individual differences in many other applications that involve human neural or physiological data, such as affective computing. PMID:23437188

  15. Charge transfer interaction using quasiatomic minimal-basis orbitals in the effective fragment potential method

    International Nuclear Information System (INIS)

    Xu, Peng; Gordon, Mark S.

    2013-01-01

    The charge transfer (CT) interaction, the most time-consuming term in the general effective fragment potential method, is made much more computationally efficient. This is accomplished by the projection of the quasiatomic minimal-basis-set orbitals (QUAMBOs) as the atomic basis onto the self-consistent field virtual molecular orbital (MO) space to select a subspace of the full virtual space called the valence virtual space. The diagonalization of the Fock matrix in terms of QUAMBOs recovers the canonical occupied orbitals and, more importantly, gives rise to the valence virtual orbitals (VVOs). The CT energies obtained using VVOs are generally as accurate as those obtained with the full virtual space canonical MOs because the QUAMBOs span the valence part of the virtual space, which can generally be regarded as “chemically important.” The number of QUAMBOs is the same as the number of minimal-basis MOs of a molecule. Therefore, the number of VVOs is significantly smaller than the number of canonical virtual MOs, especially for large atomic basis sets. This leads to a dramatic decrease in the computational cost

  16. Molecular interaction and energy transfer between human serum albumin and bioactive component Aloe dihydrocoumarin

    Science.gov (United States)

    Zhang, Xiu-Feng; Xie, Ling; Liu, Yang; Xiang, Jun-Feng; Li, Lin; Tang, Ya-Lin

    2008-10-01

    Aloe dihydrocoumarin is an antioxidant and a candidate of immunomodulatory drug on the immune system and can balance physiological reactive oxygen species (ROS) levels which may be useful to maintain homeostasis. In order to explore the mechanism of drug action at a molecular level, the binding of Aloe dihydrocoumarin with human serum albumin (HSA) has been investigated by fluorescence, ultraviolet (UV), circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, fluorescence dynamics, and molecular dynamic docking for the first time. We observed a quenching of fluorescence of HSA in the presence of Aloe dihydrocoumarin and also analyzed the quenching results using the Stern-Volmer equation and obtained high affinity binding to HSA. A Förster type fluorescence resonance energy transfer mechanism is involved in this quenching of Trp fluorescence by Aloe dihydrocoumarin. From the CD and FT-IR results, it is apparent that the interaction of Aloe dihydrocoumarin with HSA causes a conformational change of the protein, with the loss of α-helix stability and the gain of β-sheet and β-turn content. Data obtained by fluorescence spectroscopy, fluorescence dynamics, CD, and FT-IR experiments along with the docking studies suggest that Aloe dihydrocoumarin binds to residues located in subdomain IIA of HSA.

  17. Collision dynamics of three interacting atoms: Energy transfer and dissociation in collinear motions

    International Nuclear Information System (INIS)

    Beard, L.H.; Micha, D.A.

    1980-01-01

    The general theory of collisions in three-body systems is applied to vibrational excitation and dissociation in atom--diatom collisions. A multiple collision expansion is introduced for high relative energies, concentrating on single- and double-collision contributions. The general formalism is illustrated with calculations in collinear models for the H+D 2 system. They include results for hard-core and exponentially repulsive interactions, and for harmonic oscillator and Morse diatomic potentials. Excitation probabilities are given within the single collision approximation with and without a peaking factorization. Comparison with exact results show that these assumptions are generally valid above threshold energies. For the case of collisional dissociation it is found that double collision events, describing the final channel distortion in the diatomic breakup, are essential to properly cover the energy transfer region between breakup and excitation. Results for dissociation of vibrational excited diatomics show the important role played by initial diatomic momentum distributions and more specifically, by the dynamical form factors of the theory

  18. Nanoscale fluid-structure interaction: flow resistance and energy transfer between water and carbon nanotubes.

    Science.gov (United States)

    Chen, Chao; Ma, Ming; Jin, Kai; Liu, Jefferson Zhe; Shen, Luming; Zheng, Quanshui; Xu, Zhiping

    2011-10-01

    We investigate here water flow passing a single-walled carbon nanotube (CNT), through analysis based on combined atomistic and continuum mechanics simulations. The relation between drag coefficient C(D) and Reynolds number Re is obtained for a wide range of flow speed u from 5 to 600 m/s. The results suggest that Stokes law for creep flow works well for small Reynolds numbers up to 0.1 (u ≈ 100 m/s), and indicates a linear dependence between drag force and flow velocity. Significant deviation is observed at elevated Re values, which is discussed by considering the interfacial slippage, reduction of viscosity due to friction-induced local heating, and flow-induced structural vibration. We find that interfacial slippage has a limited contribution to the reduction of the resistance, and excitations of low-frequency vibration modes in the carbon nanotube play an important role in energy transfer between water and carbon nanotubes, especially at high flow speeds where drastic enhancement of the carbon nanotube vibration is observed. The results reported here reveal nanoscale fluid-structure interacting mechanisms, and lay the ground for rational design of nanofluidics and nanoelectromechanical devices operating in a fluidic environment.

  19. {beta}-Lactam antibiotics epitope mapping with STD NMR spectroscopy: a study of drug-human serum albumin interaction

    Energy Technology Data Exchange (ETDEWEB)

    Milagre, Cintia D. F.; Cabeca, Luis F.; Almeida, Wanda P.; Marsaioli, Anita J., E-mail: cmilagre@rc.unesp.br [Institute of Chemistry, University of Campinas (UNICAMP), SP (Brazil)

    2012-03-15

    Molecular recognition events are key issues in many biological processes. STD NMR (saturation transfer difference nuclear magnetic resonance spectroscopy) is one of the techniques used to understand such biological interactions. Herein, we have investigated the interactions of four {beta}-lactam antibiotics belonging to two classes (cephalosporins and penicillins) with human serum albumin (HSA) by {sup 1}H STD NMR revealing that the interaction between the aromatic moiety and HSA is responsible for the binding efficiency. Thus, the structural differences from the five to six-membered thio ring in penicillins and cephalosporins do not seem to influence antibiotic albumin interactions. (author)

  20. Carotenoids gene markers for sweetpotato (Ipomoea batatas L. Lam): applications in genetic mapping, diversity evaluation and cross-species transference.

    Science.gov (United States)

    Arizio, C M; Costa Tártara, S M; Manifesto, M M

    2014-04-01

    Carotenoids play essential biological roles in plants, and genes involved in the carotenoid biosynthesis pathway are evolutionarily conserved. Orange sweetpotato is an important source of β-carotene, a precursor of vitamin A. In spite of this, only a few research studies have focussed on the molecular aspects of carotenoid genes regarding their specific sequence and structure. In this study, we used published carotenoid gene sequences from Ipomoea and other species for "exon-primed intron-crossing" approaches. Fifteen pairs of primers representing six carotenoid genes were designed for different introns, eleven of which amplified scorable and reproducible alleles. The sequence of PCR products showed high homology to the original ones. Moreover, the structure and sequence of the introns and exons from five carotenoid structural genes were partially defined. Intron length polymorphism and intron single nucleotide polymorphisms were detected in amplified sequences. Marker dosages and allelic segregations were analysed in a mapping population. The developed markers were evaluated in a set of Ipomoeas batatas accessions so as to analyse genetic diversity and conservation applicability. Using CG strategy combined with EPIC-PCR technique, we developed carotenoid gene markers in sweetpotato. We reported the first set of polymorphic Candidate Gene markers for I. batatas, and demonstrated transferability in seven wild Ipomoea species. We described the sequence and structure of carotenoid genes and introduced new information about genomic constitution and allele dosage.

  1. Homotypic interactions of the infectious bursal disease virus proteins VP3, pVP2, VP4, and VP5: mapping of the interacting domains

    International Nuclear Information System (INIS)

    Tacken, Mirriam G.J.; Beuken, Patricia A.J. van den; Peeters, Ben P.H.; Thomas, Adri A.M.; Rottier, Peter J.M.; Boot, Hein J.

    2003-01-01

    Infectious bursal disease virus (IBDV), a nonenveloped double-stranded RNA virus of chicken, encodes five proteins. Of these, the RNA-dependent RNA polymerase (VP1) is specified by the smaller genome segment, while the large segment directs synthesis of a nonstructural protein (VP5) and a structural protein precursor from which the capsid proteins pVP2 and VP3 as well as the viral protease VP4 are derived. Using the recently redefined processing sites of the precursor, we have reevaluated the homotypic interactions of the viral proteins using the yeast two-hybrid system. Except for VP1, which interacted weakly, all proteins appeared to self-associate strongly. Using a deletion mutagenesis approach, we subsequently mapped the interacting domains in these polypeptides, where possible confirming the observations made in the two-hybrid system by performing coimmunoprecipitation analyses of tagged protein constructs coexpressed in avian culture cells. The results revealed that pVP2 possesses multiple interaction domains, consistent with available structural information about this external capsid protein. VP3-VP3 interactions were mapped to the amino-terminal part of the polypeptide. Interestingly, this domain is distinct from two other interaction domains occurring in this internal capsid protein: while binding to VP1 has been mapped to the carboxy-terminal end of the protein, interaction with the genomic dsRNA segments has been suggested to occur just upstream thereof. No interaction sites could be assigned to the VP4 protein; any deletion applied abolished its self-association. Finally, one interaction domain was detected in the central, most hydrophobic region of VP5, supporting the idea that this virulence determinant may function as a membrane pore-forming protein in infected cells

  2. COREMAP: Graphical user interface for displaying reactor core data in an interactive hexagon map

    International Nuclear Information System (INIS)

    Muscat, F.L.; Derstine, K.L.

    1995-01-01

    COREMAP is a Graphical User Interface (GUI) designed to assist users read and check reactor core data from multidimensional neutronic simulation models in color and/or as text in an interactive 2D planar grid of hexagonal subassemblies. COREMAP is a complete GEODST/RUNDESC viewing tool which enables the user to access multi data set files (e.g. planes, moments, energy groups ,... ) and display up to two data sets simultaneously, one as color and the other as text. The user (1) controls color scale characteristics such as type (linear or logarithmic) and range limits, (2) controls the text display based upon conditional statements on data spelling, and value. (3) chooses zoom features such as core map size, number of rings and surrounding subassemblies, and (4) specifies the data selection for supplied popup subwindows which display a selection of data currently off-screen for a selected cell, as a list of data and/or as a graph. COREMAP includes a RUNDESC file editing tool which creates ''proposed'' Run-description files by point and click revisions to subassembly assignments in an existing EBRII Run-description file. COREMAP includes a fully automated printing option which creates high quality PostScript color or greyscale images of the core map independent of the monitor used, e.g. color prints can be generated with a session from a color or monochrome monitor. The automated PostScript output is an alternative to the xgrabsc based printing option. COREMAP includes a plotting option which creates graphs related to a selected cell. The user specifies the X and Y coordinates types (planes, moment, group, flux ,... ) and a parameter, P, when displaying several curves for the specified (X, Y) pair COREMAP supports hexagonal geometry reactor core configurations specified by: the GEODST file and binary Standard Interface Files and the RUNDESC ordering

  3. Interactive Mapping of Inundation Metrics Using Cloud Computing for Improved Floodplain Conservation and Management

    Science.gov (United States)

    Bulliner, E. A., IV; Lindner, G. A.; Bouska, K.; Paukert, C.; Jacobson, R. B.

    2017-12-01

    Within large-river ecosystems, floodplains serve a variety of important ecological functions. A recent survey of 80 managers of floodplain conservation lands along the Upper and Middle Mississippi and Lower Missouri Rivers in the central United States found that the most critical information needed to improve floodplain management centered on metrics for characterizing depth, extent, frequency, duration, and timing of inundation. These metrics can be delivered to managers efficiently through cloud-based interactive maps. To calculate these metrics, we interpolated an existing one-dimensional hydraulic model for the Lower Missouri River, which simulated water surface elevations at cross sections spaced (elevations to inundation depths, we subtracted a merged terrain model consisting of floodplain LIDAR and bathymetric surveys of the river channel. This approach resulted in a 29000+ day time series of inundation depths across the floodplain using grid cells with 30 m spatial resolution. Initially, we used these data on a local workstation to calculate a suite of nine spatially distributed inundation metrics for the entire model domain. These metrics are calculated on a per pixel basis and encompass a variety of temporal criteria generally relevant to flora and fauna of interest to floodplain managers, including, for example, the average number of days inundated per year within a growing season. Using a local workstation, calculating these metrics for the entire model domain requires several hours. However, for the needs of individual floodplain managers working at site scales, these metrics may be too general and inflexible. Instead of creating a priori a suite of inundation metrics able to satisfy all user needs, we present the usage of Google's cloud-based Earth Engine API to allow users to define and query their own inundation metrics from our dataset and produce maps nearly instantaneously. This approach allows users to select the time periods and inundation

  4. An interaction map of circulating metabolites, immune gene networks, and their genetic regulation.

    Science.gov (United States)

    Nath, Artika P; Ritchie, Scott C; Byars, Sean G; Fearnley, Liam G; Havulinna, Aki S; Joensuu, Anni; Kangas, Antti J; Soininen, Pasi; Wennerström, Annika; Milani, Lili; Metspalu, Andres; Männistö, Satu; Würtz, Peter; Kettunen, Johannes; Raitoharju, Emma; Kähönen, Mika; Juonala, Markus; Palotie, Aarno; Ala-Korpela, Mika; Ripatti, Samuli; Lehtimäki, Terho; Abraham, Gad; Raitakari, Olli; Salomaa, Veikko; Perola, Markus; Inouye, Michael

    2017-08-01

    Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking. Here, we integrate blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts (total N = 2168), including a subset of individuals with matched multi-omic data at 7-year follow-up. We identify topologically replicable gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity. These immune gene modules show complex patterns of association with 158 circulating metabolites, including lipoprotein subclasses, lipids, fatty acids, amino acids, small molecules, and CRP. Genome-wide scans for module expression quantitative trait loci (mQTLs) reveal five modules with mQTLs that have both cis and trans effects. The strongest mQTL is in ARHGEF3 (rs1354034) and affects a module enriched for platelet function, independent of platelet counts. Modules of mast cell/basophil and neutrophil function show temporally stable metabolite associations over 7-year follow-up, providing evidence that these modules and their constituent gene products may play central roles in metabolic inflammation. Furthermore, the strongest mQTL in ARHGEF3 also displays clear temporal stability, supporting widespread trans effects at this locus. This study provides a detailed map of natural variation at the blood immunometabolic interface and its genetic basis, and may facilitate subsequent studies to explain inter-individual variation in cardiometabolic disease.

  5. Charge transfer and rapidity gap analysis in p(π+)n interactions at 195 GeV/c

    International Nuclear Information System (INIS)

    Eisenberg, Y.; Haber, B.; Hochmann, D.; Karshon, U.; Ronat, E.E.; Shapira, A.; Yekutieli, G.

    1980-01-01

    We present charge transfer probabilities between CM hemispheres in pn and π + n interactions at 195 GeV/c. The relative probabilities for charge exchanges ΔQ > 1 as a function of rapidity gap length, r, are given. Both results are compared with those of π - p interactions at 200 GeV/c. The average of r, viz. , is given as a function of the gap number and of ΔQ for various multiplicities, and the reduced average gap lengths /ysub(max) for pn interactions are compared with data at a lower energy. (orig.)

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

    Science.gov (United States)

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

    2015-11-21

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

  7. Using Concept Maps as Instructional Materials to Foster the Understanding of the Atomic Model and Matter-Energy Interaction

    Science.gov (United States)

    Aguiar, Joana G.; Correia, Paulo R. M.

    2016-01-01

    In this paper, we explore the use of concept maps (Cmaps) as instructional materials prepared by teachers, to foster the understanding of chemistry. We choose fireworks as a macroscopic event to teach basic chemical principles related to the Bohr atomic model and matter-energy interaction. During teachers' Cmap navigation, students can experience…

  8. Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping.

    Science.gov (United States)

    Jessup, R W; Burson, B L; Burow, O; Wang, Y W; Chang, C; Li, Z; Paterson, A H; Hussey, M A

    2003-04-01

    Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.

  9. Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.

    Directory of Open Access Journals (Sweden)

    Anna Cichonska

    2017-08-01

    Full Text Available Due to relatively high costs and labor required for experimental profiling of the full target space of chemical compounds, various machine learning models have been proposed as cost-effective means to advance this process in terms of predicting the most potent compound-target interactions for subsequent verification. However, most of the model predictions lack direct experimental validation in the laboratory, making their practical benefits for drug discovery or repurposing applications largely unknown. Here, we therefore introduce and carefully test a systematic computational-experimental framework for the prediction and pre-clinical verification of drug-target interactions using a well-established kernel-based regression algorithm as the prediction model. To evaluate its performance, we first predicted unmeasured binding affinities in a large-scale kinase inhibitor profiling study, and then experimentally tested 100 compound-kinase pairs. The relatively high correlation of 0.77 (p < 0.0001 between the predicted and measured bioactivities supports the potential of the model for filling the experimental gaps in existing compound-target interaction maps. Further, we subjected the model to a more challenging task of predicting target interactions for such a new candidate drug compound that lacks prior binding profile information. As a specific case study, we used tivozanib, an investigational VEGF receptor inhibitor with currently unknown off-target profile. Among 7 kinases with high predicted affinity, we experimentally validated 4 new off-targets of tivozanib, namely the Src-family kinases FRK and FYN A, the non-receptor tyrosine kinase ABL1, and the serine/threonine kinase SLK. Our sub-sequent experimental validation protocol effectively avoids any possible information leakage between the training and validation data, and therefore enables rigorous model validation for practical applications. These results demonstrate that the kernel

  10. Mitochondrial DNA mapping of social-biological interactions in Brazilian Amazonian African-descendant populations

    Directory of Open Access Journals (Sweden)

    Bruno Maia Carvalho

    2008-01-01

    Full Text Available The formation of the Brazilian Amazonian population has historically involved three main ethnic groups, Amerindian, African and European. This has resulted in genetic investigations having been carried out using classical polymorphisms and molecular markers. To better understand the genetic variability and the micro-evolutionary processes acting in human groups in the Brazilian Amazon region we used mitochondrial DNA to investigate 159 maternally unrelated individuals from five Amazonian African-descendant communities. The mitochondrial lineage distribution indicated a contribution of 50.2% from Africans (L0, L1, L2, and L3, 46.6% from Amerindians (haplogroups A, B, C and D and a small European contribution of 1.3%. These results indicated high genetic diversity in the Amerindian and African lineage groups, suggesting that the Brazilian Amazonian African-descendant populations reflect a possible population amalgamation of Amerindian women from different Amazonian indigenous tribes and African women from different geographic regions of Africa who had been brought to Brazil as slaves. The present study partially mapped the historical biological and social interactions that had occurred during the formation and expansion of Amazonian African-descendant communities.

  11. Mapping the specific cytoprotective interaction of humanin with the pro-apoptotic protein bid.

    Science.gov (United States)

    Choi, Jungyuen; Zhai, Dayong; Zhou, Xin; Satterthwait, Arnold; Reed, John C; Marassi, Francesca M

    2007-11-01

    Humanin is a short endogenous peptide, which can provide protection from cell death through its association with various receptors, including the pro-apoptotic Bcl-2 family proteins Bid, Bim, and Bax. By using NMR chemical shift mapping experiments, we demonstrate that the interaction between Humanin-derived peptides and Bid is specific, and we localize the binding site to a region on the surface of Bid, which includes residues from the conserved helical BH3 domain of the protein. The BH3 domain mediates the association of Bid with other Bcl-2 family members and is essential for the protein's cytotoxic activity. The data suggest that Humanin exerts its cytoprotective activity by engaging the Bid BH3 domain; this would hinder the association of Bid with other Bcl-2 family proteins, thereby mitigating its toxicity. The identification of a Humanin-specific binding site on the surface of Bid reinforces its importance as a direct modulator of programmed cell death, and suggests a strategy for the design of cytoprotective peptide inhibitors of Bid.

  12. Analysis of intercomponent energy transfer in the interaction of oscillating-grid turbulence with an impermeable boundary

    Science.gov (United States)

    McCorquodale, Mark W.; Munro, R. J.

    2018-01-01

    New experimental results are presented that investigate the nature of the intercomponent energy transfer that occurs in the interaction between oscillating-grid turbulence and a solid impermeable boundary, using instantaneous velocity measurements obtained from two-dimensional particle imaging velocimetry (PIV). Estimates of the pressure-strain correlation term (Πij s) of the transport equation of the Reynolds stress tensor, which represents intercomponent energy transfer, are obtained using the PIV data from a balance of the remaining terms of the transport equation. The influence of Πij s on the flow is examined by computing the energy spectra and conditional turbulent statistics associated with events in which intercomponent energy transfer is thought to be concentrated. Data reported here are in support of viscous and "return-to-isotropy" mechanisms governing the intercomponent energy transfer previously proposed, respectively, by Perot and Moin [J. Fluid Mech. 295, 199-227 (1995)] and Walker et al. [J. Fluid Mech. 320, 19-51 (1996)]. However, the data reported also indicate the presence of a weak net intercomponent energy transfer from the boundary-normal velocity components to the boundary-tangential velocity components over a thin region outside the viscous sublayer which is not captured within existing models of intercomponent energy transfer at the boundary.

  13. The interaction between a sexually transferred steroid hormone and a female protein regulates oogenesis in the malaria mosquito Anopheles gambiae.

    Science.gov (United States)

    Baldini, Francesco; Gabrieli, Paolo; South, Adam; Valim, Clarissa; Mancini, Francesca; Catteruccia, Flaminia

    2013-10-01

    Molecular interactions between male and female factors during mating profoundly affect the reproductive behavior and physiology of female insects. In natural populations of the malaria mosquito Anopheles gambiae, blood-fed females direct nutritional resources towards oogenesis only when inseminated. Here we show that the mating-dependent pathway of egg development in these mosquitoes is regulated by the interaction between the steroid hormone 20-hydroxy-ecdysone (20E) transferred by males during copulation and a female Mating-Induced Stimulator of Oogenesis (MISO) protein. RNAi silencing of MISO abolishes the increase in oogenesis caused by mating in blood-fed females, causes a delay in oocyte development, and impairs the function of male-transferred 20E. Co-immunoprecipitation experiments show that MISO and 20E interact in the female reproductive tract. Moreover MISO expression after mating is induced by 20E via the Ecdysone Receptor, demonstrating a close cooperation between the two factors. Male-transferred 20E therefore acts as a mating signal that females translate into an increased investment in egg development via a MISO-dependent pathway. The identification of this male-female reproductive interaction offers novel opportunities for the control of mosquito populations that transmit malaria.

  14. Changes in balance coordination and transfer to an unlearned balance task after slackline training: a self-organizing map analysis.

    Science.gov (United States)

    Serrien, Ben; Hohenauer, Erich; Clijsen, Ron; Taube, Wolfgang; Baeyens, Jean-Pierre; Küng, Ursula

    2017-11-01

    How humans maintain balance and change postural control due to age, injury, immobility or training is one of the basic questions in motor control. One of the problems in understanding postural control is the large set of degrees of freedom in the human motor system. Therefore, a self-organizing map (SOM), a type of artificial neural network, was used in the present study to extract and visualize information about high-dimensional balance strategies before and after a 6-week slackline training intervention. Thirteen subjects performed a flamingo and slackline balance task before and after the training while full body kinematics were measured. Range of motion, velocity and frequency of the center of mass and joint angles from the pelvis, trunk and lower leg (45 variables) were calculated and subsequently analyzed with an SOM. Subjects increased their standing time significantly on the flamingo (average +2.93 s, Cohen's d = 1.04) and slackline (+9.55 s, d = 3.28) tasks, but the effect size was more than three times larger in the slackline. The SOM analysis, followed by a k-means clustering and marginal homogeneity test, showed that the balance coordination pattern was significantly different between pre- and post-test for the slackline task only (χ 2  = 82.247; p slackline could be characterized by an increase in range of motion and a decrease in velocity and frequency in nearly all degrees of freedom simultaneously. The observation of low transfer of coordination strategies to the flamingo task adds further evidence for the task-specificity principle of balance training, meaning that slackline training alone will be insufficient to increase postural control in other challenging situations.

  15. NeuroMap: A spline-based interactive open-source software for spatiotemporal mapping of 2D and 3D MEA data

    Directory of Open Access Journals (Sweden)

    Oussama eAbdoun

    2011-01-01

    Full Text Available A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA technology. Indeed, high-density MEAs provide large-scale covering (several mm² of whole neural structures combined with microscopic resolution (about 50µm of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid deformation based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License (GPL and available at http://sites.google.com/site/neuromapsoftware.

  16. Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model

    Science.gov (United States)

    Xu, Yang; Song, Kai; Shi, Qiang

    2018-03-01

    The hydride transfer reaction catalyzed by dihydrofolate reductase is studied using a recently developed mixed quantum-classical method to investigate the nuclear quantum effects on the reaction. Molecular dynamics simulation is first performed based on a two-state empirical valence bond potential to map the atomistic model to an effective double-well potential coupled to a harmonic bath. In the mixed quantum-classical simulation, the hydride degree of freedom is quantized, and the effective harmonic oscillator modes are treated classically. It is shown that the hydride transfer reaction rate using the mapped effective double-well/harmonic-bath model is dominated by the contribution from the ground vibrational state. Further comparison with the adiabatic reaction rate constant based on the Kramers theory confirms that the reaction is primarily vibrationally adiabatic, which agrees well with the high transmission coefficients found in previous theoretical studies. The calculated kinetic isotope effect is also consistent with the experimental and recent theoretical results.

  17. MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars

    Science.gov (United States)

    Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.

    2006-12-01

    Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its

  18. An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.

    Science.gov (United States)

    Paterson, Trevor; Law, Andy

    2009-08-14

    exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

  19. Fluorescence resonance energy transfer: A promising tool for investigation of the interaction between 1-anthracene sulphonate and serum albumins

    International Nuclear Information System (INIS)

    Banerjee, Paltu; Ghosh, Saptaparni; Sarkar, Arindam; Bhattacharya, Subhash Chandra

    2011-01-01

    This present investigation has revealed that steady state as well as time-resolved fluorescence techniques can serve as highly sensitive monitors for exploring the interaction of fluorescent probe 1-anthracene sulphonate (1-AS) with model transport proteins, bovine serum albumin (BSA) and human serum albumin (HSA).We have focused on fluorescence resonance energy transfer (FRET) between excited tryptophan in transport proteins to 1-AS, for the study of relaxation dynamics of biological molecules.

  20. ENDOR investigations of the Ce.sup.3+./sup. ions in YAG: Transferred hyperfine interaction with nearest aluminum ions

    Czech Academy of Sciences Publication Activity Database

    Azamat, Dmitry; Badalyan, A. G.; Feng, D.H.; Lančok, Ján; Jastrabík, Lubomír; Dejneka, Alexandr; Baranov, P. G.; Yakovlev, D.R.; Bayer, M.

    2017-01-01

    Roč. 122, č. 24 (2017), s. 1-3, č. článku 243903. ISSN 0021-8979 R&D Projects: GA MŠk LO1409; GA ČR GA16-22092S Institutional support: RVO:68378271 Keywords : ENDOR * Ce 3+ ions in YAG * transferred hyperfine interactions Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 2.068, year: 2016

  1. Raman spectroscopy based toolkit for mapping bacterial social interactions relevant to human and plant health

    Science.gov (United States)

    Couvillion, Sheha Polisetti

    Bacteria interact and co-exist with other microbes and with higher organisms like plants and humans, playing a major role in their health and well being. These ubiquitous single celled organisms are so successful, because they can form organized communities, called biofilms, that protect them from environmental stressors and enable communication and cooperation among members of the community. The work described in this thesis develops a toolkit of analytical techniques centered around Raman microspectroscopy and imaging representing a powerful approach to non-invasively investigate bacterial communities, yielding molecular information at the sub-micrometer length scale. Bacterial cellular components of non-pigmented and pigmented rhizosphere strains are characterized, and regiospecific SERS is used for cases where resonantly enhanced background signals obscure the spectra. Silver nanoparticle colloids were synthesized in situ, in the presence of the cells to form a proximal coating and principal component analysis (PCA) revealed features attributed to flavins. SERS enabled in situ acquisition of Raman spectra and chemical images in highly autofluorescent P.aeruginosa biofilms. In combination with PCA, this allowed for non-invasive spatial mapping of bacterial communities and revealed differences between strains and nutrients in the secretion of virulence factor pyocyanin. The rich potential of using Raman microspectroscopy to study plant-microbe interactions is demonstrated. Effect of exposure to oxidative stress, on both the wild type Pantoea sp. YR343 and carotenoid mutant Delta crtB, was assessed by following the intensity of the 1520 cm -1 and 1126 cm-1 Raman bands, respectively, after treatment with various concentrations of H2O2. Significant changes were observed in these marker bands even at concentrations (1 mM) below the point at which the traditional plate-based viability assay shows an effect (5-10 mM), thus establishing the value of Raman

  2. Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci

    NARCIS (Netherlands)

    Jansen, R.C.; Ooijen, J.W. van; Stam, P.; Lister, C.; Dean, C.

    1995-01-01

    The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment

  3. Mapping the Conformational Dynamics of E-selectin upon Interaction with its Ligands

    KAUST Repository

    Aleisa, Fajr A

    2013-05-15

    Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. The adhesion of cells (expressing ligands) to the endothelium (expressing the selectin i.e.,E-selectin) occurs through spatio-temporally regulated interactions that are mediated by multiple intra- and inter-cellular components. The mechanism of cell adhesion is investigated primarily using ensemble-based experiments, which provides indirect information about how individual molecules work in such a complex system. Recent developments in single-molecule (SM) fluorescence detection allow for the visualization of individual molecules with a good spatio-temporal resolution nanometer spatial resolution and millisecond time resolution). Furthermore, advanced SM fluorescence techniques such as Förster Resonance Energy Transfer (FRET) and super-resolution microscopy provide unique opportunities to obtain information about nanometer-scale conformational dynamics of proteins as well as nano-scale architectures of biological samples. Therefore, the state-of-the-art SM techniques are powerful tools for investigating complex biological system such as the mechanism of cell adhesion. In this project, several constructs of fluorescently labeled E-selectin will be used to study the conformational dynamics of E-selectin binding to its ligand(s) using SM-FRET and combination of SM-FRET and force microscopy. These studies will be beneficial to fully understand the mechanistic details of cell adhesion and migration of cells using the established model system of hematopoietic stem cells (HSCs) adhesion to the selectin expressing endothelial cells (such as the E-selectin expressing endothelial cells in the bone marrow).

  4. Birthplace in Australia: Processes and interactions during the intrapartum transfer of women from planned homebirth to hospital.

    Science.gov (United States)

    Fox, Deborah; Sheehan, Athena; Homer, Caroline

    2018-02-01

    the aim of the study was to explore the views and experiences of women, midwives and obstetricians on the intrapartum transfer of women from planned homebirth to hospital in Australia. a Constructivist Grounded Theory approach was taken, to conceptualise the social interactions and processes grounded in the data. urban and regional areas in four states of south-eastern Australia. semi-structured qualitative interviews were conducted with 36 women, midwives and obstetricians who had experienced an intrapartum homebirth transfer within three years prior to the interview. Interviews were audio recorded and transcribed verbatim. women who were transferred to hospital from a planned homebirth made physical and psychological journeys out of their comfort zone, as they faced the uncertainty of changing expectations for their birth. The trusting relationship between a woman and her homebirth midwife was crucial to women's sense of safety and well-being in hospital. Midwives and obstetricians, when congregating in the hospital birthing rooms of transferred women, also felt out of their comfort zones. This was due to the challenges of converging with others who possessed conflicting paradigms of safety and risk in birth that were at odds with their own, and adapting to different routines, roles and responsibilities. These differences were derived from diverse professional, social and personal influences and often manifested in stereotyping behaviours and 'us and them' dynamics. When midwife-woman partnerships were respected as an inclusive part of women's care, collaboration ensued, conflict was ameliorated, and smooth transfers could be celebrated as successes of the maternity care system. supporting woman centred care in homebirth transfers means acknowledging the social challenges of collaborating in the unique context of a transferred woman's hospital birthing room. Understanding the power of the midwife-woman partnership, and its value to the health and well-being of

  5. Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Sarbottam ePiya

    2014-12-01

    Full Text Available The phytohormone auxin regulates nearly all aspects of plant growth and development. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs. Experimental evidence suggests that heterodimerization between Aux/IAA and ARF proteins are related to their unique biological functions. The objective of this study was to generate the Aux/IAA-ARF protein-protein interaction map using full length sequences and locate the interacting protein pairs to specific gene co-expression networks in order to define tissue-specific responses of the Aux/IAA-ARF interactome. Pairwise interactions between 19 ARFs and 29 Aux/IAAs resulted in the identification of 213 specific interactions of which 79 interactions were previously unknown. The incorporation of co-expression profiles with protein-protein interaction data revealed a strong correlation of gene co-expression for 70% of the ARF-Aux/IAA interacting pairs in at least one tissue/organ, indicative of the biological significance of these interactions. Importantly, ARF4-8 and 19, which were found to interact with almost all Aux-Aux/IAA showed broad co-expression relationships with Aux/IAA genes, thus, formed the central hubs of the co-expression network. Our analyses provide new insights into the biological significance of ARF-Aux/IAA associations in the morphogenesis and development of various plant tissues and organs.

  6. Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis.

    Science.gov (United States)

    Piya, Sarbottam; Shrestha, Sandesh K; Binder, Brad; Stewart, C Neal; Hewezi, Tarek

    2014-01-01

    The phytohormone auxin regulates nearly all aspects of plant growth and development. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA) proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs). Experimental evidence suggests that heterodimerization between Aux/IAA and ARF proteins are related to their unique biological functions. The objective of this study was to generate the Aux/IAA-ARF protein-protein interaction map using full length sequences and locate the interacting protein pairs to specific gene co-expression networks in order to define tissue-specific responses of the Aux/IAA-ARF interactome. Pairwise interactions between 19 ARFs and 29 Aux/IAAs resulted in the identification of 213 specific interactions of which 79 interactions were previously unknown. The incorporation of co-expression profiles with protein-protein interaction data revealed a strong correlation of gene co-expression for 70% of the ARF-Aux/IAA interacting pairs in at least one tissue/organ, indicative of the biological significance of these interactions. Importantly, ARF4-8 and 19, which were found to interact with almost all Aux-Aux/IAA showed broad co-expression relationships with Aux/IAA genes, thus, formed the central hubs of the co-expression network. Our analyses provide new insights into the biological significance of ARF-Aux/IAA associations in the morphogenesis and development of various plant tissues and organs.

  7. Interactive Mapping of the Planets: An Online Activity Using the Google Earth Platform

    Science.gov (United States)

    Osinski, G. R.; Gilbert, A.; Harrison, T. N.; Mader, M. M.; Shankar, B.; Tornabene, L. L.

    2013-12-01

    With funding from the Natural Sciences and Engineering Research Council of Canada's PromoScience program and support from the Department of Earth Sciences at The University of Western Ontario, the Centre for Planetary Science and Exploration (CPSX) has developed a new web-based initiative called Interactive Mapping of the Planets (IMAPS). Additional components include in person school visits to deliver inquiry-based workshops, week-long summer camps, and pre-prepared impact rock lending kits, all framed around the IMAPS activity. IMAPS will is now in beta testing mode and will be demonstrated in this session. The general objective of the online activity is for participants to plan and design a rover mission to Mars based on a given mission goal - e.g., to find evidence for past water flow. The activity begins with participants receiving image-analysis training to learn about the different landforms on Mars and which ones are potentially caused by water flow. They then need to pass a short test to show they can consistently identify Martian landforms. From there, the participants choose a landing site and plan a traverse - utilizing the free Google Earth plug-in - and taking into account factors such as hazards and their sites of interest. A mission control blog will provide updates on the status of their mission and a 'choose your rover' option provides the opportunity to unlock more advanced rovers by collaborating with other scientists and rating their missions. Indeed, evaluation of missions will be done using a crowd-sourcing method. In addition to being fully accessible online, CPSX will also target primary- and secondary-school grades in which astronomy and space science is taught. Teachers in K-12 classrooms will be able to sign-up for the activity ahead of time in order to receive a workshop package, which will guide them on how to use the IMAPS online activity with their class. Teachers will be able to set up groups for their classroom so that they can

  8. Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P

    2002-01-01

    The calcium-sensing receptor (CaR) belongs to family C of the G-protein coupled receptor superfamily. The receptor is believed to exist as a homodimer due to covalent and non-covalent interactions between the two amino terminal domains (ATDs). It is well established that agonist binding to family C...... receptors takes place at the ATD and that this causes the ATD dimer to twist. However, very little is known about the translation of the ATD dimer twist into G-protein coupling to the 7 transmembrane moieties (7TMs) of these receptor dimers. In this study we have attempted to delineate the agonist......-induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

  9. Local shell-to-shell energy transfer via nonlocal interactions in fluid ...

    Indian Academy of Sciences (India)

    In this paper we analytically compute the strength of nonlinear interactions in a triad, and the energy exchanges between wave-number shells in incompressible fluid turbulence. The computation has been done using first-order perturbative field theory. In three dimensions, magnitude of triad interactions is large for nonlocal ...

  10. Plant–Agrobacterium interaction mediated by ethylene and super-Agrobacterium conferring efficient gene transfer

    OpenAIRE

    Nonaka, Satoko; Ezura, Hiroshi

    2014-01-01

    Agrobacterium tumefaciens has a unique ability to transfer genes into plant genomes. This ability has been utilized for plant genetic engineering. However, the efficiency is not sufficient for all plant species. Several studies have shown that ethylene decreased the Agrobacterium-mediated transformation frequency. Thus, A. tumefaciens with an ability to suppress ethylene evolution would increase the efficiency of Agrobacterium-mediated transformation. Some studies showed that plant growth-pro...

  11. Should the Department of Defense Transfer the Defense Logistics Agency's Map Functions to the Defense Working Capital Fund

    National Research Council Canada - National Science Library

    Zimmerman, Donald

    2000-01-01

    .... The functions cost about $25 million annually and are funded by operations and maintenance (O&M) dollars. This study analyzed if the functions should be transferred to the Defense Working Capital Fund...

  12. Radioiodinated, photoactivatable phosphatidylcholine and phosphatidylserine: transfer properties and differential photoreactive interaction with human erythrocyte membrane proteins

    International Nuclear Information System (INIS)

    Schroit, A.J.; Madsen, J.; Ruoho, A.E.

    1987-01-01

    An isotopically labeled cross-linking reagent, succinimido 3-(3-[ 125 I]iodo-4-azidophenyl)propionate, has been synthesized and coupled to 1-acyl-2-(aminocaproyl)phosphatidylcholine according to previously described procedures. 125 I- and N 3 -labeled phosphatidylserine ( 125 I-N 3 -PS) was produced from the phosphatidylcholine (PC) analog by phospholipase D catalyzed base exchange in the presence of L-serine. These phospholipid analogues are photoactivatable, are labeled with 125 I at high specific activity, completely incorporate into synthetic vesicles, and spontaneously transfer between membranes. When an excess of acceptor vesicles or red blood cells (RBC) was mixed with a population of donor vesicles containing the 125 I-N 3 -phospholipids, approximately 40% of the analogues transferred to the acceptor population. After transfer in the dark to RBC, all of the 125 I-N 3 -PC incorporated into the cells could be removed by washing with serum, whereas the 125 I-N 3 -PS could not. After photolabeling of intact RBC, ∼50% of the PC and 20% of the PS cross-linked to membrane proteins as determined by their insolubility in CHCl 3 /MeOH. Analysis of probe distribution by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that 125 I-N 3 -PS preferentially labeled a M/sub r/ 30,000 peptide which contained ∼30% of the protein-bound label

  13. Test of nucleon-nucleon interaction by p vector-d vector polarization transfer in the three-nucleon system

    International Nuclear Information System (INIS)

    Sperisen, F.; Gruebler, W.; Koenig, V.; Schmelzbach, P.A.; Elsener, K.; Jenny, B.; Schweizer, C.; Ulbricht, J.; Doleschall, P.

    1982-01-01

    Measurements of three vector-to-vector and seven vector-to-tensor polarization transfer coefficients of the 2 H(p vector, d vector) 1 H elastic scattering at Esub(p) = 10 MeV are reported in the angular range between THETAsub(cm) = 92 0 and 180 0 . These second-order observables are compared with Faddeev calculations. It is shown that the vector-to-tensor components depend largely on the details of the N-N P-wave interaction. (orig.)

  14. Playing Cards on Asthma Management: A New Interactive Method for Knowledge Transfer to Primary Care Physicians

    Directory of Open Access Journals (Sweden)

    Louis-Philippe Boulet

    2007-01-01

    Full Text Available OBJECTIVES: To describe an interactive playing card workshop in the communication of asthma guidelines recommendations, and to assess the initial evaluation of this educational tool by family physicians.

  15. Interactive overlay maps for US Patent (USPTO) data based on International Patent Classifications (IPC)

    NARCIS (Netherlands)

    Leydesdorff, L.; Kushnir, D.; Rafols, I.

    2014-01-01

    We report on the development of an interface to the US Patent and Trademark Office (USPTO) that allows for the mapping of patent portfolios as overlays to basemaps constructed from citation relations among all patents contained in this database during the period 1976-2011. Both the interface and the

  16. Interactive remote data processing using Pixelize Wavelet Filtration (PWF-method) and PeriodMap analysis

    Science.gov (United States)

    Sych, Robert; Nakariakov, Valery; Anfinogentov, Sergey

    Wavelet analysis is suitable for investigating waves and oscillating in solar atmosphere, which are limited in both time and frequency. We have developed an algorithms to detect this waves by use the Pixelize Wavelet Filtration (PWF-method). This method allows to obtain information about the presence of propagating and non-propagating waves in the data observation (cube images), and localize them precisely in time as well in space. We tested the algorithm and found that the results of coronal waves detection are consistent with those obtained by visual inspection. For fast exploration of the data cube, in addition, we applied early-developed Period- Map analysis. This method based on the Fast Fourier Transform and allows on initial stage quickly to look for "hot" regions with the peak harmonic oscillations and determine spatial distribution at the significant harmonics. We propose the detection procedure of coronal waves separate on two parts: at the first part, we apply the PeriodMap analysis (fast preparation) and than, at the second part, use information about spatial distribution of oscillation sources to apply the PWF-method (slow preparation). There are two possible algorithms working with the data: in automatic and hands-on operation mode. Firstly we use multiply PWF analysis as a preparation narrowband maps at frequency subbands multiply two and/or harmonic PWF analysis for separate harmonics in a spectrum. Secondly we manually select necessary spectral subband and temporal interval and than construct narrowband maps. For practical implementation of the proposed methods, we have developed the remote data processing system at Institute of Solar-Terrestrial Physics, Irkutsk. The system based on the data processing server - http://pwf.iszf.irk.ru. The main aim of this resource is calculation in remote access through the local and/or global network (Internet) narrowband maps of wave's sources both in whole spectral band and at significant harmonics. In addition

  17. Landslide susceptibility mapping using decision-tree based CHi-squared automatic interaction detection (CHAID) and Logistic regression (LR) integration

    International Nuclear Information System (INIS)

    Althuwaynee, Omar F; Pradhan, Biswajeet; Ahmad, Noordin

    2014-01-01

    This article uses methodology based on chi-squared automatic interaction detection (CHAID), as a multivariate method that has an automatic classification capacity to analyse large numbers of landslide conditioning factors. This new algorithm was developed to overcome the subjectivity of the manual categorization of scale data of landslide conditioning factors, and to predict rainfall-induced susceptibility map in Kuala Lumpur city and surrounding areas using geographic information system (GIS). The main objective of this article is to use CHi-squared automatic interaction detection (CHAID) method to perform the best classification fit for each conditioning factor, then, combining it with logistic regression (LR). LR model was used to find the corresponding coefficients of best fitting function that assess the optimal terminal nodes. A cluster pattern of landslide locations was extracted in previous study using nearest neighbor index (NNI), which were then used to identify the clustered landslide locations range. Clustered locations were used as model training data with 14 landslide conditioning factors such as; topographic derived parameters, lithology, NDVI, land use and land cover maps. Pearson chi-squared value was used to find the best classification fit between the dependent variable and conditioning factors. Finally the relationship between conditioning factors were assessed and the landslide susceptibility map (LSM) was produced. An area under the curve (AUC) was used to test the model reliability and prediction capability with the training and validation landslide locations respectively. This study proved the efficiency and reliability of decision tree (DT) model in landslide susceptibility mapping. Also it provided a valuable scientific basis for spatial decision making in planning and urban management studies

  18. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I

    Science.gov (United States)

    Mukherjee, Abhijit; Chaudhuri, Tandrima; Moulik, Satya Priya; Banerjee, Manas

    2016-01-01

    Cetyl trimethyl ammonium bromide (CTAB) binds calf thymus (ct-) DNA like anionic biopolymers electrostatically and established equilibrium both in the ground as well as in excited state in aqueous medium at pH 7. Anionic sodium dodecyl sulfate (SDS) does not show even hydrophobic interaction with ct-DNA at low concentration. On contrary, SDS can establish well defined equilibrium with DNA bound CTAB in ground state where the same CTAB-DNA isosbestic point reappears. First report of internal charge transfer (ICT) based binding of CTAB with ct-DNA as well as ICT based interaction of anionic SDS with DNA bound CTAB that shows dynamic quenching contribution also. The reappearance of anodic peak and slight increase in cathodic peak current with increasing concentration (at lower range) of anionic SDS, possibly reflect the release of CTAB from DNA bound CTAB by SDS.

  19. Magnetic field effect corroborated with docking study to explore photoinduced electron transfer in drug-protein interaction.

    Science.gov (United States)

    Chakraborty, Brotati; Roy, Atanu Singha; Dasgupta, Swagata; Basu, Samita

    2010-12-30

    Conventional spectroscopic tools such as absorption, fluorescence, and circular dichroism spectroscopy used in the study of photoinduced drug-protein interactions can yield useful information about ground-state and excited-state phenomena. However, photoinduced electron transfer (PET) may be a possible phenomenon in the drug-protein interaction, which may go unnoticed if only conventional spectroscopic observations are taken into account. Laser flash photolysis coupled with an external magnetic field can be utilized to confirm the occurrence of PET and authenticate the spin states of the radicals/radical ions formed. In the study of interaction of the model protein human serum albumin (HSA) with acridine derivatives, acridine yellow (AY) and proflavin (PF(+)), conventional spectroscopic tools along with docking study have been used to decipher the binding mechanism, and laser flash photolysis technique with an associated magnetic field (MF) has been used to explore PET. The results of fluorescence study indicate that fluorescence resonance energy transfer takes place from the protein to the acridine-based drugs. Docking study unveils the crucial role of Ser 232 residue of HSA in explaining the differential behavior of the two drugs towards the model protein. Laser flash photolysis experiments help to identify the radicals/radical ions formed in the due course of PET (PF(•), AY(•-), TrpH(•+), Trp(•)), and the application of an external MF has been used to characterize their initial spin-state. Owing to its distance dependence, MF effect gives an idea about the proximity of the radicals/radical ions during interaction in the system and also helps to elucidate the reaction mechanisms. A prominent MF effect is observed in homogeneous buffer medium owing to the pseudoconfinement of the radicals/radical ions provided by the complex structure of the protein.

  20. Immersive participation: Smartphone-Apps and Virtual Reality - tools for knowledge transfer, citizen science and interactive collaboration

    Science.gov (United States)

    Dotterweich, Markus

    2017-04-01

    In the last few years, the use of smartphone-apps has become a daily routine in our life. However, only a few approaches have been undertaken to use apps for transferring scientific knowledge to the public audience. The development of learning apps or serious games requires large efforts and several levels of simplification which is different to traditional text books or learning webpages. Current approaches often lack a connection to the real life and/or innovative gamification concepts. Another almost untapped potential is the use of Virtual Reality, a fast growing technology which replicates a virtual environment in order to simulate physical experiences in artificial or real worlds. Hence, smartphone-apps and VR provides new opportunities for capacity building, knowledge transfer, citizen science or interactive engagement in the realm of environmental sciences. This presentation will show some examples and discuss the advantages of these immersive approaches to improve the knowledge transfer between scientists and citizens and to stimulate actions in the real world.

  1. University of California San Francisco (UCSF-1): Chemical-Genetic Interaction Mapping Strategy | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at University of California San Francisco (UCSF-1) developed a chemical-genetic interaction mapping strategy to uncover the impact of cancer gene expression on responses to a panel of emerging therapeutics. To study the impact of aberrant gene activity in isolation, they developed an isogenic model of triple-negative breast cancer (TNBC) using the hormone receptor negative MCF10A non-tumorigenic cell line derived from healthy breast tissue which is diploid and largely devoid of somatic alterations.

  2. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.

    Science.gov (United States)

    Wei, Pengcheng; Song, Guangji; Shi, Mengyang; Zhou, Yafei; Liu, Yang; Lei, Jun; Chen, Peng; Yin, Lei

    2018-02-01

    Colistin is considered a last-resort antibiotic against most gram-negative bacteria. Recent discoveries of a plasmid-mediated, transferable mobilized colistin-resistance gene ( mcr-1) on all continents have heralded the imminent emergence of pan-drug-resistant superbacteria. The inner-membrane protein MCR-1 can catalyze the transfer of phosphoethanolamine (PEA) to lipid A, resulting in colistin resistance. However, little is known about the mechanism, and few drugs exist to address this issue. We present crystal structures revealing the MCR-1 catalytic domain (cMCR-1) as a monozinc metalloprotein with ethanolamine (ETA) and d-glucose, respectively, thus highlighting 2 possible substrate-binding pockets in the MCR-1-catalyzed PEA transfer reaction. Mutation of the residues involved in ETA and d-glucose binding impairs colistin resistance in recombinant Escherichia coli containing full-length MCR-1. Partial analogs of the substrate are used for cocrystallization with cMCR-1, providing valuable information about the family of PEA transferases. One of the analogs, ETA, causes clear inhibition of polymyxin B resistance, highlighting its potential for drug development. These data demonstrate the crucial role of the PEA- and lipid A-binding pockets and provide novel insights into the structure-based mechanisms, important drug-target hot spots, and a drug template for further drug development to combat the urgent, rising threat of MCR-1-mediated antibiotic resistance.-Wei, P., Song, G., Shi, M., Zhou, Y., Liu, Y., Lei, J., Chen, P., Yin, L. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.

  3. Water-polysaccharide interactions in the primary cell wall of Arabidopsis thaliana from polarization transfer solid-state NMR.

    Science.gov (United States)

    White, Paul B; Wang, Tuo; Park, Yong Bum; Cosgrove, Daniel J; Hong, Mei

    2014-07-23

    Polysaccharide-rich plant cell walls are hydrated under functional conditions, but the molecular interactions between water and polysaccharides in the wall have not been investigated. In this work, we employ polarization transfer solid-state NMR techniques to study the hydration of primary-wall polysaccharides of the model plant, Arabidopsis thaliana. By transferring water (1)H polarization to polysaccharides through distance- and mobility-dependent (1)H-(1)H dipolar couplings and detecting it through polysaccharide (13)C signals, we obtain information about water proximity to cellulose, hemicellulose, and pectins as well as water mobility. Both intact and partially extracted cell wall samples are studied. Our results show that water-pectin polarization transfer is much faster than water-cellulose polarization transfer in all samples, but the extent of extraction has a profound impact on the water-polysaccharide spin diffusion. Removal of calcium ions and the consequent extraction of homogalacturonan (HG) significantly slowed down spin diffusion, while further extraction of matrix polysaccharides restored the spin diffusion rate. These trends are observed in cell walls with similar water content, thus they reflect inherent differences in the mobility and spatial distribution of water. Combined with quantitative analysis of the polysaccharide contents, our results indicate that calcium ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while calcium removal disrupts the gel and gives rise to highly dynamic water, which slows down spin diffusion. The recovery of spin diffusion rates after more extensive extraction is attributed to increased water-exposed surface areas of the polysaccharides. Water-pectin spin diffusion precedes water-cellulose spin diffusion, lending support to the single-network model of plant primary walls in which a substantial fraction of the cellulose surface is surrounded by pectins.

  4. Building Daily 30-meter Spatial Resolution Maps of Surface Water Bodies from MODIS Data Using a Novel Technique for Transferring Information Across Space and Time

    Science.gov (United States)

    Khandelwal, A.; Karpatne, A.; Kumar, V.

    2017-12-01

    In this paper, we present novel methods for producing surface water maps at 30 meter spatial resolution at a daily temporal resolution. These new methods will make use of the MODIS spectral data from Terra (available daily since 2000) to produce daily maps at 250 meter and 500 meter resolution, and then refine them using the relative elevation ordering of pixels at 30 meter resolution. The key component of these methods is the use of elevation structure (relative elevation ordering) of a water body. Elevation structure is not explicitly available at desired resolution for most water bodies in the world and hence it will be estimated using our previous work that uses the history of imperfect labels. In this paper, we will present a new technique that uses elevation structure (unlike existing pixel based methods) to enforce temporal consistency in surface water extents (lake area on nearby dates is likely to be very similar). This will greatly improve the quality of the MODIS scale land/water labels since daily MODIS data can have a large amount of missing (or poor quality) data due to clouds and other factors. The quality of these maps will be further improved using elevation based resolution refinement approach that will make use of elevation structure estimated at Landsat scale. With the assumption that elevation structure does not change over time, it provides a very effective way to transfer information between datasets even when they are not observed concurrently. In this work, we will derive elevation structure at Landsat scale from monthly water extent maps spanning 1984-2015, publicly available through a joint effort of Google Earth Engine and the European Commission's Joint Research Centre (JRC). This elevation structure will then be used to refine spatial resolution of Modis scale maps from 2000 onwards. We will present the analysis of these methods on a large and diverse set of water bodies across the world.

  5. Mapping Soluble Guanylyl Cyclase and Protein Disulfide Isomerase Regions of Interaction.

    Directory of Open Access Journals (Sweden)

    Erin J Heckler

    Full Text Available Soluble guanylyl cyclase (sGC is a heterodimeric nitric oxide (NO receptor that produces cyclic GMP. This signaling mechanism is a key component in the cardiovascular system. NO binds to heme in the β subunit and stimulates the catalytic conversion of GTP to cGMP several hundred fold. Several endogenous factors have been identified that modulate sGC function in vitro and in vivo. In previous work, we determined that protein disulfide isomerase (PDI interacts with sGC in a redox-dependent manner in vitro and that PDI inhibited NO-stimulated activity in cells. To our knowledge, this was the first report of a physical interaction between sGC and a thiol-redox protein. To characterize this interaction between sGC and PDI, we first identified peptide linkages between sGC and PDI, using a lysine cross-linking reagent and recently developed mass spectrometry analysis. Together with Flag-immunoprecipitation using sGC domain deletions, wild-type (WT and mutated PDI, regions of sGC involved in this interaction were identified. The observed data were further explored with computational modeling to gain insight into the interaction mechanism between sGC and oxidized PDI. Our results indicate that PDI interacts preferentially with the catalytic domain of sGC, thus providing a mechanism for PDI inhibition of sGC. A model in which PDI interacts with either the α or the β catalytic domain is proposed.

  6. An autoradiographic map of (3H)diprenorphine binding in rat brain: effects of social interaction

    International Nuclear Information System (INIS)

    Panksepp, J.; Bishop, P.

    1981-01-01

    (3H)Diprenorphine binding was analyzed autoradiographically in the brains of 33 day old rat pups. A photographic atlas of diprenorphine binding in the coronal plane is provided to highlight the dispersion of opioid receptor systems through the brain. To determine whether brain opioid release may be induced by social interactions, half the animals were sacrificed following a 30 min period of social interaction while the other half were sacrificed following 30 min of social isolation. Opioid binding was higher in isolate-tested animals than socially-tested ones, suggesting that social interaction may promote endogenous brain opioid release

  7. Complete Relaxation and Conformational Exchange Matrix (CORCEMA) Analysis of NOESY Spectra of Interacting Systems; Two-Dimensional Transferred NOESY

    Science.gov (United States)

    Moseley, H. N. B.; Curto, E. V.; Krishna, N. R.

    1995-09-01

    A very general procedure entitled complete relaxation and conformational exchange matrix (CORCEMA) analysis has been developed to analyze the 2D-NOESY spectra of interacting systems undergoing multistate conformational exchange. This is an extension of earlier work from this laboratory on the methodological treatment of multistate conformational exchange [Krishna et al., Biopolymers19, 2003 (1980)] and the theory of transferred NOESY for finite exchange off-rates [Lee and Krishna, J. Magn. Reson.98, 36 (1992)]. The current theory is based on generalized rate matrices for relaxation and conformational exchange, The CORCEMA algorithm explicitly incorporates intermolecular dipolar cross relaxation between the molecules when they are complexed. It permits an analysis of NOESY intensities for the intra- as well as intermolecular contacts between the interacting molecules under a variety of binding conditions, Its application is illustrated on two examples of transferred NOESY simulations: (1) a two-state system involving a ligand and an enzyme forming a ligand-enzyme complex, and (2) a three-state system in which the ligand-enzyme complex can undergo a conformational transition from an "open state" to a "closed state," and can include conformational changes in both the complexed ligand and the complexed enzyme, such as hinge-bending motions, Simplifying expressions for generalized matrix analyses are derived for three limiting cases of the three-state system, This three-state example is illustrated using a hypothetical model of the hinge-bending motion in a thermolysin-inhibitor complex. It is shown that: (1) The neglect of cross relaxation between the interacting species in their complexed forms can lead to misleading conclusions on the "bound" conformation of the ligand. (2) If protein-mediated spin diffusion is dominant, caution is needed in analyses based on initial slopes alone due to one‧s inability to identify the exact range of the initial growth curve under

  8. Heat transfer and fluid flow aspects of fuel--coolant interactions

    International Nuclear Information System (INIS)

    Corradini, M.L.

    1978-09-01

    A major portion of the safety analysis effort for the LMFBR is involved in assessing the consequences of a Hypothetical Core Disruptive Accident (HCDA). The thermal interaction of the hot fuel and the sodium coolant during the HCDA is investigated in two areas. A postulated loss of flow transient may produce a two-phase fuel at high pressures. The thermal interaction phenomena between fuel and coolant as the fuel is ejected into the upper plenum are investigated. A postulated transient overpower accident may produce molten fuel being released into sodium coolant in the core region. An energetic coolant vapor explosion for these reactor materials does not seem likely. However, experiments using other materials (e.g., Freon/water, tin/water) have demonstrated the possibility of this phenomenon

  9. Manipulation of Nanoparticle Electron Transfer Dynamics by Engineering of Metal-Ligand Interaction

    OpenAIRE

    Chen, Limei

    2017-01-01

    Nanoparticles represent a novel class of material consisting of hundreds to a few thousand atoms each, and their physical and chemical properties are significantly different than the bulk materials. The electronic structure, chemical and optical properties of nanoparticles can be tuned by the size, shape, surface modification and interaction with supporting materials, to fulfil the potential specific applications in catalysis, imaging and electronic devices. In the preparation of nanoparticle...

  10. Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping.

    Science.gov (United States)

    Broekgaarden, Colette; Bucher, Johan; Bac-Molenaar, Johanna; Keurentjes, Joost J B; Kruijer, Willem; Voorrips, Roeland E; Vosman, Ben

    2015-01-01

    Plants have evolved a variety of ways to defend themselves against biotic attackers. This has resulted in the presence of substantial variation in defense mechanisms among plants, even within a species. Genome-wide association (GWA) mapping is a useful tool to study the genetic architecture of traits, but has so far only had limited exploitation in studies of plant defense. Here, we study the genetic architecture of defense against the phloem-feeding insect cabbage whitefly (Aleyrodes proletella) in Arabidopsis thaliana. We determined whitefly performance, i.e. the survival and reproduction of whitefly females, on 360 worldwide selected natural accessions and subsequently performed GWA mapping using 214,051 SNPs. Substantial variation for whitefly adult survival and oviposition rate (number of eggs laid per female per day) was observed between the accessions. We identified 39 candidate SNPs for either whitefly adult survival or oviposition rate, all with relatively small effects, underpinning the complex architecture of defense traits. Among the corresponding candidate genes, i.e. genes in linkage disequilibrium (LD) with candidate SNPs, none have previously been identified as a gene playing a role in the interaction between plants and phloem-feeding insects. Whitefly performance on knock-out mutants of a number of candidate genes was significantly affected, validating the potential of GWA mapping for novel gene discovery in plant-insect interactions. Our results show that GWA analysis is a very useful tool to gain insight into the genetic architecture of plant defense against herbivorous insects, i.e. we identified and validated several genes affecting whitefly performance that have not previously been related to plant defense against herbivorous insects.

  11. Rational Design of Charge-Transfer Interactions in Halogen-Bonded Co-crystals toward Versatile Solid-State Optoelectronics.

    Science.gov (United States)

    Zhu, Weigang; Zheng, Renhui; Zhen, Yonggang; Yu, Zhenyi; Dong, Huanli; Fu, Hongbing; Shi, Qiang; Hu, Wenping

    2015-09-02

    Charge-transfer (CT) interactions between donor (D) and acceptor (A) groups, as well as CT exciton dynamics, play important roles in optoelectronic devices, such as organic solar cells, photodetectors, and light-emitting sources, which are not yet well understood. In this contribution, the self-assembly behavior, molecular stacking structure, CT interactions, density functional theory (DFT) calculations, and corresponding physicochemical properties of two similar halogen-bonded co-crystals are comprehensively investigated and compared, to construct an "assembly-structure-CT-property" relationship. Bpe-IFB wire-like crystals (where Bpe = 1,2-bis(4-pyridyl)ethylene and IFB = 1,3,5-trifluoro-2,4,6-triiodobenzene), packed in a segregated stacking form with CT ground and excited states, are measured to be quasi-one-dimensional (1D) semiconductors and show strong violet-blue photoluminescence (PL) from the lowest CT1 excitons (ΦPL = 26.1%), which can be confined and propagate oppositely along the 1D axial direction. In comparison, Bpe-F4DIB block-like crystals (F4DIB = 1,4-diiodotetrafluorobenzene), packed in a mixed stacking form without CT interactions, are determined to be insulators and exhibit unique white light emission and two-dimensional optical waveguide property. Surprisingly, it seems that the intrinsic spectroscopic states of Bpe and F4DIB do not change after co-crystallization, which is also confirmed by theoretical calculations, thus offering a new design principle for white light emitting materials. More importantly, we show that the CT interactions in co-crystals are related to their molecular packing and can be triggered or suppressed by crystal engineering, which eventually leads to distinct optoelectronic properties. These results help us to rationally control the CT interactions in organic D-A systems by tuning the molecular stacking, toward the development of a fantastic "optoelectronic world".

  12. Towards a map of the Populus biomass protein-protein interaction network

    Energy Technology Data Exchange (ETDEWEB)

    Beers, Eric [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Brunner, Amy [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Helm, Richard [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Dickerman, Allan [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)

    2015-07-31

    Biofuels can be produced from a variety of plant feedstocks. The value of a particular feedstock for biofuels production depends in part on the degree of difficulty associated with the extraction of fermentable sugars from the plant biomass. The wood of trees is potentially a rich source fermentable sugars. However, the sugars in wood exist in a tightly cross-linked matrix of cellulose, hemicellulose, and lignin, making them largely recalcitrant to release and fermentation for biofuels production. Before breeders and genetic engineers can effectively develop plants with reduced recalcitrance to fermentation, it is necessary to gain a better understanding of the fundamental biology of the mechanisms responsible for wood formation. Regulatory, structural, and enzymatic proteins are required for the complicated process of wood formation. To function properly, proteins must interact with other proteins. Yet, very few of the protein-protein interactions necessary for wood formation are known. The main objectives of this project were to 1) identify new protein-protein interactions relevant to wood formation, and 2) perform in-depth characterizations of selected protein-protein interactions. To identify relevant protein-protein interactions, we cloned a set of approximately 400 genes that were highly expressed in the wood-forming tissue (known as secondary xylem) of poplar (Populus trichocarpa). We tested whether the proteins encoded by these biomass genes interacted with each other in a binary matrix design using the yeast two-hybrid (Y2H) method for protein-protein interaction discovery. We also tested a subset of the 400 biomass proteins for interactions with all proteins present in wood-forming tissue of poplar in a biomass library screen design using Y2H. Together, these two Y2H screens yielded over 270 interactions involving over 75 biomass proteins. For the second main objective we selected several interacting pairs or groups of interacting proteins for in

  13. Mapping the Interactions between the Alzheimer’s Aβ-Peptide and Human Serum Albumin beyond Domain Resolution

    Science.gov (United States)

    Algamal, Moustafa; Milojevic, Julijana; Jafari, Naeimeh; Zhang, William; Melacini, Giuseppe

    2013-01-01

    Human serum albumin (HSA) is a potent inhibitor of Aβ self-association and this novel, to our knowledge, function of HSA is of potential therapeutic interest for the treatment of Alzheimer’s disease. It is known that HSA interacts with Aβ oligomers through binding sites evenly partitioned across the three albumin domains and with comparable affinities. However, as of this writing, no information is available on the HSA-Aβ interactions beyond domain resolution. Here, we map the HSA-Aβ interactions at subdomain and peptide resolution. We show that each separate subdomain of HSA domain 3 inhibits Aβ self-association. We also show that fatty acids (FAs) compete with Aβ oligomers for binding to domain 3, but the determinant of the HSA/Aβ oligomer interactions are markedly distinct from those of FAs. Although salt bridges with the FA carboxylate determine the FA binding affinities, hydrophobic contacts are pivotal for Aβ oligomer recognition. Specifically, we identified a site of Aβ oligomer recognition that spans the HSA (494–515) region and aligns with the central hydrophobic core of Aβ. The HSA (495–515) segment includes residues affected by FA binding and this segment is prone to self-associate into β-amyloids, suggesting that sites involved in fibrilization may provide a lead to develop inhibitors of Aβ self-association. PMID:24094411

  14. Changes in balance coordination and transfer to an unlearned balance task after slackline training: a self-organizing map analysis

    OpenAIRE

    Serrien, Ben; Hohenauer, Erich; Clijsen, Ron; Taube, Wolfgang; Baeyens, Jean-Pierre; Küng, Ursula

    2017-01-01

    How humans maintain balance and change postural control due to age, injury, immobility or training is one of the basic questions in motor control. One of the problems in understanding postural control is the large set of degrees of freedom in the human motor system. Therefore, a self-organizing map (SOM), a type of artificial neural network, was used in the present study to extract and visualize information about high-dimensional balance strategies before and after a 6-week slackline tra...

  15. Tn7 and Tn501 Insertions into Pseudomonas aeruginosa plasmid R91-5: mapping of two transfer regions.

    OpenAIRE

    Moore, R J; Krishnapillai, V

    1982-01-01

    We constructed a restriction endonuclease map of the Pseudomonas aeruginosa narrow-host-range plasmid R91-5. Insertions of transposons Tn7 and Tn501 into the plasmid DNA were characterized physically and genetically. The distribution of sites of insertion showed some regional specificity for the insertion of these transposons, especially TN501. The insertion of Tn7 was unusual in that all 42 of 43 insertions were in the same orientation. By relating phenotypic changes to the site of insertion...

  16. Institutional Regime, Off-Farm Employment, and the Interaction Effect: What are the Determinants of Households’ Forestland Transfer in China?

    Directory of Open Access Journals (Sweden)

    Han Zhang

    2017-10-01

    Full Text Available The development of the land rental market has been widely attributed to the associated institutional regime and the functioning of the off-farm labor market. However, little is known of the interaction effect of these two factors. To fill this gap, we employ a nationwide representative household dataset to investigate the effects of China’s collective forest tenure reform (CFTR and off-farm employment on forestland transfer in China. Special interest is focused on their potential interaction effect. The Smith-Blundell instrumental variable tobit model is adopted to account for the endogeneity of off-farm employment. The estimation results show that both the tenure reform and off-farm employment significantly influence forestland transactions. However, compared to the positive effect of the reform on both renting in and renting out forestland, the effect of off-farm employment is mixed, that is, its effect is negative when forestland is rented in but positive on rent-out decisions. An important finding is that the CFTR imposes a negative enhancement effect on forestland rent-in through its interaction term with off-farm employment. In contrast, the enhancement effect on rent-out is not statistically significant, which may be due to the neutralization by the endowment effect of the CFTR.

  17. Analytical use of multi-protein Fluorescence Resonance Energy Transfer to demonstrate membrane-facilitated interactions within cytokine receptor complexes.

    Science.gov (United States)

    Krause, Christopher D; Izotova, Lara S; Pestka, Sidney

    2013-10-01

    Experiments measuring Fluorescence Resonance Energy Transfer (FRET) between cytokine receptor chains and their associated proteins led to hypotheses describing their organization in intact cells. These interactions occur within a larger protein complex or within a given nano-environment. To illustrate this complexity empirically, we developed a protocol to analyze FRET among more than two fluorescent proteins (multi-FRET). In multi-FRET, we model FRET among more than two fluorophores as the sum of all possible pairwise interactions within the complex. We validated our assumption by demonstrating that FRET among pairs within a fluorescent triplet resembled FRET between each pair measured in the absence of the third fluorophore. FRET between two receptor chains increases with increasing FRET between the ligand-binding chain (e.g., IFN-γR1, IL-10R1 and IFN-λR1) and an acylated fluorescent protein that preferentially resides within subsections of the plasma membrane. The interaction of IL-10R2 with IFN-λR1 or IL-10R1 results in decreased FRET between IL-10R2 and the acylated fluorescent protein. Finally, we analyzed FRET among four fluorescent proteins to demonstrate that as FRET between IFN-γR1 and IFN-γR2 or between IFN-αR1 and IFN-αR2c increases, FRET among other pairs of proteins changes within each complex. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. PDB-Explorer: a web-based interactive map of the protein data bank in shape space.

    Science.gov (United States)

    Jin, Xian; Awale, Mahendra; Zasso, Michaël; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis

    2015-10-23

    The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3

  19. Defect-Mediated Molecular Interaction and Charge Transfer in Graphene Mesh-Glucose Sensors.

    Science.gov (United States)

    Kwon, Sun Sang; Shin, Jae Hyeok; Choi, Jonghyun; Nam, SungWoo; Park, Won Il

    2017-04-26

    We report the role of defects in enzymatic graphene field-effect transistor sensors by introducing engineered defects in graphene channels. Compared with conventional graphene sensors (Gr sensors), graphene mesh sensors (GM sensors), with an array of circular holes, initially exhibited a higher irreversible response to glucose, involving strong chemisorption to edge defects. However, after immobilization of glucose oxidase, the irreversibility of the responses was substantially diminished, without any reduction in the sensitivity of the GM sensors (i.e., -0.53 mV/mM for the GM sensor vs -0.37 mV/mM for Gr sensor). Furthermore, multiple cycle operation led to rapid sensing and improved the reversibility of GM sensors. In addition, control tests with sensors containing a linker showed that sensitivity was increased in Gr sensors but decreased in GM sensors. Our findings indicate that edge defects can be used to replace linkers for immobilization of glucose oxidase and improve charge transfer across glucose oxidase-graphene interfaces.

  20. Beam transfer functions for relativistic proton bunches with beam–beam interaction

    Energy Technology Data Exchange (ETDEWEB)

    Görgen, P., E-mail: goergen@temf.tu-darmstadt.de [Institut für Theorie Elektromagnetischer Felder (TEMF), Technische Universität Darmstadt, Schloßgartenstr. 8 64289 Darmstadt (Germany); Boine-Frankenheim, O. [Institut für Theorie Elektromagnetischer Felder (TEMF), Technische Universität Darmstadt, Schloßgartenstr. 8 64289 Darmstadt (Germany); Fischer, W. [Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2015-03-21

    We present a method for the recovery of the transverse tune spread directly from the beam transfer function (BTF). The model is applicable for coasting beams and bunched beams at high energy with a tune spread from transverse nonlinearities induced by the beam–beam effect or by an electron lens. Other sources of tune spread can be added. A method for the recovery of the incoherent tune spread without prior knowledge of the nonlinearity is presented. The approach is based on the analytic model for BTFs of coasting beams, which agrees very well with simulations results for bunched beams at relativistic energies with typically low synchrotron tune. A priori the presented tune spread recovery method is usable only in the absence of coherent modes, but additional simulation data shows its applicability even in the presence of coherent beam–beam modes. Finally agreement of both the analytic and simulation models with measurement data obtained at RHIC is presented. The proposed method successfully recovers the tune spread from analytic, simulated and measured BTF.

  1. Mapping jet-ISM interactions in X-ray binaries with ALMA: a GRS 1915+105 case study

    Science.gov (United States)

    Tetarenko, A. J.; Freeman, P.; Rosolowsky, E. W.; Miller-Jones, J. C. A.; Sivakoff, G. R.

    2018-03-01

    We present Atacama Large Millimetre/Sub-Millimetre Array (ALMA) observations of IRAS 19132+1035, a candidate jet-interstellar medium (ISM) interaction zone near the black hole X-ray binary (BHXB) GRS 1915+105. With these ALMA observations (combining data from the 12 m array and the Atacama Compact Array), we map the molecular line emission across the IRAS 19132+1035 region. We detect emission from the 12CO [J = 2 - 1], 13CO [ν = 0, J = 2 - 1], C18O [J = 2 - 1], H2CO [J = 30, 3 - 20, 2], H2CO [J = 32, 2 - 22, 1], H2CO [J = 32, 1 - 22, 0], SiO [ν = 0, J = 5 - 4], CH3OH [J = 42, 2 - 31, 2], and CS [ν = 0, J = 5 - 4] transitions. Given the morphological, spectral, and kinematic properties of this molecular emission, we present several lines of evidence that support the presence of a jet-ISM interaction at this site, including a jet-blown cavity in the molecular gas. This compelling new evidence identifies this site as a jet-ISM interaction zone, making GRS 1915+105, the third Galactic BHXB with at least one conclusive jet-ISM interaction zone. However, we find that this interaction occurs on much smaller scales than was postulated by previous work, where the BHXB jet does not appear to be dominantly powering the entire IRAS 19132+1035 region. Using estimates of the ISM conditions in the region, we utilize the detected cavity as a calorimeter to estimate the time-averaged power carried in the GRS 1915+105 jets of (8.4^{+7.7}_{-8.1})× 10^{32} erg s^{-1}. Overall, our analysis demonstrates that molecular lines are excellent diagnostic tools to identify and probe jet-ISM interaction zones near Galactic BHXBs.

  2. Mapping Functional Brain Development: Building a Social Brain through Interactive Specialization

    Science.gov (United States)

    Johnson, Mark H.; Grossmann, Tobias; Kadosh, Kathrin Cohen

    2009-01-01

    The authors review a viewpoint on human functional brain development, interactive specialization (IS), and its application to the emerging network of cortical regions referred to as the "social brain." They advance the IS view in 2 new ways. First, they extend IS into a domain to which it has not previously been applied--the emergence of social…

  3. Effective Online Interaction: Mapping Course Design to Bridge from Research to Practice

    Science.gov (United States)

    Thorpe, Mary

    2008-01-01

    Quantitative and qualitative research of a case study course confirmed that the course achieved a highly interactive learning experience, associated with more effective student support and high student retention. Computer conferencing achieved high participation from the beginning and evidence of dialogue and argumentation within online tutor…

  4. Identification of Odorant-Receptor Interactions by Global Mapping of the Human Odorome

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Tromelin, Anne; Le Bon, Anne Marie

    2014-01-01

    and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions...

  5. Mapping networks of physical interactions between genomic elements using 5C technology.

    Science.gov (United States)

    Dostie, Josée; Dekker, Job

    2007-01-01

    Genomic elements separated by large genomic distances can physically interact to mediate long-range gene regulation and other chromosomal processes. Interactions between genomic elements can be detected using the chromosome conformation capture (3C) technology. We recently developed a high-throughput adaptation of 3C, 3C-carbon copy (5C), that is used to measure networks of millions of chromatin interactions in parallel. As in 3C, cells are treated with formaldehyde to cross-link chromatin interactions. The chromatin is solubilized, digested with a restriction enzyme and ligated at low DNA concentration to promote intra-molecular ligation of cross-linked DNA fragments. Ligation products are subsequently purified to generate a 3C library. The 5C technology then employs highly multiplexed ligation-mediated amplification (LMA) to detect and amplify 3C ligation junctions. The resulting 5C library of ligated primers is analyzed using either microarray detection or ultra-high-throughput DNA sequencing. The 5C protocol described here can be completed in 13 d.

  6. Mapping phenotypic plasticity and genotype-environment interactions affecting life-history traits in Caenorhabditis elegans

    NARCIS (Netherlands)

    Gutteling, E.W.; Riksen, J.A.G.; Bakker, J.; Kammenga, J.E.

    2007-01-01

    Phenotypic plasticity and genotype-environment interactions (GEI) play an important role in the evolution of life histories. Knowledge of the molecular genetic basis of plasticity and GEI provides insight into the underlying mechanisms of life-history changes in different environments. We used a

  7. CuO Nanoparticle Interaction with Arabidopsis thaliana: Toxicity, Parent-Progeny Transfer, and Gene Expression.

    Science.gov (United States)

    Wang, Zhenyu; Xu, Lina; Zhao, Jian; Wang, Xiangke; White, Jason C; Xing, Baoshan

    2016-06-07

    CuO nanoparticles (NPs) (20, 50 mg L(-1)) inhibited seedling growth of different Arabidopsis thaliana ecotypes (Col-0, Bay-0, and Ws-2), as well as the germination of their pollens and harvested seeds. For most of growth parameters (e.g., biomass, relative growth rate, root morphology change), Col-0 was the more sensitive ecotype to CuO NPs compared to Bay-0 and Ws-2. Equivalent Cu(2+) ions and CuO bulk particles had no effect on Arabidopsis growth. After CuO NPs (50 mg L(-1)) exposure, Cu was detected in the roots, leaves, flowers and harvested seeds of Arabidopsis, and its contents were significantly higher than that in CuO bulk particles (50 mg L(-1)) and Cu(2+) ions (0.15 mg L(-1)) treatments. Based on X-ray absorption near-edge spectroscopy analysis (XANES), Cu in the harvested seeds was confirmed as being mainly in the form of CuO (88.8%), which is the first observation on the presence of CuO NPs in the plant progeny. Moreover, after CuO NPs exposure, two differentially expressed genes (C-1 and C-3) that regulated root growth and reactive oxygen species generation were identified, which correlated well with the physiological root inhibition and oxidative stress data. This current study provides direct evidence for the negative effects of CuO NPs on Arabidopsis, including accumulation and parent-progeny transfer of the particles, which may have significant implications with regard to the risk of NPs to food safety and security.

  8. Revised genetic map of the distal end of the F transfer operon: implications for DNA helicase I, nicking at oriT, and conjugal DNA transport.

    Science.gov (United States)

    Traxler, B A; Minkley, E G

    1987-07-01

    The DNA transfer stage of conjugation requires the products of the F sex factor genes traMYDIZ and the cis-acting site oriT. Previous interpretation of genetic and protein analyses suggested that traD, traI, and traZ mapped as contiguous genes at the distal end of the transfer operon and saturated this portion of the F transfer region (which ends with an IS3 element). Using antibodies prepared against the purified TraD and TraI proteins, we analyzed the products encoded by a collection of chimeric plasmids constructed with various segments of traDIZ DNA. We found the traI gene to be located 1 kilobase to the right of the position suggested on previous maps. This creates an unsaturated space between traD and traI where unidentified tra genes may be located and leaves insufficient space between traI and IS3 for coding the 94-kilodalton protein previously thought to be the product of traZ. We found that the 94-kilodalton protein arose from a translational restart and corresponds to the carboxy terminus of traI; we named it TraI*. The precise physical location of the traZ gene and the identity of its product are unknown. The oriT nicking activity known as TraZ may stem from unassigned regions between traD and traI and between traI and IS3, but a more interesting possibility is that it is actually a function of traI. On our revised map, the position of a previously detected RNA polymerase-binding site corresponds to a site at the amino terminus of traI rather than a location 1 kilobase into the coding region of the gene. Furthermore, the physical and genetic comparison of the F traD and traI genes with those of the closely related F-like conjugative plasmids R1 and R100 is greatly simplified. The translational organization we found for traI, together with its identity as the structural gene for DNA helicase I, suggests a possible functional link to several other genes from which translational restart polypeptides are expressed. These include the primases of the

  9. Electromagnetic interactions of nucleons and nuclei at low energy and momentum transfer

    International Nuclear Information System (INIS)

    Arenhoevel, H.

    1994-01-01

    In these lectures I concentrate on the manifestation of subnuclear degrees of freedom in terms of meson and isobar degrees of freedom in electromagnetic processes where their presence usually is described in terms of so-called exchange or interaction currents. In Section 2 I first discuss the general properties of the electromagnetic interaction, the gauge conditions and low-energy theorems which follow from gauge invariance, the charge and current density operators for a non-relativistic system of nucleons and the Siegert theorem. In Section 3 I sketch the basic ideas and construction methods for the exchange current operators as effective operators and in Section 4 the model of nuclear isobar configurations introducing explicitly isobar degrees of freedom into the nuclear wave function. The general features of one- and two-photon processes are discussed in Section 5. First the expressions for the cross sections of photoabsorption and electron scattering are reviewed. As a specific but important example, I then discuss the two-body break-up of the deuteron since it permits the cleanest analysis and provides one of the best evidences for the presence of subnuclear degrees of freedom due to its simple two-body structure within the classical nuclear physics framework. This is a unique situation because in more complex nuclei the analysis is often hampered by presently still unavoidable approximations of the many-body problem. I furthermore discuss the role of meson exchange currents in the photonuclear TRK sum rule, in particular, I carefully analyse what determines the enhancement. This section ends with a brief discussion of elastic photon scattering with special emphasis on the low-energy theorem for the scattering amplitude and the sum rule relations for the low-energy parameters. (orig.)

  10. Textile Pressure Mapping Sensor for Emotional Touch Detection in Human-Robot Interaction

    Directory of Open Access Journals (Sweden)

    Bo Zhou

    2017-11-01

    Full Text Available In this paper, we developed a fully textile sensing fabric for tactile touch sensing as the robot skin to detect human-robot interactions. The sensor covers a 20-by-20 cm 2 area with 400 sensitive points and samples at 50 Hz per point. We defined seven gestures which are inspired by the social and emotional interactions of typical people to people or pet scenarios. We conducted two groups of mutually blinded experiments, involving 29 participants in total. The data processing algorithm first reduces the spatial complexity to frame descriptors, and temporal features are calculated through basic statistical representations and wavelet analysis. Various classifiers are evaluated and the feature calculation algorithms are analyzed in details to determine each stage and segments’ contribution. The best performing feature-classifier combination can recognize the gestures with a 93 . 3 % accuracy from a known group of participants, and 89 . 1 % from strangers.

  11. Humanin binds MPP8: mapping interaction sites of the peptide and protein.

    Science.gov (United States)

    Maximov, Vadim V; Martynenko, Alina V; Arman, Inga P; Tarantul, Vyacheslav Z

    2013-05-01

    Humanin (HN), a 24-amino acid peptide encoded by the mitochondrial 16S rRNA gene, was discovered by screening a cDNA library from the occipital cortex of a patient with Alzheimer's disease (AD) for a protection factor against AD-relevant insults. Earlier, using the yeast two-hybrid system, we have identified the M-phase phosphoprotein 8 (MPP8) as a binding partner for HN. In the present work, we further confirmed interaction of HN with MPP8 in co-immunoprecipitation experiments and localized an MPP8-binding site in the region between 5 and 12 aa. of HN. We have also shown that an MPP8 fragment (residues 431-560) is sufficient to bind HN. Further studies on functional consequences of the interaction between the potential oncopetide and the oncoprotein may elucidate some aspects of the molecular mechanisms of carcinogenesis. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.

  12. Heterotic trait locus (HTL) mapping identifies intra-locus interactions that underlie reproductive hybrid vigor in Sorghum bicolor.

    Science.gov (United States)

    Ben-Israel, Imri; Kilian, Benjamin; Nida, Habte; Fridman, Eyal

    2012-01-01

    Identifying intra-locus interactions underlying heterotic variation among whole-genome hybrids is a key to understanding mechanisms of heterosis and exploiting it for crop and livestock improvement. In this study, we present the development and first use of the heterotic trait locus (HTL) mapping approach to associate specific intra-locus interactions with an overdominant heterotic mode of inheritance in a diallel population using Sorghum bicolor as the model. This method combines the advantages of ample genetic diversity and the possibility of studying non-additive inheritance. Furthermore, this design enables dissecting the latter to identify specific intra-locus interactions. We identified three HTLs (3.5% of loci tested) with synergistic intra-locus effects on overdominant grain yield heterosis in 2 years of field trials. These loci account for 19.0% of the heterotic variation, including a significant interaction found between two of them. Moreover, analysis of one of these loci (hDPW4.1) in a consecutive F2 population confirmed a significant 21% increase in grain yield of heterozygous vs. homozygous plants in this locus. Notably, two of the three HTLs for grain yield are in synteny with previously reported overdominant quantitative trait loci for grain yield in maize. A mechanism for the reproductive heterosis found in this study is suggested, in which grain yield increase is achieved by releasing the compensatory tradeoffs between biomass and reproductive output, and between seed number and weight. These results highlight the power of analyzing a diverse set of inbreds and their hybrids for unraveling hitherto unknown allelic interactions mediating heterosis.

  13. Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions.

    Science.gov (United States)

    Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun

    2017-05-01

    Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide chromatin interactions. Unlike other 3C-based methods, it includes a chromatin immunoprecipitation (ChIP) step that enriches for interactions mediated by specific target proteins. This unique feature allows ChIA-PET to provide the functional specificity and higher resolution needed to detect chromatin interactions, which chromosome conformation capture (3C)/Hi-C approaches have not achieved. The original ChIA-PET protocol generates short paired-end tags (2 × 20 base pairs (bp)) to detect two genomic loci that are far apart on linear chromosomes but are in spatial proximity in the folded genome. We have improved the original approach by developing long-read ChIA-PET, in which the length of the paired-end tags is increased (up to 2 × 250 bp). The longer PET reads not only improve the tag-mapping efficiency but also increase the probability of covering phased single-nucleotide polymorphisms (SNPs), which allows haplotype-specific chromatin interactions to be identified. Here, we provide the detailed protocol for long-read ChIA-PET that includes cell fixation and lysis, chromatin fragmentation by sonication, ChIP, proximity ligation with a bridge linker, Tn5 tagmentation, PCR amplification and high-throughput sequencing. For a well-trained molecular biologist, it typically takes 6 d from cell harvesting to the completion of library construction, up to a further 36 h for DNA sequencing and <20 h for processing of raw sequencing reads.

  14. Heterotic trait locus (HTL mapping identifies intra-locus interactions that underlie reproductive hybrid vigor in Sorghum bicolor.

    Directory of Open Access Journals (Sweden)

    Imri Ben-Israel

    Full Text Available Identifying intra-locus interactions underlying heterotic variation among whole-genome hybrids is a key to understanding mechanisms of heterosis and exploiting it for crop and livestock improvement. In this study, we present the development and first use of the heterotic trait locus (HTL mapping approach to associate specific intra-locus interactions with an overdominant heterotic mode of inheritance in a diallel population using Sorghum bicolor as the model. This method combines the advantages of ample genetic diversity and the possibility of studying non-additive inheritance. Furthermore, this design enables dissecting the latter to identify specific intra-locus interactions. We identified three HTLs (3.5% of loci tested with synergistic intra-locus effects on overdominant grain yield heterosis in 2 years of field trials. These loci account for 19.0% of the heterotic variation, including a significant interaction found between two of them. Moreover, analysis of one of these loci (hDPW4.1 in a consecutive F2 population confirmed a significant 21% increase in grain yield of heterozygous vs. homozygous plants in this locus. Notably, two of the three HTLs for grain yield are in synteny with previously reported overdominant quantitative trait loci for grain yield in maize. A mechanism for the reproductive heterosis found in this study is suggested, in which grain yield increase is achieved by releasing the compensatory tradeoffs between biomass and reproductive output, and between seed number and weight. These results highlight the power of analyzing a diverse set of inbreds and their hybrids for unraveling hitherto unknown allelic interactions mediating heterosis.

  15. Mapping the Interaction Anatomy of BmP02 on Kv1.3 Channel

    Science.gov (United States)

    Wu, B.; Wu, B. F.; Feng, Y. J.; Tao, J.; Ji, Y. H.

    2016-07-01

    The potassium channel Kv 1.3 plays a vital part in the activation of T lymphocytes and is an attractive pharmacological target for autoimmune diseases. BmP02, a 28-residue peptide isolated from Chinese scorpion (Buthus martensi Karsch) venom, is a potent and selective Kv1.3 channel blocker. However, the mechanism through which BmP02 recognizes and inhibits the Kv1.3 channel is still unclear. In the present study, a complex molecular model of Kv1.3-BmP02 was developed by docking analysis and molecular dynamics simulations. From these simulations, it appears the large β-turn (residues 10-16) of BmP02 might be the binding interface with Kv 1.3. These results were confirmed by scanning alanine mutagenesis of BmP02, which identified His9, Lys11 and Lys13, which lie within BmP02’s β-turn, as key residues for interacting with Kv1.3. Based on these results and molecular modeling, two negatively charged residues of Kv1.3, D421 and D422, located in turret region, were predicted to act as the binding site for BmP02. Mutation of these residues reduced sensitivity of Kv 1.3 to BmP02 inhibition, suggesting that electrostatic interactions play a crucial role in Kv1.3-BmP02 interaction. This study revealed the molecular basis of Kv 1.3 recognition by BmP02 venom, and provides a novel interaction model for Kv channel-specific blocker complex, which may help guide future drug-design for Kv1.3-related channelopathies.

  16. Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification.

    Science.gov (United States)

    van Rooden, Eva J; Florea, Bogdan I; Deng, Hui; Baggelaar, Marc P; van Esbroeck, Annelot C M; Zhou, Juan; Overkleeft, Herman S; van der Stelt, Mario

    2018-04-01

    Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA 10-2474, thereby providing a potential explanation for the adverse side effects observed with this compound. ABPP allows mapping of protein interaction landscapes of inhibitors in cells, tissues and animal models. Whereas our previous protocol described quantification of proteasome activity using stable-isotope labeling, this protocol describes the procedures for identifying the in vivo selectivity profile of covalent inhibitors with label-free quantitative proteomics. The optimization of our protocol for label-free quantification methods results in high proteome coverage and allows the comparison of multiple biological samples. We demonstrate our protocol by assessing the protein interaction landscape of the diacylglycerol lipase inhibitor DH376 in mouse brain, liver, kidney and testes. The stages of the protocol include tissue lysis, probe incubation, target enrichment, sample preparation, liquid chromatography-mass spectrometry (LC-MS) measurement, data processing and analysis. This approach can be used to study target engagement in a native proteome and to identify potential off targets for the inhibitor under investigation. The entire protocol takes at least 4 d, depending on the number of samples.

  17. Roads as Channels of Centrifugal Policy Transfer: A Spatial Interaction Model Revised

    Directory of Open Access Journals (Sweden)

    Katarzyna Kopczewska

    2013-10-01

    Full Text Available This paper proposes a methodology for measuring the spatial effects of roads and the seats of local authorities on the diffusion of business activity, which usually follows distance decay patterns from core to periphery. Regional development policies, pursued by regional authorities, directed at local units and designed to support local economies, are implemented by means of a centrifugal diffusion process. This invisible flow of policy is modeled using a one-way spatial interaction model represented by a multinomial distance decay function for the integrated spatial dataset. The research results indicate that NUTS5 (Nomenclature of Territorial Units for Statistics units (gminas perform better in terms of saturation with business activity when NUTS4 seats of authority are established there than when they are established near international roads. The natural diffusion process from core cities to the periphery covers approximately 25–30 km, and the presence of international roads extends this range by 20 km. The results confirm the hypothesis of an endogenous growth pattern.

  18. Perceptions of Private Sector towards the Pollutant Release and Transfer Register: A Case Study on Petrochemical Industry in the Map Ta Phut Industrial Estate, Rayong, Thailand

    Directory of Open Access Journals (Sweden)

    Marie Kondo

    2013-01-01

    Full Text Available Under the Rio Declaration and Agenda 21 from the United Nations Conference on Environment and Development in 1992 as well as other international agreements, Thailand is currently in the process of adopting the Pollutant Release and Transfer Register (PRTR through a pilot project in Rayong province with assistance from the Japan International Cooperation Agency (JICA. This research aimed to study perceptions of private sector towards the PRTR through a case study on petrochemical industry in the Map Ta Phut Industrial Estate. Through semi-structured questionnaires and in-depth interviews, the study found that the petrochemical industry viewed that benefits of the PRTR for the government and civil society is quite clear, while each petrochemical company has different understanding on such benefit for private sector to be as sustainable industrial management. Various incentive measures and concerns on the PRTR were also indicated in this study.

  19. Lunar Mapping and Modeling On-the-Go: A mobile framework for viewing and interacting with large geospatial datasets

    Science.gov (United States)

    Chang, G.; Kim, R.; Bui, B.; Sadaqathullah, S.; Law, E.; Malhotra, S.

    2012-12-01

    The Lunar Mapping and Modeling Portal (LMMP, https://www.lmmp.nasa.gov/) is a collaboration between four NASA centers, JPL, Marshall, Goddard, and Ames, along with the USGS and US Army to provide a centralized geospatial repository for storing processed lunar data collected from the Apollo missions to the latest data acquired by the Lunar Reconnaissance Orbiter (LRO). We offer various scientific and visualization tools to analyze rock and crater densities, lighting maps, thermal measurements, mineral concentrations, slope hazards, and digital elevation maps with the intention of serving not only scientists and lunar mission planners, but also the general public. The project has pioneered in leveraging new technologies and embracing new computing paradigms to create a system that is sophisticated, secure, robust, and scalable all the while being easy to use, streamlined, and modular. We have led innovations through the use of a hybrid cloud infrastructure, authentication through various sources, and utilizing an in-house GIS framework, TWMS (TiledWMS) as well as the commercial ArcGIS product from ESRI. On the client end, we also provide a Flash GUI framework as well as REST web services to interact with the portal. We have also developed a visualization framework on mobile devices, specifically Apple's iOS, which allows anyone from anywhere to interact with LMMP. At the most basic level, the framework allows users to browse LMMP's entire catalog of over 600 data imagery products ranging from global basemaps to LRO's Narrow Angle Camera (NAC) images that provide details of up to .5 meters/pixel. Users are able to view map metadata and can zoom in and out as well as pan around the entire lunar surface with the appropriate basemap. They can arbitrarily stack the maps and images on top of each other to show a layered view of the surface with layer transparency adjusted to suit the user's desired look. Once the user has selected a combination of layers, he can also

  20. Development of a dynamic network monitoring tool – Interactive map based on LLDP and SNMP

    CERN Document Server

    Haen, Christophe; Mesnard, E

    2010-01-01

    The European Organization for Nuclear Research (French: Organisation Européenne pour la Recherche Nucléaire), known as CERN is the world’s largest particle physics laboratory, established in 1954 near Geneva. CERN’s main function is to provide the particle accelerators and other infrastructure needed for high-energy physics research. The LHCb (standing for “Large Hadron Collider beauty”) experiment is one of six particle physics detector experiments built on the Large Hadron Collider, the world’s largest and highest-energy particle accelerator. This experiment produces a large amount of data which needs to be treated. This task is processed by some 2000 computing servers and 400 control servers. The LHCb Online team is responsible of the data, from their creation in the detector, till the storage. The purpose of my internship was to develop a software from scratch able to dynamically discover the network, draw a map of it, gather information of the network equipments, and implement basic monitorin...

  1. Mapping African ethical review committee activity onto capacity needs: the MARC initiative and HRWeb's interactive database of RECs in Africa.

    Science.gov (United States)

    IJsselmuiden, Carel; Marais, Debbie; Wassenaar, Douglas; Mokgatla-Moipolai, Boitumelo

    2012-08-01

    Health research initiatives worldwide are growing in scope and complexity, particularly as they move into the developing world. Expanding health research activity in low- and middle-income countries has resulted in a commensurate rise in the need for sound ethical review structures and functions in the form of Research Ethics Committees (RECs). Yet these seem to be lagging behind as a result of the enormous challenges facing these countries, including poor resource availability and lack of capacity. There is thus an urgent need for ongoing capacity and resource development in these regions in general, and in Africa in particular. Similarly, there is a need for research and initiatives that can identify existing capacity and funding and indicate the areas where this needs to be developed. This discussion paper argues that the Mapping African Research Ethics Capacity (MARC) project is a timely initiative aimed at identifying existing capacity. MARC provides a platform and tool on the Council on Health Research for Development's (COHRED) Health Research website (HRWeb), which can be used by RECs and key stakeholders in health research in Africa to identify capacity, constraints and development needs. MARC intends to provide the first comprehensive interactive database of RECs in Africa, which will allow for the identification of key relationships and analyses of capacity. The potential of MARC lies in the mapping of current ethical review activity onto capacity needs. This paper serves as a starting point by providing a descriptive illustration of the current state of RECs in Africa. © 2012 Blackwell Publishing Ltd.

  2. Characterization of the bionano interface and mapping extrinsic interactions of the corona of nanomaterials

    Science.gov (United States)

    O'Connell, D. J.; Bombelli, F. Baldelli; Pitek, A. S.; Monopoli, M. P.; Cahill, D. J.; Dawson, K. A.

    2015-09-01

    Nanoparticles in physiological environments are known to selectively adsorb proteins and other biomolecules forming a tightly bound biomolecular `corona' on their surface. Where the exchange times of the proteins are sufficiently long, it is believed that the protein corona constitutes the particle identity in biological milieu. Here we show that proteins in the corona retain their functional characteristics and can specifically bind to cognate proteins on arrays of thousands of immobilised human proteins. The biological identity of the nanomaterial is seen to be specific to the blood plasma concentration in which they are exposed. We show that the resulting in situ nanoparticle interactome is dependent on the protein concentration in plasma, with the emergence of a small number of dominant protein-protein interactions. These interactions are those driven by proteins that are adsorbed onto the particle surface and whose binding epitopes are subsequently expressed or presented suitably on the particle surface. We suggest that, since specific tailored protein arrays for target systems and organs can be designed, their use may be an important element in an overall study of the biomolecular corona.Nanoparticles in physiological environments are known to selectively adsorb proteins and other biomolecules forming a tightly bound biomolecular `corona' on their surface. Where the exchange times of the proteins are sufficiently long, it is believed that the protein corona constitutes the particle identity in biological milieu. Here we show that proteins in the corona retain their functional characteristics and can specifically bind to cognate proteins on arrays of thousands of immobilised human proteins. The biological identity of the nanomaterial is seen to be specific to the blood plasma concentration in which they are exposed. We show that the resulting in situ nanoparticle interactome is dependent on the protein concentration in plasma, with the emergence of a small

  3. Mapping protein–protein interactions by double-REDOR-filtered magic angle spinning NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Changmiao; Hou, Guangjin, E-mail: hou@udel.edu; Lu, Xingyu; Polenova, Tatyana, E-mail: tpolenov@udel.edu [University of Delaware, Department of Chemistry and Biochemistry (United States)

    2017-02-15

    REDOR-based experiments with simultaneous {sup 1}H–{sup 13}C and {sup 1}H−{sup 15}N dipolar dephasing are explored for investigating intermolecular protein–protein interfaces in complexes formed by a U–{sup 13}C,{sup 15}N-labeled protein and its natural abundance binding partner. The application of a double-REDOR filter (dREDOR) results in a complete dephasing of proton magnetization in the U–{sup 13}C,{sup 15}N-enriched molecule while the proton magnetization of the unlabeled binding partner is not dephased. This retained proton magnetization is then transferred across the intermolecular interface by {sup 1}H–{sup 13}C or {sup 1}H–{sup 15}N cross polarization, permitting to establish the residues of the U–{sup 13}C,{sup 15}N-labeled protein, which constitute the binding interface. To assign the interface residues, this dREDOR-CPMAS element is incorporated as a building block into {sup 13}C–{sup 13}C correlation experiments. We established the validity of this approach on U–{sup 13}C,{sup 15}N-histidine and on a structurally characterized complex of dynactin’s U–{sup 13}C,{sup 15}N-CAP-Gly domain with end-binding protein 1 (EB1). The approach introduced here is broadly applicable to the analysis of intermolecular interfaces when one of the binding partners in a complex cannot be isotopically labeled.

  4. Integration of Weather Research Forecast (WRF) Hurricane model with socio-economic data in an interactive web mapping service

    Science.gov (United States)

    Boehnert, J.; Wilhelmi, O.; Sampson, K. M.

    2009-12-01

    The integration of weather forecast models and socio-economic data is key to better understanding of the weather forecast and its impact upon society. Whether the forecast is looking at a hurricane approaching land or a snow storm over an urban corridor; the public is most interested in how this weather will affect day-to-day activities, and in extreme events how it will impact human lives, property and livelihoods. The GIS program at NCAR is developing an interactive web mapping portal which will integrate weather forecasts with socio-economic and infrastructure data. This integration of data is essential to better communication of the weather models and their impact on society. As a pilot project, we are conducting a case study on hurricane Ike, which made landfall at Galveston, Texas on 13 September, 2008, with winds greater than 70 mph. There was heavy flooding and loss of electricity due to high winds. This case study is an extreme event, which we are using to demonstrate how the Weather Research Forecasts (WRF) model runs at NCAR can be used to answer questions about how storms impact society. We are integrating WRF model output with the U.S. Census and infrastructure data in a Geographic Information System (GIS) web mapping framework. In this case study, we have identified a series of questions and custom queries which can be viewed through the interactive web portal; such as who will be affected by rain greater than 5 mm/h, or which schools will be affected by winds greater than 90 mph. These types of queries demonstrate the power of GIS and the necessity of integrating weather models with other spatial data in order to improve its effectiveness and understanding for society.

  5. Protein interaction maps for complete genomes based on gene fusion events

    Science.gov (United States)

    Enright, Anton J.; Iliopoulos, Ioannis; Kyrpides, Nikos C.; Ouzounis, Christos A.

    1999-11-01

    A large-scale effort to measure, detect and analyse protein-protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as unlinked noncomplementing mutant detection. Using the two-hybrid system, an international effort to analyse the complete yeast genome is in progress. Evidently, all these approaches are tedious, labour intensive and inaccurate. From a computational perspective, the question is how can we predict that two proteins interact from structure or sequence alone. Here we present a method that identifies gene-fusion events in complete genomes, solely based on sequence comparison. Because there must be selective pressure for certain genes to be fused over the course of evolution, we are able to predict functional associations of proteins. We show that 215 genes or proteins in the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii are involved in 64 unique fusion events. The approach is general, and can be applied even to genes of unknown function.

  6. 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

  7. Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions.

    Science.gov (United States)

    Mao, Tingting; Li, Jinyu; Wen, Zixiang; Wu, Tingting; Wu, Cunxiang; Sun, Shi; Jiang, Bingjun; Hou, Wensheng; Li, Wenbin; Song, Qijian; Wang, Dechun; Han, Tianfu

    2017-05-26

    Soybean (Glycine max (L.) Merr.) is a short day plant. Its flowering and maturity time are controlled by genetic and environmental factors, as well the interaction between the two factors. Previous studies have shown that both genetic and environmental factors, mainly photoperiod and temperature, control flowering time of soybean. Additionally, these studies have reported gene × gene and gene × environment interactions on flowering time. However, the effects of quantitative trait loci (QTL) in response to photoperiod and temperature have not been well evaluated. The objectives of the current study were to identify the effects of loci associated with flowering time under different photo-thermal conditions and to understand the effects of interaction between loci and environment on soybean flowering. Different photoperiod and temperature combinations were obtained by adjusting sowing dates (spring sowing and summer sowing) or day-length (12 h, 16 h). Association mapping was performed on 91 soybean cultivars from different maturity groups (MG000-VIII) using 172 SSR markers and 5107 SNPs from the Illumina SoySNP6K iSelectBeadChip. The effects of the interaction between QTL and environments on flowering time were also analysed using the QTXNetwork. Large-effect loci were detected on Gm 11, Gm 16 and Gm 20 as in previous reports. Most loci associated with flowering time are sensitive to photo-thermal conditions. Number of loci associated with flowering time was more under the long day (LD) than under the short day (SD) condition. The variation of flowering time among the soybean cultivars mostly resulted from the epistasis × environment and additive × environment interactions. Among the three candidate loci, i.e. Gm04_4497001 (near GmCOL3a), Gm16_30766209 (near GmFT2a and GmFT2b) and Gm19_47514601 (E3 or GmPhyA3), the Gm04_4497001 may be the key locus interacting with other loci for controlling soybean flowering time. The effects of loci associated

  8. Mapping QTL associated with photoperiod sensitivity and assessing the importance of QTL×environment interaction for flowering time in maize.

    Directory of Open Access Journals (Sweden)

    Cuiling Wang

    2010-11-01

    Full Text Available An understanding of the genetic determinism of photoperiod response of flowering is a prerequisite for the successful exchange of germplasm across different latitudes. In order to contribute to resolve the genetic basis of photoperiod sensitivity in maize, a set of 201 recombinant inbred lines (RIL, derived from a temperate and tropical inbred line cross were evaluated in 5 field trials spread in short- and long-day environments.Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A and additive-by-environment interaction effect (AE by using a mixed-model-based composite interval mapping (MCIM method.Seven putative QTL were found associated with DPS thermal time based on the data estimated in individual environments. Nine putative QTL were found associated with DPS thermal time across environments and six of them showed significant QTL×enviroment (QE interactions. Three QTL for photoperiod sensitivity were identified on chromosome 4, 9 and 10, which had the similar position to QTL for DPS thermal time in the two long-day environment. The major photoperiod sensitive loci qDPS10 responded to both short and long-day photoperiod environments and had opposite effects in different photoperiod environment. The QTL qDPS3, which had the greatest additive effect exclusively in the short-day environment, were photoperiod independent and should be classified in autonomous promotion pathway.

  9. I.4 Screening Experimental Designs for Quantitative Trait Loci, Association Mapping, Genotype-by Environment Interaction, and Other Investigations.

    Science.gov (United States)

    Federer, Walter T; Crossa, José

    2012-01-01

    Crop breeding programs using conventional approaches, as well as new biotechnological tools, rely heavily on data resulting from the evaluation of genotypes in different environmental conditions (agronomic practices, locations, and years). Statistical methods used for designing field and laboratory trials and for analyzing the data originating from those trials need to be accurate and efficient. The statistical analysis of multi-environment trails (MET) is useful for assessing genotype × environment interaction (GEI), mapping quantitative trait loci (QTLs), and studying QTL × environment interaction (QEI). Large populations are required for scientific study of QEI, and for determining the association between molecular markers and quantitative trait variability. Therefore, appropriate control of local variability through efficient experimental design is of key importance. In this chapter we present and explain several classes of augmented designs useful for achieving control of variability and assessing genotype effects in a practical and efficient manner. A popular procedure for unreplicated designs is the one known as "systematically spaced checks." Augmented designs contain "c" check or standard treatments replicated "r" times, and "n" new treatments or genotypes included once (usually) in the experiment.

  10. A Spatially Explicit Dual-Isotope Approach to Map Regions of Plant-Plant Interaction after Exotic Plant Invasion.

    Directory of Open Access Journals (Sweden)

    Christine Hellmann

    Full Text Available Understanding interactions between native and invasive plant species in field settings and quantifying the impact of invaders in heterogeneous native ecosystems requires resolving the spatial scale on which these processes take place. Therefore, functional tracers are needed that enable resolving the alterations induced by exotic plant invasion in contrast to natural variation in a spatially explicit way. 15N isoscapes, i.e., spatially referenced representations of stable nitrogen isotopic signatures, have recently provided such a tracer. However, different processes, e.g. water, nitrogen or carbon cycles, may be affected at different spatial scales. Thus multi-isotope studies, by using different functional tracers, can potentially return a more integrated picture of invader impact. This is particularly true when isoscapes are submitted to statistical methods suitable to find homogeneous subgroups in multivariate data such as cluster analysis. Here, we used model-based clustering of spatially explicit foliar δ15N and δ13C isoscapes together with N concentration of a native indicator species, Corema album, to map regions of influence in a Portuguese dune ecosystem invaded by the N2-fixing Acacia longifolia. Cluster analysis identified regions with pronounced alterations in N budget and water use efficiency in the native species, with a more than twofold increase in foliar N, and δ13C and δ15N enrichment of up to 2‰ and 8‰ closer to the invader, respectively. Furthermore, clusters of multiple functional tracers indicated a spatial shift from facilitation through N addition in the proximity of the invader to competition for resources other than N in close contact. Finding homogeneous subgroups in multi-isotope data by means of model-based cluster analysis provided an effective tool for detecting spatial structure in processes affecting plant physiology and performance. The proposed method can give an objective measure of the spatial extent

  11. A structured workflow for mapping human Sin3 histone deacetylase complex interactions using Halo-MudPIT AP-MS.

    Science.gov (United States)

    Banks, Charles A S; Thornton, Janet L; Eubanks, Cassandra G; Adams, Mark K; Miah, Sayem; Boanca, Gina; Liu, Xingyu; Katt, Maria; Parmely, Tari; Florens, Laurence A; Washburn, Michael P

    2018-03-29

    Although a variety of affinity purification mass spectrometry (AP-MS) strategies have been used to investigate complex interactions, many of these are susceptible to artifacts due to substantial overexpression of the exogenously expressed bait protein. Here we present a logical and systematic workflow that uses the multifunctional Halo tag to assess the correct localization and behavior of tagged subunits of the Sin3 histone deacetylase complex prior to further AP-MS analysis. Using this workflow, we modified our tagging/expression strategy with 21.7% of the tagged bait proteins that we constructed, allowing us to quickly develop validated reagents. Specifically, we apply the workflow to map interactions between stably expressed versions of the Sin3 subunits SUDS3, SAP30 or SAP30L and other cellular proteins.  Here we show that the SAP30 and SAP30L paralogues strongly associate with the core Sin3 complex, but SAP30L has unique associations with the proteasome and the myelin sheath.  Next, we demonstrate an advancement of the complex NSAF (cNSAF) approach, in which normalization to the scaffold protein SIN3A accounts for variations in the proportion of each bait capturing Sin3 complexes and allows a comparison between different baits capturing the same protein complex. This analysis reveals that although the Sin3 subunit SUDS3 appears to be used in both SIN3A and SIN3B based complexes, the SAP30 subunit is not used in SIN3B based complexes. Intriguingly, we do not detect the Sin3 subunits SAP18 and SAP25 among the 128 high-confidence interactions identified, suggesting that these subunits may not be common to all versions of the Sin3 complex in human cells. This workflow provides the framework for building validated reagents to assemble quantitative interaction networks for chromatin remodeling complexes and provides novel insights into focused protein interaction networks. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Improving Interactions between a Power-Assist Robot System and Its Human User in Horizontal Transfer of Objects Using a Novel Adaptive Control Method

    Directory of Open Access Journals (Sweden)

    S. M. Mizanoor Rahman

    2012-01-01

    Full Text Available Power assist systems are usually used for rehabilitation, healthcare, and so forth.This paper puts emphasis on the use of power assist systems for object transfer and thus brings a novelty in the power-assist applications. However, the interactions between the systems and the human users are usually not satisfactory because human features are not included in the control design. In this paper, we present the development of a 1-DOF power assist system for horizontal transfer of objects. We included human features such as weight perception in the system dynamics and control. We then simulated the system using MATLAB/Simulink for transferring objects with it and (i determined the optimum maneuverability conditions for object transfer, (ii determined psychophysical relationships between actual and perceived weights, and (iii analyzed load forces and motion features. We then used the findings to design a novel adaptive control scheme to improve the interactions between the user and the system. We implemented the novel control (simulated the system again using the novel control, the subjects evaluated the system, and the results showed that the novel control reduced the excessive load forces and accelerations and thus improved the human-system interactions in terms of maneuverability, safety, and so forth. Finally, we proposed to use the findings to develop power assist systems for manipulating heavy objects in industries that may improve interactions between the systems and the users.

  13. Electron-lattice interactions strongly renormalize the charge-transfer energy in the spin-chain cuprate Li.sub.2./sub.CuO.sub.2./sub.

    Czech Academy of Sciences Publication Activity Database

    Johnston, S.; Monney, C.; Bisogni, V.; Zhou, K.J.; Kraus, R.; Behr, G.; Strocov, V.N.; Málek, Jiří; Drechsler, S.L.; Geck, J.; Schmitt, T.; van den Brink, J.

    2016-01-01

    Roč. 7, Feb (2016), 1-7, č. článku 10653. ISSN 2041-1723 Institutional support: RVO:68378271 Keywords : X-ray scattering * electron-lattice interactions * spin-chain cuprates * renormalization of charge- transfer energy Subject RIV: BE - Theoretical Physics Impact factor: 12.124, year: 2016

  14. Transferred hyperfine interaction at 295 K between the rare-earth ions and the fluorine and lithium nuclei in lithium rare-earth fluorides

    DEFF Research Database (Denmark)

    Hansen, P. E.; Nevald, Rolf

    1977-01-01

    The nuclear-magnetic-resonance rotation spectra for the fluorine and lithium nuclei in LiTbF4, LiDyF4, LiHoF4, and LiErF4 have been obtained at 295 K. They are separated in contributions from the dipole and the transferred hyperfine interactions. In general, the latter consists of an isotropic part...

  15. Deriving a Benefit Transfer Function for Threatened and Endangered Species in Interaction with Their Level of Charisma

    Directory of Open Access Journals (Sweden)

    Franklin Amuakwa-Mensah

    2018-02-01

    Full Text Available Biodiversity and species conservation are among the most urgent global issues. Both are under serious threat because of human intrusion and as a result, it is likely that present and future projects will affect threatened and endangered species. Thus, it is important to account for these impacts when evaluating and conducting cost and benefit analyses of projects. Due to their public good character and non-tradability, the total economic value of threatened and endangered species cannot be reflected by a market price and therefore, alternative approaches (stated preference method are needed to determine their monetary value. This paper reviews and compares the valuation literature on threatened and endangered animals and conducts a meta-analysis regression to identify explanatory variables for the variation in willingness to pay for threatened and endangered species. The main findings of the meta-analysis show that the interaction of the level of threat and charisma have a positive effect on willingness to pay. Furthermore, developed countries have a higher willingness to pay compared to developing countries. Similarly, visitors of conservation sites have higher willingness to pay than residents. The provided example of a benefit transfer of the estimated function shows the practicability of our results.

  16. Fluorescent copper(II complexes: The electron transfer mechanism, interaction with bovine serum albumin (BSA and antibacterial activity

    Directory of Open Access Journals (Sweden)

    Madhumita Hazra

    2017-01-01

    Full Text Available Dinuclear copper(II complexes with formula [Cu2(L2(N32] (1 and [Cu2(L2(NCS2] (2 HL = (1-[(3-methyl-pyridine-2-ylimino-methyl]-naphthalen-2-ol were synthesized by controlling the molar ratio of Cu(OAC2·6H2O, HL, sodium azide (1 and ammonium thiocyanate (2. The end on bridges appear exclusively in azide and thiocyanate to copper complexes. The electron transfer mechanism of copper(II complexes is examined by cyclic voltammetry indicating copper(II complexes are Cu(II/Cu(I couple. The interactions of copper(II complexes towards bovine serum albumin (BSA were examined with the help of absorption and fluorescence spectroscopic tools. We report a superficial solution-based route for the synthesis of micro crystals of copper complexes with BSA. The antibacterial activity of the Schiff base and its copper complexes were investigated by the agar disc diffusion method against some species of pathogenic bacteria (Escherichia coli, Vibrio cholerae, Streptococcus pneumonia and Bacillus cereus. It has been observed that the antibacterial activity of all complexes is higher than the ligand.

  17. Interaction, transference, and subjectivity

    DEFF Research Database (Denmark)

    Lundgaard Andersen, Linda

    2012-01-01

    is also subjected to psychodynamic processes. In this article, I draw upon a number of research inquiries to illustrate how psychodynamic processes influence research processes: data production, research questions and methodology, relations to informants, as well as interpretation and analysis. I further......Fieldwork is one of the important methods in educational, social, and organisational research. In fieldwork, the researcher takes residence for a shorter or longer period amongst the subjects and settings to be studied. The aim of this is to study the culture of people: how people seem to make...... sense of their lives and which moral, professional, and ethical values seem to guide their behaviour and attitudes. In fieldwork, the researcher has to balance participation and observation in her attempts at representation. Consequently, the researcher’s academic and life-historical subjectivity...

  18. Proliferating cell nuclear antigen (PCNA) interacts with a meiosis-specific RecA homologues, Lim15/Dmc1, but does not stimulate its strand transfer activity

    International Nuclear Information System (INIS)

    Hamada, Fumika N.; Koshiyama, Akiyo; Namekawa, Satoshi H.; Ishii, Satomi; Iwabata, Kazuki; Sugawara, Hiroko; Nara, Takayuki Y.; Sakaguchi, Kengo; Sawado, Tomoyuki

    2007-01-01

    PCNA is a multi-functional protein that is involved in various nuclear events. Here we show that PCNA participates in events occurring during early meiotic prophase. Analysis of protein-protein interactions using surface plasmon resonance indicates that Coprinus cinereus PCNA (CoPCNA) specifically interacts with a meiotic specific RecA-like factor, C. cinereus Lim15/Dmc1 (CoLim15) in vitro. The binding efficiency increases with addition of Mg 2+ ions, while ATP inhibits the interaction. Co-immunoprecipitation experiments indicate that the CoLim15 protein interacts with the CoPCNA protein in vitro and in the cell extracts. Despite the interaction between these two factors, no enhancement of CoLim15-dependent strand transfer activity by CoPCNA was found in vitro. We propose that the interaction between Lim15/Dmc1 and PCNA mediates the recombination-associated DNA synthesis during meiosis

  19. Development of a new assessment scale for measuring interaction during staff-assisted transfer of residents in dementia special care units.

    Science.gov (United States)

    Thunborg, Charlotta; von Heideken Wågert, Petra; Götell, Eva; Ivarsson, Ann-Britt; Söderlund, Anne

    2015-02-10

    Mobility problems and cognitive deficits related to transferring or moving persons suffering from dementia are associated with dependency. Physical assistance provided by staff is an important component of residents' maintenance of mobility in dementia care facilities. Unfortunately, hands-on assistance during transfers is also a source of confusion in persons with dementia, as well as a source of strain in the caregiver. The bidirectional effect of actions in a dementia care dyad involved in transfer is complicated to evaluate. This study aimed to develop an assessment scale for measuring actions related to transferring persons with dementia by dementia care dyads. This study was performed in four phases and guided by the framework of the biopsychosocial model and the approach presented by Social Cognitive Theory. These frameworks provided a starting point for understanding reciprocal effects in dyadic interaction. The four phases were 1) a literature review identifying existing assessment scales; 2) analyses of video-recorded transfer of persons with dementia for further generation of items, 3) computing the item content validity index of the 93 proposed items by 15 experts; and 4) expert opinion on the response scale and feasibility testing of the new assessment scale by video observation of the transfer situations. The development process resulted in a 17-item scale with a seven-point response scale. The scale consists of two sections. One section is related to transfer-related actions (e.g., capability of communication, motor skills performance, and cognitive functioning) of the person with dementia. The other section addresses the caregivers' facilitative actions (e.g., preparedness of transfer aids, interactional skills, and means of communication and interaction). The literature review and video recordings provided ideas for the item pool. Expert opinion decreased the number of items by relevance ratings and qualitative feedback. No further development of

  20. E-Learning Content Design Standards Based on Interactive Digital Concepts Maps in the Light of Meaningful and Constructivist Learning Theory

    Science.gov (United States)

    Afify, Mohammed Kamal

    2018-01-01

    The present study aims to identify standards of interactive digital concepts maps design and their measurement indicators as a tool to develop, organize and administer e-learning content in the light of Meaningful Learning Theory and Constructivist Learning Theory. To achieve the objective of the research, the author prepared a list of E-learning…

  1. Electron transfer in pnicogen bonds.

    Science.gov (United States)

    Guan, Liangyu; Mo, Yirong

    2014-10-02

    As a new type of noncovalent interactions, pnicogen bond between a VA group element (N, P, and As) and an electron donor (Lewis base) has grabbed attention in recent several years. Here we employ the block-localized wave function (BLW) based energy decomposition scheme to probe the bonding nature in a series of substituted phosphines X(n)PH(3-n) complexed with ammonia. As the BLW method can derive the optimal monomer orbitals in a complex with the electron transfer among monomers quenched, we can effectively examine the HOMO-LUMO interaction in these pnicogen bonding systems. Among various energy components, electron transfer energy together with the polarization energy dominates the pnicogen bonding energy. Although usually it is assumed that the electron transfer from ammonia to substituted phosphines occurs in the form of n → σ*(XP) hyperconjugative interaction, we identify a kind of new pathway when X = NO2 and CN, i.e., n → dπ*, which results from the interaction between the π orbital of cyano or nitro substituent and d orbitals on P. But still this picture of electron transfer using a single pair of orbitals is greatly simplified, as the electron density difference (EDD) maps corresponding to the overall electron transfer processes show the accumulation of electron density on the P side opposite to the X-P bond, with insignificant or even negligible gain of electron density on the substituent group side. Thus, the EDD maps tend to support the concept of σ-hole in pnicogen bonds.

  2. Electron-Transfer-Enhanced Cation-Cation Interactions in Homo- and Heterobimetallic Actinide Complexes: A Relativistic Density Functional Theory Study.

    Science.gov (United States)

    Zheng, Ming; Chen, Fang-Yuan; Tian, Jia-Nan; Pan, Qing-Jiang

    2018-03-21

    To provide deep insight into cation-cation interactions (CCIs) involving hexavalent actinyl species that are major components in spent nuclear fuel and pose important implications for the effective removal of radiotoxic pollutants in the environment, a series of homo- and heterobimetallic actinide complexes supported by cyclopentadienyl (Cp) and polypyrrolic macrocycle (H 4 L) ligands were systematically investigated using relativistic density functional theory. The metal sort in both parts of (THF)(H 2 L)(OAn VI O) and (An') III Cp 3 from U to Np to Pu, as well as the substituent bonding to Cp from electron-donating Me to H to electron-withdrawing Cl, SiH 3 , and SiMe 3 , was changed. Over 0.70 electrons are unraveled to transfer from the electron-rich U III to the electron-deficient An VI of the actinyl moiety, leading to a more stable An V -U IV isomer; in contrast, uranylneptunium and uranylplutonium complexes behave as electron-resonance structures between VI-III and V-IV. These were further corroborated by geometrical and electronic structures. The energies of CCIs (i.e., O exo -An' bonds) were calculated to be -19.6 to -41.2 kcal/mol, affording those of OUO-Np (-23.9 kcal/mol) and OUO-Pu (-19.6 kcal/mol) with less electron transfer (ET) right at the low limit. Topological analyses of the electron density at the O exo -An' bond critical points demonstrate that the CCIs are ET or dative bonds in nature. A positive correlation has been built between the CCIs' strength and corresponding ET amount. It is concluded that the CCIs of O exo -An' are driven by the electrostatic attraction between the actinyl oxo atom (negative) and the actinide ion (positive) and enhanced by their ET. Finally, experimental syntheses of (THF)(H 2 L)(OU VI O)(An') III Cp 3 (An' = U and Np) were well reproduced by thermodynamic calculations that yielded negative free energies in a tetrahydrofuran solution but a positive one for their uranylplutonium analogue, which was synthetically

  3. QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits

    Science.gov (United States)

    2013-01-01

    Background Asparagus bean (Vigna. unguiculata. ssp sesquipedalis) is a subspecies and special vegetable type of cowpea (Vigna. unguiculata L. Walp.) important in Asia. Genetic basis of horticulturally important traits of asparagus bean is still poorly understood, hindering the utilization of targeted, DNA marker-assisted breeding in this crop. Here we report the identification of quantitative trait loci (QTLs) and epistatic interactions for four horticultural traits, namely, days to first flowering (FLD), nodes to first flower (NFF), leaf senescence (LS) and pod number per plant (PN) using a recombinant inbred line (RIL) population of asparagus bean. Results A similar genetic mode of one major QTL plus a few minor QTLs was found to dominate each of the four traits, with the number of QTLs for individual traits ranging from three to four. These QTLs were distributed on 7 of the 11 chromosomes. Major QTLs for FLD, NFF and LS were co-localized on LG 11, indicative of tight linkage. Genome wide epistasis analysis detected two and one interactive locus pairs that significantly affect FLD and LS, respectively, and the epistatic QTLs for FLD appeared to work in different ways. Synteny based comparison of QTL locations revealed conservation of chromosome regions controlling these traits in related legume crops. Conclusion Major, minor, and epistatic QTLs were found to contribute to the inheritance of the FLD, NFF, LS, and PN. Positions of many of these QTLs are conserved among closely related legume species, indicating common mechanisms they share. To our best knowledge, this is the first QTL mapping report using an asparagus bean × asparagus bean intervarietal population and provides marker-trait associations for marker-assisted approaches to selection. PMID:23375055

  4. An integrated protein localization and interaction map for Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus

    International Nuclear Information System (INIS)

    Bandyopadhyay, Anindya; Kopperud, Kristin; Anderson, Gavin; Martin, Kathleen; Goodin, Michael

    2010-01-01

    The genome of Potato yellow dwarf virus (PYDV; Nucleorhabdovirus type species) was determined to be 12,875 nucleotides (nt). The antigenome is organized into seven open reading frames (ORFs) ordered 3'-N-X-P-Y-M-G-L-5', which likely encode the nucleocapsid, phospho, movement, matrix, glyco and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. The ORFs are flanked by a 3' leader RNA of 149 nt and a 5' trailer RNA of 97 nt, and are separated by conserved intergenic junctions. Phylogenetic analyses indicated that PYDV is closely related to other leafhopper-transmitted rhabdoviruses. Functional protein assays were used to determine the subcellular localization of PYDV proteins. Surprisingly, the M protein was able to induce the intranuclear accumulation of the inner nuclear membrane in the absence of any other viral protein. Finally, bimolecular fluorescence complementation was used to generate the most comprehensive protein interaction map for a plant-adapted rhabdovirus to date.

  5. Rydberg and valence state excitation dynamics: a velocity map imaging study involving the E-V state interaction in HBr.

    Science.gov (United States)

    Zaouris, Dimitris; Kartakoullis, Andreas; Glodic, Pavle; Samartzis, Peter C; Rafn Hróðmarsson, Helgi; Kvaran, Ágúst

    2015-04-28

    Photoexcitation dynamics of the E((1)Σ(+)) (v' = 0) Rydberg state and the V((1)Σ(+)) (v') ion-pair vibrational states of HBr are investigated by velocity map imaging (VMI). H(+) photoions, produced through a number of vibrational and rotational levels of the two states were imaged and kinetic energy release (KER) and angular distributions were extracted from the data. In agreement with previous work, we found the photodissociation channels forming H*(n = 2) + Br((2)P3/2)/Br*((2)P1/2) to be dominant. Autoionization pathways leading to H(+) + Br((2)P3/2)/Br*((2)P1/2) via either HBr(+)((2)Π3/2) or HBr(+)*((2)Π1/2) formation were also present. The analysis of KER and angular distributions and comparison with rotationally and mass resolved resonance enhanced multiphoton ionization (REMPI) spectra revealed the excitation transition mechanisms and characteristics of states involved as well as the involvement of the E-V state interactions and their v' and J' dependence.

  6. Web GIS in practice II: interactive SVG maps of diagnoses of sexually transmitted diseases by Primary Care Trust in London, 1997 - 2003.

    Science.gov (United States)

    Boulos, Maged N Kamel; Russell, Chris; Smith, Michael

    2005-01-18

    BACKGROUND: The rates of Sexually transmitted diseases (STDs) in England have been rising steadily since the mid 1990s, making them a major public health concern. In 2003, 672,718 people were diagnosed with an STD in England, and around one third of those cases were diagnosed in London. RESULTS: Using GeoReveal v1.1 for Windows, we produced Web-based interactive choropleth maps of diagnoses of STDs by Primary Care Trust (PCT) in London for the years from 1997 to 2003 http://healthcybermap.org/PCT/STDs/. These maps are in Scalable Vector Graphics (SVG) format and require a freely available Adobe SVG browser plug-in to be displayed. They are based on data obtained from the House of Commons Hansard Written Answers for 15 October 2004. They show steadily rising rates of STDs in London over the covered seven-year period. Also, one can clearly see on the maps that PCTs located in central London had the highest numbers of STD diagnoses throughout the mapped seven years. A companion bar chart allows users to instantly compare the STD figure of a given PCT for a given year against the average figure for all 25 mapped PCTs for the same year, and also compare those figures across all seven years. The maps offer users a rich set of useful features and functions, including the ability to change the classification method in use, the number of ranges in the map, and the colour theme, among others. CONCLUSIONS: Wizard-driven tools like GeoReveal have made it very easy to transform complex raw data into valuable decision support information products (interactive Web maps) in very little time and without requiring much expertise. The resultant interactive maps have the potential of further supporting health planners and decision makers in their planning and management tasks by allowing them to graphically interrogate data, instantly spot trends, and make quick and effective visual comparisons of geographically differentiated phenomena between different geographical areas and over

  7. Web GIS in practice II: interactive SVG maps of diagnoses of sexually transmitted diseases by Primary Care Trust in London, 1997 – 2003

    Directory of Open Access Journals (Sweden)

    Russell Chris

    2005-01-01

    Full Text Available Abstract Background The rates of Sexually transmitted diseases (STDs in England have been rising steadily since the mid 1990s, making them a major public health concern. In 2003, 672,718 people were diagnosed with an STD in England, and around one third of those cases were diagnosed in London. Results Using GeoReveal v1.1 for Windows, we produced Web-based interactive choropleth maps of diagnoses of STDs by Primary Care Trust (PCT in London for the years from 1997 to 2003 http://healthcybermap.org/PCT/STDs/. These maps are in Scalable Vector Graphics (SVG format and require a freely available Adobe SVG browser plug-in to be displayed. They are based on data obtained from the House of Commons Hansard Written Answers for 15 October 2004. They show steadily rising rates of STDs in London over the covered seven-year period. Also, one can clearly see on the maps that PCTs located in central London had the highest numbers of STD diagnoses throughout the mapped seven years. A companion bar chart allows users to instantly compare the STD figure of a given PCT for a given year against the average figure for all 25 mapped PCTs for the same year, and also compare those figures across all seven years. The maps offer users a rich set of useful features and functions, including the ability to change the classification method in use, the number of ranges in the map, and the colour theme, among others. Conclusions Wizard-driven tools like GeoReveal have made it very easy to transform complex raw data into valuable decision support information products (interactive Web maps in very little time and without requiring much expertise. The resultant interactive maps have the potential of further supporting health planners and decision makers in their planning and management tasks by allowing them to graphically interrogate data, instantly spot trends, and make quick and effective visual comparisons of geographically differentiated phenomena between different

  8. Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P

    2002-01-01

    -induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

  9. The visualization and dissemination of the Great Lakes Regional Toxic Air Emissions Inventory: Using geographic information systems and interactive Internet mapping applications

    Energy Technology Data Exchange (ETDEWEB)

    Conley, R.M. [Great Lakes Commission, Ann Arbor, MI (United States)

    1997-12-31

    The eight Great Lakes states, the Canadian province of Ontario and the Great Lakes Commission are involved in a collective effort to develop a regional inventory of toxic air emissions for 49 targeted toxic pollutants from point and area sources. The regional inventory will soon be expanded to include emissions from mobile sources. The inventory, when aggregated for all eight states and Ontario, will eventually reside at the US Environmental Protection Agency (EPA), Great Lakes National Program Office (GLNPO). To aid in the understanding and interpretation of the inventory`s data, an effort has been undertaken to generate two map series for the entire region: (1) choropleth maps of total toxic air emissions at the county level of geography and (2) dot maps showing facility locations. To ensure an effective and efficient dissemination process among the province and various states, an interactive Internet mapping interface prototype was modified and used for the project. With an interactive online visualization tool, the inventory collectors, managers and researchers can quickly and effectively view the inventory`s data on maps, charts or spreadsheets. These graphics can be used as: (1) a QA/QC function for the inventory collectors, (2) a simple communication of complex data to support managers decision making and (3) a means for easy access to complex data and information about any geographic area in the region for the researchers or general public. This paper describes the development and use of PC Arc/Info, ArcView and MapInfo geographic information systems (GIS), mapping and Internet interfacing applications to visualize, disseminate and convey the emissions inventory data in a meaningful and useful manner. The various methods developed and implemented to convert, process and prepare the inventory data and Internet interface for use with a standard Internet web browser also are described in this paper.

  10. Plasmon-enhanced scattering and charge transfer in few-layer graphene interacting with buried printed 2D-pattern of silver nanoparticles

    Science.gov (United States)

    Carles, R.; Bayle, M.; Bonafos, C.

    2018-04-01

    Hybrid structures combing silver nanoparticles and few-layer graphene have been synthetized by combining low-energy ion beam synthesis and stencil techniques. A single plane of metallic nanoparticles plays the role of an embedded plasmonic enhancer located in dedicated areas at a controlled nanometer distance from deposited graphene layers. Optical imaging, reflectance and Raman scattering mapping are used to measure the enhancement of electronic and vibrational properties of these layers. In particular electronic Raman scattering is shown as notably efficient to analyze the optical transfer of charge carriers between the systems and the presence of intrinsic and extrinsic defects.

  11. Interaction between the PH and START domains of ceramide transfer protein competes with phosphatidylinositol 4-phosphate binding by the PH domain.

    Science.gov (United States)

    Prashek, Jennifer; Bouyain, Samuel; Fu, Mingui; Li, Yong; Berkes, Dusan; Yao, Xiaolan

    2017-08-25

    De novo synthesis of the sphingolipid sphingomyelin requires non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi by the multidomain protein ceramide transfer protein (CERT). CERT's N-terminal pleckstrin homology (PH) domain targets it to the Golgi by binding to phosphatidylinositol 4-phosphate (PtdIns(4)P) in the Golgi membrane, whereas its C-terminal StAR-related lipid transfer domain (START) carries out ceramide transfer. Hyperphosphorylation of a serine-rich motif immediately after the PH domain decreases both PtdIns(4)P binding and ceramide transfer by CERT. This down-regulation requires both the PH and START domains, suggesting a possible inhibitory interaction between the two domains. In this study we show that isolated PH and START domains interact with each other. The crystal structure of a PH-START complex revealed that the START domain binds to the PH domain at the same site for PtdIns(4)P-binding, suggesting that the START domain competes with PtdIns(4)P for association with the PH domain. We further report that mutations disrupting the PH-START interaction increase both PtdIns(4)P-binding affinity and ceramide transfer activity of a CERT-serine-rich phosphorylation mimic. We also found that these mutations increase the Golgi localization of CERT inside the cell, consistent with enhanced PtdIns(4)P binding of the mutant. Collectively, our structural, biochemical, and cellular investigations provide important structural insight into the regulation of CERT function and localization. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Interaction between the PH and START domains of ceramide transfer protein competes with phosphatidylinositol 4-phosphate binding by the PH domain

    Energy Technology Data Exchange (ETDEWEB)

    Prashek, Jennifer; Bouyain, Samuel; Fu, Mingui; Li, Yong; Berkes, Dusan; Yao, Xiaolan

    2017-06-26

    De novo synthesis of the sphingolipid sphingomyelin requires non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi by the multidomain protein ceramide transfer protein (CERT). CERT's N-terminal pleckstrin homology (PH) domain targets it to the Golgi by binding to phosphatidylinositol 4-phosphate (PtdIns(4)P) in the Golgi membrane, whereas its C-terminal StAR-related lipid transfer domain (START) carries out ceramide transfer. Hyperphosphorylation of a serine-rich motif immediately after the PH domain decreases both PtdIns(4)P binding and ceramide transfer by CERT. This down-regulation requires both the PH and START domains, suggesting a possible inhibitory interaction between the two domains. In this study we show that isolated PH and START domains interact with each other. The crystal structure of a PH–START complex revealed that the START domain binds to the PH domain at the same site for PtdIns(4)P-binding, suggesting that the START domain competes with PtdIns(4)P for association with the PH domain. We further report that mutations disrupting the PH–START interaction increase both PtdIns(4)P-binding affinity and ceramide transfer activity of a CERT-serine–rich phosphorylation mimic. We also found that these mutations increase the Golgi localization of CERT inside the cell, consistent with enhanced PtdIns(4)P binding of the mutant. Collectively, our structural, biochemical, and cellular investigations provide important structural insight into the regulation of CERT function and localization.

  13. Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat.

    Science.gov (United States)

    Singh, A; Pandey, M P; Singh, A K; Knox, R E; Ammar, K; Clarke, J M; Clarke, F R; Singh, R P; Pozniak, C J; Depauw, R M; McCallum, B D; Cuthbert, R D; Randhawa, H S; Fetch, T G

    2013-02-01

    Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding.

  14. A critical study of different Monte Carlo scoring methods of dose average linear-energy-transfer maps calculated in voxelized geometries irradiated with clinical proton beams.

    Science.gov (United States)

    Cortés-Giraldo, M A; Carabe, A

    2015-04-07

    We compare unrestricted dose average linear energy transfer (LET) maps calculated with three different Monte Carlo scoring methods in voxelized geometries irradiated with proton therapy beams with three different Monte Carlo scoring methods. Simulations were done with the Geant4 (Geometry ANd Tracking) toolkit. The first method corresponds to a step-by-step computation of LET which has been reported previously in the literature. We found that this scoring strategy is influenced by spurious high LET components, which relative contribution in the dose average LET calculations significantly increases as the voxel size becomes smaller. Dose average LET values calculated for primary protons in water with voxel size of 0.2 mm were a factor ~1.8 higher than those obtained with a size of 2.0 mm at the plateau region for a 160 MeV beam. Such high LET components are a consequence of proton steps in which the condensed-history algorithm determines an energy transfer to an electron of the material close to the maximum value, while the step length remains limited due to voxel boundary crossing. Two alternative methods were derived to overcome this problem. The second scores LET along the entire path described by each proton within the voxel. The third followed the same approach of the first method, but the LET was evaluated at each step from stopping power tables according to the proton kinetic energy value. We carried out microdosimetry calculations with the aim of deriving reference dose average LET values from microdosimetric quantities. Significant differences between the methods were reported either with pristine or spread-out Bragg peaks (SOBPs). The first method reported values systematically higher than the other two at depths proximal to SOBP by about 15% for a 5.9 cm wide SOBP and about 30% for a 11.0 cm one. At distal SOBP, the second method gave values about 15% lower than the others. Overall, we found that the third method gave the most consistent

  15. HeatMapViewer: interactive display of 2D data in biology [v1; ref status: indexed, http://f1000r.es/2u6

    Directory of Open Access Journals (Sweden)

    Guy Yachdav

    2014-02-01

    Full Text Available Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis. Availability: https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706.

  16. Autism and Intellectual Disability-Associated KIRREL3 Interacts with Neuronal Proteins MAP1B and MYO16 with Potential Roles in Neurodevelopment.

    Directory of Open Access Journals (Sweden)

    Ying F Liu

    Full Text Available Cell-adhesion molecules of the immunoglobulin superfamily play critical roles in brain development, as well as in maintaining synaptic plasticity, the dysfunction of which is known to cause cognitive impairment. Recently dysfunction of KIRREL3, a synaptic molecule of the immunoglobulin superfamily, has been implicated in several neurodevelopmental conditions including intellectual disability, autism spectrum disorder, and in the neurocognitive delay associated with Jacobsen syndrome. However, the molecular mechanisms of its physiological actions remain largely unknown. Using a yeast two-hybrid screen, we found that the KIRREL3 extracellular domain interacts with brain expressed proteins MAP1B and MYO16 and its intracellular domain can potentially interact with ATP1B1, UFC1, and SHMT2. The interactions were confirmed by co-immunoprecipitation and colocalization analyses of proteins expressed in human embryonic kidney cells, mouse neuronal cells, and rat primary neuronal cells. Furthermore, we show KIRREL3 colocalization with the marker for the Golgi apparatus and synaptic vesicles. Previously, we have shown that KIRREL3 interacts with the X-linked intellectual disability associated synaptic scaffolding protein CASK through its cytoplasmic domain. In addition, we found a genomic deletion encompassing MAP1B in one patient with intellectual disability, microcephaly and seizures and deletions encompassing MYO16 in two unrelated patients with intellectual disability, autism and microcephaly. MAP1B has been previously implicated in synaptogenesis and is involved in the development of the actin-based membrane skeleton. MYO16 is expressed in hippocampal neurons and also indirectly affects actin cytoskeleton through its interaction with WAVE1 complex. We speculate KIRREL3 interacting proteins are potential candidates for intellectual disability and autism spectrum disorder. Moreover, our findings provide further insight into understanding the molecular

  17. Validation of NOAA-Interactive Multisensor Snow and Ice Mapping System (IMS by Comparison with Ground-Based Measurements over Continental United States

    Directory of Open Access Journals (Sweden)

    Reza Khanbilvardi

    2012-04-01

    Full Text Available In this study, daily maps of snow cover distribution and sea ice extent produced by NOAA’s interactive multisensor snow and ice mapping system (IMS were validated using in situ snow depth data from observing stations obtained from NOAA’s National Climatic Data Center (NCDC for calendar years 2006 to 2010. IMS provides daily maps of snow and sea ice extent within the Northern Hemisphere using data from combination of geostationary and polar orbiting satellites in visible, infrared and microwave spectrums. Statistical correspondence between the IMS and in situ point measurements has been evaluated assuming that ground measurements are discrete and continuously distributed over a 4 km IMS snow cover maps. Advanced Very High Resolution Radiometer (AVHRR land and snow classification data are supplemental datasets used in the further analysis of correspondence between the IMS product and in situ measurements. The comparison of IMS maps with in situ snow observations conducted over a period of four years has demonstrated a good correspondence of the data sets. The daily rate of agreement between the products mostly ranges between 80% and 90% during the Northern Hemisphere through the winter seasons when about a quarter to one third of the territory of continental US is covered with snow. Further, better agreement was observed for stations recording higher snow depth. The uncertainties in validation of IMS snow product with stationed NCDC data were discussed.

  18. Utilization of a nitrogen-sulfur nonbonding interaction in the design of new 2-aminothiazol-5-yl-pyrimidines as p38α MAP kinase inhibitors.

    Science.gov (United States)

    Lin, Shuqun; Wrobleski, Stephen T; Hynes, John; Pitt, Sidney; Zhang, Rosemary; Fan, Yi; Doweyko, Arthur M; Kish, Kevin F; Sack, John S; Malley, Mary F; Kiefer, Susan E; Newitt, John A; McKinnon, Murray; Trzaskos, James; Barrish, Joel C; Dodd, John H; Schieven, Gary L; Leftheris, Katerina

    2010-10-01

    The design, synthesis, and structure-activity relationships (SAR) of a series of 2-aminothiazol-5-yl-pyrimidines as novel p38α MAP kinase inhibitors are described. These efforts led to the identification of 41 as a potent p38α inhibitor that utilizes a unique nitrogen-sulfur intramolecular nonbonding interaction to stabilize the conformation required for binding to the p38α active site. X-ray crystallographic studies that confirm the proposed binding mode of this class of inhibitors in p38 α and provide evidence for the proposed intramolecular nitrogen-sulfur interaction are discussed. Copyright © 2010 Elsevier Ltd. All rights reserved.

  19. Cortical Maps.

    Science.gov (United States)

    Bednar, James A; Wilson, Stuart P

    2016-12-01

    In this article, we review functional organization in sensory cortical regions-how the cortex represents the world. We consider four interrelated aspects of cortical organization: (1) the set of receptive fields of individual cortical sensory neurons, (2) how lateral interaction between cortical neurons reflects the similarity of their receptive fields, (3) the spatial distribution of receptive-field properties across the horizontal extent of the cortical tissue, and (4) how the spatial distributions of different receptive-field properties interact with one another. We show how these data are generally well explained by the theory of input-driven self-organization, with a family of computational models of cortical maps offering a parsimonious account for a wide range of map-related phenomena. We then discuss important challenges to this explanation, with respect to the maps present at birth, maps present under activity blockade, the limits of adult plasticity, and the lack of some maps in rodents. Because there is not at present another credible general theory for cortical map development, we conclude by proposing key experiments to help uncover other mechanisms that might also be operating during map development. © The Author(s) 2015.

  20. Map Learning with a 3D Printed Interactive Small-Scale Model: Improvement of Space and Text Memorization in Visually Impaired Students

    Directory of Open Access Journals (Sweden)

    Stéphanie Giraud

    2017-06-01

    Full Text Available Special education teachers for visually impaired students rely on tools such as raised-line maps (RLMs to teach spatial knowledge. These tools do not fully and adequately meet the needs of the teachers because they are long to produce, expensive, and not versatile enough to provide rapid updating of the content. For instance, the same RLM can barely be used during different lessons. In addition, those maps do not provide any interactivity, which reduces students’ autonomy. With the emergence of 3D printing and low-cost microcontrollers, it is now easy to design affordable interactive small-scale models (SSMs which are adapted to the needs of special education teachers. However, no study has previously been conducted to evaluate non-visual learning using interactive SSMs. In collaboration with a specialized teacher, we designed a SSM and a RLM representing the evolution of the geography and history of a fictitious kingdom. The two conditions were compared in a study with 24 visually impaired students regarding the memorization of the spatial layout and historical contents. The study showed that the interactive SSM improved both space and text memorization as compared to the RLM with braille legend. In conclusion, we argue that affordable home-made interactive small scale models can improve learning for visually impaired students. Interestingly, they are adaptable to any teaching situation including students with specific needs.

  1. Map Learning with a 3D Printed Interactive Small-Scale Model: Improvement of Space and Text Memorization in Visually Impaired Students.

    Science.gov (United States)

    Giraud, Stéphanie; Brock, Anke M; Macé, Marc J-M; Jouffrais, Christophe

    2017-01-01

    Special education teachers for visually impaired students rely on tools such as raised-line maps (RLMs) to teach spatial knowledge. These tools do not fully and adequately meet the needs of the teachers because they are long to produce, expensive, and not versatile enough to provide rapid updating of the content. For instance, the same RLM can barely be used during different lessons. In addition, those maps do not provide any interactivity, which reduces students' autonomy. With the emergence of 3D printing and low-cost microcontrollers, it is now easy to design affordable interactive small-scale models (SSMs) which are adapted to the needs of special education teachers. However, no study has previously been conducted to evaluate non-visual learning using interactive SSMs. In collaboration with a specialized teacher, we designed a SSM and a RLM representing the evolution of the geography and history of a fictitious kingdom. The two conditions were compared in a study with 24 visually impaired students regarding the memorization of the spatial layout and historical contents. The study showed that the interactive SSM improved both space and text memorization as compared to the RLM with braille legend. In conclusion, we argue that affordable home-made interactive small scale models can improve learning for visually impaired students. Interestingly, they are adaptable to any teaching situation including students with specific needs.

  2. Transferation of the theoretical and practical subjects concerning ionizing radiation physics to interactive multimedia-software for instructional purposes

    International Nuclear Information System (INIS)

    Salcher, R.

    1999-05-01

    The aim of this thesis was to produce a computer based training which allows the knowledge transfers of the theoretical and practical subjects of a radiation protection course according to the provisions of national law. An overview of the recent developments concerning 'Multimedia' is given in the first part of this work. General teaching methods and present-day national and international trends in information technology and instructional multimedia are analysed and differences between comparable methods are pointed out. The importance of producing computer based training courses by universities and external research centers is discussed. The basics of instructional multimedia and the authoring process are summarized and examples are given. An analysis of up-to-date authoring tools is also included. The individual modules of the developed computer based training like the transfer of two typical radiation protection experiments into a virtual counterpart are described in detail one by one (this partially also includes the specific programming solutions). The advantages of this form of knowledge transfer like the elimination of radiation risk by the use of virtual simulations are discussed. The efficiency of the knowledge transfer of this computer based training is verified by means of test persons. This project shows the potential of recent developments in the area of multimedia and information technology for the professional transfer of specific scientific know-how. (author)

  3. Revealing Cross-Frequency Causal Interactions During a Mental Arithmetic Task Through Symbolic Transfer Entropy: A Novel Vector-Quantization Approach.

    Science.gov (United States)

    Dimitriadis, Stavros; Sun, Yu; Laskaris, Nikolaos; Thakor, Nitish; Bezerianos, Anastasios

    2016-10-01

    Working memory (WM) is a distributed cognitive process that employs communication between prefrontal cortex and posterior brain regions in the form of cross-frequency coupling between theta ( θ) and high-alpha ( α2) brain waves. A novel method for deriving causal interactions between brain waves of different frequencies is essential for a better understanding of the neural dynamics of such complex cognitive process. Here, we proposed a novel method to estimate transfer entropy ( TE) through a symbolization scheme, which is based on neural-gas algorithm (NG) and encodes a bivariate time series in the form of two symbolic sequences. Given the symbolic sequences, the delay symbolic transfer entropy ( dSTE NG ) is defined. Our approach is akin to standard symbolic transfer entropy ( STE) that incorporates the ordinal pattern (OP) symbolization technique. We assessed the proposed method in a WM-invoked paradigm that included a mental arithmetic task at various levels of difficulty. Effective interactions between Frontal θ ( F θ ) and [Formula: see text] ( PO α2 ) brain waves were detected in multichannel EEG recordings from 16 subjects. Compared with conventional methods, our technique was less sensitive to noise and demonstrated improved computational efficiency in quantifying the dominating direction of effective connectivity between brain waves of different spectral content. Moreover, we discovered an efferent F θ connectivity pattern and an afferent PO α2 one, in all the levels of the task. Further statistical analysis revealed an increasing dSTE NG strength following the task's difficulty.

  4. Förster resonance energy transfer demonstrates a flavonoid metabolon in living plant cells that displays competitive interactions between enzymes

    NARCIS (Netherlands)

    Crosby, K.C.; Pietraszewska-Bogiel, A.; Gadella (jr.), T.W.J.; Winkel, B.S.J.

    2011-01-01

    We have used Förster resonance energy transfer detected by fluorescence lifetime imaging microscopy (FLIM-FRET) to provide the first evidence from living plants cells for the existence of a flavonoid metabolon. The distribution of flux within this system may be regulated by the direct competition of

  5. The Analysis of Interactivity in a Teaching and Learning Sequence of Rugby: The Transfer of Control and Learning Responsibility

    Science.gov (United States)

    Llobet-Martí, Bernat; López-Ros, Víctor; Vila, Ignasi

    2018-01-01

    Background: The social constructivist perspective emphasises that learning is a process of self-construction of knowledge in a social context. Game-centred approaches, such as teaching games for understanding, have been used in accordance with this perspective. The process of transferring learning responsibility takes place when the learner is…

  6. Estimating protein-protein interaction affinity in single living cells using Förster resonance energy transfer measurements

    DEFF Research Database (Denmark)

    Jensen, Jens Ledet; Raarup, Merete Krog; Rubak, Ege

    Using Förster resonance energy transfer (FRET) images we study the possibility of estimating the equilibrium dissociation constant Kd and the intrinsic FRET efficiency Em from single cells. We model the measurement uncertainty in the acquired images and use the method of total least squares...

  7. Infralimbic Prefrontal Cortex Interacts with Nucleus Accumbens Shell to Unmask Expression of Outcome-Selective Pavlovianto- Instrumental Transfer

    Science.gov (United States)

    Keistler, Colby; Barker, Jacqueline M.; Taylor, Jane R.

    2015-01-01

    Although several studies have examined the subcortical circuitry underlying Pavlovian-to-instrumental transfer (PIT), the role of medial prefrontal cortex in this behavior is largely unknown. Elucidating the cortical contributions to PIT will be key for understanding how reward-paired cues control behavior in both adaptive and maladaptive context…

  8. Transferring water management knowledge: how actors, interaction and context influence the effectiveness of Dutch-funded projects in Romania

    NARCIS (Netherlands)

    Vinke-de Kruijf, Joanne

    2013-01-01

    Countries around the world face pressing, often similar, water problems. International projects in which knowledge is transferred from one country to another can contribute to solving these problems. Building on the experiences of three Dutch-funded flood risk management projects in Romania, this

  9. Evaluating the interaction between progesterone, TNF alpha and cortisol on early loss of transferred embryos in beef cows

    Science.gov (United States)

    Fifty-eight non-lactating cows previously synchronized for estrus were assigned to two treatments to assess the effects of progesterone supplementation and its correlation with TNF-a and cortisol on the survival of the transferred embryos. On day 7 after exhibiting estrus (day 0), cows in both group...

  10. Mapping Medicare Disparities Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CMS Office of Minority Health has designed an interactive map, the Mapping Medicare Disparities Tool, to identify areas of disparities between subgroups of...

  11. Recovery Action Mapping Tool

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Recovery Action Mapping Tool is a web map that allows users to visually interact with and query actions that were developed to recover species listed under the...

  12. Mapping of interaction domains of putative telomere-binding proteins AtTRB1 and AtPOT1b from Arabidopsis thaliana.

    Science.gov (United States)

    Schrumpfová, Petra Procházková; Kuchar, Milan; Palecek, Jan; Fajkus, Jirí

    2008-04-30

    We previously searched for interactions between plant telomere-binding proteins and found that AtTRB1, from the single-myb-histone (Smh) family, interacts with the Arabidopsis POT1-like-protein, AtPOT1b, involved in telomere capping. Here we identify domains responsible for that interaction. We also map domains in AtTRB1 responsible for interactions with other Smh-family-members. Our results show that the N-terminal OB-fold-domain of AtPOT1b mediates the interaction with AtTRB1. This domain is characteristic for POT1- proteins and is involved with binding the G-rich-strand of telomeric DNA. AtPOT1b also interacts with AtTRB2 and AtTRB3. The central histone-globular-domain of AtTRB1 is involved with binding to AtTRB2 and 3, as well as to AtPOT1b. AtTRB1-heterodimers with other Smh-family-members are more stable than AtTRB1-homodimers. Our results reveal interaction networks of plant telomeres.

  13. The Application of an Emerging Technique for Protein–Protein Interaction Interface Mapping: The Combination of Photo-Initiated Cross-Linking Protein Nanoprobes with Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ptáčková Renata

    2014-05-01

    Full Text Available Protein–protein interaction was investigated using a protein nanoprobe capable of photo-initiated cross-linking in combination with high-resolution and tandem mass spectrometry. This emerging experimental approach introduces photo-analogs of amino acids within a protein sequence during its recombinant expression, preserves native protein structure and is suitable for mapping the contact between two proteins. The contact surface regions involved in the well-characterized interaction between two molecules of human 14-3-3ζ regulatory protein were used as a model. The employed photo-initiated cross-linking techniques extend the number of residues shown to be within interaction distance in the contact surface of the 14-3-3ζ dimer (Gln8–Met78. The results of this study are in agreement with our previously published data from molecular dynamic calculations based on high-resolution chemical cross-linking data and Hydrogen/Deuterium exchange mass spectrometry. The observed contact is also in accord with the 14-3-3ζ X-ray crystal structure (PDB 3dhr. The results of the present work are relevant to the structural biology of transient interaction in the 14-3-3ζ protein, and demonstrate the ability of the chosen methodology (the combination of photo-initiated cross-linking protein nanoprobes and mass spectrometry analysis to map the protein-protein interface or regions with a flexible structure.

  14. Molecular mapping of stripe rust resistance gene YrSE5756 in synthetic hexaploid wheat and its transfer to common wheat

    International Nuclear Information System (INIS)

    Wang, Y.J.; Wang, C.Y.; Zhang, H.

    2015-01-01

    Synthetic hexaploid wheat is an important germplasm resource for transfer of beneficial genes from alien species to common wheat (Triticum aestivum L.). Synthetic hexaploid wheat SE5756 confers a high level of resistance against a wide range of races of Puccinia striiformis West. f. sp. tritici Eriks. et Henn.(Pst). The objectives of this study were to determine the inheritance pattern, adjacent molecular markers, and chromosomal location of the stripe rust resistance gene in SE5756 and to develop new germplasm. We constructed a segregating population of 116 F2 plants and corresponding F2:3 families from a cross between SE5756 and Xinong979 with Pst races CYR32. Genetic analysis revealed that a single dominant gene, tentatively designated as YrSE5756, was responsible for seedling stage stripe rust resistance in SE5756. A genetic map, encompassing Xwmc626, Xwmc269, Xgwm11, Xbarx137, Xwmc419, Xwmc85, Xgpw5237, Xwmc134, WE173, Xwmc631, and YrSE5756, spanned 70.1 cM on chromosome 1BS. Xwmc419 and Xwmc85 were flanking markers tightly linked to YrSE5756 at genetic distances of 2.3 and 1.8 cM. Typical adult plant responses of the SE5756, varieties of the carrier Yr10 and Yr15, Chuanmai 42 (Yr24/Yr26), Yuanfeng 175 (Yr24/Yr26) and Huixianhong resistant to mixture Pst races (CYR32, CYR33 and V26) were experimented. The results showed that YrSE5756 was likely a new resistance stripe rust gene different from Yr24/Yr26, Yr10 and Yr15. From cross and backcross populations of SE5756/Xinong 979, we developed four new wheat lines with large seeds, stripe rust resistance, and improved agronomic traits: N07178-1, N07178-2, N08256-1, and N08256-2. These new germplasm lines could serve as sources of resistance to stripe rust in wheat breeding. SE5756 has the very vital significance in the development of breeding and expand our resistance germplasm resource gene pool. (author)

  15. Infrared-spectroscopic single-shot laser mapping ellipsometry: Proof of concept for fast investigations of structured surfaces and interactions in organic thin films

    Science.gov (United States)

    Furchner, Andreas; Kratz, Christoph; Gkogkou, Dimitra; Ketelsen, Helge; Hinrichs, Karsten

    2017-11-01

    We present a novel infrared-spectroscopic laser mapping ellipsometer based on a single-shot measurement concept. The ellipsometric set-up employs multiple analyzers and detectors to simultaneously measure the sample's optical response under different analyzer azimuths. An essential component is a broadly tunable quantum cascade laser (QCL) covering the important marker region of 1800-1540 cm-1. The ellipsometer allows for fast single-wavelength as well as spectroscopic studies with thin-film sensitivity at temporal resolutions of 60 ms per wavelength. We applied the single-shot mapping ellipsometer for the characterization of metal-island enhancement surfaces as well as of molecular interactions in organic thin films. In less than 3 min, a linescan with 1600 steps revealed profile and infrared-enhancement properties of a gradient gold-island film for sensing applications. Spectroscopic measurements were performed to probe the amide I band of thin films of poly(N-isopropylacrylamide) [PNIPAAm], a stimuli-responsive polymer for bioapplications. The QCL spectra agree well with conventional FT-IR ellipsometric results, showing different band components associated with hydrogen-bond interactions between polymer and adsorbed water. Multi-wavelength ellipsometric maps were used to analyze homogeneity and surface contaminations of the polymer films.

  16. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper looks at computer-assisted cartography as part...... of environmental knowledge production. It uses InfoAmazonia, the databased platform on Amazon rainforests, as an example of affective geo-visualization within information mapping that enhances embodiment in the experience of the information. Amazonia is defined as a digitally created affective (map)space within...

  17. Measuring ligand-dependent and ligand-independent interactions between nuclear receptors and associated proteins using Bioluminescence Resonance Energy Transfer (BRET).

    Science.gov (United States)

    Koterba, Kristen L; Rowan, Brian G

    2006-07-26

    Bioluminescent resonance energy transfer (BRET2) is a recently developed technology for the measurement of protein-protein interactions in a live, cell-based system. BRET2 is characterized by the efficient transfer of excited energy between a bioluminescent donor molecule (Renilla luciferase) and a fluorescent acceptor molecule (a mutant of Green Fluorescent Protein (GFP2). The BRET2 assay offers advantages over fluorescence resonance energy transfer (FRET) because it does not require an external light source thereby eliminating problems of photobleaching and autoflourescence. The absence of contamination by light results in low background that permits detection of very small changes in the BRET2 signal. BRET2 is dependent on the orientation and distance between two fusion proteins and therefore requires extensive preliminary standardization experiments to conclude a positive BRET2 signal independent of variations in protein titrations and arrangement in tertiary structures. Estrogen receptor (ER) signaling is modulated by steroid receptor coactivator 1 (SRC-1). To establish BRET2 in a ligand inducible system we used SRC-1 as the donor moiety and ER as the acceptor moiety. Expression and functionality of the fusion proteins were assessed by transient transfection in HEK-293 cells followed by Western blot analysis and measurement of ER-dependent reporter gene activity. These preliminary determinations are required prior to measuring nuclear receptor protein-protein interactions by BRET2. This article describes in detail the BRET2 methodology for measuring interaction between full-length ER and coregulator proteins in real-time, in an in vivo environment.

  18. The interaction between liquid motion and mass transfer induced by single rising bubble via PIV/LIE

    International Nuclear Information System (INIS)

    Yoshimoto, Kenjo; Yamamoto, Manabu; Sone, Daiji; Saito, Takayuki

    2009-01-01

    Deep understanding of gas-liquid two phase flows is essential for safe operation and high efficiency of nuclear reactors, chemical reactors and so on. In this study, we focus on the process of mass transfer induced by a single rising bubble. The mass transfer process of a zigzag ascending single bubble is investigated via LIF (Laser Induced Fluorescence) and PIV (Particle Image Velocimetry). From these results, we discuss the relationship between the mass transfer and the surrounding liquid motion of the single bubble. We examined single CO 2 -bubbles of 2-3 mm in equivalent diameter, which shows zigzagging motion in rest water. To directly visualize the dynamic mass transfer of CO 2 from the bubble surface to the surrounding liquid, HPTS (8-hydroxypyrene-1, 3, 6-trisulfonic acid) was used as a fluorescent substance for LIF. From LIF results, it was observed that the CO 2 -rich regions were spread by advective flow in the rest water as horseshoe-like vortices. From LIF results combined with the PIV results, it was observed that the horseshoe-like vortices were transported by the fast upward flow (buoyancy driven flow). Especially, in the case of a larger-diameter bubble with large shape oscillations, the high turbulence intensity (in a strict sense, fluctuation intensity of the liquid-phase velocity) was observed. The CO 2 -rich regions spread over a wide range by the strong flow. As a result, it is considered that the high turbulence intensity which was caused by the shape oscillations enhances the mass transportation from the bubble to the surrounding liquid. (author)

  19. Participatory Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    2016-01-01

    , it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This article looks at computer-assisted cartography as part of environmental knowledge production. It uses InfoAmazonia, the data-journalism platform on Amazon rainforests, as an example...

  20. Evaluation of an automated ultraviolet-C light disinfection device and patient hand hygiene for reduction of pathogen transfer from interactive touchscreen computer kiosks.

    Science.gov (United States)

    Alhmidi, Heba; Cadnum, Jennifer L; Piedrahita, Christina T; John, Amrita R; Donskey, Curtis J

    2018-04-01

    Touchscreens are a potential source of pathogen transmission. In our facility, patients and visitors rarely perform hand hygiene after using interactive touchscreen computer kiosks. An automated ultraviolet-C touchscreen disinfection device was effective in reducing bacteriophage MS2, bacteriophage ϕX174, methicillin-resistant Staphylococcus aureus, and Clostridium difficile spores inoculated onto a touchscreen. In simulations, an automated ultraviolet-C touchscreen disinfection device alone or in combination with hand hygiene reduced transfer of the viruses from contaminated touchscreens to fingertips. Published by Elsevier Inc.

  1. Crystal structure of a complex between lumiflavin and 2,6-diamino-9-ethylpurine: a flavin adenine dinucleotide model exhibiting charge-transfer interactions.

    Science.gov (United States)

    Scarbrough, F E; Shieh, H; Voet, D

    1976-11-01

    The x-ray structure of the deep red crystalline complex lumiflavin-2,6-diamino-9-ethylpurine has been determined. The flavin and adenine derivatives form hydrogen-bonded base pairs of the Watson-Crick type. The molecules in the crystal also associate via extensively overlapped flavin/adenine and flavin/flavin stacking interactions in which there are several contacts that are closer than van der Waals distances. This, together with the red color of the crystals, is indicative of the formation of a charge-transfer complex.

  2. Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping

    NARCIS (Netherlands)

    Broekgaarden, Colette; Bucher, Johan; Bac-Molenaar, Johanna; Keurentjes, Joost J.B.; Kruijer, Willem; Voorrips, Roeland E.; Vosman, Ben

    2015-01-01

    Plants have evolved a variety of ways to defend themselves against biotic attackers. This has resulted in the presence of substantial variation in defense mechanisms among plants, even within a species. Genome-wide association (GWA) mapping is a useful tool to study the genetic architecture of

  3. Making Large Class Basic Histology Lectures More Interactive: The Use of Draw-Along Mapping Techniques and Associated Educational Activities

    Science.gov (United States)

    Kotzé, Sanet Henriët; Mole, Calvin Gerald

    2015-01-01

    At Stellenbosch University, South Africa, basic histology is taught to a combination class of almost 400 first-year medical, physiotherapy, and dietetic students. Many students often find the amount of work in basic histology lectures overwhelming and consequently loose interest. The aim was to determine if a draw-along mapping activity would…

  4. Structural map of Kaposi sarcoma-associated herpesvirus RNA provides clues to molecular interactions | Center for Cancer Research

    Science.gov (United States)

    Scientists from CCR have generated a comprehensive structural map of Kaposi sarcoma-associated herpesvirus polyadenylated nuclear (PAN) RNA, a long non-coding RNA that helps the virus evade detection by its host’s immune system. The findings open new oppportunites to study the life cycle of this cancer-causing virus.  Learn more...

  5. Sharing our data—An overview of current (2016) USGS policies and practices for publishing data on ScienceBase and an example interactive mapping application

    Science.gov (United States)

    Chase, Katherine J.; Bock, Andrew R.; Sando, Roy

    2017-01-05

    This report provides an overview of current (2016) U.S. Geological Survey policies and practices related to publishing data on ScienceBase, and an example interactive mapping application to display those data. ScienceBase is an integrated data sharing platform managed by the U.S. Geological Survey. This report describes resources that U.S. Geological Survey Scientists can use for writing data management plans, formatting data, and creating metadata, as well as for data and metadata review, uploading data and metadata to ScienceBase, and sharing metadata through the U.S. Geological Survey Science Data Catalog. Because data publishing policies and practices are evolving, scientists should consult the resources cited in this paper for definitive policy information.An example is provided where, using the content of a published ScienceBase data release that is associated with an interpretive product, a simple user interface is constructed to demonstrate how the open source capabilities of the R programming language and environment can interact with the properties and objects of the ScienceBase item and be used to generate interactive maps.

  6. The calcium-binding protein ALG-2 regulates protein secretion and trafficking via interactions with MISSL and MAP1B proteins.

    Science.gov (United States)

    Takahara, Terunao; Inoue, Kuniko; Arai, Yumika; Kuwata, Keiko; Shibata, Hideki; Maki, Masatoshi

    2017-10-13

    Mobilization of intracellular calcium is essential for a wide range of cellular processes, including signal transduction, apoptosis, and vesicular trafficking. Several lines of evidence have suggested that apoptosis-linked gene 2 (ALG-2, also known as PDCD6 ), a calcium-binding protein, acts as a calcium sensor linking calcium levels with efficient vesicular trafficking, especially at the endoplasmic reticulum (ER)-to-Golgi transport step. However, how ALG-2 regulates these processes remains largely unclear. Here, we report that M APK1- i nteracting and s pindle- s tabilizing (MISS)- l ike (MISSL), a previously uncharacterized protein, interacts with ALG-2 in a calcium-dependent manner. Live-cell imaging revealed that upon a rise in intracellular calcium levels, GFP-tagged MISSL (GFP-MISSL) dynamically relocalizes in a punctate pattern and colocalizes with ALG-2. MISSL knockdown caused disorganization of the components of the ER exit site, the ER-Golgi intermediate compartment, and Golgi. Importantly, knockdown of either MISSL or ALG-2 attenuated the secretion of se creted a lkaline p hosphatase (SEAP), a model secreted cargo protein, with similar reductions in secretion by single- and double-protein knockdowns, suggesting that MISSL and ALG-2 act in the same pathway to regulate the secretion process. Furthermore, ALG-2 or MISSL knockdown delayed ER-to-Golgi transport of procollagen type I. We also found that ALG-2 and MISSL interact with microtubule-associated protein 1B (MAP1B) and that MAP1B knockdown reverts the reduced secretion of SEAP caused by MISSL or ALG-2 depletion. These results suggest that a change in the intracellular calcium level plays a role in regulation of the secretory pathway via interaction of ALG-2 with MISSL and MAP1B. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat

    OpenAIRE

    Singh, A.; Pandey, M. P.; Singh, A. K.; Knox, R. E.; Ammar, K.; Clarke, J. M.; Clarke, F. R.; Singh, R. P.; Pozniak, C. J.; DePauw, R. M.; McCallum, B. D.; Cuthbert, R. D.; Randhawa, H. S.; Fetch, T. G.

    2012-01-01

    Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf ...

  8. Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy.

    Science.gov (United States)

    Stich, Benjamin; Yu, Jianming; Melchinger, Albrecht E; Piepho, Hans-Peter; Utz, H Friedrich; Maurer, Hans P; Buckler, Edward S

    2007-05-01

    Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The single-nucleotide polymorphism haplotype data of B73 and 25 diverse maize inbreds were used to simulate the production of various RIL populations. Compared to the three-step genome scan, the power to detect three-way interactions was higher with the four-step genome scan. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distance-based designs than from nested designs or diallel designs. The power and PFP to detect three-way interactions using a nested design with 5000 RILs were for both the 4-QTL and the 12-QTL scenario of a magnitude that seems promising for their identification.

  9. Mortalin antibody-conjugated quantum dot transfer from human mesenchymal stromal cells to breast cancer cells requires cell–cell interaction

    International Nuclear Information System (INIS)

    Pietilä, Mika; Lehenkari, Petri; Kuvaja, Paula; Kaakinen, Mika; Kaul, Sunil C.; Wadhwa, Renu; Uemura, Toshimasa

    2013-01-01

    The role of tumor stroma in regulation of breast cancer growth has been widely studied. However, the details on the type of heterocellular cross-talk between stromal and breast cancer cells (BCCs) are still poorly known. In the present study, in order to investigate the intercellular communication between human mesenchymal stromal cells (hMSCs) and breast cancer cells (BCCs, MDA-MB-231), we recruited cell-internalizing quantum dots (i-QD) generated by conjugation of cell-internalizing anti-mortalin antibody and quantum dots (QD). Co-culture of illuminated and color-coded hMSCs (QD655) and BCCs (QD585) revealed the intercellular transfer of QD655 signal from hMSCs to BCCs. The amount of QD double positive BCCs increased gradually within 48 h of co-culture. We found prominent intercellular transfer of QD655 in hanging drop co-culture system and it was non-existent when hMSCs and BBCs cells were co-cultured in trans-well system lacking imminent cell–cell contact. Fluorescent and electron microscope analyses also supported that the direct cell-to-cell interactions may be required for the intercellular transfer of QD655 from hMSCs to BCCs. To the best of our knowledge, the study provides a first demonstration of transcellular crosstalk between stromal cells and BCCs that involve direct contact and may also include a transfer of mortalin, an anti-apoptotic and growth-promoting factor enriched in cancer cells

  10. Proton-transfer and H2-elimination reactions of trimethylamine alane: role of dihydrogen bonding and Lewis acid-base interactions.

    Science.gov (United States)

    Filippov, Oleg A; Tsupreva, Victoria N; Golubinskaya, Lyudmila M; Krylova, Antonina I; Bregadze, Vladimir I; Lledos, Agusti; Epstein, Lina M; Shubina, Elena S

    2009-04-20

    Proton-transfer and H(2)-elimination reactions of aluminum hydride AlH(3)(NMe(3)) (TMAA) with XH acids were studied by means of IR and NMR spectroscopy and DFT calculations. The dihydrogen-bonded (DHB) intermediates in the interaction of the TMAA with XH acids (CH(3)OH, (i)PrOH, CF(3)CH(2)OH, adamantyl acetylene, indole, 2,3,4,5,6-pentafluoroaniline, and 2,3,5,6-tetrachloroaniline) were examined experimentally at low temperatures, and the spectroscopic characteristics, dihydrogen bond strength and structures, and the electronic and energetic characteristics of these complexes were determined by combining experimental and theoretical approaches. The possibility of two different types of DHB complexes with polydentate proton donors (typical monodentate and bidentate coordination with the formation of a symmetrical chelate structure) was shown by DFT calculations and was experimentally proven in solution. The DHB complexes are intermediates of proton-transfer and H(2)-elimination reactions. The extent of this reaction is very dependent on the acid strength and temperature. With temperature increases the elimination of H(2) was observed for OH and NH acids, yielding the reaction products with Al-O and Al-N bonds. The reaction mechanism was computationally studied. Besides the DHB pathway for proton transfer, another pathway starting from a Lewis complex was discovered. Preference for one of the pathways is related to the acid strength and the nucleophilicity of the proton donor. As a consequence of the dual Lewis acid-base nature of neutral aluminum hydride, participation of a second ROH molecule acting as a bifunctional catalyst forming a six-member cycle connecting aluminum and hydride sites notably reduces the reaction barrier. This mechanism could operate for proton transfer from weak OH acids to TMAA in the presence of an excess of proton donor.

  11. How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium

    NARCIS (Netherlands)

    He, Yuejun; Cornelissen, J. Hans C.; Zhong, Zhangcheng; Dong, Ming; Jiang, Changhong

    2017-01-01

    In the karst landscape, widespread in the world including southern China, soil nutrient supply is strongly constrained. In such environments, arbuscular mycorrhizal (AM) fungi may facilitate plant nutrient uptake. However, the possible role of different AM fungal species, and their interactions,

  12. Probing nucleic acid interactions and pre-mRNA splicing by Förster resonance energy transfer (FRET) microscopy

    Czech Academy of Sciences Publication Activity Database

    Šimková, Eva; Staněk, David

    2012-01-01

    Roč. 13, č. 11 (2012), s. 14929-14945 E-ISSN 1422-0067 R&D Projects: GA AV ČR KAN200520801 Institutional support: RVO:68378050 Keywords : FRET * FLIM * acceptor photobleaching * RNA interactions * spliceosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.464, year: 2012

  13. Characterization of G-protein coupled receptor kinase interaction with the neurokinin-1 receptor using bioluminescence resonance energy transfer

    DEFF Research Database (Denmark)

    Jorgensen, Rasmus; Holliday, Nicholas D; Hansen, Jakob L

    2007-01-01

    activation, the full-length NK-1 receptor, but not a functional C-terminal tail-truncated receptor, is preassociated with GRK5 in a relatively low-affinity state. We demonstrate that GRK5 can compete for agonist induced GRK2 interaction with the NK-1 receptor, whereas GRK2 does not compete for receptor...

  14. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper looks at computer-assisted cartography as part...

  15. Participatory maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    , performative, and participatory practice. In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-human- geographies’ practices include notions of species, space and territory, and movement...... towards a new political ecology. This type of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper...

  16. The impact of electrostatic interactions on ultrafast charge transfer at Ag 29 nanoclusters–fullerene and CdTe quantum dots–fullerene interfaces

    KAUST Repository

    Ahmed, Ghada H.

    2015-11-09

    A profound understanding of charge transfer (CT) at semiconductor quantum dots (QDs) and nanoclusters (NCs) interfaces is extremely important to optimize the energy conversion efficiency in QDs and NCs-based solar cell devices. Here, we report on the ground- and excited-state interactions at the interface of two different bimolecular non-covalent donor-acceptor (D-A) systems using steady-state and femtosecond transient absorption (fs-TA) spectroscopy with broadband capabilities. We systematically investigate the electrostatic interactions between the positively charged fullerene derivative C60-(N,N dimethylpyrrolidinium iodide) (CF) employed as an efficient molecular acceptor and two different donor molecules: Ag29 nanoclusters (NCs) and CdTe quantum dots (QDs). For comparison purposes, we also monitor the interaction of each donor molecule with the neutral fullerene derivative C60-(malonic acid)n, which has minimal electrostatic interactions. Our steady-state and time-resolved data demonstrate that both QDs and NCs have strong interfacial electrostatic interactions and dramatic fluorescence quenching when the CF derivative is present. In other words, our results reveal that only CF can be in close molecular proximity with the QDs and NCs, allowing ultrafast photoinduced CT to occur. It turned out that the intermolecular distances, electronic coupling and subsequently CT from the excited QDs or NCs to fullerene derivatives can be controlled by the interfacial electrostatic interactions. Our findings highlight some of the key variable components for optimizing CT at QDs and NCs interfaces, which can also be applied to other D-A systems that rely on interfacial CT. © The Royal Society of Chemistry 2016.

  17. Development of a Time-Resolved Fluorescence Resonance Energy Transfer Ultrahigh-Throughput Screening Assay for Targeting the NSD3 and MYC Interaction.

    Science.gov (United States)

    Xiong, Jinglin; Pecchi, Valentina Gonzalez; Qui, Min; Ivanov, Andrey A; Mo, Xiulei; Niu, Qiankun; Chen, Xiang; Fu, Haian; Du, Yuhong

    Epigenetic modulators play critical roles in reprogramming of cellular functions, emerging as a new class of promising therapeutic targets. Nuclear receptor binding SET domain protein 3 (NSD3) is a member of the lysine methyltransferase family. Interestingly, the short isoform of NSD3 without the methyltransferase fragment, NSD3S, exhibits oncogenic activity in a wide range of cancers. We recently showed that NSD3S interacts with MYC, a central regulator of tumorigenesis, suggesting a mechanism by which NSD3S regulates cell proliferation through engaging MYC. Thus, small molecule inhibitors of the NSD3S/MYC interaction will be valuable tools for understanding the function of NSD3 in tumorigenesis for potential cancer therapeutic discovery. Here we report the development of a cell lysate-based time-resolved fluorescence resonance energy transfer (TR-FRET) assay in an ultrahigh-throughput screening (uHTS) format to monitor the interaction of NSD3S with MYC. In our TR-FRET assay, anti-Flag-terbium and anti-glutathione S-transferase (GST)-d2, a paired fluorophores, were used to indirectly label Flag-tagged NSD3 and GST-MYC in HEK293T cell lysates. This TR-FRET assay is robust in a 1,536-well uHTS format, with signal-to-background >8 and a Z' factor >0.7. A pilot screening with the Spectrum library of 2,000 compounds identified several positive hits. One positive compound was confirmed to disrupt the NSD3/MYC interaction in an orthogonal protein-protein interaction assay. Thus, our optimized uHTS assay could be applied to future scaling up of a screening campaign to identify small molecule inhibitors targeting the NSD3/MYC interaction.

  18. Development of an expert analysis tool based on an interactive subsidence hazard map for urban land use in the city of Celaya, Mexico

    Science.gov (United States)

    Alloy, A.; Gonzalez Dominguez, F.; Nila Fonseca, A. L.; Ruangsirikulchai, A.; Gentle, J. N., Jr.; Cabral, E.; Pierce, S. A.

    2016-12-01

    Land Subsidence as a result of groundwater extraction in central Mexico's larger urban centers initiated in the 80's as a result of population and economic growth. The city of Celaya has undergone subsidence for a few decades and a consequence is the development of an active normal fault system that affects its urban infrastructure and residential areas. To facilitate its analysis and a land use decision-making process we created an online interactive map enabling users to easily obtain information associated with land subsidence. Geological and socioeconomic data of the city was collected, including fault location, population data, and other important infrastructure and structural data has been obtained from fieldwork as part of a study abroad interchange undergraduate course. The subsidence and associated faulting hazard map was created using an InSAR derived subsidence velocity map and population data from INEGI to identify hazard zones using a subsidence gradient spatial analysis approach based on a subsidence gradient and population risk matrix. This interactive map provides a simple perspective of different vulnerable urban elements. As an accessible visualization tool, it will enhance communication between scientific and socio-economic disciplines. Our project also lays the groundwork for a future expert analysis system with an open source and easily accessible Python coded, SQLite database driven website which archives fault and subsidence data along with visual damage documentation to civil structures. This database takes field notes and provides an entry form for uniform datasets, which are used to generate a JSON. Such a database is useful because it allows geoscientists to have a centralized repository and access to their observations over time. Because of the widespread presence of the subsidence phenomena throughout cities in central Mexico, the spatial analysis has been automated using the open source software R. Raster, rgeos, shapefiles, and rgdal

  19. Communication: electron transfer mediated decay enabled by spin-orbit interaction in small krypton/xenon clusters.

    Science.gov (United States)

    Zobel, J Patrick; Kryzhevoi, Nikolai V; Pernpointner, Markus

    2014-04-28

    In this work we study the influence of relativistic effects, in particular spin-orbit coupling, on electronic decay processes in KrXe2 clusters of various geometries. For the first time it is shown that inclusion of spin-orbit coupling has decisive influence on the accessibility of a specific decay pathway in these clusters. The radiationless relaxation process is initiated by a Kr 4s ionization followed by an electron transfer from xenon to krypton and a final second ionization of the system. We demonstrate the existence of competing electronic decay pathways depending in a subtle way on the geometry and level of theory. For our calculations a fully relativistic framework was employed where omission of spin-orbit coupling leads to closing of two decay pathways. These findings stress the relevance of an adequate relativistic description for clusters with heavy elements and their fragmentation dynamics.

  20. Peptide-Driven Charge-Transfer Organogels Built from Synergetic Hydrogen Bonding and Pyrene-Naphthalenediimide Donor-Acceptor Interactions.

    Science.gov (United States)

    Bartocci, Silvia; Berrocal, José Augusto; Guarracino, Paola; Grillaud, Maxime; Franco, Lorenzo; Mba, Miriam

    2018-02-26

    The peptide-driven formation of charge transfer (CT) supramolecular gels featuring both directional hydrogen-bonding and donor-acceptor (D-A) complexation is reported. Our design consists of the coassembly of two dipeptide-chromophore conjugates, namely diphenylalanine (FF) dipeptide conveniently functionalized at the N-terminus with either a pyrene (Py-1, donor) or naphthalene diimide (NDI-1, acceptor). UV/Vis spectroscopy confirmed the formation of CT complexes. FTIR and 1 H NMR spectroscopy studies underlined the pivotal role of hydrogen bonding in the gelation process, and electronic paramagnetic resonance (EPR) measurements unraveled the advantage of preorganized CT supramolecular architectures for charge transport over solutions containing non-coassembled D and A molecular systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins

    International Nuclear Information System (INIS)

    Tieleman, D Peter; MacCallum, Justin L; Ash, Walter L; Kandt, Christian; Xu Zhitao; Monticelli, Luca

    2006-01-01

    We have reparameterized the dihedral parameters in a commonly used united-atom lipid force field so that they can be used with the all-atom OPLS force field for proteins implemented in the molecular dynamics simulation software GROMACS. Simulations with this new combination give stable trajectories and sensible behaviour of both lipids and protein. We have calculated the free energy of transfer of amino acid side chains between water and 'lipid-cyclohexane', made of lipid force field methylene groups, as a hydrophobic mimic of the membrane interior, for both the OPLS-AA and a modified OPLS-AA force field which gives better hydration free energies under simulation conditions close to those preferred for the lipid force field. The average error is 4.3 kJ mol -1 for water-'lipid-cyclohexane' compared to 3.2 kJ mol -1 for OPLS-AA cyclohexane and 2.4 kJ mol -1 for the modified OPLS-AA water-'lipid-cyclohexane'. We have also investigated the effect of different methods to combine parameters between the united-atom lipid force field and the united-atom protein force field ffgmx. In a widely used combination, the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering. Using straight combination rules improves the results. Combined, we suggest that using OPLS-AA together with the united-atom lipid force field implemented in GROMACS is a reasonable approach to membrane protein simulations. We also suggest that using partial volume information and free energies of transfer may help to improve the parameterization of lipid-protein interactions and point out the need for accurate experimental data to validate and improve force field descriptions of such interactions

  2. Mapping epistasis and environment × QTX interaction based on four -omics genotypes for the detected QTX loci controlling complex traits in tobacco

    Directory of Open Access Journals (Sweden)

    Liyuan Zhou

    2013-12-01

    Full Text Available Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four -omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP (QTS loci, quantitative trait transcript (QTT differences, quantitative trait protein (QTP variability, and quantitative trait metabolite (QTM changes, which can be summarized as QTX locus variation. The total heritabilities of the four -omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction. Epistasis and environment × treatment interaction had important impacts on complex traits at all -omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation.

  3. HealthMap: a cluster randomised trial of interactive health plans and self-management support to prevent coronary heart disease in people with HIV.

    Science.gov (United States)

    Dodson, Sarity; Klassen, Karen M; McDonald, Karalyn; Millard, Tanya; Osborne, Richard H; Battersby, Malcolm W; Fairley, Christopher K; Simpson, Julie A; Lorgelly, Paula; Tonkin, Andrew; Roney, Janine; Slavin, Sean; Sterjovski, Jasminka; Brereton, Margot; Lewin, Sharon R; Crooks, Levinia; Watson, Jo; Kidd, Michael R; Williams, Irith; Elliott, Julian H

    2016-03-05

    The leading causes of morbidity and mortality for people in high-income countries living with HIV are now non-AIDS malignancies, cardiovascular disease and other non-communicable diseases associated with ageing. This protocol describes the trial of HealthMap, a model of care for people with HIV (PWHIV) that includes use of an interactive shared health record and self-management support. The aims of the HealthMap trial are to evaluate engagement of PWHIV and healthcare providers with the model, and its effectiveness for reducing coronary heart disease risk, enhancing self-management, and improving mental health and quality of life of PWHIV. The study is a two-arm cluster randomised trial involving HIV clinical sites in several states in Australia. Doctors will be randomised to the HealthMap model (immediate arm) or to proceed with usual care (deferred arm). People with HIV whose doctors are randomised to the immediate arm receive 1) new opportunities to discuss their health status and goals with their HIV doctor using a HealthMap shared health record; 2) access to their own health record from home; 3) access to health coaching delivered by telephone and online; and 4) access to a peer moderated online group chat programme. Data will be collected from participating PWHIV (n = 710) at baseline, 6 months, and 12 months and from participating doctors (n = 60) at baseline and 12 months. The control arm will be offered the HealthMap intervention at the end of the trial. The primary study outcomes, measured at 12 months, are 1) 10-year risk of non-fatal acute myocardial infarction or coronary heart disease death as estimated by a Framingham Heart Study risk equation; and 2) Positive and Active Engagement in Life Scale from the Health Education Impact Questionnaire (heiQ). The study will determine the viability and utility of a novel technology-supported model of care for maintaining the health and wellbeing of people with HIV. If shown to be effective, the HealthMap model

  4. In vivo detection of RNA-binding protein interactions with cognate RNA sequences by fluorescence resonance energy transfer

    Czech Academy of Sciences Publication Activity Database

    Huranová, Martina; Jablonski, J.A.; Benda, Aleš; Hof, Martin; Staněk, David; Caputi, M.

    2009-01-01

    Roč. 15, č. 11 (2009), s. 2063-2071 ISSN 1355-8382 R&D Projects: GA AV ČR KAN200520801; GA MŠk(CZ) LC06063 Institutional research plan: CEZ:AV0Z50520514; CEZ:AV0Z40400503 Keywords : FRET * FLIM * RNA-protein interactions Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.198, year: 2009

  5. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...... interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...

  6. Interactions

    DEFF Research Database (Denmark)

    The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists such as ......The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists...... such as Lorentz and Einstein as well as mathematicians such as Poincare, Minkowski, Hilbert and Weyl contributed to this development. They created the new physical theories and the mathematical disciplines that play such paramount roles in their mathematical formulations. These physicists and mathematicians were...... also key figures in the philosophical discussions of nature and science - from philosophical tendencies like logical empiricism via critical rationalism to various neo-Kantian trends....

  7. Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping.

    Science.gov (United States)

    Gallone, Giuseppe; Simpson, T Ian; Armstrong, J Douglas; Jarman, Andrew P

    2011-07-18

    Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction. We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation. Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the

  8. Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping

    Directory of Open Access Journals (Sweden)

    Armstrong J Douglas

    2011-07-01

    Full Text Available Abstract Background Protein-protein interaction (PPI data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction. Results We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation. Conclusions Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy

  9. ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.

    Science.gov (United States)

    Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Tagore, Somnath; Sekar, Vaishnovi; Vazquez, Miguel; Valencia, Alfonso

    2017-07-07

    Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein-protein interactions (ChiPPI) that uses the domain-domain co-occurrence scores in order to identify preserved interactors of chimeric proteins. Mapping the influence of fusion proteins on cell metabolism and pathways reveals that ChiPPI networks often lose tumor suppressor proteins and gain oncoproteins. Furthermore, fusions often induce novel connections between non-interactors skewing interaction networks and signaling pathways. We compared fusion protein PPI networks in leukemia/lymphoma, sarcoma and solid tumors finding distinct enrichment patterns for each disease type. While certain pathways are enriched in all three diseases (Wnt, Notch and TGF β), there are distinct patterns for leukemia (EGFR signaling, DNA replication and CCKR signaling), for sarcoma (p53 pathway and CCKR signaling) and solid tumors (FGFR and EGFR signaling). Thus, the ChiPPI method represents a comprehensive tool for studying the anomaly of skewed cellular networks produced by fusion proteins in cancer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex.

    Science.gov (United States)

    Armour, Sean M; Bennett, Eric J; Braun, Craig R; Zhang, Xiao-Yong; McMahon, Steven B; Gygi, Steven P; Harper, J Wade; Sinclair, David A

    2013-04-01

    Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex.

  11. Role of hydrogen-bonding and photoinduced electron transfer (PET) on the interaction of resorcinol based acridinedione dyes with Bovine Serum Albumin (BSA) in water

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran, Rajendran, E-mail: kumaranwau@rediffmail.com [Department of Chemistry, Dwaraka Doss Goverdhan Doss, Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu (India); Vanjinathan, Mahalingam [Department of Chemistry, Dwaraka Doss Goverdhan Doss, Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu (India); Ramamurthy, Perumal [National Centre for Ultrafast Processes, University of Madras, Taramani Campus Chennai 600113, Tamil Nadu (India)

    2015-08-15

    Resorcinol based acridinedione (ADDR) dyes are a class of laser dyes and have structural similarity with purine derivatives, nicotinamide adenine dinucleotide (NADH) analogs. These dyes are classified into photoinduced electron transfer (PET) and non-photoinduced electron transfer dyes, and the photophysical properties of family of these dyes exhibiting PET behavior are entirely different from that of non-PET dyes. The PET process in ADDR dyes is governed by the solvent polarity such that an ADDR dye exhibits PET process through space in an aprotic solvent like acetonitrile and does not exhibit the same in protic solvents like water and methanol. A comparison on the fluorescence emission, lifetime and nature of interaction of various ADDR dyes with a large globular protein like Bovine Serum Albumin (BSA) was carried out in aqueous solution. The interaction of PET based ADDR dyes with BSA in water is found to be largely hydrophobic, but hydrogen-bonding interaction of BSA with dye molecule influences the fluorescence emission of the dye and shifts the emission towards red region. Fluorescence spectral studies reveal that the excited state properties of PET based ADDR dyes are largely influenced by the addition of BSA. The microenvironment around the dye results in significant change in the fluorescence lifetime and emission. Fluorescence enhancement with a red shift in the emission results after the addition of BSA to ADDR dyes containing free amino hydrogen in the 10th position of basic acridinedione dye. The amino hydrogen (N–H) in the 10th position of ADDR dye is replaced by methyl group (N–CH{sub 3}), a significant decrease in the fluorescence intensity with no apparent shift in the emission maximum was observed after the addition of BSA. The nature of interaction between ADDR dyes with BSA is hydrogen-bonding and the dye remains unbound even at the highest concentration of BSA. Circular Dichroism (CD) studies show that the addition of dye to BSA results in

  12. Role of hydrogen-bonding and photoinduced electron transfer (PET) on the interaction of resorcinol based acridinedione dyes with Bovine Serum Albumin (BSA) in water

    International Nuclear Information System (INIS)

    Kumaran, Rajendran; Vanjinathan, Mahalingam; Ramamurthy, Perumal

    2015-01-01

    Resorcinol based acridinedione (ADDR) dyes are a class of laser dyes and have structural similarity with purine derivatives, nicotinamide adenine dinucleotide (NADH) analogs. These dyes are classified into photoinduced electron transfer (PET) and non-photoinduced electron transfer dyes, and the photophysical properties of family of these dyes exhibiting PET behavior are entirely different from that of non-PET dyes. The PET process in ADDR dyes is governed by the solvent polarity such that an ADDR dye exhibits PET process through space in an aprotic solvent like acetonitrile and does not exhibit the same in protic solvents like water and methanol. A comparison on the fluorescence emission, lifetime and nature of interaction of various ADDR dyes with a large globular protein like Bovine Serum Albumin (BSA) was carried out in aqueous solution. The interaction of PET based ADDR dyes with BSA in water is found to be largely hydrophobic, but hydrogen-bonding interaction of BSA with dye molecule influences the fluorescence emission of the dye and shifts the emission towards red region. Fluorescence spectral studies reveal that the excited state properties of PET based ADDR dyes are largely influenced by the addition of BSA. The microenvironment around the dye results in significant change in the fluorescence lifetime and emission. Fluorescence enhancement with a red shift in the emission results after the addition of BSA to ADDR dyes containing free amino hydrogen in the 10th position of basic acridinedione dye. The amino hydrogen (N–H) in the 10th position of ADDR dye is replaced by methyl group (N–CH 3 ), a significant decrease in the fluorescence intensity with no apparent shift in the emission maximum was observed after the addition of BSA. The nature of interaction between ADDR dyes with BSA is hydrogen-bonding and the dye remains unbound even at the highest concentration of BSA. Circular Dichroism (CD) studies show that the addition of dye to BSA results in a

  13. Mapping of immunogenic and protein-interacting regions at the surface of the seven-bladed β-propeller domain of the HIV-1 cellular interactor EED

    Directory of Open Access Journals (Sweden)

    Gouet Patrice

    2008-02-01

    Full Text Available Abstract Background The human EED protein, a member of the superfamily of Polycomb group proteins, is involved in multiple cellular protein complexes. Its C-terminal domain, which is common to the four EED isoforms, contains seven repeats of a canonical WD-40 motif. EED is an interactor of three HIV-1 proteins, matrix (MA, integrase (IN and Nef. An antiviral activity has been found to be associated with isoforms EED3 and EED4 at the late stage of HIV-1 replication, due to a negative effect on virus assembly and genomic RNA packaging. The aim of the present study was to determine the regions of the EED C-terminal core domain which were accessible and available to protein interactions, using three-dimensional (3D protein homology modelling with a WD-40 protein of known structure, and epitope mapping of anti-EED antibodies. Results Our data suggested that the C-terminal domain of EED was folded as a seven-bladed β-propeller protein. During the completion of our work, crystallographic data of EED became available from co-crystals of the EED C-terminal core with the N-terminal domain of its cellular partner EZH2. Our 3D-model was in good congruence with the refined structural model determined from crystallographic data, except for a unique α-helix in the fourth β-blade. More importantly, the position of flexible loops and accessible β-strands on the β-propeller was consistent with our mapping of immunogenic epitopes and sites of interaction with HIV-1 MA and IN. Certain immunoreactive regions were found to overlap with the EZH2, MA and IN binding sites, confirming their accessibility and reactivity at the surface of EED. Crystal structure of EED showed that the two discrete regions of interaction with MA and IN did not overlap with each other, nor with the EZH2 binding pocket, but were contiguous, and formed a continuous binding groove running along the lateral face of the β-propeller. Conclusion Identification of antibody-, MA-, IN- and EZH2

  14. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...

  15. Technology Transfer

    Science.gov (United States)

    Smith, Nanette R.

    1995-01-01

    The objective of this summer's work was to attempt to enhance Technology Application Group (TAG) ability to measure the outcomes of its efforts to transfer NASA technology. By reviewing existing literature, by explaining the economic principles involved in evaluating the economic impact of technology transfer, and by investigating the LaRC processes our William & Mary team has been able to lead this important discussion. In reviewing the existing literature, we identified many of the metrics that are currently being used in the area of technology transfer. Learning about the LaRC technology transfer processes and the metrics currently used to track the transfer process enabled us to compare other R&D facilities to LaRC. We discuss and diagram impacts of technology transfer in the short run and the long run. Significantly, it serves as the basis for analysis and provides guidance in thinking about what the measurement objectives ought to be. By focusing on the SBIR Program, valuable information regarding the strengths and weaknesses of this LaRC program are to be gained. A survey was developed to ask probing questions regarding SBIR contractors' experience with the program. Specifically we are interested in finding out whether the SBIR Program is accomplishing its mission, if the SBIR companies are providing the needed innovations specified by NASA and to what extent those innovations have led to commercial success. We also developed a survey to ask COTR's, who are NASA employees acting as technical advisors to the SBIR contractors, the same type of questions, evaluating the successes and problems with the SBIR Program as they see it. This survey was developed to be implemented interactively on computer. It is our hope that the statistical and econometric studies that can be done on the data collected from all of these sources will provide insight regarding the direction to take in developing systematic evaluations of programs like the SBIR Program so that they can

  16. Mapping with Drupal

    CERN Document Server

    Palazzolo, Alan

    2011-01-01

    Build beautiful interactive maps on your Drupal website, and tell engaging visual stories with your data. This concise guide shows you how to create custom geographical maps from top to bottom, using Drupal 7 tools and out-of-the-box modules. You'll learn how mapping works in Drupal, with examples on how to use intuitive interfaces to map local events, businesses, groups, and other custom data. Although building maps with Drupal can be tricky, this book helps you navigate the system's complexities for creating sophisticated maps that match your site design. Get the knowledge and tools you ne

  17. Accurate Mapping of Multilevel Rydberg Atoms on Interacting Spin-1 /2 Particles for the Quantum Simulation of Ising Models

    Science.gov (United States)

    de Léséleuc, Sylvain; Weber, Sebastian; Lienhard, Vincent; Barredo, Daniel; Büchler, Hans Peter; Lahaye, Thierry; Browaeys, Antoine

    2018-03-01

    We study a system of atoms that are laser driven to n D3 /2 Rydberg states and assess how accurately they can be mapped onto spin-1 /2 particles for the quantum simulation of anisotropic Ising magnets. Using nonperturbative calculations of the pair potentials between two atoms in the presence of electric and magnetic fields, we emphasize the importance of a careful selection of experimental parameters in order to maintain the Rydberg blockade and avoid excitation of unwanted Rydberg states. We benchmark these theoretical observations against experiments using two atoms. Finally, we show that in these conditions, the experimental dynamics observed after a quench is in good agreement with numerical simulations of spin-1 /2 Ising models in systems with up to 49 spins, for which numerical simulations become intractable.

  18. Electron transfer from plant phenolates to carotenoid radical cations. Antioxidant interaction entering the Marcus theory inverted region.

    Science.gov (United States)

    Cheng, Hong; Han, Rui-Min; Zhang, Jian-Ping; Skibsted, Leif H

    2014-01-29

    β-Carotene, lycopene, and zeaxanthin are maximally regenerated by plant phenolates from their radical cations formed during laser flash photolysis in 9:1 (v/v) chloroform/methanol for a driving force corresponding to the reorganization energy according to the Marcus theory. For β-carotene, the reorganization energy has values of 0.41 ± 0.04 and 0.40 ± 0.04 eV for the plant phenols in the presence of 1 and 2 equiv of base, respectively, at 23 °C. For a driving force lower than the reorganization energy, regeneration of the carotenoids is less efficient as is seen for m-hydroxybenzoic acid, vanillic acid, and p-coumaric acid. For a driving force above the maximum rate as determined to have kET = 6.3 × 10(9) L·mol(-1)·s(-1) for syringic acid and β-carotene, the reaction becomes gradually slower and regeneration less efficient as is seen for the more reducing caffeic acid, rutin, and quercetin corresponding to an inverted region for the rate of electron transfer. Lycopene and zeaxanthin show a similar behavior for the same series of plant phenols with slightly lower reorganization energy, in agreement with the lower reduction potential of their radical cations, while, for the ketocarotenoids astaxanthin and canthaxanthin, fast reactions with a solvent of radical cations inhibit regeneration from being detected. Intermediate reducing plant phenols accordingly yield maximal protection of carotenoids against photobleaching in foods and beverages.

  19. Interaction of nitrogen oxides with sublimed layers of (meso-tetraphenylporphyrinato)cobalt(II); IR evidence of oxo-transfer from (nitro)porphyrinatocobalt(III) to free nitric oxide.

    Science.gov (United States)

    Kurtikyan, Tigran S; Mardyukov, Arthur N; Goodwin, John A

    2003-12-15

    Interaction of a low-pressure NO2 with sublimed layers of (meso-tetraphenylporphyrinato)cobalt(II) (Co(TPP)) leads to formation of 5-coordinate nitro complex Co(III)(TPP)(NO2). Upon exposure of these layers to pyridine vapors, the fast reaction with formation of 6-coordinate nitro-pyridine porphyrins (Py)Co(III)(TPP)(NO2) occurs. By means of IR spectroscopy and use of nitrogen oxide isotopomers, it is shown that an oxo-transfer reaction occurs from 5-coordinate species to free nitric oxide (NO) while the 6-coordinate complex is rather inert. It is also demonstrated that the stepwise addition of low-pressure NO2 to nitrosyl complex Co(TPP)(NO) leads to formation of the nitro complex most likely by an exchange reaction.

  20. Mapping and characterization of the interaction interface between two polypyrimidine-tract binding proteins and a nova-type protein of Solanum tuberosum.

    Directory of Open Access Journals (Sweden)

    Shweta Shah

    Full Text Available Polypyrimidine tract-binding (PTB proteins are RNA-binding proteins that generally contain four RNA recognition motifs (RRMs. In potato, six cDNAs encoding full-length PTB proteins have been identified. In the present study Nova1-like protein, designated StNova1, was identified as a potential interacting partner of the StPTB proteins via yeast two-hybrid screening. Nova protein is a RNA-binding protein that contains three K-homology (KH domains. In humans, these proteins are involved in regulation of neuronal RNA metabolism but the role of Nova-like proteins in plants is poorly understood. We have validated this interaction and mapped the protein binding region on StNova1 and StPTB1 and -6 using a novel domain interaction phage display (DIPP technique. The interaction between the two RNA-binding proteins StPTB1/6 and StNova1 is mediated through linker regions that are distinctly separated from the RRMs. Furthermore, using a random 21-mer phage-peptide library, we have identified a number of peptides with the consensus sequence motif [S/G][V/I][L/V]G that recognize the StPTB proteins. One over-represented peptide that recognizes StPTB6 contains the GVLGPWP sequence that is similar to the GIGGRYP sequence in the glycine-rich linker region between the KH2 and KH3 domains of StNova1. We show, through site-specific mutations, the importance of glycine and proline residues in StNova1-StPTB interactions.

  1. Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin.

    Directory of Open Access Journals (Sweden)

    Haruka Kameda

    Full Text Available Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd, a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I at 1.46 Å resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported; we identified the short α-helix (67-71 near the active center, which is conserved in other plant-type [2Fe-2S] Fds. Although the 3D structures of the four molecules in the asymmetric unit are similar to each other, detailed comparison of the four structures revealed the segments whose conformations are variable. Structural comparison between the Fds from different sources showed that the distribution of the variable segments in AsFd-I is highly conserved in other Fds, suggesting the presence of intrinsically flexible regions in the plant-type [2Fe-2S] Fd. A few structures of the complexes with Fd-dependent enzymes clearly demonstrate that the protein-protein interactions are achieved through these variable regions in Fd. The results described here will provide a guide for interpreting the biochemical and mutational studies that aim at the manner of interactions with Fd-dependent enzymes.

  2. Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

    Energy Technology Data Exchange (ETDEWEB)

    Bejerman, Nicolás, E-mail: n.bejerman@uq.edu.au [Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria INTA, Camino a 60 Cuadras k 5,5, Córdoba X5020ICA (Argentina); Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 (Australia); Giolitti, Fabián; Breuil, Soledad de; Trucco, Verónica; Nome, Claudia; Lenardon, Sergio [Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria INTA, Camino a 60 Cuadras k 5,5, Córdoba X5020ICA (Argentina); Dietzgen, Ralf G. [Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 (Australia)

    2015-09-15

    Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses.

  3. Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

    International Nuclear Information System (INIS)

    Bejerman, Nicolás; Giolitti, Fabián; Breuil, Soledad de; Trucco, Verónica; Nome, Claudia; Lenardon, Sergio; Dietzgen, Ralf G.

    2015-01-01

    Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses

  4. Binding interactions between yeast tRNA ligase and a precursor transfer ribonucleic acid containing two photoreactive uridine analogues

    International Nuclear Information System (INIS)

    Tanner, N.K.; Hanna, M.M.; Abelson, J.

    1988-01-01

    Yeast tRNA ligase, from Saccharomyces cerevisiae, is one of the protein components that is involved in the splicing reaction of intron-containing yeast precursor tRNAs. It is an unusual protein because it has three distinct catalytic activities. It functions as a polynucleotide kinase, as a cyclic phosphodiesterase, and as an RNA ligase. We have studied the binding interactions between ligase and precursor tRNAs containing two photoreactive uridine analogues, 4-thiouridine and 5-bromouridine. When irradiated with long ultraviolet light, RNA containing these analogues can form specific covalent bonds with associated proteins. In this paper, we show that 4-thiouridine triphosphate and 5-bromouridine triphosphate were readily incorporated into a precursor tRNA(Phe) that was synthesized, in vitro, with bacteriophage T7 RNA polymerase. The analogue-containing precursor tRNAs were authentic substrates for the two splicing enzymes that were tested (endonuclease and ligase), and they formed specific covalent bonds with ligase when they were irradiated with long-wavelength ultraviolet light. We have determined the position of three major cross-links and one minor cross-link on precursor tRNA(Phe) that were located within the intron and near the 3' splice site. On the basis of these data, we present a model for the in vivo splicing reaction of yeast precursor tRNAs

  5. DYNAMO: a Mars upper atmosphere package for investigating solar wind interaction and escape processes, and mapping Martian fields

    DEFF Research Database (Denmark)

    Chassefiere, E.; Nagy, A.; Mandea, M.

    2004-01-01

    DYNAMO is a small multi-instrument payload aimed at characterizing current atmospheric escape, which is still poorly constrained, and improving gravity and magnetic field representations, in order to better understand the magnetic, geologic and thermal history of Mars. The internal structure...... of periapsis 170 km), and in a lesser extent 2a, offers an unprecedented opportunity to investigate by in situ probing the chemical and dynamical properties of the deep ionosphere, thermosphere, and the interaction between the atmosphere and the solar wind, and therefore the present atmospheric escape rate...

  6. A kinetic investigation of interacting, stimulated T cells identifies conditions for rapid functional enhancement, minimal phenotype differentiation, and improved adoptive cell transfer tumor eradication.

    Directory of Open Access Journals (Sweden)

    Jing Zhou

    Full Text Available For adoptive cell transfer (ACT immunotherapy of tumor-reactive T cells, an effective therapeutic outcome depends upon cell dose, cell expansion in vivo through a minimally differentiated phenotype, long term persistence, and strong cytolytic effector function. An incomplete understanding of the biological coupling between T cell expansion, differentiation, and response to stimulation hinders the co-optimization of these factors. We report on a biophysical investigation of how the short-term kinetics of T cell functional activation, through molecular stimulation and cell-cell interactions, competes with phenotype differentiation. T cells receive molecular stimulation for a few minutes to a few hours in bulk culture. Following this priming period, the cells are then analyzed at the transcriptional level, or isolated as single cells, with continuing molecular stimulation, within microchambers for analysis via 11-plex secreted protein assays. We resolve a rapid feedback mechanism, promoted by T cell-T cell contact interactions, which strongly amplifies T cell functional performance while yielding only minimal phenotype differentiation. When tested in mouse models of ACT, optimally primed T cells lead to complete tumor eradication. A similar kinetic process is identified in CD8+ and CD4+ T cells collected from a patient with metastatic melanoma.

  7. Interaction of Protease-Activated Receptor 2 with G Proteins and Beta-Arrestin 1 Studied by Bioluminescence Resonance Energy Transfer

    Directory of Open Access Journals (Sweden)

    Mohammed Akli eAyoub

    2013-12-01

    Full Text Available G protein-coupled receptors (GPCRs are well recognized as being able to activate several signaling pathways through the activation of different G proteins as well as other signaling proteins such as beta-arrestins. Therefore, understanding how such multiple GPCR-mediated signaling can be integrated constitute an important aspect. Here, we applied bioluminescence resonance energy transfer (BRET to shed more light on the G protein coupling profile of trypsin receptor, or protease-activated receptor 2 (PAR2, and its interaction with beta-arrestin1. Using YFP and Rluc fusion constructs expressed in COS-7 cells, BRET data revealed a pre-assembly of PAR2 with both Galphai1 and Galphao and a rapid and transient activation of these G proteins upon receptor activation. In contrast, no preassembly of PAR2 with Galpha12 could be detected and their physical association can be measured with a very slow and sustained kinetics similar to that of beta-arrestin1 recruitment. These data demonstrate the coupling of PAR2 with Galphai1, Galphao and Galpha12 in COS-7 cells with differences in the kinetics of GPCR-G protein coupling, a parameter that very likely influences the cellular response. Moreover, this further illustrates that preassembly or agonist-induced G protein interaction depends on receptor-G protein pairs indicating another level of complexity and regulation of the signaling of GPCR-G protein complexes and its multiplicity.

  8. Investigation of glutathione-derived electrostatic and hydrogen-bonding interactions and their role in defining Grx5 [2Fe-2S] cluster optical spectra and transfer chemistry.

    Science.gov (United States)

    Sen, Sambuddha; Bonfio, Claudia; Mansy, Sheref S; Cowan, J A

    2018-03-01

    Human glutaredoxin 5 (Grx5) is one of the core components of the Isc (iron-sulfur cluster) assembly and trafficking machinery, and serves as an intermediary cluster carrier, putatively delivering cluster from the Isu scaffold protein to target proteins. The tripeptide glutathione is intimately involved in this role, providing cysteinyl coordination to the iron center of the Grx5-bound [2Fe-2S] cluster. Grx5 has a well-defined glutathione-binding pocket with protein amino acid residues providing many ionic and hydrogen binding contacts to the bound glutathione. In this report, we investigated the importance of these interactions in cluster chirality and exchange reactivity by systematically perturbing the crucial contacts by use of natural and non-natural amino acid substitutions to disrupt the binding contacts from both the protein and glutathione. Native Grx5 could be reconstituted with all of the glutathione analogs used, as well as other thiol ligands, such as DTT or L-cysteine, by in vitro chemical reconstitution, and the holo proteins were found to transfer [2Fe-2S] cluster to apo ferredoxin 1 at comparable rates. However, the circular dichroism spectra of these derivatives displayed prominent differences that reflect perturbations in local cluster chirality. These studies provided a detailed molecular understanding of glutathione-protein interactions in holo Grx5 that define both cluster spectroscopy and exchange chemistry.

  9. Interaction of cholesterol ester transfer protein polymo- rphisms, body mass index, and birth weight with the risk of dyslipidemia in children and adolescents: the CASPIAN-III study

    Directory of Open Access Journals (Sweden)

    Motahar Heidari-Beni

    2015-11-01

    Full Text Available Objective(s: This study aims to investigate joint association between cholesterol ester transfer protein (CETP polymorphisms and body mass index (BMI or birth weight with the risk of dyslipidemia in Iranian children and adolescents. Materials and Methods:This study was conducted as a sub-study of the “school-based nationwide health survey” (CASPIAN-III. We randomly selected 750 samples from the whole blood samples. Real-time PCR and high resolution melt (HRM analysis were performed to determine Taq1B (rs708272 and A373P (rs5880 polymorphisms. Results:Taq1B polymorphism increased HDL-C, and total cholesterol (TC as well as decreased triglyceride and LDL-C concentrations. LDL-C and triglyceride levels were significantly higher and HDL-C and TC levels were significantly lower among those with A373P polymorphism. CT/TT genotype in Taq1B polymorphism showed a protective effect on dyslipidemia (OR= 0.12, 95%CI: 0.07-0.20. G allele of A373P polymorphism increased the risk of dyslipidemia (OR=4.10, 95%CI: 2.14, 7.83 after adjusting the confounders. We observed interactive effects of CETP gene polymorphisms and BMI or birth weight on dyslipidemia. Conclusion:Findings showed Taq1B polymorphism might have a protective effect and A373P polymorphism had deleterious effect on dyslipidemia in Iranian children and adolescents. These associations interacted with BMI and birth weight.

  10. Guanidinium/ammonium competition and proton transfer in the interaction of the amino acid arginine with the tetracarboxylic 18-crown-6 ionophore.

    Science.gov (United States)

    Avilés-Moreno, Juan Ramón; Berden, Giel; Oomens, Jos; Martínez-Haya, Bruno

    2018-02-07

    The recognition of arginine plays a central role in modern proteomics and genomics. Arginine is unique among natural amino acids due to the high basicity of its guanidinium side chain, which sustains specific interactions and proton exchange biochemical processes. The search for suitable macrocyclic ionophores constitutes a promising route towards the development of arginine receptors. This study evaluates the conformational features involved in the binding of free arginine by the polyether macrocycle (18-crown-6)-tetracarboxylic acid. Infrared action vibrational spectroscopy and quantum-chemical computations are combined to characterize the complexes with net charges +1 and +2. The spectrum of the +1 complex can be explained in terms of a configuration predominantly stabilized by a robust bidentate coordination of guanidinium with a carboxylate group formed from the deprotonation of one side group of the crown ether. The released proton is transferred to the amino terminus of arginine, which then coordinates with the crown ether ring. In an alternative type of conformation, partly consistent with experiment, the amino terminus is neutral and the guanidinium group inserts into the crown ether cavity. In the +2 complexes, arginine is always doubly protonated and the most stable conformations are characterized by a tripodal coordination of the ammonium -NH 3 + group of arginine with the oxygen atoms of the macrocycle ring, while the interactions of the amino acid with the side carboxylic acid groups of the crown ether acquire a remarkable lesser role.

  11. Experimental study of nonlinear interaction of plasma flow with charged thin current sheets: 2. Hall dynamics, mass and momentum transfer

    Directory of Open Access Journals (Sweden)

    S. Savin

    2006-01-01

    Full Text Available Proceeding with the analysis of Amata et al. (2005, we suggest that the general feature for the local transport at a thin magnetopause (MP consists of the penetration of ions from the magnetosheath with gyroradius larger than the MP width, and that, in crossing it, the transverse potential difference at the thin current sheet (TCS is acquired by these ions, providing a field-particle energy exchange without parallel electric fields. It is suggested that a part of the surface charge is self-consistently produced by deflection of ions in the course of inertial drift in the non-uniform electric field at MP. Consideration of the partial moments of ions with different energies demonstrates that the protons having gyroradii of roughly the same size or larger than the MP width carry fluxes normal to MP that are about 20% of the total flow in the plasma jet under MP. This is close to the excess of the ion transverse velocity over the cross-field drift speed in the plasma flow just inside MP (Amata et al., 2005, which conforms to the contribution of the finite-gyroradius inflow across MP. A linkage through the TCS between different plasmas results from the momentum conservation of the higher-energy ions. If the finite-gyroradius penetration occurs along the MP over ~1.5 RE from the observation site, then it can completely account for the formation of the jet under the MP. To provide the downstream acceleration of the flow near the MP via the cross-field drift, the weak magnetic field is suggested to rotate from its nearly parallel direction to the unperturbed flow toward being almost perpendicular to the accelerated flow near the MP. We discuss a deceleration of the higher-energy ions in the MP normal direction due to the interaction with finite-scale electric field bursts in the magnetosheath flow frame, equivalent to collisions, providing a charge separation. These effective collisions, with a nonlinear frequency proxy of the order of the proton

  12. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers.

    Science.gov (United States)

    Umeyama, Taichi; Ito, Takashi

    2017-10-03

    Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Interactive signal transfer between host and pathogen during successful infection of barley leaves by Blumeria graminis and Bipolaris sorokiniana.

    Science.gov (United States)

    Felle, Hubert H; Herrmann, Almut; Schäfer, Patrick; Hückelhoven, Ralph; Kogel, Karl-Heinz

    2008-01-01

    Using ion-selective microprobes, interactive signalling between barley and Blumeria graminis or Bipolaris sorokiniana has been investigated. The question was raised whether a biotrophically growing fungus manipulates the electrical driving forces (membrane potential, transmembrane pH), required for H+ cotransport of energy-rich compounds. Electrodes were positioned in the substomatal cavity of open stomata or on the leaf surface, and pH was measured continuously up to several days during fungal development. We demonstrate that surface and apoplastic fluids are electrically coupled and respond in a similar manner to stimuli. Apoplastic pH, monitored from the moment of inoculation with conidia, reveals several phases: 2-4h after inoculation of the barley leaf with either fungus, the host displays rapid transient responses after its first contact with the fungal cell wall; apoplastic pH and pCa increases, cytoplasmic pH and pCa decreases. About 1 day after inoculation, the apoplastic pH increases by up to 2 pH units, which is thought to reflect a resistance response against the intruder. Whereas barley leaf cells possess a membrane potential of -152+/-5 mV, hyphae of B. graminis yield -251+/-8 mV, indicative of a substantial driving force advantage for the fungus. Although the resting membrane potential of barley remains constant during the first days after inoculation, leaves infected with B. sorokiniana get confronted with an energy problem, indicated by a retarded repolarization following a "light-off" stimulus. Five days after inoculation, apoplastic pH has increased to 5.97+/-0.47 (n=11) and does no longer respond to "light-off" when measured within lesions. In contrast, it stays at near normal values outside the lesions and responds to "light-off". It is concluded that biotrophically growing fungi do not manipulate the cotransport driving forces since (i) any change in apoplastic pH would be experienced by both partners; (ii) the resting membrane potential is

  14. Heat Transfer and Observation of Droplet-Surface Interactions During Air-Mist Cooling at CSP Secondary System Temperatures

    Science.gov (United States)

    Huerta L., Mario E.; Mejía G., M. Esther; Castillejos E., A. Humberto

    2016-04-01

    Air-mists are key elements in the secondary cooling of modern thin steel slab continuous casters. The selection of water, W, and air, A, flow rates, and pressures in pneumatic nozzles open up a wide spectrum of cooling possibilities by their influence on droplet diameter, d, droplet velocity, v, and water impact flux, w. Nonetheless, due to the harsh environment resulting from the high temperatures and dense mists involved, there is very little information about the correlation between heat flux extracted, - q, and mist characteristics, and none about the dynamics of drop-wall interactions. For obtaining both kinds of information, this work combines a steady-state heat flux measuring method with a visualization technique based on a high-speed camera and a laser illumination system. For wall temperatures, T w, between ~723 K and ~1453 K (~450 °C and ~1180 °C), which correspond to film boiling regime, it was confirmed that - q increases with increase in v, w, and T w and with decrease in d. It should be noticed, however, that the increase in w generally decreases the spray cooling effectiveness because striking drops do not evaporate efficiently due to the interference by liquid remains from previous drops. Visualization of the events happening close to the surface also reveals that the contact time of the liquid with the surface is very brief and that rebounding, splashing, sliding, and levitation of drops lead to ineffective contact with the surface. At the center of the mist footprint, where drops impinge nearly normal to the surface those with enough momentum establish intimate contact with it before forming a vapor layer that pushes away the remaining liquid. Also, some drops are observed sliding upon the surface or levitating close to it; these are drops with low momentum which are influenced by the deflecting air stream. At footprint positions where oblique impingement occurs, frequently drops are spotted sliding or levitating and liquid films flowing in

  15. Long-range protein electron transfer observed at the single-molecule level: In situ mapping of redox-gated tunneling resonance

    DEFF Research Database (Denmark)

    Chi, Qijin; Farver, O; Ulstrup, Jens

    2005-01-01

    A biomimetic long-range electron transfer (ET) system consisting of the blue copper protein azurin, a tunneling barrier bridge, and a gold single-crystal electrode was designed on the basis of molecular wiring self-assembly principles. This system is sufficiently stable and sensitive in a quasi...... on the redox potential. Maximum resonance appears around the equilibrium redox potential of azurin with an on/off current ratio of approximate to 9. Simulation analyses, based on a two-step interfacial ET model for the scanning tunneling microscopy redox process, were performed and provide quantitative...

  16. What Is Technology Transfer? | Poster

    Science.gov (United States)

    The NCI Technology Transfer Center (TTC) facilitates partnerships between NIH research laboratories and external partners. With a team of technology transfer specialists, NCI TTC guides interactions from discovery to patenting, as well as from collaboration and invention development to licensing.

  17. Interactively Improving Agricultural Field Mapping in Sub-Saharan Africa with Crowd-Sourcing and Active Learning

    Science.gov (United States)

    Debats, S. R.; Estes, L. D.; Caylor, K. K.

    2015-12-01

    As satellite imagery becomes increasingly available, management of large image databases becomes more important for efficient image processing. We have developed a computer vision-based classification algorithm to distinguish smallholder agricultural land cover in Sub-Saharan Africa, using a group of high-resolution images from South Africa as a case study. For supervised classification, smallholder agriculture, with ambiguous patterns of small, irregular fields, requires a wide range of training data samples to adequately describe the variability in appearance. We employ crowd-sourcing to obtain new training data to expand the geographic range of our algorithm. A crowd-sourcing user is asked to hand-digitize the boundaries of agricultural fields in an assigned 1 km2 image. Yet random assignment of images to users could result in a highly redundant training data set with limited discriminative power. Furthermore, larger training data sets require a greater number of users to hand-digitize fields, which increases costs through crowd-sourcing engines like Amazon Mechanical Turk, as well as longer algorithm training times, which increases computing costs. Therefore, we employ an active learning approach to interactively select the most informative images to be hand-digitized for training data by crowd-sourcing users, based on changes in algorithm accuracy. We investigate the use of various image similarity measures used in content-based image retrieval systems, which quantify the distance, such as Euclidean distance or Manhattan distance, between a variety of extracted feature spaces to determine how similar the content of two images are. We determine the minimum training data set needed to maximize algorithm accuracy, as well as automate the selection of additional training images to classify a new target image that expands the geographic range of our algorithm.

  18. The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ

    Directory of Open Access Journals (Sweden)

    Düring Daniel N

    2013-01-01

    Full Text Available Abstract Background Like human infants, songbirds learn their species-specific vocalizations through imitation learning. The birdsong system has emerged as a widely used experimental animal model for understanding the underlying neural mechanisms responsible for vocal production learning. However, how neural impulses are translated into the precise motor behavior of the complex vocal organ (syrinx to create song is poorly understood. First and foremost, we lack a detailed understanding of syringeal morphology. Results To fill this gap we combined non-invasive (high-field magnetic resonance imaging and micro-computed tomography and invasive techniques (histology and micro-dissection to construct the annotated high-resolution three-dimensional dataset, or morphome, of the zebra finch (Taeniopygia guttata syrinx. We identified and annotated syringeal cartilage, bone and musculature in situ in unprecedented detail. We provide interactive three-dimensional models that greatly improve the communication of complex morphological data and our understanding of syringeal function in general. Conclusions Our results show that the syringeal skeleton is optimized for low weight driven by physiological constraints on song production. The present refinement of muscle organization and identity elucidates how apposed muscles actuate different syringeal elements. Our dataset allows for more precise predictions about muscle co-activation and synergies and has important implications for muscle activity and stimulation experiments. We also demonstrate how the syrinx can be stabilized during song to reduce mechanical noise and, as such, enhance repetitive execution of stereotypic motor patterns. In addition, we identify a cartilaginous structure suited to play a crucial role in the uncoupling of sound frequency and amplitude control, which permits a novel explanation of the evolutionary success of songbirds.

  19. The polar 2e/12c bond in phenalenyl-azaphenalenyl hetero-dimers: Stronger stacking interaction and fascinating interlayer charge transfer

    Science.gov (United States)

    Zhong, Rong-Lin; Xu, Hong-Liang; Li, Zhi-Ru

    2016-08-01

    An increasing number of chemists have focused on the two-electron/multicenter bond (2e/mc) that was first introduced to interpret the bonding mechanism of radical dimers. Herein, we report the polar two-electron/twelve center (2e/12c) bonding character in a series of phenalenyl-azaphenalenyl radical hetero-dimers. Interestingly, the bonding energy of weaker polar hetero-dimer (P-TAP) is dominated by the overlap of the two different singly occupied molecular orbital of radicals, while that of stronger polar hetero-dimer (P-HAP) is dominated by the electrostatic attraction. Results show that the difference between the electronegativity of the monomers plays a prominent role in the essential attribution of the polar 2e/12c bond. Correspondingly, a stronger stacking interaction in the hetero-dimer could be effectively achieved by increasing the difference of nitrogen atoms number between the monomers. It is worthy of note that an interesting interlayer charge transfer character is induced in the polar hetero-dimers, which is dependent on the difference between the electronegativity of the monomers. It is our expectation that the new knowledge about the bonding nature of radical hetero-dimers might provide important information for designing radical based functional materials with various applications.

  20. Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis.

    Science.gov (United States)

    Xue, Weiwei; Jin, Xiaojie; Ning, Lulu; Wang, Meixia; Liu, Huanxiang; Yao, Xiaojun

    2013-01-28

    The rapid emergence of cross-resistance to the integrase strand transfer inhibitors (INSTIs) has become a serious problem in the therapy of human immunodeficiency virus type 1 (HIV-1) infection. Understanding the detailed molecular mechanism of INSTIs cross-resistance is therefore critical for the development of new effective therapy against cross-resistance. On the basis of the homology modeling constructed structure of tetrameric HIV-1 intasome, the detailed molecular mechanism of the cross-resistance mutation E138K/Q148K to three important INSTIs (Raltegravir (RAL, FDA approved in 2007), Elvitegravir (EVG, FDA approved in 2012), and Dolutegravir (DTG, phase III clinical trials)) was investigated by using molecular dynamics (MD) simulation and residue interaction network (RIN) analysis. The results from conformation analysis and binding free energy calculation can provide some useful information about the detailed binding mode and cross-resistance mechanism for the three INSTIs to HIV-1 intasome. Binding free energy decomposition analysis revealed that Pro145 residue in the 140s 1oop (Gly140 to Gly149) of the HIV-1 intasome had strong hydrophobic interactions with INSTIs and played an important role in the binding of INSTIs to HIV-1 intasome active site. A systematic comparison and analysis of the RIN proves that the communications between the residues in the resistance mutant is increased when compared with that of the wild-type HIV-1 intasome. Further analysis indicates that residue Pro145 may play an important role and is relevant to the structure rearrangement in HIV-1 intasome active site. In addition, the chelating ability of the oxygen atoms in INSTIs (e.g., RAL and EVG) to Mg(2+) in the active site of the mutated intasome was reduced due to this conformational change and is also responsible for the cross-resistance mechanism. Notably, the cross-resistance mechanism we proposed could give some important information for the future rational design of novel

  1. Individual differences in spontaneous analogical transfer.

    Science.gov (United States)

    Kubricht, James R; Lu, Hongjing; Holyoak, Keith J

    2017-05-01

    Research on analogical problem solving has shown that people often fail to spontaneously notice the relevance of a semantically remote source analog when solving a target problem, although they are able to form mappings and derive inferences when given a hint to recall the source. Relatively little work has investigated possible individual differences that predict spontaneous transfer, or how such differences may interact with interventions that facilitate transfer. In this study, fluid intelligence was measured for participants in an analogical problem-solving task, using an abridged version of the Raven's Progressive Matrices (RPM) test. In two experiments, we systematically compared the effect of augmenting verbal descriptions of the source with animations or static diagrams. Solution rates to Duncker's radiation problem were measured across varying source presentation conditions, and participants' understanding of the relevant source material was assessed. The pattern of transfer was best fit by a moderated mediation model: the positive impact of fluid intelligence on spontaneous transfer was mediated by its influence on source comprehension; however, this path was in turn modulated by provision of a supplemental animation via its influence on comprehension of the source. Animated source depictions were most beneficial in facilitating spontaneous transfer for those participants with low scores on the fluid intelligence measure.

  2. A differential algebraic integration algorithm for symplectic mappings in systems with three-dimensional magnetic field

    International Nuclear Information System (INIS)

    Chang, P.; Lee, S.Y.; Yan, Y.T.

    2006-01-01

    A differential algebraic integration algorithm is developed for symplectic mapping through a three-dimensional (3-D) magnetic field. The self-consistent reference orbit in phase space is obtained by making a canonical transformation to eliminate the linear part of the Hamiltonian. Transfer maps from the entrance to the exit of any 3-D magnetic field are then obtained through slice-by-slice symplectic integration. The particle phase-space coordinates are advanced by using the integrable polynomial procedure. This algorithm is a powerful tool to attain nonlinear maps for insertion devices in synchrotron light source or complicated magnetic field in the interaction region in high energy colliders

  3. A Differential Algebraic Integration Algorithm for Symplectic Mappings in Systems with Three-Dimensional Magnetic Field

    International Nuclear Information System (INIS)

    Chang, P

    2004-01-01

    A differential algebraic integration algorithm is developed for symplectic mapping through a three-dimensional (3-D) magnetic field. The self-consistent reference orbit in phase space is obtained by making a canonical transformation to eliminate the linear part of the Hamiltonian. Transfer maps from the entrance to the exit of any 3-D magnetic field are then obtained through slice-by-slice symplectic integration. The particle phase-space coordinates are advanced by using the integrable polynomial procedure. This algorithm is a powerful tool to attain nonlinear maps for insertion devices in synchrotron light source or complicated magnetic field in the interaction region in high energy colliders

  4. Stripe rust and leaf rust resistance QTL mapping, epistatic interactions, and co-localization with stem rust resistance loci in spring wheat evaluated over three continents.

    Science.gov (United States)

    Singh, A; Knox, R E; DePauw, R M; Singh, A K; Cuthbert, R D; Campbell, H L; Shorter, S; Bhavani, S

    2014-11-01

    In wheat, advantageous gene-rich or pleiotropic regions for stripe, leaf, and stem rust and epistatic interactions between rust resistance loci should be accounted for in plant breeding strategies. Leaf rust (Puccinia triticina Eriks.) and stripe rust (Puccinia striiformis f. tritici Eriks) contribute to major production losses in many regions worldwide. The objectives of this research were to identify and study epistatic interactions of quantitative trait loci (QTL) for stripe and leaf rust resistance in a doubled haploid (DH) population derived from the cross of Canadian wheat cultivars, AC Cadillac and Carberry. The relationship of leaf and stripe rust resistance QTL that co-located with stem rust resistance QTL previously mapped in this population was also investigated. The Carberry/AC Cadillac population was genotyped with DArT(®) and simple sequence repeat markers. The parents and population were phenotyped for stripe rust severity and infection response in field rust nurseries in Kenya (Njoro), Canada (Swift Current), and New Zealand (Lincoln); and for leaf rust severity and infection response in field nurseries in Canada (Swift Current) and New Zealand (Lincoln). AC Cadillac was a source of stripe rust resistance QTL on chromosomes 2A, 2B, 3A, 3B, 5B, and 7B; and Carberry was a source of resistance on chromosomes 2B, 4B, and 7A. AC Cadillac contributed QTL for resistance to leaf rust on chromosome 2A and Carberry contributed QTL on chromosomes 2B and 4B. Stripe rust resistance QTL co-localized with previously reported stem rust resistance QTL on 2B, 3B, and 7B, while leaf rust resistance QTL co-localized with 4B stem rust resistance QTL. Several epistatic interactions were identified both for stripe and leaf rust resistance QTL. We have identified useful combinations of genetic loci with main and epistatic effects. Multiple disease resistance regions identified on chromosomes 2A, 2B, 3B, 4B, 5B, and 7B are prime candidates for further investigation and

  5. Meso(topoclimatic maps and mapping

    Directory of Open Access Journals (Sweden)

    Ladislav Plánka

    2007-06-01

    Full Text Available The atmospheric characteristics can be studied from many points of view, most often we talk about time and spatial standpoint. Application of time standpoint leads either to different kinds of the synoptic and prognostic maps production, which presents actual state of atmosphere in short time section in the past or in the near future or to the climatic maps production which presents longterm weather regime. Spatial standpoint then differs map works according to natural phenomenon proportions, whereas the scale of their graphic presentation can be different. It depends on production purpose of each work.In the paper there are analysed methods of mapping and climatic maps production, which display longterm regime of chosen atmospheric features. These athmosphere features are formed in interaction with land surface and also have direct influence on people and their activities throughout the country. At the same time they’re influenced by anthropogenic intervention to the landscape.

  6. The Interstellar Mapping and Acceleration Probe - A Mission to Discover the Origin of Particle Acceleration and its Fundamental Connection to the Global Interstellar Interaction

    Science.gov (United States)

    Schwadron, N.

    2017-12-01

    Our piece of cosmic real-estate, the heliosphere, is the domain of all human existence - an astrophysical case-history of the successful evolution of life in a habitable system. The Interstellar Boundary Explorer (IBEX) was the first mission to explore the global heliosphere and in concert with Voyager 1 and Voyager 2 is discovering a fundamentally new and uncharted physical domain of the outer heliosphere. In parallel, Cassini/INCA maps the global heliosphere at energies ( 5-55 keV) above those measured by IBEX. The enigmatic IBEX ribbon and the INCA belt were unanticipated discoveries demonstrating that much of what we know or think we understand about the outer heliosphere needs to be revised. The global structure of the heliosphere is highly complex and influenced by competing factors ranging from the local interstellar magnetic field, suprathermal populations both within and beyond the heliopause, and the detailed flow properties of the LISM. Global heliospheric structure and microphysics in turn influences the acceleration of energetic particles and creates feedbacks that modify the interstellar interaction as a whole. The next quantum leap enabled by IMAP will open new windows on the frontier of Heliophysics and probe the acceleration of suprathermal and higher energy particles at a time when the space environment is rapidly evolving. IMAP ultimately connects the acceleration processes observed directly at 1 AU with unprecedented sensitivity and temporal resolution with the global structure of our heliosphere. The remarkable synergy between IMAP, Voyager 1 and Voyager 2 will remain for at least the next decade as Voyager 1 pushes further into the interstellar domain and Voyager 2 moves through the heliosheath. IMAP, like ACE before it, will be a keystone of the Heliophysics System Observatory by providing comprehensive energetic particle, pickup ion, suprathermal ion, neutral atom, solar wind, solar wind heavy ion, and magnetic field observations to diagnose

  7. Mapping Urban Social Divisions

    Directory of Open Access Journals (Sweden)

    Susan Ball

    2010-05-01

    Full Text Available Against the background of increased levels of interest in space and images beyond the field of geography, this article (re- introduces earlier work on the semiotics of maps undertaken by geographers in the 1960s. The data limitations, purpose and cultural context in which a user interprets a map's codes and conventions are highlighted in this work, which remains relevant to the interpretation of maps—new and old—forty years later. By means of drawing on geography's contribution to the semiotics of maps, the article goes on to examine the concept of urban social divisions as represented in map images. Using a small number of map images, including two of the most widely known maps of urban social division in Europe and North America, the roles of context, data and purpose in the production and interpretation of maps are discussed. By presenting the examples chronologically the article shows that although advances in data collection and manipulation have allowed researchers to combine different social variables in maps of social division, and to interact with map images, work by geographers on the semiotics of maps is no less relevant today than when it was first proposed forty years ago. URN: urn:nbn:de:0114-fqs1002372

  8. Native protein mapping and visualization of protein interactions in the area of human plasma high-density lipoprotein by combining nondenaturing micro 2DE and quantitative LC-MS/MS.

    Science.gov (United States)

    Jin, Ya; Bu, Shujie; Zhang, Jun; Yuan, Qi; Manabe, Takashi; Tan, Wen

    2014-07-01

    A human plasma sample was subjected to nondenaturing micro 2DE and a gel area (5 mm × 18 mm) that includes high-density lipoprotein (HDL) was cut into 1 mm × 1 mm squares, then the proteins in the 90 gel pieces were analyzed by quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data. Totally 154 proteins were assigned in the 90 gel pieces and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The map of apolipoprotein (Apo) A-I showed a wide apparent mass distribution characteristic to HDL and was compared with the maps of the other 153 proteins. Eleven proteins showed maps of wide distribution that overlapped with the map of Apo A-I, and all have been reported to be the components of HDL. Further, seven minor proteins associated with HDL were detected at the gel positions of high Apo A-I quantity. These results for the first time visualized the localization of HDL apolipoproteins on a nondenaturing 2DE gel and strongly suggested their interactions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Interaction of C1q and mannan-binding lectin (MBL) with C1r, C1s, MBL-associated serine proteases 1 and 2, and the MBL-associated protein MAp19

    DEFF Research Database (Denmark)

    Thiel, S; Petersen, Steen Vang; Vorup-Jensen, T

    2000-01-01

    Mannan-binding lectin (MBL) and C1q activate the complement cascade via attached serine proteases. The proteases C1r and C1s were initially discovered in a complex with C1q, whereas the MBL-associated serine proteases 1 and 2 (MASP-1 and -2) were discovered in a complex with MBL. There is controv......Mannan-binding lectin (MBL) and C1q activate the complement cascade via attached serine proteases. The proteases C1r and C1s were initially discovered in a complex with C1q, whereas the MBL-associated serine proteases 1 and 2 (MASP-1 and -2) were discovered in a complex with MBL......, whereas MASP-1, MASP-2, and a third protein, MAp19 (19-kDa MBL-associated protein), were found to be associated only with MBL. The bulk of MASP-1 and MAp19 was found in association with each other and was not bound to MBL or MASP-2. The interactions of MASP-1, MASP-2, and MAp19 with MBL differ from those...... of C1r and C1s with C1q in that both high salt concentrations and calcium chelation (EDTA) are required to fully dissociate the MASPs or MAp19 from MBL. In the presence of calcium, most of the MASP-1, MASP-2, and MAp19 emerged on gel-permeation chromatography as large complexes that were not associated...

  10. Onomastic Mapping

    Directory of Open Access Journals (Sweden)

    Yuliana Yu. Gordova

    2012-12-01

    Full Text Available Mapping the onomastic material and creating linguistic atlases of each region remains a significant and urgent problem of Russian onomastics. The paper summarizes the experience of onomastic cartography, and explains the concept of onomastic map as well as linguistic and technical principles of mapping. The author considers traditional objects of mapping and main map topics and describes new opportunities which become possible due to the creation of modern means and techniques of mapping. The paper is illustrated with toponymic maps, compiled by different researchers between 1970 and 2000.

  11. A new interactive map overlaid on the Google Earth programme, shows for the first time nine of the world's computing grids. (1/2 page)

    CERN Multimedia

    Weston, Naomi

    2006-01-01

    "Dr Gidon Moont, a research associate in the High Energy Physics Group at Imperial College London, developed the visualisation for the map. It was showcased at the Supercomputing 2006 annual conference in Tampa, Florida, this November. (1/2 page)

  12. Element interactions and soil properties affecting the soil-to-plant transfer of six elements relevant to radioactive waste in boreal forest

    International Nuclear Information System (INIS)

    Roivainen, Paeivi; Makkonen, Sari; Holopainen, Toini; Juutilainen, Jukka

    2012-01-01

    Cobalt (Co), lead (Pb), molybdenum (Mo), nickel (Ni), uranium (U), and zinc (Zn) are among the elements that have radioactive isotopes in radioactive waste. Soil-to-plant transfer is a key process for possible adverse effects if these radionuclides are accidentally released into the environment. The present study aimed at investigating factors affecting such transfer in boreal forest. The plant species studied were blueberry (Vaccinium myrtillus), May lily (Maianthemum bifolium), narrow buckler fern (Dryopteris carthusiana), rowan (Sorbus aucuparia) and Norway spruce (Picea abies). Regression analyses were carried out to investigate the effects of the chemical composition and physical properties of soil on the soil-to-leaf/needle concentration ratios of Co, Mo, Ni, Pb, U and Zn. Soil potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P) and sulphur (S) concentrations were the most important factors affecting the soil-to-plant transfer of the elements studied. Soil clay and organic matter contents were found to significantly affect plant uptake of Mo, Pb and U. Knowledge of the effects of these factors is helpful for interpretation of the predictions of radioecological models describing soil-to-plant transfer and for improving such models. (orig.)

  13. Element interactions and soil properties affecting the soil-to-plant transfer of six elements relevant to radioactive waste in boreal forest

    Energy Technology Data Exchange (ETDEWEB)

    Roivainen, Paeivi; Makkonen, Sari; Holopainen, Toini; Juutilainen, Jukka [University of Eastern Finland, Department of Environmental Science, Kuopio (Finland)

    2012-03-15

    Cobalt (Co), lead (Pb), molybdenum (Mo), nickel (Ni), uranium (U), and zinc (Zn) are among the elements that have radioactive isotopes in radioactive waste. Soil-to-plant transfer is a key process for possible adverse effects if these radionuclides are accidentally released into the environment. The present study aimed at investigating factors affecting such transfer in boreal forest. The plant species studied were blueberry (Vaccinium myrtillus), May lily (Maianthemum bifolium), narrow buckler fern (Dryopteris carthusiana), rowan (Sorbus aucuparia) and Norway spruce (Picea abies). Regression analyses were carried out to investigate the effects of the chemical composition and physical properties of soil on the soil-to-leaf/needle concentration ratios of Co, Mo, Ni, Pb, U and Zn. Soil potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P) and sulphur (S) concentrations were the most important factors affecting the soil-to-plant transfer of the elements studied. Soil clay and organic matter contents were found to significantly affect plant uptake of Mo, Pb and U. Knowledge of the effects of these factors is helpful for interpretation of the predictions of radioecological models describing soil-to-plant transfer and for improving such models. (orig.)

  14. Selective induced polarization through electron transfer in acetone and pyrazole ester derivatives via C-H center dot center dot center dot O=C interaction

    Czech Academy of Sciences Publication Activity Database

    Tewari, A. K.; Srivastava, P.; Singh, V. P.; Singh, P.; Kumar, R.; Khanna, R. S.; Srivastava, Pa.; Gnanasekaran, Ramachandran; Hobza, Pavel

    2014-01-01

    Roč. 38, č. 10 (2014), s. 4885-4892 ISSN 1144-0546 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : O hydrogen bonds * noncovalent interactions * pi interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.086, year: 2014

  15. Transfer Pricing

    OpenAIRE

    Larsen, Mads Grenaa; Nørgaard, Mads Frid; Hansen, Manjarita

    2013-01-01

    This project seeks to highlight some of the criticisms given towards the OECD Transfer Pricing Guidelines and the challenges Danish companies experience by pricing their goods and the problems this causes for trade. The project is based on a series of interviews that represent the different agents who are operating in Transfer Pricing business. These interviews, combined with the Transfer Pricing Guidelines, gives us the basis to analyse the challenges we want to clarify based on the hypothes...

  16. Transfer Pricing

    DEFF Research Database (Denmark)

    Rohde, Carsten; Rossing, Christian Plesner

    trade internally as the units have to decide what prices should be paid for such inter-unit transfers. One important challenge is to uncover the consequences that different transfer prices have on the willingness in the organizational units to coordinate activities and trade internally. At the same time...... the determination of transfer price will affect the size of the profit or loss in the organizational units and thus have an impact on the evaluation of managers‟ performance. In some instances the determination of transfer prices may lead to a disagreement between coordination of the organizational units...

  17. Interaction of chemical reactions and radiant heat transfer with temperature turbulent pulsations and its effect on heat traner in high-temperature gas flows

    International Nuclear Information System (INIS)

    Petukhov, B.S.; Zal'tsman, I.G.; Shikov, V.K.

    1980-01-01

    Methods of taking account of mutual effect of chemical transformations, radiation and turbulence in the calculations of heat transfer in gas flows are considered. Exponential functions of medium parameters are used to describe chemical sources and optical properties of media. It is shown using as an example the dissociation reaction C 2 reversible 2C that the effect of temperature and composition pulsations on recombination rates is negligibly small. It is also shown on the example of turbulent flow of hot molecular gas in a flat channel with cold walls that at moderate temperatures the effect of temperature pulsations on heat radiation flow can be significant (30-40%). The calculational results also show that there is a region in a turbulent boundary layer where the radiation greatly affects the coefficient of turbulent heat transfer

  18. Knowledge Transfers in IJVs

    DEFF Research Database (Denmark)

    Park, Chansoo; Vertinsky, Ilan; Minbaeva, Dana

    firms to their international joint ventures (IJVs) in South Korea. We developed a theoretical model that examines the impacts of the knowledge senders¡¯ disseminative capacities on knowledge transfer to IJVs. We tested our theory with data from 199 IJVs in South Korea. We found that the willingness...... of parent firms to share knowledge is manifested in an increased capacity to articulate and codify knowledge and create opportunities to transfer this knowledge. Mediated by the effective use of organizational communication channels, articulation and codification capabilities have a significant impact...... on the transfer of knowledge. The creation of opportunities for face-to-face interactions between organizations also has an impact on knowledge transfer, but only when senders and receivers have similar products and technologies...

  19. Aggregated journal–journal citation relations in scopus and web of science matched and compared in terms of networks, maps, and interactive overlays

    NARCIS (Netherlands)

    Leydesdorff, L.; de Moya-Anegón, F.; de Nooy, W.

    We compare the network of aggregated journal–journal citation relations provided by the Journal Citation Reports (JCR) 2012 of the Science Citation Index (SCI) and Social Sciences Citation Index (SSCI) with similar data based on Scopus 2012. First, global and overlay maps were developed for the 2

  20. Heat and mass transfer are in the interaction of multi-pulsed spray with vertical surfaces in the regime of evaporative cooling

    Science.gov (United States)

    Karpov, P. N.; Nazarov, A. D.; Serov, A. F.; Terekhov, V. I.

    2017-10-01

    Sprays with a periodic supply drop phase have great opportunities to control the processes of heat transfer. We can achieve optimal evaporative modes of cooling by changing the pulse duration and the repetition frequency while minimizing flow of the liquid phase. Experimental data of investigation of local heat transfer for poorly heated large surface obtained on the original stand with multi nozzle managed the irrigation system impact of the gas-droplet flow present in this work. Researches on the contribution to the intensification of spray options were conducted. Also the growth rate was integral and local heat. Information instantaneous distribution of the heat flux in the description of the processes have helped us. Managed to describe two basic modes of heat transfer: Mode “insular” foil cooling and thick foil with forming of streams. Capacitive sensors allow to monitor the dynamics of the foil thickness, the birth-belt flow, forming and the evolution of waves generated by “bombing” the surface with the droplets.

  1. Technology transfer 1994

    Energy Technology Data Exchange (ETDEWEB)

    1994-01-01

    This document, Technology Transfer 94, is intended to communicate that there are many opportunities available to US industry and academic institutions to work with DOE and its laboratories and facilities in the vital activity of improving technology transfer to meet national needs. It has seven major sections: Introduction, Technology Transfer Activities, Access to Laboratories and Facilities, Laboratories and Facilities, DOE Office, Technologies, and an Index. Technology Transfer Activities highlights DOE`s recent developments in technology transfer and describes plans for the future. Access to Laboratories and Facilities describes the many avenues for cooperative interaction between DOE laboratories or facilities and industry, academia, and other government agencies. Laboratories and Facilities profiles the DOE laboratories and facilities involved in technology transfer and presents information on their missions, programs, expertise, facilities, and equipment, along with data on whom to contact for additional information on technology transfer. DOE Offices summarizes the major research and development programs within DOE. It also contains information on how to access DOE scientific and technical information. Technologies provides descriptions of some of the new technologies developed at DOE laboratories and facilities.

  2. Large momentum transfer phenomena

    International Nuclear Information System (INIS)

    Imachi, Masahiro; Otsuki, Shoichiro; Matsuoka, Takeo; Sawada, Shoji.

    1978-01-01

    The large momentum transfer phenomena in hadron reaction drastically differ from small momentum transfer phenomena, and are described in this paper. Brief review on the features of the large transverse momentum transfer reactions is described in relation with two-body reactions, single particle productions, particle ratios, two jet structure, two particle correlations, jet production cross section, and the component of momentum perpendicular to the plane defined by the incident protons and the triggered pions and transverse momentum relative to jet axis. In case of two-body process, the exponent N of the power law of the differential cross section is a value between 10 to 11.5 in the large momentum transfer region. The breaks of the exponential behaviors into the power ones are observed at the large momentum transfer region. The break would enable to estimate the order of a critical length. The large momentum transfer phenomena strongly suggest an important role of constituents of hadrons in the hard region. Hard rearrangement of constituents from different initial hadrons induces large momentum transfer reactions. Several rules to count constituents in the hard region have been proposed so far to explain the power behavior. Scale invariant quark interaction and hard reactions are explained, and a summary of the possible types of hard subprocess is presented. (Kato, T.)

  3. Somatosensory maps.

    Science.gov (United States)

    Harding-Forrester, Samuel; Feldman, Daniel E

    2018-01-01

    Somatosensory areas containing topographic maps of the body surface are a major feature of parietal cortex. In primates, parietal cortex contains four somatosensory areas, each with its own map, with the primary cutaneous map in area 3b. Rodents have at least three parietal somatosensory areas. Maps are not isomorphic to the body surface, but magnify behaviorally important skin regions, which include the hands and face in primates, and the whiskers in rodents. Within each map, intracortical circuits process tactile information, mediate spatial integration, and support active sensation. Maps may also contain fine-scale representations of touch submodalities, or direction of tactile motion. Functional representations are more overlapping than suggested by textbook depictions of map topography. The whisker map in rodent somatosensory cortex is a canonic system for studying cortical microcircuits, sensory coding, and map plasticity. Somatosensory maps are plastic throughout life in response to altered use or injury. This chapter reviews basic principles and recent findings in primate, human, and rodent somatosensory maps. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  5. The time-organized map algorithm: extending the self-organizing map to spatiotemporal signals.

    Science.gov (United States)

    Wiemer, Jan C

    2003-05-01

    The new time-organized map (TOM) is presented for a better understanding of the self-organization and geometric structure of cortical signal representations. The algorithm extends the common self-organizing map (SOM) from the processing of purely spatial signals to the processing of spatiotemporal signals. The main additional idea of the TOM compared with the SOM is the functionally reasonable transfer of temporal signal distances into spatial signal distances in topographic neural representations. This is achieved by neural dynamics of propagating waves, allowing current and former signals to interact spatiotemporally in the neural network. Within a biologically plausible framework, the TOM algorithm (1) reveals how dynamic neural networks can self-organize to embed spatial signals in temporal context in order to realize functional meaningful invariances, (2) predicts time-organized representational structures in cortical areas representing signals with systematic temporal relation, and (3) suggests that the strength with which signals interact in the cortex determines the type of signal topology realized in topographic maps (e.g., spatially or temporally defined signal topology). Moreover, the TOM algorithm supports the explanation of topographic reorganizations based on time-to-space transformations (Wiemer, Spengler, Joublin, Stagge, & Wacquant, 2000).

  6. Transfer Pricing

    DEFF Research Database (Denmark)

    Rohde, Carsten; Rossing, Christian Plesner

    trade internally as the units have to decide what prices should be paid for such inter-unit transfers. One important challenge is to uncover the consequences that different transfer prices have on the willingness in the organizational units to coordinate activities and trade internally. At the same time...

  7. Transfer Pricing

    DEFF Research Database (Denmark)

    Nielsen, Søren Bo

    2014-01-01

    Against a background of rather mixed evidence about transfer pricing practices in multinational enterprises (MNEs) and varying attitudes on the part of tax authorities, this paper explores how multiple aims in transfer pricing can be pursued across four different transfer pricing regimes. A MNE has...... a production subsidiary in one country, from where it sells the produced good locally as well as to a sales subsidiary in a second country. The latter subsidiary is engaged in duopolistic competition with a local competitor. The MNE has two aims in setting the transfer price: strategic delegation and tax...... minimization. We examine the extent to which the four transfer pricing regimes we set up allow the MNE to pursue these aims. While neither strategic delegation nor tax minimization will be eliminated, trade-offs are inevitable, albeit to varying degree....

  8. Transfer Pricing

    DEFF Research Database (Denmark)

    Nielsen, Søren Bo

    2014-01-01

    a production subsidiary in one country, from where it sells the produced good locally as well as to a sales subsidiary in a second country. The latter subsidiary is engaged in duopolistic competition with a local competitor. The MNE has two aims in setting the transfer price: strategic delegation and tax......Against a background of rather mixed evidence about transfer pricing practices in multinational enterprises (MNEs) and varying attitudes on the part of tax authorities, this paper explores how multiple aims in transfer pricing can be pursued across four different transfer pricing regimes. A MNE has...... minimization. We examine the extent to which the four transfer pricing regimes we set up allow the MNE to pursue these aims. While neither strategic delegation nor tax minimization will be eliminated, trade-offs are inevitable, albeit to varying degree....

  9. Effects of Concept-Mapping-Based Interactive E-Books on Active and Reflective-Style Students' Learning Performances in Junior High School Law Courses

    Science.gov (United States)

    Hwang, Gwo-Jen; Sung, Han-Yu; Chang, Hsuan

    2017-01-01

    Researchers have pointed out that interactive e-books have rich content and interactive features which can promote students' learning interest. However, researchers have also indicated the need to integrate effective learning supports or tools to help students organize what they have learned so as to increase their learning performance, in…

  10. The fine tuning of carotenoid–chlorophyll interactions in light-harvesting complexes: an important requisite to guarantee efficient photoprotection via triplet–triplet energy transfer in the complex balance of the energy transfer processes

    International Nuclear Information System (INIS)

    Di Valentin, Marilena; Carbonera, Donatella

    2017-01-01

    Triplet–triplet energy transfer (TTET) from the chlorophyll to the carotenoid triplet state is the process exploited by photosynthetic systems to protect themselves from singlet oxygen formation under light-stress conditions. A deep comprehension of the molecular strategies adopted to guarantee TTET efficiency, while at the same time maintaining minimal energy loss and efficient light-harvesting capability, is still lacking. The paramagnetic nature of the triplet state makes electron paramagnetic resonance (EPR) the method of choice when investigating TTET. In this review, we focus on our extended comparative study of two photosynthetic antenna complexes, the Peridinin–chlorophyll a -protein of dinoflagellates and the light-harvesting complex II of higher plants, in order to point out important aspects of the molecular design adopted in the photoprotection strategy. We have demonstrated that a proper analysis of the EPR data allows one to identify the pigments involved in TTET and, consequently, gain an insight into the structure of the photoprotective sites. The structural information has been complemented by a detailed description of the electronic structure provided by hyperfine spectroscopy. All these elements represent the fundamental building blocks toward a deeper understanding of the requirements for efficient photoprotection, which is fundamental to guarantee the prolonged energy conversion action of photosynthesis. (topical review)

  11. The fine tuning of carotenoid-chlorophyll interactions in light-harvesting complexes: an important requisite to guarantee efficient photoprotection via triplet-triplet energy transfer in the complex balance of the energy transfer processes

    Science.gov (United States)

    Di Valentin, Marilena; Carbonera, Donatella

    2017-08-01

    Triplet-triplet energy transfer (TTET) from the chlorophyll to the carotenoid triplet state is the process exploited by photosynthetic systems to protect themselves from singlet oxygen formation under light-stress conditions. A deep comprehension of the molecular strategies adopted to guarantee TTET efficiency, while at the same time maintaining minimal energy loss and efficient light-harvesting capability, is still lacking. The paramagnetic nature of the triplet state makes electron paramagnetic resonance (EPR) the method of choice when investigating TTET. In this review, we focus on our extended comparative study of two photosynthetic antenna complexes, the Peridinin-chlorophyll a-protein of dinoflagellates and the light-harvesting complex II of higher plants, in order to point out important aspects of the molecular design adopted in the photoprotection strategy. We have demonstrated that a proper analysis of the EPR data allows one to identify the pigments involved in TTET and, consequently, gain an insight into the structure of the photoprotective sites. The structural information has been complemented by a detailed description of the electronic structure provided by hyperfine spectroscopy. All these elements represent the fundamental building blocks toward a deeper understanding of the requirements for efficient photoprotection, which is fundamental to guarantee the prolonged energy conversion action of photosynthesis.

  12. Vol2velle: Printable Interactive Volume Visualization.

    Science.gov (United States)

    Stoppel, Sergej; Bruckner, Stefan

    2017-01-01

    Interaction is an indispensable aspect of data visualization. The presentation of volumetric data, in particular, often significantly benefits from interactive manipulation of parameters such as transfer functions, rendering styles, or clipping planes. However, when we want to create hardcopies of such visualizations, this essential aspect is lost. In this paper, we present a novel approach for creating hardcopies of volume visualizations which preserves a certain degree of interactivity. We present a method for automatically generating Volvelles, printable tangible wheel charts that can be manipulated to explore different parameter settings. Our interactive system allows the flexible mapping of arbitrary visualization parameters and supports advanced features such as linked views. The resulting designs can be easily reproduced using a standard printer and assembled within a few minutes.

  13. Phthalimides: Supramolecular Interactions in Crystals, Hypersensitive Solution 1H-NMR Dynamics and Energy Transfer to Europium(III and Terbium(III States

    Directory of Open Access Journals (Sweden)

    David J. Williams

    2003-07-01

    Full Text Available Detailed crystal structures and 1H-NMR characteristics of some alkylaminephthalimides, including dendritic polyphthalimides, are reported. These investigations were undertaken in order to obtain a better understanding of the relationship between solid-state supramolecular interactions, their persistence in solution and associated dynamics of magnetically hypersensitive phthalimide aromatic AA'BB'-AA'XX' proton NMR resonances. Some alkylamine phthalimides feature folded molecular geometries, which we attribute to n-π interactions among proximal amine-phthalimide sites; those alkylamine-phthalimides that have no possibility for such interactions feature fully extended phthalimide functionalities. Accordingly, alkylamine phthalimide compounds with folded solid-state geometries feature solvent and temperature dependent hypersensitive AA'BB'-AA'XX' 1H-NMR line profiles, which we attribute to the n-π interactions. Luminescence of Eu3+(5D0 and Tb3+(5D4 states show well defined metal ion environments in their complexes with dendritic phthalimides, as well as relatively weak phthalimide-lanthanide(III interactions.

  14. MUTYH Associated Polyposis (MAP)

    DEFF Research Database (Denmark)

    Poulsen, Marie Louise Mølgaard; Bisgaard, M L

    2008-01-01

    MUTYH Associated Polyposis (MAP), a Polyposis predisposition caused by biallelic mutations in the Base Excision Repair (BER) gene MUTYH, confers a marked risk of colorectal cancer (CRC). The MAP phenotype is difficult to distinguish from other hereditary CRC syndromes. Especially from Familial...... Adenomatous Polyposis (FAP) and to a lesser extend Lynch Syndrome, which are caused by germline mutations in the APC and Mismatch Repair (MMR) genes, respectively.Here we review research findings regarding MUTYH interactions, genotypic and phenotypic characteristics of MAP, as well as surveillance......, cooperation between the BER and the MMR systems exists, as MUTYH interacts with MMR gene-products. Possibly, monoallelic defects in both pathways are of significance to CRC development.Specific MUTYH variants are found to be characteristic in distinct ethnic populations, which could facilitate future genetic...

  15. The energy, transferred to secondary charged pions in pion-nucleon and pion-carbon interactions at momentum 40 GeV/s

    International Nuclear Information System (INIS)

    Boos, E.G.; Izbasarov, M.; Temiraliyev, T.; Samoilov, V.V.; Tursunov, R.A.

    2005-01-01

    Full text: The analysis has been undertaken for the energy ratio K π ± (partial coefficient of inelasticity) taken away by charged pions at laboratory coordinate system in pion-nucleon and pion-carbon interactions at momentum 40 GeV/s. It is shown that distribution of partial inelasticity coefficients for elementary act is more narrow than the same distribution for carbon nucleus. The mean number of charged mesons (n π ± t) grows with enlarging of partial inelasticity coefficient, being larger for interactions of π - -mesons with carbon nuclei in comparison with corresponding distribution in elementary act. The similar picture is observed for one-nucleon and multi-nucleon events selected from π - - C -interactions by the value of total electric charge of all secondary particles (except for the identified protons) and by the value of target mass

  16. The Investigation of the Interaction between Human Serum Transferring with Colchicine in the Presence of Pb+2 Ions: Synchronous Fluorescence Measurements

    Directory of Open Access Journals (Sweden)

    Goldouzian Z. Goldouzian F., Momen-Heravi M. and Chamani J.

    2012-01-01

    Full Text Available The interaction between Holo-Transferin (HTF and Colchicine (COL was investigated in the present of Pb+2 ions under physiological conditions by using synchronous fluorescence spectra. The synchronous fluorescence spectra show a slight change of tryptophan residue micro-environment. Synchronous fluorescence spectra show that the structure of the tyrosine residue environment was altered by interaction of the COL and Pb+2 ions with HTF. The fluorescence intensity of HTF decreased regularly beside a small blue shift with increasing concentrations of COL and Pb+2 ions. The intrinsic fluorescence of HTF was quenched in the presence of drug and ion. Interaction of drugs with HTF and HTF-Pb+2 can elucidate the properties of drug-protein and ion- protein complex, as it may provide useful information about the structural feature that determines the therapeutic effectiveness of ion and drugs. Therefore, it has become a significant research field in life science, chemistry, biotechnology and clinical medicine.

  17. Using business intelligence for efficient inter-facility patient transfer.

    Science.gov (United States)

    Haque, Waqar; Derksen, Beth Ann; Calado, Devin; Foster, Lee

    2015-01-01

    In the context of inter-facility patient transfer, a transfer operator must be able to objectively identify a destination which meets the needs of a patient, while keeping in mind each facility's limitations. We propose a solution which uses Business Intelligence (BI) techniques to analyze data related to healthcare infrastructure and services, and provides a web based system to identify optimal destination(s). The proposed inter-facility transfer system uses a single data warehouse with an Online Analytical Processing (OLAP) cube built on top that supplies analytical data to multiple reports embedded in web pages. The data visualization tool includes map based navigation of the health authority as well as an interactive filtering mechanism which finds facilities meeting the selected criteria. The data visualization is backed by an intuitive data entry web form which safely constrains the data, ensuring consistency and a single version of truth. The overall time required to identify the destination for inter-facility transfers is reduced from hours to a few minutes with this interactive solution.

  18. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    Science.gov (United States)

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory).

  19. An Introduction to Drug Discovery by Probing Protein-Substrate Interactions Using Saturation Transfer Difference-Nuclear Magnetic Resonance (STD-NMR)

    Science.gov (United States)

    Guegan, Jean-Paul; Daniellou, Richard

    2012-01-01

    NMR spectroscopy is a powerful tool for characterizing and identifying molecules and nowadays is even used to characterize complex systems in biology. In the experiment presented here, students learned how to apply this modern technique to probe interactions between small molecules and proteins. With the use of simple organic synthesis, students…

  20. Synchronized communication between people with dementia and their volunteer caregivers. A video-based explorative study on temporal aspects of interaction and the transfer to education.

    Science.gov (United States)

    Jost, A; Neumann, E; Himmelmann, K-H

    2010-08-01

    Processes of demographic change are leading to decreasing human resources in professional as well as lay care; this decrease necessitates new concepts of care, especially for the growing number of people with dementia (p.w.d.). Since the amendment to the German Care Insurance Law (2002), family carers have been entitled to regular weekly relief, provided by volunteers who have been given a thirty-hour-training. As difficulties in information processing in p.w.d. form an important part of the symptoms in dementia sufferers--with a high impact on communication as well as competent functioning in activities associated with daily life, we wanted to establish how much awareness and sensitivity voluntary attendants show in "tuning in" to the p.w.d. and her/his individual capacity to interact. In an exploratory study the authors analyzed videotaped interactions between volunteer caregivers and dementia-sufferers which were recorded in everyday situations during the process of ongoing care. Using methods of Video Interaction Analysis and Grounded Theory, we developed categories which describe how in tune the helpers are with the timing skills--or lack of them--of p.w.d.. We think that understanding the different ways in which p.w.d. structure their time can improve their communication and interaction. The categories --"speed and adjustment of speed", "mutuality" and "time control"--seemed crucial in understanding the subsequent course of the interactions. In a second step, these categories have recently been used by students and staff of the Lausitz University of Applied Sciences to provide training that sensitizes volunteer attendants to the topic and to learn about volunteers; judgement on the importance of continuing education in this field.

  1. Station Transfers

    Data.gov (United States)

    Department of Homeland Security — ixed rail transit external system transfers for systems within the Continental United States, Alaska, Hawaii, the District of Columbia, and Puerto Rico. The modes of...

  2. A Global Survey and Interactive Map Suite of Deep Underground Facilities; Examples of Geotechnical and Engineering Capabilities, Achievements, Challenges: (Mines, Shafts, Tunnels, Boreholes, Sites and Underground Facilities for Nuclear Waste and Physics R&D)

    Science.gov (United States)

    Tynan, M. C.; Russell, G. P.; Perry, F.; Kelley, R.; Champenois, S. T.

    2017-12-01

    This global survey presents a synthesis of some notable geotechnical and engineering information reflected in four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies, sites, or disposal facilities; 3) deep large diameter boreholes, and 4) physics underground laboratories and facilities from around the world. These data are intended to facilitate user access to basic information and references regarding deep underground "facilities", history, activities, and plans. In general, the interactive maps and database [http://gis.inl.gov/globalsites/] provide each facility's approximate site location, geology, and engineered features (e.g.: access, geometry, depth, diameter, year of operations, groundwater, lithology, host unit name and age, basin; operator, management organization, geographic data, nearby cultural features, other). Although the survey is not all encompassing, it is a comprehensive review of many of the significant existing and historical underground facilities discussed in the literature addressing radioactive waste management and deep mined geologic disposal safety systems. The global survey is intended to support and to inform: 1) interested parties and decision makers; 2) radioactive waste disposal and siting option evaluations, and 3) safety case development as a communication tool applicable to any mined geologic disposal facility as a demonstration of historical and current engineering and geotechnical capabilities available for use in deep underground facility siting, planning, construction, operations and monitoring.

  3. Epitope mapping of imidazolium cations in ionic liquid-protein interactions unveils the balance between hydrophobicity and electrostatics towards protein destabilisation.

    Science.gov (United States)

    Silva, Micael; Figueiredo, Angelo Miguel; Cabrita, Eurico J

    2014-11-14

    We investigated imidazolium-based ionic liquid (IL) interactions with human serum albumin (HSA) to discern the level of cation interactions towards protein stability. STD-NMR spectroscopy was used to observe the imidazolium IL protons involved in direct binding and to identify the interactions responsible for changes in Tm as accessed by differential scanning calorimetry (DSC). Cations influence protein stability less than anions but still significantly. It was found that longer alkyl side chains of imidazolium-based ILs (more hydrophobic) are associated with a higher destabilisation effect on HSA than short-alkyl groups (less hydrophobic). The reason for such destabilisation lies on the increased surface contact area of the cation with the protein, particularly on the hydrophobic contacts promoted by the terminus of the alkyl chain. The relevance of the hydrophobic contacts is clearly demonstrated by the introduction of a polar moiety in the alkyl chain: a methoxy or alcohol group. Such structural modification reduces the degree of hydrophobic contacts with HSA explaining the lesser extent of protein destabilisation when compared to longer alkyl side chain groups: above [C2mim](+). Competition STD-NMR experiments using [C2mim](+), [C4mim](+) and [C2OHmim](+) also validate the importance of the hydrophobic interactions. The combined effect of cation and anion interactions was explored using (35)Cl NMR. Such experiments show that the nature of the cation has no influence on the anion-protein contacts, still the nature of the anion modulates the cation-protein interaction. Herein we propose that more destabilising anions are likely to be a result of a partial contribution from the cation as a direct consequence of the different levels of interaction (cation-anion pair and cation-protein).

  4. Causal mapping

    DEFF Research Database (Denmark)

    Rasmussen, Lauge Baungaard

    2006-01-01

    The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method......The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method...

  5. Collection Mapping.

    Science.gov (United States)

    Harbour, Denise

    2002-01-01

    Explains collection mapping for library media collections. Discusses purposes for creating collection maps, including helping with selection and weeding decisions, showing how the collection supports the curriculum, and making budget decisions; and methods of data collection, including evaluating a collaboratively taught unit with the classroom…

  6. CALS Mapping

    DEFF Research Database (Denmark)

    Collin, Ib; Nielsen, Povl Holm; Larsen, Michael Holm

    1998-01-01

    To enhance the industrial applications of CALS, CALS Center Danmark has developed a cost efficient and transparent assessment, CALS Mapping, to uncover the potential of CALS - primarily dedicated to small and medium sized enterprises. The idea behind CALS Mapping is that the CALS State of the ent...

  7. Adenoviral gene transfer of PLD1-D4 enhances insulin sensitivity in mice by disrupting phospholipase D1 interaction with PED/PEA-15.

    Directory of Open Access Journals (Sweden)

    Angela Cassese

    Full Text Available Over-expression of phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes (PED/PEA-15 causes insulin resistance by interacting with the D4 domain of phospholipase D1 (PLD1. Indeed, the disruption of this association restores insulin sensitivity in cultured cells over-expressing PED/PEA-15. Whether the displacement of PLD1 from PED/PEA-15 improves insulin sensitivity in vivo has not been explored yet. In this work we show that treatment with a recombinant adenoviral vector containing the human D4 cDNA (Ad-D4 restores normal glucose homeostasis in transgenic mice overexpressing PED/PEA-15 (Tg ped/pea-15 by improving both insulin sensitivity and secretion. In skeletal muscle of these mice, D4 over-expression inhibited PED/PEA-15-PLD1 interaction, decreased Protein Kinase C alpha activation and restored insulin induced Protein Kinase C zeta activation, leading to amelioration of insulin-dependent glucose uptake. Interestingly, Ad-D4 administration improved insulin sensitivity also in high-fat diet treated obese C57Bl/6 mice. We conclude that PED/PEA-15-PLD1 interaction may represent a novel target for interventions aiming at improving glucose tolerance.

  8. Insights on the Interaction between Transthyretin and Aβ in Solution. A Saturation Transfer Difference (STD) NMR Analysis of the Role of Iododiflunisal.

    Science.gov (United States)

    Gimeno, Ana; Santos, Luis M; Alemi, Mobina; Rivas, Josep; Blasi, Daniel; Cotrina, Ellen Y; Llop, Jordi; Valencia, Gregorio; Cardoso, Isabel; Quintana, Jordi; Arsequell, Gemma; Jiménez-Barbero, Jesús

    2017-07-13

    Several strategies against Alzheimer disease (AD) are directed to target Aβ-peptides. The ability of transthyretin (TTR) to bind Aβ-peptides and the positive effect exerted by some TTR stabilizers for modulating the TTR-Aβ interaction have been previously studied. Herein, key structural features of the interaction between TTR and the Aβ(12-28) peptide (3), the essential recognition element of Aβ, have been unravelled by STD-NMR spectroscopy methods in solution. Molecular aspects related to the role of the TTR stabilizer iododiflunisal (IDIF, 5) on the TTR-Aβ complex have been also examined. The NMR results, assisted by molecular modeling protocols, have provided a structural model for the TTR-Aβ interaction, as well as for the ternary complex formed in the presence of IDIF. This basic structural information could be relevant for providing light on the mechanisms involved in the ameliorating effects of AD symptoms observed in AD/TTR ± animal models after IDIF treatment and eventually for designing new molecules toward AD therapeutic drugs.

  9. Construction of microsatellite-based linkage map and mapping of ...

    Indian Academy of Sciences (India)

    Abstract. Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat,. SSR)-based genetic map was constructed using the ...

  10. Construction of microsatellite-based linkage map and mapping of ...

    Indian Academy of Sciences (India)

    Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross ...

  11. Neutron signal transfer analysis

    CERN Document Server

    Pleinert, H; Lehmann, E

    1999-01-01

    A new method called neutron signal transfer analysis has been developed for quantitative determination of hydrogenous distributions from neutron radiographic measurements. The technique is based on a model which describes the detector signal obtained in the measurement as a result of the action of three different mechanisms expressed by signal transfer functions. The explicit forms of the signal transfer functions are determined by Monte Carlo computer simulations and contain only the distribution as a variable. Therefore an unknown distribution can be determined from the detector signal by recursive iteration. This technique provides a simple and efficient tool for analysis of this type while also taking into account complex effects due to the energy dependency of neutron interaction and single and multiple scattering. Therefore this method provides an efficient tool for precise quantitative analysis using neutron radiography, as for example quantitative determination of moisture distributions in porous buil...

  12. Energy transfer models in nitrogen plasmas: Analysis of {N_2(X 1Σg^+)-N(4S_u){-e-} interaction

    Science.gov (United States)

    Heritier, K. L.; Jaffe, R. L.; Laporta, V.; Panesi, M.

    2014-11-01

    The relaxation of N_2(X ^1Σ _g^+) molecules in a background gas composed of N(^4S_u) atoms and free electrons is studied by using an ideal isochoric and isothermic chemical reactor. A rovibrational state-to-state model is developed to study energy transfer process induced by free electron and atomic collisions. The required cross sections and the corresponding rate coefficients are taken from two well-known kinetic databases: NASA Ames kinetic mechanism for the description of the N_2(X ^1Σ _g^+)-N(^4S_u) processes and the Phys4Entry database for the electron driven processes, N_2(X ^1Σ _g^+)-e-. The evolution of the population densities of each individual rovibrational level is explicitly determined via the numerical solution of the master equation for temperatures ranging from 10000 to 30 000 K. It was found that the distribution of the rovibrational energy levels of N_2(X ^1Σ _g^+) is strongly influenced by the electron driven collisional processes, which promote the excitation of the low lying vibrational levels. The macroscopic vibrational energy relaxation is governed by the molecule-atom collisions, when free electrons, initially cold are relaxing to the final heat-bath temperature. Thus, the main role of the free electrons is to ensure the equilibration of vibrational and free electron excitation, thus validating the existence of the local equilibrium TV-Te. However, if electrons and heavy particles are assumed to be in equilibrium at the heat bath temperature, electron driven processes dominate the vibrational relaxation. Finally, we have assessed the validity of the Landau-Teller model for the description of the inelastic energy transfer between molecules and free electrons. In the case of free-electron temperatures lower than 10 000 K, Landau-Teller relaxation model gives an accurate description of the vibrational relaxation, while at higher temperatures the error in the predictions can be significant and the model should not be used.

  13. Copenhagen Sonic Experience Map

    DEFF Research Database (Denmark)

    Kreutzfeldt, Jacob

    2011-01-01

    of assessment and management of environmental noise brings forth the disturbing and potentially damaging effect of environmental sound.1 But as maps of coloured streets start to circulate, and real estate prices drop in designated blue and red areas,2 it is worth remembering that sound itself is not a killer....... Most of the time sound is a trivial part of everyday life involved in interactions, experiences, atmospheres, actions, etc. Although trivial, the role of the aural in the urban life world is more complex than what is suggested by sound level maps, and as such it may be a vital part of urbanity itself...

  14. Mapping of interaction between cytochrome P450 2B4 and cytochrome b5: the first evidence of two mutual orientations

    Czech Academy of Sciences Publication Activity Database

    Šulc, Miroslav; Ječmen, Tomáš; Šnajdrová, Renata; Novák, Petr; Martínek, V.; Hodek, P.; Stiborová, M.; Hudeček, J.

    2012-01-01

    Roč. 33, č. 3 (2012), s. 101-107 ISSN 0172-780X R&D Projects: GA ČR(CZ) GAP207/12/0627 Institutional support: RVO:61388971 Keywords : cytochrome P450 2B4 * protein-protein interaction * mass spectrometry Subject RIV: CE - Biochemistry Impact factor: 0.932, year: 2012

  15. Development of a Time-Resolved Fluorescence Resonance Energy Transfer Ultrahigh-Throughput Screening Assay for Targeting the NSD3 and MYC Interaction. | Office of Cancer Genomics

    Science.gov (United States)

    Epigenetic modulators play critical roles in reprogramming of cellular functions, emerging as a new class of promising therapeutic targets. Nuclear receptor binding SET domain protein 3 (NSD3) is a member of the lysine methyltransferase family. Interestingly, the short isoform of NSD3 without the methyltransferase fragment, NSD3S, exhibits oncogenic activity in a wide range of cancers. We recently showed that NSD3S interacts with MYC, a central regulator of tumorigenesis, suggesting a mechanism by which NSD3S regulates cell proliferation through engaging MYC.

  16. The Roles of Structural Order and Intermolecular Interactions in Determining Ionization Energies and Charge-Transfer State Energies in Organic Semiconductors

    KAUST Repository

    Graham, Kenneth

    2016-08-17

    The energy landscape in organic semiconducting materials greatly influences charge and exciton behavior, which are both critical to the operation of organic electronic devices. These energy landscapes can change dramatically depending on the phases of material present, including pure phases of one molecule or polymer and mixed phases exhibiting different degrees of order and composition. In this work, ultraviolet photoelectron spectroscopy measurements of ionization energies (IEs) and external quantum efficiency measurements of charge-transfer (CT) state energies (ECT) are applied to molecular photovoltaic material systems to characterize energy landscapes. The results show that IEs and ECT values are highly dependent on structural order and phase composition. In the sexithiophene:C60 system both the IEs of sexithiophene and C60 shift by over 0.4 eV while ECT shifts by 0.5 eV depending on molecular composition. By contrast, in the rubrene:C60 system the IE of rubrene and C60 vary by ≤0.11 eV and ECT varies by ≤0.04 eV as the material composition varies. These results suggest that energy landscapes can exist whereby the binding energies of the CT states are overcome by energy offsets between charges in CT states in mixed regions and free charges in pure phases. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. MD 2197: Experimental studies of Landau damping by means of Beam Transfer Function measurements in the presence of beam-beam interactions and diffusive mechanisms

    CERN Document Server

    Tambasco, Claudia; Barranco Garcia, Javier; Boccardi, Andrea; Buffat, Xavier; Bruce, Roderik; Gasior, Marek; Hostettler, Michi; Lefevre, Thibaut; Louro Alves, Diogo Miguel; Metral, Elias; Persson, Tobias Hakan Bjorn; Pieloni, Tatiana; Pojer, Mirko; Salvachua Ferrando, Belen Maria; Solfaroli Camillocci, Matteo; CERN. Geneva. ATS Department

    2018-01-01

    Beam Transfer Function (BTF) measurements are direct measurement of the stability diagrams that define the stability threshold of coherent beam instabilities driven by the impedance. At the LHC, some coherent instabilities at flat top energy are still not fully understood and the BTF measurements provide a method to experimentally probe the Landau damping of the proton beams. The BTF response is sensitive to the particle distribution changes and contain information about the transverse tune spread in the beams. The BTF system has been installed in the LHC in the 2015 in order to investigate the Landau damping at different stages of the operational cycle, machine configurations (different octupole currents, crossing angles, tunes etc...) and in presence of beam-beam excited resonances that may provoke diffusion mechanisms with a consequence change of Landau damping. Past MDs showed some difficulties for the reconstruction of the stability diagram from BTF measurements and several improvements on the BTF sy...

  18. Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments.

    Science.gov (United States)

    Singh, A; Knox, R E; DePauw, R M; Singh, A K; Cuthbert, R D; Campbell, H L; Singh, D; Bhavani, S; Fetch, T; Clarke, F

    2013-08-01

    Stem rust (Puccinia graminis f. sp. tritici) is responsible for major production losses in hexaploid wheat (Triticum aestivum L.) around the world. The spread of stem rust race Ug99 and variants is a threat to worldwide wheat production and efforts are ongoing to identify and incorporate resistance. The objectives of this research were to identify quantitative trait loci (QTL) and to study their epistatic interactions for stem rust resistance in a population derived from the Canadian wheat cultivars AC Cadillac and Carberry. A doubled haploid (DH) population was developed and genotyped with DArT(®) and SSR markers. The parents and DH lines were phenotyped for stem rust severity and infection response to Ug99 and variant races in 2009, 2010 and 2011 in field rust nurseries near Njoro, Kenya, and to North American races in 2011 and 2012 near Swift Current, SK, Canada. Seedling infection type to race TTKSK was assessed in a bio-containment facility in 2009 and 2012 near Morden, MB. Eight QTL for stem rust resistance and three QTL for pseudo-black chaff on nine wheat chromosomes were identified. The phenotypic variance (PV) explained by the stem rust resistance QTL ranged from 2.4 to 48.8 %. AC Cadillac contributed stem rust resistance QTL on chromosomes 2B, 3B, 5B, 6D, 7B and 7D. Carberry contributed resistance QTL on 4B and 5A. Epistatic interactions were observed between loci on 4B and 5B, 4B and 7B, 6D and 3B, 6D and 5B, and 6D and 7B. The stem rust resistance locus on 6D interacted synergistically with 5B to improve the disease resistance through both crossover and non-crossover interactions depending on the environment. Results from this study will assist in planning breeding for stem rust resistance by maximizing QTL main effects and epistatic interactions.

  19. BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for science and land management in the vicinity of Utqiaġvik (Barrow) on the North Slope of Alaska.

    Science.gov (United States)

    Cody, R. P.; Escarzaga, S. M.; Gaylord, A. G.; Kassin, A.; Barba, M.; Tweedie, C. E.

    2017-12-01

    The Utqiaġvik (Barrow) area of northern Alaska is one of the most intensely researched locations in the Arctic and the Barrow Area Information Database (BAID, www.barrowmapped.org) tracks and facilitates a gamut of research, management, and educational activities in the area. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 18,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, save or print maps and query results, and filter or view information by space, time, and/or other tags. Recent advances include provision of differential global positioning (dGPS) system and high resolution aerial imagery support to visiting scientists, analysis and multitemporal mapping of over 120 km of coastline for erosion monitoring; maintenance of a wireless micrometeorological sensor network; links to Barrow area datasets housed at national data archives; a NOAA funded community outreach program for citizen science and public outreach on costal erosion; and substantial upgrades to the BAID website. Web mapping applications that have launched to the public include: an Imagery Time Viewer that allows users to compare imagery of the Barrow area between 1948 and the present; a Coastal Erosion Viewer that allows users to view long-term (1955-2015) and recent (2013-2015) rates of erosion for the Barrow area; and a Community Planning tool that allows users to view and print dynamic reports based on an array of basemaps including a new 0.5m resolution wetlands map designed to

  20. FluView National Flu Activity Map

    Data.gov (United States)

    U.S. Department of Health & Human Services — The FluView National Flu Activity Map is a complementary widget to the state-by-state flu map widget introduced in the 2007-2008 flu season. This interactive map...

  1. Non local separable interactions in the description of some nuclear properties. Recoil and finite range effects in the CRC formalism for the study of heavy ion transfers

    International Nuclear Information System (INIS)

    Meyer, J.

    1976-01-01

    Some simplifications given by the nonlocal separable interactions (NLSI) allowed an exhaustive study of the three body problem to be performed. This work is intended to show that NLSI are also useful in studying the properties of nuclei. Some satisfactory results obtained in the infinite nuclear matter and also in the Hartree-Fock study of some 3s-1d nuclei are then given. A coupled reaction formalism has been developed for the analysis of heavy ion induced reactions. The recoil and finite range effects, which are necessary tools in heavy-ion induced reactions, have been introduced from the work of Coker et al. for the ( 3 He,t) reaction [fr

  2. Genetic Mapping

    Science.gov (United States)

    ... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers Genomic ... genetic mapping? Among the main goals of the Human Genome Project (HGP) was to develop new, better and cheaper ...

  3. Technology transfer

    International Nuclear Information System (INIS)

    Boury, C.

    1986-01-01

    This paper emphasizes in the specific areas of design, engineering and component production. This paper presents what Framatome has to offer in these areas and its export oriented philosophy. Then, a typical example of this technology transfer philosophy is the collaboration with the South Korean firm, Korea Heavy Industries Corporation (KHIC) for the supply of KNU 9 and KNU 10 power stations

  4. Copenhagen Sonic Experience Map

    DEFF Research Database (Denmark)

    Kreutzfeldt, Jacob

    2011-01-01

    In the wake of present European interest for mapping urban noise, it seems increasingly relevant to investigate the multiple ways in which sound intersects with the everyday experiences of urban citizens. Focusing on the polluting effects of infrastructural noise, the EU-initiated project...... of assessment and management of environmental noise brings forth the disturbing and potentially damaging effect of environmental sound.1 But as maps of coloured streets start to circulate, and real estate prices drop in designated blue and red areas,2 it is worth remembering that sound itself is not a killer....... Most of the time sound is a trivial part of everyday life involved in interactions, experiences, atmospheres, actions, etc. Although trivial, the role of the aural in the urban life world is more complex than what is suggested by sound level maps, and as such it may be a vital part of urbanity itself...

  5. Rupture behaviors of the 2010 Jiashian and 2016 Meinong Earthquakes: Implication for interaction of two asperities on the Chishan Transfer Fault Zone in SW Taiwan.

    Science.gov (United States)

    Jian, P. R.; Hung, S. H.; Chen, Y. L.; Meng, L.; Tseng, T. L.

    2017-12-01

    Chishan Transfer Fault Zone as a likely candidate rupture plane. In 2010, the Jiasian earthquake initiated at the deeper NE asperity and propagated NW-ward and up-dip. Six years later, the stronger shallower asperity responsible for the Meinong event was statically triggered, which consequently caused the ruinous destruction in SW Taiwan.

  6. Graphene Conductance Uniformity Mapping

    DEFF Research Database (Denmark)

    Buron, Jonas Christian Due; Petersen, Dirch Hjorth; Bøggild, Peter

    2012-01-01

    We demonstrate a combination of micro four-point probe (M4PP) and non-contact terahertz time-domain spectroscopy (THz-TDS) measurements for centimeter scale quantitative mapping of the sheet conductance of large area chemical vapor deposited graphene films. Dual configuration M4PP measurements...... of less than a minute for a 4-in. wafer. The combination of M4PP and THz-TDS conductance measurements, supported by micro Raman spectroscopy and optical imaging, reveals that the film is electrically continuous on the nanoscopic scale with microscopic defects likely originating from the transfer process...

  7. Our interests in protein-protein interactions

    Indian Academy of Sciences (India)

    protein interactions. Evolution of P-P partnerships. Evolution of P-P structures. Evolutionary dynamics of P-P interactions. Dynamics of P-P interaction network. Host-pathogen interactions. CryoEM mapping of gigantic protein assemblies.

  8. A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways

    Science.gov (United States)

    Musungu, Bryan M.; Bhatnagar, Deepak; Brown, Robert L.; Payne, Gary A.; OBrian, Greg; Fakhoury, Ahmad M.; Geisler, Matt

    2016-01-01

    A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus. PMID:27917194

  9. A Network Approach of Gene Co-expression in theZea mays/Aspergillus flavusPathosystem to Map Host/Pathogen Interaction Pathways.

    Science.gov (United States)

    Musungu, Bryan M; Bhatnagar, Deepak; Brown, Robert L; Payne, Gary A; OBrian, Greg; Fakhoury, Ahmad M; Geisler, Matt

    2016-01-01

    A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus , a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays , and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays , there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus . Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus .

  10. Designing a Multichannel Map Service Concept

    Directory of Open Access Journals (Sweden)

    Hanna-Marika Halkosaari

    2013-01-01

    Full Text Available This paper introduces a user-centered design process for developing a multichannel map service. The aim of the service is to provide hikers with interactive maps through several channels. In a multichannel map service, the same spatial information is available through various channels, such as printed maps, Web maps, mobile maps, and other interactive media. When properly networked, the channels share a uniform identity so that the user experiences the different channels as a part of a single map service. The traditional methods of user-centered design, such as design probes, personas, and scenarios, proved useful even in the emerging field of developing multichannel map services. The findings emphasize the need to involve users and multidisciplinary teams in the conceptual phases of designing complex services aimed at serving various kinds of users.

  11. Radiative Heat Transfer in Combustion Applications: Parallel Efficiencies of Two Gas Models, Turbulent Radiation Interactions in Particulate Laden Flows, and Coarse Mesh Finite Difference Acceleration for Improved Temporal Accuracy

    Science.gov (United States)

    Cleveland, Mathew A.

    We investigate several aspects of the numerical solution of the radiative transfer equation in the context of coal combustion: the parallel efficiency of two commonly-used opacity models, the sensitivity of turbulent radiation interaction (TRI) effects to the presence of coal particulate, and an improvement of the order of temporal convergence using the coarse mesh finite difference (CMFD) method. There are four opacity models commonly employed to evaluate the radiative transfer equation in combustion applications; line-by-line (LBL), multigroup, band, and global. Most of these models have been rigorously evaluated for serial computations of a spectrum of problem types [1]. Studies of these models for parallel computations [2] are limited. We assessed the performance of the Spectral-Line-Based weighted sum of gray gasses (SLW) model, a global method related to K-distribution methods [1], and the LBL model. The LBL model directly interpolates opacity information from large data tables. The LBL model outperforms the SLW model in almost all cases, as suggested by Wang et al. [3]. The SLW model, however, shows superior parallel scaling performance and a decreased sensitivity to load imbalancing, suggesting that for some problems, global methods such as the SLW model, could outperform the LBL model. Turbulent radiation interaction (TRI) effects are associated with the differences in the time scales of the fluid dynamic equations and the radiative transfer equations. Solving on the fluid dynamic time step size produces large changes in the radiation field over the time step. We have modified the statistically homogeneous, non-premixed flame problem of Deshmukh et al. [4] to include coal-type particulate. The addition of low mass loadings of particulate minimally impacts the TRI effects. Observed differences in the TRI effects from variations in the packing fractions and Stokes numbers are difficult to analyze because of the significant effect of variations in problem

  12. Modes of Representation in Cognitive Mapping.

    Science.gov (United States)

    Cohen, Michelle E.; Nodine, Calvin F.

    Recent investigations of the cognitive components of human-environmental interactions owe much to the work of city planner Kevin Lynch, who hypothesized cognitive mapping as a two-way interactive process between individuals and their environment. Lynch identified five elements which individuals used in the construction of cognitive maps,…

  13. In silico analysis, mapping of regulatory elements and corresponding dna-protein interaction in polyphenol oxidase gene promoter from different rice varieties

    International Nuclear Information System (INIS)

    Mahmood, T.; Rehman, M.; Aziz, E.

    2015-01-01

    Polyphenol oxidase (PPO) is an important enzyme that has positive impact regarding plant resistance against different biotic and abiotic stresses. In the present study PPO promoter from six different rice varieties was amplified and then analyzed for cis- and trans-acting elements. The study revealed a total of 79 different cis-acting regulatory elements including 11 elements restricted to only one or other variety. Among six varieties Pakhal-Basmati had highest number (5) of these elements, whereas C-622 and Rachna-Basmati have no such sequences. Rachna-Basmati, IR-36-Basmati and Kashmir- Basmati had 1, 2 and 3 unique elements, respectively. Different elementsrelated to pathogen, salt and water stresses were found, which may be helpful in controlling PPO activity according to changing environment. Moreover, HADDOCK was used to understand molecular mechanism of PPO regulation and it was found that DNA-protein interactions are stabilized by many potential hydrogen bonds. Adenine and arginine were the most reactive residues in DNA and proteins respectively.Structural comparison of different protein-DNA complexes show that even a highly conserved transcriptional factor can adopt different conformations when they contact a different DNA binding sequence, however their stable interactions depend on the number of hydrogen bonds formed and distance. (author)

  14. Micron-scale mapping of megagauss magnetic fields using optical polarimetry to probe hot electron transport in petawatt-class laser-solid interactions.

    Science.gov (United States)

    Chatterjee, Gourab; Singh, Prashant Kumar; Robinson, A P L; Blackman, D; Booth, N; Culfa, O; Dance, R J; Gizzi, L A; Gray, R J; Green, J S; Koester, P; Kumar, G Ravindra; Labate, L; Lad, Amit D; Lancaster, K L; Pasley, J; Woolsey, N C; Rajeev, P P

    2017-08-21

    The transport of hot, relativistic electrons produced by the interaction of an intense petawatt laser pulse with a solid has garnered interest due to its potential application in the development of innovative x-ray sources and ion-acceleration schemes. We report on spatially and temporally resolved measurements of megagauss magnetic fields at the rear of a 50-μm thick plastic target, irradiated by a multi-picosecond petawatt laser pulse at an incident intensity of ~10 20 W/cm 2 . The pump-probe polarimetric measurements with micron-scale spatial resolution reveal the dynamics of the magnetic fields generated by the hot electron distribution at the target rear. An annular magnetic field profile was observed ~5 ps after the interaction, indicating a relatively smooth hot electron distribution at the rear-side of the plastic target. This is contrary to previous time-integrated measurements, which infer that such targets will produce highly structured hot electron transport. We measured large-scale filamentation of the hot electron distribution at the target rear only at later time-scales of ~10 ps, resulting in a commensurate large-scale filamentation of the magnetic field profile. Three-dimensional hybrid simulations corroborate our experimental observations and demonstrate a beam-like hot electron transport at initial time-scales that may be attributed to the local resistivity profile at the target rear.

  15. The MAP kinase ERK and its scaffold protein MP1 interact with the chromatin regulator Corto during Drosophila wing tissue development.

    Science.gov (United States)

    Mouchel-Vielh, Emmanuèle; Rougeot, Julien; Decoville, Martine; Peronnet, Frédérique

    2011-03-14

    Mitogen-activated protein kinase (MAPK) cascades (p38, JNK, ERK pathways) are involved in cell fate acquisition during development. These kinase modules are associated with scaffold proteins that control their activity. In Drosophila, dMP1, that encodes an ERK scaffold protein, regulates ERK signaling during wing development and contributes to intervein and vein cell differentiation. Functional relationships during wing development between a chromatin regulator, the Enhancer of Trithorax and Polycomb Corto, ERK and its scaffold protein dMP1, are examined here. Genetic interactions show that corto and dMP1 act together to antagonize rolled (which encodes ERK) in the future intervein cells, thus promoting intervein fate. Although Corto, ERK and dMP1 are present in both cytoplasmic and nucleus compartments, they interact exclusively in nucleus extracts. Furthermore, Corto, ERK and dMP1 co-localize on several sites on polytene chromosomes, suggesting that they regulate gene expression directly on chromatin. Finally, Corto is phosphorylated. Interestingly, its phosphorylation pattern differs between cytoplasm and nucleus and changes upon ERK activation. Our data therefore suggest that the Enhancer of Trithorax and Polycomb Corto could participate in regulating vein and intervein genes during wing tissue development in response to ERK signaling.

  16. The MAP kinase ERK and its scaffold protein MP1 interact with the chromatin regulator Corto during Drosophila wing tissue development

    Directory of Open Access Journals (Sweden)

    Peronnet Frédérique

    2011-03-01

    Full Text Available Abstract Background Mitogen-activated protein kinase (MAPK cascades (p38, JNK, ERK pathways are involved in cell fate acquisition during development. These kinase modules are associated with scaffold proteins that control their activity. In Drosophila, dMP1, that encodes an ERK scaffold protein, regulates ERK signaling during wing development and contributes to intervein and vein cell differentiation. Functional relationships during wing development between a chromatin regulator, the Enhancer of Trithorax and Polycomb Corto, ERK and its scaffold protein dMP1, are examined here. Results Genetic interactions show that corto and dMP1 act together to antagonize rolled (which encodes ERK in the future intervein cells, thus promoting intervein fate. Although Corto, ERK and dMP1 are present in both cytoplasmic and nucleus compartments, they interact exclusively in nucleus extracts. Furthermore, Corto, ERK and dMP1 co-localize on several sites on polytene chromosomes, suggesting that they regulate gene expression directly on chromatin. Finally, Corto is phosphorylated. Interestingly, its phosphorylation pattern differs between cytoplasm and nucleus and changes upon ERK activation. Conclusions Our data therefore suggest that the Enhancer of Trithorax and Polycomb Corto could participate in regulating vein and intervein genes during wing tissue development in response to ERK signaling.

  17. Quasispecies theory for horizontal gene transfer and recombination

    Science.gov (United States)

    Muñoz, Enrique; Park, Jeong-Man; Deem, Michael W.

    2008-12-01

    We introduce a generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population. We study the effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population, through an analytic field theoretic mapping. We investigate both horizontal gene transfer from a population and recombination between pairs of individuals. Somewhat surprisingly, these nonlinear generalizations of quasispecies theory to modern biology are analytically solvable. For two-parent recombination, we find two selected phases, one of which is spectrally rigid. We present exact analytical formulas for the equilibrium mean fitness of the population, in terms of a maximum principle, which are generally applicable to any permutation invariant replication rate function. For smooth fitness landscapes, we show that when positive epistatic interactions are present, recombination or horizontal gene transfer introduces a mild load against selection. Conversely, if the fitness landscape exhibits negative epistasis, horizontal gene transfer or recombination introduces an advantage by enhancing selection towards the fittest genotypes. These results prove that the mutational deterministic hypothesis holds for quasispecies models. For the discontinuous single sharp peak fitness landscape, we show that horizontal gene transfer has no effect on the fitness, while recombination decreases the fitness, for both the parallel and the Eigen models. We present numerical and analytical results as well as phase diagrams for the different cases.