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Sample records for muon-nucleus interactions based

  1. Photo nuclear energy loss term for muon-nucleus interactions based on xi scaling model of QCD

    NASA Technical Reports Server (NTRS)

    Roychoudhury, R.

    1985-01-01

    Extensive air showers (EMC) experiments discovered a significant deviation of the ratio of structure functions of iron and deuteron from unity. It was established that the quark parton distribution in nuclei are different from the corresponding distribution in the nucleus. It was examined whether these results have an effect on the calculation of photo nucleus energy loss term for muon-nucleus nuclear interaction. Though the EMC and SLAC data were restricted to rather large q sq region it is expected that the derivation would persist even in the low q sq domain. For the ratio of iron and deuteron structure function a rather naive least square fit of the form R(x) = a + bx was taken and it is assumed that the formula is valid for the whole q sq region the absence of any knowledge of R(x) for small q sq.

  2. Results-Based Interaction Design

    ERIC Educational Resources Information Center

    Weiss, Meredith

    2008-01-01

    Interaction design is a user-centered approach to development in which users and their goals are the driving force behind a project's design. Interaction design principles are fundamental to the design and implementation of effective websites, but they are not sufficient. This article argues that, to reach its full potential, a website should also…

  3. Adding Interactivity to Web Based Distance Learning.

    ERIC Educational Resources Information Center

    Cafolla, Ralph; Knee, Richard

    Web Based Distance Learning (WBDL) is a form of distance learning based on providing instruction mainly on the World Wide Web. This paradigm has limitations, especially the lack of interactivity inherent in the Web. The purpose of this paper is to discuss some of the technologies the authors have used in their courses at Florida Atlantic…

  4. Interactive Pedagogy in a Literature Based Classroom.

    ERIC Educational Resources Information Center

    Mayer, Virginia

    1993-01-01

    Preserving a literary-based curriculum, creating a sensitivity to the literature, and encouraging communicative skills relative to the literature are significant goals in foreign language study. Therefore, a program involving strategic interaction and cooperative learning techniques applied to the study of literature fosters communication and…

  5. Interactive analysis of geodata based intelligence

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  6. Theoretical calculations of base-base interactions in nucleic acids: II. Stacking interactions in polynucleotides.

    PubMed Central

    Gupta, G; Sasisekharan, V

    1978-01-01

    Base-base interactions were computed for single- and double stranded poly,ucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interacting energies of a regular duplex and the alternative structures were compared. It was found that the type II model is energetically more favourable than the rest. PMID:662698

  7. Susceptibility based upon Chemical Interaction with Disease ...

    EPA Pesticide Factsheets

    One of the challenges facing toxicology and risk assessment is that numerous host and environmental factors may modulate vulnerability and risk. An area of increasing interest is the potential for chemicals to interact with background aging and disease processes, an interaction that may yield cumulative damage, altered chemical potency, and increased disease incidence. This review outlines the interactions possible between chemicals and background disease and identifies the type of information needed to evaluate such interactions. Key among these is the existence of a clinically relevant and easy to measure biomarker of disease risk which allows the identification of vulnerable individuals based upon the level of risk biomarker. The impact of toxic chemicals on this biomarker can then be used to predict how the chemical modifies disease risk as long as related mechanistic and toxicological data are consistent with toxicant effect on the disease process. Several case studies are briefly presented which describe the toxic chemical, the clinical biomarker and the impacted disease including: fine particulate matter/decreased heart rate variability/increased cardiopulmonary events; cadmium/decreased glomerular filtration rate/increased chronic kidney disease; methyl mercury/decreased paraoxonase-1/increased cardiovascular risk; trichloroethylene/increased anti-nuclear antibody/autoimmunity; dioxin/increased CYP1A1/hypertension. These case studies point o

  8. ECCE Toolkit: Prototyping Sensor-Based Interaction.

    PubMed

    Bellucci, Andrea; Aedo, Ignacio; Díaz, Paloma

    2017-02-23

    Building and exploring physical user interfaces requires high technical skills and hours of specialized work. The behavior of multiple devices with heterogeneous input/output channels and connectivity has to be programmed in a context where not only the software interface matters, but also the hardware components are critical (e.g., sensors and actuators). Prototyping physical interaction is hindered by the challenges of: (1) programming interactions among physical sensors/actuators and digital interfaces; (2) implementing functionality for different platforms in different programming languages; and (3) building custom electronic-incorporated objects. We present ECCE (Entities, Components, Couplings and Ecosystems), a toolkit for non-programmers that copes with these issues by abstracting from low-level implementations, thus lowering the complexity of prototyping small-scale, sensor-based physical interfaces to support the design process. A user evaluation provides insights and use cases of the kind of applications that can be developed with the toolkit.

  9. ECCE Toolkit: Prototyping Sensor-Based Interaction

    PubMed Central

    Bellucci, Andrea; Aedo, Ignacio; Díaz, Paloma

    2017-01-01

    Building and exploring physical user interfaces requires high technical skills and hours of specialized work. The behavior of multiple devices with heterogeneous input/output channels and connectivity has to be programmed in a context where not only the software interface matters, but also the hardware components are critical (e.g., sensors and actuators). Prototyping physical interaction is hindered by the challenges of: (1) programming interactions among physical sensors/actuators and digital interfaces; (2) implementing functionality for different platforms in different programming languages; and (3) building custom electronic-incorporated objects. We present ECCE (Entities, Components, Couplings and Ecosystems), a toolkit for non-programmers that copes with these issues by abstracting from low-level implementations, thus lowering the complexity of prototyping small-scale, sensor-based physical interfaces to support the design process. A user evaluation provides insights and use cases of the kind of applications that can be developed with the toolkit. PMID:28241502

  10. Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions.

    PubMed

    Matta, Chérif F; Castillo, Norberto; Boyd, Russell J

    2006-01-12

    We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

  11. Learning through Interaction: Improving Practice with Design-Based Research

    ERIC Educational Resources Information Center

    Voigt, Christian; Swatman, Paula M. C.

    2006-01-01

    This article presents the first stage of a design-based research project to introduce case-based learning using existing interactive technologies in a major Australian university. The paper initially outlines the relationship between case-based learning, student interaction and the study of interactions--and includes a review of research into…

  12. Interactive physically-based sound simulation

    NASA Astrophysics Data System (ADS)

    Raghuvanshi, Nikunj

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

  13. CABINS: Case-based interactive scheduler

    NASA Technical Reports Server (NTRS)

    Miyashita, Kazuo; Sycara, Katia

    1992-01-01

    In this paper we discuss the need for interactive factory schedule repair and improvement, and we identify case-based reasoning (CBR) as an appropriate methodology. Case-based reasoning is the problem solving paradigm that relies on a memory for past problem solving experiences (cases) to guide current problem solving. Cases similar to the current case are retrieved from the case memory, and similarities and differences of the current case to past cases are identified. Then a best case is selected, and its repair plan is adapted to fit the current problem description. If a repair solution fails, an explanation for the failure is stored along with the case in memory, so that the user can avoid repeating similar failures in the future. So far we have identified a number of repair strategies and tactics for factory scheduling and have implemented a part of our approach in a prototype system, called CABINS. As a future work, we are going to scale up CABINS to evaluate its usefulness in a real manufacturing environment.

  14. Interactions between space-based and feature-based attention

    PubMed Central

    Leonard, Carly J.; Balestreri, Angela; Luck, Steven J.

    2014-01-01

    Although early research suggested that attention to nonspatial features (i.e., red) was confined to stimuli appearing at an attended spatial location, more recent research has emphasized the global nature of feature-based attention. For example, a distractor sharing a target feature may capture attention even if it occurs at a task-irrelevant location. Such findings have been used to argue that feature-based attention operates independently of spatial attention. However, feature-based attention may nonetheless interact with spatial attention, yielding larger feature-based effects at attended locations than at unattended locations. The present study tested this possibility. In two experiments, participants viewed a rapid serial visual presentation (RSVP) stream and identified a target letter defined by its color. Target-colored distractors were presented at various task-irrelevant locations during the RSVP stream. We found that feature-driven attentional capture effects were largest when the target-colored distractor was closer to the attended location. These results demonstrate that spatial attention modulates the strength of feature-based attention capture, calling into question the prior evidence that feature-based attention operates in a global manner that is independent of spatial attention. PMID:25285472

  15. Nuclear reaction inputs based on effective interactions

    NASA Astrophysics Data System (ADS)

    Hilaire, S.; Goriely, S.; Péru, S.; Dubray, N.; Dupuis, M.; Bauge, E.

    2016-11-01

    Extensive nuclear structure studies have been performed for decades using effective interactions as sole input. They have shown a remarkable ability to describe rather accurately many types of nuclear properties. In the early 2000s, a major effort has been engaged to produce nuclear reaction input data out of the Gogny interaction, in order to challenge its quality also with respect to nuclear reaction observables. The status of this project, well advanced today thanks to the use of modern computers as well as modern nuclear reaction codes, is reviewed and future developments are discussed.

  16. Genetic interaction mapping with microfluidic-based single cell sequencing

    PubMed Central

    Haliburton, John R.; Shao, Wenjun; Deutschbauer, Adam; Arkin, Adam; Abate, Adam R.

    2017-01-01

    Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms. PMID:28170417

  17. Genetic interaction mapping with microfluidic-based single cell sequencing.

    PubMed

    Haliburton, John R; Shao, Wenjun; Deutschbauer, Adam; Arkin, Adam; Abate, Adam R

    2017-01-01

    Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms.

  18. An Interactive Computer-Based Revision Aid

    ERIC Educational Resources Information Center

    Stevens, J. M.; Harris, F. T. C.

    1977-01-01

    A computer-based review system has been developed, based on the multiple-choice technique, at the University of London for medical students. The user can enter an answer or can have a list of questions to take away and enter later. Student response has been favorable. (LBH)

  19. Physically-based interactive Schlieren flow visualization

    SciTech Connect

    Mccormick, Patrick S; Brownlee, Carson S; Pegoraro, Vincent; Shankar, Siddharth; Hansen, Charles D

    2009-01-01

    Understanding fluid flow is a difficult problem and of increasing importance as computational fluid dynamics produces an abundance of simulation data. Experimental flow analysis has employed techniques such as shadowgraph and schlieren imaging for centuries which allow empirical observation of inhomogeneous flows. Shadowgraphs provide an intuitive way of looking at small changes in flow dynamics through caustic effects while schlieren cutoffs introduce an intensity gradation for observing large scale directional changes in the flow. The combination of these shading effects provides an informative global analysis of overall fluid flow. Computational solutions for these methods have proven too complex until recently due to the fundamental physical interaction of light refracting through the flow field. In this paper, we introduce a novel method to simulate the refraction of light to generate synthetic shadowgraphs and schlieren images of time-varying scalar fields derived from computational fluid dynamics (CFD) data. Our method computes physically accurate schlieren and shadowgraph images at interactive rates by utilizing a combination of GPGPU programming, acceleration methods, and data-dependent probabilistic schlieren cutoffs. Results comparing this method to previous schlieren approximations are presented.

  20. Constraint-based interactive assembly planning

    SciTech Connect

    Jones, R.E.; Wilson, R.H.; Calton, T.L.

    1997-03-01

    The constraints on assembly plans vary depending on the product, assembly facility, assembly volume, and many other factors. This paper describes the principles and implementation of a framework that supports a wide variety of user-specified constraints for interactive assembly planning. Constraints from many sources can be expressed on a sequencing level, specifying orders and conditions on part mating operations in a number of ways. All constraints are implemented as filters that either accept or reject assembly operations proposed by the planner. For efficiency, some constraints are supplemented with special-purpose modifications to the planner`s algorithms. Replanning is fast enough to enable a natural plan-view-constrain-replan cycle that aids in constraint discovery and documentation. We describe an implementation of the framework in a computer-aided assembly planning system and experiments applying the system to several complex assemblies. 12 refs., 2 figs., 3 tabs.

  1. Isoniazid interaction with phosphatidylcholine-based membranes

    NASA Astrophysics Data System (ADS)

    Marques, Amanda Vicente; Marengo Trindade, Paulo; Marques, Sheylla; Brum, Tainá; Harte, Etienne; Rodrigues, Marieli Oliveira; D'Oca, Marcelo Gonçalves Montes; da Silva, Pedro Almeida; Pohlmann, Adriana R.; Alves, Isabel Dantas; de Lima, Vânia Rodrigues

    2013-11-01

    Interaction between the anti-tuberculosis drug isoniazid (INH) and phosphatidylcholine membranes was investigated in terms of: (i) drug affinity to a lipid bilayer and (ii) drug-induced changes in the dynamic properties of liposomes, such as membrane hydration state, polar head and non-polar acyl chain order and lipid phase transition behavior. These parameters were studied by plasmon waveguide resonance spectroscopy (PWR), UV-visible, horizontal attenuated total reflectance-Fourier transform infrared (HATR-FTIR), nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC) techniques. PWR measurements showed an INH membrane dissociation constant value of 0.031 μM to phosphatidylcholine bilayers. INH induced higher membrane perturbation in the plane which is perpendicular to the membrane plane. The INH saturation concentration in phosphatidylcholine liposomes was 170 μM. At this concentration, HATR-FTIR and NMR findings showed that INH may interact with the lipid polar head, increasing the number of hydrogen bonds in the phosphate region and enhancing the choline motional freedom. DSC measurements showed that, at 115 μM, INH was responsible for a decrease in lipid phase transition temperature of approximately 2 °C and had no influence in the lipid enthalpy variation (ΔH). However, at 170 μM, INH induced the reduction of the ΔH by approximately 52%, suggesting that the drug may increase the distance among lipid molecules and enhance the freedom of the lipid acyl chains methylene groups. This paper provides information on the effects of INH on membrane dynamics which is important to understand liposome targeting of the drug and for the development of anti-TB pharmacologic systems that not only are less susceptible to resistance but also have low toxicity.

  2. A Usability Study of Interactive Web-Based Modules

    ERIC Educational Resources Information Center

    Girard, Tulay; Pinar, Musa

    2011-01-01

    This research advances the understanding of the usability of marketing case study modules in the area of interactive web-based technologies through the assignment of seven interactive case modules in a Principles of Marketing course. The case modules were provided for marketing students by the publisher, McGraw Hill Irwin, of the…

  3. Web-based Interactive Simulator for Rotating Machinery.

    ERIC Educational Resources Information Center

    Sirohi, Vijayalaxmi

    1999-01-01

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

  4. On Interactive Teaching Model of Translation Course Based on Wechat

    ERIC Educational Resources Information Center

    Lin, Wang

    2017-01-01

    Constructivism is a theory related to knowledge and learning, focusing on learners' subjective initiative, based on which the interactive approach has been proved to play a crucial role in language learning. Accordingly, the interactive approach can also be applied to translation teaching since translation itself is a bilingual transformational…

  5. A web-based protein interaction network visualizer

    PubMed Central

    2014-01-01

    Background Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online. Results Given the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions (http://biosual.cbio.uct.ac.za/pinv.html). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs. Conclusions The resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s research collaborative environments. The source code is freely available for download at

  6. Multiquadric Spline-Based Interactive Segmentation of Vascular Networks

    PubMed Central

    Meena, Sachin; Surya Prasath, V. B.; Kassim, Yasmin M.; Maude, Richard J.; Glinskii, Olga V.; Glinsky, Vladislav V.; Huxley, Virginia H.; Palaniappan, Kannappan

    2016-01-01

    Commonly used drawing tools for interactive image segmentation and labeling include active contours or boundaries, scribbles, rectangles and other shapes. Thin vessel shapes in images of vascular networks are difficult to segment using automatic or interactive methods. This paper introduces the novel use of a sparse set of user-defined seed points (supervised labels) for precisely, quickly and robustly segmenting complex biomedical images. A multiquadric spline-based binary classifier is proposed as a unique approach for interactive segmentation using as features color values and the location of seed points. Epifluorescence imagery of the dura mater microvasculature are difficult to segment for quantitative applications due to challenging tissue preparation, imaging conditions, and thin, faint structures. Experimental results based on twenty epifluorescence images is used to illustrate the benefits of using a set of seed points to obtain fast and accurate interactive segmentation compared to four interactive and automatic segmentation approaches. PMID:28227856

  7. Multiquadric Spline-Based Interactive Segmentation of Vascular Networks.

    PubMed

    Meena, Sachin; Surya Prasath, V B; Kassim, Yasmin M; Maude, Richard J; Glinskii, Olga V; Glinsky, Vladislav V; Huxley, Virginia H; Palaniappan, Kannappan

    2016-08-01

    Commonly used drawing tools for interactive image segmentation and labeling include active contours or boundaries, scribbles, rectangles and other shapes. Thin vessel shapes in images of vascular networks are difficult to segment using automatic or interactive methods. This paper introduces the novel use of a sparse set of user-defined seed points (supervised labels) for precisely, quickly and robustly segmenting complex biomedical images. A multiquadric spline-based binary classifier is proposed as a unique approach for interactive segmentation using as features color values and the location of seed points. Epifluorescence imagery of the dura mater microvasculature are difficult to segment for quantitative applications due to challenging tissue preparation, imaging conditions, and thin, faint structures. Experimental results based on twenty epifluorescence images is used to illustrate the benefits of using a set of seed points to obtain fast and accurate interactive segmentation compared to four interactive and automatic segmentation approaches.

  8. Interactive Internet Based Pendulum for Learning Mechatronics

    NASA Astrophysics Data System (ADS)

    Sethson, Magnus R.

    2003-01-01

    This paper describes an Internet based remote experimental setup of a double lined pendulum mechanism for students experiments at the M. Sc. Level. Some of the first year experience using this web-based setup in classes is referred. In most of the courses given at the division of mechanical engineering systems at Linkoeping Institute of Technology we provide experimental setups to enhance the teaching Of M.Sc. students. Many of these experimental setups involve mechatronical systems. Disciplines like fluid power, electronics, and mechanics and also software technologies are used in each experiment. As our campus has recently been split into two different cities some new concepts for distance learning have been studied. The one described here tries to implement remotely controlled mechatronic setups for teaching basic programming of real-time operating systems and analysis of the dynamics of mechanical systems. The students control the regulators for the pendulum through a web interface and get measurement results and a movie back through their email. The present setup uses a double linked pendulum that is controlled by a DC-motor and monitored through both camera and angular position sensors. All software needed is hosted on a double-processor PC running the RedHat 7.1. distribution complemented with real-time scheduling using DIAPM-RTAI 1.7. The Internet site is presented to the students using PHP, Apache and MySQL. All of the used software originates from the open source domain. The experience from integrating these technologies and security issues is discussed together with the web-camera interface. One of the important experiences from this project so far is the need for a good visual feedback. This is both in terms of video speed but also in resolution. It has been noticed that when the students makes misstates and wants to search the failure they want clear, large images with high resolution to support their personal believes in the cause of the failure. Even

  9. Individual versus Interactive Task-Based Performance through Voice-Based Computer-Mediated Communication

    ERIC Educational Resources Information Center

    Granena, Gisela

    2016-01-01

    Interaction is a necessary condition for second language (L2) learning (Long, 1980, 1996). Research in computer-mediated communication has shown that interaction opportunities make learners pay attention to form in a variety of ways that promote L2 learning. This research has mostly investigated text-based rather than voice-based interaction. The…

  10. Gallium based low-interaction anions

    DOEpatents

    King, Wayne A.; Kubas, Gregory J.

    2000-01-01

    The present invention provides: a composition of the formula M.sup.+x (Ga(Y).sub.4.sup.-).sub.x where M is a metal selected from the group consisting of lithium, sodium, potassium, cesium, calcium, strontium, thallium, and silver, x is an integer selected from the group consisting of 1 or 2, each Y is a ligand selected from the group consisting of aryl, alkyl, hydride and halide with the proviso that at least one Y is a ligand selected from the group consisting of aryl, alkyl and halide; a composition of the formula (R).sub.x Q.sup.+ Ga(Y).sub.4.sup.- where Q is selected from the group consisting of carbon, nitrogen, sulfur, phosphorus and oxygen, each R is a ligand selected from the group consisting of alkyl, aryl, and hydrogen, x is an integer selected from the group consisting of 3 and 4 depending upon Q, and each Y is a ligand selected from the group consisting of aryl, alkyl, hydride and halide with the proviso that at least one Y is a ligand selected from the group consisting of aryl, alkyl and halide; an ionic polymerization catalyst composition including an active cationic portion and a gallium based weakly coordinating anion; and bridged anion species of the formula M.sup.+x.sub.y [X(Ga(Y.sub.3).sub.z ].sup.-y.sub.x where M is a metal selected from the group consisting of lithium, sodium, potassium, magnesium, cesium, calcium, strontium, thallium, and silver, x is an integer selected from the group consisting of 1 or 2, X is a bridging group between two gallium atoms, y is an integer selected from the group consisting 1 and 2, z is an integer of at least 2, each Y is a ligand selected from the group consisting of aryl, alkyl, hydride and halide with the proviso that at least one Y is a ligand selected from the group consisting of aryl, alkyl and halide.

  11. Drug-target interaction prediction from PSSM based evolutionary information.

    PubMed

    Mousavian, Zaynab; Khakabimamaghani, Sahand; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-01-01

    The labor-intensive and expensive experimental process of drug-target interaction prediction has motivated many researchers to focus on in silico prediction, which leads to the helpful information in supporting the experimental interaction data. Therefore, they have proposed several computational approaches for discovering new drug-target interactions. Several learning-based methods have been increasingly developed which can be categorized into two main groups: similarity-based and feature-based. In this paper, we firstly use the bi-gram features extracted from the Position Specific Scoring Matrix (PSSM) of proteins in predicting drug-target interactions. Our results demonstrate the high-confidence prediction ability of the Bigram-PSSM model in terms of several performance indicators specifically for enzymes and ion channels. Moreover, we investigate the impact of negative selection strategy on the performance of the prediction, which is not widely taken into account in the other relevant studies. This is important, as the number of non-interacting drug-target pairs are usually extremely large in comparison with the number of interacting ones in existing drug-target interaction data. An interesting observation is that different levels of performance reduction have been attained for four datasets when we change the sampling method from the random sampling to the balanced sampling.

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  13. User Interaction Design for a Home-Based Telecare System

    NASA Astrophysics Data System (ADS)

    Raptis, Spyros; Tsiakoulis, Pirros; Chalamandaris, Aimilios; Karabetsos, Sotiris

    This paper presents the design of the user-interaction component of a home-based telecare system for congestive heart failure patients. It provides a short overview of the overall system and offers details on the different interaction types supported by the system. Interacting with the user occurs either as part of a scheduled procedure or as a consequence of identifying or predicting a potentially hazardous deterioration of the patients' health state. The overall logic of the interaction is structured around event-scenario associations, where a scenario consists of concrete actions to be performed, some of which may involve the patient. A key objective in this type of interaction that it is very simple, intuitive and short, involving common everyday objects and familiar media such as speech.

  14. Evaluation of an Interactive Case-Based Online Network (ICON) in a Problem Based Learning Environment

    ERIC Educational Resources Information Center

    Nathoo, Arif N.; Goldhoff, Patricia; Quattrochi, James J.

    2005-01-01

    Purpose: This study sought to assess the introduction of a web-based innovation in medical education that complements traditional problem-based learning curricula. Utilizing the case method as its fundamental educational approach, the Interactive Case-based Online Network (ICON) allows students to interact with each other, faculty and a virtual…

  15. Cyberpsychology: a human-interaction perspective based on cognitive modeling.

    PubMed

    Emond, Bruno; West, Robert L

    2003-10-01

    This paper argues for the relevance of cognitive modeling and cognitive architectures to cyberpsychology. From a human-computer interaction point of view, cognitive modeling can have benefits both for theory and model building, and for the design and evaluation of sociotechnical systems usability. Cognitive modeling research applied to human-computer interaction has two complimentary objectives: (1) to develop theories and computational models of human interactive behavior with information and collaborative technologies, and (2) to use the computational models as building blocks for the design, implementation, and evaluation of interactive technologies. From the perspective of building theories and models, cognitive modeling offers the possibility to anchor cyberpsychology theories and models into cognitive architectures. From the perspective of the design and evaluation of socio-technical systems, cognitive models can provide the basis for simulated users, which can play an important role in usability testing. As an example of application of cognitive modeling to technology design, the paper presents a simulation of interactive behavior with five different adaptive menu algorithms: random, fixed, stacked, frequency based, and activation based. Results of the simulation indicate that fixed menu positions seem to offer the best support for classification like tasks such as filing e-mails. This research is part of the Human-Computer Interaction, and the Broadband Visual Communication research programs at the National Research Council of Canada, in collaboration with the Carleton Cognitive Modeling Lab at Carleton University.

  16. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

    PubMed Central

    Flannery, Andrea; Gerlach, Jared Q.; Joshi, Lokesh; Kilcoyne, Michelle

    2015-01-01

    Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i) conventional carbohydrate or glycan microarrays; (ii) whole mucin microarrays; and (iii) microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments. PMID:27600247

  17. Computer-Based Interaction Analysis with DEGREE Revisited

    ERIC Educational Resources Information Center

    Barros, B.; Verdejo, M. F.

    2016-01-01

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

  18. Student Satisfaction in Interactive Engagement-Based Physics Classes

    ERIC Educational Resources Information Center

    Gaffney, Jon D. H.; Gaffney, Amy L. Housley

    2016-01-01

    Interactive engagement-based (IE) physics classes have the potential to invigorate and motivate students, but students may resist or oppose the pedagogy. Understanding the major influences on student satisfaction is a key to successful implementation of such courses. In this study, we note that one of the major differences between IE and…

  19. A Microcomputer-Based Interactive Presentation Development System.

    ERIC Educational Resources Information Center

    Moreau, Dennis R.; Dominick, Wayne D.

    1988-01-01

    Reviews research and development projects sponsored by the National Aeronautics and Space Administration (NASA) that address microcomputer-based support for instructional activities at the University of Southwestern Louisiana. Highlights include a graphics project, local area networks, and the Interactive Presentation Development System, which is…

  20. Interaction in Graduate Nursing Web-based Instruction.

    ERIC Educational Resources Information Center

    Boyle, Diane K.; Wambach, Karen A.

    2001-01-01

    Web-based instruction in graduate nursing courses was built on learner-centered and adult learning philosophies and interaction at several points: precourse, course start-up, course maintenance, and course closure. Students were relatively satisfied, found the courses convenient, were moderately engaged in active learning, and felt prepared for…

  1. Web-Based Interactive Writing Environment: Development and Evaluation

    ERIC Educational Resources Information Center

    Yang, Jie Chi; Ko, Hwa Wei; Chung, I. Ling

    2005-01-01

    This study reports the development and evaluation of a web-based interactive writing environment designed for elementary school students. The environment includes three writing themes, "story pass on", "story chameleon" and "thousand ideas", to encourage reading comprehension, creativity and problem-solving skills of…

  2. Web-Based Learning Interaction and Learning Styles.

    ERIC Educational Resources Information Center

    Sabry, Khaled; Baldwin, Lynne

    2003-01-01

    Reports a study exploring the learning styles and perceptions of undergraduate and postgraduate students at Brunel University (United Kingdom) in relation to using the Web for learning. Explores the sequential/global learning style dimension in relation to three categories of Web-based interaction: learner-tutor, learner-leaner, and…

  3. Interactive Video-Based Industrial Training in Basic Electronics.

    ERIC Educational Resources Information Center

    Mirkin, Barry

    The Wisconsin Foundation for Vocational, Technical, and Adult Education is currently involved in the development, implementation, and distribution of a sophisticated interactive computer and video learning system. Designed to offer trainees an open entry and open exit opportunity to pace themselves through a comprehensive competency-based,…

  4. Wandering: A Web-Based Platform for the Creation of Location-Based Interactive Learning Objects

    ERIC Educational Resources Information Center

    Barak, Miri; Ziv, Shani

    2013-01-01

    Wandering is an innovative web-based platform that was designed to facilitate outdoor, authentic, and interactive learning via the creation of location-based interactive learning objects (LILOs). Wandering was integrated as part of a novel environmental education program among middle school students. This paper describes the Wandering platform's…

  5. Potential drug interactions with statins: Estonian register-based study

    PubMed Central

    Volmer, Daisy; Hartikainen, Sirpa; Zharkovsky, Alexander

    2015-01-01

    In Estonia, HMG-CoA reductase inhibitors are widely used to modify lipid levels but there are no current data on additional medicines prescribed alongside the statins. The aim of this study was to identify the frequency of potential clinically relevant interactions at a national level among an outpatient population treated with statins between January and June 2008, based on the prescription database of the Estonian Health Insurance Fund. This retrospective prevalence study included 203,646 outpatients aged 50 years or older, of whom 29,367 received statin therapy. The study analysed individuals who had used at least one prescription medicine for a minimum of 7 days concomitantly with statins. Potential drug interactions were analysed using Epocrates online, Stockley’s Drug Interactions, and the drug interaction database developed in Estonia. Statins metabolised by the CYP3A4 isoenzyme were prescribed to 64% of all statin users. Medicines known to have potentially clinically significant interactions with statins were prescribed to 4.6% of patients. The drugs prescribed concomitantly most often with simvastatin were warfarin (5.7%) and amiodarone (3.9%), whereas digoxin (1.2%) and ethinylestradiol (2%) were prescribed with atorvastatin. Potential interactions were not detected in the treatment regimens of rosuvastatin, pravastatin, and fluvastatin users. PMID:28352703

  6. Traffic and Driving Simulator Based on Architecture of Interactive Motion

    PubMed Central

    Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

    2015-01-01

    This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination. PMID:26491711

  7. Traffic and Driving Simulator Based on Architecture of Interactive Motion.

    PubMed

    Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

    2015-01-01

    This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination.

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

    PubMed

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

    2015-04-01

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

  9. Analysis of Geophysical Data Bases and Models for Spacecraft Interactions.

    DTIC Science & Technology

    1986-10-31

    electrons, protons, ions (major species), and measured dose. - Evaluation of magnetic field models (Delta B Model). - Quasi- static Data Bases, Analysis ...AIB4 889 ANALYSIS OF GEOPHYSICRL DATA BASES AND MODELS FOR 1/3 SPACECRAFT INTERACTIONS(U) RADEX INC CARLISLE MA J N BAS ET AL 31 OCT 86 AFGL-TR-86...1114 11116 MICROCOPY RESOLUTION TEST CHART NATI()NAL BUREAU flE SIANDARD % 43 A oJ P=I -- % AFGL-TR-86-0221 0 00 ANALYSIS OF GEOPHYSICAL DATA BASES

  10. Web-based Interactive Landform Simulation Model - Grand Canyon

    NASA Astrophysics Data System (ADS)

    Luo, W.; Pelletier, J. D.; Duffin, K.; Ormand, C. J.; Hung, W.; Iverson, E. A.; Shernoff, D.; Zhai, X.; Chowdary, A.

    2013-12-01

    Earth science educators need interactive tools to engage and enable students to better understand how Earth systems work over geologic time scales. The evolution of landforms is ripe for interactive, inquiry-based learning exercises because landforms exist all around us. The Web-based Interactive Landform Simulation Model - Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is a continuation and upgrade of the simple cellular automata (CA) rule-based model (WILSIM-CA, http://www.niu.edu/landform/) that can be accessed from anywhere with an Internet connection. Major improvements in WILSIM-GC include adopting a physically based model and the latest Java technology. The physically based model is incorporated to illustrate the fluvial processes involved in land-sculpting pertaining to the development and evolution of one of the most famous landforms on Earth: the Grand Canyon. It is hoped that this focus on a famous and specific landscape will attract greater student interest and provide opportunities for students to learn not only how different processes interact to form the landform we observe today, but also how models and data are used together to enhance our understanding of the processes involved. The latest development in Java technology (such as Java OpenGL for access to ubiquitous fast graphics hardware, Trusted Applet for file input and output, and multithreaded ability to take advantage of modern multi-core CPUs) are incorporated into building WILSIM-GC and active, standards-aligned curricula materials guided by educational psychology theory on science learning will be developed to accompany the model. This project is funded NSF-TUES program.

  11. Deep-Learning-Based Drug-Target Interaction Prediction.

    PubMed

    Wen, Ming; Zhang, Zhimin; Niu, Shaoyu; Sha, Haozhi; Yang, Ruihan; Yun, Yonghuan; Lu, Hongmei

    2017-04-07

    Identifying interactions between known drugs and targets is a major challenge in drug repositioning. In silico prediction of drug-target interaction (DTI) can speed up the expensive and time-consuming experimental work by providing the most potent DTIs. In silico prediction of DTI can also provide insights about the potential drug-drug interaction and promote the exploration of drug side effects. Traditionally, the performance of DTI prediction depends heavily on the descriptors used to represent the drugs and the target proteins. In this paper, to accurately predict new DTIs between approved drugs and targets without separating the targets into different classes, we developed a deep-learning-based algorithmic framework named DeepDTIs. It first abstracts representations from raw input descriptors using unsupervised pretraining and then applies known label pairs of interaction to build a classification model. Compared with other methods, it is found that DeepDTIs reaches or outperforms other state-of-the-art methods. The DeepDTIs can be further used to predict whether a new drug targets to some existing targets or whether a new target interacts with some existing drugs.

  12. Student satisfaction in interactive engagement-based physics classes

    NASA Astrophysics Data System (ADS)

    Gaffney, Jon D. H.; Gaffney, Amy L. Housley

    2016-12-01

    Interactive engagement-based (IE) physics classes have the potential to invigorate and motivate students, but students may resist or oppose the pedagogy. Understanding the major influences on student satisfaction is a key to successful implementation of such courses. In this study, we note that one of the major differences between IE and traditional physics classes lies in the interpersonal relationships between the instructor and students. Therefore, we introduce the interpersonal communication constructs of instructor credibility and facework as possible frameworks for understanding how instructors and students navigate the new space of interactions. By interpreting survey data (N =161 respondents in eight sections of an IE introductory algebra-based physics course), we found both frameworks to be useful in explaining variance in student ratings of their satisfaction in the course, although we are unable to distinguish at this point whether instructor credibility acts as a mediating variable between facework and course satisfaction.

  13. Using Agent Based Modeling (ABM) to Develop Cultural Interaction Simulations

    NASA Technical Reports Server (NTRS)

    Drucker, Nick; Jones, Phillip N.

    2012-01-01

    Today, most cultural training is based on or built around "cultural engagements" or discrete interactions between the individual learner and one or more cultural "others". Often, success in the engagement is the end or the objective. In reality, these interactions usually involve secondary and tertiary effects with potentially wide ranging consequences. The concern is that learning culture within a strict engagement context might lead to "checklist" cultural thinking that will not empower learners to understand the full consequence of their actions. We propose the use of agent based modeling (ABM) to collect, store, and, simulating the effects of social networks, promulgate engagement effects over time, distance, and consequence. The ABM development allows for rapid modification to re-create any number of population types, extending the applicability of the model to any requirement for social modeling.

  14. Structure-based prediction of host-pathogen protein interactions.

    PubMed

    Mariano, Rachelle; Wuchty, Stefan

    2017-03-16

    The discovery, validation, and characterization of protein-based interactions from different species are crucial for translational research regarding a variety of pathogens, ranging from the malaria parasite Plasmodium falciparum to HIV-1. Here, we review recent advances in the prediction of host-pathogen protein interfaces using structural information. In particular, we observe that current methods chiefly perform machine learning on sequence and domain information to produce large sets of candidate interactions that are further assessed and pruned to generate final, highly probable sets. Structure-based studies have also emphasized the electrostatic properties and evolutionary transformations of pathogenic interfaces, supplying crucial insight into antigenic determinants and the ways pathogens compete for host protein binding. Advancements in spectroscopic and crystallographic methods complement the aforementioned techniques, permitting the rigorous study of true positives at a molecular level. Together, these approaches illustrate how protein structure on a variety of levels functions coordinately and dynamically to achieve host takeover.

  15. Role of exchange interaction in nitrogen vacancy center based magnetometry

    NASA Astrophysics Data System (ADS)

    Ho, Cong Son; Tan, Seng Ghee; Jalil, Mansoor B. A.; Chen, Zilong; Krivitsky, Leonid A.

    2016-12-01

    We propose a multilayer device comprising a thin-film-based ferromagnetic heterostructure (FMH) deposited on a diamond layer doped with nitrogen vacancy centers (NVC's). We find that when the NVC's are in close proximity (1-2 nm) to the FMH, the exchange energy is comparable to, and may even surpass, the magnetostatic interaction energy. This calls forth the need to consider and utilize both effects in magnetometry based on NVC's in diamond. As the distance between the FMH and NVC is decreased to the subnanometer scale, the exponential increase in the exchange energy suggests spintronic applications of NVC's beyond magnetometry, such as detection of spin Hall effect or spin currents.

  16. Direct interaction of microtubule- and actin-based transport motors

    NASA Technical Reports Server (NTRS)

    Huang, J. D.; Brady, S. T.; Richards, B. W.; Stenolen, D.; Resau, J. H.; Copeland, N. G.; Jenkins, N. A.

    1999-01-01

    The microtubule network is thought to be used for long-range transport of cellular components in animal cells whereas the actin network is proposed to be used for short-range transport, although the mechanism(s) by which this transport is coordinated is poorly understood. For example, in sea urchins long-range Ca2+-regulated transport of exocytotic vesicles requires a microtubule-based motor, whereas an actin-based motor is used for short-range transport. In neurons, microtubule-based kinesin motor proteins are used for long-range vesicular transport but microtubules do not extend into the neuronal termini, where actin filaments form the cytoskeletal framework, and kinesins are rapidly degraded upon their arrival in neuronal termini, indicating that vesicles may have to be transferred from microtubules to actin tracks to reach their final destination. Here we show that an actin-based vesicle-transport motor, MyoVA, can interact directly with a microtubule-based transport motor, KhcU. As would be expected if these complexes were functional, they also contain kinesin light chains and the localization of MyoVA and KhcU overlaps in the cell. These results indicate that cellular transport is, in part, coordinated through the direct interaction of different motor molecules.

  17. Optimization-based interactive segmentation interface for multiregion problems.

    PubMed

    Baxter, John S H; Rajchl, Martin; Peters, Terry M; Chen, Elvis C S

    2016-04-01

    Interactive segmentation is becoming of increasing interest to the medical imaging community in that it combines the positive aspects of both manual and automated segmentation. However, general-purpose tools have been lacking in terms of segmenting multiple regions simultaneously with a high degree of coupling between groups of labels. Hierarchical max-flow segmentation has taken advantage of this coupling for individual applications, but until recently, these algorithms were constrained to a particular hierarchy and could not be considered general-purpose. In a generalized form, the hierarchy for any given segmentation problem is specified in run-time, allowing different hierarchies to be quickly explored. We present an interactive segmentation interface, which uses generalized hierarchical max-flow for optimization-based multiregion segmentation guided by user-defined seeds. Applications in cardiac and neonatal brain segmentation are given as example applications of its generality.

  18. Interactive Reference Point Procedure Based on the Conic Scalarizing Function

    PubMed Central

    2014-01-01

    In multiobjective optimization methods, multiple conflicting objectives are typically converted into a single objective optimization problem with the help of scalarizing functions. The conic scalarizing function is a general characterization of Benson proper efficient solutions of non-convex multiobjective problems in terms of saddle points of scalar Lagrangian functions. This approach preserves convexity. The conic scalarizing function, as a part of a posteriori or a priori methods, has successfully been applied to several real-life problems. In this paper, we propose a conic scalarizing function based interactive reference point procedure where the decision maker actively takes part in the solution process and directs the search according to her or his preferences. An algorithmic framework for the interactive solution of multiple objective optimization problems is presented and is utilized for solving some illustrative examples. PMID:24723795

  19. Interactive reference point procedure based on the conic scalarizing function.

    PubMed

    Ustun, Ozden

    2014-01-01

    In multiobjective optimization methods, multiple conflicting objectives are typically converted into a single objective optimization problem with the help of scalarizing functions. The conic scalarizing function is a general characterization of Benson proper efficient solutions of non-convex multiobjective problems in terms of saddle points of scalar Lagrangian functions. This approach preserves convexity. The conic scalarizing function, as a part of a posteriori or a priori methods, has successfully been applied to several real-life problems. In this paper, we propose a conic scalarizing function based interactive reference point procedure where the decision maker actively takes part in the solution process and directs the search according to her or his preferences. An algorithmic framework for the interactive solution of multiple objective optimization problems is presented and is utilized for solving some illustrative examples.

  20. Template-Based Modeling of Protein-RNA Interactions

    PubMed Central

    Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.

    2016-01-01

    Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342

  1. Template-Based Modeling of Protein-RNA Interactions.

    PubMed

    Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong

    2016-09-01

    Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.

  2. A GDP fluctuation model based on interacting firms

    NASA Astrophysics Data System (ADS)

    Li, Honggang; Gao, Yan

    2008-09-01

    A distinctive feature of the market economies is the short-run fluctuations in output around the trend of long-run growth over time, and we regard this feature is internal to complex economic systems composed of interacting heterogeneous units. To explore such internal mechanisms of macroeconomic fluctuations, we present a multi-agent Keynesian theory-based model, which can provide a good approximation to the key empirical features of the western business cycles in the 20th Century, such as the structure of the autocorrelation function of overall output growth, correlations between the output growth of individual agents over time, the distribution of recessions, etc.

  3. SOLO: An Interactive Microcomputer-Based Bedside Monitor

    PubMed Central

    Comerchero, Harry; Vernia, Michael; Tivig, Gerhard; Kalinsky, David; Miller, Avram; Rackow, Eric C.; Welch, Jim

    1979-01-01

    An interactive, microcomputer-based bedside monitor is described which facilitates continuous on-line monitoring of a given patient's hemodynamic parameters. Used primarily in shock/trauma and intensive care units, the user has easy access to the patient data via a special interactive keypad and video display integrally a part of the bedside monitor. Phasic waveforms are analyzed in order to derive heart rate, arterial pressure, pulmonary artery pressure, central venous pressure, temperature and respiration rate. Special procedure functions are available to facilitate on-line, interactive measurement of Cardiac Output, Pulmonary Wedge Pressure, and Fluid Input/Output. All continuously monitored parameters, as well as specially acquired parameters, can be graphically trended over the last 72 hours. Medication administration and special event markers can be displayed together with trends to correlate such actions with changes in the patient status. The SOLO MONITOR is currently implemented on a Digital Equipment Corporation LSI-11 with 28K words of memory and is commercially available through Mennen Medical Inc. ImagesFig. 1Fig. 11

  4. A prototype system based on visual interactive SDM called VGC

    NASA Astrophysics Data System (ADS)

    Jia, Zelu; Liu, Yaolin; Liu, Yanfang

    2009-10-01

    In many application domains, data is collected and referenced by its geo-spatial location. Spatial data mining, or the discovery of interesting patterns in such databases, is an important capability in the development of database systems. Spatial data mining recently emerges from a number of real applications, such as real-estate marketing, urban planning, weather forecasting, medical image analysis, road traffic accident analysis, etc. It demands for efficient solutions for many new, expensive, and complicated problems. For spatial data mining of large data sets to be effective, it is also important to include humans in the data exploration process and combine their flexibility, creativity, and general knowledge with the enormous storage capacity and computational power of today's computers. Visual spatial data mining applies human visual perception to the exploration of large data sets. Presenting data in an interactive, graphical form often fosters new insights, encouraging the information and validation of new hypotheses to the end of better problem-solving and gaining deeper domain knowledge. In this paper a visual interactive spatial data mining prototype system (visual geo-classify) based on VC++6.0 and MapObject2.0 are designed and developed, the basic algorithms of the spatial data mining is used decision tree and Bayesian networks, and data classify are used training and learning and the integration of the two to realize. The result indicates it's a practical and extensible visual interactive spatial data mining tool.

  5. Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations

    PubMed Central

    Shashkova, Tatiana; Popenko, Anna; Tyakht, Alexander; Peskov, Kirill; Kosinsky, Yuri; Bogolubsky, Lev; Raigorodskii, Andrei; Ischenko, Dmitry; Alexeev, Dmitry; Govorun, Vadim

    2016-01-01

    Background Intestinal microbiota plays an important role in the human health. It is involved in the digestion and protects the host against external pathogens. Examination of the intestinal microbiome interactions is required for understanding of the community influence on host health. Studies of the microbiome can provide insight on methods of improving health, including specific clinical procedures for individual microbial community composition modification and microbiota correction by colonizing with new bacterial species or dietary changes. Methodology/Principal Findings In this work we report an agent-based model of interactions between two bacterial species and between species and the gut. The model is based on reactions describing bacterial fermentation of polysaccharides to acetate and propionate and fermentation of acetate to butyrate. Antibiotic treatment was chosen as disturbance factor and used to investigate stability of the system. System recovery after antibiotic treatment was analyzed as dependence on quantity of feedback interactions inside the community, therapy duration and amount of antibiotics. Bacterial species are known to mutate and acquire resistance to the antibiotics. The ability to mutate was considered to be a stochastic process, under this suggestion ratio of sensitive to resistant bacteria was calculated during antibiotic therapy and recovery. Conclusion/Significance The model confirms a hypothesis of feedbacks mechanisms necessity for providing functionality and stability of the system after disturbance. High fraction of bacterial community was shown to mutate during antibiotic treatment, though sensitive strains could become dominating after recovery. The recovery of sensitive strains is explained by fitness cost of the resistance. The model demonstrates not only quantitative dynamics of bacterial species, but also gives an ability to observe the emergent spatial structure and its alteration, depending on various feedback mechanisms

  6. Interactive Webmap-Based Science Planning for BepiColombo

    NASA Astrophysics Data System (ADS)

    McAuliffe, J.; Martinez, S.; Ortiz de Landaluce, I.; de la Fuente, S.

    2015-10-01

    For BepiColombo, ESA's Mission to Mercury, we will build a web-based, map-based interface to the Science Planning System. This interface will allow the mission's science teams to visually define targets for observations and interactively specify what operations will make up the given observation. This will be a radical departure from previous ESA mission planning methods. Such an interface will rely heavily on GIS technologies. This interface will provide footprint coverage of all existing archived data for Mercury, including a set of built-in basemaps. This will allow the science teams to analyse their planned observations and operational constraints with relevant contextual information from their own instrument, other BepiColombo instruments or from previous missions. The interface will allow users to import and export data in commonly used GIS formats, such that it can be visualised together with the latest planning information (e.g. import custom basemaps) or analysed in other GIS software. The interface will work with an object-oriented concept of an observation that will be a key characteristic of the overall BepiColombo scienceplanning concept. Observation templates or classes will be tracked right through the planning-executionprocessing- archiving cycle to the final archived science products. By using an interface that synthesises all relevant available information, the science teams will have a better understanding of the operational environment; it will enhance their ability to plan efficiently minimising or removing manual planning. Interactive 3D visualisation of the planned, scheduled and executed observations, simulation of the viewing conditions and interactive modification of the observation parameters are also being considered.

  7. Investigating antimalarial drug interactions of emetine dihydrochloride hydrate using CalcuSyn-based interactivity calculations

    PubMed Central

    Matthews, Holly; Deakin, Jon; Rajab, May; Idris-Usman, Maryam

    2017-01-01

    The widespread introduction of artemisinin-based combination therapy has contributed to recent reductions in malaria mortality. Combination therapies have a range of advantages, including synergism, toxicity reduction, and delaying the onset of resistance acquisition. Unfortunately, antimalarial combination therapy is limited by the depleting repertoire of effective drugs with distinct target pathways. To fast-track antimalarial drug discovery, we have previously employed drug-repositioning to identify the anti-amoebic drug, emetine dihydrochloride hydrate, as a potential candidate for repositioned use against malaria. Despite its 1000-fold increase in in vitro antimalarial potency (ED50 47 nM) compared with its anti-amoebic potency (ED50 26–32 uM), practical use of the compound has been limited by dose-dependent toxicity (emesis and cardiotoxicity). Identification of a synergistic partner drug would present an opportunity for dose-reduction, thus increasing the therapeutic window. The lack of reliable and standardised methodology to enable the in vitro definition of synergistic potential for antimalarials is a major drawback. Here we use isobologram and combination-index data generated by CalcuSyn software analyses (Biosoft v2.1) to define drug interactivity in an objective, automated manner. The method, based on the median effect principle proposed by Chou and Talalay, was initially validated for antimalarial application using the known synergistic combination (atovaquone-proguanil). The combination was used to further understand the relationship between SYBR Green viability and cytocidal versus cytostatic effects of drugs at higher levels of inhibition. We report here the use of the optimised Chou Talalay method to define synergistic antimalarial drug interactivity between emetine dihydrochloride hydrate and atovaquone. The novel findings present a potential route to harness the nanomolar antimalarial efficacy of this affordable natural product. PMID:28257497

  8. Graphics processing unit-based alignment of protein interaction networks.

    PubMed

    Xie, Jiang; Zhou, Zhonghua; Ma, Jin; Xiang, Chaojuan; Nie, Qing; Zhang, Wu

    2015-08-01

    Network alignment is an important bridge to understanding human protein-protein interactions (PPIs) and functions through model organisms. However, the underlying subgraph isomorphism problem complicates and increases the time required to align protein interaction networks (PINs). Parallel computing technology is an effective solution to the challenge of aligning large-scale networks via sequential computing. In this study, the typical Hungarian-Greedy Algorithm (HGA) is used as an example for PIN alignment. The authors propose a HGA with 2-nearest neighbours (HGA-2N) and implement its graphics processing unit (GPU) acceleration. Numerical experiments demonstrate that HGA-2N can find alignments that are close to those found by HGA while dramatically reducing computing time. The GPU implementation of HGA-2N optimises the parallel pattern, computing mode and storage mode and it improves the computing time ratio between the CPU and GPU compared with HGA when large-scale networks are considered. By using HGA-2N in GPUs, conserved PPIs can be observed, and potential PPIs can be predicted. Among the predictions based on 25 common Gene Ontology terms, 42.8% can be found in the Human Protein Reference Database. Furthermore, a new method of reconstructing phylogenetic trees is introduced, which shows the same relationships among five herpes viruses that are obtained using other methods.

  9. Microscopic positive-energy potential based on the Gogny interaction

    NASA Astrophysics Data System (ADS)

    Blanchon, G.; Dupuis, M.; Arellano, H. F.; Vinh Mau, N.

    2015-01-01

    We present a nucleon elastic scattering calculation based on Green's function formalism in the random-phase approximation. For the first time, the finite-range Gogny effective interaction is used consistently throughout the whole calculation to account for the complex, nonlocal, and energy-dependent optical potential. Effects of intermediate single-particle resonances are included and found to play a crucial role in the account for measured reaction cross sections. Double counting of the particle-hole second-order contribution is carefully addressed. The resulting integro-differential Schrödinger equation for the scattering process is solved without localization procedures. The method is applied to neutron and proton elastic scattering from 40Ca. A successful account for differential and integral cross sections, including analyzing powers, is obtained for incident energies up to 30 MeV. Discrepancies at higher energies are related to a much-too-high volume integral of the real potential for large partial waves. This work opens the way to simultaneously assess effective interactions suitable for both nuclear structure and reactions.

  10. Interaction of vitamin D with membrane-based signaling pathways

    PubMed Central

    Larriba, María Jesús; González-Sancho, José Manuel; Bonilla, Félix; Muñoz, Alberto

    2014-01-01

    Many studies in different biological systems have revealed that 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) modulates signaling pathways triggered at the plasma membrane by agents such as Wnt, transforming growth factor (TGF)-β, epidermal growth factor (EGF), and others. In addition, 1α,25(OH)2D3 may affect gene expression by paracrine mechanisms that involve the regulation of cytokine or growth factor secretion by neighboring cells. Moreover, post-transcriptional and post-translational effects of 1α,25(OH)2D3 add to or overlap with its classical modulation of gene transcription rate. Together, these findings show that vitamin D receptor (VDR) cannot be considered only as a nuclear-acting, ligand-modulated transcription factor that binds to and controls the transcription of target genes. Instead, available data support the view that much of the complex biological activity of 1α,25(OH)2D3 resides in its capacity to interact with membrane-based signaling pathways and to modulate the expression and secretion of paracrine factors. Therefore, we propose that future research in the vitamin D field should focus on the interplay between 1α,25(OH)2D3 and agents that act at the plasma membrane, and on the analysis of intercellular communication. Global analyses such as RNA-Seq, transcriptomic arrays, and genome-wide ChIP are expected to dissect the interactions at the gene and molecular levels. PMID:24600406

  11. Ultrasonic power measurement system based on acousto-optic interaction

    NASA Astrophysics Data System (ADS)

    He, Liping; Zhu, Fulong; Chen, Yanming; Duan, Ke; Lin, Xinxin; Pan, Yongjun; Tao, Jiaquan

    2016-05-01

    Ultrasonic waves are widely used, with applications including the medical, military, and chemical fields. However, there are currently no effective methods for ultrasonic power measurement. Previously, ultrasonic power measurement has been reliant on mechanical methods such as hydrophones and radiation force balances. This paper deals with ultrasonic power measurement based on an unconventional method: acousto-optic interaction. Compared with mechanical methods, the optical method has a greater ability to resist interference and also has reduced environmental requirements. Therefore, this paper begins with an experimental determination of the acoustic power in water contained in a glass tank using a set of optical devices. Because the light intensity of the diffraction image generated by acousto-optic interaction contains the required ultrasonic power information, specific software was written to extract the light intensity information from the image through a combination of filtering, binarization, contour extraction, and other image processing operations. The power value can then be obtained rapidly by processing the diffraction image using a computer. The results of this work show that the optical method offers advantages that include accuracy, speed, and a noncontact measurement method.

  12. Interactive brain shift compensation using GPU based programming

    NASA Astrophysics Data System (ADS)

    van der Steen, Sander; Noordmans, Herke Jan; Verdaasdonk, Rudolf

    2009-02-01

    Processing large images files or real-time video streams requires intense computational power. Driven by the gaming industry, the processing power of graphic process units (GPUs) has increased significantly. With the pixel shader model 4.0 the GPU can be used for image processing 10x faster than the CPU. Dedicated software was developed to deform 3D MR and CT image sets for real-time brain shift correction during navigated neurosurgery using landmarks or cortical surface traces defined by the navigation pointer. Feedback was given using orthogonal slices and an interactively raytraced 3D brain image. GPU based programming enables real-time processing of high definition image datasets and various applications can be developed in medicine, optics and image sciences.

  13. Shape-based interactive three-dimensional medical image segmentation

    NASA Astrophysics Data System (ADS)

    Hinshaw, Kevin P.; Brinkley, James F.

    1997-04-01

    Accurate image segmentation continues to be one of the biggest challenges in medical image analysis. Simple, low- level vision techniques have had limited success in this domain because of the visual complexity of medical images. This paper presents a 3-D shape model that uses prior knowledge of an object's structure to guide the search for its boundaries. The shape model has been incorporated into scanner, an interactive software package for image segmentation. We describe a graphical user interface that was developed for finding the surface of the brain and explain how the 3-D model assists with the segmentation process. Preliminary experiments show that with this shape- based approach, a low-resolution boundary for a surface can be found with two-thirds less work for the user than with a comparable manual method.

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

    NASA Astrophysics Data System (ADS)

    Yucel, Osman; Crawford, Chad; Sen, Sandip

    2015-07-01

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

  15. Interaction Pattern Analysis in cMOOCs Based on the Connectivist Interaction and Engagement Framework

    ERIC Educational Resources Information Center

    Wang, Zhijun; Anderson, Terry; Chen, Li; Barbera, Elena

    2017-01-01

    Connectivist learning is interaction-centered learning. A framework describing interaction and cognitive engagement in connectivist learning was constructed using logical reasoning techniques. The framework and analysis was designed to help researchers and learning designers understand and adapt the characteristics and principles of interaction in…

  16. Using Interactive Simulations in Assessment: The Use of Computer-Based Interactive Simulations in the Assessment of Statistical Concepts

    ERIC Educational Resources Information Center

    Neumann, David L.

    2010-01-01

    Interactive computer-based simulations have been applied in several contexts to teach statistical concepts in university level courses. In this report, the use of interactive simulations as part of summative assessment in a statistics course is described. Students accessed the simulations via the web and completed questions relating to the…

  17. Interactive model evaluation tool based on IPython notebook

    NASA Astrophysics Data System (ADS)

    Balemans, Sophie; Van Hoey, Stijn; Nopens, Ingmar; Seuntjes, Piet

    2015-04-01

    In hydrological modelling, some kind of parameter optimization is mostly performed. This can be the selection of a single best parameter set, a split in behavioural and non-behavioural parameter sets based on a selected threshold or a posterior parameter distribution derived with a formal Bayesian approach. The selection of the criterion to measure the goodness of fit (likelihood or any objective function) is an essential step in all of these methodologies and will affect the final selected parameter subset. Moreover, the discriminative power of the objective function is also dependent from the time period used. In practice, the optimization process is an iterative procedure. As such, in the course of the modelling process, an increasing amount of simulations is performed. However, the information carried by these simulation outputs is not always fully exploited. In this respect, we developed and present an interactive environment that enables the user to intuitively evaluate the model performance. The aim is to explore the parameter space graphically and to visualize the impact of the selected objective function on model behaviour. First, a set of model simulation results is loaded along with the corresponding parameter sets and a data set of the same variable as the model outcome (mostly discharge). The ranges of the loaded parameter sets define the parameter space. A selection of the two parameters visualised can be made by the user. Furthermore, an objective function and a time period of interest need to be selected. Based on this information, a two-dimensional parameter response surface is created, which actually just shows a scatter plot of the parameter combinations and assigns a color scale corresponding with the goodness of fit of each parameter combination. Finally, a slider is available to change the color mapping of the points. Actually, the slider provides a threshold to exclude non behaviour parameter sets and the color scale is only attributed to the

  18. Interactive Multimedia and Model-based Learning in Biology.

    ERIC Educational Resources Information Center

    Buckley, Barbara C.

    2000-01-01

    Documents a case of model-building in biology through microanalysis of one student's interaction with "Science for Living: The Circulatory System (SFL)", an interactive multimedia resource prototype for research. Describes the student's learning goals, gains, and activities with particular attention to interactions with representations,…

  19. Catalysis based on reversible covalent interactions of organoboron compounds.

    PubMed

    Taylor, Mark S

    2015-02-17

    CONSPECTUS: An Account of the development of organoboron-catalyzed methods for chemo- or regioselective activation of pyruvic acids, diols, and carbohydrate derivatives is presented. These methods are based on reversible, covalent interactions that have been exploited extensively in host-guest chemistry, but were comparatively underutilized in catalysis. Important differences between the established properties of organboron compounds in molecular recognition and their behavior as catalysts emerged over the course of this work: for instance, borinic acids, which have largely been ignored in molecular recognition, proved to be a particularly useful class of catalysts. Nonetheless, the high selectivity that has enabled applications of organoboron compounds in molecular recognition (e.g., the selective binding of cis-1,2-diol groups in carbohydrates) also appears to play a key role in the outcomes of catalytic reactions. This research program began as a modest, narrowly defined project aimed at developing direct aldol reactions based on established interactions between pyruvic acids and boronic acids. While this goal was achieved, it was unexpected observations related to the nature of the nucleophile in this transformation (a putative tetracoordinate boron enolate) that attracted our attention and pointed toward broader applications in the catalyst-controlled, regioselective functionalization of polyols. This line of research proved to be fruitful: diarylborinic-acid-based precatalysts were found to promote efficient monoalkylations, sulfonylations, and alkylations of a range of diol substrates, as well as cis-1,2-diol motifs in pyranoside-derived triols. Extension of this chemistry to glycosyl donors as electrophiles enabled the regioselective, catalyst-controlled synthesis of disaccharides from readily accessible feedstocks, and was also employed to modify the oligosaccharide component of a complex, glycosylated natural product. Mechanistic studies have played an

  20. Maxwell's equations-based dynamic laser-tissue interaction model.

    PubMed

    Ahmed, Elharith M; Barrera, Frederick J; Early, Edward A; Denton, Michael L; Clark, C D; Sardar, Dhiraj K

    2013-12-01

    Since its invention in the early 1960s, the laser has been used as a tool for surgical, therapeutic, and diagnostic purposes. To achieve maximum effectiveness with the greatest margin of safety it is important to understand the mechanisms of light propagation through tissue and how that light affects living cells. Lasers with novel output characteristics for medical and military applications are too often implemented prior to proper evaluation with respect to tissue optical properties and human safety. Therefore, advances in computational models that describe light propagation and the cellular responses to laser exposure, without the use of animal models, are of considerable interest. Here, a physics-based laser-tissue interaction model was developed to predict the dynamic changes in the spatial and temporal temperature rise during laser exposure to biological tissues. Unlike conventional models, the new approach is grounded on the rigorous electromagnetic theory that accounts for wave interference, polarization, and nonlinearity in propagation using a Maxwell's equations-based technique.

  1. Evaluating Types of Students' Interactions in a Wiki-Based Collaborative Learning Project

    ERIC Educational Resources Information Center

    Prokofieva, Maria

    2013-01-01

    Wiki technology has been promoted as a collaborative software platform. This study investigates interactions that occur in a wiki-based collaborative learning project. The study draws on interaction literature and investigates the types of interactions with which students are engaged in wiki-based group projects, clusters that reflect online…

  2. Optimization Model for Web Based Multimodal Interactive Simulations.

    PubMed

    Halic, Tansel; Ahn, Woojin; De, Suvranu

    2015-07-15

    This paper presents a technique for optimizing the performance of web based multimodal interactive simulations. For such applications where visual quality and the performance of simulations directly influence user experience, overloading of hardware resources may result in unsatisfactory reduction in the quality of the simulation and user satisfaction. However, optimization of simulation performance on individual hardware platforms is not practical. Hence, we present a mixed integer programming model to optimize the performance of graphical rendering and simulation performance while satisfying application specific constraints. Our approach includes three distinct phases: identification, optimization and update. In the identification phase, the computing and rendering capabilities of the client device are evaluated using an exploratory proxy code. This data is utilized in conjunction with user specified design requirements in the optimization phase to ensure best possible computational resource allocation. The optimum solution is used for rendering (e.g. texture size, canvas resolution) and simulation parameters (e.g. simulation domain) in the update phase. Test results are presented on multiple hardware platforms with diverse computing and graphics capabilities to demonstrate the effectiveness of our approach.

  3. Optimization Model for Web Based Multimodal Interactive Simulations

    PubMed Central

    Halic, Tansel; Ahn, Woojin; De, Suvranu

    2015-01-01

    This paper presents a technique for optimizing the performance of web based multimodal interactive simulations. For such applications where visual quality and the performance of simulations directly influence user experience, overloading of hardware resources may result in unsatisfactory reduction in the quality of the simulation and user satisfaction. However, optimization of simulation performance on individual hardware platforms is not practical. Hence, we present a mixed integer programming model to optimize the performance of graphical rendering and simulation performance while satisfying application specific constraints. Our approach includes three distinct phases: identification, optimization and update. In the identification phase, the computing and rendering capabilities of the client device are evaluated using an exploratory proxy code. This data is utilized in conjunction with user specified design requirements in the optimization phase to ensure best possible computational resource allocation. The optimum solution is used for rendering (e.g. texture size, canvas resolution) and simulation parameters (e.g. simulation domain) in the update phase. Test results are presented on multiple hardware platforms with diverse computing and graphics capabilities to demonstrate the effectiveness of our approach. PMID:26085713

  4. Ocean interactions with the base of Amery Ice Shelf, Antarctica

    NASA Technical Reports Server (NTRS)

    Hellmer, Hartmut H.; Jacobs, Stanley S.

    1992-01-01

    Using a two-dimensional ocean themohaline circulation model, we varied the cavity shape beneath Amery Ice Shelf in an attempt to reproduce the 150-m-thick marine ice layer observed at the 'G1' ice core site. Most simulations caused melting rates which decrease the ice thickness by as much as 400 m between grounding line and G1, but produce only minor accumulation at the ice core site and closer to the ice front. Changes in the sea floor and ice topographies revealed a high sensitivity of the basal mass balance to water column thickness near the grounding line, to submarine sills, and to discontinuities in ice thickness. Model results showed temperature/salinity gradients similar to observations from beneath other ice shelves where ice is melting into seawater. Modeled outflow characteristics at the ice front are in general agreement with oceanographic data from Prydz Bay. We concur with Morgan's inference that the G1 core may have been taken in a basal crevasse filled with marine ice. This ice is formed from water cooled by ocean/ice shelf interactions along the interior ice shelf base.

  5. Optical immunoassay systems based upon evanescent wave interactions

    NASA Astrophysics Data System (ADS)

    Christensen, Douglas A.; Herron, James N.

    1996-04-01

    Immunoassays based upon evanescent wave interactions are finding increased biosensing application. In these devices, the evanescent tail associated with total internal reflection of an incident beam at the substrate/solution interface provides sensitivity for surface-bound protein over bulk molecules, allowing homogeneous assays and real-time measurement of binding dynamics. Among such systems are surface plasmon resonance sensors and a resonant mirror device. Several research groups are also developing fluorescent fiberoptic or planar waveguide sensors for biomedical applications. We describe a second-generation planar waveguide fluoroimmunoassay system being developed in our laboratory which uses a molded polystyrene sensor. The 633-nm beam from a laser diode is focused into the 500 micrometer- thick planar waveguide by an integral lens. Antibodies to the desired analyte (hCG) are immobilized on the waveguide surface and fluorescence from bound analyte/tracer antibodies in a sandwich format is imaged onto the detector. The geometry of the waveguide allows several zones to be detected, providing the capability for on-sensor calibration. This sensor has shown picomolar sensitivity for the detection of hCG.

  6. Sensing Landscape History with an Interactive Location Based Service

    PubMed Central

    van Lammeren, Ron; Goossen, Martin; Roncken, Paul

    2009-01-01

    This paper introduces the STEAD approach for interpreting data acquired by a “human sensor”, who uses an informal interactive location-based service (iLBS) to sense cultural-historic facts and anecdotes of, and in the landscape. This user-generated data is collected outdoors and in situ. The approach consists of four related facets (who, what, where, when). Three of the four facets are discussed and illustrated by user generated data collected during a Dutch survey in 2008. These data represent the personal cultural-historic knowledge and anecdotes of 150 people using a customized iLBS for experiencing the cultural history of a landscape. The “who” facet shows three dominant mentality groups (cosmopolitans, modern materialists and post modern hedonists) that generated user content. The “what” facet focuses on three subject types of pictures and four picture framing classes. Pictures of the place type showed to be dominant and foreground framing class was slightly favourite. The “where” facet is explored via density, distribution, and distance of the pictures made. The illustrations of the facets indirectly show the role of the “human sensor” with respect to the domain of interest. The STEAD approach needs further development of the when-facet and of the relations between the four facets. Finally the results of the approach may support data archives of iLBS applications. PMID:22399994

  7. Quadrupole beam-based alignment in the RHIC interaction regions

    SciTech Connect

    Ziegler, J.; Satogata, T.

    2011-03-28

    Continued beam-based alignment (BBA) efforts have provided significant benefit to both heavy ion and polarized proton operations at RHIC. Recent studies demonstrated previously unknown systematic beam position monitor (BPM) offset errors and produced accurate measurements of individual BPM offsets in the experiment interaction regions. Here we describe the algorithm used to collect and analyze data during the 2010 and early 2011 RHIC runs and the results of these measurements. BBA data has been collected over the past two runs for all three of the active experimental IRs at RHIC, updating results from the 2005 run which were taken with incorrectly installed offsets. The technique was successfully applied to expose a systematic misuse of the BPM survey offsets in the control system. This is likely to benefit polarized proton operations as polarization transmission through acceleration ramps depends on RMS orbit control in the arcs, but a quantitative understanding of its impact is still under active investigation. Data taking is ongoing as are refinements to the BBA technique aimed at reducing systematic errors and properly accounting for dispersive effects. Further development may focus on non-triplet BPMs such as those located near snakes, or arc quadrupoles that do not have individually shunted power supplies (a prerequisite for the current method) and as such, will require a modified procedure.

  8. Sensing landscape history with an interactive location based service.

    PubMed

    van Lammeren, Ron; Goossen, Martin; Roncken, Paul

    2009-01-01

    This paper introduces the STEAD approach for interpreting data acquired by a "human sensor", who uses an informal interactive location-based service (iLBS) to sense cultural-historic facts and anecdotes of, and in the landscape. This user-generated data is collected outdoors and in situ. The approach consists of four related facets (who, what, where, when). Three of the four facets are discussed and illustrated by user generated data collected during a Dutch survey in 2008. These data represent the personal cultural-historic knowledge and anecdotes of 150 people using a customized iLBS for experiencing the cultural history of a landscape. The "who" facet shows three dominant mentality groups (cosmopolitans, modern materialists and post modern hedonists) that generated user content. The "what" facet focuses on three subject types of pictures and four picture framing classes. Pictures of the place type showed to be dominant and foreground framing class was slightly favourite. The "where" facet is explored via density, distribution, and distance of the pictures made. The illustrations of the facets indirectly show the role of the "human sensor" with respect to the domain of interest. The STEAD approach needs further development of the when-facet and of the relations between the four facets. Finally the results of the approach may support data archives of iLBS applications.

  9. Natural Interaction Based Online Military Boxing Learning System

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  10. Interactive Language Simulation Systems: Technology for a National Language Base.

    ERIC Educational Resources Information Center

    Rowe, A. Allen

    1985-01-01

    Discusses the efforts of the Defense Language Institute Foreign Language Center to make interactive video an integral part of foreign language instruction. Interactive video is seen as a method which could profoundly alter the old classroom model of language instruction. (Author/SED)

  11. Dendrimer-protein interactions versus dendrimer-based nanomedicine.

    PubMed

    Shcharbin, Dzmitry; Shcharbina, Natallia; Dzmitruk, Volha; Pedziwiatr-Werbicka, Elzbieta; Ionov, Maksim; Mignani, Serge; de la Mata, F Javier; Gómez, Rafael; Muñoz-Fernández, Maria Angeles; Majoral, Jean-Pierre; Bryszewska, Maria

    2017-04-01

    Dendrimers are hyperbranched polymers belonging to the huge class of nanomedical devices. Their wide application in biology and medicine requires understanding of the fundamental mechanisms of their interactions with biological systems. Summarizing, electrostatic force plays the predominant role in dendrimer-protein interactions, especially with charged dendrimers. Other kinds of interactions have been proven, such as H-bonding, van der Waals forces, and even hydrophobic interactions. These interactions depend on the characteristics of both participants: flexibility and surface charge of a dendrimer, rigidity of protein structure and the localization of charged amino acids at its surface. pH and ionic strength of solutions can significantly modulate interactions. Ligands and cofactors attached to a protein can also change dendrimer-protein interactions. Binding of dendrimers to a protein can change its secondary structure, conformation, intramolecular mobility and functional activity. However, this strongly depends on rigidity versus flexibility of a protein's structure. In addition, the potential applications of dendrimers to nanomedicine are reviwed related to dendrimer-protein interactions.

  12. A Mobile, Map-Based Tasking Interface for Human-Robot Interaction

    DTIC Science & Technology

    2010-12-01

    the one of the fastest but least accurate methods of interaction (Muratore, 1987; Ahlström and Lenman, 1987; Karat et al., 1986) . However, these...claims of Muratore (1987); Ahlström and Lenman (1987); and Karat et al. (1986) which state that touch-based interaction is faster, but less accurate...interaction versus mouse-based interaction were also compared. Once again, the claimes of Muratore (1987); Ahlström and Lenman (1987); and Karat et al

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

    SciTech Connect

    McAdams, Harley; AlQuraishi, Mohammed

    2015-04-21

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

  14. Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis.

    PubMed

    Guerrero, Cortnie; Milenkovic, Tijana; Przulj, Natasa; Kaiser, Peter; Huang, Lan

    2008-09-09

    Quantitative analysis of tandem-affinity purified cross-linked (x) protein complexes (QTAX) is a powerful technique for the identification of protein interactions, including weak and/or transient components. Here, we apply a QTAX-based tag-team mass spectrometry strategy coupled with protein network analysis to acquire a comprehensive and detailed assessment of the protein interaction network of the yeast 26S proteasome. We have determined that the proteasome network is composed of at least 471 proteins, significantly more than the total number of proteins identified by previous reports using proteasome subunits as baits. Validation of the selected proteasome-interacting proteins by reverse copurification and immunoblotting experiments with and without cross-linking, further demonstrates the power of the QTAX strategy for capturing protein interactions of all natures. In addition, >80% of the identified interactions have been confirmed by existing data using protein network analysis. Moreover, evidence obtained through network analysis links the proteasome to protein complexes associated with diverse cellular functions. This work presents the most complete analysis of the proteasome interaction network to date, providing an inclusive set of physical interaction data consistent with physiological roles for the proteasome that have been suggested primarily through genetic analyses. Moreover, the methodology described here is a general proteomic tool for the comprehensive study of protein interaction networks.

  15. In Interactive, Web-Based Approach to Metadata Authoring

    NASA Technical Reports Server (NTRS)

    Pollack, Janine; Wharton, Stephen W. (Technical Monitor)

    2001-01-01

    NASA's Global Change Master Directory (GCMD) serves a growing number of users by assisting the scientific community in the discovery of and linkage to Earth science data sets and related services. The GCMD holds over 8000 data set descriptions in Directory Interchange Format (DIF) and 200 data service descriptions in Service Entry Resource Format (SERF), encompassing the disciplines of geology, hydrology, oceanography, meteorology, and ecology. Data descriptions also contain geographic coverage information, thus allowing researchers to discover data pertaining to a particular geographic location, as well as subject of interest. The GCMD strives to be the preeminent data locator for world-wide directory level metadata. In this vein, scientists and data providers must have access to intuitive and efficient metadata authoring tools. Existing GCMD tools are not currently attracting. widespread usage. With usage being the prime indicator of utility, it has become apparent that current tools must be improved. As a result, the GCMD has released a new suite of web-based authoring tools that enable a user to create new data and service entries, as well as modify existing data entries. With these tools, a more interactive approach to metadata authoring is taken, as they feature a visual "checklist" of data/service fields that automatically update when a field is completed. In this way, the user can quickly gauge which of the required and optional fields have not been populated. With the release of these tools, the Earth science community will be further assisted in efficiently creating quality data and services metadata. Keywords: metadata, Earth science, metadata authoring tools

  16. A reliability measure of protein-protein interactions and a reliability measure-based search engine.

    PubMed

    Park, Byungkyu; Han, Kyungsook

    2010-02-01

    Many methods developed for estimating the reliability of protein-protein interactions are based on the topology of protein-protein interaction networks. This paper describes a new reliability measure for protein-protein interactions, which does not rely on the topology of protein interaction networks, but expresses biological information on functional roles, sub-cellular localisations and protein classes as a scoring schema. The new measure is useful for filtering many spurious interactions, as well as for estimating the reliability of protein interaction data. In particular, the reliability measure can be used to search protein-protein interactions with the desired reliability in databases. The reliability-based search engine is available at http://yeast.hpid.org. We believe this is the first search engine for interacting proteins, which is made available to public. The search engine and the reliability measure of protein interactions should provide useful information for determining proteins to focus on.

  17. The Development of a Research Agenda and Generic Disc for Computer-Based Interactive Video.

    ERIC Educational Resources Information Center

    Grabowski, Barbara; Pearson, Robert

    This paper describes the development of a conceptual framework for conducting research using computer based interactive video and a generic disc as research tools. It is argued that computer based interactive video represents the beginnings of a truly computer based learning system. An altered version of the 1984 Grabowski and Whitney conceptual…

  18. The in Silico Insight into Carbon Nanotube and Nucleic Acid Bases Interaction

    PubMed Central

    Karimi, Ali Asghar; Ghalandari, Behafarid; Tabatabaie, Seyed Saleh; Farhadi, Mohammad

    2016-01-01

    Background To explore practical applications of carbon nanotubes (CNTs) in biomedical fields the properties of their interaction with biomolecules must be revealed. Recent years, the interaction of CNTs with biomolecules is a subject of research interest for practical applications so that previous research explored that CNTs have complementary structure properties with single strand DNA (ssDNA). Objectives Hence, the quantum mechanics (QM) method based on ab initio was used for this purpose. Therefore values of binding energy, charge distribution, electronic energy and other physical properties of interaction were studied for interaction of nucleic acid bases and SCNT. Materials and Methods In this study, the interaction between nucleic acid bases and a (4, 4) single-walled carbon nanotube (SCNT) were investigated through calculations within quantum mechanics (QM) method at theoretical level of Hartree-Fock (HF) method using 6-31G basis set. Hence, the physical properties such as electronic energy, total dipole moment, charge distributions and binding energy of nucleic acid bases interaction with SCNT were investigated based on HF method. Results It has been found that the guanine base adsorption is bound stronger to the outer surface of nanotube in comparison to the other bases, consistent with the recent theoretical studies. In the other words, the results explored that guanine interaction with SCNT has optimum level of electronic energy so that their interaction is stable. Also, the calculations illustrated that SCNT interact to nucleic acid bases by noncovalent interaction because of charge distribution an electrostatic area is created in place of interaction. Conclusions Consequently, small diameter SCNT interaction with nucleic acid bases is noncovalent. Also, the results revealed that small diameter SCNT interaction especially SCNT (4, 4) with nucleic acid bases can be useful in practical application area of biomedical fields such detection and drug delivery

  19. A Qualitative Examination of Two Year-Olds Interaction with Tablet Based Interactive Technology

    ERIC Educational Resources Information Center

    Geist, Eugene A.

    2012-01-01

    The purpose of this study was to observe children naturally interacting with these touch screen devices. Little direct instruction was given to the children on the use of the devices however an adult did assist when needed. The device was introduced to the children as would be any other educational material such as play-dough, new items in the…

  20. ESL Students' Interaction in Second Life: Task-Based Synchronous Computer-Mediated Communication

    ERIC Educational Resources Information Center

    Jee, Min Jung

    2010-01-01

    The purpose of the present study was to explore ESL students' interactions in task-based synchronous computer-mediated communication (SCMC) in Second Life, a virtual environment by which users can interact through representational figures. I investigated Low-Intermediate and High-Intermediate ESL students' interaction patterns before, during, and…

  1. Faculty Choice and Student Perception of Web-Based Technologies for Interaction in Online Economics Courses

    ERIC Educational Resources Information Center

    Morris, Olivia

    2012-01-01

    This research investigated faculty choice of web-based technologies for interaction in online economics courses and students' perception of those technologies. The literature review of online interaction has established the importance of learner-learner, learner-instructor and learner-content interaction in distance learning. However, some…

  2. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    NASA Technical Reports Server (NTRS)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  3. Social Network Extraction and Analysis Based on Multimodal Dyadic Interaction

    PubMed Central

    Escalera, Sergio; Baró, Xavier; Vitrià, Jordi; Radeva, Petia; Raducanu, Bogdan

    2012-01-01

    Social interactions are a very important component in people’s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times’ Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links’ weights are a measure of the “influence” a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network. PMID:22438733

  4. Social network extraction and analysis based on multimodal dyadic interaction.

    PubMed

    Escalera, Sergio; Baró, Xavier; Vitrià, Jordi; Radeva, Petia; Raducanu, Bogdan

    2012-01-01

    Social interactions are a very important component in people's lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times' Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links' weights are a measure of the "influence" a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

  5. Interactive Image Segmentation Framework Based On Control Theory.

    PubMed

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

    2015-02-21

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

  6. Interactive image segmentation framework based on control theory

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  7. Interactive Learning with Java Applets: Using Interactive, Web-Based Java Applets to Present Science in a Concrete, Meaningful Manner

    ERIC Educational Resources Information Center

    Corder, Greg

    2005-01-01

    Science teachers face challenges that affect the quality of instruction. Tight budgets, limited resources, school schedules, and other obstacles limit students' opportunities to experience science that is visual and interactive. Incorporating web-based Java applets into science instruction offers a practical solution to these challenges. The…

  8. Vizic: Jupyter-based interactive visualization tool for astronomical catalogs

    NASA Astrophysics Data System (ADS)

    Yu, Weixiang; Carrasco-Kind, Matias; Brunner, Robert J.

    2017-01-01

    Vizic is a Python visualization library that builds the connection between images and catalogs through an interactive map of the sky region. The software visualizes catalog data over a custom background canvas using the shape, size and orientation of each object in the catalog and displays interactive and customizable objects in the map. Property values such as redshift and magnitude can be used to filter or apply colormaps, and objects can be selected for further analysis through standard Python functions from inside a Jupyter notebook. Vizic allows custom overlays to be appended dynamically on top of the sky map; included are Voronoi, Delaunay, Minimum Spanning Tree and HEALPix layers, which are helpful for visualizing large-scale structure. Overlays can be generated, added or removed dynamically with one line of code. Catalog data is kept in a non-relational database. The Jupyter Notebook allows the user to create scripts to analyze and plot the data selected/displayed in the interactive map, making Vizic a powerful and flexible interactive analysis tool. Vizic be used for data inspection, clustering analysis, galaxy alignment studies, outlier identification or simply large-scale visualizations.

  9. NMR-based analysis of protein-ligand interactions.

    PubMed

    Cala, Olivier; Guillière, Florence; Krimm, Isabelle

    2014-02-01

    Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.

  10. GAIA: a gram-based interaction analysis tool – an approach for identifying interacting domains in yeast

    PubMed Central

    Zhang, Kelvin X; Ouellette, BF Francis

    2009-01-01

    Background Protein-Protein Interactions (PPIs) play important roles in many biological functions. Protein domains, which are defined as independently folding structural blocks of proteins, physically interact with each other to perform these biological functions. Therefore, the identification of Domain-Domain Interactions (DDIs) is of great biological interests because it is generally accepted that PPIs are mediated by DDIs. As a result, much effort has been put on the prediction of domain pair interactions based on computational methods. Many DDI prediction tools using PPIs network and domain evolution information have been reported. However, tools that combine the primary sequences, domain annotations, and structural annotations of proteins have not been evaluated before. Results In this study, we report a novel approach called Gram-bAsed Interaction Analysis (GAIA). GAIA extracts peptide segments that are composed of fixed length of continuous amino acids, called n-grams (where n is the number of amino acids), from the annotated domain and DDI data set in Saccharomyces cerevisiae (budding yeast) and identifies a list of n-grams that may contribute to DDIs and PPIs based on the frequencies of their appearance. GAIA also reports the coordinate position of gram pairs on each interacting domain pair. We demonstrate that our approach improves on other DDI prediction approaches when tested against a gold-standard data set and achieves a true positive rate of 82% and a false positive rate of 21%. We also identify a list of 4-gram pairs that are significantly over-represented in the DDI data set and may mediate PPIs. Conclusion GAIA represents a novel and reliable way to predict DDIs that mediate PPIs. Our results, which show the localizations of interacting grams/hotspots, provide testable hypotheses for experimental validation. Complemented with other prediction methods, this study will allow us to elucidate the interactome of cells. PMID:19208164

  11. Non-Native Speaker Interaction Management Strategies in a Network-Based Virtual Environment

    ERIC Educational Resources Information Center

    Peterson, Mark

    2008-01-01

    This article investigates the dyad-based communication of two groups of non-native speakers (NNSs) of English involved in real time interaction in a type of text-based computer-mediated communication (CMC) tool known as a MOO. The object of this semester long study was to examine the ways in which the subjects managed their L2 interaction during…

  12. Approaches to Interactive Video Anchors in Problem-Based Science Learning

    ERIC Educational Resources Information Center

    Kumar, David Devraj

    2010-01-01

    This paper is an invited adaptation of the IEEE Education Society Distinguished Lecture Approaches to Interactive Video Anchors in Problem-Based Science Learning. Interactive video anchors have a cognitive theory base, and they help to enlarge the context of learning with information-rich real-world situations. Carefully selected movie clips and…

  13. Market-based Predictors of Interactivity at Southeast Asian Online Newspapers.

    ERIC Educational Resources Information Center

    Massey, Brian L.

    2000-01-01

    Market-based and press-freedom variables were tested as predictors of "interactive" online journalism at the Web companions of 17 English-language Asian newspapers. A multidimensional conception of interactivity was used in the analysis. Findings suggest that market-based variables predict only certain facets of an online newspaper's…

  14. A Jupyter-based Interactive Visualization Tool for Astronomical Catalogs

    NASA Astrophysics Data System (ADS)

    Yu, Weixiang; Carrasco Kind, Matias; Brunner, Robert

    2017-01-01

    The ever-growing datasets in observational astronomy have challenged scientists in many aspects, including an efficient and interactive data exploration and visualization. Many tools have been developed to confront this challenge. However, they usually focus on displaying the actual images or focus on visualizing patterns within catalogs. Here we present Vizic, a Python visualization library that builds the connection between images and catalogs through an interactive map of the sky region. Vizic visualizes catalog data over a custom background canvas using the shape, size and orientation of each object in the catalog. The displayed objects in the map are highly interactive and customizable comparing to those in the observation images. These objects can be filtered by or colored by their property values, such as redshift and/or magnitude or can be sub-selected using a lasso-like tool. In addition, Vizic also allows custom overlays to be appended dynamically on top of the image. We have implemented a minimum spanning tree overlay and a Voronoi diagram overlay. Both overlays can be generated, added or removed with just a click of a button. All the data is kept in a non relational database, and the interfaces were developed in JavaScript and Python to work on Jupyter notebooks which allows to create custom widgets, user generated scripts to analyze and plot the data selected/displayed in the interactive map.Vizic can be adopted in variety of exercises, for example, data inspection, clustering analysis, galaxy alignment studies or public data release for large surveys.

  15. Human-Swarm Interactions Based on Managing Attractors

    DTIC Science & Technology

    2014-03-06

    further claim that using quorum sensing allows a human to manage trade-offs between the scalability of interactions and mitigating the vulnerability...influence can cause the swarm to switch between attractors. We further claim that using quorum sensing allows a human to manage trade- offs between the...attractors of dynamic systems, bio-inspired swarms, quorum sensing 1. INTRODUCTION Swarms provide complex behaviors out of simple agents following simple

  16. Model-based description of environment interaction for mobile robots

    NASA Astrophysics Data System (ADS)

    Borghi, Giuseppe; Ferrari, Carlo; Pagello, Enrico; Vianello, Marco

    1999-01-01

    We consider a mobile robot that attempts to accomplish a task by reaching a given goal, and interacts with its environment through a finite set of actions and observations. The interaction between robot and environment is modeled by Partially Observable Markov Decision Processes (POMDP). The robot takes its decisions in presence of uncertainty about the current state, by maximizing its reward gained during interactions with the environment. It is able to self-locate into the environment by collecting actions and perception histories during the navigation. To make the state estimation more reliable, we introduce an additional information in the model without adding new states and without discretizing the considered measures. Thus, we associate to the state transition probabilities also a continuous metric given through the mean and the variance of some significant sensor measurements suitable to be kept under continuous form, such as odometric measurements, showing that also such unreliable data can supply a great deal of information to the robot. The overall control system of the robot is structured as a two-levels layered architecture, where the low level implements several collision avoidance algorithms, while the upper level takes care of the navigation problem. In this paper, we concentrate on how to use POMDP models at the upper level.

  17. Discovering Pair-Wise Genetic Interactions: An Information Theory-Based Approach

    PubMed Central

    Ignac, Tomasz M.; Skupin, Alexander; Sakhanenko, Nikita A.; Galas, David J.

    2014-01-01

    Phenotypic variation, including that which underlies health and disease in humans, results in part from multiple interactions among both genetic variation and environmental factors. While diseases or phenotypes caused by single gene variants can be identified by established association methods and family-based approaches, complex phenotypic traits resulting from multi-gene interactions remain very difficult to characterize. Here we describe a new method based on information theory, and demonstrate how it improves on previous approaches to identifying genetic interactions, including both synthetic and modifier kinds of interactions. We apply our measure, called interaction distance, to previously analyzed data sets of yeast sporulation efficiency, lipid related mouse data and several human disease models to characterize the method. We show how the interaction distance can reveal novel gene interaction candidates in experimental and simulated data sets, and outperforms other measures in several circumstances. The method also allows us to optimize case/control sample composition for clinical studies. PMID:24670935

  18. PPI-IRO: a two-stage method for protein-protein interaction extraction based on interaction relation ontology.

    PubMed

    Li, Chuan-Xi; Chen, Peng; Wang, Ru-Jing; Wang, Xiu-Jie; Su, Ya-Ru; Li, Jinyan

    2014-01-01

    Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identification of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifies and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At first, IRO is applied in a binary classifier to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the significant performance of IRO on relation sentences classification and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and BioInfer, respectively, which are superior to most existing extraction methods.

  19. Magnetic hysteresis based on dipolar interactions in granular magnetic systems

    NASA Astrophysics Data System (ADS)

    Allia, Paolo; Coisson, Marco; Knobel, Marcelo; Tiberto, Paola; Vinai, Franco

    1999-11-01

    The magnetic hysteresis of granular magnetic systems is investigated in the high-temperature limit (T>> blocking temperature of magnetic nanoparticles). Measurements of magnetization curves have been performed at room temperature on various samples of granular bimetallic alloys of the family Cu100-xCox (x=5-20 at. %) obtained in ribbon form by planar flow casting in a controlled atmosphere, and submitted to different thermal treatments. The loop amplitude and shape, which are functions of sample composition and thermal history, are studied taking advantage of a novel method of graphical representation, particularly apt to emphasize the features of thin, elongated loops. The hysteresis is explained in terms of the effect of magnetic interactions of the dipolar type among magnetic-metal particles, acting to hinder the response of the system of moments to isothermal changes of the applied field. Such a property is accounted for in a mean-field scheme, by introducing a memory term in the argument of the Langevin function which describes the anhysteretic behavior of an assembly of noninteracting superparamagnetic particles. The rms field arising from the cumulative effect of dipolar interactions is linked by the theory to a measurable quantity, the reduced remanence of a major symmetric hysteresis loop. The theory's self-consistence and adequacy have been properly tested at room temperature on all examined systems. The agreement with experimental results is always striking, indicating that at high temperatures the magnetic hysteresis of granular systems is dominated by interparticle, rather than single-particle, effects. Dipolar interactions seem to fully determine the magnetic hysteresis in the high-temperature limit for low Co content (x<=10). For higher concentrations of magnetic metal, the experimental results indicate that additional hysteretic mechanisms have to be introduced.

  20. Child second language interaction in science-based tasks

    NASA Astrophysics Data System (ADS)

    McPhail, Cynthia Leigh

    While quasi-experimental in design, this study utilized qualitative data collection and analysis methods to examine the questions of whether students' speech act behavior and language use would vary by linguistic grouping. Second grade Puerto Rican native speakers of Spanish, and native English speakers completed sets of paired, hands-on, science activities. Children were paired in two linguistic groupings: heterogeneous (English native speaker/non-native speaker), and homogeneous (English non-native speaker/non-native speaker, or English native speaker/native speaker). Speech acts and use of target and native language in the two linguistic groupings were compared. Interviews with both the students and their teachers provided further understanding of the speech act behavior. Most prior research has dealt with university level adults learning English. Previous research that has dealt with children and second language interaction has often focused on teacher talk directed to the children, and no child/child interaction studies have attempted to control for variables such as linguistic grouping. Results indicated that linguistically heterogeneous groupings led to higher percentages of English use for non-native speakers. Homogeneous grouping led to higher percentages of native Spanish use. English native speakers' speech act behavior remained consistent in terms of dominance or passivity of behavior regardless of linguistic grouping, but there is the possibility that non-English speakers may behave in a slightly more passive manner when in heterogeneous grouping.

  1. Sculpting Mountains: Interactive Terrain Modeling Based on Subsurface Geology.

    PubMed

    Cordonnier, Guillaume; Cani, Marie-Paule; Benes, Bedrich; Braun, Jean; Galin, Eric

    2017-03-29

    Most mountain ranges are formed by the compression and folding of colliding tectonic plates. Subduction of one plate causes large-scale asymmetry while their layered composition (or stratigraphy) explains the multi-scale folded strata observed on real terrains. We introduce a novel interactive modeling technique to generate visually plausible, large scale terrains that capture these phenomena. Our method draws on both geological knowledge for consistency and on sculpting systems for user interaction. The user is provided hands-on control on the shape and motion of tectonic plates, represented using a new geologically-inspired model for the Earth crust. The model captures their volume preserving and complex folding behaviors under collision, causing mountains to grow. It generates a volumetric uplift map representing the growth rate of subsurface layers. Erosion and uplift movement are jointly simulated to generate the terrain. The stratigraphy allows us to render folded strata on eroded cliffs. We validated the usability of our sculpting interface through a user study, and compare the visual consistency of the earth crust model with geological simulation results and real terrains.

  2. A global test for gene-gene interactions based on random matrix theory.

    PubMed

    Frost, H Robert; Amos, Christopher I; Moore, Jason H

    2016-12-01

    Statistical interactions between markers of genetic variation, or gene-gene interactions, are believed to play an important role in the etiology of many multifactorial diseases and other complex phenotypes. Unfortunately, detecting gene-gene interactions is extremely challenging due to the large number of potential interactions and ambiguity regarding marker coding and interaction scale. For many data sets, there is insufficient statistical power to evaluate all candidate gene-gene interactions. In these cases, a global test for gene-gene interactions may be the best option. Global tests have much greater power relative to multiple individual interaction tests and can be used on subsets of the markers as an initial filter prior to testing for specific interactions. In this paper, we describe a novel global test for gene-gene interactions, the global epistasis test (GET), that is based on results from random matrix theory. As we show via simulation studies based on previously proposed models for common diseases including rheumatoid arthritis, type 2 diabetes, and breast cancer, our proposed GET method has superior performance characteristics relative to existing global gene-gene interaction tests. A glaucoma GWAS data set is used to demonstrate the practical utility of the GET method.

  3. Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer.

    PubMed

    Zhu, Fei; Liu, Quan; Zhang, Xiaofang; Shen, Bairong

    2015-08-01

    Constructing interaction network from biomedical texts is a very important and interesting work. The authors take advantage of text mining and reinforcement learning approaches to establish protein interaction network. Considering the high computational efficiency of co-occurrence-based interaction extraction approaches and high precision of linguistic patterns approaches, the authors propose an interaction extracting algorithm where they utilise frequently used linguistic patterns to extract the interactions from texts and then find out interactions from extended unprocessed texts under the basic idea of co-occurrence approach, meanwhile they discount the interaction extracted from extended texts. They put forward a reinforcement learning-based algorithm to establish a protein interaction network, where nodes represent proteins and edges denote interactions. During the evolutionary process, a node selects another node and the attained reward determines which predicted interaction should be reinforced. The topology of the network is updated by the agent until an optimal network is formed. They used texts downloaded from PubMed to construct a prostate cancer protein interaction network by the proposed methods. The results show that their method brought out pretty good matching rate. Network topology analysis results also demonstrate that the curves of node degree distribution, node degree probability and probability distribution of constructed network accord with those of the scale-free network well.

  4. A global test for gene‐gene interactions based on random matrix theory

    PubMed Central

    Amos, Christopher I.; Moore, Jason H.

    2016-01-01

    ABSTRACT Statistical interactions between markers of genetic variation, or gene‐gene interactions, are believed to play an important role in the etiology of many multifactorial diseases and other complex phenotypes. Unfortunately, detecting gene‐gene interactions is extremely challenging due to the large number of potential interactions and ambiguity regarding marker coding and interaction scale. For many data sets, there is insufficient statistical power to evaluate all candidate gene‐gene interactions. In these cases, a global test for gene‐gene interactions may be the best option. Global tests have much greater power relative to multiple individual interaction tests and can be used on subsets of the markers as an initial filter prior to testing for specific interactions. In this paper, we describe a novel global test for gene‐gene interactions, the global epistasis test (GET), that is based on results from random matrix theory. As we show via simulation studies based on previously proposed models for common diseases including rheumatoid arthritis, type 2 diabetes, and breast cancer, our proposed GET method has superior performance characteristics relative to existing global gene‐gene interaction tests. A glaucoma GWAS data set is used to demonstrate the practical utility of the GET method. PMID:27386793

  5. Interactive applications for sketch-based editable polycube map.

    PubMed

    Garcia, Ismael; Xia, Jiazhi; He, Ying; Xin, Shi-Qing; Patow, Gustavo

    2013-07-01

    In this paper, we propose a sketch-based editable polycube mapping method that, given a general mesh and a simple polycube that coarsely resembles the shape of the object, plus sketched features indicating relevant correspondences between the two, provides a uniform, regular, and user-controllable quads-only mesh that can be used as a basis structure for subdivision. Large scale models with complex geometry and topology can be processed efficiently with simple, intuitive operations. We show that the simple, intuitive nature of the polycube map is a substantial advantage from the point of view of the interface by demonstrating a series of applications, including kit-basing, shape morphing, painting over the parameterization domain, and GPU-friendly tessellated subdivision displacement, where the user is also able to control the number of patches in the base mesh by the construction of the base polycube.

  6. MINDS: A microcomputer interactive data system for 8086-based controllers

    NASA Technical Reports Server (NTRS)

    Soeder, J. F.

    1985-01-01

    A microcomputer interactive data system (MINDS) software package for the 8086 family of microcomputers is described. To enhance program understandability and ease of code maintenance, the software is written in PL/M-86, Intel Corporation's high-level system implementation language. The MINDS software is intended to run in residence with real-time digital control software to provide displays of steady-state and transient data. In addition, the MINDS package provides classic monitor capabilities along with extended provisions for debugging an executing control system. The software uses the CP/M-86 operating system developed by Digital Research, Inc., to provide program load capabilities along with a uniform file structure for data and table storage. Finally, a library of input and output subroutines to be used with consoles equipped with PL/M-86 and assembly language is described.

  7. Nonreciprocity and magnetic-free isolation based on optomechanical interactions

    PubMed Central

    Ruesink, Freek; Miri, Mohammad-Ali; Alù, Andrea; Verhagen, Ewold

    2016-01-01

    Nonreciprocal components, such as isolators and circulators, provide highly desirable functionalities for optical circuitry. This motivates the active investigation of mechanisms that break reciprocity, and pose alternatives to magneto-optic effects in on-chip systems. In this work, we use optomechanical interactions to strongly break reciprocity in a compact system. We derive minimal requirements to create nonreciprocity in a wide class of systems that couple two optical modes to a mechanical mode, highlighting the importance of optically biasing the modes at a controlled phase difference. We realize these principles in a silica microtoroid optomechanical resonator and use quantitative heterodyne spectroscopy to demonstrate up to 10 dB optical isolation at telecom wavelengths. We show that nonreciprocal transmission is preserved for nondegenerate modes, and demonstrate nonreciprocal parametric amplification. These results open a route to exploiting various nonreciprocal effects in optomechanical systems in different electromagnetic and mechanical frequency regimes, including optomechanical metamaterials with topologically non-trivial properties. PMID:27897165

  8. Human-Interaction Challenges in UAV-Based Autonomous Surveillance

    NASA Technical Reports Server (NTRS)

    Freed, Michael; Harris, Robert; Shafto, Michael G.

    2004-01-01

    Autonomous UAVs provide a platform for intelligent surveillance in application domains ranging from security and military operations to scientific information gathering and land management. Surveillance tasks are often long duration, requiring that any approach be adaptive to changes in the environment or user needs. We describe a decision- theoretic model of surveillance, appropriate for use on our autonomous helicopter, that provides a basis for optimizing the value of information returned by the UAV. From this approach arise a range of challenges in making this framework practical for use by human operators lacking specialized knowledge of autonomy and mathematics. This paper describes our platform and approach, then describes human-interaction challenges arising from this approach that we have identified and begun to address.

  9. Emerging Supramolecular Therapeutic Carriers Based on Host-Guest Interactions.

    PubMed

    Karim, Anis Abdul; Dou, Qingqing; Li, Zibiao; Loh, Xian Jun

    2016-05-06

    Recent advances in host-guest chemistry have significantly influenced the construction of supramolecular soft biomaterials. The highly selective and non-covalent interactions provide vast possibilities of manipulating supramolecular self-assemblies at the molecular level, allowing a rational design to control the sizes and morphologies of the resultant objects as carrier vehicles in a delivery system. In this Focus Review, the most recent developments of supramolecular self-assemblies through host-guest inclusion, including nanoparticles, micelles, vesicles, hydrogels, and various stimuli-responsive morphology transition materials are presented. These sophisticated materials with diverse functions, oriented towards therapeutic agent delivery, are further summarized into several active domains in the areas of drug delivery, gene delivery, co-delivery and site-specific targeting deliveries. Finally, the possible strategies for future design of multifunctional delivery carriers by combining host-guest chemistry with biological interface science are proposed.

  10. Inquiry and groups: student interactions in cooperative inquiry-based science

    NASA Astrophysics Data System (ADS)

    Woods-McConney, Amanda; Wosnitza, Marold; Sturrock, Keryn L.

    2016-03-01

    Science education research has recommended cooperative inquiry based science in the primary science context for more than two decades but after more than 20 years, student achievement in science has not substantially improved. This study, through direct observation and analysis, investigated content-related student interactions in an authentic inquiry based primary science class setting. Thirty-one upper primary students were videotaped working in cooperative inquiry based science activities. Cooperative talk and negotiation of the science content was analysed to identify any high-level group interactions. The data show that while all groups have incidences of high-level content-related group interactions, the frequency and duration of these interactions were limited. No specific pattern of preceding events was identified and no episodes of high-level content-related group interactions were immediately preceded by the teacher's interactions with the groups. This in situ study demonstrated that even without any kind of scaffolding, specific skills in knowing how to implement cooperative inquiry based science, high-level content-related group interactions did occur very briefly. Support for teachers to develop their knowledge and skills in facilitating cooperative inquiry based science learning is warranted to ensure that high-level content-related group interactions and the associated conceptual learning are not left to chance in science classrooms.

  11. Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites

    NASA Astrophysics Data System (ADS)

    Li, Z. K.; Fu, H. M.; Sha, P. F.; Zhu, Z. W.; Wang, A. M.; Li, H.; Zhang, H. W.; Zhang, H. F.; Hu, Z. Q.

    2015-03-01

    The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by adding minor elements that have stronger interaction with W into the alloy. The calculation about atomic interaction energy indicates that Ta and Nb preferred to segregate on the W substrate surface. Sessile drop experiment proves the prediction and corresponding in-situ coating appears at the interface. Besides, the atomic interaction mechanism was proven to be effective in many other systems by the sessile drop technique. Considering the interfacial morphology, Nb was added into the alloy to fabricate W/Zr-based BMGCs. As expected, the Nb addition effectively suppressed the W-Zr reaction and damage to W fibers. Both the compressive and tensile properties are improved obviously.

  12. Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites.

    PubMed

    Li, Z K; Fu, H M; Sha, P F; Zhu, Z W; Wang, A M; Li, H; Zhang, H W; Zhang, H F; Hu, Z Q

    2015-03-11

    The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by adding minor elements that have stronger interaction with W into the alloy. The calculation about atomic interaction energy indicates that Ta and Nb preferred to segregate on the W substrate surface. Sessile drop experiment proves the prediction and corresponding in-situ coating appears at the interface. Besides, the atomic interaction mechanism was proven to be effective in many other systems by the sessile drop technique. Considering the interfacial morphology, Nb was added into the alloy to fabricate W/Zr-based BMGCs. As expected, the Nb addition effectively suppressed the W-Zr reaction and damage to W fibers. Both the compressive and tensile properties are improved obviously.

  13. Combining region-based and imprecise boundary-based cues for interactive medical image segmentation.

    PubMed

    Jones, Jonathan-Lee; Xie, Xianghua; Essa, Ehab

    2014-12-01

    In this paper, we present an approach combining both region selection and user point selection for user-assisted segmentation as either an enclosed object or an open curve, investigate the method of image segmentation in specific medical applications (user-assisted segmentation of the media-adventitia border in intravascular ultrasound images, and lumen border in optical coherence tomography images), and then demonstrate the method with generic images to show how it could be utilized in other types of medical image and is not limited to the applications described. The proposed method combines point-based soft constraint on object boundary and stroke-based regional constraint. The user points act as attraction points and are treated as soft constraints rather than hard constraints that the segmented boundary has to pass through. The user can also use strokes to specify region of interest. The probabilities of region of interest for each pixel are then calculated, and their discontinuity is used to indicate object boundary. The combinations of different types of user constraints and image features allow flexible and robust segmentation, which is formulated as an energy minimization problem on a multilayered graph and is solved using a shortest path search algorithm. We show that this combinatorial approach allows efficient and effective interactive segmentation, which can be used with both open and closed curves to segment a variety of images in different ways. The proposed method is demonstrated in the two medical applications, that is, intravascular ultrasound and optical coherence tomography images, where image artefacts such as acoustic shadow and calcification are commonplace and thus user guidance is desirable. We carried out both qualitative and quantitative analysis of the results for the medical data; comparing the proposed method against a number of interactive segmentation techniques.

  14. Literature Mining and Ontology based Analysis of Host-Brucella Gene–Gene Interaction Network

    PubMed Central

    Karadeniz, İlknur; Hur, Junguk; He, Yongqun; Özgür, Arzucan

    2015-01-01

    Brucella is an intracellular bacterium that causes chronic brucellosis in humans and various mammals. The identification of host-Brucella interaction is crucial to understand host immunity against Brucella infection and Brucella pathogenesis against host immune responses. Most of the information about the inter-species interactions between host and Brucella genes is only available in the text of the scientific publications. Many text-mining systems for extracting gene and protein interactions have been proposed. However, only a few of them have been designed by considering the peculiarities of host–pathogen interactions. In this paper, we used a text mining approach for extracting host-Brucella gene–gene interactions from the abstracts of articles in PubMed. The gene–gene interactions here represent the interactions between genes and/or gene products (e.g., proteins). The SciMiner tool, originally designed for detecting mammalian gene/protein names in text, was extended to identify host and Brucella gene/protein names in the abstracts. Next, sentence-level and abstract-level co-occurrence based approaches, as well as sentence-level machine learning based methods, originally designed for extracting intra-species gene interactions, were utilized to extract the interactions among the identified host and Brucella genes. The extracted interactions were manually evaluated. A total of 46 host-Brucella gene interactions were identified and represented as an interaction network. Twenty four of these interactions were identified from sentence-level processing. Twenty two additional interactions were identified when abstract-level processing was performed. The Interaction Network Ontology (INO) was used to represent the identified interaction types at a hierarchical ontology structure. Ontological modeling of specific gene–gene interactions demonstrates that host–pathogen gene–gene interactions occur at experimental conditions which can be ontologically

  15. Literature Mining and Ontology based Analysis of Host-Brucella Gene-Gene Interaction Network.

    PubMed

    Karadeniz, İlknur; Hur, Junguk; He, Yongqun; Özgür, Arzucan

    2015-01-01

    Brucella is an intracellular bacterium that causes chronic brucellosis in humans and various mammals. The identification of host-Brucella interaction is crucial to understand host immunity against Brucella infection and Brucella pathogenesis against host immune responses. Most of the information about the inter-species interactions between host and Brucella genes is only available in the text of the scientific publications. Many text-mining systems for extracting gene and protein interactions have been proposed. However, only a few of them have been designed by considering the peculiarities of host-pathogen interactions. In this paper, we used a text mining approach for extracting host-Brucella gene-gene interactions from the abstracts of articles in PubMed. The gene-gene interactions here represent the interactions between genes and/or gene products (e.g., proteins). The SciMiner tool, originally designed for detecting mammalian gene/protein names in text, was extended to identify host and Brucella gene/protein names in the abstracts. Next, sentence-level and abstract-level co-occurrence based approaches, as well as sentence-level machine learning based methods, originally designed for extracting intra-species gene interactions, were utilized to extract the interactions among the identified host and Brucella genes. The extracted interactions were manually evaluated. A total of 46 host-Brucella gene interactions were identified and represented as an interaction network. Twenty four of these interactions were identified from sentence-level processing. Twenty two additional interactions were identified when abstract-level processing was performed. The Interaction Network Ontology (INO) was used to represent the identified interaction types at a hierarchical ontology structure. Ontological modeling of specific gene-gene interactions demonstrates that host-pathogen gene-gene interactions occur at experimental conditions which can be ontologically represented. Our

  16. Classified Bibliography on Bibliographic Data Base Interaction, Compatibility and Standardization.

    ERIC Educational Resources Information Center

    Landau, H.B.

    This is the third in a series of eight reports of a research study for the National Agricultural Library (NAL) on the effective utilization of bibliographic data bases in machine-readable form. It consists of about 750 references collected to provide background data for the seven technical tasks of the study. The bibliography is set up to…

  17. Supporting Language Students' Interactions in Web-Based Conferencing.

    ERIC Educational Resources Information Center

    Lamy, Marie-Noelle; Goodfellow, Robin

    1999-01-01

    Looks at on-line tutor strategies for the support of students learning a second language with the help of a Web-based asynchronous textual conference. Looks specifically at strategies used by three tutors who participated in a project with students of French. (Author/VWL)

  18. Inquiry-Based Learning with or without Facilitator Interactions

    ERIC Educational Resources Information Center

    Weerasinghe, Thushani Alwis; Ramberg, Robert; Hewagamage, Kamalanath Priyantha

    2012-01-01

    This paper discusses findings of a study investigating how students, in four online courses, engaged in inquiry-based learning with and without support from a facilitator. The investigation was conducted by analyzing discussions of the online courses using the community of inquiry model. The results of the study imply that students in online…

  19. Interactive Storybook-Based Intervention Effects on Kindergartners' Language Development

    ERIC Educational Resources Information Center

    van Druten-Frietman, Loes; Strating, Heleen; Denessen, Eddie; Verhoeven, Ludo

    2016-01-01

    A dialogic storybook-based intervention integrating dialogic storybook reading with early literacy activities is studied with a longitudinal quasi-experimental study design. The effects of this intervention, in addition to a regular early childhood education (ECE) program, on kindergartners' vocabulary and phonological awareness development are…

  20. EVA: An Interactive Web-Based Collaborative Learning Environment

    ERIC Educational Resources Information Center

    Sheremetov, Leonid; Arenas, Adolfo Guzman

    2002-01-01

    In this paper, a Web-based learning environment developed within the project called Virtual Learning Spaces (EVA, in Spanish) is described. The environment is composed of knowledge, collaboration, consulting and experimentation spaces as a collection of agents and conventional software components working over the knowledge domains. All user…

  1. A Fast Goal Recognition Technique Based on Interaction Estimates

    NASA Technical Reports Server (NTRS)

    E-Martin, Yolanda; R-Moreno, Maria D.; Smith, David E.

    2015-01-01

    Goal Recognition is the task of inferring an actor's goals given some or all of the actor's observed actions. There is considerable interest in Goal Recognition for use in intelligent personal assistants, smart environments, intelligent tutoring systems, and monitoring user's needs. In much of this work, the actor's observed actions are compared against a generated library of plans. Recent work by Ramirez and Geffner makes use of AI planning to determine how closely a sequence of observed actions matches plans for each possible goal. For each goal, this is done by comparing the cost of a plan for that goal with the cost of a plan for that goal that includes the observed actions. This approach yields useful rankings, but is impractical for real-time goal recognition in large domains because of the computational expense of constructing plans for each possible goal. In this paper, we introduce an approach that propagates cost and interaction information in a plan graph, and uses this information to estimate goal probabilities. We show that this approach is much faster, but still yields high quality results.

  2. Kernel Method Based Human Model for Enhancing Interactive Evolutionary Optimization

    PubMed Central

    Zhao, Qiangfu; Liu, Yong

    2015-01-01

    A fitness landscape presents the relationship between individual and its reproductive success in evolutionary computation (EC). However, discrete and approximate landscape in an original search space may not support enough and accurate information for EC search, especially in interactive EC (IEC). The fitness landscape of human subjective evaluation in IEC is very difficult and impossible to model, even with a hypothesis of what its definition might be. In this paper, we propose a method to establish a human model in projected high dimensional search space by kernel classification for enhancing IEC search. Because bivalent logic is a simplest perceptual paradigm, the human model is established by considering this paradigm principle. In feature space, we design a linear classifier as a human model to obtain user preference knowledge, which cannot be supported linearly in original discrete search space. The human model is established by this method for predicting potential perceptual knowledge of human. With the human model, we design an evolution control method to enhance IEC search. From experimental evaluation results with a pseudo-IEC user, our proposed model and method can enhance IEC search significantly. PMID:25879050

  3. Kernel method based human model for enhancing interactive evolutionary optimization.

    PubMed

    Pei, Yan; Zhao, Qiangfu; Liu, Yong

    2015-01-01

    A fitness landscape presents the relationship between individual and its reproductive success in evolutionary computation (EC). However, discrete and approximate landscape in an original search space may not support enough and accurate information for EC search, especially in interactive EC (IEC). The fitness landscape of human subjective evaluation in IEC is very difficult and impossible to model, even with a hypothesis of what its definition might be. In this paper, we propose a method to establish a human model in projected high dimensional search space by kernel classification for enhancing IEC search. Because bivalent logic is a simplest perceptual paradigm, the human model is established by considering this paradigm principle. In feature space, we design a linear classifier as a human model to obtain user preference knowledge, which cannot be supported linearly in original discrete search space. The human model is established by this method for predicting potential perceptual knowledge of human. With the human model, we design an evolution control method to enhance IEC search. From experimental evaluation results with a pseudo-IEC user, our proposed model and method can enhance IEC search significantly.

  4. IP-based streaming technology for interactive MPEG-4 contents

    NASA Astrophysics Data System (ADS)

    Kim, Hyun-Cheol; Jeong, Seyoon; Cha, Jihun; Kim, Kyuheon

    2004-11-01

    In this paper, we present an MPEG-4 contents streaming system and propose MPEG-4 contents streaming scheme by using priority. The presented streaming system which consists of a server and a client supports MPEG-4 contents compliant with ISO/IEC 14496-1 and enables a user to interact with MPEG-4 contents over IP networks. The server consists of GUI, Server Management Layer, Sync Layer, and Delivery Layer. The client supports to display MPEG-4 contents stored in local storage or received through IP networks. Moreover, we propose an MPEG-4 contents streaming scheme that the object a user prefers to watch is sent first by increasing priority and objects with low priority are dropped at a server side when network bandwidth is not enough to transmit all objects that are supposed to appear in the scene. We made experiment of the proposed scheme with the presented MPEG-4 contents streaming system, and the experiment results are shown in this paper. If we use the proposed scheme for MPEG-4 contents streaming, it is possible for a user to watch a video of interest in high quality and video of indifference in low quality.

  5. Structural and functional bases of laser-microvessels interaction

    NASA Astrophysics Data System (ADS)

    Kozlov, Valentine I.; Terman, Oleg A.; Builin, Vitalij; Lebedeva, Natalia A.; Samoilov, Nickolai

    1993-07-01

    Structural and functional microcirculatory changes in tissues and organs (muscles, liver, derma, epinephros, brain cortex) under various dosages and powers of laser irradiation in the red (633 nm) and near infrared (890 nm) spectrum regions have been studied in experiments and clinic. In case of nonsensitized tissues the `photoactivation' range of power densities and doses of laser irradiation has been established. We have identified a short-term reaction of microvessels and a long-term reaction (adaptation). The former consists of intensification of microcirculation and metabolism rise in parenchymatous cells; the latter is connected with neoangiogenesis acceleration. The intensification of the blood microcirculation includes a dilation of microvessels of all orders, an amplification of arteriolar vasomotions and an opening of `reserved' capillaries. Data on the structural reconstruction of myocytes and endotheliocytes have shown that the high differential parenchymatous cells and its membrane structures are sensitive to low energy laser irradiation and, on the other hand, under low energy laser irradiation there is an activation of synthetic processes in the cells. Thus, during the laser-tissue interaction in such complex system as human organism the microcirculation plays the key role among the other systems.

  6. Interactions of NO2 with sewage sludge based composite adsorbents.

    PubMed

    Pietrzak, Robert; Bandosz, Teresa J

    2008-06-15

    Interactions of NO2 present in most air were analyzed at room temperature on composite sewage sludge-derived adsorbents. They consist of carbonaceous and inorganic phases with the majority of the latter. The adsorption capacity was evaluated using the dynamic breakthrough experiments. The materials before and after NO2 exposure were characterized using adsorption of nitrogen, thermal analysis and FTIR. The results showed differences in the surface activities of sludge-derived materials towards immobilization and reduction of nitric dioxide. Nitrates and nitrite are the main products of surface reactions. This is linked to the presence of active oxides and hydroxides, which are formed when the surface is exposed to water. The highest activity of the sample pyrolyzed at 650 degrees C is owing to the high content of those species formed as a result of decomposition of inorganic salts (likely chlorides, sulfates and phosphates) during thermal treatment. When sludge is pyrolyzed at 950 degrees C those oxides are engaged in stable mineral phases formed in solid-state reactions, which limits the surface activity towards NO2 retention. The reactivity of the high temperature pyrolyzed samples can be linked to the physical adsorption of water. In a water film nitrous and nitric acid can be formed and they can further react with inorganic and carbonaceous phases to the limited extent.

  7. A sparse matrix based full-configuration interaction algorithm.

    PubMed

    Rolik, Zoltán; Szabados, Agnes; Surján, Péter R

    2008-04-14

    We present an algorithm related to the full-configuration interaction (FCI) method that makes complete use of the sparse nature of the coefficient vector representing the many-electron wave function in a determinantal basis. Main achievements of the presented sparse FCI (SFCI) algorithm are (i) development of an iteration procedure that avoids the storage of FCI size vectors; (ii) development of an efficient algorithm to evaluate the effect of the Hamiltonian when both the initial and the product vectors are sparse. As a result of point (i) large disk operations can be skipped which otherwise may be a bottleneck of the procedure. At point (ii) we progress by adopting the implementation of the linear transformation by Olsen et al. [J. Chem Phys. 89, 2185 (1988)] for the sparse case, getting the algorithm applicable to larger systems and faster at the same time. The error of a SFCI calculation depends only on the dropout thresholds for the sparse vectors, and can be tuned by controlling the amount of system memory passed to the procedure. The algorithm permits to perform FCI calculations on single node workstations for systems previously accessible only by supercomputers.

  8. Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks*

    PubMed Central

    Wagih, Omar; Sugiyama, Naoyuki; Ishihama, Yasushi; Beltrao, Pedro

    2016-01-01

    Protein kinases are an important class of enzymes involved in the phosphorylation of their targets, which regulate key cellular processes and are typically mediated by a specificity for certain residues around the target phospho-acceptor residue. While efforts have been made to identify such specificities, only ∼30% of human kinases have a significant number of known binding sites. We describe a computational method that utilizes functional interaction data and phosphorylation data to predict specificities of kinases. We applied this method to human kinases to predict substrate preferences for 57% of all known kinases and show that we are able to reconstruct well-known specificities. We used an in vitro mass spectrometry approach to validate four understudied kinases and show that predicted models closely resemble true specificities. We show that this method can be applied to different organisms and can be extended to other phospho-recognition domains. Applying this approach to different types of posttranslational modifications (PTMs) and binding domains could uncover specificities of understudied PTM recognition domains and provide significant insight into the mechanisms of signaling networks. PMID:26572964

  9. Effects of Varying Interactive Strategies Provided by Computer-Based Tutorials for a Software Application Program.

    ERIC Educational Resources Information Center

    Tiemann, Philip W.; Markle, Susan M.

    1990-01-01

    Discussion of interaction in computer-based tutorials (CBT) focuses on a study that compared the performance of adult learners from training with three CBTs that varied the level of interactivity. The degrees of learner control, system control, and domain control are discussed, and the Lotus spreadsheet tutorials used are described. (24…

  10. Seven-Step Problem-Based Learning in an Interaction Design Course

    ERIC Educational Resources Information Center

    Schultz, Nette; Christensen, Hans Peter

    2004-01-01

    The objective in this paper is the implementation of the highly structured seven-step problem-based learning (PBL) procedure as part of the learning process in a human-computer interaction (HCI) design course at the Technical University of Denmark, taking into account the common learning processes in PBL and the interaction design process. These…

  11. Managing Mutual Orientation in the Absence of Physical Copresence: Multiparty Voice-Based Chat Room Interaction

    ERIC Educational Resources Information Center

    Jenks, Christopher Joseph; Brandt, Adam

    2013-01-01

    This study investigates the interactional work involved in ratifying mutual participation in online, multiparty, voice-based chat rooms. The purpose of this article is to provide a preliminary sketch of how talk and participation is managed in a spoken communication environment that comprises interactants who are not physically copresent but are…

  12. Evaluation of the Interactivity of Web-Based Learning Systems: Principles and Process.

    ERIC Educational Resources Information Center

    Evans, Chris; Sabry, Khaled

    2003-01-01

    Considers the process of evaluating the interactivity of Web-based learning systems (WBLSs), adapting a heuristic approach usually employed for usability evaluations. Proposes a three-way model of interactivity, reports an evaluation using three different WBLSs, and concludes that heuristic evaluation provides a cheap, intuitive and practical…

  13. Creative Multimodal Learning Environments and Blended Interaction for Problem-Based Activity in HCI Education

    ERIC Educational Resources Information Center

    Ioannou, Andri; Vasiliou, Christina; Zaphiris, Panayiotis; Arh, Tanja; Klobucar, Tomaž; Pipan, Matija

    2015-01-01

    This exploratory case study aims to examine how students benefit from a multimodal learning environment while they engage in collaborative problem-based activity in a Human Computer Interaction (HCI) university course. For 12 weeks, 30 students, in groups of 5-7 each, participated in weekly face-to-face meetings and online interactions.…

  14. An Instructional Design Theory for Interactions in Web-Based Learning Environments.

    ERIC Educational Resources Information Center

    Lee, Miyoung; Paulus, Trena

    This study developed and formatively evaluated an instructional design theory to guide designers in selecting when and how to utilize interactions as instructional methods in a Web-based distance learning higher education environment. Research questions asked: What are the types and outcomes of interactions between participants in a Web-based…

  15. Virtual Reality Simulations and Animations in a Web-Based Interactive Manufacturing Engineering Module

    ERIC Educational Resources Information Center

    Ong, S. K.; Mannan, M. A.

    2004-01-01

    This paper presents a web-based interactive teaching package that provides a comprehensive and conducive yet dynamic and interactive environment for a module on automated machine tools in the Manufacturing Division at the National University of Singapore. The use of Internet technologies in this teaching tool makes it possible to conjure…

  16. Spin current source based on a quantum point contact with local spin-orbit interaction

    SciTech Connect

    Nowak, M. P.; Szafran, B.

    2013-11-11

    Proposal for construction of a source of spin-polarized current based on quantum point contact (QPC) with local spin-orbit interaction is presented. We show that spin-orbit interaction present within the narrowing acts like a spin filter. The spin polarization of the current is discussed as a function of the Fermi energy and the width of the QPC.

  17. Research on Teachers' Characteristics in Relation to a Cognitive-Learning Based Interactive Videodisc System.

    ERIC Educational Resources Information Center

    Grant, Martha B.; Cambre, Marjorie A.

    This pilot study explored teacher characteristics as they influenced the use of "Exploring Nepal," a cognitive learning-based interactive video system for middle school students. Specifically, the study sought to narrow down a variety of teacher characteristics that may influence the quality of their interaction with the videodisk. The…

  18. Virtual-Reality-Based Social Interaction Training for Children with High-Functioning Autism

    ERIC Educational Resources Information Center

    Ke, Fengfeng; Im, Tami

    2013-01-01

    Employing the multiple-baseline across-subjects design, the authors examined the implementation and potential effect of a virtual-reality-based social interaction program on the interaction and communication performance of children with high functioning autism. The data were collected via behavior observation and analysis, questionnaires, and…

  19. Learning with Web-Based Interactive Objects: An Investigation into Student Perceptions of Effectiveness

    ERIC Educational Resources Information Center

    Salajan, Florin D.; Perschbacher, Susanne; Cash, Mindy; Talwar, Reena; El-Badrawy, Wafa; Mount, Greg J.

    2009-01-01

    In its efforts to continue the modernization of its curriculum, the Faculty of Dentistry at the University of Toronto has developed a series of web-based interactive learning applications. This article presents the production cycle of these new interactive learning objects and the preliminary study conducted to measure the students' perception of…

  20. Enhancing L2 Interaction in Avatar-Based Virtual Worlds: Student Teachers' Perceptions

    ERIC Educational Resources Information Center

    Tseng, Jun-Jie; Tsai, Ya-Hsun; Chao, Rih-Chang

    2013-01-01

    Three-dimensional (3-D) multi-user virtual environments (3-D MUVEs) have been used to provide language learners with realistic scenarios in which verbal and non-verbal interactions are simulated. However, little is known of the underlying factors that shape interaction in avatar-based virtual worlds. This study examined the perceptions of 38…

  1. Computer-based Approaches for Training Interactive Digital Map Displays

    DTIC Science & Technology

    2005-09-01

    SUPPLEMENTARY NOTES Subject Matter POC: Jean L. Dyer 14. ABSTRACT (Maximum 200 words): Five computer-based training approaches for learning digital skills...Training assessment Exploratory Learning Guided ExploratoryTraining Guided Discovery SECURITY CLASSIFICATION OF 19. LIMITATION OF 20. NUMBER 21...the other extreme of letting Soldiers learn a digital interface on their own. The research reported here examined these two conditions and three other

  2. Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

    SciTech Connect

    Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.; Ross, Nancy L.; Cox, David F.; Rosso, Kevin M.

    2011-04-01

    Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for several other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and β-AsS and the distorted hexagonal close-packed arrays adopted by α- and β-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.

  3. Development of StopAdvisor: A theory-based interactive internet-based smoking cessation intervention.

    PubMed

    Michie, Susan; Brown, Jamie; Geraghty, Adam W A; Miller, Sascha; Yardley, Lucy; Gardner, Benjamin; Shahab, Lion; McEwen, Andy; Stapleton, John A; West, Robert

    2012-09-01

    Reviews of internet-based behaviour-change interventions have shown that they can be effective but there is considerable heterogeneity and effect sizes are generally small. In order to advance science and technology in this area, it is essential to be able to build on principles and evidence of behaviour change in an incremental manner. We report the development of an interactive smoking cessation website, StopAdvisor, designed to be attractive and effective across the social spectrum. It was informed by a broad motivational theory (PRIME), empirical evidence, web-design expertise, and user-testing. The intervention was developed using an open-source web-development platform, 'LifeGuide', designed to facilitate optimisation and collaboration. We identified 19 theoretical propositions, 33 evidence- or theory-based behaviour change techniques, 26 web-design principles and nine principles from user-testing. These were synthesised to create the website, 'StopAdvisor' (see http://www.lifeguideonline.org/player/play/stopadvisordemonstration). The systematic and transparent application of theory, evidence, web-design expertise and user-testing within an open-source development platform can provide a basis for multi-phase optimisation contributing to an 'incremental technology' of behaviour change.

  4. A Theoretical Analysis of Social Interactions in Computer-based Learning Environments: Evidence for Reciprocal Understandings.

    ERIC Educational Resources Information Center

    Jarvela, Sanna; Bonk, Curtis Jay; Lehtinen, Erno; Lehti, Sirpa

    1999-01-01

    Presents a theoretical and empirical analysis of social interactions in computer-based learning environments. Explores technology use to support reciprocal understanding between teachers and students based on three technology-based learning environments in Finland and the United States, and discusses situated learning, cognitive apprenticeships,…

  5. Customizable Computer-Based Interaction Analysis for Coaching and Self-Regulation in Synchronous CSCL Systems

    ERIC Educational Resources Information Center

    Lonchamp, Jacques

    2010-01-01

    Computer-based interaction analysis (IA) is an automatic process that aims at understanding a computer-mediated activity. In a CSCL system, computer-based IA can provide information directly to learners for self-assessment and regulation and to tutors for coaching support. This article proposes a customizable computer-based IA approach for a…

  6. Unusual Base-Pairing Interactions in Monomer–Template Complexes

    PubMed Central

    2016-01-01

    Many high-resolution crystal structures have contributed to our understanding of the reaction pathway for catalysis by DNA and RNA polymerases, but the structural basis of nonenzymatic template-directed RNA replication has not been studied in comparable detail. Here we present crystallographic studies of the binding of ribonucleotide monomers to RNA primer–template complexes, with the goal of improving our understanding of the mechanism of nonenzymatic RNA copying, and of catalysis by polymerases. To explore how activated ribonucleotides recognize and bind to RNA templates, we synthesized an unreactive phosphonate-linked pyrazole analogue of guanosine 5′-phosphoro-2-methylimidazolide (2-MeImpG), a highly activated nucleotide that has been used extensively to study nonenzymatic primer extension. We cocrystallized this analogue with structurally rigidified RNA primer–template complexes carrying single or multiple monomer binding sites, and obtained high-resolution X-ray structures of these complexes. In addition to Watson–Crick base pairing, we repeatedly observed noncanonical guanine:cytidine base pairs in our crystal structures. In most structures, the phosphate and leaving group moieties of the monomers were highly disordered, while in others the distance from O3′ of the primer to the phosphorus of the incoming monomer was too great to allow for reaction. We suggest that these effects significantly influence the rate and fidelity of nonenzymatic RNA replication, and that even primitive ribozyme polymerases could enhance RNA replication by enforcing Watson–Crick base pairing between monomers and primer–template complexes, and by bringing the reactive functional groups into closer proximity. PMID:28058281

  7. Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria

    SciTech Connect

    Shi, Cindy

    2015-07-17

    The interactions among different microbial populations in a community could play more important roles in determining ecosystem functioning than species numbers and their abundances, but very little is known about such network interactions at a community level. The goal of this project is to develop novel framework approaches and associated software tools to characterize the network interactions in microbial communities based on high throughput, large scale high-throughput metagenomics data and apply these approaches to understand the impacts of environmental changes (e.g., climate change, contamination) on network interactions among different nitrifying populations and associated microbial communities.

  8. Grandmaster: Interactive text-based analytics of social media

    SciTech Connect

    Fabian, Nathan D.; Davis, Warren Leon,; Raybourn, Elaine M.; Lakkaraju, Kiran; Whetzel, Jonathan

    2015-11-01

    People use social media resources like Twitter, Facebook, forums etc. to share and discuss various activities or topics. By aggregating topic trends across many individuals using these services, we seek to construct a richer profile of a person’s activities and interests as well as provide a broader context of those activities. This profile may then be used in a variety of ways to understand groups as a collection of interests and affinities and an individual’s participation in those groups. Our approach considers that much of these data will be unstructured, free-form text. By analyzing free-form text directly, we may be able to gain an implicit grouping of individuals with shared interests based on shared conversation, and not on explicit social software linking them. In this paper, we discuss a proof-of-concept application called Grandmaster built to pull short sections of text, a person’s comments or Twitter posts, together by analysis and visualization to allow a gestalt understanding of the full collection of all individuals: how groups are similar and how they differ, based on their text inputs.

  9. Steady-State and Kinetics-Based Affinity Determination in Effector-Effector Target Interactions.

    PubMed

    Reinhard, André; Nürnberger, Thorsten

    2017-01-01

    Dissecting the functional basis of pathogenicity and resistance in the context of plant innate immunity benefits greatly from detailed knowledge about biomolecular interactions, as both resistance and virulence depend on specific interactions between pathogen and host biomolecules. While in vivo systems provide biological context to host-pathogen interactions, these experiments typically cannot provide quantitative biochemical characterization of biomolecular interactions. However, in many cases, the biological function does not only depend on whether an interaction occurs at all, but rather on the "intensity" of the interaction, as quantified by affinity. Specifically, microbial effector proteins may bind more than one host target to exert virulence functions, and looking at these interactions more closely than would be possible in a purely black-and-white qualitative assay (as classically based on plant or yeast systems) can reveal new insights into the evolutionary arms race between host and pathogen. Recent advances in biomolecular interaction assays that can be performed in vitro allow quantification of binding events with ever greater fidelity and application range. Here, we describe assays based on microscale thermophoresis (MST) and surface plasmon resonance (SPR). Using these technologies allows affinity determination both in steady-state and in kinetic configurations, providing two conceptually independent pathways to arrive at quantitative affinity data describing the interactions of pathogen and host biomolecules.

  10. Use of physiologically based pharmacokinetic modeling for assessment of drug-drug interactions.

    PubMed

    Baneyx, Guillaume; Fukushima, Yumi; Parrott, Neil

    2012-04-01

    Interactions between co-administered medicines can reduce efficacy or lead to adverse effects. Understanding and managing such interactions is essential in bringing safe and effective medicines to the market. Ideally, interaction potential should be recognized early and minimized in compounds that reach late stages of drug development. Physiologically based pharmacokinetic models combine knowledge of physiological factors with compound-specific properties to simulate how a drug behaves in the human body. These software tools are increasingly used during drug discovery and development and, when integrating relevant in vitro data, can simulate drug interaction potential. This article provides some background and presents illustrative examples. Physiologically based models are an integral tool in the discovery and development of drugs, and can significantly aid our understanding and prediction of drug interactions.

  11. Image-based interactive device for effective communication

    NASA Astrophysics Data System (ADS)

    Ferrari, F.; Nielsen, J.; Questa, Paolo; Sandini, Giulio

    1996-12-01

    The main objective of IBIDEM is to develop a video phone useful for speech reading by hearing-impaired people based on a new generation of the space-variant sensor and using standard telephone lines. The space variant nature of the sensor will allow it to have high resolution in the area of interest, lips or fingers, while still maintaining a wide field of view in order to perceive, for example, the facial expression of the interlocutor, but reducing drastically the amount of data to be sent on the line. A second objective if IBIDEM is the use of the same equipment for remote monitoring of health status. The system can be used for obtaining information about the status of a client in the form of images and could be extended to include various physiological parameters like heart rate, blood pressure, etc. The IBIDEM project is constructing a video phone using a camera with the retina-like sensor, a motorized system for moving the point of view of the camera as well as a display for the transmitted images. This video phone will be a high- quality, low-cost aid for the hearing impaired as well as being useful for remote monitoring.

  12. Integrated electronic circuits and devices based on interactive paper

    NASA Astrophysics Data System (ADS)

    Garnier, Francis

    1997-08-01

    Various organic conjugated materials, e.g. conjugated polymers and short conjugated oligomers, have been up to now proposed as active semiconducting layers in organic-base devices, such as thin film transistors, TFTs, or light emitting diodes. The mode of operation of TFTs shows that a high carrier mobility together with a low conductivity are required for their figure of merit. Experimental results from literature indicate that, whereas conjugated polymers exhibit a low carrier mobility, of the order of 10-4 to 10-5 cm2V-1s-1, conjugated oligomers appear much more promising. It is thus shown that carrier mobility is directly related to the long range structural order in conjugated oligomer films, i.e. to the decrease of grain boundaries, leading to values of the order of 10-1 cm-2V-1s-1, comparable to that of amorphous hydrogenated silicon. Conjugated oligomers are well defined materials, offering various physical and chemical ways for control of the structural organization of thin films made from them. Besides, conductivity in thin films of conjugated oligomers is mainly determined by the purity of the materials, allowing values lower than 10-7 Scm-1, with a high on/off ratio. The low melting and evaporation temperatures of conjugated oligomers, together with the solubility of some of these materials, allows the construction of TFTs by the use of room temperature techniques, following a process compatible with paper technology.

  13. CaseWorld™: Interactive, media rich, multidisciplinary case based learning.

    PubMed

    Gillham, David; Tucker, Katie; Parker, Steve; Wright, Victoria; Kargillis, Christina

    2015-11-01

    Nurse educators are challenged to keep up with highly specialised clinical practice, emerging research evidence, regulation requirements and rapidly changing information technology while teaching very large numbers of diverse students in a resource constrained environment. This complex setting provides the context for the CaseWorld project, which aims to simulate those aspects of clinical practice that can be represented by e-learning. This paper describes the development, implementation and evaluation of CaseWorld, a simulated learning environment that supports case based learning. CaseWorld provides nursing students with the opportunity to view unfolding authentic cases presented in a rich multimedia context. The first round of comprehensive summative evaluation of CaseWorld is discussed in the context of earlier formative evaluation, reference group input and strategies for integration of CaseWorld with subject content. This discussion highlights the unique approach taken in this project that involved simultaneous prototype development and large scale implementation, thereby necessitating strong emphasis on staff development, uptake and engagement. The lessons learned provide an interesting basis for further discussion of broad content sharing across disciplines and universities, and the contribution that local innovations can make to global education advancement.

  14. Regime-based analysis of aerosol-cloud interactions

    NASA Astrophysics Data System (ADS)

    Gryspeerdt, Edward; Stier, Philip

    2012-11-01

    Previous global satellite studies into the indirect aerosol effect have relied on determining the sensitivity of derived Cloud Droplet Number Concentration (Nd) to co-located Aerosol Optical Depth (AOD). These studies generally find a positive Nd sensitivity to AOD changes over ocean, but some find a negative sensitivity over land, in contrast to that predicted by models and theory. Here we investigate the Nd sensitivity to AOD in different cloud regimes, determined using a k-means clustering process on retrieved cloud properties. We find the strongest positive Nd sensitivity in the stratiform regimes over both land and ocean, providing the majority of the total sensitivity. The negative sensitivity previously observed over land is generated by the low cloud fraction regimes, suggesting that it is due to the difficulty of retrieving Nd at low cloud fractions. When considering a mean sensitivity, weighted by liquid cloud fraction to account for sampling biases, we find an increased sensitivity over land, in some regions becoming positive. This highlights the importance of regime based analysis when studying aerosol indirect effects.

  15. Interactive facial caricaturing system based on eye camera

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Tsuyoshi; Tominaga, Masafumi; Koshimizu, Hiroyasu

    2003-04-01

    Face is the most effective visual media for supporting human interface and communication. We have proposed a typical KANSEI machine vision system to generate the facial caricature so far. The basic principle of this system uses the "mean face assumption" to extract individual features of a given face. This system did not provide for feedback from the gallery of the caricature; therefore, to allow for such feedback, in this paper, we propose a caricaturing system by using the KANSEI visual information acquired from the Eye-camera mounted on the head of a gallery, because it is well know that the gaze distribution represents not only where but also how he is looking at the face. The caricatures created in this way could be based on several measures which are provided from the distribution of the number of fixations to the facial parts, the number of times the gaze came to a particular area of the face, and the matrix of the transitions from a facial region to the other. These measures of the gallery"s KANSEI information were used to create caricatures with feedback from the gallery.

  16. PPIevo: protein-protein interaction prediction from PSSM based evolutionary information.

    PubMed

    Zahiri, Javad; Yaghoubi, Omid; Mohammad-Noori, Morteza; Ebrahimpour, Reza; Masoudi-Nejad, Ali

    2013-10-01

    Protein-protein interactions regulate a variety of cellular processes. There is a great need for computational methods as a complement to experimental methods with which to predict protein interactions due to the existence of many limitations involved in experimental techniques. Here, we introduce a novel evolutionary based feature extraction algorithm for protein-protein interaction (PPI) prediction. The algorithm is called PPIevo and extracts the evolutionary feature from Position-Specific Scoring Matrix (PSSM) of protein with known sequence. The algorithm does not depend on the protein annotations, and the features are based on the evolutionary history of the proteins. This enables the algorithm to have more power for predicting protein-protein interaction than many sequence based algorithms. Results on the HPRD database show better performance and robustness of the proposed method. They also reveal that the negative dataset selection could lead to an acute performance overestimation which is the principal drawback of the available methods.

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

    PubMed

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

    2016-08-04

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

  18. Content Interactivity: The Effect of Higher Levels of Interactivity on Learner Performance Outcomes and Satisfaction in Web-Based Military Training

    ERIC Educational Resources Information Center

    Kenyon, Peggy L.

    2012-01-01

    The effect of content interactivity on performance outcomes and satisfaction has been studied by researchers who compared the results of Web-based and computer-based learning to classroom learning. Few scholars have compared the effects of the same content produced at different levels (low and high) of interactivity and the resulting effects. The…

  19. Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering.

    PubMed

    Yang, Lei; Tang, Xianglong

    2014-01-01

    Cliques (maximal complete subnets) in protein-protein interaction (PPI) network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO) annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP) and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning.

  20. Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

    PubMed Central

    Vijayabaskar, M. S.; Vishveshwara, Saraswathi

    2012-01-01

    There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or “sequence conservation” as the basis for their understanding. Recently “interaction energy” based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the “interaction conservation” viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design. PMID:22615547

  1. Homology-Based Prediction of Potential Protein–Protein Interactions between Human Erythrocytes and Plasmodium falciparum

    PubMed Central

    Ramakrishnan, Gayatri; Srinivasan, Narayanaswamy; Padmapriya, Ponnan; Natarajan, Vasant

    2015-01-01

    Plasmodium falciparum, a causative agent of malaria, is a well-characterized obligate intracellular parasite known for its ability to remodel host cells, particularly erythrocytes, to successfully persist in the host environment. However, the current levels of understanding from the laboratory experiments on the host–parasite interactions and the strategies pursued by the parasite to remodel host erythrocytes are modest. Several computational means developed in the recent past to predict host–parasite/pathogen interactions have generated testable hypotheses on feasible protein–protein interactions. We demonstrate the utility of protein structure-based protocol in the recognition of potential interacting proteins across P. falciparum and host erythrocytes. In concert with the information on the expression and subcellular localization of host and parasite proteins, we have identified 208 biologically feasible interactions potentially brought about by 59 P. falciparum and 30 host erythrocyte proteins. For selected cases, we have evaluated the physicochemical viability of the predicted interactions in terms of surface complementarity, electrostatic complementarity, and interaction energies at protein interface regions. Such careful inspection of molecular and mechanistic details generates high confidence on the predicted host–parasite protein–protein interactions. The predicted host–parasite interactions generate many experimentally testable hypotheses that can contribute to the understanding of possible mechanisms undertaken by the parasite in host erythrocyte remodeling. Thus, the key protein players recognized in P. falciparum can be explored for their usefulness as targets for chemotherapeutic intervention. PMID:26740742

  2. Modeling of Tool-Tissue Interactions for Computer-Based Surgical Simulation: A Literature Review.

    PubMed

    Misra, Sarthak; Ramesh, K T; Okamura, Allison M

    2008-10-01

    Surgical simulators present a safe and potentially effective method for surgical training, and can also be used in robot-assisted surgery for pre- and intra-operative planning. Accurate modeling of the interaction between surgical instruments and organs has been recognized as a key requirement in the development of high-fidelity surgical simulators. Researchers have attempted to model tool-tissue interactions in a wide variety of ways, which can be broadly classified as (1) linear elasticity-based, (2) nonlinear (hyperelastic) elasticity-based finite element (FE) methods, and (3) other techniques that not based on FE methods or continuum mechanics. Realistic modeling of organ deformation requires populating the model with real tissue data (which are difficult to acquire in vivo) and simulating organ response in real time (which is computationally expensive). Further, it is challenging to account for connective tissue supporting the organ, friction, and topological changes resulting from tool-tissue interactions during invasive surgical procedures. Overcoming such obstacles will not only help us to model tool-tissue interactions in real time, but also enable realistic force feedback to the user during surgical simulation. This review paper classifies the existing research on tool-tissue interactions for surgical simulators specifically based on the modeling techniques employed and the kind of surgical operation being simulated, in order to inform and motivate future research on improved tool-tissue interaction models.

  3. Modeling of Tool-Tissue Interactions for Computer-Based Surgical Simulation: A Literature Review

    PubMed Central

    Misra, Sarthak; Ramesh, K. T.; Okamura, Allison M.

    2009-01-01

    Surgical simulators present a safe and potentially effective method for surgical training, and can also be used in robot-assisted surgery for pre- and intra-operative planning. Accurate modeling of the interaction between surgical instruments and organs has been recognized as a key requirement in the development of high-fidelity surgical simulators. Researchers have attempted to model tool-tissue interactions in a wide variety of ways, which can be broadly classified as (1) linear elasticity-based, (2) nonlinear (hyperelastic) elasticity-based finite element (FE) methods, and (3) other techniques that not based on FE methods or continuum mechanics. Realistic modeling of organ deformation requires populating the model with real tissue data (which are difficult to acquire in vivo) and simulating organ response in real time (which is computationally expensive). Further, it is challenging to account for connective tissue supporting the organ, friction, and topological changes resulting from tool-tissue interactions during invasive surgical procedures. Overcoming such obstacles will not only help us to model tool-tissue interactions in real time, but also enable realistic force feedback to the user during surgical simulation. This review paper classifies the existing research on tool-tissue interactions for surgical simulators specifically based on the modeling techniques employed and the kind of surgical operation being simulated, in order to inform and motivate future research on improved tool-tissue interaction models. PMID:20119508

  4. Whole Language versus Code-Based Skills and Interactional Patterns in Singapore's Early Literacy Program

    ERIC Educational Resources Information Center

    Vaish, Viniti

    2014-01-01

    This paper analyzes whole language and code-based skills approaches in early literacy and the specific patterns of interaction present in both approaches. Nineteen hours of video data were coded to analyze the nature of whole language versus code-based skills instruction and document the allocation of time spent on each approach in a reading…

  5. The Effect of Interactive Whiteboard-Based Instruction on Mathematics Performance of English Learners

    ERIC Educational Resources Information Center

    Link, Tammy

    2012-01-01

    A quasi-experimental research study was conducted to investigate the performance of English learners (ELs) on mathematics assessments when using interactive whiteboard (IWB)-based instruction as compared to text-based instruction. A sample of 47 seventh-and eighth-grade EL students from ABC Middle School (name has been changed) was included in…

  6. A Multiple-Sessions Interactive Computer-Based Learning Tool for Ability Cultivation in Circuit Simulation

    ERIC Educational Resources Information Center

    Xu, Q.; Lai, L. L.; Tse, N. C. F.; Ichiyanagi, K.

    2011-01-01

    An interactive computer-based learning tool with multiple sessions is proposed in this paper, which teaches students to think and helps them recognize the merits and limitations of simulation tools so as to improve their practical abilities in electrical circuit simulation based on the case of a power converter with progressive problems. The…

  7. A Computer-Based Interactive Multimedia Program to Reduce HIV Transmission for Women with Intellectual Disability

    ERIC Educational Resources Information Center

    Wells, J.; Clark, K. D.; Sarno, K.

    2012-01-01

    Background: Despite recent recognition of the need for preventive sexual health materials for people with intellectual disability (ID), there have been remarkably few health-based interventions designed for people with mild to moderate ID. The purpose of this study was to evaluate the effects of a computer-based interactive multimedia (CBIM)…

  8. Development of an Interactive Computer-Based Learning Strategy to Assist in Teaching Water Quality Modelling

    ERIC Educational Resources Information Center

    Zigic, Sasha; Lemckert, Charles J.

    2007-01-01

    The following paper presents a computer-based learning strategy to assist in introducing and teaching water quality modelling to undergraduate civil engineering students. As part of the learning strategy, an interactive computer-based instructional (CBI) aid was specifically developed to assist students to set up, run and analyse the output from a…

  9. Collaborative Scaffolding in Online Task-Based Voice Interactions between Advanced Learners

    ERIC Educational Resources Information Center

    Kenning, Marie-Madeleine

    2010-01-01

    This paper reports some of the findings of a distinctive innovative use of audio-conferencing involving a population (campus-based advanced learners) and a type of application (task-based language learning) that have received little attention to date: the use of Wimba Voice Tools to provide additional opportunities for spoken interactions between…

  10. Young Foreign Language Learners' Interactions during Task-Based Paired Assessments

    ERIC Educational Resources Information Center

    Butler, Yuko Goto; Zeng, Wei

    2014-01-01

    Despite the popularity of task-based language teaching (TBLT) in foreign language (FL) education at elementary school, it remains unclear how young learners' FL abilities can best be evaluated with tasks. The present study seeks to understand developmental differences in interactions among elementary-school students during task-based language…

  11. Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics.

    PubMed

    Zaslavsky, Boris Y; Uversky, Vladimir N; Chait, Arnon

    2016-01-01

    Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein-partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein-protein- and protein-partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.

  12. Adaptive mesh compression and transmission in Internet-based interactive walkthrough virtual environments

    NASA Astrophysics Data System (ADS)

    Yang, Sheng; Kuo, C.-C. Jay

    2002-07-01

    An Internet-based interactive walkthrough virtual environment is presented in this work to facilitate interactive streaming and browsing of 3D graphic models across the Internet. The models are compressed by the view-dependent progressive mesh compression algorithm to enable the decorrelation of partitions and finer granularity. Following the fundamental framework of mesh representation, an interactive protocol based on the real time streaming protocol (RTSP) is developed to enhance the interaction between the server and the client. Finally, the data of the virtual world is re-organized and transmitted according to the viewer's requests. Experimental results demonstrate that the proposed algorithm reduces the required transmission bandwidth, and provides an acceptable visual quality even at low bit rates.

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

    PubMed

    Lee, Seungcheol Austin; Liang, Yuhua Jake

    2015-04-01

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

  14. MAS C-Terminal Tail Interacting Proteins Identified by Mass Spectrometry- Based Proteomic Approach

    PubMed Central

    Tirupula, Kalyan C.; Zhang, Dongmei; Osbourne, Appledene; Chatterjee, Arunachal; Desnoyer, Russ; Willard, Belinda; Karnik, Sadashiva S.

    2015-01-01

    Propagation of signals from G protein-coupled receptors (GPCRs) in cells is primarily mediated by protein-protein interactions. MAS is a GPCR that was initially discovered as an oncogene and is now known to play an important role in cardiovascular physiology. Current literature suggests that MAS interacts with common heterotrimeric G-proteins, but MAS interaction with proteins which might mediate G protein-independent or atypical signaling is unknown. In this study we hypothesized that MAS C-terminal tail (Ct) is a major determinant of receptor-scaffold protein interactions mediating MAS signaling. Mass-spectrometry based proteomic analysis was used to comprehensively identify the proteins that interact with MAS Ct comprising the PDZ-binding motif (PDZ-BM). We identified both PDZ and non-PDZ proteins from human embryonic kidney cell line, mouse atrial cardiomyocyte cell line and human heart tissue to interact specifically with MAS Ct. For the first time our study provides a panel of PDZ and other proteins that potentially interact with MAS with high significance. A ‘cardiac-specific finger print’ of MAS interacting PDZ proteins was identified which includes DLG1, MAGI1 and SNTA. Cell based experiments with wild-type and mutant MAS lacking the PDZ-BM validated MAS interaction with PDZ proteins DLG1 and TJP2. Bioinformatics analysis suggested well-known multi-protein scaffold complexes involved in nitric oxide signaling (NOS), cell-cell signaling of neuromuscular junctions, synapses and epithelial cells. Majority of these protein hits were predicted to be part of disease categories comprising cancers and malignant tumors. We propose a ‘MAS-signalosome’ model to stimulate further research in understanding the molecular mechanism of MAS function. Identifying hierarchy of interactions of ‘signalosome’ components with MAS will be a necessary step in future to fully understand the physiological and pathological functions of this enigmatic receptor. PMID

  15. Research on gaze-based interaction to 3D display system

    NASA Astrophysics Data System (ADS)

    Kwon, Yong-Moo; Jeon, Kyeong-Won; Kim, Sung-Kyu

    2006-10-01

    There have been reported several researches on gaze tracking techniques using monocular camera or stereo camera. The most popular used gaze estimation techniques are based on PCCR (Pupil Center & Cornea Reflection). These techniques are for gaze tracking for 2D screen or images. In this paper, we address the gaze-based 3D interaction to stereo image for 3D virtual space. To the best of our knowledge, our paper first addresses the 3D gaze interaction techniques to 3D display system. Our research goal is the estimation of both of gaze direction and gaze depth. Until now, the most researches are focused on only gaze direction for the application to 2D display system. It should be noted that both of gaze direction and gaze depth should be estimated for the gaze-based interaction in 3D virtual space. In this paper, we address the gaze-based 3D interaction techniques with glassless stereo display. The estimation of gaze direction and gaze depth from both eyes is a new important research topic for gaze-based 3D interaction. We present our approach for the estimation of gaze direction and gaze depth and show experimentation results.

  16. Quadrupole-dipole transform based on optical near-field interactions in engineered nanostructures.

    PubMed

    Tate, Naoya; Sugiyama, Hiroki; Naruse, Makoto; Nomura, Wataru; Yatsui, Takashi; Kawazoe, Tadashi; Ohtsu, Motoichi

    2009-06-22

    Nanophotonics has the potential to provide novel devices and systems with unique functions based on optical near-field interactions. Here we experimentally demonstrate, for the first time, what we call a quadrupole-dipole transform achieved by optical near-field interactions between engineered nanostructures. We describe its principles, the nanostructure design, fabrication of one- and two-layer gold nanostructures, an experimental demonstration, and optical characterization and analysis.

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

    PubMed

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

    2015-07-01

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

  18. The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods

    PubMed Central

    Bhat, Riyaz A; Lahaye, Thomas; Panstruga, Ralph

    2006-01-01

    Non-invasive fluorophore-based protein interaction assays like fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC, also referred to as "split YFP") have been proven invaluable tools to study protein-protein interactions in living cells. Both methods are now frequently used in the plant sciences and are likely to develop into standard techniques for the identification, verification and in-depth analysis of polypeptide interactions. In this review, we address the individual strengths and weaknesses of both approaches and provide an outlook about new directions and possible future developments for both techniques. PMID:16800872

  19. Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

    PubMed

    Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

    2012-01-01

    Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.

  20. Plant-based antimicrobial studies--methods and approaches to study the interaction between natural products.

    PubMed

    van Vuuren, Sandy; Viljoen, Alvaro

    2011-07-01

    The therapeutic value of synergistic interactions has been known since antiquity, and many different cultural healing systems still rely on this principle in the belief that combination therapy may enhance efficacy. This paper intends to provide an overview, from an antimicrobial perspective, on the research undertaken and interactive principles involved in pharmacognosy studies. Methods used to determine antimicrobial interactions include basic combination studies, the sum of the fractional inhibitory concentration index (ΣFIC), isobole interpretations, and death kinetic (time-kill) assays. The various interactions are discussed with reference to molecules, different plant parts or fractions, different plant species, and combinations with nonbotanical antimicrobial agents. It is recommended for future development in the field of phytosynergy that consideration should be given to the selection criteria for the two inhibitors. A more conservative approach should be adopted when classifying synergy. When examining interactions in plant-based studies, antagonistic interactions should not be ignored. Combinations involving more than two test samples should be examined where applicable, and very importantly, the mechanism of action of synergistic interactions should be given precedence. It is encouraging to observe the upsurge in papers exploring the complex interactions of medicinal plants, and undoubtedly this will become increasingly important in our continued quest to understand the mechanism of action of phytotherapy. The scientific validation of efficacious antimicrobial combinations could lead to patentable entities making research in the field of phytosynergy not only academically rewarding but also commercially relevant.

  1. A Single Kernel-Based Approach to Extract Drug-Drug Interactions from Biomedical Literature

    PubMed Central

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng

    2012-01-01

    When one drug influences the level or activity of another drug this is known as a drug-drug interaction (DDI). Knowledge of such interactions is crucial for patient safety. However, the volume and content of published biomedical literature on drug interactions is expanding rapidly, making it increasingly difficult for DDIs database curators to detect and collate DDIs information manually. In this paper, we propose a single kernel-based approach to extract DDIs from biomedical literature. This novel kernel-based approach can effectively make full use of syntactic structural information of the dependency graph. In particular, our approach can efficiently represent both single subgraph topological information and the relation of two subgraphs in the dependency graph. Experimental evaluations showed that our single kernel-based approach can achieve state-of-the-art performance on the publicly available DDI corpus without exploiting multiple kernels or additional domain resources. PMID:23133662

  2. Interactions of sugar-based bolaamphiphiles with biomimetic systems of plasma membranes.

    PubMed

    Nasir, Mehmet Nail; Crowet, Jean-Marc; Lins, Laurence; Obounou Akong, Firmin; Haudrechy, Arnaud; Bouquillon, Sandrine; Deleu, Magali

    2016-11-01

    Glycolipids constitute a class of molecules with various biological activities. Among them, sugar-based bolaamphiphiles characterized by their biocompatibility, biodegradability and lower toxicity, became interesting for the development of efficient and low cost lipid-based drug delivery systems. Their activity seems to be closely related to their interactions with the lipid components of the plasma membrane of target cells. Despite many works devoted to the chemical synthesis and characterization of sugar-based bolaamphiphiles, their interactions with plasma membrane have not been completely elucidated. In this work, two sugar-based bolaamphiphiles differing only at the level of their sugar residues were chemically synthetized. Their interactions with membranes have been investigated using model membranes containing or not sterol and with in silico approaches. Our findings indicate that the nature of sugar residues has no significant influence for their membrane interacting properties, while the presence of sterol attenuates the interactions of both bolaamphiphiles with the membrane systems. The understanding of this distinct behavior of bolaamphiphiles towards sterol-containing membrane systems could be useful for their applications as drug delivery systems.

  3. Embedded Process Modeling, Analogy-Based Option Generation and Analytical Graphic Interaction for Enhanced User-Computer Interaction: An Interactive Storyboard of Next Generation User-Computer Interface Technology. Phase 1

    DTIC Science & Technology

    1988-03-01

    ANALOGY-BASED OPTION GENERATION & ANALYTICAL GRAPHIC INTERACTION FOR ENHANCED USER-COMPUTER INTERACTION: AN INTERACTIVE STORYBOARD OF NEXT GENERATION...the design and development of the advanced UCI system concept from which we, in turn, designed and developed a " storyboard " prototype. Storyboard ...prototypes are simulations of interactive systems designed to help validate requirements. Storyboard prototypes are intended to narrow the gap between

  4. Prediction of oncogenic interactions and cancer-related signaling networks based on network topology.

    PubMed

    Acencio, Marcio Luis; Bovolenta, Luiz Augusto; Camilo, Esther; Lemke, Ney

    2013-01-01

    Cancer has been increasingly recognized as a systems biology disease since many investigators have demonstrated that this malignant phenotype emerges from abnormal protein-protein, regulatory and metabolic interactions induced by simultaneous structural and regulatory changes in multiple genes and pathways. Therefore, the identification of oncogenic interactions and cancer-related signaling networks is crucial for better understanding cancer. As experimental techniques for determining such interactions and signaling networks are labor-intensive and time-consuming, the development of a computational approach capable to accomplish this task would be of great value. For this purpose, we present here a novel computational approach based on network topology and machine learning capable to predict oncogenic interactions and extract relevant cancer-related signaling subnetworks from an integrated network of human genes interactions (INHGI). This approach, called graph2sig, is twofold: first, it assigns oncogenic scores to all interactions in the INHGI and then these oncogenic scores are used as edge weights to extract oncogenic signaling subnetworks from INHGI. Regarding the prediction of oncogenic interactions, we showed that graph2sig is able to recover 89% of known oncogenic interactions with a precision of 77%. Moreover, the interactions that received high oncogenic scores are enriched in genes for which mutations have been causally implicated in cancer. We also demonstrated that graph2sig is potentially useful in extracting oncogenic signaling subnetworks: more than 80% of constructed subnetworks contain more than 50% of original interactions in their corresponding oncogenic linear pathways present in the KEGG PATHWAY database. In addition, the potential oncogenic signaling subnetworks discovered by graph2sig are supported by experimental evidence. Taken together, these results suggest that graph2sig can be a useful tool for investigators involved in cancer research

  5. Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process.

    PubMed

    Venclovas, Ceslovas; Colvin, Michael E; Thelen, Michael P

    2002-10-01

    Replication and related processes in eukaryotic cells require replication factor C (RFC) to load a molecular clamp for DNA polymerase in an ATP-driven process, involving multiple molecular interactions. The detailed understanding of this mechanism is hindered by the lack of data regarding structure, mutual arrangement, and dynamics of the players involved. In this study, we analyzed interactions that take place during loading onto DNA of either the PCNA clamp or the Rad9-Rad1-Hus1 checkpoint complex, using computationally derived molecular models. Combining the modeled structures for each RFC subunit with known structural, biochemical, and genetic data, we propose detailed models of how two of the RFC subunits, RFC1 and RFC3, interact with the C-terminal regions of PCNA. RFC1 is predicted to bind PCNA similarly to the p21-PCNA interaction, while the RFC3-PCNA binding is proposed to be similar to the E. coli delta-beta interaction. Additional sequence and structure analysis, supported by experimental data, suggests that RFC5 might be the third clamp loader subunit to bind the equivalent PCNA region. We discuss functional implications stemming from the proposed model of the RFC1-PCNA interaction and compare putative clamp-interacting regions in RFC1 and its paralogs, Rad17 and Ctf18. Based on the individual intermolecular interactions, we propose RFC and PCNA arrangement that places three RFC subunits in association with each of the three C-terminal regions in PCNA. The two other RFC subunits are positioned at the two PCNA interfaces, with the third PCNA interface left unobstructed. In addition, we map interactions at the level of individual subunits between the alternative clamp loader/clamp system, Rad17-RFC(2-5)/Rad9-Rad1-Hus1. The proposed models of interaction between two clamp/clamp loader pairs provide both structural framework for interpretation of existing experimental data and a number of specific findings that can be subjected to direct experimental

  6. A hybrid configuration interaction treatment based on seniority number and excitation schemes

    SciTech Connect

    Alcoba, Diego R.; Capuzzi, Pablo; Torre, Alicia; Lain, Luis; Oña, Ofelia B.; Van Raemdonck, Mario; Bultinck, Patrick; Van Neck, Dimitri

    2014-12-28

    We present a configuration interaction method in which the Hamiltonian of an N-electron system is projected on Slater determinants selected according to the seniority-number criterion along with the traditional excitation-based procedure. This proposed method is especially useful to describe systems which exhibit dynamic (weak) correlation at determined geometric arrangements (where the excitation-based procedure is more suitable) but show static (strong) correlation at other arrangements (where the seniority-number technique is preferred). The hybrid method amends the shortcomings of both individual determinant selection procedures, yielding correct shapes of potential energy curves with results closer to those provided by the full configuration interaction method.

  7. Efficient fold-change detection based on protein-protein interactions.

    PubMed

    Buijsman, W; Sheinman, M

    2014-02-01

    Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the past few years, fold-change detecting mechanisms, based on transcriptional networks, have been proposed. Here we present a fold-change detecting mechanism, based on protein-protein interactions, consisting of two interacting proteins. This mechanism does not consume chemical energy and is not subject to transcriptional and translational noise, in contrast to previously proposed mechanisms. We show by analytical and numerical calculations that the mechanism is robust and can have a fast, precise, and efficient response for parameters that are relevant to eukaryotic cells.

  8. Efficient fold-change detection based on protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Buijsman, W.; Sheinman, M.

    2014-02-01

    Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the past few years, fold-change detecting mechanisms, based on transcriptional networks, have been proposed. Here we present a fold-change detecting mechanism, based on protein-protein interactions, consisting of two interacting proteins. This mechanism does not consume chemical energy and is not subject to transcriptional and translational noise, in contrast to previously proposed mechanisms. We show by analytical and numerical calculations that the mechanism is robust and can have a fast, precise, and efficient response for parameters that are relevant to eukaryotic cells.

  9. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

    SciTech Connect

    Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri; Sumpter, Bobby G; Fuentes-Cabrera, Miguel A; Vazquez-Mayagoitia, Alvaro

    2010-01-01

    Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

  10. Reputation-based conditional interaction supports cooperation in well-mixed prisoner's dilemmas.

    PubMed

    Chen, Xiaojie; Schick, Alana; Doebeli, Michael; Blachford, Alistair; Wang, Long

    2012-01-01

    In the well-mixed prisoner's dilemma game, individuals are typically assumed to have no choice about whether to interact with other individuals in the population. In this paper, we instead consider reputation-based conditional interaction and its consequences for the evolution of cooperation. Each individual has a tolerance range, and only interacts with other individuals whose reputation lies within its tolerance range in a chosen sample of the population. Reputation contains information about the number of interaction partners an individual has just cooperated with. We find that the introduction of conditional interaction promotes cooperation in well-mixed populations, and there exist moderate tolerance ranges for which this effect is maximized. For a given tolerance range, there is a critical cost-to-benefit ratio below which cooperation can be promoted. Interestingly, we find that if cooperation evolves, different cooperators' interaction clusters are typically maintained in the population, each around a different reputation level. We further investigate some properties of these cooperators' clusters. Moreover, we examine the effects of the sample number on the evolution of cooperation. Our results highlight the importance of the detailed consideration of modes of interaction for the evolution of cooperation in well-mixed populations.

  11. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

    PubMed

    Bryce, Richard A

    2011-04-01

    The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

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

    PubMed Central

    Martínez-Bueso, Pau; Moyà-Alcover, Biel

    2014-01-01

    Observation is recommended in motor rehabilitation. For this reason, the aim of this study was to experimentally test the feasibility and benefit of including mirror feedback in vision-based rehabilitation systems: we projected the user on the screen. We conducted a user study by using a previously evaluated system that improved the balance and postural control of adults with cerebral palsy. We used a within-subjects design with the two defined feedback conditions (mirror and no-mirror) with two different groups of users (8 with disabilities and 32 without disabilities) using usability measures (time-to-start (Ts) and time-to-complete (Tc)). A two-tailed paired samples t-test confirmed that in case of disabilities the mirror feedback facilitated the interaction in vision-based systems for rehabilitation. The measured times were significantly worse in the absence of the user's own visual feedback (Ts = 7.09 (P < 0.001) and Tc = 4.48 (P < 0.005)). In vision-based interaction systems, the input device is the user's own body; therefore, it makes sense that feedback should be related to the body of the user. In case of disabilities the mirror feedback mechanisms facilitated the interaction in vision-based systems for rehabilitation. Results recommends developers and researchers use this improvement in vision-based motor rehabilitation interactive systems. PMID:25295310

  13. Improving vision-based motor rehabilitation interactive systems for users with disabilities using mirror feedback.

    PubMed

    Jaume-i-Capó, Antoni; Martínez-Bueso, Pau; Moyà-Alcover, Biel; Varona, Javier

    2014-01-01

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

  14. Apparatus and method for interaction phenomena with world modules in data-flow-based simulation

    DOEpatents

    Xavier, Patrick G.; Gottlieb, Eric J.; McDonald, Michael J.; Oppel, III, Fred J.

    2006-08-01

    A method and apparatus accommodate interaction phenomenon in a data-flow-based simulation of a system of elements, by establishing meta-modules to simulate system elements and by establishing world modules associated with interaction phenomena. World modules are associated with proxy modules from a group of meta-modules associated with one of the interaction phenomenon. The world modules include a communication world, a sensor world, a mobility world, and a contact world. World modules can be further associated with other world modules if necessary. Interaction phenomenon are simulated in corresponding world modules by accessing member functions in the associated group of proxy modules. Proxy modules can be dynamically allocated at a desired point in the simulation to accommodate the addition of elements in the system of elements such as a system of robots, a system of communication terminals, or a system of vehicles, being simulated.

  15. Magnetic Yoking and Tunable Interactions in FePt-Based Hard/Soft Bilayers

    PubMed Central

    Gilbert, Dustin A.; Liao, Jung-Wei; Kirby, Brian J.; Winklhofer, Michael; Lai, Chih-Huang; Liu, Kai

    2016-01-01

    Magnetic interactions in magnetic nanostructures are critical to nanomagnetic and spintronic explorations. Here we demonstrate an extremely sensitive magnetic yoking effect and tunable interactions in FePt based hard/soft bilayers mediated by the soft layer. Below the exchange length, a thin soft layer strongly exchange couples to the perpendicular moments of the hard layer; above the exchange length, just a few nanometers thicker, the soft layer moments turn in-plane and act to yoke the dipolar fields from the adjacent hard layer perpendicular domains. The evolution from exchange to dipolar-dominated interactions is experimentally captured by first-order reversal curves, the ΔM method, and polarized neutron reflectometry, and confirmed by micromagnetic simulations. These findings demonstrate an effective yoking approach to design and control magnetic interactions in wide varieties of magnetic nanostructures and devices. PMID:27604428

  16. Magnetic Yoking and Tunable Interactions in FePt-Based Hard/Soft Bilayers

    NASA Astrophysics Data System (ADS)

    Gilbert, Dustin A.; Liao, Jung-Wei; Kirby, Brian J.; Winklhofer, Michael; Lai, Chih-Huang; Liu, Kai

    2016-09-01

    Magnetic interactions in magnetic nanostructures are critical to nanomagnetic and spintronic explorations. Here we demonstrate an extremely sensitive magnetic yoking effect and tunable interactions in FePt based hard/soft bilayers mediated by the soft layer. Below the exchange length, a thin soft layer strongly exchange couples to the perpendicular moments of the hard layer; above the exchange length, just a few nanometers thicker, the soft layer moments turn in-plane and act to yoke the dipolar fields from the adjacent hard layer perpendicular domains. The evolution from exchange to dipolar-dominated interactions is experimentally captured by first-order reversal curves, the ΔM method, and polarized neutron reflectometry, and confirmed by micromagnetic simulations. These findings demonstrate an effective yoking approach to design and control magnetic interactions in wide varieties of magnetic nanostructures and devices.

  17. A Look at an Interactive Classroom-Based Drug Abuse Prevention Program: Interactive Contents and Suggestions for Research

    ERIC Educational Resources Information Center

    Sussman, Steve; Rohrbach, Louise A.; Patel, Ravi; Holiday, Karen

    2003-01-01

    Interactivity has been shown to be a critical element of effective drug abuse prevention programs. This study examined the contents of Project Towards No Drug Abuse, a program that has revealed strong effects only when delivered in a highly interactive version. Types of teacher and student interactive messages were identified. It is speculated…

  18. A CAPS-based binding assay provides semi-quantitative validation of protein-DNA interactions.

    PubMed

    Xie, Yongyao; Zhang, Yaling; Zhao, Xiucai; Liu, Yao-Guang; Chen, Letian

    2016-02-15

    Investigation of protein-DNA interactions provides crucial information for understanding the mechanisms of gene regulation. Current methods for studying protein-DNA interactions, such as DNaseI footprinting or gel shift assays, involve labeling DNA with radioactive or fluorescent tags, making these methods costly, laborious, and potentially damaging to the environment. Here, we describe a novel cleaved amplified polymorphic sequence (CAPS)-based binding assay (CBA), which is a label-free method that can simplify the semi-quantitative validation of protein-DNA interactions. The CBA tests the interaction between a protein and its target DNA, based on the CAPS pattern produced due to differences in the accessibility of a restriction endonuclease site (intrinsic or artificial) in amplified DNA in the presence and absence of the protein of interest. Thus, the CBA can produce a semi-quantitative readout of the interaction strength based on the dose of the binding protein. We demonstrate the principle and feasibility of CBA using B3, MADS3 proteins and the corresponding RY or CArG-box containing DNAs.

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

    PubMed

    Liu, Yang; Xu, Haiming; Chen, Suchao; Chen, Xianfeng; Zhang, Zhenguo; Zhu, Zhihong; Qin, Xueying; Hu, Landian; Zhu, Jun; Zhao, Guo-Ping; Kong, Xiangyin

    2011-03-01

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

  20. Plume Interaction and Base Flow Analysis of a Twin Engine Flight Vehicle

    NASA Astrophysics Data System (ADS)

    Chandra Murty, Mamidi Sri Rama; Chakraborty, Debasis

    2016-06-01

    3D RANS simulations are performed to study the multi jet interactions of a twin engine gimbal configuration of an aerospace vehicle at different time instants. Simulations captured all the essential features of the flow field and interaction between the neighboring jets did not occur because of low altitudes and moderate under-expansion of the jets considered in the simulations. For higher gimbal angle, two jets were the closest but still did not interact. Detail exploration of the downstream flow field revealed that the distinct features of the jets are retained at the farthest downstream locations; although the pressure field reached the uniformity. Average base pressure ratios for the three different time instances are 0.91, 0.547 and 0.522 and maximum base temperature is of the order 800 K.

  1. A centrifugation-based physicochemical characterization method for the interaction between proteins and nanoparticles

    NASA Astrophysics Data System (ADS)

    Bekdemir, Ahmet; Stellacci, Francesco

    2016-10-01

    Nanomedicine requires in-depth knowledge of nanoparticle-protein interactions. These interactions are studied with methods limited to large or fluorescently labelled nanoparticles as they rely on scattering or fluorescence-correlation signals. Here, we have developed a method based on analytical ultracentrifugation (AUC) as an absorbance-based, label-free tool to determine dissociation constants (KD), stoichiometry (Nmax), and Hill coefficient (n), for the association of bovine serum albumin (BSA) with gold nanoparticles. Absorption at 520 nm in AUC renders the measurements insensitive to unbound and aggregated proteins. Measurements remain accurate and do not become more challenging for small (sub-10 nm) nanoparticles. In AUC, frictional ratio analysis allows for the qualitative assessment of the shape of the analyte. Data suggests that small-nanoparticles/protein complexes significantly deviate from a spherical shape even at maximum coverage. We believe that this method could become one of the established approaches for the characterization of the interaction of (small) nanoparticles with proteins.

  2. Using a dual safeguard web-based interactive teaching approach in an introductory physics class

    NASA Astrophysics Data System (ADS)

    Li, Lie-Ming; Li, Bin; Luo, Ying

    2015-06-01

    We modified the Just-in-Time Teaching approach and developed a dual safeguard web-based interactive (DGWI) teaching system for an introductory physics course. The system consists of four instructional components that improve student learning by including warm-up assignments and online homework. Student and instructor activities involve activities both in the classroom and on a designated web site. An experimental study with control groups evaluated the effectiveness of the DGWI teaching method. The results indicate that the DGWI method is an effective way to improve students' understanding of physics concepts, develop students' problem-solving abilities through instructor-student interactions, and identify students' misconceptions through a safeguard framework based on questions that satisfy teaching requirements and cover all of the course material. The empirical study and a follow-up survey found that the DGWI method increased student-teacher interaction and improved student learning outcomes.

  3. Predicting disease-related proteins based on clique backbone in protein-protein interaction network.

    PubMed

    Yang, Lei; Zhao, Xudong; Tang, Xianglong

    2014-01-01

    Network biology integrates different kinds of data, including physical or functional networks and disease gene sets, to interpret human disease. A clique (maximal complete subgraph) in a protein-protein interaction network is a topological module and possesses inherently biological significance. A disease-related clique possibly associates with complex diseases. Fully identifying disease components in a clique is conductive to uncovering disease mechanisms. This paper proposes an approach of predicting disease proteins based on cliques in a protein-protein interaction network. To tolerate false positive and negative interactions in protein networks, extending cliques and scoring predicted disease proteins with gene ontology terms are introduced to the clique-based method. Precisions of predicted disease proteins are verified by disease phenotypes and steadily keep to more than 95%. The predicted disease proteins associated with cliques can partly complement mapping between genotype and phenotype, and provide clues for understanding the pathogenesis of serious diseases.

  4. Scale-Free Correlations in Flocking Systems with Position-Based Interactions

    NASA Astrophysics Data System (ADS)

    Huepe, Cristián; Ferrante, Eliseo; Wenseleers, Tom; Turgut, Ali Emre

    2015-02-01

    We consider a model of self-propelled agents with spring-like interactions that depend only on relative positions, and not on relative orientations. We observe that groups of these agents self-organize to achieve collective motion (CM) through a mechanism based on the cascading of self-propulsion energy towards lower elastic modes. By computing the correlation functions of the speed and velocity fluctuations for different group sizes, we show that the corresponding correlation lengths are proportional to the linear size of the group and have no intrinsic length scale. We argue that such scale-free correlations are a natural consequence of the position-based interactions and associated CM dynamics. We hypothesize that this effect, acting in the context of more complex realistic interactions, could be at the origin of the scale-free correlations measured experimentally in flocks of starlings, instead of the previously argued proximity to a critical regime.

  5. Using a Dual Safeguard Web-Based Interactive Teaching Approach in an Introductory Physics Class

    ERIC Educational Resources Information Center

    Li, Lie-Ming; Li, Bin; Luo, Ying

    2015-01-01

    We modified the Just-in-Time Teaching approach and developed a dual safeguard web-based interactive (DGWI) teaching system for an introductory physics course. The system consists of four instructional components that improve student learning by including warm-up assignments and online homework. Student and instructor activities involve activities…

  6. Interactive Computer-Assisted Instruction in Acid-Base Physiology for Mobile Computer Platforms

    ERIC Educational Resources Information Center

    Longmuir, Kenneth J.

    2014-01-01

    In this project, the traditional lecture hall presentation of acid-base physiology in the first-year medical school curriculum was replaced by interactive, computer-assisted instruction designed primarily for the iPad and other mobile computer platforms. Three learning modules were developed, each with ~20 screens of information, on the subjects…

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

    NASA Astrophysics Data System (ADS)

    Ding, Diankuan; Li, Lixin

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

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  9. Video-Based Interaction, Negotiation for Comprehensibility, and Second Language Speech Learning: A Longitudinal Study

    ERIC Educational Resources Information Center

    Saito, Kazuya; Akiyama, Yuka

    2017-01-01

    This study examined the impact of video-based conversational interaction on the longitudinal development (one academic semester) of second language production by college-level Japanese English-as-a-foreign-language learners. Students in the experimental group engaged in weekly dyadic conversation exchanges with native speakers in the United States…

  10. Effects of Web-Based Interactive Modules on Engineering Students' Learning Motivations

    ERIC Educational Resources Information Center

    Bai, Haiyan; Aman, Amjad; Xu, Yunjun; Orlovskaya, Nina; Zhou, Mingming

    2016-01-01

    The purpose of this study is to assess the impact of a newly developed modules, Interactive Web-Based Visualization Tools for Gluing Undergraduate Fuel Cell Systems Courses system (IGLU), on learning motivations of engineering students using two samples (n[subscript 1] = 144 and n[subscript 2] = 135) from senior engineering classes. The…

  11. Personality Types and Learners' Interaction in Web-Based Threaded Discussion

    ERIC Educational Resources Information Center

    Lee, JeongMin; Lee, Youngmin

    2006-01-01

    This study examined the effects of group composition based on the learners' personality types as measured by the Myers-Briggs type indicator as they interacted in threaded discussions. Three groups comprised introverts, extroverts, and mixed introvert-extrovert classifications. Ninety-six participants were divided into 24 groups of 4 participants…

  12. Web-Based Interactive System for Analyzing Achievement Gaps in Public Schools System

    ERIC Educational Resources Information Center

    Wang, Kening; Mulvenon, Sean W.; Stegman, Charles; Xia, Yanling

    2010-01-01

    The National Office for Research on Measurement and Evaluation Systems (NORMES) at the University of Arkansas developed a web-based interactive system to provide information on state, district, and school level achievement gaps between white students and black students, socioeconomically disadvantaged students and non-disadvantaged students, male…

  13. Levels of Interaction and Proximity: Content Analysis of Video-Based Classroom Cases

    ERIC Educational Resources Information Center

    Kale, Ugur

    2008-01-01

    This study employed content analysis techniques to examine video-based cases of two websites that exemplify learner-centered pedagogies for pre-service teachers to carry out in their teaching practices. The study focused on interaction types and physical proximity levels between students and teachers observed in the videos. The findings regarding…

  14. Specifying and Refining a Measurement Model for a Computer-Based Interactive Assessment

    ERIC Educational Resources Information Center

    Levy, Roy; Mislevy, Robert J.

    2004-01-01

    The challenges of modeling students' performance in computer-based interactive assessments include accounting for multiple aspects of knowledge and skill that arise in different situations and the conditional dependencies among multiple aspects of performance. This article describes a Bayesian approach to modeling and estimating cognitive models…

  15. The Generative Effects of Instructional Organizers with Computer-Based Interactive Video.

    ERIC Educational Resources Information Center

    Kenny, Richard F.

    This study compared the use of three instructional organizers--the advance organizer (AO), the participatory pictorial graphic organizer (PGO), and the final form pictorial graphic organizer (FGO)--in the design and use of computer-based interactive video (CBIV) programs. That is, it attempted to determine whether a less generative or more…

  16. Ninter-Networked Interaction: Theory-based Cases in Teaching and Learning.

    ERIC Educational Resources Information Center

    Saarenkunnas, Maarit; Jarvela, Sanna; Hakkinen, Paivi; Kuure, Leena; Taalas, Peppi; Kunelius, Esa

    2000-01-01

    Describes the pedagogical framework of an interdisciplinary, international project entitled NINTER (Networked Interaction: Theory-Based Cases in Teaching and Learning). Discusses a pedagogical model for teacher and staff development programs in a networked environment; distributed cognition; cognitive apprenticeship; challenges for educational…

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

    ERIC Educational Resources Information Center

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

    2001-01-01

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

  18. Facilitating Grounded Online Interactions in Video-Case-Based Teacher Professional Development

    ERIC Educational Resources Information Center

    Nemirovsky, Ricardo; Galvis, Alvaro

    2004-01-01

    The use of interactive video cases for teacher professional development is an emergent medium inspired by case study methods used extensively in law, management, and medicine, and by the advent of multimedia technology available to support online discussions. This paper focuses on Web-based "grounded" discussions--in which the participants base…

  19. Learning Mathematics with Interactive Whiteboards and Computer-Based Graphing Utility

    ERIC Educational Resources Information Center

    Erbas, Ayhan Kursat; Ince, Muge; Kaya, Sukru

    2015-01-01

    The purpose of this study was to explore the effect of a technology-supported learning environment utilizing an interactive whiteboard (IWB) and NuCalc graphing software compared to a traditional direct instruction-based environment on student achievement in graphs of quadratic functions and attitudes towards mathematics and technology. Sixty-five…

  20. Interactive Computer Based Assessment Tasks: How Problem-Solving Process Data Can Inform Instruction

    ERIC Educational Resources Information Center

    Zoanetti, Nathan

    2010-01-01

    This article presents key steps in the design and analysis of a computer based problem-solving assessment featuring interactive tasks. The purpose of the assessment is to support targeted instruction for students by diagnosing strengths and weaknesses at different stages of problem-solving. The first focus of this article is the task piloting…

  1. Human Relations Skills in Individual Interactions for the Occupational Specialist. Competency-Based Modular Series.

    ERIC Educational Resources Information Center

    Nutter, Juanita B.; Boland, Jeanne M.

    This self-instructional module, one volume of a series of competency-based modules in human relations skills for occupational specialists, is designed to help the specialist interact effectively with a variety of students, teachers, co-workers and employees. Other modules in this set of three are Level I Human Relations Skills for the Occupational…

  2. Molecular Interactions between a Novel Soybean Oil-Based Polymer and Doxorubicin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel soybean oil-based polymer, hydrolyzed polymers of epoxidized soybean oil (HPESO), was developed and investigated for drug delivery. This work was aimed at determining the molecular interactions between HPESO and doxorubicin (DOX), an anticancer drug. Powder X-ray diffraction, ATR-FTIR and ...

  3. An Interactive Web-Based Method of Outreach to College Students at Risk for Suicide

    ERIC Educational Resources Information Center

    Haas, Ann; Koestner, Bethany; Rosenberg, Jill; Moore, David; Garlow, Steven J.; Sedway, Jan; Nicholas, Linda; Hendin, Herbert; Mann, J. John; Nemeroff, Charles B.

    2008-01-01

    Objective and Participants: From 2002 to 2005, the authors tested an interactive, Web-based method to encourage college students at risk for suicide to seek treatment. Methods: The authors invited students at 2 universities to complete an online questionnaire that screened for depression and other suicide risk factors. Respondents received a…

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

    ERIC Educational Resources Information Center

    Gioffre, Penelope

    2012-01-01

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

  5. Rationale, Design and Implementation of a Computer Vision-Based Interactive E-Learning System

    ERIC Educational Resources Information Center

    Xu, Richard Y. D.; Jin, Jesse S.

    2007-01-01

    This article presents a schematic application of computer vision technologies to e-learning that is synchronous, peer-to-peer-based, and supports an instructor's interaction with non-computer teaching equipments. The article first discusses the importance of these focused e-learning areas, where the properties include accurate bidirectional…

  6. The TEACH Method: An Interactive Approach for Teaching the Needs-Based Theories Of Motivation

    ERIC Educational Resources Information Center

    Moorer, Cleamon, Jr.

    2014-01-01

    This paper describes an interactive approach for explaining and teaching the Needs-Based Theories of Motivation. The acronym TEACH stands for Theory, Example, Application, Collaboration, and Having Discussion. This method can help business students to better understand and distinguish the implications of Maslow's Hierarchy of Needs,…

  7. Shared Hypermedia: Communication and Interaction in Web-Based Learning Environments.

    ERIC Educational Resources Information Center

    Riva, Giuseppe

    2001-01-01

    Presents a framework for the development of Web-based learning environments that is focused on shared hypermedia, a new form of computer-mediated communication. Highlights include how communication and interaction are changed by computers; changes in training as a result of the Internet; situated action theory; and creating communities of…

  8. Learning through Interaction in Children with Autism: Preliminary Data from a Social-Communication-Based Intervention

    ERIC Educational Resources Information Center

    Casenhiser, Devin M.; Shanker, Stuart G.; Stieben, Jim

    2013-01-01

    The study evaluates a social-communication-based approach to autism intervention aimed at improving the social interaction skills of children with autism spectrum disorder. We report preliminary results from an ongoing randomized controlled trial of 51 children aged 2 years 0 months to 4 years 11 months. Participants were assigned to either a…

  9. Coaching and Inspiring an Interactive Family Literacy Project of Excellence in a School-Based Setting

    ERIC Educational Resources Information Center

    Anderson, M. Parker; Adelman, David

    2007-01-01

    This article features the Project of Excellence, a program that was designed to engage families in an interactive community-based school literacy program. The authors discuss how they created the Project of Excellence. Although the goal of the Project was to improve the reading skills of young children, the focus of the Project was directed toward…

  10. A Mineral-Exploration Exercise Based on an Interactive Computer-Simulated Drilling Program.

    ERIC Educational Resources Information Center

    Hayes, W. B.; Allard, G. O.

    1981-01-01

    The effectiveness of an interactive computer-based instruction program designed to give students experience with exploratory drilling is compared to a previously used field-oriented simulated exploration program. The development, operation, and implementation of the computer program are discussed. (DC)

  11. Inquiry and Groups: Student Interactions in Cooperative Inquiry-Based Science

    ERIC Educational Resources Information Center

    Woods-McConney, Amanda; Wosnitza, Marold; Sturrock, Keryn L.

    2016-01-01

    Science education research has recommended cooperative inquiry based science in the primary science context for more than two decades but after more than 20 years, student achievement in science has not substantially improved. This study, through direct observation and analysis, investigated content-related student interactions in an authentic…

  12. Reconstruction of missing data in social networks based on temporal patterns of interactions

    NASA Astrophysics Data System (ADS)

    Stomakhin, Alexey; Short, Martin B.; Bertozzi, Andrea L.

    2011-11-01

    We discuss a mathematical framework based on a self-exciting point process aimed at analyzing temporal patterns in the series of interaction events between agents in a social network. We then develop a reconstruction model that allows one to predict the unknown participants in a portion of those events. Finally, we apply our results to the Los Angeles gang network.

  13. Effects of large vessel on temperature distribution based on photothermal coupling interaction model

    NASA Astrophysics Data System (ADS)

    Li, Zhifang; Zhang, Xiyang; Li, Zuoran; Li, Hui

    2016-10-01

    This paper is based on the finite element analysis method for studying effects of large blood vessel on temperature based on photothermal coupling interaction model, and it couples the physical field of optical transmission with the physical field of heat transfer in biological tissue by using COMSOL Multiphysics 4.4 software. The results demonstrate the cooling effect of large blood vessel, which can be potential application for the treatment of liver tumors.

  14. Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions.

    PubMed Central

    Zhang, Y; Zhou, H; Ou-Yang, Z C

    2001-01-01

    Recent single-macromolecule observations revealed that the force/extension characteristics of single-stranded DNA (ssDNA) are closely related to solution ionic concentration and DNA sequence composition. To understand this, we studied the elastic property of ssDNA through the Monte Carlo implementation of a modified freely jointed chain (FJC), with electrostatic, base-pairing, and base-pair stacking interactions all incorporated. The simulated force-extension profiles for both random and designed sequences have attained quantitative agreements with the experimental data. In low-salt solution, electrostatic interaction dominates, and at low forces, the molecule can be more easily aligned than an unmodified FJC. In high-salt solution, secondary hairpin structure appears in ssDNA by the formation of base pairs between complementary bases, and external stretching causes a hairpin-coil structural transition, which is continuous for ssDNA made of random sequences. In designed sequences such as poly(dA-dT) and poly(dG-dC), the stacking potential between base pairs encourages the aggregation of base pairs into bulk hairpins and makes the hairpin-coil transition a discontinuous (first-order) process. The sensitivity of elongation to the base-pairing rule is also investigated. The comparison of modeling calculations and the experimental data suggests that the base pairing of single-stranded polynucleotide molecules tends to form a nested and independent planar hairpin structure rather than a random intersecting pattern. PMID:11463654

  15. Classification of metal-oxide bonded interactions based on local potential- and kinetic-energy densities

    SciTech Connect

    Gibbs, Gerald V.; Cox, David; Crawford, T Daniel; Rosso, Kevin M.; Ross, Nancy; Downs, R. T.

    2006-02-28

    A classification of the HF bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio |V(rc)|/G(rc) where |V(rc)| is the magnitude of the local potential energy density and G(rc) is the local kinetic density evaluated at the bond critical points, rc. A calculation of the ratio for the MO bonded interactions comprising a relatively large number of molecules and earth materials, together with the constraints imposed by the values of Ñ2ρ(rc) and the local electronic energy density H(rc) = G(rc) + V(rc) in the HF study, yielded the same classification for the oxides as found for the fluorides. This is true despite the different trends of the bond critical point and local energy properties with the bond length displayed by the HF and MO bonded interactions. LiO, NaO and MgO bonded interactions classify as closed shell ionic bonds, BeO, AlO, SiO, BO and PO bonded interactions classify as bonds of intermediate character and NO bonded interactions classify as shared covalent bonds. CO and SO bonded interactions classify as both intermediate and covalent bonded interactions. The CO triple bonded interaction classifies as a bond of intermediate character and the CO single bonded interaction classifies as a covalent bond whereas their H(rc) value indicates that they are both covalent bonds. The |V(rc)|/G(rc) ratios for the BeO, AlO and SiO bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between |V(rc)|/G(rc) and the character of the bonded interaction is consistent with trends expected from electronegativity considerations. The connection between the net charges and the experimental SiO bond length evaluated for the Si and O atoms comprising two orthosilicates are examined in terms of the |V(rc)|/G(rc) values.

  16. Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach.

    PubMed

    Pai, Priyadarshini P; Dash, Tirtharaj; Mondal, Sukanta

    2017-04-07

    Protein interactions with ribonucleic acids (RNA) are well-known to be crucial for a wide range of cellular processes such as transcriptional regulation, protein synthesis or translation, and post-translational modifications. Identification of the RNA-interacting residues can provide insights into these processes and aid in relevant biotechnological manipulations. Owing to their eventual potential in combating diseases and industrial production, several computational attempts have been made over years using sequence- and structure-based information. Recent comparative studies suggest that despite these developments, many problems are faced with respect to the usability, prerequisites, and accessibility of various tools, thereby calling for an alternative approach and perspective supplementation in the prediction scenario. With this motivation, in this paper, we propose the use of a simple-yet-efficient conditional probabilistic approach based on the application of local occurrence of amino acids in the interacting region in a non-numeric sequence feature space, for discriminating between RNA interacting and non-interacting residues. The proposed method has been meticulously tested for robustness using a cross-estimation method showing MCC of 0.341 and F- measure of 66.84%. Upon exploring large scale applications using benchmark datasets available to date, this approach showed an encouraging performance comparable with the state-of-art. The software is available at https://github.com/ABCgrp/DORAEMON.

  17. Probing intramolecular interactions in arylselenides using a property descriptor based approach.

    PubMed

    Roy, Dipankar; Patel, Chandan; Liebman, Joel F; Sunoj, Raghavan B

    2008-09-18

    Although a large volume of experimental evidence is available on the existence of intramolecular nonbonding interactions between chalcogen atoms in main group organometallic compounds, the primary focus has been on the contact distances involving the chalcogen atoms. The important class of intramolecular Se...X (where X is O, S, N) nonbonding interaction in a series of organoselenium compounds is quantified using a new scheme based on a molecular property descriptor. In the present study, we have employed the nucleus-independent chemical shift [NICS(0)] values, as a property descriptor to evaluate the strength of exocyclic nonbonding interactions in a series of aryl selenides. The ab initio MP2 as well as density functional theory methods have been used in conjunction with Dunning's cc-pVDZ basis set. The quantified values of Se...X nonbonding interactions are compared with other schemes based on thermochemical equations such as homodesmic and ortho-para methods. The changes in NICS(0) values at the aryl ring center are found to be sensitive to the strength of exocyclic Se...X interaction.

  18. Biotin-Avidin Based Universal Cell-Matrix Interaction for Promoting Three-Dimensional Cell Adhesion.

    PubMed

    Dou, Xiao-Qiu; Zhang, Jia; Feng, Chuanliang

    2015-09-23

    To promote cell adhesion in three-dimensional (3D) extracellular matrix (ECM) is crucial for avoiding cell anoikis, which is one of the most important issues for fundamental cell biology. Herein, a biotin-avidin based universal cell-matrix interaction for different types of cells is developed in order to achieve the promoted adhesion in 3D ECM. For the purpose, biotinylated nanofibrous hydrogels are constructed by coassembling 1,4-benzyldicarboxamide (C2) based non-biotinylated and biotinylated supramolecular gelators. The used cells are modified by avidin (AV-cells) through biotinylating cells and then interacting with avidin. After in situ encapsulating AV-cells in the hydrogels, the adhered amount can be increased by tens of percent even with adding several percentages of the biotinylated C2 gelators in the coassembly due to the specific biotin-avidin interaction. Reverse transcription polymerase chain reaction (RT-PCR) confirms that AV-cells can proliferate without varying gene expression and denaturation. Compared with the interaction between RGD and cells, this avidin-biotin interaction should be much more universal and it is feasible to be employed to promote cell adhesion for most types of cells in 3D matrix.

  19. Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

    PubMed

    Zhang, Shu-Bo; Tang, Qiang-Rong

    2016-07-21

    Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most powerful indicators for protein interaction. However, conventional methods based on GO similarity fail to take advantage of the specificity of GO terms in the ontology graph. We proposed a GO-based method to predict protein-protein interaction by integrating different kinds of similarity measures derived from the intrinsic structure of GO graph. We extended five existing methods to derive the semantic similarity measures from the descending part of two GO terms in the GO graph, then adopted a feature integration strategy to combines both the ascending and the descending similarity scores derived from the three sub-ontologies to construct various kinds of features to characterize each protein pair. Support vector machines (SVM) were employed as discriminate classifiers, and five-fold cross validation experiments were conducted on both human and yeast protein-protein interaction datasets to evaluate the performance of different kinds of integrated features, the experimental results suggest the best performance of the feature that combines information from both the ascending and the descending parts of the three ontologies. Our method is appealing for effective prediction of protein-protein interaction.

  20. HEMORHEOLOGICAL IMPLICATIONS OF PERFLUOROCARBON BASED OXYGEN CARRIER INTERACTION WITH COLLOID PLASMA EXPANDERS AND BLOOD

    PubMed Central

    Vásquez, Diana M.; Ortiz, Daniel; Alvarez, Oscar A.; Briceño, Juan C.; Cabrales, Pedro

    2013-01-01

    Perfluorocarbon (PFC) emulsion based oxygen carriers lack colloid osmotic pressure (COP) and must be administered with colloid-based plasma expanders (PEs). Although PFC emulsions have been widely studied, there is limited information about PFC emulsion interaction with PEs and blood. Their interaction forms aggregates due to electrostatic and rheological phenomena, and change blood rheology and blood flow. This study analyzes the effects of the interaction between PFC emulsions with blood in the presence of clinically-used PEs. The rheological behavior of the mixtures was analyzed in parallel with in vivo analysis of blood flow in microvessels using intravital microscopy when administered in a clinically relevant scenario. The interaction between the PFC emulsion and PE with blood produced PFC droplets and red blood cell (RBCs) aggregation, and increased blood viscosity. The PFC droplets formed aggregates when mixed with PEs containing electrolytes, and the aggregation increased with the electrolyte concentration. Mixtures of PFC with PEs that produced PFC aggregates also induced RCBs aggregation when mixed with blood, increasing blood viscosity at low shear rates. The more viscous suspension at low shear rates produced a blunted blood flow velocity profile in vivo relative to non-aggregating mixtures of PFC and PEs. For the PEs evaluated, albumin produced minimal to undetectable aggregation. PFC and PEs interaction with blood can affect sections of the microcirculation with low shear rate (e.g. arterioles, venules, and pulmonary circulation) because aggregates could cause capillary occlusion, decrease perfusion, pulmonary emboli, or focal ischemia. PMID:23606592

  1. Nurturing Healthy Relationships through a Community-based Interactive Theater Program

    PubMed Central

    Fredland, Nina M.

    2010-01-01

    Promoting healthy relationships and preventing unhealthy behaviors, such as bullying and teen dating violence, among young adolescents was the goal of this study. This developmentally appropriate project used interactive theater to deliver a healthy message. Students in 7th grade health classes (N = 114) participated in the interactive theater intervention, a program that consisted of three consecutive performances and one follow-up day. This article reports on community-based research related to the development of a theater script in collaboration with a local theater group, the feasibility of using this innovative format as an intervention method, and lessons learned in collaborating with community partners. PMID:20437291

  2. Evaluating the Use of Computer-based Interactive Technology for Improving Outpatient Procedure Education

    PubMed Central

    Cowl, Clayton T.; Petersen, Bret T.; Smith, Glenn; Hauser, Stephen C.

    2002-01-01

    We randomly assigned 125 first-time elective colonoscopy or esophagoduodenoscopy patients to receive education about their procedure using the written format used currently or with computer-based interactive technology (CBT) with video animation. Using validated questionnaires, patient anxiety decreased (p<0.001) and satisfaction increased (p<0.05) in the CBT group. CBT patients were more willing to pay out-of-pocket for procedure education (p<0.05). Use of new interactive technologies to educate patients regarding procedures and providing informed consent might be applied successfully to other clinical endeavors.

  3. The interaction with tubulin of a series of stilbenes based on combretastatin A-4.

    PubMed Central

    Woods, J. A.; Hadfield, J. A.; Pettit, G. R.; Fox, B. W.; McGown, A. T.

    1995-01-01

    A series of stilbenes, based on combretastatin A-4, were synthesised. A structure-activity study was carried out to characterise the interaction of these agents with tubulin. The substitution of small alkyl substituents for the 4'-methoxy group of combretastatin A-4 and the loss of the 3'-hydroxyl group does not have a major effect on the interaction with tubulin. trans-Stilbenes were shown to bind tubulin, but do not inhibit microtubule assembly. This work, together with previous studies, has been used to propose an idealised structure for a tubulin-binding agent of this type. Images Figure 7 PMID:7710932

  4. Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes

    PubMed Central

    Luo, Jiawei; Qi, Yi

    2015-01-01

    Background Computational approaches aided by computer science have been used to predict essential proteins and are faster than expensive, time-consuming, laborious experimental approaches. However, the performance of such approaches is still poor, making practical applications of computational approaches difficult in some fields. Hence, the development of more suitable and efficient computing methods is necessary for identification of essential proteins. Method In this paper, we propose a new method for predicting essential proteins in a protein interaction network, local interaction density combined with protein complexes (LIDC), based on statistical analyses of essential proteins and protein complexes. First, we introduce a new local topological centrality, local interaction density (LID), of the yeast PPI network; second, we discuss a new integration strategy for multiple bioinformatics. The LIDC method was then developed through a combination of LID and protein complex information based on our new integration strategy. The purpose of LIDC is discovery of important features of essential proteins with their neighbors in real protein complexes, thereby improving the efficiency of identification. Results Experimental results based on three different PPI(protein-protein interaction) networks of Saccharomyces cerevisiae and Escherichia coli showed that LIDC outperformed classical topological centrality measures and some recent combinational methods. Moreover, when predicting MIPS datasets, the better improvement of performance obtained by LIDC is over all nine reference methods (i.e., DC, BC, NC, LID, PeC, CoEWC, WDC, ION, and UC). Conclusions LIDC is more effective for the prediction of essential proteins than other recently developed methods. PMID:26125187

  5. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.

    PubMed

    Kieslich, Chris A; Tamamis, Phanourios; Guzman, Yannis A; Onel, Melis; Floudas, Christodoulos A

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.

  6. Interactive Learning Environment: Web-based Virtual Hydrological Simulation System using Augmented and Immersive Reality

    NASA Astrophysics Data System (ADS)

    Demir, I.

    2014-12-01

    Recent developments in internet technologies make it possible to manage and visualize large data on the web. Novel visualization techniques and interactive user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The hydrological simulation system is a web-based 3D interactive learning environment for teaching hydrological processes and concepts. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create or load predefined scenarios, control environmental parameters, and evaluate environmental mitigation alternatives. The web-based simulation system provides an environment for students to learn about the hydrological processes (e.g. flooding and flood damage), and effects of development and human activity in the floodplain. The system utilizes latest web technologies and graphics processing unit (GPU) for water simulation and object collisions on the terrain. Users can access the system in three visualization modes including virtual reality, augmented reality, and immersive reality using heads-up display. The system provides various scenarios customized to fit the age and education level of various users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various visualization and interaction modes.

  7. InterRNA: a database of base interactions in RNA structures

    PubMed Central

    Appasamy, Sri Devan; Hamdani, Hazrina Yusof; Ramlan, Effirul Ikhwan; Firdaus-Raih, Mohd

    2016-01-01

    A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the database InterRNA (INTERactions in RNA structures database—http://mfrlab.org/interrna/) that contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM (http://mfrlab.org/grafss/nassam) and COGNAC (http://mfrlab.org/grafss/cognac) computer programs. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations. PMID:26553798

  8. Design and Implementation of an Interactive Web-Based Near Real-Time Forest Monitoring System

    PubMed Central

    Pratihast, Arun Kumar; DeVries, Ben; Avitabile, Valerio; de Bruin, Sytze; Herold, Martin; Bergsma, Aldo

    2016-01-01

    This paper describes an interactive web-based near real-time (NRT) forest monitoring system using four levels of geographic information services: 1) the acquisition of continuous data streams from satellite and community-based monitoring using mobile devices, 2) NRT forest disturbance detection based on satellite time-series, 3) presentation of forest disturbance data through a web-based application and social media and 4) interaction of the satellite based disturbance alerts with the end-user communities to enhance the collection of ground data. The system is developed using open source technologies and has been implemented together with local experts in the UNESCO Kafa Biosphere Reserve, Ethiopia. The results show that the system is able to provide easy access to information on forest change and considerably improves the collection and storage of ground observation by local experts. Social media leads to higher levels of user interaction and noticeably improves communication among stakeholders. Finally, an evaluation of the system confirms the usability of the system in Ethiopia. The implemented system can provide a foundation for an operational forest monitoring system at the national level for REDD+ MRV applications. PMID:27031694

  9. Interactive case-based learning improves resident knowledge and confidence in reproductive endocrinology and infertility().

    PubMed

    Goldman, Kara N; Tiegs, Ashley W; Uquillas, Kristen; Nachtigall, Margaret; Fino, M Elizabeth; Winkel, Abigail F; Lerner, Veronica

    2017-02-21

    Resident physicians' scores on the REI section of the CREOG exam are traditionally low, and nearly 40% of house staff nation-wide perceive their REI knowledge to be poor. We aimed to assess whether an interactive case-based group-learning curriculum would narrow the REI knowledge gap by improving understanding and retention of core REI concepts under the time constraints affecting residents. A three-hour case-based workshop was developed to address four primary CREOG objectives. A multiple-choice test was administered immediately before and after the intervention and 7 weeks post-workshop, to evaluate both knowledge and confidence. Following the intervention, residents self-reported increased confidence with counseling and treatment of PCOS, ovulation induction cycle monitoring, counseling and treatment of POI, and breaking bad news related to infertility (p < 0.05). The multiple-choice exam was re-administered 7 weeks post-intervention, and scores remained significantly improved compared to pre-workshop scores (p < 0.05). At that time, all residents either strongly agreed (91.7%) or agreed (8.3%) that the case-based interactive format was preferable to traditional lecture-based teaching. In conclusion, a nontraditional curriculum aimed at teaching core REI concepts to residents through interactive case-based learning can be successfully integrated into a residency curriculum, and significantly improves knowledge and confidence of critical concepts in REI.

  10. Design and Implementation of an Interactive Web-Based Near Real-Time Forest Monitoring System.

    PubMed

    Pratihast, Arun Kumar; DeVries, Ben; Avitabile, Valerio; de Bruin, Sytze; Herold, Martin; Bergsma, Aldo

    2016-01-01

    This paper describes an interactive web-based near real-time (NRT) forest monitoring system using four levels of geographic information services: 1) the acquisition of continuous data streams from satellite and community-based monitoring using mobile devices, 2) NRT forest disturbance detection based on satellite time-series, 3) presentation of forest disturbance data through a web-based application and social media and 4) interaction of the satellite based disturbance alerts with the end-user communities to enhance the collection of ground data. The system is developed using open source technologies and has been implemented together with local experts in the UNESCO Kafa Biosphere Reserve, Ethiopia. The results show that the system is able to provide easy access to information on forest change and considerably improves the collection and storage of ground observation by local experts. Social media leads to higher levels of user interaction and noticeably improves communication among stakeholders. Finally, an evaluation of the system confirms the usability of the system in Ethiopia. The implemented system can provide a foundation for an operational forest monitoring system at the national level for REDD+ MRV applications.

  11. Interactive Web-based Learning Modules Prior to General Medicine Advanced Pharmacy Practice Experiences

    PubMed Central

    Walton, Alison M.; Nisly, Sarah A.

    2015-01-01

    Objective. To implement and evaluate interactive web-based learning modules prior to advanced pharmacy practice experiences (APPEs) on inpatient general medicine. Design. Three clinical web-based learning modules were developed for use prior to APPEs in 4 health care systems. The aim of the interactive modules was to strengthen baseline clinical knowledge before the APPE to enable the application of learned material through the delivery of patient care. Assessment. For the primary endpoint, postassessment scores increased overall and for each individual module compared to preassessment scores. Postassessment scores were similar among the health care systems. The survey demonstrated positive student perceptions of this learning experience. Conclusion. Prior to inpatient general medicine APPEs, web-based learning enabled the standardization and assessment of baseline student knowledge across 4 health care systems. PMID:25995515

  12. Approaches to Interactive Video Anchors in Problem-based Science Learning

    NASA Astrophysics Data System (ADS)

    Kumar, David Devraj

    2010-02-01

    This paper is an invited adaptation of the IEEE Education Society Distinguished Lecture Approaches to Interactive Video Anchors in Problem-Based Science Learning. Interactive video anchors have a cognitive theory base, and they help to enlarge the context of learning with information-rich real-world situations. Carefully selected movie clips and custom-developed regular videos and virtual simulations have been successfully used as anchors in problem-based science learning. Examples discussed include a range of situations such as Indiana Jones tackling a trap, a teenager misrepresenting lead for gold, an agriculture inspection at the US border, counterintuitive events, analyzing a river ecosystem for pollution, and finding the cause of illness in a nineteenth century river city. Suggestions for teachers are provided.

  13. Application of web-based visualizations to interactive television: a practical approach

    NASA Astrophysics Data System (ADS)

    Chakaveh, Sepideh; Geuer, Olaf; Werning, Stefan; Borggrefe, Sorina; Haeger, Ralf

    2003-06-01

    In the near future interactive television will provide many entertaining and innovative broadcasting formats for TV viewers. Moreover through the recent advancements in web-based visualisation techniques, complex application scenarios can already be realised. With the aid of a demonstrator called "deinewahl02" we proved a challenging concept on how to import web-based applications onto more complex platforms such as MHP set-up boxes. "deinewahl02" which represents a pretend political TV debate of the German general elections 2002, gives one the possibilities to playfully & entertainly be guided into the programme. Using the various functionalities such as "Voting" or "Hotspots" the possibilities of interaction, are well demonstrated within the programme. This provides a two way communication channel which can be established instantly, between the viewer and the broadcaster. "deinewahl02" has successfully demonstrated, ways where web-based applications may quickly and cheaply be implemented onto much more complex platforms.

  14. Regulatory Interactions in ProKaryotes from RegTransBase

    DOE Data Explorer

    Dubchak, Inna; Gelfand, Mikhail

    RegTransBase, a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular: the activation or repression of transcription by an identified direct regulator determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA mapping or prediction of binding sites for a regulatory protein characterization of regulatory mutations. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species. (Specialized Interface)

  15. Testing gene-environment interactions in family-based association studies using trait-based ascertained samples

    PubMed Central

    Zhang, Weiming; Langefeld, Carl D.; Grunwald, Gary K.; Fingerlin, Tasha E.

    2014-01-01

    The study of gene-environment interactions is an increasingly important aspect of genetic epidemiological investigation. Historically, it has been difficult to study gene-environment interactions using a family-based design for quantitative traits or when parent-offspring trios were incomplete. The QBAT-I[1] provides researchers a tool to estimate and test for a gene-environment interaction in families of arbitrary structure that are sampled without regard to the phenotype of interest, but is vulnerable to inflated type I error if families are ascertained based on the phenotype. In this study, we verified the potential for type I error of the QBAT-I when applied to samples ascertained on a trait of interest. The magnitude of the inflation increases as the main genetic effect increases and as the ascertainment becomes more extreme. We propose an ascertainment-corrected score test that allows use of the QBAT-I to test for gene-environment interactions in ascertained samples. Our results indicate that the score test and an ad-hoc method we propose can often restore the nominal type I error rate, and in cases where complete restoration is not possible, dramatically reduce the inflation of the type I error rate in ascertained samples. PMID:23922213

  16. Interaction of Schiff base ligand with tin dioxide nanoparticles: optical studies.

    PubMed

    Rani, J Suvetha; Ramakrishnan, V

    2013-10-01

    Interaction between 1,4 Bis ((2-Methyl) thio) Phenylamino methyl benzene (BMTPMB) Schiff base with tin dioxide nanoparticles (SnO2 NPs) of various concentrations in methanol have been studied using UV-Visible and Fluorescence spectroscopic techniques. The low value of Stern-Volmer quenching constant and non-linear plot of Benesi-Hildebrand equation suggests the less affinity of SnO2 NPs towards the adsorption of BMTPMB Schiff base. The Scott equation has been employed to determine molar absorptivity of the Schiff base-NPs system.

  17. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions.

    PubMed

    Robertson, Neil O; Shah, Manan; Matthews, Jacqueline M

    2016-10-10

    We have developed Förster resonance energy transfer (FRET)-based experiments for measuring the binding affinity, off-rates, and inferred on-rates for interactions between a family of transcriptional regulators and their intrinsically disordered binding partners. It was difficult to evaluate these interactions previously, as the transcriptional regulators are obligate binding proteins that aggregate in the absence of a binding partner. The assays rely on fusion constructs where binding domains are linked by a flexible tether containing a specific protease site, with fluorescent proteins at either end that display FRET when the complex is formed. Loss of FRET is monitored after cutting the tether followed by dilution or competition with a non-fluorescent peptide. These methods allowed a wide range of binding affinities (10(-9) -10(-5)  m) to be determined. Our data indicate that interactions of closely related proteins can have surprisingly different binding properties.

  18. A walking prescription for statically-stable walkers based on walker/terrain interaction

    NASA Technical Reports Server (NTRS)

    Nagy, Peter V.; Whittaker, William L.; Desa, Subhas

    1992-01-01

    The walker/terrain interaction phenomena for the control of a statically stable walking machine are described. The algorithms, measures, and knowledge of walker/terrain interaction phenomena are then combined to form a prescription for how to walk on general terrain. This prescription consists of two parts: nominal control and reactive control. The function of nominal control is the evaluation and execution of planned motions, based on predicted foot force redistributions, to achieve reliable locomotion. The function of reactive control is the monitoring of walker/terrain interaction in real-time to detect anomalous conditions and then respond with the appropriate reflexive actions. Simulations and experiments have been used to test and verify various aspects of the walking prescription.

  19. Counter-selectable marker for bacterial-based interaction trap systems.

    PubMed

    Meng, Xiangdong; Smith, Robin M; Giesecke, Astrid V; Joung, J Keith; Wolfe, Scot A

    2006-02-01

    Counter-selectable markers can be used in two-hybrid systems to search libraries for a protein or compound that interferes with a macromolecular interaction or to identify macromolecules from a population that cannot mediate a particular interaction. In this report, we describe the adaptation of the yeast URA3/5-FOA counter-selection system for use in bacterial interaction trap experiments. Two different URA3 reporter systems were developed that allow robust counter-selection: (i) a single copy F' episome reporter and (ii) a co-cistronic HIS3-URA3 reporter vector. The HIS3-URA3 reporter can be used for either positive or negative selections in appropriate bacterial strains. These reagents extend the utility of the bacterial two-hybrid system as an alternative to its yeast-based counterpart.

  20. The influence of arene-ring size on stacking interaction with canonical base pairs

    NASA Astrophysics Data System (ADS)

    Formánek, Martin; Burda, Jaroslav V.

    2014-04-01

    Stacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson-Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking interaction increases with the size of π-conjugation system. Its extent is in agreement with experimental finding on anticancer activity of Ru(II) piano-stool complexes where intercalation of these aromatic molecules should play an important role. The explored structures are considered as ternary system so that decomposition of the interaction energy to pairwise and non-additivity contributions is also examined.

  1. Intriguing radical-radical interactions among double-electron oxidized adenine-thymine base pairs

    NASA Astrophysics Data System (ADS)

    Wang, Mei; Zhao, Jing; Zhang, Laibin; Su, Xiyu; Su, Hanlei; Bu, Yuxiang

    2015-01-01

    We present a theoretical investigation of the structural and electronic properties of double-electron oxidized adenine-thymine base pair as well as its deprotonated Watson-Crick derivatives. Double-electron oxidation can destabilize the AT unit, leading to a barrier-hindered metastable A+T+ state with a dissociation channel featuring negative dissociation energy. This unusual energetic phenomenon originates from the competition of electrostatic repulsion and attractively hydrogen-bonding interaction co-existing between Arad + and Trad +. The associated double-proton-transfer process is also explored, suggesting a possible two-step mechanism. Magnetic coupling interactions of various diradical structures are controlled by both intra- and inter-molecular interactions.

  2. Interactive point-based rendering of higher-order tetrahedral data.

    PubMed

    Zhou, Yuan; Garland, Michael

    2006-01-01

    Computational simulations frequently generate solutions defined over very large tetrahedral volume meshes containing many millions of elements. Furthermore, such solutions may often be expressed using non-linear basis functions. Certain solution techniques, such as discontinuous Galerkin methods, may even produce non-conforming meshes. Such data is difficult to visualize interactively, as it is far too large to fit in memory and many common data reduction techniques, such as mesh simplification, cannot be applied to non-conforming meshes. We introduce a point-based visualization system for interactive rendering of large, potentially non-conforming, tetrahedral meshes. We propose methods for adaptively sampling points from non-linear solution data and for decimating points at run time to fit GPU memory limits. Because these are streaming processes, memory consumption is independent of the input size. We also present an order-independent point rendering method that can efficiently render volumes on the order of 20 million tetrahedra at interactive rates.

  3. A non-verbal Turing test: differentiating mind from machine in gaze-based social interaction.

    PubMed

    Pfeiffer, Ulrich J; Timmermans, Bert; Bente, Gary; Vogeley, Kai; Schilbach, Leonhard

    2011-01-01

    In social interaction, gaze behavior provides important signals that have a significant impact on our perception of others. Previous investigations, however, have relied on paradigms in which participants are passive observers of other persons' gazes and do not adjust their gaze behavior as is the case in real-life social encounters. We used an interactive eye-tracking paradigm that allows participants to interact with an anthropomorphic virtual character whose gaze behavior is responsive to where the participant looks on the stimulus screen in real time. The character's gaze reactions were systematically varied along a continuum from a maximal probability of gaze aversion to a maximal probability of gaze-following during brief interactions, thereby varying contingency and congruency of the reactions. We investigated how these variations influenced whether participants believed that the character was controlled by another person (i.e., a confederate) or a computer program. In a series of experiments, the human confederate was either introduced as naïve to the task, cooperative, or competitive. Results demonstrate that the ascription of humanness increases with higher congruency of gaze reactions when participants are interacting with a naïve partner. In contrast, humanness ascription is driven by the degree of contingency irrespective of congruency when the confederate was introduced as cooperative. Conversely, during interaction with a competitive confederate, judgments were neither based on congruency nor on contingency. These results offer important insights into what renders the experience of an interaction truly social: Humans appear to have a default expectation of reciprocation that can be influenced drastically by the presumed disposition of the interactor to either cooperate or compete.

  4. Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins

    PubMed Central

    Ielasi, Francesco S.; Alioscha-Perez, Mitchel; Donohue, Dagmara; Claes, Sandra; Sahli, Hichem; Schols, Dominique

    2016-01-01

    ABSTRACT The first step in the infection of humans by microbial pathogens is their adherence to host tissue cells, which is frequently based on the binding of carbohydrate-binding proteins (lectin-like adhesins) to human cell receptors that expose glycans. In only a few cases have the human receptors of pathogenic adhesins been described. A novel strategy—based on the construction of a lectin-glycan interaction (LGI) network—to identify the potential human binding receptors for pathogenic adhesins with lectin activity was developed. The new approach is based on linking glycan array screening results of these adhesins to a human glycoprotein database via the construction of an LGI network. This strategy was used to detect human receptors for virulent Escherichia coli (FimH adhesin), and the fungal pathogens Candida albicans (Als1p and Als3p adhesins) and C. glabrata (Epa1, Epa6, and Epa7 adhesins), which cause candidiasis. This LGI network strategy allows the profiling of potential adhesin binding receptors in the host with prioritization, based on experimental binding data, of the most relevant interactions. New potential targets for the selected adhesins were predicted and experimentally confirmed. This methodology was also used to predict lectin interactions with envelope glycoproteins of human-pathogenic viruses. It was shown that this strategy was successful in revealing that the FimH adhesin has anti-HIV activity. PMID:27406561

  5. Evaluating hydro-mechanical interactions of adjacent clay-based sealing materials

    NASA Astrophysics Data System (ADS)

    Kim, C.-S.; Dixon, D.

    Canada’s Nuclear Waste Management Organization (NWMO) is investigating various geological isolation concepts for Canada’s used reactor fuel (NWMO, 2005). These options are all based on the concept of multiple barriers that include Highly Compacted Bentonite (HCB), Dense Backfill (DBF), Light Backfill (LBF), and Gap Fill (GF). The hydraulic, mechanical, and other characteristics of these clay-based sealing materials have been examined previously, but typically in relative isolation (e.g., Dixon, 1999; Blatz, 2000; Siemens, 2006; Stroes-Gascoyne et al., 2006; Baumgartner et al., 2007). Information on how these clay-based sealing materials interact with each other is needed to understand the evolution and performance of the overall sealing system. A total of twenty-three (23) tests that examine the physical interaction of physically dissimilar clay-based sealing materials were installed and monitored at Atomic Energy of Canada Limited’s (AECL) geotechnical laboratory. This paper describes the process of water uptake, interaction between the components installed, and the role of groundwater salinity on water uptake as interpreted from these tests.

  6. Teacher-student interaction: The overlooked dimension of inquiry-based professional development

    NASA Astrophysics Data System (ADS)

    de Oliveira, Alandeom Wanderlei

    This study explores the teacher-student interactional dimension of inquiry-based science instruction. In it, microethnographic and grounded theory analyses are conducted in order to assess the impact of a professional development program designed to enhance in-service elementary teachers' interactional views (i.e., their understandings of inquiry-based social roles and relationships) and discursive practices (i.e., teachers' abilities to interact with student engaged in classroom inquiries) through a combination of expert instruction, immersion in scientific inquiry, and collaborative analysis of video-recorded classroom discourse. A sociolinguistic theoretical perspective on language use is adopted, viewing classroom discourse as comprising multiple linguistic signs (questions, responses, personal pronouns, hedges, backchannels, reactive tokens, directives, figures of speech, parallel repetitions) that convey not only semantic meanings (the literal information being exchanged) but also pragmatic meanings (information about teachers and students' social roles and relationships). A grounded theory analysis of the professional development activities uncovered a gradual shift in teachers' interactional views from a cognitive, monofunctional and decontextualized perspective to a social, multifunctional and contextualized conception of inquiry-based discourse. Furthermore, teachers developed increased levels of pragmatic awareness, being able to recognize the authoritative interactional functions served by discursive moves such as display questions, cued elicitation, convergent questioning, verbal cloze, affirmation, explicit evaluations of students' responses, verbatim repetitions, IRE triplets, IR couplets, second-person pronouns, "I/you" contrastive pairs, and direct or impolite directives. A comparative microethnographic analysis of teachers' classroom practices revealed that after participating in the program teachers demonstrated an improved ability to share

  7. Do aurophilic interactions compete against hydrogen bonds? Experimental evidence and rationalization based on ab initio calculations.

    PubMed

    Codina, Antonio; Fernández, Eduardo J; Jones, Peter G; Laguna, Antonio; López-De-Luzuriaga, José M; Monge, Miguel; Olmos, M Elena; Pérez, Javier; Rodríguez, Miguel A

    2002-06-12

    [M(C6F5)(N(H)=CPh2)] (M = Ag (1) and Au (2)) complexes have been synthesized and characterized by X-ray diffraction analysis. Complex 1 shows a ladder-type structure in which two [Ag(C6F5)(N(H)=CPh2)] units are linked by a Ag(I)-Ag(I) interaction in an antiparallel disposition. The dimeric units are associated through hydrogen bonds of the type N-H...F(ortho). On the other hand, gold(I) complex 2 displays discrete dimers also in an antiparallel conformation in which both Au(I)-Au(I) interactions and N-H.F(ortho) hydrogen bonds appear within the dimeric units. The features of these coexisting interactions have been theoretically studied by ab initio calculations based on four different model systems in order to analyze them separately. The interactions have been analyzed at HF and MP2 levels of theory showing that, in this case, even at larger distances. The Au(I)-Au(I) interaction is stronger than Ag(I)-Ag(I) and that N-H.F hydrogen bonding and Au(I)-Au(I) contacts have a similar strength in the same molecule, which permits a competition between these two structural motifs giving rise to different structural arrangements.

  8. A physiologically based pharmacokinetic model linking plasma protein binding interactions with drug disposition.

    PubMed

    Buur, J L; Baynes, R E; Smith, G W; Riviere, J E

    2009-04-01

    Combination drug therapy increases the chance for an adverse drug reactions due to drug-drug interactions. Altered disposition for sulfamethazine (SMZ) when concurrently administered with flunixin meglumine (FLU) in swine could lead to increased tissue residues. There is a need for a pharmacokinetic modeling technique that can predict the consequences of possible drug interactions. A physiologically based pharmacokinetic model was developed that links plasma protein binding interactions to drug disposition for SMZ and FLU in swine. The model predicted a sustained decrease in total drug and a temporary increase in free drug concentration. An in vivo study confirmed the presence of a drug interaction. Neither the model nor the in vivo study revealed clinically significant changes that alter tissue disposition. This novel linkage approach has use in the prediction of the clinical impact of plasma protein binding interactions. Ultimately it could be used in the design of dosing regimens and in the protection of the food supply through prediction and minimization of tissue residues.

  9. Commercial Motion Sensor Based Low-Cost and Convenient Interactive Treadmill †

    PubMed Central

    Kim, Jonghyun; Gravunder, Andrew; Park, Hyung-Soon

    2015-01-01

    Interactive treadmills were developed to improve the simulation of overground walking when compared to conventional treadmills. However, currently available interactive treadmills are expensive and inconvenient, which limits their use. We propose a low-cost and convenient version of the interactive treadmill that does not require expensive equipment and a complicated setup. As a substitute for high-cost sensors, such as motion capture systems, a low-cost motion sensor was used to recognize the subject’s intention for speed changing. Moreover, the sensor enables the subject to make a convenient and safe stop using gesture recognition. For further cost reduction, the novel interactive treadmill was based on an inexpensive treadmill platform and a novel high-level speed control scheme was applied to maximize performance for simulating overground walking. Pilot tests with ten healthy subjects were conducted and results demonstrated that the proposed treadmill achieves similar performance to a typical, costly, interactive treadmill that contains a motion capture system and an instrumented treadmill, while providing a convenient and safe method for stopping. PMID:26393592

  10. ESI-MS Characterization of a Novel Pyrrole-Inosine Nucleoside that Interacts with Guanine Bases

    PubMed Central

    Pierce, Sarah E.; Sherman, Courtney L.; Jayawickramarajah, Janarthanan; Lawrence, Candace M.; Sessler, Jonathan L.; Brodbelt, Jennifer S.

    2008-01-01

    Based on binding studies undertaken by electrospray ionization-mass spectrometry, a synthetic pyrrole-inosine nucleoside, 1, capable of forming an extended three-point Hoogsteen-type hydrogen-bonding interaction with guanine, is shown to form specific complexes with two different quadruplex DNA structures [dTG4T]4 and d(T2G4)4 as well as guanine rich duplex DNA. The binding interactions of two other analogs were evaluated in order to unravel the structural features that contribute to specific DNA recognition. The importance of the Hoogsteen interactions was confirmed through the absence of specific binding when the pyrrole NH hydrogen-bonding site was blocked or removed. While 2, with a large blocking group, was not found to interact with virtually any form of DNA, 3, with the pyrrole functionality missing, was found to interact non-specifically with several types of DNA. The specific binding of 1 to guanine rich DNA emphasizes the necessity of careful ligand design for specific sequence recognition. PMID:18790136

  11. Commercial Motion Sensor Based Low-Cost and Convenient Interactive Treadmill.

    PubMed

    Kim, Jonghyun; Gravunder, Andrew; Park, Hyung-Soon

    2015-09-17

    Interactive treadmills were developed to improve the simulation of overground walking when compared to conventional treadmills. However, currently available interactive treadmills are expensive and inconvenient, which limits their use. We propose a low-cost and convenient version of the interactive treadmill that does not require expensive equipment and a complicated setup. As a substitute for high-cost sensors, such as motion capture systems, a low-cost motion sensor was used to recognize the subject's intention for speed changing. Moreover, the sensor enables the subject to make a convenient and safe stop using gesture recognition. For further cost reduction, the novel interactive treadmill was based on an inexpensive treadmill platform and a novel high-level speed control scheme was applied to maximize performance for simulating overground walking. Pilot tests with ten healthy subjects were conducted and results demonstrated that the proposed treadmill achieves similar performance to a typical, costly, interactive treadmill that contains a motion capture system and an instrumented treadmill, while providing a convenient and safe method for stopping.

  12. A novel microfluidics-based method for probing weak protein-protein interactions.

    PubMed

    Tan, Darren Cherng-wen; Wijaya, I Putu Mahendra; Andreasson-Ochsner, Mirjam; Vasina, Elena Nikolaevna; Nallani, Madhavan; Hunziker, Walter; Sinner, Eva-Kathrin

    2012-08-07

    We report the use of a novel microfluidics-based method to detect weak protein-protein interactions between membrane proteins. The tight junction protein, claudin-2, synthesised in vitro using a cell-free expression system in the presence of polymer vesicles as membrane scaffolds, was used as a model membrane protein. Individual claudin-2 molecules interact weakly, although the cumulative effect of these interactions is significant. This effect results in a transient decrease of average vesicle dispersivity and reduction in transport speed of claudin-2-functionalised vesicles. Polymer vesicles functionalised with claudin-2 were perfused through a microfluidic channel and the time taken to traverse a defined distance within the channel was measured. Functionalised vesicles took 1.19 to 1.69 times longer to traverse this distance than unfunctionalised ones. Coating the channel walls with protein A and incubating the vesicles with anti-claudin-2 antibodies prior to perfusion resulted in the functionalised vesicles taking 1.75 to 2.5 times longer to traverse this distance compared to the controls. The data show that our system is able to detect weak as well as strong protein-protein interactions. This system offers researchers a portable, easily operated and customizable platform for the study of weak protein-protein interactions, particularly between membrane proteins.

  13. A New Protein-Protein Interaction Sensor Based on Tripartite Split-GFP Association

    PubMed Central

    Cabantous, Stéphanie; Nguyen, Hau B.; Pedelacq, Jean-Denis; Koraïchi, Faten; Chaudhary, Anu; Ganguly, Kumkum; Lockard, Meghan A.; Favre, Gilles; Terwilliger, Thomas C.; Waldo, Geoffrey S.

    2013-01-01

    Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence. PMID:24092409

  14. A new protein-protein interaction sensor based on tripartite split-GFP association.

    PubMed

    Cabantous, Stéphanie; Nguyen, Hau B; Pedelacq, Jean-Denis; Koraïchi, Faten; Chaudhary, Anu; Ganguly, Kumkum; Lockard, Meghan A; Favre, Gilles; Terwilliger, Thomas C; Waldo, Geoffrey S

    2013-10-04

    Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.

  15. Platoon Interactions and Real-World Traffic Simulation and Validation Based on the LWR-IM.

    PubMed

    Ng, Kok Mun; Reaz, Mamun Bin Ibne

    2016-01-01

    Platoon based traffic flow models form the underlying theoretical framework in traffic simulation tools. They are essentially important in facilitating efficient performance calculation and evaluation in urban traffic networks. For this purpose, a new platoon-based macroscopic model called the LWR-IM has been developed in [1]. Preliminary analytical validation conducted previously has proven the feasibility of the model. In this paper, the LWR-IM is further enhanced with algorithms that describe platoon interactions in urban arterials. The LWR-IM and the proposed platoon interaction algorithms are implemented in the real-world class I and class II urban arterials. Another purpose of the work is to perform quantitative validation to investigate the validity and ability of the LWR-IM and its underlying algorithms to describe platoon interactions and simulate performance indices that closely resemble the real traffic situations. The quantitative validation of the LWR-IM is achieved by performing a two-sampled t-test on queues simulated by the LWR-IM and real queues observed at these real-world locations. The results reveal insignificant differences of simulated queues with real queues where the p-values produced concluded that the null hypothesis cannot be rejected. Thus, the quantitative validation further proved the validity of the LWR-IM and the embedded platoon interactions algorithm for the intended purpose.

  16. A Course-based Cross-Cultural Interaction among Pharmacy Students in Qatar and Canada

    PubMed Central

    Taylor, Jeff; Khalifa, Sherief I.; Jorgenson, Derek

    2015-01-01

    Objective. To develop, implement, and evaluate a course-based, cross-cultural student interaction using real-time videoconferencing between universities in Canada and Qatar. Design. A professional skills simulation practice session on smoking cessation was run for students in Qatar (n=22) and Canada (n=22). Students role played cases in small group situations and then interacted with colleagues from the other country regarding culturally challenging situations and communication strategies. Assessment. Students were assessed on analytical content and communication skills through faculty member and peer evaluation. Cultural competency outcomes were assessed using a postsession survey. Overall, 92.3% of respondents agreed that learning was enhanced through the cross-cultural exchange, and 94.9% agreed that insight was gained into the health-related issues and needs of people from another culture. Conclusion. A course-based, cross-cultural interaction was an effective method to incorporate cultural competency principles into student learning. Future initiatives should increase direct student interaction and focus on culturally sensitive topics. PMID:25861107

  17. Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

    PubMed

    Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

    2006-05-18

    On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

  18. Platoon Interactions and Real-World Traffic Simulation and Validation Based on the LWR-IM

    PubMed Central

    Ng, Kok Mun; Reaz, Mamun Bin Ibne

    2016-01-01

    Platoon based traffic flow models form the underlying theoretical framework in traffic simulation tools. They are essentially important in facilitating efficient performance calculation and evaluation in urban traffic networks. For this purpose, a new platoon-based macroscopic model called the LWR-IM has been developed in [1]. Preliminary analytical validation conducted previously has proven the feasibility of the model. In this paper, the LWR-IM is further enhanced with algorithms that describe platoon interactions in urban arterials. The LWR-IM and the proposed platoon interaction algorithms are implemented in the real-world class I and class II urban arterials. Another purpose of the work is to perform quantitative validation to investigate the validity and ability of the LWR-IM and its underlying algorithms to describe platoon interactions and simulate performance indices that closely resemble the real traffic situations. The quantitative validation of the LWR-IM is achieved by performing a two-sampled t-test on queues simulated by the LWR-IM and real queues observed at these real-world locations. The results reveal insignificant differences of simulated queues with real queues where the p-values produced concluded that the null hypothesis cannot be rejected. Thus, the quantitative validation further proved the validity of the LWR-IM and the embedded platoon interactions algorithm for the intended purpose. PMID:26731745

  19. Noncovalent interactions from electron density topology and solvent effects on spectral properties of Schiff bases

    NASA Astrophysics Data System (ADS)

    Gandhimathi, S.; Balakrishnan, C.; Theetharappan, M.; Neelakantan, M. A.; Venkataraman, R.

    2017-03-01

    Two Schiff bases were prepared by the condensation of o-allyl substituted 2,4-dihydroxy acetophenone with 1,2-diaminopropane (L1) and ethanediamine (L2) and characterized by elemental analysis, and ESI-MS, IR, UV-Vis, 1H and 13C NMR spectral techniques. The effect of solvents with respect to different polarities on UV-Vis and emission spectra of L1 and L2 was investigated at room temperature show that the compounds exist in keto and enol forms in solution and may be attributed to the intramolecular proton transfer in the ground state. The solute-solvent interactions, change in dipole moment and solvatochromic properties of the compounds were studied based on the solvent polarity parameters. For L1 and L2, the ground and excited state electronic structure calculations were carried out by DFT and TD-DFT at B3LYP/6-311G (d,p) level, respectively. The IR, NMR and electronic absorption spectra computed were compared with the experimental observations. The intramolecular charge transfer within the molecule is evidenced from the HOMO and LUMO energy levels and surface analysis. The noncovalent interactions like hydrogen bonding and van der Waals interactions were identified from the molecular geometry and electron localization function. These interactions in molecules have been studied by using reduced density gradient and graphed by Multiwfn.

  20. Noncovalent interactions from electron density topology and solvent effects on spectral properties of Schiff bases.

    PubMed

    Gandhimathi, S; Balakrishnan, C; Theetharappan, M; Neelakantan, M A; Venkataraman, R

    2017-03-15

    Two Schiff bases were prepared by the condensation of o-allyl substituted 2,4-dihydroxy acetophenone with 1,2-diaminopropane (L1) and ethanediamine (L2) and characterized by elemental analysis, and ESI-MS, IR, UV-Vis, (1)H and (13)C NMR spectral techniques. The effect of solvents with respect to different polarities on UV-Vis and emission spectra of L1 and L2 was investigated at room temperature show that the compounds exist in keto and enol forms in solution and may be attributed to the intramolecular proton transfer in the ground state. The solute-solvent interactions, change in dipole moment and solvatochromic properties of the compounds were studied based on the solvent polarity parameters. For L1 and L2, the ground and excited state electronic structure calculations were carried out by DFT and TD-DFT at B3LYP/6-311G (d,p) level, respectively. The IR, NMR and electronic absorption spectra computed were compared with the experimental observations. The intramolecular charge transfer within the molecule is evidenced from the HOMO and LUMO energy levels and surface analysis. The noncovalent interactions like hydrogen bonding and van der Waals interactions were identified from the molecular geometry and electron localization function. These interactions in molecules have been studied by using reduced density gradient and graphed by Multiwfn.

  1. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of the double helix

    PubMed Central

    He, Yi; Maciejczyk, Maciej; Ołdziej, Stanisław; Scheraga, Harold A.; Liwo, Adam

    2013-01-01

    A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and excluded-volume interactions, are sufficient to form double-helical structures of DNA and RNA molecules. Additionally, local interactions determine helix handedness and direction of strand packing. This result, and earlier research on reduced protein models, suggest that mean-field multipole-multipole interactions are the principal factors responsible for the formation of regular structure of biomolecules. PMID:23496746

  2. Evaluation of an interactive, case-based review session in teaching medical microbiology

    PubMed Central

    Blewett, Earl L; Kisamore, Jennifer L

    2009-01-01

    Background Oklahoma State University-Center for Health Sciences (OSU-CHS) has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial. Methods Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session. Results Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session. Conclusion The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified. PMID:19712473

  3. Synthesis of bio-based aldehyde from seaweed polysaccharide and its interaction with bovine serum albumin.

    PubMed

    Kholiya, Faisal; Chaudhary, Jai Prakash; Vadodariya, Nilesh; Meena, Ramavatar

    2016-10-05

    Here, we demonstrate a successful synthesis of bio-based aldehyde namely dialdehyde-carboxymethylagarose (DCMA) using carboxymethyagarose (CMA). Further reaction parameters (i.e. reaction temperature, pH and periodate concentration) were optimized to achieve maximum aldehyde content and product yield. The synthesis of DCMA was confirmed by employing FTIR, (1)H NMR, XRD, SEM, AFM, TGA, DSC, EA and GPC techniques. To investigate the aldehyde functionality, DCMA was allowed to interact with BSA and obtained results were found to be comparable with that of synthetic aldehyde (Formaldehyde). Further interaction of DCMA with BSA was confirmed by using UV-vis, FTIR, fluorescent spectroscopy, CD and DLS analysis. Results of this study revealed that bio-based aldehyde behaves like formaldehyde. This study adds value to abundant marine biopolymers and opens the new research area for polymer researchers.

  4. Fuzzy Neural Network-Based Interacting Multiple Model for Multi-Node Target Tracking Algorithm

    PubMed Central

    Sun, Baoliang; Jiang, Chunlan; Li, Ming

    2016-01-01

    An interacting multiple model for multi-node target tracking algorithm was proposed based on a fuzzy neural network (FNN) to solve the multi-node target tracking problem of wireless sensor networks (WSNs). Measured error variance was adaptively adjusted during the multiple model interacting output stage using the difference between the theoretical and estimated values of the measured error covariance matrix. The FNN fusion system was established during multi-node fusion to integrate with the target state estimated data from different nodes and consequently obtain network target state estimation. The feasibility of the algorithm was verified based on a network of nine detection nodes. Experimental results indicated that the proposed algorithm could trace the maneuvering target effectively under sensor failure and unknown system measurement errors. The proposed algorithm exhibited great practicability in the multi-node target tracking of WSNs. PMID:27809271

  5. Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases.

    PubMed

    Priyakumar, U Deva; Hyeon, Changbong; Thirumalai, D; Mackerell, Alexander D

    2009-12-16

    Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to elucidate in atomic detail the destabilization mechanism of folded RNA in aqueous urea solutions. Urea denatures RNA by forming multiple hydrogen bonds with the RNA bases and has little influence on the phosphodiester backbone. Most significantly we discovered that urea engages in stacking interactions with the bases. We also estimate, for the first time, the m-value for RNA, which is a measure of the strength of urea-RNA interactions. Our work provides a conceptual understanding of the mechanism by which urea enhances RNA folding rates.

  6. Histidine-Based Lipopeptides Enhance Cleavage of Nucleic Acids: Interactions with DNA and Hydrolytic Properties.

    PubMed

    Bélières, M; Déjugnat, C; Chouini-Lalanne, N

    2015-12-16

    Interaction studies and cleavage activity experiments were carried out between plasmid DNA and a series of histidine-based lipopeptides. Specific fluorescent probes (ethidium bromide, Hoechst 33342, and pyrene) were used to monitor intercalation, minor groove binding, and self-assembly of lipopeptides, respectively. Association between DNA and lipopeptides was thus evidenced, highlighting the importance of both histidine and hydrophobic tail in the interaction process. DNA cleavage in the presence of lipopeptides was then detected by gel electrophoresis and quantified, showing the importance of histidine and the involvement of its side-chain imidazole in the hydrolysis mechanism. These systems could then be developed as synthetic nucleases while raising concern of introducing histidine in the design of lipopeptide-based transfection vectors.

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

    PubMed

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

    2013-11-01

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

  8. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    SciTech Connect

    Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2015-09-25

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  9. Digital Control of Exchange Interaction in a Spin-based Silicon Quantum Computer

    DTIC Science & Technology

    2013-05-19

    investigate dc and ac properties of single and double vertical Si quantum dots with 3D confinement. The dots constitute the main building blocks of a...quantum computing, quantyum dots, Majorana fermions Leonid P. Rokhinson, James C. Sturm Indiana University - Purdue University Fort Wayne Sponsored Programs...of Exchange Interaction in a Spin-based Silicon Quantum Computer Report Title ABSTRACT We propose to investigate dc and ac properties of single and

  10. An examination of social interaction profiles based on the factors measured by the screen for social interaction.

    PubMed

    Mahoney, Emery B; Breitborde, Nicholas J K; Leone, Sarah L; Ghuman, Jaswinder Kaur

    2014-10-01

    Deficits in the capacity to engage in social interactions are a core deficit associated with Autistic Disorder (AD) and Pervasive Developmental Disorder-Not Otherwise Specified (PDD-NOS). These deficits emerge at a young age, making screening for social interaction deficits and interventions targeted at improving capacity in this area important for early identification and intervention. Screening and early intervention efforts are particularly important given the poor short and long term outcomes for children with Autism Spectrum Disorders (ASDs) who experience social interaction deficits. The Screen for Social Interaction (SSI) is a well-validated screening measure that examines a child's capacity for social interaction using a developmental approach. The present study identified four underlying factors measured by the SSI, namely, Connection with Caregiver, Interaction/Imagination, Social Approach/Interest, and Agreeable Nature. The resulting factors were utilized to compare social interaction profiles across groups of children with AD, PDD-NOS, children with non-ASD developmental and/or psychiatric conditions and typically developing children. The results indicate that children with AD and those with PDD-NOS had similar social interaction profiles, but were able to be distinguished from typically developing children on every factor and were able to be distinguished from children with non-ASD psychiatric conditions on every factor except the Connection with Caregiver factor. In addition, children with non-ASD developmental and/or psychiatric conditions could be distinguished from typically developing children on the Connection with Caregiver factor and the Social Approach/Interest factor. These findings have implications for screening and intervention for children with ASDs and non-ASD psychiatric conditions.

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

    PubMed Central

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

    2016-01-01

    Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects of variants across the genome, it is believed that gene-gene interactions can help elucidate part of the missing heritability by allowing for the test of interactions between genetic variants to mimic the complex nature of biology. To explain the etiology of glaucoma, we first performed a genome-wide association study (GWAS) on glaucoma case-control samples obtained from electronic medical records (EMR) to establish the utility of EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype. Our findings from GWAS suggest consistent evidence of several known associations in POAG. We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value <0.01) and observed interesting findings in the electronic MEdical Records and GEnomics Network (eMERGE) network dataset. Genes from the top epistatic interactions from eMERGE data (Likelihood Ratio Test i.e. LRT p-value <1e-05) were then tested for replication in the NEIGHBOR consortium dataset. To replicate our findings, we performed a gene-based SNP-SNP interaction analysis in NEIGHBOR and observed significant gene-gene interactions (p-value <0.001) among the top 17 gene-gene models identified in the discovery phase. Variants from gene-gene interaction analysis that we found to be associated with POAG explain 3.5% of additional genetic variance in eMERGE dataset above what is explained by the SNPs in genes that are replicated from previous GWAS studies (which

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

    PubMed

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

    2016-09-01

    Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects of variants across the genome, it is believed that gene-gene interactions can help elucidate part of the missing heritability by allowing for the test of interactions between genetic variants to mimic the complex nature of biology. To explain the etiology of glaucoma, we first performed a genome-wide association study (GWAS) on glaucoma case-control samples obtained from electronic medical records (EMR) to establish the utility of EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype. Our findings from GWAS suggest consistent evidence of several known associations in POAG. We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value <0.01) and observed interesting findings in the electronic MEdical Records and GEnomics Network (eMERGE) network dataset. Genes from the top epistatic interactions from eMERGE data (Likelihood Ratio Test i.e. LRT p-value <1e-05) were then tested for replication in the NEIGHBOR consortium dataset. To replicate our findings, we performed a gene-based SNP-SNP interaction analysis in NEIGHBOR and observed significant gene-gene interactions (p-value <0.001) among the top 17 gene-gene models identified in the discovery phase. Variants from gene-gene interaction analysis that we found to be associated with POAG explain 3.5% of additional genetic variance in eMERGE dataset above what is explained by the SNPs in genes that are replicated from previous GWAS studies (which

  13. iHand: an interactive bare-hand-based augmented reality interface on commercial mobile phones

    NASA Astrophysics Data System (ADS)

    Choi, Junyeong; Park, Jungsik; Park, Hanhoon; Park, Jong-Il

    2013-02-01

    The performance of mobile phones has rapidly improved, and they are emerging as a powerful platform. In many vision-based applications, human hands play a key role in natural interaction. However, relatively little attention has been paid to the interaction between human hands and the mobile phone. Thus, we propose a vision- and hand gesture-based interface in which the user holds a mobile phone in one hand but sees the other hand's palm through a built-in camera. The virtual contents are faithfully rendered on the user's palm through palm pose estimation, and reaction with hand and finger movements is achieved that is recognized by hand shape recognition. Since the proposed interface is based on hand gestures familiar to humans and does not require any additional sensors or markers, the user can freely interact with virtual contents anytime and anywhere without any training. We demonstrate that the proposed interface works at over 15 fps on a commercial mobile phone with a 1.2-GHz dual core processor and 1 GB RAM.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Information-based or resource-based systems may mediate Cycas-herbivore interactions.

    PubMed

    Marler, Thomas E; Lindström, Anders; Terry, L Irene

    2012-07-01

    Invasive arthropod herbivores comprise one of the greatest threats to cycad conservation both in situ and ex situ. We discuss two mechanisms, not necessarily mutually exclusive, that may underlie the disparity in Chilades pandava damage among Cycas species. In an information-based system, plant infochemicals may differentially influence oviposition behavior of Ch. pandava adults or host finding behavior of this butterfly's natural enemies. Alternatively, heterogeneity in damage may be mediated by a resource-based system whereby plant substrate is more palatable to larvae for susceptible species or more defended by less damaged species.

  16. The Pathway Active Learning Environment: An interactive web-based tool for physics education

    NASA Astrophysics Data System (ADS)

    Nakamura, Christopher Matthew

    The work described here represents an effort to design, construct, and test an interactive online multimedia learning environment that can provide physics instruction to students in their homes. The system was designed with one-on-one human tutoring in mind as the mode of instruction. The system uses an original combination of a video-based tutor that incorporates natural language processing video-centered lessons and additional illustrative multimedia. Our Synthetic Interview (SI) tutor provides pre-recorded video answers from expert physics instructors in response to students' typed natural language questions. Our lessons cover Newton's laws and provide a context for the tutoring interaction to occur, connect physics ideas to real-world behavior of mechanical systems, and allow for quantitative testing of physics. Additional multimedia can be used to supplement the SI tutors' explanations and illustrate the physics of interest. The system is targeted at students of algebra-based and concept-based physics at the college and high school level. The system logs queries to the SI tutor, responses to lesson questions and several other interactions with the system, tagging those interactions with a username and timestamp. We have provided several groups of students with access to our system under several different conditions ranging from the controlled conditions of our interview facility to the naturalistic conditions of use at home. In total nearly two-hundred students have accessed the system. To gain insight into the ways students might use the system and understand the utility of its various components we analyzed qualitative interview data collected with 22 algebra-based physics students who worked with our system in our interview facility. We also performed a descriptive analysis of data from the system's log of user interactions. Finally we explored the use of machine learning to explore the possibility of using automated assessment to augment the interactive

  17. Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

    NASA Astrophysics Data System (ADS)

    Liu, Shuang

    Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural

  18. The role of hydrogen atoms in interactions involving imidazolium-based ionic liquids

    NASA Astrophysics Data System (ADS)

    Kempter, V.; Kirchner, B.

    2010-05-01

    In the first part of this report experimental results are discussed which focus onto the importance of hydrogen atoms in the interaction of imidazolium-based ionic liquids. These include examples for the cation-anion interaction in neat ionic liquids as well as the interactions between ionic liquids and their molecular environment, water in particular. Most of the studies emphasize the importance of the C(2)-H group of the imidazolium ring for the intra- and intermolecular interactions; commonly, the interactions of the type C-H … X (X =: O, halide) are attributed to "hydrogen bonding". In the second part it is analyzed whether these interactions and their consequences fulfill the criteria set by standard definitions of hydrogen bonding. Two cation-anion co-conformations at the C(2)-H group are found. One co-conformer (in-plane) often resembles a hydrogen bond while the other one (on-top) points to a non-hydrogen bonding behavior. Furthermore, the degree of hydrogen bonding for the in-plane structure is very dependent on the anion. Spatial distribution functions show that, in general, both co-conformations are occupied. However, the question of how long a particular co-conformer is populated in the liquid state has yet to be answered. Therefore, it is concluded that the term "hydrogen bond" should, at present, be treated with care to characterize the cation-anion contacts, because of the above-mentioned difficulties. Once more it must be stressed that oversimplifications and generalizations, even for this subclass of ionic liquids have to be avoided, because these liquids are more complicated than it appears from first sight.

  19. ProPose: a docking engine based on a fully configurable protein-ligand interaction model.

    PubMed

    Seifert, Markus H J; Schmitt, Frank; Herz, Thomas; Kramer, Bernd

    2004-12-01

    Virtual high-throughput screening of molecular databases and in particular high-throughput protein-ligand docking are both common methodologies that identify and enrich hits in the early stages of the drug design process. Current protein-ligand docking algorithms often implement a program-specific model for protein-ligand interaction geometries. However, in order to create a platform for arbitrary queries in molecular databases, a new program is desirable that allows more manual control of the modeling of molecular interactions. For that reason, ProPose, an advanced incremental construction docking engine, is presented here that implements a fast and fully configurable molecular interaction and scoring model. This program uses user-defined, discrete, pharmacophore-like representations of molecular interactions that are transformed on-the-fly into a continuous potential energy surface, allowing for the incorporation of target specific interaction mechanisms into docking protocols in a straightforward manner. A torsion angle library, based on semi-empirical quantum chemistry calculations, is used to provide minimum energy torsion angles for the incremental construction algorithm. Docking results of a diverse set of protein-ligand complexes from the Protein Data Bank demonstrate the feasibility of this new approach. As a result, the seamless integration of pharmacophore-like interaction types into the docking and scoring scheme implemented in ProPose opens new opportunities for efficient, receptor-specific screening protocols. [figure: see text]. ProPose--a fully configurable protein-ligand docking program--transforms pharmacophores into a smooth potential energy surface.

  20. A model of urban scaling laws based on distance dependent interactions

    PubMed Central

    Ribeiro, Fabiano L.; Meirelles, Joao; Ferreira, Fernando F.

    2017-01-01

    Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log–log plot, the so-called superlinear scaling. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.

  1. Interactive computer-assisted instruction in acid-base physiology for mobile computer platforms.

    PubMed

    Longmuir, Kenneth J

    2014-03-01

    In this project, the traditional lecture hall presentation of acid-base physiology in the first-year medical school curriculum was replaced by interactive, computer-assisted instruction designed primarily for the iPad and other mobile computer platforms. Three learning modules were developed, each with ∼20 screens of information, on the subjects of the CO2-bicarbonate buffer system, other body buffer systems, and acid-base disorders. Five clinical case modules were also developed. For the learning modules, the interactive, active learning activities were primarily step-by-step learner control of explanations of complex physiological concepts, usually presented graphically. For the clinical cases, the active learning activities were primarily question-and-answer exercises that related clinical findings to the relevant basic science concepts. The student response was remarkably positive, with the interactive, active learning aspect of the instruction cited as the most important feature. Also, students cited the self-paced instruction, extensive use of interactive graphics, and side-by-side presentation of text and graphics as positive features. Most students reported that it took less time to study the subject matter with this online instruction compared with subject matter presented in the lecture hall. However, the approach to learning was highly examination driven, with most students delaying the study of the subject matter until a few days before the scheduled examination. Wider implementation of active learning computer-assisted instruction will require that instructors present subject matter interactively, that students fully embrace the responsibilities of independent learning, and that institutional administrations measure instructional effort by criteria other than scheduled hours of instruction.

  2. Interaction Domains and Suicide: A Population-Based Panel Study of Suicides in Stockholm, 1991-1999

    ERIC Educational Resources Information Center

    Hedstrom, Peter; Liu, Ka-Yuet; Nordvik, Monica K.

    2008-01-01

    This article examines how suicides influence suicide risks of others within two interaction domains: the family and the workplace. A distinction is made between dyad-based social-interaction effects and degree-based exposure effects. A unique database including all individuals who ever lived in Stockholm during the 1990s is analyzed. For about 5.6…

  3. Rational design of FRET sensor proteins based on mutually exclusive domain interactions.

    PubMed

    Merkx, Maarten; Golynskiy, Misha V; Lindenburg, Laurens H; Vinkenborg, Jan L

    2013-10-01

    Proteins that switch between distinct conformational states are ideal to monitor and control molecular processes within the complexity of biological systems. Inspired by the modular architecture of natural signalling proteins, our group explores generic design strategies for the construction of FRET-based sensor proteins and other protein switches. In the present article, I show that designing FRET sensors based on mutually exclusive domain interactions provides a robust method to engineer sensors with predictable properties and an inherently large change in emission ratio. The modularity of this approach should make it easily transferable to other applications of protein switches in fields ranging from synthetic biology, optogenetics and molecular diagnostics.

  4. Modulating the interaction between CDK2 and cyclin A with a quinoline-based inhibitor.

    PubMed

    Deng, Yongqi; Shipps, Gerald W; Zhao, Lianyun; Siddiqui, M Arshad; Popovici-Muller, Janeta; Curran, Patrick J; Duca, Jose S; Hruza, Alan W; Fischmann, Thierry O; Madison, Vincent S; Zhang, Rumin; McNemar, Charles W; Mayhood, Todd W; Syto, Rosalinda; Annis, Allen; Kirschmeier, Paul; Lees, Emma M; Parry, David A; Windsor, William T

    2014-01-01

    A new class of quinoline-based kinase inhibitors has been discovered that both disrupt cyclin dependent 2 (CDK2) interaction with its cyclin A subunit and act as ATP competitive inhibitors. The key strategy for discovering this class of protein-protein disrupter compounds was to screen the monomer CDK2 in an affinity-selection/mass spectrometry-based technique and to perform secondary assays that identified compounds that bound only to the inactive CDK2 monomer and not the active CDK2/cyclin A heterodimer. Through a series of chemical modifications the affinity (Kd) of the original hit improved from 1 to 0.005μM.

  5. PHI-base update: additions to the pathogen–host interaction database

    PubMed Central

    Winnenburg, Rainer; Urban, Martin; Beacham, Andrew; Baldwin, Thomas K.; Holland, Sabrina; Lindeberg, Magdalen; Hansen, Hilde; Rawlings, Christopher; Hammond-Kosack, Kim E.; Köhler, Jacob

    2008-01-01

    The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/. PMID:17942425

  6. Source and listener directivity for interactive wave-based sound propagation.

    PubMed

    Mehra, Ravish; Antani, Lakulish; Kim, Sujeong; Manocha, Dinesh

    2014-04-01

    We present an approach to model dynamic, data-driven source and listener directivity for interactive wave-based sound propagation in virtual environments and computer games. Our directional source representation is expressed as a linear combination of elementary spherical harmonic (SH) sources. In the preprocessing stage, we precompute and encode the propagated sound fields due to each SH source. At runtime, we perform the SH decomposition of the varying source directivity interactively and compute the total sound field at the listener position as a weighted sum of precomputed SH sound fields. We propose a novel plane-wave decomposition approach based on higher-order derivatives of the sound field that enables dynamic HRTF-based listener directivity at runtime. We provide a generic framework to incorporate our source and listener directivity in any offline or online frequency-domain wave-based sound propagation algorithm. We have integrated our sound propagation system in Valve's Source game engine and use it to demonstrate realistic acoustic effects such as sound amplification, diffraction low-passing, scattering, localization, externalization, and spatial sound, generated by wave-based propagation of directional sources and listener in complex scenarios. We also present results from our preliminary user study.

  7. Computational prediction of molecular pathogen-host interactions based on dual transcriptome data

    PubMed Central

    Schulze, Sylvie; Henkel, Sebastian G.; Driesch, Dominik; Guthke, Reinhard; Linde, Jörg

    2015-01-01

    Inference of inter-species gene regulatory networks based on gene expression data is an important computational method to predict pathogen-host interactions (PHIs). Both the experimental setup and the nature of PHIs exhibit certain characteristics. First, besides an environmental change, the battle between pathogen and host leads to a constantly changing environment and thus complex gene expression patterns. Second, there might be a delay until one of the organisms reacts. Third, toward later time points only one organism may survive leading to missing gene expression data of the other organism. Here, we account for PHI characteristics by extending NetGenerator, a network inference tool that predicts gene regulatory networks from gene expression time series data. We tested multiple modeling scenarios regarding the stimuli functions of the interaction network based on a benchmark example. We show that modeling perturbation of a PHI network by multiple stimuli better represents the underlying biological phenomena. Furthermore, we utilized the benchmark example to test the influence of missing data points on the inference performance. Our results suggest that PHI network inference with missing data is possible, but we recommend to provide complete time series data. Finally, we extended the NetGenerator tool to incorporate gene- and time point specific variances, because complex PHIs may lead to high variance in expression data. Sample variances are directly considered in the objective function of NetGenerator and indirectly by testing the robustness of interactions based on variance dependent disturbance of gene expression values. We evaluated the method of variance incorporation on dual RNA sequencing (RNA-Seq) data of Mus musculus dendritic cells incubated with Candida albicans and proofed our method by predicting previously verified PHIs as robust interactions. PMID:25705211

  8. Real-time interactive projection system based on infrared structured-light method

    NASA Astrophysics Data System (ADS)

    Qiao, Xiaorui; Zhou, Qian; Ni, Kai; He, Liang; Wu, Guanhao; Mao, Leshan; Cheng, Xuemin; Ma, Jianshe

    2012-11-01

    Interactive technologies have been greatly developed in recent years, especially in projection field. However, at present, most interactive projection systems are based on special designed interactive pens or whiteboards, which is inconvenient and limits the improvement of user experience. In this paper, we introduced our recent progress on theoretically modeling a real-time interactive projection system. The system permits the user to easily operate or draw on the projection screen directly by fingers without any other auxiliary equipment. The projector projects infrared striping patterns onto the screen and the CCD captures the deformational image. We resolve the finger's position and track its movement by processing the deformational image in real-time. A new way to determine whether the finger touches the screen is proposed. The first deformational fringe on the fingertip and the first fringe at the finger shadow are the same one. The correspondence is obtained, so the location parameters can be decided by triangulation. The simulation results are given, and errors are analyzed.

  9. CLIMLAB: a Python-based software toolkit for interactive, process-oriented climate modeling

    NASA Astrophysics Data System (ADS)

    Rose, B. E. J.

    2015-12-01

    Global climate is a complex emergent property of the rich interactions between simpler components of the climate system. We build scientific understanding of this system by breaking it down into component process models (e.g. radiation, large-scale dynamics, boundary layer turbulence), understanding each components, and putting them back together. Hands-on experience and freedom to tinker with climate models (whether simple or complex) is invaluable for building physical understanding. CLIMLAB is an open-ended software engine for interactive, process-oriented climate modeling. With CLIMLAB you can interactively mix and match model components, or combine simpler process models together into a more comprehensive model. It was created primarily to support classroom activities, using hands-on modeling to teach fundamentals of climate science at both undergraduate and graduate levels. CLIMLAB is written in Python and ties in with the rich ecosystem of open-source scientific Python tools for numerics and graphics. The IPython notebook format provides an elegant medium for distributing interactive example code. I will give an overview of the current capabilities of CLIMLAB, the curriculum we have developed thus far, and plans for the future. Using CLIMLAB requires some basic Python coding skills. We consider this an educational asset, as we are targeting upper-level undergraduates and Python is an increasingly important language in STEM fields. However CLIMLAB is well suited to be deployed as a computational back-end for a graphical gaming environment based on earth-system modeling.

  10. Interactions between organic additives and active powders in water-based lithium iron phosphate electrode slurries

    NASA Astrophysics Data System (ADS)

    Li, Chia-Chen; Lin, Yu-Sheng

    2012-12-01

    The interactions of organic additives with active powders are investigated and are found to have great influence on the determination of the mixing process for preparing electrode slurries with good dispersion and electrochemical properties of lithium iron phosphate (LiFePO4) electrodes. Based on the analyses of zeta potential, sedimentation, and rheology, it is shown that LiFePO4 prefers to interact with styrene-butadiene rubber (SBR) relative to other organic additives such as sodium carboxymethyl cellulose (SCMC), and thus shows preferential adsorption by SBR, whereas SBR has much lower efficiency than SCMC in dispersing LiFePO4. Therefore, for SCMC to interact with and disperse LiFePO4 before the interaction of LiFePO4 with SBR, it is suggested to mix SCMC with LiFePO4 prior to the addition of SBR during the slurry preparation process. For the electrode prepared via the suggested process, i.e., the sequenced adding process in which SCMC is mixed with active powders prior to the addition of SBR, a much better electrochemical performance is obtained than that of the one prepared via the process referred as the simultaneous adding process, in which mixing of SCMC and SBR with active powders in simultaneous.

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

    PubMed Central

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

    2015-01-01

    Gait function is traditionally assessed using well-lit, unobstructed walkways with minimal distractions. In patients with subclinical physiological abnormalities, these conditions may not provide enough stress on their ability to adapt to walking. The introduction of challenging walking conditions in gait can induce responses in physiological systems in addition to the locomotor system. There is a need for a device that is capable of monitoring multiple physiological systems in various walking conditions. To address this need, an Android-based gait-monitoring device was developed that enabled the recording of a patient's physiological systems during walking. The gait-monitoring device was tested during self-regulated overground walking sessions of fifteen healthy subjects that included 6 females and 9 males aged 18 to 35 years. The gait-monitoring device measures the patient's stride interval, acceleration, electrocardiogram, skin conductance and respiratory rate. The data is stored on an Android phone and is analyzed offline through the extraction of features in the time, frequency and time-frequency domains. The analysis of the data depicted multisystem physiological interactions during overground walking in healthy subjects. These interactions included locomotion-electrodermal, locomotion-respiratory and cardiolocomotion couplings. The current results depicting strong interactions between the locomotion system and the other considered systems (i.e., electrodermal, respiratory and cardivascular systems) warrant further investigation into multisystem interactions during walking, particularly in challenging walking conditions with older adults. PMID:26390946

  12. DINIES: drug-target interaction network inference engine based on supervised analysis.

    PubMed

    Yamanishi, Yoshihiro; Kotera, Masaaki; Moriya, Yuki; Sawada, Ryusuke; Kanehisa, Minoru; Goto, Susumu

    2014-07-01

    DINIES (drug-target interaction network inference engine based on supervised analysis) is a web server for predicting unknown drug-target interaction networks from various types of biological data (e.g. chemical structures, drug side effects, amino acid sequences and protein domains) in the framework of supervised network inference. The originality of DINIES lies in prediction with state-of-the-art machine learning methods, in the integration of heterogeneous biological data and in compatibility with the KEGG database. The DINIES server accepts any 'profiles' or precalculated similarity matrices (or 'kernels') of drugs and target proteins in tab-delimited file format. When a training data set is submitted to learn a predictive model, users can select either known interaction information in the KEGG DRUG database or their own interaction data. The user can also select an algorithm for supervised network inference, select various parameters in the method and specify weights for heterogeneous data integration. The server can provide integrative analyses with useful components in KEGG, such as biological pathways, functional hierarchy and human diseases. DINIES (http://www.genome.jp/tools/dinies/) is publicly available as one of the genome analysis tools in GenomeNet.

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

    PubMed Central

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

    2016-01-01

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

  14. Similarity-based modeling in large-scale prediction of drug-drug interactions

    PubMed Central

    Vilar, Santiago; Uriarte, Eugenio; Santana, Lourdes; Lorberbaum, Tal; Hripcsak, George; Friedman, Carol; Tatonetti, Nicholas P

    2015-01-01

    Drug-drug interactions (DDIs) are a major cause of adverse drug effects and a public health concern, as they increase hospital care expenses and reduce patients’ quality of life. DDI detection is, therefore, an important objective in patient safety, one whose pursuit affects drug development and pharmacovigilance. In this article, we describe a protocol applicable on a large scale to predict novel DDIs based on similarity of drug interaction candidates to drugs involved in established DDIs. the method integrates a reference standard database of known DDIs with drug similarity information extracted from different sources, such as 2D and 3D molecular structure, interaction profile, target and side-effect similarities. the method is interpretable in that it generates drug interaction candidates that are traceable to pharmacological or clinical effects. We describe a protocol with applications in patient safety and preclinical toxicity screening. the time frame to implement this protocol is 5–7 h, with additional time potentially necessary, depending on the complexity of the reference standard DDI database and the similarity measures implemented. PMID:25122524

  15. DNA-probe-target interaction based detection of Brucella melitensis by using surface plasmon resonance.

    PubMed

    Sikarwar, Bhavna; Singh, Virendra V; Sharma, Pushpendra K; Kumar, Ashu; Thavaselvam, Duraipandian; Boopathi, Mannan; Singh, Beer; Jaiswal, Yogesh K

    2017-01-15

    Surface plasmon resonance (SPR) immunosensor using 4-mercaptobenzoic acid (4-MBA) modified gold (4-MBA/Au) SPR chip was developed first time for the detection of Brucella melitensis (B. melitensis) based on the screening of its complementary DNA target by using two different newly designed DNA probes of IS711 gene. Herein, interaction between DNA probes and target molecule are also investigated and result revealed that the interaction is spontaneous. The kinetics and thermodynamic results derived from the experimental data showed that the interaction between complementary DNA targets and probe 1 is more effective than that of probe 2. Equilibrium dissociation constant (KD) and maximum binding capacity of analyte (Bmax) values for the interaction of complementary DNA target with the immobilized DNA probes were calculated by using kinetic evaluation software, and found to be 15.3 pM (KD) and 81.02m° (Bmax) with probe 1 and 54.9pM and 55.29m° (Bmax), respectively. Moreover, real serum samples analysis were also carried out using immobilized probe 1 and probe 2 with SPR which showed the applicability of this methodology and provides an alternative way for the detection of B. melitensis in less than 10min. This remarkable sensing response of present methodology offer a real time and label free detection of biological warfare agent and provide an opportunity to make miniaturized sensor, indicating considerable promise for diverse environmental, bio-defence, clinical diagnostics, food safety, water and security applications.

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

    NASA Astrophysics Data System (ADS)

    Mehra, Ravish

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

  17. Ground-based remote sensing scheme for monitoring aerosol-cloud interactions

    NASA Astrophysics Data System (ADS)

    Sarna, K.; Russchenberg, H. W. J.

    2015-11-01

    A method for continuous observation of aerosol-cloud interactions with ground-based remote sensing instruments is presented. The main goal of this method is to enable the monitoring of cloud microphysical changes due to the changing aerosol concentration. We use high resolution measurements from lidar, radar and radiometer which allow to collect and compare data continuously. This method is based on a standardised data format from Cloudnet and can be implemented at any observatory where the Cloudnet data set is available. Two example study cases were chosen from the Atmospheric Radiation Measurement (ARM) Program deployment at Graciosa Island, Azores, Portugal in 2009 to present the method. We show the Pearson Product-Moment Correlation Coefficient, r, and the Coefficient of Determination, r2 for data divided into bins of LWP, each of 10 g m-2. We explain why the commonly used way of quantity aerosol cloud interactions by use of an ACI index (ACIr,τ = dln re,τ/dlnα) is not the best way of quantifying aerosol-cloud interactions.

  18. Evaluation of Web-Based Interactive Instruction in Intraoral and Panoramic Radiographic Anatomy.

    PubMed

    Farkhondeh, Alireza; Geist, James R

    2015-07-01

    The objective was to evaluate the effectiveness of Web-based interactive modules in the instruction of dental hygiene students on intraoral and panoramic radiographic landmarks. The experimental group studied these landmarks as presented on interactive Web-based modules instead of in classroom presentations. The control group (the previous year's class) received instruction in the traditional classroom format. The outcomes measures included quizzes, examinations and an in-class project. Independent samples t-tests compared the scores of the two groups. A survey was administered to the experimental group to determine their perceptions of instruction with the modules. There was no significant difference in scores between the two groups on the project (p = .926) or the intraoral quiz and exam scores (p = .1 22), but the experimental group scored significantly lower on the panoramic outcomes (p = .039). Only 26% of the students preferred computer-assisted instruction to classroom instruction. The narration and interactive quizzes in the intraoral module may have contributed to the similar performance of the experimental and control groups, while their absence may have adversely affected the effectiveness of the panoramic module.

  19. RiBAC: Role Interaction Based Access Control Model for Community Computing

    NASA Astrophysics Data System (ADS)

    Jung, Youna; Masoumzadeh, Amirreza; Joshi, James B. D.; Kim, Minkoo

    Community computing is an agent-based development paradigm for ubiquitous computing systems. In a community computing system, ubiquitous services are provided by cooperation among agents. While agents cooperate, they interact with each other continuously to access data of other agents and/or to execute other agent’s actions. However, in cases of security-critical ubiquitous services such as medical or military services, an access control mechanism is necessary to prevent unauthorized access to critical data or action. In this paper, we propose a family of Role interaction Based Access Control (RiBAC) models for Community Computing, by extending the existing RBAC model to consider role interactions. As a basic model, we propose the core RiBAC model. For the convenience of management and to provide more fine-grained access control, we propose Hierarchical RiBAC (H-RiBAC), Constrained RiBAC (C-RiBAC), and Constrained Hierarchical RiBAC (CH-RiBAC) models. Finally, we extend the existing community computing framework to accommodate the specification and enforcement of RiBAC policies.

  20. A Development of Game-Based Learning Environment to Activate Interaction among Learners

    NASA Astrophysics Data System (ADS)

    Takaoka, Ryo; Shimokawa, Masayuki; Okamoto, Toshio

    Many studies and systems that incorporate elements such as “pleasure” and “fun” in the game to improve a learner's motivation have been developed in the field of learning environments. However, few are the studies of situations where many learners gather at a single computer and participate in a game-based learning environment (GBLE), and where the GBLE designs the learning process by controlling the interactions between learners such as competition, collaboration, and learning by teaching. Therefore, the purpose of this study is to propose a framework of educational control that induces and activates interaction between learners intentionally to create a learning opportunity that is based on the knowledge understanding model of each learner. In this paper, we explain the design philosophy and the framework of our GBLE called “Who becomes the king in the country of mathematics?” from a game viewpoint and describe the method of learning support control in the learning environment. In addition, we report the results of the learning experiment with our GBLE, which we carried out in a junior high school, and include some comments by a principal and a teacher. From the results of the experiment and some comments, we noticed that a game may play a significant role in weakening the learning relationship among students and creating new relationships in the world of the game. Furthermore, we discovered that learning support control of the GBLE has led to activation of the interaction between learners to some extent.

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

    PubMed

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2015-09-24

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

  2. Development of Multilayer Microcapsules by a Phase Coacervation Method Based on Ionic Interactions for Textile Applications

    PubMed Central

    Chatterjee, Sudipta; Salaün, Fabien; Campagne, Christine

    2014-01-01

    The present study describes the development of multilayer microcapsules by 11 alternate additions of chitosan (Chi) and sodium dodecyl sulfate (SDS) in a combined emulsification and phase coacervation method based on ionic interactions. After an alkali treatment, microcapsules are applied on polyester (PET) fabric by a padding process to investigate their wash-durability on fabric. Air atmospheric plasma treatment is performed on PET fabric to modify the surface properties of the textiles. Zeta potential, X-ray photoelectron spectroscopy (XPS), wetting measurements, scanning electron microscopy (SEM), and atomic force microscopy (AFM) with surface roughness measurements are realized to characterize and determine wash durability of microcapsule samples onto PET. After alkali treatment, the microcapsules are selected for textile application because they are submicron sized with the desired morphology. The results obtained from various characterization techniques indicate that microcapsules are wash-durable on PET fabric pre activated by air plasma atmospheric as Chi based microcapsules can interact directly with PET by ionic interactions. PMID:24932719

  3. Can Interactive Web-based CAD Tools Improve the Learning of Engineering Drawing? A Case Study

    NASA Astrophysics Data System (ADS)

    Pando Cerra, Pablo; Suárez González, Jesús M.; Busto Parra, Bernardo; Rodríguez Ortiz, Diana; Álvarez Peñín, Pedro I.

    2014-06-01

    Many current Web-based learning environments facilitate the theoretical teaching of a subject but this may not be sufficient for those disciplines that require a significant use of graphic mechanisms to resolve problems. This research study looks at the use of an environment that can help students learn engineering drawing with Web-based CAD tools, including a self-correction component. A comparative study of 121 students was carried out. The students were divided into two experimental groups using Web-based interactive CAD tools and into two control groups using traditional learning tools. A statistical analysis of all the samples was carried out in order to study student behavior during the research and the effectiveness of these self-study tools in the learning process. The results showed that a greater number of students in the experimental groups passed the test and improved their test scores. Therefore, the use Web-based graphic interactive tools to learn engineering drawing can be considered a significant improvement in the teaching of this kind of academic discipline.

  4. Extracting Drug-Drug Interaction from the Biomedical Literature Using a Stacked Generalization-Based Approach

    PubMed Central

    He, Linna; Yang, Zhihao; Zhao, Zhehuan; Lin, Hongfei; Li, Yanpeng

    2013-01-01

    Drug-drug interaction (DDI) detection is particularly important for patient safety. However, the amount of biomedical literature regarding drug interactions is increasing rapidly. Therefore, there is a need to develop an effective approach for the automatic extraction of DDI information from the biomedical literature. In this paper, we present a Stacked Generalization-based approach for automatic DDI extraction. The approach combines the feature-based, graph and tree kernels and, therefore, reduces the risk of missing important features. In addition, it introduces some domain knowledge based features (the keyword, semantic type, and DrugBank features) into the feature-based kernel, which contribute to the performance improvement. More specifically, the approach applies Stacked generalization to automatically learn the weights from the training data and assign them to three individual kernels to achieve a much better performance than each individual kernel. The experimental results show that our approach can achieve a better performance of 69.24% in F-score compared with other systems in the DDI Extraction 2011 challenge task. PMID:23785452

  5. A flexible flight display research system using a ground-based interactive graphics terminal

    NASA Technical Reports Server (NTRS)

    Hatfield, J. J.; Elkins, H. C.; Batson, V. M.; Poole, W. L.

    1975-01-01

    Requirements and research areas for the air transportation system of the 1980 to 1990's were reviewed briefly to establish the need for a flexible flight display generation research tool. Specific display capabilities required by aeronautical researchers are listed and a conceptual system for providing these capabilities is described. The conceptual system uses a ground-based interactive graphics terminal driven by real-time radar and telemetry data to generate dynamic, experimental flight displays. These displays are scan converted to television format, processed, and transmitted to the cockpits of evaluation aircraft. The attendant advantages of a Flight Display Research System (FDRS) designed to employ this concept are presented. The detailed implementation of an FDRS is described. The basic characteristics of the interactive graphics terminal and supporting display electronic subsystems are presented and the resulting system capability is summarized. Finally, the system status and utilization are reviewed.

  6. Viscoelastic model based force control for soft tissue interaction and its application in physiological motion compensation.

    PubMed

    Moreira, Pedro; Zemiti, Nabil; Liu, Chao; Poignet, Philippe

    2014-09-01

    Controlling the interaction between robots and living soft tissues has become an important issue as the number of robotic systems inside the operating room increases. Many researches have been done on force control to help surgeons during medical procedures, such as physiological motion compensation and tele-operation systems with haptic feedback. In order to increase the performance of such controllers, this work presents a novel force control scheme using Active Observer (AOB) based on a viscoelastic interaction model. The control scheme has shown to be stable through theoretical analysis and its performance was evaluated by in vitro experiments. In order to evaluate how the force control scheme behaves under the presence of physiological motion, experiments considering breathing and beating heart disturbances are presented. The proposed control scheme presented a stable behavior in both static and moving environment. The viscoelastic AOB presented a compensation ratio of 87% for the breathing motion and 79% for the beating heart motion.

  7. Biomolecule immobilization in biosensor development: tailored strategies based on affinity interactions.

    PubMed

    Prieto-Simín, B; Campàs, M; Marty, J-L

    2008-01-01

    The exponential development of biosensors as powerful analytical tools in the last four decades mainly relies on the high sensitivity and selectivity offered when detecting the target analyte. The transducer and the biological receptor are the bases of the biosensor development. Nevertheless, the bioreceptor immobilisation is also important, playing a key role in the retention of the biological activity, and thus affecting the sensitivity. Parameters such as shelf-life and surface regeneration also depend on the biomolecule immobilisation. Researchers are focusing their efforts towards random and oriented immobilisation procedures. Adsorption, entrapment, cross-linking and electrostatic interactions provide randomly immobilised biomolecules, sometimes partially hindering their biological activity. Covalent binding and affinity interactions may enable oriented biomolecule immobilisations, providing controlled, reproducible and highly active modified surfaces. This paper reviews the main immobilisation strategies used in the biosensors development, putting special emphasis on our contribution to mild and oriented immobilisation techniques.

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

    PubMed

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

    2012-07-01

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

  9. Oscillation mode analysis considering the interaction between a DFIG-based wind turbine and the grid

    NASA Astrophysics Data System (ADS)

    Wu, Wangping; Xie, Da; Lu, Yupu; Zhao, Zuyi; Yu, Songtao

    2017-01-01

    Sub-synchronous interactions between wind farms and transmission networks with series compensation have drawn great attention. As most large wind farms in Europe and Asia employ doubly fed induction generator turbines, there has recently been a growing interest in studying this phenomenon. To study the stability of wind turbine with doubly fed induction generator after a small disturbance, a complete small signal system is built in this paper. By using eigenvalue and participation factor analysis, the relation between the modes and state variables can be discovered. Thereafter, the oscillation modes are classified into electrical resonance, sub-synchronous resonance, sub-synchronous oscillation, sub-synchronous control interaction, and low frequency oscillation. To verify the oscillation frequency of each oscillation mode, time-domain simulation based on MATLAB/Simulink is presented. The simulation results justify the effectiveness of the small-signal models.

  10. Data-driven interactive 3D medical image segmentation based on structured patch model.

    PubMed

    Park, Sang Hyun; Yun, Il Dong; Lee, Sang Uk

    2013-01-01

    In this paper, we present a novel three dimensional interactive medical image segmentation method based on high level knowledge of training set. Since the interactive system should provide intermediate results to an user quickly, insufficient low level models are used for most of previous methods. To exploit the high level knowledge within a short time, we construct a structured patch model that consists of multiple corresponding patch sets. The structured patch model includes the spatial relationships between neighboring patch sets and the prior knowledge of the corresponding patch set on each local region. The spatial relationships accelerate the search of corresponding patch in test time, while the prior knowledge improves the segmentation accuracy. The proposed framework provides not only fast editing tool, but the incremental learning system through adding the segmentation result to the training set. Experiments demonstrate that the proposed method is useful for fast and accurate segmentation of target objects from the multiple medical images.

  11. Quantum thermal diode based on two interacting spinlike systems under different excitations

    NASA Astrophysics Data System (ADS)

    Ordonez-Miranda, Jose; Ezzahri, Younès; Joulain, Karl

    2017-02-01

    We demonstrate that two interacting spinlike systems characterized by different excitation frequencies and coupled to a thermal bath each, can be used as a quantum thermal diode capable of efficiently rectifying the heat current. This is done by deriving analytical expressions for both the heat current and rectification factor of the diode, based on the solution of a master equation for the density matrix. Higher rectification factors are obtained for lower heat currents, whose magnitude takes their maximum values for a given interaction coupling proportional to the temperature of the hotter thermal bath. It is shown that the rectification ability of the diode increases with the excitation frequencies difference, which drives the asymmetry of the heat current, when the temperatures of the thermal baths are inverted. Furthermore, explicit conditions for the optimization of the rectification factor and heat current are explicitly found.

  12. KIPSE1: A Knowledge-based Interactive Problem Solving Environment for data estimation and pattern classification

    NASA Technical Reports Server (NTRS)

    Han, Chia Yung; Wan, Liqun; Wee, William G.

    1990-01-01

    A knowledge-based interactive problem solving environment called KIPSE1 is presented. The KIPSE1 is a system built on a commercial expert system shell, the KEE system. This environment gives user capability to carry out exploratory data analysis and pattern classification tasks. A good solution often consists of a sequence of steps with a set of methods used at each step. In KIPSE1, solution is represented in the form of a decision tree and each node of the solution tree represents a partial solution to the problem. Many methodologies are provided at each node to the user such that the user can interactively select the method and data sets to test and subsequently examine the results. Otherwise, users are allowed to make decisions at various stages of problem solving to subdivide the problem into smaller subproblems such that a large problem can be handled and a better solution can be found.

  13. Mutual Lewis acid-base interactions of cations and anions in ionic liquids.

    PubMed

    Holzweber, Markus; Lungwitz, Ralf; Doerfler, Denise; Spange, Stefan; Koel, Mihkel; Hutter, Herbert; Linert, Wolfgang

    2013-01-02

    Solute properties are known to be strongly influenced by solvent molecules due to solvation. This is due to mutual interaction as both the properties of the solute and of the solvent strongly depend on each other. The present paper is based on the idea that ionic liquids are cations solvated by anions and anions solvated by cations. To show this (in this system strongly pronounced) interaction the long time established donor-acceptor concept for solvents and ions in solution by Viktor Gutmann is extended to ionic liquids. A number of solvent parameters, such as the Kamlet-Abboud-Taft and the Dimroth-Reichardt E(T) scale for ionic liquids neglect this mutual influence, which, however, seems to be in fact necessary to get a proper description of ionic liquid properties. It is shown how strong such parameters vary when the influence of the counter ion is taken into account. Furthermore, acceptor and donor numbers for ionic liquids are presented.

  14. Integrated VR platform for 3D and image-based models: a step toward interactive image-based virtual environments

    NASA Astrophysics Data System (ADS)

    Yoon, Jayoung; Kim, Gerard J.

    2003-04-01

    Traditionally, three dimension models have been used for building virtual worlds, and a data structure called the "scene graph" is often employed to organize these 3D objects in the virtual space. On the other hand, image-based rendering has recently been suggested as a probable alternative VR platform for its photo-realism, however, due to limited interactivity, it has only been used for simple navigation systems. To combine the merits of these two approaches to object/scene representations, this paper proposes for a scene graph structure in which both 3D models and various image-based scenes/objects can be defined, traversed, and rendered together. In fact, as suggested by Shade et al., these different representations can be used as different LOD's for a given object. For instance, an object might be rendered using a 3D model at close range, a billboard at an intermediate range, and as part of an environment map at far range. The ultimate objective of this mixed platform is to breath more interactivity into the image based rendered VE's by employing 3D models as well. There are several technical challenges in devising such a platform: designing scene graph nodes for various types of image based techniques, establishing criteria for LOD/representation selection, handling their transitions, implementing appropriate interaction schemes, and correctly rendering the overall scene. Currently, we have extended the scene graph structure of the Sense8's WorldToolKit, to accommodate new node types for environment maps billboards, moving textures and sprites, "Tour-into-the-Picture" structure, and view interpolated objects. As for choosing the right LOD level, the usual viewing distance and image space criteria are used, however, the switching between the image and 3D model occurs at a distance from the user where the user starts to perceive the object's internal depth. Also, during interaction, regardless of the viewing distance, a 3D representation would be used, it if

  15. D Modelling and Interactive Web-Based Visualization of Cultural Heritage Objects

    NASA Astrophysics Data System (ADS)

    Koeva, M. N.

    2016-06-01

    Nowadays, there are rapid developments in the fields of photogrammetry, laser scanning, computer vision and robotics, together aiming to provide highly accurate 3D data that is useful for various applications. In recent years, various LiDAR and image-based techniques have been investigated for 3D modelling because of their opportunities for fast and accurate model generation. For cultural heritage preservation and the representation of objects that are important for tourism and their interactive visualization, 3D models are highly effective and intuitive for present-day users who have stringent requirements and high expectations. Depending on the complexity of the objects for the specific case, various technological methods can be applied. The selected objects in this particular research are located in Bulgaria - a country with thousands of years of history and cultural heritage dating back to ancient civilizations. This motivates the preservation, visualisation and recreation of undoubtedly valuable historical and architectural objects and places, which has always been a serious challenge for specialists in the field of cultural heritage. In the present research, comparative analyses regarding principles and technological processes needed for 3D modelling and visualization are presented. The recent problems, efforts and developments in interactive representation of precious objects and places in Bulgaria are presented. Three technologies based on real projects are described: (1) image-based modelling using a non-metric hand-held camera; (2) 3D visualization based on spherical panoramic images; (3) and 3D geometric and photorealistic modelling based on architectural CAD drawings. Their suitability for web-based visualization are demonstrated and compared. Moreover the possibilities for integration with additional information such as interactive maps, satellite imagery, sound, video and specific information for the objects are described. This comparative study

  16. Detecting Pathway-Based Gene-Gene and Gene-Environment Interactions in Pancreatic Cancer

    PubMed Central

    Duell, Eric J.; Bracci, Paige M.; Moore, Jason H.; Burk, Robert D.; Kelsey, Karl T.; Holly, Elizabeth A.

    2015-01-01

    Data mining and data reduction methods to detect interactions in epidemiologic data are being developed and tested. In these analyses, multifactor dimensionality reduction, focused interaction testing framework, and traditional logistic regression models were used to identify potential interactions with up to three factors. These techniques were used in a population-based case-control study of pancreatic cancer from the San Francisco Bay Area (308 cases, 964 controls). From 7 biochemical pathways, along with tobacco smoking, 26 polymorphisms in 20 genes were included in these analyses. Combinations of genetic markers and cigarette smoking were identified as potential risk factors for pancreatic cancer, including genes in base excision repair (OGG1), nucleotide excision repair (XPD, XPA, XPC), and double-strand break repair (XRCC3). XPD.751, XPD.312, and cigarette smoking were the best single-factor predictors of pancreatic cancer risk, whereas XRCC3.241*smoking and OGG1.326*XPC.PAT were the best two-factor predictors. There was some evidence for a three-factor combination of OGG1.326*XPD.751*smoking, but the covariate-adjusted relative-risk estimates lacked precision. Multifactor dimensionality reduction and focused interaction testing framework showed little concordance, whereas logistic regression allowed for covariate adjustment and model confirmation. Our data suggest that multiple common alleles from DNA repair pathways in combination with cigarette smoking may increase the risk for pancreatic cancer, and that multiple approaches to data screening and analysis are necessary to identify potentially new risk factor combinations. PMID:18559563

  17. Mass-based hygroscopicity parameter interaction model and measurement of atmospheric aerosol water uptake

    NASA Astrophysics Data System (ADS)

    Mikhailov, E.; Merkulov, V.; Vlasenko, S.; Rose, D.; Pöschl, U.

    2011-11-01

    In this study we derive and apply a mass-based hygroscopicity parameter interaction model for efficient description of concentration-dependent water uptake by atmospheric aerosol particles. The model approach builds on the single hygroscopicity parameter model of Petters and Kreidenweis (2007). We introduce an observable mass-based hygroscopicity parameter κm, which can be deconvoluted into a dilute intrinsic hygroscopicity parameter (κm,∞) and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems. For sodium chloride, the κm-interaction model (KIM) captures the observed concentration and humidity dependence of the hygroscopicity parameter and is in good agreement with an accurate reference model based on the Pitzer ion-interaction approach (Aerosol Inorganic Model, AIM). For atmospheric aerosol samples collected from boreal rural air and from pristine tropical rainforest air (secondary organic aerosol) we present first mass-based measurements of water uptake over a wide range of relative humidity (1-99%) obtained with a new filter-based differential hygroscopicity analyzer (FDHA) technique. By application of KIM to the measurement data we can distinguish three different regimes of hygroscopicity in the investigated aerosol samples: (I) A quasi-eutonic regime at low relative humidity (~60% RH) where the solutes co-exist in an aqueous and non-aqueous phase; (II) a gradually deliquescent regime at intermediate humidity (~60%-90% RH) where different solutes undergo gradual dissolution in the aqueous phase; and (III) a dilute regime at high humidity (≳90% RH) where the solutes are fully dissolved approaching their dilute intrinsic hygroscopicity. The characteristic features of the three hygroscopicity regimes are similar for both samples, while the RH threshold values vary as expected for samples of different chemical composition. In each regime, the

  18. A state parameter-based model for static recrystallization interacting with precipitation

    NASA Astrophysics Data System (ADS)

    Buken, Heinrich; Sherstnev, Pavel; Kozeschnik, Ernst

    2016-03-01

    In the present work, we develop a state parameter-based model for the treatment of simultaneous precipitation and recrystallization based on a single-parameter representation of the total dislocation density and a multi-particle multi-component framework for precipitation kinetics. In contrast to conventional approaches, the interaction of particles with recrystallization is described with a non-zero grain boundary mobility even for the case where the Zener pressure exceeds the driving pressure for recrystallization. The model successfully reproduces the experimentally observed particle-induced recrystallization stasis and subsequent continuation in micro-alloyed steel with a single consistent set of input parameters. In addition, as a state parameter-based approach, our model naturally supports introspection into the physical mechanisms governing the competing recrystallization and recovery processes.

  19. Interaction between vegetable oil based plasticizer molecules and polyvinyl chloride, and their plasticization effect

    NASA Astrophysics Data System (ADS)

    Haryono, Agus; Triwulandari, Evi; Jiang, Pingping

    2017-01-01

    Plasticizer molecules are low molecular weight compounds that are widely used in polymer industries especially in polyvinyl chloride (PVC) resin. As an additive in PVC resin, the important role of plasticizer molecules is to improve the flexibility and processability of PVC by lowering the glass transition temperature (Tg). However, the commercial plasticizer like di(2-ethylhexyl)phthalate (DEHP) is known to cause liver cancer, at least in laboratory rats. DEHP can leach out from PVC into blood, certain drug solutions and fatty foods, which has been detected in the bloodstream of patients undergoing transfusion. Vegetable oil based plasticizers have some attractive properties such as non-toxic, bio-degradable, good heat and light stability, renewable resources, and environmentally friendly. Here we discussed the main results and development of vegetable oil based plasticizer, and especially palm oil based plasticizer. The interaction between plasticizer and polymer was discussed from the properties of the plasticized polymeric material.

  20. An Interactive, Web-based High Performance Modeling Environment for Computational Epidemiology.

    PubMed

    Deodhar, Suruchi; Bisset, Keith R; Chen, Jiangzhuo; Ma, Yifei; Marathe, Madhav V

    2014-07-01

    We present an integrated interactive modeling environment to support public health epidemiology. The environment combines a high resolution individual-based model with a user-friendly web-based interface that allows analysts to access the models and the analytics back-end remotely from a desktop or a mobile device. The environment is based on a loosely-coupled service-oriented-architecture that allows analysts to explore various counter factual scenarios. As the modeling tools for public health epidemiology are getting more sophisticated, it is becoming increasingly hard for non-computational scientists to effectively use the systems that incorporate such models. Thus an important design consideration for an integrated modeling environment is to improve ease of use such that experimental simulations can be driven by the users. This is achieved by designing intuitive and user-friendly interfaces that allow users to design and analyze a computational experiment and steer the experiment based on the state of the system. A key feature of a system that supports this design goal is the ability to start, stop, pause and roll-back the disease propagation and intervention application process interactively. An analyst can access the state of the system at any point in time and formulate dynamic interventions based on additional information obtained through state assessment. In addition, the environment provides automated services for experiment set-up and management, thus reducing the overall time for conducting end-to-end experimental studies. We illustrate the applicability of the system by describing computational experiments based on realistic pandemic planning scenarios. The experiments are designed to demonstrate the system's capability and enhanced user productivity.

  1. [Advances in development of gene-gene interaction analysis methods based on SNP data: a review].

    PubMed

    Luan, Yi-Zhao; Zuo, Xiao-Yu; Liu, Ke; Li, Gu; Rao, Shao-Qi

    2013-12-01

    The SNP-based association analysis has become one of the most important approaches to interpret the underlying molecular mechanisms for human complex diseases. Nevertheless, the widely-used singe-locus analysis is only capable of capturing a small portion of susceptible SNPs with prominent marginal effects, leaving the important genetic component, epistasis or joint effects, to be undetectable. Identifying the complex interplays among multiple genes in the genome-wide context is an essential task for systematically unraveling the molecular mechanisms for complex diseases. Many approaches have been used to detect genome-wide gene-gene interactions and provided new insights into the genetic basis of complex diseases. This paper reviewed recent advances of the methods for detecting gene-gene interaction, categorized into three types, model-based and model-free statistical methods, and data mining methods, based on their characteristics in theory and numerical algorithm. In particular, the basic principle, numerical implementation and cautions for application for each method were elucidated. In addition, this paper briefly discussed the limitations and challenges associated with detecting genome-wide epistasis, in order to provide some methodological consultancies for scientists in the related fields.

  2. Interactive Web-based Floodplain Simulation System for Realistic Experiments of Flooding and Flood Damage

    NASA Astrophysics Data System (ADS)

    Demir, I.

    2013-12-01

    Recent developments in web technologies make it easy to manage and visualize large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The floodplain simulation system is a web-based 3D interactive flood simulation environment to create real world flooding scenarios. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create and modify predefined scenarios, control environmental parameters, and evaluate flood mitigation techniques. The web-based simulation system provides an environment to children and adults learn about the flooding, flood damage, and effects of development and human activity in the floodplain. The system provides various scenarios customized to fit the age and education level of the users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various flooding and land use scenarios.

  3. Estimating Development Cost of an Interactive Website Based Cancer Screening Promotion Program

    PubMed Central

    Lairson, David R.; Chung, Tong Han; Smith, Lisa G.; Springston, Jeffrey K.; Champion, Victoria L.

    2015-01-01

    Objectives The aim of this study was to estimate the initial development costs for an innovative talk show format tailored intervention delivered via the interactive web, for increasing cancer screening in women 50 to 75 who were non-adherent to screening guidelines for colorectal cancer and/or breast cancer. Methods The cost of the intervention development was estimated from a societal perspective. Micro costing methods plus vendor contract costs were used to estimate cost. Staff logs were used to track personnel time. Non-personnel costs include all additional resources used to produce the intervention. Results Development cost of the interactive web based intervention was $.39 million, of which 77% was direct cost. About 98% of the cost was incurred in personnel time cost, contract cost and overhead cost. Conclusions The new web-based disease prevention medium required substantial investment in health promotion and media specialist time. The development cost was primarily driven by the high level of human capital required. The cost of intervention development is important information for assessing and planning future public and private investments in web-based health promotion interventions. PMID:25749548

  4. Lewis Acid–Base Interactions between Polysulfides and Metal Organic Framework in Lithium Sulfur Batteries

    SciTech Connect

    Zheng, Jianming; Tian, Jian; Wu, Dangxin; Gu, Meng; Xu, Wu; Wang, Chongmin; Gao, Fei; Engelhard, Mark H.; Zhang, Ji-Guang; Liu, Jun; Xiao, Jie

    2014-05-14

    Lithium–sulfur (Li–S) battery is one of the most promising energy storage systems because of its high specific capacity of 1675 mAh g–1 based on sulfur. However, the rapid capacity degradation, mainly caused by polysulfide dissolution, remains a significant challenge prior to practical applications. This work demonstrates that a novel Ni-based metal organic framework (Ni-MOF), Ni6(BTB)4(BP)3 (BTB = benzene-1,3,5-tribenzoate and BP = 4,4'-bipyridyl), can remarkably immobilize polysulfides within the cathode structure through physical and chemical interactions at molecular level. The capacity retention achieves up to 89% after 100 cycles at 0.1 C. Finally, the excellent performance is attributed to the synergistic effects of the interwoven mesopores (~2.8 nm) and micropores (~1.4 nm) of Ni-MOF, which first provide an ideal matrix to confine polysulfides, and the strong interactions between Lewis acidic Ni(II) center and the polysulfide base, which significantly slow down the migration of soluble polysulfides out of the pores, leading to the excellent cycling performance of Ni-MOF/S composite.

  5. Lewis acid-base interactions between polysulfides and metal organic framework in lithium sulfur batteries.

    PubMed

    Zheng, Jianming; Tian, Jian; Wu, Dangxin; Gu, Meng; Xu, Wu; Wang, Chongmin; Gao, Fei; Engelhard, Mark H; Zhang, Ji-Guang; Liu, Jun; Xiao, Jie

    2014-05-14

    Lithium-sulfur (Li-S) battery is one of the most promising energy storage systems because of its high specific capacity of 1675 mAh g(-1) based on sulfur. However, the rapid capacity degradation, mainly caused by polysulfide dissolution, remains a significant challenge prior to practical applications. This work demonstrates that a novel Ni-based metal organic framework (Ni-MOF), Ni6(BTB)4(BP)3 (BTB = benzene-1,3,5-tribenzoate and BP = 4,4'-bipyridyl), can remarkably immobilize polysulfides within the cathode structure through physical and chemical interactions at molecular level. The capacity retention achieves up to 89% after 100 cycles at 0.1 C. The excellent performance is attributed to the synergistic effects of the interwoven mesopores (∼2.8 nm) and micropores (∼1.4 nm) of Ni-MOF, which first provide an ideal matrix to confine polysulfides, and the strong interactions between Lewis acidic Ni(II) center and the polysulfide base, which significantly slow down the migration of soluble polysulfides out of the pores, leading to the excellent cycling performance of Ni-MOF/S composite.

  6. A mobile telephone-based interactive self-care system improves asthma control.

    PubMed

    Liu, W-T; Huang, C-D; Wang, C-H; Lee, K-Y; Lin, S-M; Kuo, H-P

    2011-02-01

    The self-management of asthma can improve clinical outcomes. Recently, mobile telephones have been widely used as an efficient, instant personal communication tool. This study investigated whether a self-care system will achieve better asthma control through a mobile telephone-based interactive programme. This was a prospective, controlled study in outpatient clinics. From 120 consecutive patients with moderate-to-severe persistent asthma, 89 were eventually recruited for the study, with 43 in the mobile telephone group (with a mobile telephone-based interactive asthma self-care system). In the mobile telephone group, mean ± sem peak expiratory flow rate significantly increased at 4 (378.2 ± 9.3 L·min⁻¹; n = 43; p = 0.020), 5 (378.2 ± 9.2 L·min⁻¹; n = 43; p = 0.008) and 6 months (382.7 ± 8.6 L·min⁻¹; n = 43; p = 0.001) compared to the control group. Mean±sem forced expiratory volume in 1 s significantly increased at 6 months (65.2 ± 3.2% predicted; n = 43; p < 0.05). Patients in the mobile telephone group had better quality of life after 3 months, as determined using the Short Form-12® physical component score, and fewer episodes of exacerbation and unscheduled visits than the control group. Patients in the mobile telephone group significantly increased their mean daily dose of either systemic or inhaled corticosteroids compared with the control group. The mobile telephone-based interactive self-care system provides a convenient and practical self-monitoring and -management of asthma, and improves asthma control.

  7. Community-based prevention support: using the interactive systems framework to facilitate grassroots evidenced-based substance abuse prevention.

    PubMed

    Firesheets, E Kelly; Francis, Mary; Barnum, Ann; Rolf, Laura

    2012-12-01

    The community plays an important role in the success of substance abuse prevention efforts. However, current funding structures and a focus on limited approaches to prevention delivery have created a large gap between what substance abuse prevention professionals practice and what the community at large knows about prevention. The concept of "community" has not always been well-defined in the field of prevention, and there are few mechanisms to engage grassroots community members in evidence-based substance abuse prevention. This article explains how Wandersman et al.'s (Am J Community Psychol 41:171-181, 2008) Interactive Systems Framework can be applied to grassroots prevention efforts. The authors describe a Community Prevention Support System that collaborates with the Professional Prevention Support System to promote the adoption of evidence-based substance abuse prevention practices at the grassroots, community level.

  8. Fluid-structure interaction-based biomechanical perception model for tactile sensing.

    PubMed

    Wang, Zheng

    2013-01-01

    The reproduced tactile sensation of haptic interfaces usually selectively reproduces a certain object attribute, such as the object's material reflected by vibration and its surface shape by a pneumatic nozzle array. Tactile biomechanics investigates the relation between responses to an external load stimulus and tactile perception and guides the design of haptic interface devices via a tactile mechanism. Focusing on the pneumatic haptic interface, we established a fluid-structure interaction-based biomechanical model of responses to static and dynamic loads and conducted numerical simulation and experiments. This model provides a theoretical basis for designing haptic interfaces and reproducing tactile textures.

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

    PubMed

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

    2014-06-01

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

  10. Programmable controller with a multiprocessor-based high speed interactive language system

    SciTech Connect

    Matsuzaki, K.; Hata, S.; Ohkochi, O.; Okamura, M.; Sugimoto, N.

    1983-01-01

    A multiprocessor-based programmable controller (PC) capable of sequence control and data processing has been developed. This PC consists of a custom processor for a relay ladder program and a 68000 16-bit microprocessor for a basic program. The basic program is executed by an interpreter which is an order faster than a conventional interpreter of a personal computer. The relay ladder program and the basic program can activate and communicate with each other. Although the controller features more control functions than conventional PCs, it can be easily operated interactively on site. 2 references.

  11. Constraints on Neutron Star Radii Based on Chiral Effective Field Theory Interactions

    SciTech Connect

    Hebeler, K.; Lattimer, J. M.; Pethick, C. J.; Schwenk, A.

    2010-10-15

    We show that microscopic calculations based on chiral effective field theory interactions constrain the properties of neutron-rich matter below nuclear densities to a much higher degree than is reflected in commonly used equations of state. Combined with observed neutron star masses, our results lead to a radius R=9.7-13.9 km for a 1.4M{sub {center_dot}} star, where the theoretical range is due, in about equal amounts, to uncertainties in many-body forces and to the extrapolation to high densities.

  12. Fluid–Structure Interaction-Based Biomechanical Perception Model for Tactile Sensing

    PubMed Central

    Wang, Zheng

    2013-01-01

    The reproduced tactile sensation of haptic interfaces usually selectively reproduces a certain object attribute, such as the object's material reflected by vibration and its surface shape by a pneumatic nozzle array. Tactile biomechanics investigates the relation between responses to an external load stimulus and tactile perception and guides the design of haptic interface devices via a tactile mechanism. Focusing on the pneumatic haptic interface, we established a fluid–structure interaction-based biomechanical model of responses to static and dynamic loads and conducted numerical simulation and experiments. This model provides a theoretical basis for designing haptic interfaces and reproducing tactile textures. PMID:24260228

  13. Dual-responsive colloidal microcapsules based on host-guest interaction on solid templates.

    PubMed

    Li, Guangyu; Dong, Zhirui; Zhu, Yuting; Tong, Weijun; Gao, Changyou

    2016-08-01

    Colloidal microcapsules (MCs) have received considerable attention in the fields of microencapsulation, drug delivery as well as microreactors due to their unique nanoparticles-composed structure. In this study, dual-responsive colloidal MCs based on host-guest interaction were successfully fabricated via a layer-by-layer assembly method on sacrificial solid templates. Ferrocene-modified polyethylenimine (PEI-Fc) and cyclodextrin-modified polystyrene nanoparticles (PS-CD NPs) were used as building blocks for assembly. The colloidal MCs could be disassembled into nano-components upon addition of competitive adamantane (Ad) molecules or in the solution with a pH lower than 4.

  14. Maskiton: Interactive, Web-based Classification of Single-Particle Electron Microscopy Images

    PubMed Central

    Yoshioka, Craig; Lyumkis, Dmitry; Carragher, Bridget; Potter, Clinton S.

    2013-01-01

    Electron microscopy (EM) is an important tool for determining the composition, arrangement and structure of biological macromolecules. When studying structurally heterogeneous samples using EM, classification is a critical step toward achieving higher resolution and identifying biologically significant conformations. We have developed an interactive, web-based tool, called Maskiton, for creating custom masks and performing 2D classifications on aligned single-particle EM images. The Maskiton interface makes it considerably easier and faster to explore the significance of heterogeneity in single-particle datasets. Maskiton features include: resumable uploads to facilitate transfer of large datasets to the server, custom mask creation in the browser, continual progress updates, and interactive viewing of classification results. To demonstrate the value of this tool, we provide examples of its use on several experimental datasets and include analyses of the independent terminus mobility within the Ltn1 E3 ubiquitin ligase, the in-vitro assembly of 30S ribosomal subunits, and classification complexity reduction within Immunoglobulin M. This work also serves as a proof-of-concept for the development of future cross-platform, interactive user interfaces for electron microscopy data processing. PMID:23428431

  15. a Method to Estimate Temporal Interaction in a Conditional Random Field Based Approach for Crop Recognition

    NASA Astrophysics Data System (ADS)

    Diaz, P. M. A.; Feitosa, R. Q.; Sanches, I. D.; Costa, G. A. O. P.

    2016-06-01

    This paper presents a method to estimate the temporal interaction in a Conditional Random Field (CRF) based approach for crop recognition from multitemporal remote sensing image sequences. This approach models the phenology of different crop types as a CRF. Interaction potentials are assumed to depend only on the class labels of an image site at two consecutive epochs. In the proposed method, the estimation of temporal interaction parameters is considered as an optimization problem, whose goal is to find the transition matrix that maximizes the CRF performance, upon a set of labelled data. The objective functions underlying the optimization procedure can be formulated in terms of different accuracy metrics, such as overall and average class accuracy per crop or phenological stages. To validate the proposed approach, experiments were carried out upon a dataset consisting of 12 co-registered LANDSAT images of a region in southeast of Brazil. Pattern Search was used as the optimization algorithm. The experimental results demonstrated that the proposed method was able to substantially outperform estimates related to joint or conditional class transition probabilities, which rely on training samples.

  16. Prediction of Chemical-Protein Interactions Network with Weighted Network-Based Inference Method

    PubMed Central

    Cheng, Feixiong; Zhou, Yadi; Li, Weihua; Liu, Guixia; Tang, Yun

    2012-01-01

    Chemical-protein interaction (CPI) is the central topic of target identification and drug discovery. However, large scale determination of CPI is a big challenge for in vitro or in vivo experiments, while in silico prediction shows great advantages due to low cost and high accuracy. On the basis of our previous drug-target interaction prediction via network-based inference (NBI) method, we further developed node- and edge-weighted NBI methods for CPI prediction here. Two comprehensive CPI bipartite networks extracted from ChEMBL database were used to evaluate the methods, one containing 17,111 CPI pairs between 4,741 compounds and 97 G protein-coupled receptors, the other including 13,648 CPI pairs between 2,827 compounds and 206 kinases. The range of the area under receiver operating characteristic curves was 0.73 to 0.83 for the external validation sets, which confirmed the reliability of the prediction. The weak-interaction hypothesis in CPI network was identified by the edge-weighted NBI method. Moreover, to validate the methods, several candidate targets were predicted for five approved drugs, namely imatinib, dasatinib, sertindole, olanzapine and ziprasidone. The molecular hypotheses and experimental evidence for these predictions were further provided. These results confirmed that our methods have potential values in understanding molecular basis of drug polypharmacology and would be helpful for drug repositioning. PMID:22815915

  17. Maskiton: Interactive, web-based classification of single-particle electron microscopy images.

    PubMed

    Yoshioka, Craig; Lyumkis, Dmitry; Carragher, Bridget; Potter, Clinton S

    2013-05-01

    Electron microscopy (EM) is an important tool for determining the composition, arrangement and structure of biological macromolecules. When studying structurally heterogeneous samples using EM, classification is a critical step toward achieving higher resolution and identifying biologically significant conformations. We have developed an interactive, web-based tool, called Maskiton, for creating custom masks and performing 2D classifications on aligned single-particle EM images. The Maskiton interface makes it considerably easier and faster to explore the significance of heterogeneity in single-particle datasets. Maskiton features include: resumable uploads to facilitate transfer of large datasets to the server, custom mask creation in the browser, continual progress updates, and interactive viewing of classification results. To demonstrate the value of this tool, we provide examples of its use on several experimental datasets and include analyses of the independent terminus mobility within the Ltn1 E3 ubiquitin ligase, the in vitro assembly of 30S ribosomal subunits, and classification complexity reduction within Immunoglobulin M. This work also serves as a proof-of-concept for the development of future cross-platform, interactive user interfaces for electron microscopy data processing.

  18. "Turn off-on" fluorescent sensor for platinum drugs-DNA interactions based on quantum dots.

    PubMed

    Zhao, Dan; Li, Jiaotian; Yang, Tianming; He, Zhike

    2014-02-15

    A "turn off-on" mode has been established by using the interaction between platinum anticancer drugs and DNA as input signal and the fluorescence reversible change of quantum dots (QDs) as output signal. The QDs fluorescence can be quenched by platinum anticancer drugs via photo-induced electron transfer process, rendering the system into "turn off" status, and the system can then be "turned on" when fluorescence is restored due to covalent conjugation between DNA and platinum anticancer drugs. This dual-directional fluorescence change realized the detection of cisplatin and DNA, overcoming the selectivity problem commonly existed in the traditional mono-directional fluorescence detection mode. The reversible fluorescent "turn off-on" mode has been further employed to study the interactions between DNA and different platinum anticancer drugs (cisplatin, oxaliplatin and carboplatin). Furthermore, the impacts of different types of DNAs (different in base sequence, chain length and ssDNA/dsDNA) on the mode are also explored. This simple, fast and convenient spectroscopic method owns promising applications in the study on interaction between medical molecules and DNA, and in biochemical detections.

  19. Quantitative structure-activity relationship of organophosphate compounds based on molecular interaction fields descriptors.

    PubMed

    Zhao, Jinsong; Yu, Shuxia

    2013-03-01

    By using multi-block partial least-squares (MBPLS) method, quantitative structure-activity relationship (QSAR) between 35 organophosphate compounds (OP) and their 24h acute toxicities towards the housefly (Musca nebulo L.) was built on the molecular interaction fields (MIF) descriptors, which were obtained with O, N and DRY as probes, and then normalised with block unscaled weights (BUW) technique. The best QSAR model had 8 principal components, with the coefficient of determination R(2)=0.995 and that of leave-one-out cross-validation Q(2)=0.865, and the corresponding standard deviation of error 0.076 and 0.361, respectively. Block importance in the prediction (BIP) for O, N and DRY probe were 1.030, 0.962 and 1.007, respectively. Contour map of variable coefficients showed that hydrogen bonding between the O atom in PO and the NH groups in acetylcholinesterase (AChE) played an important role in the interaction between OP and AChE. Meanwhile, the hydrophobicity of OP also had significant contribution. QSAR based on the MIF descriptors could be a potential means to interpret the mechanisms of ligand-receptor interaction when the receptor was well known.

  20. Evaluation of cell interaction with polymeric biomaterials based on hyaluronic acid and chitosan.

    PubMed

    do Nascimento, Mônica Helena Monteiro; Ferreira, Mariselma; Malmonge, Sônia Maria; Lombello, Christiane Bertachini

    2017-05-01

    Tissue engineering involves the development of new materials or devices capable of specific interactions with biological tissues, searching the use of biocompatible materials as scaffolds for in vitro cell growth, and functional tissue development, that is subsequently implanted into patient. The aim of the current study was to evaluate the initial aspects of cell interaction with the polymeric biomaterials blends based on hyaluronic acid with chitosan. The hypothesis approach involves synthesis and analysis of swelling and thermal degradation (thermal gravimetric analysis) of the polymer blend; and Vero cell interaction with the biomaterial, through analysis of cytotoxicity, adhesion and cell morphology. The blend resulted in a biomaterial with a high swelling ratio that can allow nutrient distribution and absorption. The thermal gravimetric analysis results showed that the blend had two stages of degradation at temperatures very close to those observed for pure polymers, confirming that the physical mixing of hydrogels occurred, resulting in the presence of both hyaluronic acid and chitosan in the blend. The evaluation of indirect cytotoxicity showed that the blend was non cytotoxic for Vero cells, and the quantitative analysis performed with the MTT could verify a cell viability of 98%. The cells cultured on the blend showed adhesion, spreading and proliferation on this biomaterial, distinguished from the pattern of the control cells. These results showed that the blends produced from hyaluronic acid and chitosan hydrogels are promising for applications in tissue engineering, aiming at future cartilaginous tissue.

  1. Phantom-based multimodal interactions for medical education and training: the Munich Knee Joint Simulator.

    PubMed

    Riener, Robert; Frey, Martin; Pröll, Thomas; Regenfelder, Felix; Burgkart, Rainer

    2004-06-01

    Simulation environments based on virtual reality technologies can support medical education and training. In this paper, the novel approach of an "interactive phantom" is presented that allows a realistic display of haptic contact information typically generated when touching and moving human organs or segments. The key idea of the haptic interface is to attach passive phantom objects to a mechanical actuator. The phantoms look and feel as real anatomical objects. Additional visualization of internal anatomical and physiological information and sound generated during the interaction with the phantom yield a multimodal approach that can increase performance, didactic value, and immersion into the virtual environment. Compared to classical approaches, this multimodal display is convenient to use, provides realistic tactile properties, and can be partly adjusted to different, e.g., pathological properties. The interactive phantom is exemplified by a virtual human knee joint that can support orthopedic education, especially for the training of clinical knee joint evaluation. It is suggested that the technical principle can be transferred to many other fields of medical education and training such as obstetrics and dentistry.

  2. The research-design interaction: lessons learned from an evidence-based design studio.

    PubMed

    Haq, Saif; Pati, Debajyoti

    2010-01-01

    As evidence-based design (EBD) emerges as a model of design practice, considerable attention has been given to its research component. However, this overshadows another essential component of EBD-the change agent, namely the designer. EBD introduced a new skill set to the practitioner: the ability to interact with scientific evidence. Industry sources suggest adoption of the EBD approach across a large number of design firms. How comfortable are these designers in integrating research with design decision making? Optimizing the interaction between the primary change agent (the designer) and the evidence is crucial to producing the desired outcomes. Preliminary to examining this question, an architectural design studio was used as a surrogate environment to examine how designers interact with evidence. Twelve students enrolled in a healthcare EBD studio during the spring of 2009. A three-phase didactic structure was adopted: knowing a hospital, knowing the evidence, and designing with knowledge and evidence. Products of the studio and questionnaire responses from the students were used as the data for analysis. The data suggest that optimization of the research-design relationship warrants consideration in four domains: (1) a knowledge structure that is easy to comprehend; (2) phase-complemented representation of evidence; (3) access to context and precedence information; and (4) a designer-friendly vocabulary.

  3. Model-based safety analysis of human-robot interactions: the MIRAS walking assistance robot.

    PubMed

    Guiochet, Jérémie; Hoang, Quynh Anh Do; Kaaniche, Mohamed; Powell, David

    2013-06-01

    Robotic systems have to cope with various execution environments while guaranteeing safety, and in particular when they interact with humans during rehabilitation tasks. These systems are often critical since their failure can lead to human injury or even death. However, such systems are difficult to validate due to their high complexity and the fact that they operate within complex, variable and uncertain environments (including users), in which it is difficult to foresee all possible system behaviors. Because of the complexity of human-robot interactions, rigorous and systematic approaches are needed to assist the developers in the identification of significant threats and the implementation of efficient protection mechanisms, and in the elaboration of a sound argumentation to justify the level of safety that can be achieved by the system. For threat identification, we propose a method called HAZOP-UML based on a risk analysis technique adapted to system description models, focusing on human-robot interaction models. The output of this step is then injected in a structured safety argumentation using the GSN graphical notation. Those approaches have been successfully applied to the development of a walking assistant robot which is now in clinical validation.

  4. An interactive system for creating object models from range data based on simulated annealing

    SciTech Connect

    Hoff, W.A.; Hood, F.W.; King, R.H.

    1997-05-01

    In hazardous applications such as remediation of buried waste and dismantlement of radioactive facilities, robots are an attractive solution. Sensing to recognize and locate objects is a critical need for robotic operations in unstructured environments. An accurate 3-D model of objects in the scene is necessary for efficient high level control of robots. Drawing upon concepts from supervisory control, the authors have developed an interactive system for creating object models from range data, based on simulated annealing. Site modeling is a task that is typically performed using purely manual or autonomous techniques, each of which has inherent strengths and weaknesses. However, an interactive modeling system combines the advantages of both manual and autonomous methods, to create a system that has high operator productivity as well as high flexibility and robustness. The system is unique in that it can work with very sparse range data, tolerate occlusions, and tolerate cluttered scenes. The authors have performed an informal evaluation with four operators on 16 different scenes, and have shown that the interactive system is superior to either manual or automatic methods in terms of task time and accuracy.

  5. Neurotypical Peers are Less Willing to Interact with Those with Autism based on Thin Slice Judgments

    PubMed Central

    Sasson, Noah J.; Faso, Daniel J.; Nugent, Jack; Lovell, Sarah; Kennedy, Daniel P.; Grossman, Ruth B.

    2017-01-01

    Individuals with autism spectrum disorder (ASD), including those who otherwise require less support, face severe difficulties in everyday social interactions. Research in this area has primarily focused on identifying the cognitive and neurological differences that contribute to these social impairments, but social interaction by definition involves more than one person and social difficulties may arise not just from people with ASD themselves, but also from the perceptions, judgments, and social decisions made by those around them. Here, across three studies, we find that first impressions of individuals with ASD made from thin slices of real-world social behavior by typically-developing observers are not only far less favorable across a range of trait judgments compared to controls, but also are associated with reduced intentions to pursue social interaction. These patterns are remarkably robust, occur within seconds, do not change with increased exposure, and persist across both child and adult age groups. However, these biases disappear when impressions are based on conversational content lacking audio-visual cues, suggesting that style, not substance, drives negative impressions of ASD. Collectively, these findings advocate for a broader perspective of social difficulties in ASD that considers both the individual’s impairments and the biases of potential social partners. PMID:28145411

  6. A Context-Aware Interactive Health Care System Based on Ontology and Fuzzy Inference.

    PubMed

    Chiang, Tzu-Chiang; Liang, Wen-Hua

    2015-09-01

    In the present society, most families are double-income families, and as the long-term care is seriously short of manpower, it contributes to the rapid development of tele-homecare equipment, and the smart home care system gradually emerges, which assists the elderly or patients with chronic diseases in daily life. This study aims at interaction between persons under care and the system in various living spaces, as based on motion-sensing interaction, and the context-aware smart home care system is proposed. The system stores the required contexts in knowledge ontology, including the physiological information and environmental information of the person under care, as the database of decision. The motion-sensing device enables the person under care to interact with the system through gestures. By the inference mechanism of fuzzy theory, the system can offer advice and rapidly execute service, thus, implementing the EHA. In addition, the system is integrated with the functions of smart phone, tablet PC, and PC, in order that users can implement remote operation and share information regarding the person under care. The health care system constructed in this study enables the decision making system to probe into the health risk of each person under care; then, from the view of preventive medicine, and through a composing system and simulation experimentation, tracks the physiological trend of the person under care, and provides early warning service, thus, promoting smart home care.

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

    NASA Astrophysics Data System (ADS)

    Jones, Henry Lee, II

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

  8. Interactions of selected policy-stakeholder groups implementing middle school science standards-based systemic reform

    NASA Astrophysics Data System (ADS)

    Boydston, Theodore Lewis, III

    1999-12-01

    This research is an interpretive inquiry into the views and interactions of stakeholders in a district office of a large school system responsible for implementing science systemic reform. Three major sources of data were used in this research: surveys, stakeholder interviews, and autobiographical reflection on experiences as part of the reform initiative. This is an emergent research that is evident in the shift in the focus of research questions and their supporting assumptions during the research. The literature review describes standards-based reform, arguments about reform, and the major dimensions of reform research. The results of the survey of stakeholders revealed that the views among the stakeholder groups followed the system hierarchy and could be separated into two large groups; staff responsible for implementing the reform initiative and the other stakeholder groups. Each of these groups was composed of identifiable subgroups. The interviews with stakeholders revealed how their different attitudes, values, and beliefs frame the context of stakeholder interactions. An over reliance on an authoritarian view of decision-making leaves many stakeholders feeling disempowered and critical of others. This atmosphere promotes blaming, which inhibits collegial interaction. Work experiences in the district office revealed how stakeholders' unaddressed assumptions, attitudes, and beliefs promote fragmentation and competition rather than cooperation. Hidden assumptions about management by control and mandate, competition, and teaching and learning appear to restrain the interactions of stakeholders. Support of the National Science Education Standards was identified as a unifying view among the stakeholders, yet the professional development program focused on content and pedagogical knowledge without addressing stakeholder concerns and beliefs about the intended constructivist framework of the program. Stakeholders' attitudes about the issue of equity demonstrated

  9. MPQ-cytometry: a magnetism-based method for quantification of nanoparticle-cell interactions

    NASA Astrophysics Data System (ADS)

    Shipunova, V. O.; Nikitin, M. P.; Nikitin, P. I.; Deyev, S. M.

    2016-06-01

    Precise quantification of interactions between nanoparticles and living cells is among the imperative tasks for research in nanobiotechnology, nanotoxicology and biomedicine. To meet the challenge, a rapid method called MPQ-cytometry is developed, which measures the integral non-linear response produced by magnetically labeled nanoparticles in a cell sample with an original magnetic particle quantification (MPQ) technique. MPQ-cytometry provides a sensitivity limit 0.33 ng of nanoparticles and is devoid of a background signal present in many label-based assays. Each measurement takes only a few seconds, and no complicated sample preparation or data processing is required. The capabilities of the method have been demonstrated by quantification of interactions of iron oxide nanoparticles with eukaryotic cells. The total amount of targeted nanoparticles that specifically recognized the HER2/neu oncomarker on the human cancer cell surface was successfully measured, the specificity of interaction permitting the detection of HER2/neu positive cells in a cell mixture. Moreover, it has been shown that MPQ-cytometry analysis of a HER2/neu-specific iron oxide nanoparticle interaction with six cell lines of different tissue origins quantitatively reflects the HER2/neu status of the cells. High correlation of MPQ-cytometry data with those obtained by three other commonly used in molecular and cell biology methods supports consideration of this method as a prospective alternative for both quantifying cell-bound nanoparticles and estimating the expression level of cell surface antigens. The proposed method does not require expensive sophisticated equipment or highly skilled personnel and it can be easily applied for rapid diagnostics, especially under field conditions.Precise quantification of interactions between nanoparticles and living cells is among the imperative tasks for research in nanobiotechnology, nanotoxicology and biomedicine. To meet the challenge, a rapid method

  10. Population-based analysis of Alzheimer’s disease risk alleles implicates genetic interactions

    PubMed Central

    Ebbert, Mark T. W.; Ridge, Perry G.; Wilson, Andrew R.; Sharp, Aaron R.; Bailey, Matthew; Norton, Maria C.; Tschanz, JoAnn T.; Munger, Ronald G.; Corcoran, Christopher D.; Kauwe, John S. K.

    2013-01-01

    Background Reported odds ratios and population attributable fractions (PAF) for late-onset Alzheimer’s disease (LOAD) risk loci (BIN1, ABCA7, CR1, MS4A4E, CD2AP, PICALM, MS4A6A, CD33, and CLU) come from clinically ascertained samples. Little is known about the combined PAF for these LOAD risk alleles and the utility of these combined markers for case-control prediction. Here we evaluate these loci in a large population-based sample to estimate PAF and explore the effects of additive and non-additive interactions on LOAD status prediction performance. Methods 2,419 samples from the Cache County Memory Study were genotyped for APOE and nine LOAD risk loci from AlzGene.org. We used logistic regression and ROC analysis to assess the LOAD status prediction performance of these loci using additive and non-additive models, and compared ORs and PAFs between AlzGene.org and Cache County. Results Odds ratios were comparable between Cache County and AlzGene.org when identical SNPs were genotyped. PAFs from AlzGene.org ranged from 2.25–37%; those from Cache County ranged from 0.05–20%. Including non-APOE alleles significantly improved LOAD status prediction performance (AUC = 0.80) over APOE alone (AUC = 0.78) when not constrained to an additive relationship (p < 0.03). We identified potential allelic interactions (p-values uncorrected): CD33-MS4A4E (Synergy Factor = 5.31; p < 0.003) and CLU-MS4A4E (SF = 3.81; p < 0.016). Conclusions While non-additive interactions between loci significantly improve diagnostic ability, the improvement does not reach the desired sensitivity or specificity for clinical use. Nevertheless, these results suggest that understanding gene-gene interactions may be important in resolving Alzheimer’s disease etiology. PMID:23954108

  11. NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.

    PubMed

    Harris, Kimberly A; Bobay, Benjamin G; Sarachan, Kathryn L; Sims, Alexis F; Bilbille, Yann; Deutsch, Christopher; Iwata-Reuyl, Dirk; Agris, Paul F

    2015-08-14

    The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in the biosynthesis of t(6)A37, the details of the enzymatic mechanism remain unsolved. Therefore, the solution structure of Escherichia coli TsaC was characterized by NMR to further study the interactions with ATP and L-threonine, both substrates of TsaC in the biosynthesis of L-threonylcarbamoyl-AMP. Several conserved amino acids were identified that create a hydrophobic binding pocket for the adenine of ATP. Additionally, two residues were found to interact with L-threonine. Both binding sites are located in a deep cavity at the center of the protein. Models derived from the NMR data and molecular modeling reveal several sites with considerable conformational flexibility in TsaC that may be important for L-threonine recognition, ATP activation, and/or protein/protein interactions. These observations further the understanding of the enzymatic reaction catalyzed by TsaC, a threonylcarbamoyl-AMP synthase, and provide structure-based insight into the mechanism of t(6)A37 biosynthesis.

  12. Comparison of Interactive Computer-Based and Classroom Training on Human Rights Awareness in Persons with Intellectual Disabilities

    ERIC Educational Resources Information Center

    Tardif-Williams, Christine Y.; Owen, Frances; Feldman, Maurice; Tarulli, Donato; Griffiths, Dorothy; Sales, Carol; McQueen-Fuentes, Glenys; Stoner, Karen

    2007-01-01

    We tested the effectiveness of an interactive, video CD-ROM in teaching persons with intellectual disabilities (ID) about their human rights. Thirty-nine participants with ID were trained using both a classroom activity-based version of the training program and the interactive CD-ROM in a counterbalanced presentation. All individuals were pre- and…

  13. Student Interaction and Knowledge Construction in Case-Based Learning in Educational Psychology Using Online Discussions: The Role of Structure

    ERIC Educational Resources Information Center

    Pena-Shaff, Judith; Altman, William

    2015-01-01

    We analyzed students' patterns of participation, interaction and knowledge construction in asynchronous online case-based discussions in two Educational Psychology classes with different participation and interaction guidelines. We conducted quantitative analyses of the outlines of postings and transcripts of online messages from these group…

  14. Docking of ethanamine Schiff base imines & metal (II) complexes, cytotoxicity & DNA interaction studies

    NASA Astrophysics Data System (ADS)

    Sujarani, S.; Ramu, A.

    2015-01-01

    The present study deals with a series of biologically and stereo chemically important novel transition metal (II) Schiff base chelates. The Cu (II), Co (II), Mn (II) and Ni (II) ions containing complexes were synthesized by using diphenylethanamine and 2-hydroxy/2, 4-dihydroxy/2-hydroxy-4-methoxybenzaldehydes. The synthesized complexes were characterized using micro analytical, IR, NMR, ESI-Mass, UV-Visible, cyclic voltammetry and the EPR spectroscopic techniques. The spectral data evidenced the action of ligands as a neutral bidentate Schiff bases, coordinating through azomethine nitrogen and oxygen atom of hydroxyl group. The interaction studies revealed the groove binding nature of complexes with CT-DNA. The ligand and synthesized metal complexes showed cytotoxicity against cancerous cells. The strong binding affinity of the imine and metal complexes was also confirmed by molecular docking studies.

  15. Structure-Based Design of Inhibitors of Protein–Protein Interactions: Mimicking Peptide Binding Epitopes

    PubMed Central

    Pelay-Gimeno, Marta; Glas, Adrian; Koch, Oliver; Grossmann, Tom N

    2015-01-01

    Protein–protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A–D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices. PMID:26119925

  16. A concept-based interactive biomedical image retrieval approach using visualness and spatial information

    NASA Astrophysics Data System (ADS)

    Rahman, Md M.; Antani, Sameer K.; Demner-Fushman, Dina; Thoma, George R.

    2015-03-01

    This paper presents a novel approach to biomedical image retrieval by mapping image regions to local concepts and represent images in a weighted entropy-based concept feature space. The term concept refers to perceptually distinguishable visual patches that are identified locally in image regions and can be mapped to a glossary of imaging terms. Further, the visual significance (e.g., visualness) of concepts is measured as Shannon entropy of pixel values in image patches and is used to refine the feature vector. Moreover, the system can assist user in interactively select a Region-Of-Interest (ROI) and search for similar image ROIs. Further, a spatial verification step is used as a post-processing step to improve retrieval results based on location information. The hypothesis that such approaches would improve biomedical image retrieval, is validated through experiments on a data set of 450 lung CT images extracted from journal articles from four different collections.

  17. Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.

    PubMed

    Good, Andrew C; Liu, Jinyu; Hirth, Bradford; Asmussen, Gary; Xiang, Yibin; Biemann, Hans-Peter; Bishop, Kimberly A; Fremgen, Trisha; Fitzgerald, Maria; Gladysheva, Tatiana; Jain, Annuradha; Jancsics, Katherine; Metz, Markus; Papoulis, Andrew; Skerlj, Renato; Stepp, J David; Wei, Ronnie R

    2012-03-22

    We have studied the subtleties of fragment docking and binding using data generated in a Pim-1 kinase inhibitor program. Crystallographic and docking data analyses have been undertaken using inhibitor complexes derived from an in-house surface plasmon resonance (SPR) fragment screen, a virtual needle screen, and a de novo designed fragment inhibitor hybrid. These investigations highlight that fragments that do not fill their binding pocket can exhibit promiscuous hydrophobic interactions due to the lack of steric constraints imposed on them by the boundaries of said pocket. As a result, docking modes that disagree with an observed crystal structure but maintain key crystallographically observed hydrogen bonds still have potential value in ligand design and optimization. This observation runs counter to the lore in fragment-based drug design that all fragment elaboration must be based on the parent crystal structure alone.

  18. Interactive computer-based interventions for weight loss or weight maintenance in overweight or obese people

    PubMed Central

    Wieland, L. Susan; Falzon, Louise; Sciamanna, Chris N; Trudeau, Kimberlee J; Folse, Suzanne Brodney; Schwartz, Joseph E; Davidson, Karina W

    2014-01-01

    Background The World Health Organization (WHO) estimates that the number of obese or overweight individuals worldwide will increase to 1.5 billion by 2015. Chronic diseases associated with overweight or obesity include diabetes, heart disease, hypertension and stroke. Objectives To assess the effects of interactive computer-based interventions for weight loss or weight maintenance in overweight or obese people. Search methods We searched several electronic databases, including CENTRAL, MEDLINE, EMBASE, CINAHL, LILACS and PsycINFO, through 25 May 2011. We also searched clinical trials registries to identify studies. We scanned reference lists of included studies and relevant systematic reviews. Selection criteria Studies were included if they were randomized controlled trials or quasi-randomized controlled trials that evaluated interactive computer-based weight loss or weight maintenance programs in adults with overweight or obesity. We excluded trials if the duration of the intervention was less than four weeks or the loss to follow-up was greater than 20% overall. Data collection and analysis Two authors independently extracted study data and assessed risk of bias. Where interventions, control conditions, outcomes and time frames were similar between studies, we combined study data using meta-analysis. Main results We included 14 weight loss studies with a total of 2537 participants, and four weight maintenance studies with a total of 1603 participants. Treatment duration was between four weeks and 30 months. At six months, computer-based interventions led to greater weight loss than minimal interventions (mean difference (MD) −1.5 kg; 95% confidence interval (CI) −2.1 to −0.9; two trials) but less weight loss than in-person treatment (MD 2.1 kg; 95% CI 0.8 to 3.4; one trial). At six months, computer-based interventions were superior to a minimal control intervention in limiting weight regain (MD −0.7 kg; 95% CI −1.2 to −0.2; two trials), but not

  19. Web- and system-code based, interactive, nuclear power plant simulators

    SciTech Connect

    Kim, K. D.; Jain, P.; Rizwan, U.

    2006-07-01

    Using two different approaches, on-line, web- and system-code based graphical user interfaces have been developed for reactor system analysis. Both are LabVIEW (graphical programming language developed by National Instruments) based systems that allow local users as well as those at remote sites to run, interact and view the results of the system code in a web browser. In the first approach, only the data written by the system code in a tab separated ASCII output file is accessed and displayed graphically. In the second approach, LabVIEW virtual instruments are coupled with the system code as dynamic link libraries (DLL). RELAP5 is used as the system code to demonstrate the capabilities of these approaches. From collaborative projects between teams in geographically remote locations to providing system code experience to distance education students, these tools can be very beneficial in many areas of teaching and R and D. (authors)

  20. Knowledge based and interactive control for the Superfluid Helium On-orbit Transfer Project

    NASA Technical Reports Server (NTRS)

    Castellano, Timothy P.; Raymond, Eric A.; Shapiro, Jeff C.; Robinson, Frank A.; Rosenthal, Donald A.

    1989-01-01

    NASA's Superfluid Helium On-Orbit Transfer (SHOOT) project is a Shuttle-based experiment designed to acquire data on the properties of superfluid helium in micro-gravity. Aft Flight Deck Computer Software for the SHOOT experiment is comprised of several monitoring programs which give the astronaut crew visibility into SHOOT systems and a rule based system which will provide process control, diagnosis and error recovery for a helium transfer without ground intervention. Given present Shuttle manifests, this software will become the first expert system to be used in space. The SHOOT Command and Monitoring System (CMS) software will provide a near real time highly interactive interface for the SHOOT principal investigator to control the experiment and to analyze and display its telemetry. The CMS software is targeted for all phases of the SHOOT project: hardware development, pre-flight pad servicing, in-flight operations, and post-flight data analysis.

  1. FRIAA: A FRamework for Web-based Interactive Astronomy Analysis using AMQP Messaging

    NASA Astrophysics Data System (ADS)

    Young, M. D.; Gopu, A.; Hayashi, S.; Cox, J. A.

    2013-10-01

    This paper describes a web-based FRamework for Interactive Astronomy Analysis (FRIAA) being developed as part of the One Degree Imager - Pipeline, Portal, and Archive (ODI-PPA) Science Gateway. The framework provides astronomers with the ability to invoke data processing modules including IRAF and SExtractor on large data within their ODI-PPA web account without requiring them to download the data or to access remote compute resources. Currently available functionality includes contour plots, point source detection and photometry, surface photometry, and catalog source matching. The web browser front-end developed using the Zend PHP platform and the Bootstrap library makes Remote Procedure Calls (RPC) to the back-end modules using AMQP based messaging. The compute-intensive data processing codes are executed on powerful and dedicated nodes on a compute cluster at Indiana University.

  2. Synthesis and DNA interaction of a mixed proflavine-phenanthroline Tröger base.

    PubMed

    Baldeyrou, Brigitte; Tardy, Christelle; Bailly, Christian; Colson, Pierre; Houssier, Claude; Charmantray, Franck; Demeunynck, Martine

    2002-04-01

    We report the synthesis of an asymmetric Tröger base containing the two well characterised DNA binding chromophores, proflavine and phenanthroline. The mode of interaction of the hybrid molecule was investigated by circular and linear dichroism experiments and a biochemical assay using DNA topoisomerase I. The data are compatible with a model in which the proflavine moiety intercalates between DNA base pairs and the phenanthroline ring occupies the DNA groove. DNase I cleavage experiments were carried out to investigate the sequence preference of the hybrid ligand and a well resolved footprint was detected at a site encompassing two adjacent 5'-GTC.5-GAC triplets. The sequence preference of the asymmetric molecule is compared to that of the symmetric analogues.

  3. Static characteristics design of hydrostatic guide-ways based on fluid-structure interactions

    NASA Astrophysics Data System (ADS)

    Lin, Shuo; Yin, YueHong

    2016-10-01

    With the raising requirements in micro optical systems, the available machines become hard to achieve the process dynamic and accuracy in all aspects. This makes compact design based on fluid/structure interactions (FSI) important. However, there is a difficulty in studying FSI with oil film as fluid domain. This paper aims at static characteristic design of a hydrostatic guide-way with capillary restrictors based on FSI. The pressure distribution of the oil film land is calculated by solving the Reynolds-equation with Galerkin technique. The deformation of structure is calculated by commercial FEM software, MSC. Nastran. A matlab program is designed to realize the coupling progress by modifying the load boundary in the submitting file and reading the deformation result. It's obvious that the stiffness of the hydrostatic bearing decreases with the weakening of the bearing structure. This program is proposed to make more precise prediction of bearing stiffness.

  4. Nuclear Spin Relaxation and Molecular Interactions of a Novel Triazolium-Based Ionic Liquid

    SciTech Connect

    Allen, Jesse J; Schneider, Yanika; Kail, Brian W; Luebke, David R; Nulwala, Hunaid; Damodaran, Krishnan

    2013-04-11

    Nuclear spin relaxation, small-angle X-ray scattering (SAXS), and electrospray ionization mass spectrometry (ESI-MS) techniques are used to determine supramolecular arrangement of 3-methyl-1-octyl-4-phenyl-1H-triazol-1,2,3-ium bis(trifluoromethanesulfonyl)imide [OMPhTz][Tf{sub 2}N], an example of a triazolium-based ionic liquid. The results obtained showed first-order thermodynamic dependence for nuclear spin relaxation of the anion. First-order relaxation dependence is interpreted as through-bond dipolar relaxation. Greater than first-order dependence was found in the aliphatic protons, aromatic carbons (including nearest neighbors), and carbons at the end of the aliphatic tail. Greater than first order thermodynamic dependence of spin relaxation rates is interpreted as relaxation resulting from at least one mechanism additional to through-bond dipolar relaxation. In rigid portions of the cation, an additional spin relaxation mechanism is attributed to anisotropic effects, while greater than first order thermodynamic dependence of the octyl side chain’s spin relaxation rates is attributed to cation–cation interactions. Little interaction between the anion and the cation was observed by spin relaxation studies or by ESI-MS. No extended supramolecular structure was observed in this study, which was further supported by MS and SAXS. nuclear Overhauser enhancement (NOE) factors are used in conjunction with spin–lattice relaxation time (T{sub 1}) measurements to calculate rotational correlation times for C–H bonds (the time it takes for the vector represented by the bond between the two atoms to rotate by one radian). The rotational correlation times are used to represent segmental reorientation dynamics of the cation. A combination of techniques is used to determine the segmental interactions and dynamics of this example of a triazolium-based ionic liquid.

  5. Interactive Dose Shaping - efficient strategies for CPU-based real-time treatment planning

    NASA Astrophysics Data System (ADS)

    Ziegenhein, P.; Kamerling, C. P.; Oelfke, U.

    2014-03-01

    Conventional intensity modulated radiation therapy (IMRT) treatment planning is based on the traditional concept of iterative optimization using an objective function specified by dose volume histogram constraints for pre-segmented VOIs. This indirect approach suffers from unavoidable shortcomings: i) The control of local dose features is limited to segmented VOIs. ii) Any objective function is a mathematical measure of the plan quality, i.e., is not able to define the clinically optimal treatment plan. iii) Adapting an existing plan to changed patient anatomy as detected by IGRT procedures is difficult. To overcome these shortcomings, we introduce the method of Interactive Dose Shaping (IDS) as a new paradigm for IMRT treatment planning. IDS allows for a direct and interactive manipulation of local dose features in real-time. The key element driving the IDS process is a two-step Dose Modification and Recovery (DMR) strategy: A local dose modification is initiated by the user which translates into modified fluence patterns. This also affects existing desired dose features elsewhere which is compensated by a heuristic recovery process. The IDS paradigm was implemented together with a CPU-based ultra-fast dose calculation and a 3D GUI for dose manipulation and visualization. A local dose feature can be implemented via the DMR strategy within 1-2 seconds. By imposing a series of local dose features, equal plan qualities could be achieved compared to conventional planning for prostate and head and neck cases within 1-2 minutes. The idea of Interactive Dose Shaping for treatment planning has been introduced and first applications of this concept have been realized.

  6. Interactive breast cancer segmentation based on relevance feedback: from user-centered design to evaluation

    NASA Astrophysics Data System (ADS)

    Gouze, A.; Kieffer, S.; Van Brussel, C.; Moncarey, R.; Grivegnée, A.; Macq, B.

    2009-02-01

    Computer systems play an important role in medical imaging industry since radiologists depend on it for visualization, interpretation, communication and archiving. In particular, computer-aided diagnosis (CAD) systems help in lesion detection tasks. This paper presents the design and the development of an interactive segmentation tool for breast cancer screening and diagnosis. The tool conception is based upon a user-centered approach in order to ensure that the application is of real benefit to radiologists. The analysis of user expectations, workflow and decision-making practices give rise to the need for an interactive reporting system based on the BIRADS, that would not only include the numerical features extracted from the segmentation of the findings in a structured manner, but also support human relevance feedback as well. This way, the numerical results from segmentation can be either validated by end-users or enhanced thanks to domain-experts subjective interpretation. Such a domain-expert centered system requires the segmentation to be sufficiently accurate and locally adapted, and the features to be carefully selected in order to best suit user's knowledge and to be of use in enhancing segmentation. Improving segmentation accuracy with relevance feedback and providing radiologists with a user-friendly interface to support image analysis are the contributions of this work. The preliminary result is first the tool conception, and second the improvement of the segmentation precision.

  7. Hand gesture recognition based on motion history images for a simple human-computer interaction system

    NASA Astrophysics Data System (ADS)

    Timotius, Ivanna K.; Setyawan, Iwan

    2013-03-01

    A human-computer interaction can be developed using several kind of tools. One choice is using images captured using a camera. This paper proposed a simple human-computer interaction system based on hand movement captured by a web camera. The system aims to classify the captured movement into one of three classes. The first two classes contain hand movements to the left and right, respectively. The third class contains non-hand movements or hand movements to other directions. The method used in this paper is based on Motion History Images (MHIs) and nearest neighbor classifier. The resulting MHIs are processed in two manners, namely by summing the pixel values along the vertical axis and reshaping into vectors. We also use two distance criteria in this paper, respectively the Euclidian distance and cross correlation. This paper compared the performance of the combinations of different MHI data processing and distance criteria using 10 runs of 2-fold cross validation. Our experiments show that reshaping the MHI data into vectors combined with a Euclidean distance criterion gives the highest average accuracy, namely 55.67%.

  8. Label Propagation Prediction of Drug-Drug Interactions Based on Clinical Side Effects.

    PubMed

    Zhang, Ping; Wang, Fei; Hu, Jianying; Sorrentino, Robert

    2015-07-21

    Drug-drug interaction (DDI) is an important topic for public health, and thus attracts attention from both academia and industry. Here we hypothesize that clinical side effects (SEs) provide a human phenotypic profile and can be translated into the development of computational models for predicting adverse DDIs. We propose an integrative label propagation framework to predict DDIs by integrating SEs extracted from package inserts of prescription drugs, SEs extracted from FDA Adverse Event Reporting System, and chemical structures from PubChem. Experimental results based on hold-out validation demonstrated the effectiveness of the proposed algorithm. In addition, the new algorithm also ranked drug information sources based on their contributions to the prediction, thus not only confirming that SEs are important features for DDI prediction but also paving the way for building more reliable DDI prediction models by prioritizing multiple data sources. By applying the proposed algorithm to 1,626 small-molecule drugs which have one or more SE profiles, we obtained 145,068 predicted DDIs. The predicted DDIs will help clinicians to avoid hazardous drug interactions in their prescriptions and will aid pharmaceutical companies to design large-scale clinical trial by assessing potentially hazardous drug combinations. All data sets and predicted DDIs are available at http://astro.temple.edu/~tua87106/ddi.html.

  9. Study of the interaction between indole-based compounds and biologically relevant G-quadruplexes.

    PubMed

    Carvalho, Josué; Nottelet, Pierre; Mergny, Jean-Louis; Queiroz, João A; Salgado, Gilmar F; Cruz, Carla

    2017-04-01

    G-quadruplexes (G4s) are high-order secondary structures that modulate several key cell processes such as telomere function, gene expression and DNA replication. In the past years G4s have emerged as promising targets for drug development due to the discovery of small molecules which bind and stabilize these structures. In this work, we report the synthesis of indole-based compounds and the study of their interaction with the biological relevant G4s c-MYC and human telomeric repeat 22AG using several biophysical techniques. The ligands are G4 specific and they can discriminate different G4 structures namely parallel and hybrid-1 topologies. The NMR study of interaction between the most promising indole-derivative (compound 3) and c-MYC quadruplex suggests that the ligand binds on the external tetrads with additional actions in the loops/grooves in a 2:1 ratio. The molecular docking calculations of compound 3 to c-MYC quadruplex corroborates with the (1)H and NOESY NMR studies. Overall, the results suggest that indole-based ligands are promising candidates for future lead optimizations in drug development.

  10. Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming.

    PubMed

    Chen, Ruoying; Zhang, Zhiwang; Wu, Di; Zhang, Peng; Zhang, Xinyang; Wang, Yong; Shi, Yong

    2011-01-21

    Protein-protein interactions are fundamentally important in many biological processes and it is in pressing need to understand the principles of protein-protein interactions. Mutagenesis studies have found that only a small fraction of surface residues, known as hot spots, are responsible for the physical binding in protein complexes. However, revealing hot spots by mutagenesis experiments are usually time consuming and expensive. In order to complement the experimental efforts, we propose a new computational approach in this paper to predict hot spots. Our method, Rough Set-based Multiple Criteria Linear Programming (RS-MCLP), integrates rough sets theory and multiple criteria linear programming to choose dominant features and computationally predict hot spots. Our approach is benchmarked by a dataset of 904 alanine-mutated residues and the results show that our RS-MCLP method performs better than other methods, e.g., MCLP, Decision Tree, Bayes Net, and the existing HotSprint database. In addition, we reveal several biological insights based on our analysis. We find that four features (the change of accessible surface area, percentage of the change of accessible surface area, size of a residue, and atomic contacts) are critical in predicting hot spots. Furthermore, we find that three residues (Tyr, Trp, and Phe) are abundant in hot spots through analyzing the distribution of amino acids.

  11. ActiviTree: interactive visual exploration of sequences in event-based data using graph similarity.

    PubMed

    Vrotsou, Katerina; Johansson, Jimmy; Cooper, Matthew

    2009-01-01

    The identification of significant sequences in large and complex event-based temporal data is a challenging problem with applications in many areas of today's information intensive society. Pure visual representations can be used for the analysis, but are constrained to small data sets. Algorithmic search mechanisms used for larger data sets become expensive as the data size increases and typically focus on frequency of occurrence to reduce the computational complexity, often overlooking important infrequent sequences and outliers. In this paper we introduce an interactive visual data mining approach based on an adaptation of techniques developed for web searching, combined with an intuitive visual interface, to facilitate user-centred exploration of the data and identification of sequences significant to that user. The search algorithm used in the exploration executes in negligible time, even for large data, and so no pre-processing of the selected data is required, making this a completely interactive experience for the user. Our particular application area is social science diary data but the technique is applicable across many other disciplines.

  12. RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.

    PubMed

    Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

    2009-01-01

    We present a new database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases. The database consists of a classification of binding sites derived from protein-RNA complexes. Each binding site is assigned to a cluster of similar binding sites in other protein-RNA complexes. Cluster members share similar spatial arrangements of physico-chemical properties, thus can reveal novel similarity between proteins and RNAs with different sequences and folds. The clusters provide 3D consensus binding patterns important for protein-nucleotide recognition. The database search engine allows two types of useful queries: first, given a PDB code of a protein-RNA complex, RsiteDB can detail and classify the properties of the protein binding pockets accommodating extruded RNA nucleotides not involved in local RNA base pairing. Second, given an unbound protein structure, RsiteDB can perform an on-line structural search against the constructed database of 3D consensus binding patterns. Regions similar to known patterns are predicted to serve as binding sites. Alignment of the query to these patterns with their corresponding RNA nucleotides allows making unique predictions of the protein-RNA interactions at the atomic level of detail. This database is accessible at http://bioinfo3d.cs.tau.ac.il/RsiteDB.

  13. UTOPIAN: user-driven topic modeling based on interactive nonnegative matrix factorization.

    PubMed

    Choo, Jaegul; Lee, Changhyun; Reddy, Chandan K; Park, Haesun

    2013-12-01

    Topic modeling has been widely used for analyzing text document collections. Recently, there have been significant advancements in various topic modeling techniques, particularly in the form of probabilistic graphical modeling. State-of-the-art techniques such as Latent Dirichlet Allocation (LDA) have been successfully applied in visual text analytics. However, most of the widely-used methods based on probabilistic modeling have drawbacks in terms of consistency from multiple runs and empirical convergence. Furthermore, due to the complicatedness in the formulation and the algorithm, LDA cannot easily incorporate various types of user feedback. To tackle this problem, we propose a reliable and flexible visual analytics system for topic modeling called UTOPIAN (User-driven Topic modeling based on Interactive Nonnegative Matrix Factorization). Centered around its semi-supervised formulation, UTOPIAN enables users to interact with the topic modeling method and steer the result in a user-driven manner. We demonstrate the capability of UTOPIAN via several usage scenarios with real-world document corpuses such as InfoVis/VAST paper data set and product review data sets.

  14. Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach

    PubMed Central

    Kim, Sun; Yeganova, Lana; Wilbur, W. John

    2015-01-01

    Identifying unknown drug interactions is of great benefit in the early detection of adverse drug reactions. Despite existence of several resources for drug-drug interaction (DDI) information, the wealth of such information is buried in a body of unstructured medical text which is growing exponentially. This calls for developing text mining techniques for identifying DDIs. The state-of-the-art DDI extraction methods use Support Vector Machines (SVMs) with non-linear composite kernels to explore diverse contexts in literature. While computationally less expensive, linear kernel-based systems have not achieved a comparable performance in DDI extraction tasks. In this work, we propose an efficient and scalable system using a linear kernel to identify DDI information. The proposed approach consists of two steps: identifying DDIs and assigning one of four different DDI types to the predicted drug pairs. We demonstrate that when equipped with a rich set of lexical and syntactic features, a linear SVM classifier is able to achieve a competitive performance in detecting DDIs. In addition, the one-against-one strategy proves vital for addressing an imbalance issue in DDI type classification. Applied to the DDIExtraction 2013 corpus, our system achieves an F1 score of 0.670, as compared to 0.651 and 0.609 reported by the top two participating teams in the DDIExtraction 2013 challenge, both based on non-linear kernel methods. PMID:25796456

  15. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.

    PubMed

    Gao, Mu; Skolnick, Jeffrey

    2008-07-01

    The structures of DNA-protein complexes have illuminated the diversity of DNA-protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA-protein interactions. To address this issue, we have developed a knowledge-based method, DNA-binding Domain Hunter (DBD-Hunter), for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. In benchmark tests on approximately 4000 proteins, our method achieved an accuracy of 98% and a precision of 84%, which significantly outperforms three previous methods. We further validate the method on DNA-binding protein structures determined in DNA-free (apo) state. We show that the accuracy of our method is only slightly affected on apo-structures compared to the performance on holo-structures cocrystallized with DNA. Finally, we apply the method to approximately 1700 structural genomics targets and predict that 37 targets with previously unknown function are likely to be DNA-binding proteins. DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/.

  16. Model-based quantification of metabolic interactions from dynamic microbial-community data

    PubMed Central

    Hanemaaijer, Mark; Olivier, Brett G.; Röling, Wilfred F. M.; Bruggeman, Frank J.; Teusink, Bas

    2017-01-01

    An important challenge in microbial ecology is to infer metabolic-exchange fluxes between growing microbial species from community-level data, concerning species abundances and metabolite concentrations. Here we apply a model-based approach to integrate such experimental data and thereby infer metabolic-exchange fluxes. We designed a synthetic anaerobic co-culture of Clostridium acetobutylicum and Wolinella succinogenes that interact via interspecies hydrogen transfer and applied different environmental conditions for which we expected the metabolic-exchange rates to change. We used stoichiometric models of the metabolism of the two microorganisms that represents our current physiological understanding and found that this understanding - the model - is sufficient to infer the identity and magnitude of the metabolic-exchange fluxes and it suggested unexpected interactions. Where the model could not fit all experimental data, it indicates specific requirement for further physiological studies. We show that the nitrogen source influences the rate of interspecies hydrogen transfer in the co-culture. Additionally, the model can predict the intracellular fluxes and optimal metabolic exchange rates, which can point to engineering strategies. This study therefore offers a realistic illustration of the strengths and weaknesses of model-based integration of heterogenous data that makes inference of metabolic-exchange fluxes possible from community-level experimental data. PMID:28278266

  17. Gene network biological validity based on gene-gene interaction relevance.

    PubMed

    Gómez-Vela, Francisco; Díaz-Díaz, Norberto

    2014-01-01

    In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in KEGG are one of the most widely used knowledgeable sources for analyzing relationships between genes. This paper introduces a new methodology, GeneNetVal, to assess the biological validity of gene networks based on the relevance of the gene-gene interactions stored in KEGG metabolic pathways. Hence, a complete KEGG pathway conversion into a gene association network and a new matching distance based on gene-gene interaction relevance are proposed. The performance of GeneNetVal was established with three different experiments. Firstly, our proposal is tested in a comparative ROC analysis. Secondly, a randomness study is presented to show the behavior of GeneNetVal when the noise is increased in the input network. Finally, the ability of GeneNetVal to detect biological functionality of the network is shown.

  18. GL4D: a GPU-based architecture for interactive 4D visualization.

    PubMed

    Chu, Alan; Fu, Chi-Wing; Hanson, Andrew J; Heng, Pheng-Ann

    2009-01-01

    This paper describes GL4D, an interactive system for visualizing 2-manifolds and 3-manifolds embedded in four Euclidean dimensions and illuminated by 4D light sources. It is a tetrahedron-based rendering pipeline that projects geometry into volume images, an exact parallel to the conventional triangle-based rendering pipeline for 3D graphics. Novel features include GPU-based algorithms for real-time 4D occlusion handling and transparency compositing; we thus enable a previously impossible level of quality and interactivity for exploring lit 4D objects. The 4D tetrahedrons are stored in GPU memory as vertex buffer objects, and the vertex shader is used to perform per-vertex 4D modelview transformations and 4D-to-3D projection. The geometry shader extension is utilized to slice the projected tetrahedrons and rasterize the slices into individual 2D layers of voxel fragments. Finally, the fragment shader performs per-voxel operations such as lighting and alpha blending with previously computed layers. We account for 4D voxel occlusion along the 4D-to-3D projection ray by supporting a multi-pass back-to-front fragment composition along the projection ray; to accomplish this, we exploit a new adaptation of the dual depth peeling technique to produce correct volume image data and to simultaneously render the resulting volume data using 3D transfer functions into the final 2D image. Previous CPU implementations of the rendering of 4D-embedded 3-manifolds could not perform either the 4D depth-buffered projection or manipulation of the volume-rendered image in real-time; in particular, the dual depth peeling algorithm is a novel GPU-based solution to the real-time 4D depth-buffering problem. GL4D is implemented as an integrated OpenGL-style API library, so that the underlying shader operations are as transparent as possible to the user.

  19. Interactions of the Watson-Crick nucleic acid base pairs with carbon nanotubes and graphene: DFT and MP2 study

    NASA Astrophysics Data System (ADS)

    Stepanian, S. G.; Karachevtsev, M. V.; Karachevtsev, V. A.; Adamowicz, L.

    2014-08-01

    Structures and interaction energies of complexes formed by Watson-Crick base pairs and carbon surfaces (nanotubes and graphene) are investigated using the DFT M05-2X and MP2 quantum chemical computational methods. High structural flexibility of the complexes is demonstrated. Structures with approximately parallel and perpendicular orientations of the base pairs and the nanotube main axis are revealed. The complexes formed by the GC base pair and large-diameter zigzag nanotubes with the perpendicular orientation of the two systems are found to be the lowest energy configurations. Decomposition of the interaction energies into two-body contributions is applied to explain the nature of the interaction. The question of how the interaction between a base pair and a carbon surface affects the H-bonding between the nucleobases in the pair is elucidated.

  20. Factors Facilitating Verbal Interaction in Group Work in a Ninth-Grade Content-Based ESL Class.

    ERIC Educational Resources Information Center

    Akcan, Sumru

    This case study investigated factors that increased verbal interaction for students in group work in a ninth grade, content-based, English-as-a-Second-Language (ESL) class. Out of 11 tasks assigned to the students during the semester, four language-based and four genre-based tasks were analyzed. At the end of the study, the nature of verbal…

  1. Structure of unstable nuclei around N = 28 described by a shell model with the monopole-based universal interaction

    SciTech Connect

    Utsuno, Yutaka; Otsuka, Takaharu; Brown, B. Alex; Honma, Michio; Mizusaki, Takahiro

    2011-05-06

    The structure of exotic nuclei around N = 28 is investigated in the sd-pf shell-model space using a new effective interaction. The cross-shell part of the interaction is provided by the monopole-based universal interaction which has been successful in accounting for single-particle evolution in several mass regions. Focusing on the nuclear structure that is sensitive to the shell evolution, we show successful results for the proton-hole states in K isotopes and large deformation in {sup 42}Si. The results demonstrate that the present scheme may be a promising way for constructing an effective interaction for other mass regions.

  2. Secondary Neutron Production from Space Radiation Interactions: Advances in Model and Experimental Data Base Development

    NASA Technical Reports Server (NTRS)

    Heilbronn, Lawrence H.; Townsend, Lawrence W.; Braley, G. Scott; Iwata, Yoshiyuki; Iwase, Hiroshi; Nakamura, Takashi; Ronningen, Reginald M.; Cucinotta, Francis A.

    2003-01-01

    For humans engaged in long-duration missions in deep space or near-Earth orbit, the risk from exposure to galactic and solar cosmic rays is an important factor in the design of spacecraft, spacesuits, and planetary bases. As cosmic rays are transported through shielding materials and human tissue components, a secondary radiation field is produced. Neutrons are an important component of that secondary field, especially in thickly-shielded environments. Calculations predict that 50% of the dose-equivalent in a lunar or Martian base comes from neutrons, and a recent workshop held at the Johnson Space Center concluded that as much as 30% of the dose in the International Space Station may come from secondary neutrons. Accelerator facilities provide a means for measuring the effectiveness of various materials in their ability to limit neutron production, using beams and energies that are present in cosmic radiation. The nearly limitless range of beams, energies, and target materials that are present in space, however, means that accelerator-based experiments will not provide a complete database of cross sections and thick-target yields that are necessary to plan and design long-duration missions. As such, accurate nuclear models of neutron production are needed, as well as data sets that can be used to compare with, and verify, the predictions from such models. Improvements in a model of secondary neutron production from heavy-ion interactions are presented here, along with the results from recent accelerator-based measurements of neutron-production cross sections. An analytical knockout-ablation model capable of predicting neutron production from high-energy hadron-hadron interactions (both nucleon-nucleus and nucleus-nucleus collisions) has been previously developed. In the knockout stage, the collision between two nuclei result in the emission of one or more nucleons from the projectile and/or target. The resulting projectile and target remnants, referred to as

  3. Gas/Surface Interaction Study Applied to Si-based Materials Used in Driven Micro- and Nano-scale Devices

    DTIC Science & Technology

    2010-01-01

    1 Final Report Gas/Surface Interaction Study Applied to Si-based Materials Used in Driven Micro - and Nano -scale devices...TITLE AND SUBTITLE Gas/Surface Interaction Study Applied to Si-based Materials Used in Driven Micro - and Nano -scale devices 5a. CONTRACT NUMBER...Scanning Probe Microscopy open new opportunities in surface diagnostics at micro - and nano - scales. Because of essential increase in a role that gas

  4. Lanthanide-based imaging of protein-protein interactions in live cells.

    PubMed

    Rajendran, Megha; Yapici, Engin; Miller, Lawrence W

    2014-02-17

    In order to deduce the molecular mechanisms of biological function, it is necessary to monitor changes in the subcellular location, activation, and interaction of proteins within living cells in real time. Förster resonance energy-transfer (FRET)-based biosensors that incorporate genetically encoded, fluorescent proteins permit high spatial resolution imaging of protein-protein interactions or protein conformational dynamics. However, a nonspecific fluorescence background often obscures small FRET signal changes, and intensity-based biosensor measurements require careful interpretation and several control experiments. These problems can be overcome by using lanthanide [Tb(III) or Eu(III)] complexes as donors and green fluorescent protein (GFP) or other conventional fluorophores as acceptors. Essential features of this approach are the long-lifetime (approximately milliseconds) luminescence of Tb(III) complexes and time-gated luminescence microscopy. This allows pulsed excitation, followed by a brief delay, which eliminates nonspecific fluorescence before the detection of Tb(III)-to-GFP emission. The challenges of intracellular delivery, selective protein labeling, and time-gated imaging of lanthanide luminescence are presented, and recent efforts to investigate the cellular uptake of lanthanide probes are reviewed. Data are presented showing that conjugation to arginine-rich, cell-penetrating peptides (CPPs) can be used as a general strategy for the cellular delivery of membrane-impermeable lanthanide complexes. A heterodimer of a luminescent Tb(III) complex, Lumi4, linked to trimethoprim and conjugated to nonaarginine via a reducible disulfide linker rapidly (∼10 min) translocates into the cytoplasm of Maden Darby canine kidney cells from the culture medium. With this reagent, the intracellular interaction between GFP fused to FK506 binding protein 12 (GFP-FKBP12) and the rapamycin binding domain of mTOR fused to Escherichia coli dihydrofolate reductase (FRB

  5. Energies of interactions between purine and pyrimidine bases in B- and Z-DNA

    NASA Astrophysics Data System (ADS)

    Förner, W.; Otto, P.; Ladik, J.

    The results of ab initio SCF LCAO calculations on the dimers of the nucleotide bases for all possible sixteen stacked configurations in B-DNA geometry, on eight stacked conformations in Z-DNA geometry and on the Watson-Crick-type pairs in both DNA configurations are reported. In addition to the SCF interaction energy in the supermolecule approach, the contributions of the dispersion energy have been computed using London's formula with empirical parameters. In the case of the Watson-Crick-type pairs corrections for the basis-set superposition error are reported, which seem to be negligible for the stacked configuration as a calculation on the adenine dimer shows. The results for the Watson-Crick-type pairs are in good agreement with experimental values and with theoretical ones, obtained by other methods. The stacking energies are mostly attractive but show no significant stabilization of special sequences for B- or Z-DNA. Four dimers are recalculated with the Clementi minimal basis which leads to no considerable qualitative changes in the results. As a better approach to the situation in real DNA we took at least in a qualitative approximation the charge transfer from the sugar phosphate group to the bases into account. Qualitatively this charge transfer destabilizes the pairs to some extent, namely it leads in our approximation to a small repulsion between the stacked bases and lowers the attraction in the Watson-Crick base pairs to some extent.

  6. Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks

    NASA Astrophysics Data System (ADS)

    Erten, Sinan; Bebek, Gurkan; Koyutürk, Mehmet

    In recent years, many algorithms have been developed to narrow down the set of candidate disease genes implicated by genome wide association studies (GWAS), using knowledge on protein-protein interactions (PPIs). All of these algorithms are based on a common principle; functional association between proteins is correlated with their connectivity/proximity in the PPI network. However, recent research also reveals that networks are organized into recurrent network schemes that underlie the mechanisms of cooperation among proteins with different function, as well as the crosstalk between different cellular processes. In this paper, we hypothesize that proteins that are associated with similar diseases may exhibit patterns of "topological similarity" in PPI networks. Motivated by these observations, we introduce the notion of "topological profile", which represents the location of a protein in the network with respect to other proteins. Based on this notion, we develop a novel measure to assess the topological similarity of proteins in a PPI network. We then use this measure to develop algorithms that prioritize candidate disease genes based on the topological similarity of their products and the products of known disease genes. Systematic experimental studies using an integrated human PPI network and the Online Mendelian Inheritance (OMIM) database show that the proposed algorithm, Vavien, clearly outperforms state-of-the-art network based prioritization algorithms. Vavien is available as a web service at http://www.diseasegenes.org .

  7. Identification of human protein interaction domains using an ORFeome-based yeast two-hybrid fragment library.

    PubMed

    Waaijers, Selma; Koorman, Thijs; Kerver, Jana; Boxem, Mike

    2013-07-05

    Physical interactions between proteins are essential for biological processes. Hence, there have been major efforts to elucidate the complete networks of protein-protein interactions, or "interactomes", of various organisms. Detailed descriptions of protein interaction networks should include information on the discrete domains that mediate these interactions, yet most large-scale efforts model interactions between whole proteins only. We previously developed a yeast two-hybrid-based strategy to systematically map interaction domains and generated a domain-based interactome network for 750 proteins involved in C. elegans early embryonic development. Here, we expand the concept of Y2H-based interaction domain mapping to the genome-wide level. We generated a human fragment library by randomly fragmenting the full-length open reading frames (ORFs) present in the human ORFeome collection. Screens using several proteins required for cell division or polarity establishment as baits demonstrate the ability to accurately identify interaction domains for human proteins using this approach, while the experimental quality of the Y2H data was independently verified in coaffinity purification assays. The library generation strategy can easily be adapted to generate libraries from full-length ORF collections of other organisms.

  8. Impact of cation-π interactions on the cell voltage of carbon nanotube-based Li batteries.

    PubMed

    Gao, Shaohua; Shi, Guosheng; Fang, Haiping

    2016-01-21

    Carbon nanotube (CNT)-based Li batteries have attracted wide attention because of their high capacity, high cyclability and high energy density and are believed to be one of the most promising electrochemical energy storage systems. In CNT-based Li batteries, the main interaction between the Li(+) ions and the CNT is the cation-π interaction. However, up to now, it is still not clear how this interaction affects the storage characteristics of CNT-based Li batteries. Here, using density functional theory (DFT) calculations, we report a highly favorable impact of cation-π interactions on the cell voltage of CNT-based Li batteries. Considering both Li(+)-π interaction and Li-π interaction, we show that cell voltage enhances with the increase of the CNT diameter. In addition, when the Li(+) ion adsorbs on the external wall, the cell voltage is larger than that when it adsorbs on the internal wall. This suggests that CNTs with a large diameter and a low array density are more advantageous to enhance storage performance of CNT-based Li batteries. Compared with Li(+) ions on the (4,4) CNT internal wall, the cell voltage of Li(+) on the (10,10) CNT external wall is 0.55 V higher, which indicates an improvement of about 38%. These results will be helpful for the design of more efficient CNT-based Li batteries.

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

    PubMed

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

    2016-01-01

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

  10. The interaction of platinum-based drugs with native biologically relevant proteins.

    PubMed

    Brauckmann, Christine; Wehe, Christoph A; Kieshauer, Michael; Lanvers-Kaminsky, Claudia; Sperling, Michael; Karst, Uwe

    2013-02-01

    This study focuses on the identification of the products that are formed upon binding of therapeutically relevant platinum complexes to proteins like β-lactoglobulin A (LGA), human serum albumin (HSA), or human hemoglobin (HB). The respective proteins were incubated with the platinum-based anticancer drugs cisplatin, carboplatin, and oxaliplatin. LGA was selected as the model protein in addition to the two most abundant blood proteins HSA and HB. In case of the model protein, the effect of free thiol groups on the affinity of cisplatin, carboplatin, and oxaliplatin was investigated by means of liquid chromatography electrospray ionization time-of-flight mass spectrometry (LC/ESI-ToF-MS). The reduced form of LGA, which contains four free thiol groups more than the native LGA, shows a much higher affinity to the platinum-based drugs. By means of liquid chromatography coupled to inductively coupled plasma mass spectrometry, the reaction behavior of the platinum-based drugs towards HSA and HB was investigated under different conditions considering the chloride concentration (4 or 100 mM) and the incubation time (24 and 48 h). In case of carboplatin, less than 6 % protein-bound platinum was detected. However, both cisplatin and oxaliplatin display a high affinity to the proteins investigated. Further information was obtained by means of LC/ESI-ToF-MS. In case of oxaliplatin, the complex [Pt(DACH)](2+) (DACH=C(6)N(2)H(14)) was identified interacting with HSA and HB. For cisplatin, different results were observed for the two proteins. The complex [Pt(NH(3))(2)Cl](+) interacted predominantly with HSA and [Pt(NH(3))(2)](2+) with HB.

  11. Web-based interactive 2D/3D medical image processing and visualization software.

    PubMed

    Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

    2010-05-01

    There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies.

  12. Development and assessment of an interactive web-based breastfeeding monitoring system (LACTOR).

    PubMed

    Ahmed, Azza; Ouzzani, Mourad

    2013-07-01

    The purpose of this study is to describe an interactive web-based breastfeeding monitoring system (LACTOR), illustrate its components, explain the theoretical framework, and discuss its assessment as a model for an innovative breastfeeding support intervention. Based on the self-regulation model from Bandura Social Cognitive Theory, we have developed an interactive web-based breastfeeding monitoring system using a breastfeeding diary. The system has two main components: the Mothers' Portal, where mothers can enter their breastfeeding data and receive notifications, and the Lactation Consultants' Portal, where mothers' data can be monitored. The system is designed to send notifications to mothers in case of breastfeeding problems using triggers such as inability to latch, sleepy infant, jaundice, and maternal sore nipples. A prospective, descriptive, mixed methods study was conducted to examine the feasibility, usability, and acceptability of LACTOR among breastfeeding mothers. Eligible mothers were asked to enter their breastfeeding data into the system daily for 30 days and then submit an online system evaluation survey. Twenty-six mother/infant dyads completed the study. Feasibility of the system was established by the mothers' compliance in entering breastfeeding data. The system proved to be user-friendly. The mothers said that the monitoring was beneficial and gave them an opportunity to track their children's feeding patterns and detect any problems early. Mothers also appreciated the notifications and interventions received through the system. We concluded that the system is feasible and acceptable among breastfeeding mothers and a promising tool for maintaining communication between mothers and lactation consultants.

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

    SciTech Connect

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-14

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

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

    PubMed

    Nap, R J; Tagliazucchi, M; Szleifer, I

    2014-01-14

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

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

    PubMed

    Sriwastava, Brijesh Kumar; Basu, Subhadip; Maulik, Ujjwal

    2015-10-01

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

  16. Interaction between artemether-lumefantrine and nevirapine-based antiretroviral therapy in HIV-1-infected patients.

    PubMed

    Kredo, T; Mauff, K; Van der Walt, J S; Wiesner, L; Maartens, G; Cohen, K; Smith, P; Barnes, K I

    2011-12-01

    Artemether-lumefantrine and nevirapine-based antiretroviral therapy (ART) are the most commonly recommended first-line treatments for malaria and HIV, respectively, in Africa. Artemether, lumefantrine, and nevirapine are metabolized by the cytochrome P450 3A4 enzyme system, which nevirapine induces, creating potential for important drug interactions. In a parallel-design pharmacokinetic study, concentration-time profiles were obtained in two groups of HIV-infected patients: ART-naïve patients and those stable on nevirapine-based therapy. Both groups received the recommended artemether-lumefantrine dose. Patients were admitted for intense pharmacokinetic sampling (0 to 72 h) with outpatient sampling until 21 days. Concentrations of lumefantrine, artemether, dihydroartemisinin, and nevirapine were determined by validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. The primary outcome was observed day 7 lumefantrine concentrations, as these are associated with therapeutic response in malaria. We enrolled 36 patients (32 females). Median (range) day 7 lumefantrine concentrations were 622 ng/ml (185 to 2,040 ng/ml) and 336 ng/ml (29 to 934 ng/ml) in the nevirapine and ART-naïve groups, respectively (P = 0.0002). The median artemether area under the plasma concentration-time curve from 0 to 8 h [AUC((0-8 h))] (P < 0.0001) and dihydroartemisinin AUC((60-68 h)) (P = 0.01) were lower in the nevirapine group. Combined artemether and dihydroartemisinin exposure decreased over time only in the nevirapine group (geometric mean ratio [GMR], 0.76 [95% confidence interval {CI}, 0.65 to 0.90]; P < 0.0001) and increased with the weight-adjusted artemether dose (GMR, 2.12 [95% CI, 1.31 to 3.45]; P = 0.002). Adverse events were similar between groups, with no difference in electrocardiographic Fridericia corrected QT and P-R intervals at the expected time of maximum lumefantrine concentration (T(max)). Nevirapine-based ART decreased artemether and

  17. GPU-based interactive cut-surface extraction from high-order finite element fields.

    PubMed

    Nelson, Blake; Haimes, Robert; Kirby, Robert M

    2011-12-01

    We present a GPU-based ray-tracing system for the accurate and interactive visualization of cut-surfaces through 3D simulations of physical processes created from spectral/hp high-order finite element methods. When used by the numerical analyst to debug the solver, the ability for the imagery to precisely reflect the data is critical. In practice, the investigator interactively selects from a palette of visualization tools to construct a scene that can answer a query of the data. This is effective as long as the implicit contract of image quality between the individual and the visualization system is upheld. OpenGL rendering of scientific visualizations has worked remarkably well for exploratory visualization for most solver results. This is due to the consistency between the use of first-order representations in the simulation and the linear assumptions inherent in OpenGL (planar fragments and color-space interpolation). Unfortunately, the contract is broken when the solver discretization is of higher-order. There have been attempts to mitigate this through the use of spatial adaptation and/or texture mapping. These methods do a better job of approximating what the imagery should be but are not exact and tend to be view-dependent. This paper introduces new rendering mechanisms that specifically deal with the kinds of native data generated by high-order finite element solvers. The exploratory visualization tools are reassessed and cast in this system with the focus on image accuracy. This is accomplished in a GPU setting to ensure interactivity.

  18. Wireless, Web-Based Interactive Control of Optical Coherence Tomography with Mobile Devices

    PubMed Central

    Mehta, Rajvi; Nankivil, Derek; Zielinski, David J.; Waterman, Gar; Keller, Brenton; Limkakeng, Alexander T.; Kopper, Regis; Izatt, Joseph A.; Kuo, Anthony N.

    2017-01-01

    Purpose Optical coherence tomography (OCT) is widely used in ophthalmology clinics and has potential for more general medical settings and remote diagnostics. In anticipation of remote applications, we developed wireless interactive control of an OCT system using mobile devices. Methods A web-based user interface (WebUI) was developed to interact with a handheld OCT system. The WebUI consisted of key OCT displays and controls ported to a webpage using HTML and JavaScript. Client–server relationships were created between the WebUI and the OCT system computer. The WebUI was accessed on a cellular phone mounted to the handheld OCT probe to wirelessly control the OCT system. Twenty subjects were imaged using the WebUI to assess the system. System latency was measured using different connection types (wireless 802.11n only, wireless to remote virtual private network [VPN], and cellular). Results Using a cellular phone, the WebUI was successfully used to capture posterior eye OCT images in all subjects. Simultaneous interactivity by a remote user on a laptop was also demonstrated. On average, use of the WebUI added only 58, 95, and 170 ms to the system latency using wireless only, wireless to VPN, and cellular connections, respectively. Qualitatively, operator usage was not affected. Conclusions Using a WebUI, we demonstrated wireless and remote control of an OCT system with mobile devices. Translational Relevance The web and open source software tools used in this project make it possible for any mobile device to potentially control an OCT system through a WebUI. This platform can be a basis for remote, teleophthalmology applications using OCT. PMID:28138415

  19. Computational Analysis of Structure-Based Interactions for Novel H1-Antihistamines

    PubMed Central

    Yang, Yinfeng; Li, Yan; Pan, Yanqiu; Wang, Jinghui; Lin, Feng; Wang, Chao; Zhang, Shuwei; Yang, Ling

    2016-01-01

    As a chronic disorder, insomnia affects approximately 10% of the population at some time during their lives, and its treatment is often challenging. Since the antagonists of the H1 receptor, a protein prevalent in human central nervous system, have been proven as effective therapeutic agents for treating insomnia, the H1 receptor is quite possibly a promising target for developing potent anti-insomnia drugs. For the purpose of understanding the structural actors affecting the antagonism potency, presently a theoretical research of molecular interactions between 129 molecules and the H1 receptor is performed through three-dimensional quantitative structure-activity relationship (3D-QSAR) techniques. The ligand-based comparative molecular similarity indices analysis (CoMSIA) model (Q2 = 0.525, R2ncv = 0.891, R2pred = 0.807) has good quality for predicting the bioactivities of new chemicals. The cross-validated result suggests that the developed models have excellent internal and external predictability and consistency. The obtained contour maps were appraised for affinity trends for the investigated compounds, which provides significantly useful information in the rational drug design of novel anti-insomnia agents. Molecular docking was also performed to investigate the mode of interaction between the ligand and the active site of the receptor. Furthermore, as a supplementary tool to study the docking conformation of the antagonists in the H1 receptor binding pocket, molecular dynamics simulation was also applied, providing insights into the changes in the structure. All of the models and the derived information would, we hope, be of help for developing novel potent histamine H1 receptor antagonists, as well as exploring the H1-antihistamines interaction mechanism. PMID:26797608

  20. Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

    DOE PAGES

    Labonté, Jessica M.; Swan, Brandon K.; Poulos, Bonnie; ...

    2015-04-07

    Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. Furthermore, a combination of comparative genomics, metagenomic fragmentmore » recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. This study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.« less

  1. Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

    SciTech Connect

    Labonté, Jessica M.; Swan, Brandon K.; Poulos, Bonnie; Luo, Haiwei; Koren, Sergey; Hallam, Steven J.; Sullivan, Matthew B.; Woyke, Tanja; Eric Wommack, K.; Stepanauskas, Ramunas

    2015-04-07

    Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. Furthermore, a combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. This study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  3. Essential protein identification based on essential protein-protein interaction prediction by Integrated Edge Weights.

    PubMed

    Jiang, Yuexu; Wang, Yan; Pang, Wei; Chen, Liang; Sun, Huiyan; Liang, Yanchun; Blanzieri, Enrico

    2015-07-15

    Essential proteins play a crucial role in cellular survival and development process. Experimentally, essential proteins are identified by gene knockouts or RNA interference, which are expensive and often fatal to the target organisms. Regarding this, an alternative yet important approach to essential protein identification is through computational prediction. Existing computational methods predict essential proteins based on their relative densities in a protein-protein interaction (PPI) network. Degree, betweenness, and other appropriate criteria are often used to measure the relative density. However, no matter what criterion is used, a protein is actually ordered by the attributes of this protein per se. In this research, we presented a novel computational method, Integrated Edge Weights (IEW), to first rank protein-protein interactions by integrating their edge weights, and then identified sub PPI networks consisting of those highly-ranked edges, and finally regarded the nodes in these sub networks as essential proteins. We evaluated IEW on three model organisms: Saccharomyces cerevisiae (S. cerevisiae), Escherichia coli (E. coli), and Caenorhabditis elegans (C. elegans). The experimental results showed that IEW achieved better performance than the state-of-the-art methods in terms of precision-recall and Jackknife measures. We had also demonstrated that IEW is a robust and effective method, which can retrieve biologically significant modules by its highly-ranked protein-protein interactions for S. cerevisiae, E. coli, and C. elegans. We believe that, with sufficient data provided, IEW can be used to any other organisms' essential protein identification. A website about IEW can be accessed from http://digbio.missouri.edu/IEW/index.html.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  5. Nano-scale displacement sensing based on van der Waals interactions.

    PubMed

    Hu, Lin; Zhao, Jin; Yang, Jinlong

    2015-05-21

    We propose that a nano-scale displacement sensor with high resolution in weak-force systems can be realized based on vertically stacked two-dimensional (2D) atomic corrugated layer materials bound through van der Waals (vdW) interactions. Using first-principles calculations, we found that the electronic structures of bi-layer blue phosphorus (BLBP) vary appreciably with lateral and vertical interlayer displacements. The variation of the electronic structure is attributed to the change of the interlayer distance dz for both the lateral and vertical displacement. For lateral displacement, the change of dz is induced by atomic layer corrugation. Despite the different stacking configurations of BLBP, we find that the change of the indirect band gap is proportional to dz(-2). Furthermore, this dz(-2) dependence is found to be applicable to other graphene-like corrugated bi-layer materials such as MoS2. BLBP represents a large family of bi-layer 2D atomic corrugated materials for which the electronic structure is sensitive to the interlayer vertical and lateral displacement, and thus could be used for a nano-scale displacement sensor. This can be done by monitoring the tunable electronic structure using absorption spectroscopy. Because this type of sensor is established on atomic layers coupled through vdW interactions, it provides unique applications in the measurements of nano-scale displacement induced by tiny external forces.

  6. [Detecting gene-gene/environment interactions by model-based multifactor dimensionality reduction].

    PubMed

    Fan, Wei; Shen, Chao; Guo, Zhirong

    2015-11-01

    This paper introduces a method called model-based multifactor dimensionality reduction (MB-MDR), which was firstly proposed by Calle et al., and can be applied for detecting gene-gene or gene-environment interactions in genetic studies. The basic principle and characteristics of MB-MDR as well as the operation in R program are briefly summarized. Besides, the detailed procedure of MB-MDR is illustrated by using example. Compared with classical MDR, MB-MDR has similar principle, which merges multi-locus genotypes into a one-dimensional construct and can be used in the study with small sample size. However, there is some difference between MB-MDR and classical MDR. First, it has higher statistical power than MDR and other MDR in the presence of different noises due to the different way the genotype cells merged. Second, compared with MDR, it can deal with all binary and quantitative traits, adjust marginal effects of factors and confounders. MBMDR could be a useful method in the analyses of gene-gene/environment interactions.

  7. Glycodendritic structures based on Boltorn hyperbranched polymers and their interactions with Lens culinaris lectin.

    PubMed

    Arce, Eva; Nieto, Pedro M; Díaz, Vicente; Castro, Rossana García; Bernad, Antonio; Rojo, Javier

    2003-01-01

    Multivalent scaffolds bearing carbohydrates have been prepared to mediate biological processes where carbohydrates are involved. These systems consist of dendritic structures based on Boltorn H20 and H30 hyperbranched polymers to which carbohydrates are linked through a convenient spacer. Mannose has been chosen as a sugar unit to test the viability of this strategy. These glycodendritic compounds have been prepared in a few steps with good yields, showing a high solubility in physiological media and low toxicity. The binding of these dendritic polymers to the mannose-binding lectin Lens culinaris (LCA) was studied using STD-NMR experiments and quantitative precipitation assays. The results demonstrate the existence of a clear interaction between the mannose derivative systems and the Lens lectin where the dendritic scaffold does not have an important role in mannose binding but supplies the necessary multivalence for lectin cluster formation. These glycodendritic structures are able to interact with a receptor, and therefore they can be considered as promising tools for biological studies.

  8. Benchmark data base for accurate van der Waals interaction in inorganic fragments

    NASA Astrophysics Data System (ADS)

    Brndiar, Jan; Stich, Ivan

    2012-02-01

    A range of inorganic materials, such as Sb, As, P, S, Se are built from van der Waals (vdW) interacting units forming the crystals, which neither the standard DFT GGA description as well as cheap quantum chemistry methods, such as MP2, do not describe correctly. We use this data base, for which have performed ultra accurate CCSD(T) calculations in complete basis set limit, to test the alternative approximate theories, such as Grimme [1], Langreth-Lundqvist [2], and Tkachenko-Scheffler [3]. While none of these theories gives entirely correct description, Grimme consistently provides more accurate results than Langreth-Lundqvist, which tend to overestimate the distances and underestimate the interaction energies for this set of systems. Contrary Tkachenko-Scheffler appear to yield surprisingly accurate and computationally cheap and convenient description applicable also for systems with appreciable charge transfer. [4pt] [1] S. Grimme, J. Comp. Chem. 27, 1787 (2006) [0pt] [2] K. Lee, et al., Phys. Rev. B 82 081101 (R) (2010) [0pt] [3] Tkachenko and M. Scheffler Phys. Rev. Lett. 102 073005 (2009).

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

    PubMed

    Yoo, Bum-Soo; Kim, Jong-Hwan

    2015-09-01

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

  10. Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier.

    PubMed

    Sriwastava, Brijesh K; Basu, Subhadip; Maulik, Ujjwal

    2015-01-01

    Predicting residues that participate in protein-protein interactions (PPI) helps to identify, which amino acids are located at the interface. In this paper, we show that the performance of the classical support vector machine (SVM) algorithm can further be improved with the use of a custom-designed fuzzy membership function, for the partner-specific PPI interface prediction problem. We evaluated the performances of both classical SVM and fuzzy SVM (F-SVM) on the PPI databases of three different model proteomes of Homo sapiens, Escherichia coli and Saccharomyces Cerevisiae and calculated the statistical significance of the developed F-SVM over classical SVM algorithm. We also compared our performance with the available state-of-the-art fuzzy methods in this domain and observed significant performance improvements. To predict interaction sites in protein complexes, local composition of amino acids together with their physico-chemical characteristics are used, where the F-SVM based prediction method exploits the membership function for each pair of sequence fragments. The average F-SVM performance (area under ROC curve) on the test samples in 10-fold cross validation experiment are measured as 77.07, 78.39, and 74.91 percent for the aforementioned organisms respectively. Performances on independent test sets are obtained as 72.09, 73.24 and 82.74 percent respectively. The software is available for free download from http://code.google.com/p/cmater-bioinfo.

  11. Intensity-based hierarchical clustering in CT-scans: application to interactive segmentation in cardiology

    NASA Astrophysics Data System (ADS)

    Hadida, Jonathan; Desrosiers, Christian; Duong, Luc

    2011-03-01

    The segmentation of anatomical structures in Computed Tomography Angiography (CTA) is a pre-operative task useful in image guided surgery. Even though very robust and precise methods have been developed to help achieving a reliable segmentation (level sets, active contours, etc), it remains very time consuming both in terms of manual interactions and in terms of computation time. The goal of this study is to present a fast method to find coarse anatomical structures in CTA with few parameters, based on hierarchical clustering. The algorithm is organized as follows: first, a fast non-parametric histogram clustering method is proposed to compute a piecewise constant mask. A second step then indexes all the space-connected regions in the piecewise constant mask. Finally, a hierarchical clustering is achieved to build a graph representing the connections between the various regions in the piecewise constant mask. This step builds up a structural knowledge about the image. Several interactive features for segmentation are presented, for instance association or disassociation of anatomical structures. A comparison with the Mean-Shift algorithm is presented.

  12. A physically based numerical approach for modeling fracture-matrix interaction in fractured reservoirs

    SciTech Connect

    Wu, Yu-Shu; Pruess, Karsten

    2004-05-04

    Modeling fracture-matrix interaction within a multiple-phase flow system is a key issue for fractured reservoir simulation. Commonly used mathematical models for dealing with such interactions employ dual- or multiple-continuum concepts, in which fractures and matrix are represented as overlapping, different, but interconnected continua, described by parallel sets of conservation equations. The conventional single-point upstream weighting scheme is most commonly used to estimate flow mobility for fracture-matrix flow. However, such a scheme may have serious limitations or flaws, which lead to unphysical solutions or significant numerical errors. To overcome the limitations of the conventional upstream weighting scheme, this paper presents a physically based modeling approach for estimating physically correct relative permeability in calculating multiphase flow between fractures and the matrix, using continuity of capillary pressure at the fracture-matrix interface. The proposed approach has been implemented into two multiphase reservoir simulators and verified using analytical solutions and laboratory experimental data. The new method is demonstrated to be accurate, numerically efficient, and easy to implement in dual- or multiple-continuum reservoir simulators.

  13. Protein-protein interaction network-based detection of functionally similar proteins within species.

    PubMed

    Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

    2012-07-01

    Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Fluorescent reversible regulation based on the interactions of topotecan hydrochloride, neutral red and quantum dots.

    PubMed

    Wang, Linlin; Shen, Yizhong; Liu, Shaopu; Yang, Jidong; Liang, Wanjun; Li, Dan; He, Youqiu

    2015-02-05

    The interactions of topotecan hydrochloride (THC), neutral red (NR) and thioglycolic acid (TGA) capped CdTe/CdS quantum dots (QDs) built a solid base for the controlling of the fluorescent reversible regulation of the system. This study was developed by means of ultraviolet-visible (UV-vis) absorption, fluorescence (FL), resonance Rayleigh scattering (RRS) spectroscopy and transmission electron microscopy (TEM). Corresponding experimental results revealed that the fluorescence of TGA-CdTe/CdS QDs could be effectively quenched by NR, while the RRS of the QDs enhanced gradually with the each increment of NR concentration. After the addition of THC, the strong covalent conjugation between NR and THC which was in carboxylate state enabled NR to be dissociated from the surface of TGA-CdTe/CdS QDs to form more stable complex with THC, thereby enhancing the fluorescence of the TGA-CdTe/CdS QDs-NR system. What is more, through analyzing the optical properties and experimental data of the reaction between TGA-CdTe/CdS QDs and NR, the possible reaction mechanism of the whole system was discussed. This combination of multiple spectroscopic techniques could contribute to the investigation for the fluorescent reversible regulation of QDs and a method could also be established to research the interactions between camptothecin drugs and dyes.

  16. Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants

    USGS Publications Warehouse

    Stavreva, Diana A.; Varticovski, Lyuba; Levkova, Ludmila; George, Anuja A.; Davis, Luke; Pegoraro, Gianluca; Blazer, Vicki; Iwanowicz, Luke R.; Hager, Gordon L.

    2016-01-01

    Even though the presence of endocrine disrupting chemicals (EDCs) with thyroid hormone (TH)-like activities in the environment is a major health concern, the methods for their efficient detection and monitoring are still limited. Here we describe a novel cell assay, based on the translocation of a green fluorescent protein (GFP)—tagged chimeric molecule of glucocorticoid receptor (GR) and the thyroid receptor beta (TRβ) from the cytoplasm to the nucleus in the presence of TR ligands. Unlike the constitutively nuclear TRβ, this GFP-GR-TRβ chimera is cytoplasmic in the absence of hormone while translocating to the nucleus in a time- and concentration-dependent manner upon stimulation with triiodothyronine (T3) and thyroid hormone analogue, TRIAC, while the reverse triiodothyronine (3,3′,5′-triiodothyronine, or rT3) was inactive. Moreover, GFP-GR-TRβ chimera does not show any cross-reactivity with the GR-activating hormones, thus providing a clean system for the screening of TR beta-interacting EDCs. Using this assay, we demonstrated that Bisphenol A (BPA) and 3,3′,5,5′-Tetrabromobisphenol (TBBPA) induced GFP-GR-TRβ translocation at micro molar concentrations. We screened over 100 concentrated water samples from different geographic locations in the United States and detected a low, but reproducible contamination in 53% of the samples. This system provides a novel high-throughput approach for screening for endocrine disrupting chemicals (EDCs) interacting with TR beta.

  17. Fluorescent reversible regulation based on the interactions of topotecan hydrochloride, neutral red and quantum dots

    NASA Astrophysics Data System (ADS)

    Wang, Linlin; Shen, Yizhong; Liu, Shaopu; Yang, Jidong; Liang, Wanjun; Li, Dan; He, Youqiu

    2015-02-01

    The interactions of topotecan hydrochloride (THC), neutral red (NR) and thioglycolic acid (TGA) capped CdTe/CdS quantum dots (QDs) built a solid base for the controlling of the fluorescent reversible regulation of the system. This study was developed by means of ultraviolet-visible (UV-vis) absorption, fluorescence (FL), resonance Rayleigh scattering (RRS) spectroscopy and transmission electron microscopy (TEM). Corresponding experimental results revealed that the fluorescence of TGA-CdTe/CdS QDs could be effectively quenched by NR, while the RRS of the QDs enhanced gradually with the each increment of NR concentration. After the addition of THC, the strong covalent conjugation between NR and THC which was in carboxylate state enabled NR to be dissociated from the surface of TGA-CdTe/CdS QDs to form more stable complex with THC, thereby enhancing the fluorescence of the TGA-CdTe/CdS QDs-NR system. What is more, through analyzing the optical properties and experimental data of the reaction between TGA-CdTe/CdS QDs and NR, the possible reaction mechanism of the whole system was discussed. This combination of multiple spectroscopic techniques could contribute to the investigation for the fluorescent reversible regulation of QDs and a method could also be established to research the interactions between camptothecin drugs and dyes.

  18. Study of wave-particle interaction between fast Magnetosonic and energetic electrons based on numerical simulation

    NASA Astrophysics Data System (ADS)

    Fu, S.

    2015-12-01

    There are many energetic electrons in the radiation belt of Earth. When the geomagnetic activity becomes stronger, the energy flux of energetic electrons will increase to more than ten times in the outer radiation belt, therefore it is very important to study how the energetic electrons generate and the lifetime of energetic electrons for space weather research. The acceleration of electrons in radiation belt is mainly depending on wave-particle interaction: the whistler mode chorus is the main driver for local acceleration mechanism, which could accelerate and loss energetic electrons; the geomagnetic pulsation ULF wave will cause energetic electron inward radial diffusion which will charge the electrons; recently observation results show us that the fast magnetosonic waves may also accelerate energetic electrons. For the reason that we try to study the wave-particle interaction between fast Magnetosonic and energetic electrons based on numerical simulation, in which the most important past is at the storm time the combination of highly warped Earth magnetic field and fast magnetosonic wave field will be applied for the electromagnetic environment of moving test particles. The energy, pitch angle and cross diffusion coefficients will be calculated respectively in this simulation to study how the electrons receive energy from fast magnetosonic wave. The diffusion coefficients within different dipole Earth magnetic field and non-dipole storm magnetic field are compared, while dynamics of electrons at selected initial energys are shown in our study.

  19. The effect of intermolecular interactions on the electric dipole polarizabilities of nucleic acid base complexes

    NASA Astrophysics Data System (ADS)

    Czyżnikowska, Żaneta; Góra, Robert W.; Zaleśny, Robert; Bartkowiak, Wojciech; Baranowska-Łączkowska, Angelika; Leszczynski, Jerzy

    2013-01-01

    In this Letter, we report on the interaction-induced electric dipole polarizabilities of 70 Watson-Crick B-DNA pairs (27 adenine-thymine and 43 guanine-cytosine complexes) and 38 structures of cytosine dimer in stacked alignment. In the case of hydrogen-bonded Watson-Crick base pairs the electrostatic as well as the induction and exchange-induction interactions, increase the average polarizability of the studied complexes, whereas the exchange-repulsion effects have the opposite effect and consistently diminish this property. On the other hand, in the case of the studied cytosine dimers in stacked alignment the dominant electrostatic contribution has generally much larger magnitude and the opposite sign, resulting in a significant reduction of the average polarizability of these complexes. As a part of this model study, we also assess the performance of recently developed LPol-ds reduced-size polarized basis set. Although being much smaller than the aug-cc-pVTZ set, the LPol-ds performs equally well as far as the excess polarizabilities of the studied hydrogen-bonded complexes are concerned.

  20. A Descriptive Assessment of Instruction-Based Interactions in the Preschool Classroom

    PubMed Central

    Ndoro, Virginia W; Hanley, Gregory P; Tiger, Jeffrey H; Heal, Nicole A

    2006-01-01

    The current study describes preschool teacher–child interactions during several commonly scheduled classroom activities in which teachers deliver instructions. An observation system was developed that incorporated measurement of evidence-based compliance strategies and included the types of instructions delivered (e.g., integral or deficient directives, embedded directives, “do” or “don't” commands), the children's behavior with respect to the instructions (e.g., compliance, noncompliance, active avoidance, problem behavior), and the differential responses of the teacher to the child's behavior following an instruction (e.g., appropriate or inappropriate provision of attention and escape). After 4 classroom teachers were observed at least five times in each of five target activities, simple and conditional probabilities were calculated. Results indicated that (a) the frequency of instruction and probability of compliance varied as a function of activity type, (b) “do” commands and directive prompts were delivered almost to the exclusion of “don't” commands and nondirective prompts, (c) the likelihood of compliance was highest following an embedded or an integral directive prompt, and (d) although putative social reinforcers were more likely to follow noncompliance than compliance and were highly likely following problem behavior, compliance occurred over twice as much as noncompliance, and problem behavior during instructions was very low. Implications for using descriptive assessments for understanding and improving teacher–child interactions in the preschool classroom are discussed. PMID:16602387

  1. A digital interactive human brain atlas based on Chinese visible human datasets for anatomy teaching.

    PubMed

    Li, Qiyu; Ran, Xu; Zhang, Shaoxiang; Tan, Liwen; Qiu, Mingguo

    2014-01-01

    As we know, the human brain is one of the most complicated organs in the human body, which is the key and difficult point in neuroanatomy and sectional anatomy teaching. With the rapid development and extensive application of imaging technology in clinical diagnosis, doctors are facing higher and higher requirement on their anatomy knowledge. Thus, to cultivate medical students to meet the needs of medical development today and to improve their ability to read and understand radiographic images have become urgent challenges for the medical teachers. In this context, we developed a digital interactive human brain atlas based on the Chinese visible human datasets for anatomy teaching (available for free download from http://www.chinesevisiblehuman.com/down/DHBA.rar). The atlas simultaneously provides views in all 3 primary planes of section. The main structures of the human brain have been anatomically labeled in all 3 views. It is potentially useful for anatomy browsing, user self-testing, and automatic student assessment. In a word, it is interactive, 3D, user friendly, and free of charge, which can provide a new, intuitive means for anatomy teaching.

  2. A Physically Based Approach for Modeling Multiphase Fracture-Matrix Interaction in Fractured Porous Media

    SciTech Connect

    Wu, Yu-Shu; Pan, Lehua; Pruess, Karsten

    2004-03-15

    Modeling fracture-matrix interaction within a complex multiple phase flow system is a key issue for fractured reservoir simulation. Commonly used mathematical models for dealing with such interactions employ a dual- or multiple-continuum concept, in which fractures and matrix are represented as overlapping, different, but interconnected continua, described by parallel sets of conservation equations. The conventional single-point upstream weighting scheme, in which the fracture relative permeability is used to represent the counterpart at the fracture-matrix interface, is the most common scheme by which to estimate flow mobility for fracture-matrix flow terms. However, such a scheme has a serious flaw, which may lead to unphysical solutions or significant numerical errors. To overcome the limitation of the conventional upstream weighting scheme, this paper presents a physically based modeling approach for estimating physically correct relative permeability in calculating multiphase flow between fractures and the matrix, using continuity of capillary pressure at the fracture-matrix interface. The proposed approach has been implemented into two multiphase reservoir simulators and verified using analytical solutions and laboratory experimental data. The new method is demonstrated to be accurate, numerically efficient, and easy to implement in dual- or multiple-continuum models.

  3. Parametric amplification of orbital angular momentum beams based on light-acoustic interaction

    SciTech Connect

    Gao, Wei E-mail: zhuzhihandd@sina.com; Mu, Chunyuan; Yang, Yuqiang; Li, Hongwei; Zhu, Zhihan E-mail: zhuzhihandd@sina.com

    2015-07-27

    A high fidelity amplification of beams carrying orbital angular momentum (OAM) is very crucial for OAM multiplexing and other OAM-based applications. Here, we report a demonstration of stimulated Brillouin amplification for OAM beams, and the energy conversion efficiency of photon-phonon coupling and the phase structure of amplified signals are investigated in collinear and noncollinear frame systems, respectively. Our results demonstrate that the OAM signals can be efficiently amplified without obvious noise introduced, and the modes of output signal are independent of the pump modes or the geometrical frames. Meanwhile, an OAM state depending on the optical modes and the geometrical frames is loaded into phonons by coherent light-acoustic interaction, which reveals more fundamental significance and a great application potential in OAM-multiplexing.

  4. Biological interaction of living cells with COSAN-based synthetic vesicles

    PubMed Central

    Tarrés, Màrius; Canetta, Elisabetta; Paul, Eleanor; Forbes, Jordan; Azzouni, Karima; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J.

    2015-01-01

    Cobaltabisdicarbollide (COSAN) [3,3′-Co(1,2-C2B9H11)2]−, is a complex boron-based anion that has the unusual property of self-assembly into membranes and vesicles. These membranes have similar dimensions to biological membranes found in cells, and previously COSAN has been shown to pass through synthetic lipid membranes and those of living cells without causing breakdown of membrane barrier properties. Here, we investigate the interaction of this inorganic membrane system with living cells. We show that COSAN has no immediate effect on cell viability, and cells fully recover when COSAN is removed following exposure for hours to days. COSAN elicits a range of cell biological effects, including altered cell morphology, inhibition of cell growth and, in some cases, apoptosis. These observations reveal a new biology at the interface between inorganic, synthetic COSAN membranes and naturally occurring biological membranes. PMID:25588708

  5. An interactive method based on the live wire for segmentation of the breast in mammography images.

    PubMed

    Zewei, Zhang; Tianyue, Wang; Li, Guo; Tingting, Wang; Lu, Xu

    2014-01-01

    In order to improve accuracy of computer-aided diagnosis of breast lumps, the authors introduce an improved interactive segmentation method based on Live Wire. This paper presents the Gabor filters and FCM clustering algorithm is introduced to the Live Wire cost function definition. According to the image FCM analysis for image edge enhancement, we eliminate the interference of weak edge and access external features clear segmentation results of breast lumps through improving Live Wire on two cases of breast segmentation data. Compared with the traditional method of image segmentation, experimental results show that the method achieves more accurate segmentation of breast lumps and provides more accurate objective basis on quantitative and qualitative analysis of breast lumps.

  6. Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

    PubMed

    Vellay, S G P; Latimer, N E Miller; Paillard, G

    2009-06-01

    Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

  7. AUV Underwater Positioning Algorithm Based on Interactive Assistance of SINS and LBL

    PubMed Central

    Zhang, Tao; Chen, Liping; Li, Yao

    2015-01-01

    This paper studies an underwater positioning algorithm based on the interactive assistance of a strapdown inertial navigation system (SINS) and LBL, and this algorithm mainly includes an optimal correlation algorithm with aided tracking of an SINS/Doppler velocity log (DVL)/magnetic compass pilot (MCP), a three-dimensional TDOA positioning algorithm of Taylor series expansion and a multi-sensor information fusion algorithm. The final simulation results show that compared to traditional underwater positioning algorithms, this scheme can not only directly correct accumulative errors caused by a dead reckoning algorithm, but also solves the problem of ambiguous correlation peaks caused by multipath transmission of underwater acoustic signals. The proposed method can calibrate the accumulative error of the AUV position more directly and effectively, which prolongs the underwater operating duration of the AUV. PMID:26729120

  8. Authentication Based on Non-Interactive Zero-Knowledge Proofs for the Internet of Things

    PubMed Central

    Martín-Fernández, Francisco; Caballero-Gil, Pino; Caballero-Gil, Cándido

    2016-01-01

    This paper describes the design and analysis of a new scheme for the authenticated exchange of confidential information in insecure environments within the Internet of Things, which allows a receiver of a message to authenticate the sender and compute a secret key shared with it. The proposal is based on the concept of a non-interactive zero-knowledge proof, so that in a single communication, relevant data may be inferred to verify the legitimacy of the sender. Besides, the new scheme uses the idea under the Diffie–Hellman protocol for the establishment of a shared secret key. The proposal has been fully developed for platforms built on the Android Open Source Project, so it can be used in any device or sensor with this operating system. This work provides a performance study of the implementation and a comparison between its promising results and others obtained with similar schemes. PMID:26751454

  9. Probing tissue interaction with laser-based cauterization in the early developing Drosophila embryo.

    PubMed

    Rauzi, M

    2017-01-01

    Tissue morphogenesis is governed by mechanical forces generated by cell cytoskeletal networks. It has been shown that subcellular forces are responsible for cell shape changes. Nevertheless cells in a developing organism do not act in isolation: cells contact and adhere one another, and forces are transmitted from cell-to-cell throughout tissues. Understanding how forces are integrated at the tissue level and finally at the full animal scale is nowadays a major challenge that will allow shedding new light on how embryo morphogenesis takes place. In this chapter, I present a new laser-based technique to probe tissue coupling in a living Drosophila embryo. Such technique allows generating mechanical fix boundaries that can eventually impair or modulate cell flows and tissue displacements to probe tissue interaction.

  10. Model of laser/composite interaction based on scattering by multiple cylinders

    NASA Astrophysics Data System (ADS)

    Dedieu, Cyril; Chinesta, Francisco; Barasinski, Anaïs; Leygue, Adrien; Dupillier, Jean-Marc

    2016-10-01

    In the context of processing long-fiber reinforced thermoplastic composites with laser-heating, the spatial distribution of the heat flux is one of the main parameters which controls the induced processing temperature. Unfortunately, the illuminated geometry might be not trivial, and the optical properties related to absorption and scattering phenomena of such a material are not well-established. In order to study and characterize the laser/composite interaction at the scale of the micro-structure, a model based on multiple cylinders is envisaged. The method consists in the calculation of a semi-analytical solution for the electromagnetic scattering from an array of circular cylinders due to an obliquely incident plane wave.

  11. Image-Based Multi-Target Tracking through Multi-Bernoulli Filtering with Interactive Likelihoods

    PubMed Central

    Hoak, Anthony; Medeiros, Henry; Povinelli, Richard J.

    2017-01-01

    We develop an interactive likelihood (ILH) for sequential Monte Carlo (SMC) methods for image-based multiple target tracking applications. The purpose of the ILH is to improve tracking accuracy by reducing the need for data association. In addition, we integrate a recently developed deep neural network for pedestrian detection along with the ILH with a multi-Bernoulli filter. We evaluate the performance of the multi-Bernoulli filter with the ILH and the pedestrian detector in a number of publicly available datasets (2003 PETS INMOVE, Australian Rules Football League (AFL) and TUD-Stadtmitte) using standard, well-known multi-target tracking metrics (optimal sub-pattern assignment (OSPA) and classification of events, activities and relationships for multi-object trackers (CLEAR MOT)). In all datasets, the ILH term increases the tracking accuracy of the multi-Bernoulli filter. PMID:28273796

  12. Methods for simulation-based analysis of fluid-structure interaction.

    SciTech Connect

    Barone, Matthew Franklin; Payne, Jeffrey L.

    2005-10-01

    Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonal decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.

  13. Rationale and Considerations for the Internet-Based Delivery of Parent-Child Interaction Therapy.

    PubMed

    Comer, Jonathan S; Furr, Jami M; Cooper-Vince, Christine; Madigan, Ryan J; Chow, Candice; Chan, Priscilla; Idrobo, Fabio; Chase, Rhea M; McNeil, Cheryl B; Eyberg, Sheila M

    2015-08-01

    Given the enormous individual, familial, and societal costs associated with early disruptive behavior disorders, transformative efforts are needed to develop innovative options for overcoming traditional barriers to effective care and for broadening the availability of supported interventions. This paper presents the rationale and key considerations for a promising innovation in the treatment of early-onset disruptive behavior disorders-that is, the development of an Internet-based format for the delivery of Parent-Child Interaction Therapy (PCIT) directly to families in their own homes. Specifically, we consider traditional barriers to effective care, and discuss how technological innovations can overcome problems of treatment availability, accessibility, and acceptability. We then detail our current Internet-delivered PCIT treatment program (I-PCIT), which is currently being evaluated across multiple randomized clinical trials relative to waitlist comparison, and to traditional in-office PCIT. Embedded video clips of children treated with I-PCIT are used to illustrate novel aspects of the treatment.

  14. An interactive web-based system using cloud for large-scale visual analytics

    NASA Astrophysics Data System (ADS)

    Kaseb, Ahmed S.; Berry, Everett; Rozolis, Erik; McNulty, Kyle; Bontrager, Seth; Koh, Youngsol; Lu, Yung-Hsiang; Delp, Edward J.

    2015-03-01

    Network cameras have been growing rapidly in recent years. Thousands of public network cameras provide tremendous amount of visual information about the environment. There is a need to analyze this valuable information for a better understanding of the world around us. This paper presents an interactive web-based system that enables users to execute image analysis and computer vision techniques on a large scale to analyze the data from more than 65,000 worldwide cameras. This paper focuses on how to use both the system's website and Application Programming Interface (API). Given a computer program that analyzes a single frame, the user needs to make only slight changes to the existing program and choose the cameras to analyze. The system handles the heterogeneity of the geographically distributed cameras, e.g. different brands, resolutions. The system allocates and manages Amazon EC2 and Windows Azure cloud resources to meet the analysis requirements.

  15. X based interactive computer graphics applications for aerodynamic design and education

    NASA Technical Reports Server (NTRS)

    Benson, Thomas J.; Higgs, C. Fred, III

    1995-01-01

    Six computer applications packages have been developed to solve a variety of aerodynamic problems in an interactive environment on a single workstation. The packages perform classical one dimensional analysis under the control of a graphical user interface and can be used for preliminary design or educational purposes. The programs were originally developed on a Silicon Graphics workstation and used the GL version of the FORMS library as the graphical user interface. These programs have recently been converted to the XFORMS library of X based graphics widgets and have been tested on SGI, IBM, Sun, HP and PC-Lunix computers. The paper will show results from the new VU-DUCT program as a prime example. VU-DUCT has been developed as an educational package for the study of subsonic open and closed loop wind tunnels.

  16. AUV Underwater Positioning Algorithm Based on Interactive Assistance of SINS and LBL.

    PubMed

    Zhang, Tao; Chen, Liping; Li, Yao

    2015-12-30

    This paper studies an underwater positioning algorithm based on the interactive assistance of a strapdown inertial navigation system (SINS) and LBL, and this algorithm mainly includes an optimal correlation algorithm with aided tracking of an SINS/Doppler velocity log (DVL)/magnetic compass pilot (MCP), a three-dimensional TDOA positioning algorithm of Taylor series expansion and a multi-sensor information fusion algorithm. The final simulation results show that compared to traditional underwater positioning algorithms, this scheme can not only directly correct accumulative errors caused by a dead reckoning algorithm, but also solves the problem of ambiguous correlation peaks caused by multipath transmission of underwater acoustic signals. The proposed method can calibrate the accumulative error of the AUV position more directly and effectively, which prolongs the underwater operating duration of the AUV.

  17. A dehydrogenation mechanism of metal hydrides based on interactions between Hdelta+ and H-.

    PubMed

    Lu, Jun; Fang, Zhigang Zak; Sohn, Hong Yong

    2006-10-16

    This paper describes a reaction mechanism that explains the dehydrogenation reactions of alkali and alkaline-earth metal hydrides. These light metal hydrides, e.g., lithium-based compounds such as LiH, LiAlH4, and LiNH2, are the focus of intense research recently as the most promising candidate materials for on-board hydrogen storage applications. Although several interesting and promising reactions and materials have been reported, most of these reported reactions and materials have been discovered by empirical means because of a general lack of understanding of any underlying principles. This paper describes an understanding of the dehydrogenation reactions on the basis of the interaction between negatively charged hydrogen (H-, electron donor) and positively charged hydrogen (Hdelta+, electron acceptor) and experimental evidence that captures and explains many observations that have been reported to date. This reaction mechanism can be used as a guidance for screening new material systems for hydrogen storage.

  18. Desorption electrospray ionization-based imaging of interaction between vascular graft and human body.

    PubMed

    Bodzon-Kulakowska, Anna; Drabik, Anna; Mystkowska, Joanna; Chlabicz, Michal; Gacko, Marek; Dabrowski, Jan R; Mielczarek, Przemyslaw; Silberring, Jerzy; Suder, Piotr

    2016-01-01

    The desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) is known as a fast and convenient MS-based method for lipid imaging in various biological materials. Here, we applied this technique to visualize lipid distribution in a vascular graft removed from a patient's body. This is a good example of the DESI system capabilities toward imaging of interaction between artificial material and living tissues. Detailed analysis allowed for visualization of the spatial distribution of selected lipids in this implanted, artificial material. Not only DESI-MSI allowed visualization of lipid distribution in the investigated material but also enabled identification of the detected molecular species using MS/MS. Here, this technique was successfully used to evaluate the saturation and spatial distribution of endogenous lipids in the artificial vascular graft. Unambiguous identification of the lipids was done with the aid of fragmentation procedure. We also showed that various lipids localize preferably in graft material or internal plaque existing inside the graft.

  19. Authentication Based on Non-Interactive Zero-Knowledge Proofs for the Internet of Things.

    PubMed

    Martín-Fernández, Francisco; Caballero-Gil, Pino; Caballero-Gil, Cándido

    2016-01-07

    This paper describes the design and analysis of a new scheme for the authenticated exchange of confidential information in insecure environments within the Internet of Things, which allows a receiver of a message to authenticate the sender and compute a secret key shared with it. The proposal is based on the concept of a non-interactive zero-knowledge proof, so that in a single communication, relevant data may be inferred to verify the legitimacy of the sender. Besides, the new scheme uses the idea under the Diffie-Hellman protocol for the establishment of a shared secret key. The proposal has been fully developed for platforms built on the Android Open Source Project, so it can be used in any device or sensor with this operating system. This work provides a performance study of the implementation and a comparison between its promising results and others obtained with similar schemes.

  20. Interactive dynamic three-dimensional scene for the ground-based three-dimensional display

    NASA Astrophysics Data System (ADS)

    Hou, Peining; Sang, Xinzhu; Guo, Nan; Chen, Duo; Yan, Binbin; Wang, Kuiru; Dou, Wenhua; Xiao, Liquan

    2016-10-01

    Three-dimensional (3D) displays provides valuable tools for many fields, such as scientific experiment, education, information transmission, medical imaging and physical simulation. Ground based 360° 3D display with dynamic and controllable scene can find some special applications, such as design and construction of buildings, aeronautics, military sand table and so on. It can be utilized to evaluate and visualize the dynamic scene of the battlefield, surgical operation and the 3D canvas of art. In order to achieve the ground based 3D display, the public focus plane should be parallel to the camera's imaging planes, and optical axes should be offset to the center of public focus plane in both vertical and horizontal directions. Virtual cameras are used to display 3D dynamic scene with Unity 3D engine. Parameters of virtual cameras for capturing scene are designed and analyzed, and locations of virtual cameras are determined by the observer's eye positions in the observing space world. An interactive dynamic 3D scene for ground based 360° 3D display is demonstrated, which provides high-immersion 3D visualization.

  1. Creating an interactive Web-based e-learning course: a practical introduction for radiologists.

    PubMed

    Hoa, Denis; Micheau, Antoine; Gahide, Gerald

    2006-01-01

    With the development of e-learning and its ability to provide rich animated content rapidly to a wide audience, new methods for teaching medical imaging have evolved. E-learning tools allow building of learner-focused structured courses. Standards such as shareable content object reference model (SCORM) or Aviation Industry Computer-based Training Committee (AICC) guidelines and recommendations provide the framework required to combine text, images, videos, animations, and quizzes for learning assessment, even if each of these elements is created with different software. The main features to consider when choosing a learning management system are content management, assessment and reporting tools, customization options, course delivery, administration, and security. The tools for building a Web-based course with pages containing text, images, videos, and Flash animations are now accessible to any radiologist. Open-source learning management systems and content authoring software are available at no cost. The authors developed e-MRI.com, a free Web-based e-learning course with interactive animations and simulations, self-tests, and clinical cases to demonstrate the potential of the latest advances in e-learning and pedagogy applied to magnetic resonance imaging physics.

  2. Properties of Apolar Solutes in Alkyl Imidazolium-Based Ionic Liquids: The Importance of Local Interactions.

    PubMed

    Lesch, Volker; Heuer, Andreas; Holm, Christian; Smiatek, Jens

    2016-02-03

    The solvation and the dynamic properties of apolar model solutes in alkyl imidazolium-based ionic liquids (IL) are studied by using all-atom molecular dynamics simulations. In regards to specific IL effects, we focused on the often used 1-ethyl-3-methyl imidazolium cation in combination with the anions tetrafluoroborate, acetate, and bis(trifluoromethanesulfonyl)imide. Our findings reveal that the size of the anion crucially influences the accumulation behavior of the cations, which results in modified IL solvation properties. Deviations between the different alkyl imidazolium-based IL combinations can be also observed with regard to the results for the radial distribution functions, the number of surrounding molecules, and the molecular orientation. The analysis of the van Hove function further shows pronounced differences in the dynamic behavior of the solutes. The simulations verify that the solute mobilities are mainly influenced by the composition of the local solvent shell and the properties of the underlying Lennard-Jones interactions. Additional simulations with regard to modified short-range dispersion energies for alkyl imidazolium-based ILs validate our conclusions.

  3. Regulation of muscle force in the absence of actin-myosin-based cross-bridge interaction.

    PubMed

    Leonard, T R; Herzog, W

    2010-07-01

    For the past half century, the sliding filament-based cross-bridge theory has been the cornerstone of our understanding of how muscles contract. According to this theory, active force can only occur if there is overlap between the contractile filaments, actin and myosin. Otherwise, forces are thought to be caused by passive structural elements and are assumed to vary solely because of the length of the muscle. We observed increases in muscle force by a factor of 3 to 4 above the purely passive forces for activated and stretched myofibrils in the absence of actin-myosin overlap. We show that this dramatic increase in force is crucially dependent on the presence of the structural protein titin, cannot be explained with calcium activation, and is regulated by actin-myosin-based cross-bridge forces before stretching. We conclude from these observations that titin is a strong regulator of muscle force and propose that this regulation is based on cross-bridge force-dependent titin-actin interactions. These results suggest a mechanism for stability of sarcomeres on the "inherently unstable" descending limb of the force-length relationship, and they further provide an explanation for the protection of muscles against stretch-induced muscle injuries.

  4. Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

    PubMed Central

    Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

    2010-01-01

    With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

  5. vPresent: A cloud based 3D virtual presentation environment for interactive product customization

    NASA Astrophysics Data System (ADS)

    Nan, Xiaoming; Guo, Fei; He, Yifeng; Guan, Ling

    2013-09-01

    In modern society, many companies offer product customization services to their customers. There are two major issues in providing customized products. First, product manufacturers need to effectively present their products to the customers who may be located in any geographical area. Second, customers need to be able to provide their feedbacks on the product in real-time. However, the traditional presentation approaches cannot effectively convey sufficient information for the product or efficiently adjust product design according to customers' real-time feedbacks. In order to address these issues, we propose vPresent , a cloud based 3D virtual presentation environment, in this paper. In vPresent, the product expert can show the 3D virtual product to the remote customers and dynamically customize the product based on customers' feedbacks, while customers can provide their opinions in real time when they are viewing a vivid 3D visualization of the product. Since the proposed vPresent is a cloud based system, the customers are able to access the customized virtual products from anywhere at any time, via desktop, laptop, or even smart phone. The proposed vPresent is expected to effectively deliver 3D visual information to customers and provide an interactive design platform for the development of customized products.

  6. Application of Biologically Based Lumping To Investigate the Toxicokinetic Interactions of a Complex Gasoline Mixture.

    PubMed

    Jasper, Micah N; Martin, Sheppard A; Oshiro, Wendy M; Ford, Jermaine; Bushnell, Philip J; El-Masri, Hisham

    2016-03-15

    People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate the performance of our PBPK model and chemical lumping method. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course toxicokinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 nontarget chemicals. The same biologically based lumping approach can be used to simplify any complex mixture with tens, hundreds, or thousands of constituents.

  7. Form of the effective interaction in harmonic-oscillator-based effective theory

    NASA Astrophysics Data System (ADS)

    Haxton, W. C.

    2008-03-01

    I explore the form of the effective interaction in harmonic-oscillator-based effective theory (HOBET) in leading order (LO) through next-to-next-to-next-to-leading order (NLO3). Because the included space in a HOBET (as in the shell model) is defined by the oscillator energy, both long-distance (low-momentum) and short-distance (high-momentum) degrees of freedom reside in the high-energy excluded space. A HOBET effective interaction is developed in which a short-range contact-gradient expansion, free of operator mixing and corresponding to a systematic expansion in nodal quantum numbers, is combined with an exact summation of the relative kinetic energy. By this means the very strong coupling of the included (P) and excluded (Q) spaces by the kinetic energy is removed. One finds a simple and rather surprising result, that the interplay of QT and QV is governed by a single parameter κ, the ratio of an observable, the binding energy |E|, to a parameter in the effective theory, the oscillator energy ℏω. Once the functional dependence on κ is identified, the remaining order-by-order subtraction of the short-range physics residing in Q becomes systematic and rapidly converging. Numerical calculations are used to demonstrate how well the resulting expansion reproduces the running of Heff from high scales to a typical shell-model scale of 8ℏω. At NLO3 various global properties of Heff are reproduced to a typical accuracy of 0.01%, or about 1 keV, at 8ℏω. Channel-by-channel variations in convergence rates are similar to those found in effective field theory approaches. The state dependence of the effective interaction has been a troubling problem in nuclear physics and is embodied in the energy dependence of Heff(|E|) in the Bloch-Horowitz formalism. It is shown that almost all of this state dependence is also extracted in the procedures followed here, isolated in the analytic dependence of Heff on κ. Thus there exists a simple, Hermitian Heff that can be use

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

    PubMed Central

    2011-01-01

    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 by Census tract, in real

  9. Influences of acid-base property of membrane on interfacial interactions related with membrane fouling in a membrane bioreactor based on thermodynamic assessment.

    PubMed

    Zhao, Leihong; Qu, Xiaolu; Zhang, Meijia; Lin, Hongjun; Zhou, Xiaoling; Liao, Bao-Qiang; Mei, Rongwu; Hong, Huachang

    2016-08-01

    Failure of membrane hydrophobicity in predicting membrane fouling requires a more reliable indicator. In this study, influences of membrane acid base (AB) property on interfacial interactions in two different interaction scenarios in a submerged membrane bioreactor (MBR) were studied according to thermodynamic approaches. It was found that both the polyvinylidene fluoride (PVDF) membrane and foulant samples in the MBR had relatively high electron donor (γ(-)) component and low electron acceptor (γ(+)) component. For both of interaction scenarios, AB interaction was the major component of the total interaction. The results showed that, the total interaction monotonically decreased with membrane γ(-), while was marginally affected by membrane γ(+), suggesting that γ(-) could act as a reliable indicator for membrane fouling prediction. This study suggested that membrane modification for fouling mitigation should orient to improving membrane surface γ(-) component rather than hydrophilicity.

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

    PubMed

    Bagdy, Gyorgy; Juhasz, Gabriella; Gonda, Xenia

    2012-12-01

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

  11. Multi-gas interaction modeling on decorated semiconductor interfaces: A novel Fermi distribution-based response isotherm and the inverse hard/soft acid/base concept

    NASA Astrophysics Data System (ADS)

    Laminack, William; Gole, James

    2015-12-01

    A unique MEMS/NEMS approach is presented for the modeling of a detection platform for mixed gas interactions. Mixed gas analytes interact with nanostructured decorating metal oxide island sites supported on a microporous silicon substrate. The Inverse Hard/Soft acid/base (IHSAB) concept is used to assess a diversity of conductometric responses for mixed gas interactions as a function of these nanostructured metal oxides. The analyte conductometric responses are well represented using a combination diffusion/absorption-based model for multi-gas interactions where a newly developed response absorption isotherm, based on the Fermi distribution function is applied. A further coupling of this model with the IHSAB concept describes the considerations in modeling of multi-gas mixed analyte-interface, and analyte-analyte interactions. Taking into account the molecular electronic interaction of both the analytes with each other and an extrinsic semiconductor interface we demonstrate how the presence of one gas can enhance or diminish the reversible interaction of a second gas with the extrinsic semiconductor interface. These concepts demonstrate important considerations in the array-based formats for multi-gas sensing and its applications.

  12. INTERACTIONS BETWEEN TOPOGRAPHY AND ROUGHNESS IN A 2D RASTER-BASED HYDRAULIC MODEL

    NASA Astrophysics Data System (ADS)

    Casas, M.; Yu, D.; Lane, S. N.; Benito-Ferrandez, G.

    2009-12-01

    Analysis of river flow using hydraulic modelling and its implications in derived environmental applications are inextricably connected with the way in which the river boundary shape is represented. This relationship is scale-dependent upon the modelling resolution which in turn determines the importance of a subscale performance of the model and the way subscale (surface and flow) processes are parameterised. This work aims to explore scaling effects associated with the parameterisation of topography and roughness (i.e. surface at different scales) and possible interactions between its components (mesh resolution, topographic content of the DEM and roughness parameterisation) within a 2D raster-based diffusion-wave model. A distributed roughness variable which is scale dependent on the mesh resolution and the surface roughness of the DEM is incorporated to the hydraulic model. The roughness parameterisation is carried out on the basis of a LiDAR-derived vegetation height model and applied in a raster based 2D diffusion wave model. Topographic models with different topographic contents and a constant mesh resolution are generated using LiDAR data and different vertical thresholds. Five DEMs are generated with different topographic contents (±Δz), (DEM±5cm, DEM±10cm, DEM±25cm, DEM±50cm) and four mesh resolutions (1, 2, 4 and 8m) are assessed. A sensitivity analysis on the model results to mesh resolution due to interpolation and resampling procedures of topographic data is performed. Interactions between topographic and roughness parameterisation are related to model results and finally, geostatistical methods are used to document scaling effects in hydraulic modelling results and model performance. This method explicitly recognises the three-way interaction between the discretised mesh resolution and the topographic content in the DEM with the roughness parameterisation. The work shows how the subscale behaviour of the 2D hydraulic model is not well

  13. Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs.

    PubMed

    Koller, Alrun N; Bozilovic, Jelena; Engels, Joachim W; Gohlke, Holger

    2010-05-01

    The thermodynamics of base pairing is of fundamental importance. Fluorinated base analogs are valuable tools for investigating pairing interactions. To understand the influence of direct base-base interactions in relation to the role of water, pairing free energies between natural nucleobases and fluorinated analogs are estimated by potential of mean force calculations. Compared to pairing of AU and GC, pairing involving fluorinated analogs is unfavorable by 0.5-1.0 kcal mol(-1). Decomposing the pairing free energies into enthalpic and entropic contributions reveals fundamental differences for Watson-Crick pairs compared to pairs involving fluorinated analogs. These differences originate from direct base-base interactions and contributions of water. Pairing free energies of fluorinated base analogs with natural bases are less unfavorable by 0.5-1.0 kcal mol(-1) compared to non-fluorinated analogs. This is attributed to stabilizing C-F(...)H-N dipolar interactions and stronger N(...)H-C hydrogen bonds, demonstrating direct and indirect influences of fluorine. 7-methyl-7H-purine and its 9-deaza analog (Z) have been suggested as members of a new class of non-fluorinated base analogs. Z is found to be the least destabilizing universal base in the context of RNA known to date. This is the first experimental evidence for nitrogen-containing heterocylces as bioisosteres of aromatic rings bearing fluorine atoms.

  14. Hydrogen-hydrogen interaction in planar biphenyl: a theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods.

    PubMed

    Eskandari, Kiamars; Van Alsenoy, Christian

    2014-10-05

    The nature of H-H interaction between ortho-hydrogen atoms in planar biphenyl is investigated by two different atomic energy partitioning methods, namely fractional occupation iterative Hirshfeld (FOHI) and interacting quantum atoms (IQA), and compared with the traditional virial-based approach of quantum theory of atoms in molecules (QTAIM). In agreement with Bader's hypothesis of H-H bonding, partitioning the atomic energy into intra-atomic and interatomic terms reveals that there is a net attractive interaction between the ortho-hydrogens in the planar biphenyl. This falsifies the classical view of steric repulsion between the hydrogens. In addition, in contrast to the traditional QTAIM energy analysis, both FOHI and IQA show that the total atomic energy of the ortho-hydrogens remains almost constant when they participate in the H-H interaction. Although, the interatomic part of atomic energy of the hydrogens plays a stabilizing role during the formation of the H-H bond, it is almost compensated by the destabilizing effects of the intra-atomic parts and consequently, the total energy of the hydrogens remains constant. The trends in the changes of intra-atomic and interatomic energy terms of ortho-hydrogens during H-H bond formation are very similar to those observed for the H2 molecule.

  15. PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

    PubMed

    Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E

    2017-01-04

    The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed.

  16. The Effects of Web-Based Interactive Virtual Tours on the Development of Prospective Mathematics Teachers' Spatial Skills

    ERIC Educational Resources Information Center

    Kurtulus, Aytac

    2013-01-01

    The aim of this study was to investigate the effects of web-based interactive virtual tours on the development of prospective mathematics teachers' spatial skills. The study was designed based on experimental method. The "one-group pre-test post-test design" of this method was taken as the research model. The study was conducted with 3rd year…

  17. PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

    PubMed Central

    Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E.

    2017-01-01

    The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. PMID:27915230

  18. Discovering drug–drug interactions: a text-mining and reasoning approach based on properties of drug metabolism

    PubMed Central

    Tari, Luis; Anwar, Saadat; Liang, Shanshan; Cai, James; Baral, Chitta

    2010-01-01

    Motivation: Identifying drug–drug interactions (DDIs) is a critical process in drug administration and drug development. Clinical support tools often provide comprehensive lists of DDIs, but they usually lack the supporting scientific evidences and different tools can return inconsistent results. In this article, we propose a novel approach that integrates text mining and automated reasoning to derive DDIs. Through the extraction of various facts of drug metabolism, not only the DDIs that are explicitly mentioned in text can be extracted but also the potential interactions that can be inferred by reasoning. Results: Our approach was able to find several potential DDIs that are not present in DrugBank. We manually evaluated these interactions based on their supporting evidences, and our analysis revealed that 81.3% of these interactions are determined to be correct. This suggests that our approach can uncover potential DDIs with scientific evidences explaining the mechanism of the interactions. Contact: luis.tari@roche.com PMID:20823320

  19. Quantification of the HIV transcriptional activator complex in live cells by image-based protein-protein interaction analysis.

    PubMed

    Asamitsu, Kaori; Omagari, Katsumi; Okuda, Tomoya; Hibi, Yurina; Okamoto, Takashi

    2016-07-01

    The virus-encoded Tat protein is essential for HIV transcription in infected cells. The interaction of Tat with the cellular transcription elongation factor P-TEFb (positive transcriptional elongation factor b) containing cyclin T1 (CycT1) and cyclin-dependent kinase 9 (CDK9) is critical for its activity. In this study, we use the Fluoppi (fluorescent-based technology detecting protein-protein interaction) system, which enables the quantification of interactions between biomolecules, such as proteins, in live cells. Quantitative measurement of the molecular interactions among Tat, CycT1 and CDK9 has showed that any third molecule enhances the binding between the other two molecules. These findings suggest that each component of the Tat:P-TEFb complex stabilizes the overall complex, thereby supporting the efficient transcriptional elongation during viral RNA synthesis. These interactions may serve as appropriate targets for novel anti-HIV therapy.

  20. Supramolecular polymers constructed by orthogonal self-assembly based on host-guest and metal-ligand interactions.

    PubMed

    Wei, Peifa; Yan, Xuzhou; Huang, Feihe

    2015-02-07

    Supramolecular polymers constructed by orthogonal self-assembly based on host-guest and metal-ligand interactions are attracting increasing attention currently because of their interesting properties and potential applications. Host-guest interactions impart these polymers with good selectivity and convenient enviro-responsiveness, and metal-ligand interactions endow them with various coordination geometries, strong yet tunable coordination binding abilities, as well as magnetic, redox, photophysical, and electrochromic properties. Therefore, supramolecular polymers constructed by orthogonal host-guest and metal-ligand interactions have wide applications in the fields of soft matter, fluorescence sensing, heterocatalysis, electronics, gas storage, etc. In this critical review, we will address the recent development of supramolecular polymeric systems involving metal-ligand interactions and host-guest molecular recognition. Specifically, we classify the related supramolecular polymers depending on the types of macrocyclic hosts, and highlight their intriguing properties originating from the elegant combination of host-guest complexation and metal centers.