Lysine methylation modulates the protein-protein interactions of yeast cytochrome C Cyc1p.

PubMed

Winter, Daniel L; Abeygunawardena, Dhanushi; Hart-Smith, Gene; Erce, Melissa A; Wilkins, Marc R

2015-07-01

In recent years, protein methylation has been established as a major intracellular PTM. It has also been proposed to modulate protein-protein interactions (PPIs) in the interactome. To investigate the effect of PTMs on PPIs, we recently developed the conditional two-hybrid (C2H) system. With this, we demonstrated that arginine methylation can modulate PPIs in the yeast interactome. Here, we used the C2H system to investigate the effect of lysine methylation. Specifically, we asked whether Ctm1p-mediated trimethylation of yeast cytochrome c Cyc1p, on lysine 78, modulates its interactions with Erv1p, Ccp1p, Cyc2p and Cyc3p. We show that the interactions between Cyc1p and Erv1p, and between Cyc1p and Cyc3p, are significantly increased upon trimethylation of lysine 78. This increase of interaction helps explain the reported facilitation of Cyc1p import into the mitochondrial intermembrane space upon methylation. This first application of the C2H system to the study of methyllysine-modulated interactions further confirms its robustness and flexibility. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of mass spectrometry technologies for the discovery of low-molecular weight modulators of enzymes and protein-protein interactions.

PubMed

Zehender, Hartmut; Mayr, Lorenz M

2007-10-01

In recent years, mass spectrometry has gained widespread use as an assay and screening technology in drug discovery because it enables sensitive, label-free detection of low-molecular weight modulators of biomolecules as well as sensitive and accurate detection of high-molecular weight modifications of biomolecules. Electrospray and matrix-assisted laser desorption ionization are the most widely used ionization techniques to identify chemical compounds interfering with enzymatic function, receptor-ligand binding or molecules modulating a protein-protein interaction of interest. Mass spectrometry based techniques are no longer restricted to screening in biochemical assay systems but have now become also applicable to imaging of biomolecules and chemical compounds in cell-based assay systems and even in highly complex tissue sections.

Microelectromechanical (MEMS) manipulators for control of nanoparticle coupling interactions

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

Lopez, Daniel; Wiederrecht, Gary; Gosztola, David J.

A nanopositioning system for producing a coupling interaction between a first nanoparticle and a second nanoparticle. A first MEMS positioning assembly includes an electrostatic comb drive actuator configured to selectively displace a first nanoparticle in a first dimension and an electrode configured to selectively displace the first nanoparticle in a second dimensions. Accordingly, the first nanoparticle may be selectively positioned in two dimensions to modulate the distance between the first nanoparticle and a second nanoparticle that may be coupled to a second MEMS positioning assembly. Modulating the distance between the first and second nanoparticles obtains a coupling interaction between themore » nanoparticles that alters at least one material property of the nanoparticles applicable to a variety of sensing and control applications.« less

Interactive visualization of numerical simulation results: A tool for mission planning and data analysis

NASA Technical Reports Server (NTRS)

Berchem, J.; Raeder, J.; Walker, R. J.; Ashour-Abdalla, M.

1995-01-01

We report on the development of an interactive system for visualizing and analyzing numerical simulation results. This system is based on visualization modules which use the Application Visualization System (AVS) and the NCAR graphics packages. Examples from recent simulations are presented to illustrate how these modules can be used for displaying and manipulating simulation results to facilitate their comparison with phenomenological model results and observations.

Multi-function robots with speech interaction and emotion feedback

NASA Astrophysics Data System (ADS)

Wang, Hongyu; Lou, Guanting; Ma, Mengchao

2018-03-01

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

Investigation of direct integrated optics modulators. [applicable to data preprocessors

NASA Technical Reports Server (NTRS)

Batchman, T. E.

1980-01-01

Direct modulation techniques applicable to integrated optics data preprocessors were investigated. Several methods of modulating a coherent optical beam by interaction with an incoherent beam were studied. It was decided to investigate photon induced conductivity changes in thin semiconductor cladding layers on optical waveguides. Preliminary calculations indicate significant changes can be produced in the phase shift in a propagating wave when the conductivity is changed by ten percent or more. Experimental devices to verify these predicted phase changes and experiments designed to prove the concept are described.

Virtual environment architecture for rapid application development

NASA Technical Reports Server (NTRS)

Grinstein, Georges G.; Southard, David A.; Lee, J. P.

1993-01-01

We describe the MITRE Virtual Environment Architecture (VEA), a product of nearly two years of investigations and prototypes of virtual environment technology. This paper discusses the requirements for rapid prototyping, and an architecture we are developing to support virtual environment construction. VEA supports rapid application development by providing a variety of pre-built modules that can be reconfigured for each application session. The modules supply interfaces for several types of interactive I/O devices, in addition to large-screen or head-mounted displays.

Pure-quartic solitons

PubMed Central

Blanco-Redondo, Andrea; Martijn, de Sterke C.; Sipe, J.E.; Krauss, Thomas F.; Eggleton, Benjamin J.; Husko, Chad

2016-01-01

Temporal optical solitons have been the subject of intense research due to their intriguing physics and applications in ultrafast optics and supercontinuum generation. Conventional bright optical solitons result from the interaction of anomalous group-velocity dispersion and self-phase modulation. Here we experimentally demonstrate a class of bright soliton arising purely from the interaction of negative fourth-order dispersion and self-phase modulation, which can occur even for normal group-velocity dispersion. We provide experimental and numerical evidence of shape-preserving propagation and flat temporal phase for the fundamental pure-quartic soliton and periodically modulated propagation for the higher-order pure-quartic solitons. We derive the approximate shape of the fundamental pure-quartic soliton and discover that is surprisingly Gaussian, exhibiting excellent agreement with our experimental observations. Our discovery, enabled by precise dispersion engineering, could find applications in communications, frequency combs and ultrafast lasers. PMID:26822758

BBU design of linear induction accelerator cells for radiography application

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

Shang, C.C.; Chen, Y.J.; Gaporaso, G.J.

1997-05-06

There is an ongoing effort to develop accelerating modules for high-current electron accelerators for advanced radiography application. Accelerating modules with low beam-cavity coupling impedances along with gap designs with acceptable field stresses comprise a set of fundamental design criteria. We examine improved cell designs which have been developed for accelerator application in several radiographic operating regimes. We evaluate interaction impedances, analyze the effects of beam structure coupling on beam dynamics (beam break-up instability and corkscrew motion). We also provide estimates of coupling through interesting new high-gradient insulators and evaluate their potential future application in induction cells.

[Development of automatic urine monitoring system].

PubMed

Wei, Liang; Li, Yongqin; Chen, Bihua

2014-03-01

An automatic urine monitoring system is presented to replace manual operation. The system is composed of the flow sensor, MSP430f149 single chip microcomputer, human-computer interaction module, LCD module, clock module and memory module. The signal of urine volume is captured when the urine flows through the flow sensor and then displayed on the LCD after data processing. The experiment results suggest that the design of the monitor provides a high stability, accurate measurement and good real-time, and meets the demand of the clinical application.

Plasmonic interferometers: From physics to biosensing applications

NASA Astrophysics Data System (ADS)

Zeng, Xie

Optical interferometry has a long history and wide range of applications. In recent years, plasmonic interferometer arouses great interest due to its compact size and enhanced light-matter interaction. They have demonstrated attractive applications in biomolecule sensing, optical modulation/switching, and material characterization, etc. In this work, we first propose a practical far-field method to extract the intrinsic phase dispersion, revealing important phase information during interactions among free-space light, nanostructure, and SPs. The proposed approach is confirmed by both simulation and experiment. Then we design novel plasmonic interferometer structure for sensitive optical sensing applications. To overcome two major limitations suffered by previously reported double-slit plasmonic Mach-Zehnder interferometer (PMZI), two new schemes are proposed and investigated. (1) A PMZI based on end-fire coupling improves the SP coupling efficiency and enhance the interference contrast more than 50 times. (2) In another design, a multi-layered metal-insulator-metal PMZI releases the requirement for single-slit illumination, which enables sensitive, high-throughput sensing applications based on intensity modulation. We develop a sensitive, low-cost and high-throughput biosensing platform based on intensity modulation using ring-hole plasmonic interferometers. This biosensor is then integrated with cell-phone-based microscope, which is promising to develop a portable sensor for point-of-care diagnostics, epidemic disease control and food safety monitoring.

A designed repeat protein as an affinity capture reagent

PubMed Central

Speltz, Elizabeth B.; Brown, Rebecca S.H.; Hajare, Holly S.; Schlieker, Christian; Regan, Lynne

2017-01-01

Repeat proteins are an attractive target for protein engineering and design. We have focused our attention on the design and engineering of one particular class - tetratricopeptide repeat (TPR) proteins. In previous work we have shown that the structure and stability of TPR proteins can be manipulated in a rational fashion [Cortajarena 2011; Main 2003]. Building on those studies, we have designed and characterized a number of different peptide-binding TPR modules and we have also assembled these modules into supramolecular arrays [Cortajarena 2009; Cortajarena 2008; Jackrel 2009; Kajander 2007]. Here we focus on the development of one such TPR-peptide interaction for a practical application – affinity purification. We illustrate the general utility of our designed protein interaction. Furthermore, this example highlights how basic research on protein-peptide interactions can lead to the development of novel reagents with important practical applications. PMID:26517897

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

Towards a Comprehensive Computational Simulation System for Turbomachinery

NASA Technical Reports Server (NTRS)

Shih, Ming-Hsin

1994-01-01

The objective of this work is to develop algorithms associated with a comprehensive computational simulation system for turbomachinery flow fields. This development is accomplished in a modular fashion. These modules includes grid generation, visualization, network, simulation, toolbox, and flow modules. An interactive grid generation module is customized to facilitate the grid generation process associated with complicated turbomachinery configurations. With its user-friendly graphical user interface, the user may interactively manipulate the default settings to obtain a quality grid within a fraction of time that is usually required for building a grid about the same geometry with a general-purpose grid generation code. Non-Uniform Rational B-Spline formulations are utilized in the algorithm to maintain geometry fidelity while redistributing grid points on the solid surfaces. Bezier curve formulation is used to allow interactive construction of inner boundaries. It is also utilized to allow interactive point distribution. Cascade surfaces are transformed from three-dimensional surfaces of revolution into two-dimensional parametric planes for easy manipulation. Such a transformation allows these manipulated plane grids to be mapped to surfaces of revolution by any generatrix definition. A sophisticated visualization module is developed to al-low visualization for both grid and flow solution, steady or unsteady. A network module is built to allow data transferring in the heterogeneous environment. A flow module is integrated into this system, using an existing turbomachinery flow code. A simulation module is developed to combine the network, flow, and visualization module to achieve near real-time flow simulation about turbomachinery geometries. A toolbox module is developed to support the overall task. A batch version of the grid generation module is developed to allow portability and has been extended to allow dynamic grid generation for pitch changing turbomachinery configurations. Various applications with different characteristics are presented to demonstrate the success of this system.

Preparation for Instruction. A Module of Instruction in Teacher Education. Prepared for Project RAFT.

ERIC Educational Resources Information Center

Handley, Herbert M., Ed.

This module, developed by the Research Applications for Teaching (RAFT) project, was written to assist students to write lesson plans that are effective and interactive. Students are given directions for the preparation of behavioral objectives and for the selection of appropriate instructional methodologies to meet the widely varying needs of…

Nanoparticle interface to biology: applications in probing and modulating biological processes.

PubMed

Kah, James Chen Yong; Yeo, Eugenia Li Ling; Koh, Wee Ling; Poinard, Barbara Elodie Ariane; Neo, Dawn Jing Hui

2013-01-01

Nanomaterials can be considered as "pseudo" subcellular entities that are similar to endogenous biomolecules because of their size and ability to interact with other biomolecules. The interaction between nanoparticles and biomolecules gives rise to the nano-bio interface between a nanoparticle and its biological environment. This is often defined in terms of the biomolecules that are present on the surface of the nanoparticles. The nano-bio interface alters the surface characteristics and is what the biological system sees and interacts with. The nanoparticle can thus be viewed as a "scaffold" to which molecules are attached. Intelligent design of this nano-bio interface is therefore crucial to the functionality of nanoscale systems in biology. In this review, we discuss the most common nano-bio interfaces formed from molecules including DNA, polymers, proteins, and antibodies, and discuss their applications in probing and modulating biological processes. We focus our discussion on the nano-bio interface formed on gold nanoparticles as our nanoparticle "scaffold" of interest in part because of our research interest as well as their unique physicochemical properties. While not exhaustive, this review provides a good overview of the latest advances in the use of gold nanomaterial interface to probe and modulate biological processes.

Design and implementation of a 3D ocean virtual reality and visualization engine

NASA Astrophysics Data System (ADS)

Chen, Ge; Li, Bo; Tian, Fenglin; Ji, Pengbo; Li, Wenqing

2012-12-01

In this study, a 3D virtual reality and visualization engine for rendering the ocean, named VV-Ocean, is designed for marine applications. The design goals of VV-Ocean aim at high fidelity simulation of ocean environment, visualization of massive and multidimensional marine data, and imitation of marine lives. VV-Ocean is composed of five modules, i.e. memory management module, resources management module, scene management module, rendering process management module and interaction management module. There are three core functions in VV-Ocean: reconstructing vivid virtual ocean scenes, visualizing real data dynamically in real time, imitating and simulating marine lives intuitively. Based on VV-Ocean, we establish a sea-land integration platform which can reproduce drifting and diffusion processes of oil spilling from sea bottom to surface. Environment factors such as ocean current and wind field have been considered in this simulation. On this platform oil spilling process can be abstracted as movements of abundant oil particles. The result shows that oil particles blend with water well and the platform meets the requirement for real-time and interactive rendering. VV-Ocean can be widely used in ocean applications such as demonstrating marine operations, facilitating maritime communications, developing ocean games, reducing marine hazards, forecasting the weather over oceans, serving marine tourism, and so on. Finally, further technological improvements of VV-Ocean are discussed.

Cancer Cell Biology: A Student-Centered Instructional Module Exploring the Use of Multimedia to Enrich Interactive, Constructivist Learning of Science

PubMed Central

Bockholt, Susanne M.; West, J. Paige; Bollenbacher, Walter E.

2003-01-01

Multimedia has the potential of providing bioscience education novel learning environments and pedagogy applications to foster student interest, involve students in the research process, advance critical thinking/problem-solving skills, and develop conceptual understanding of biological topics. Cancer Cell Biology, an interactive, multimedia, problem-based module, focuses on how mutations in protooncogenes and tumor suppressor genes can lead to uncontrolled cell proliferation by engaging students as research scientists/physicians with the task of diagnosing the molecular basis of tumor growth for a group of patients. The process of constructing the module, which was guided by scientist and student feedback/responses, is described. The completed module and insights gained from its development are presented as a potential “multimedia pedagogy” for the development of other multimedia science learning environments. PMID:12822037

Neuroticism modulates the effects of intranasal vasopressin treatment on the neural response to positive and negative social interactions.

PubMed

Feng, Chunliang; DeMarco, Ashley C; Haroon, Ebrahim; Rilling, James K

2015-07-01

Neuroticism is a fundamental personality trait associated with proneness to feel negative affect. Here we ask how Neuroticism influences the neural response to positive and negative social interactions and how Neuroticism modulates the effect of intranasal oxytocin (OT) and vasopressin (AVP) on the neural response to social interactions. In a double-blind, placebo-controlled study, 153 male participants were randomized to receive 24 IU intranasal OT, 20 IU AVP or placebo. Afterwards, they were imaged with fMRI while playing an iterated Prisoner's Dilemma Game. On a different day, subjects completed the NEO personality inventory to measure Neuroticism. Neuroticism was positively correlated with the neural response to negative social interactions in the anterior cingulate cortex/medial prefrontal cortex and with the neural response to positive social interactions in the insula, indicating that Neuroticism modulates neuropsychological processing of both negative and positive social interactions. Neuroticism did not modulate the effect of intranasal OT treatment on the neural response to either positive or negative social interactions. On the other hand, AVP treatment significantly interacted with Neuroticism to modulate the BOLD response to both positive and negative social interactions. Specifically, AVP increased anterior cingulate cortex/medial prefrontal cortex and lateral temporal lobe responses to negative social interactions to a greater extent in participants scoring high rather than low on Neuroticism. AVP also increased the insula response to positive social interactions to a greater extent in participants scoring high rather than low on Neuroticism. These results imply that AVP may increase emotion regulation in response to negative social interactions and the salience of positive social interactions to a greater extent in individuals high compared to low in Neuroticism. The current findings urge caution against uniform clinical application of nonapeptides and suggest that their efficacy may vary as a function of personality. Copyright © 2015 Elsevier Ltd. All rights reserved.

Naver: a PC-cluster-based VR system

NASA Astrophysics Data System (ADS)

Park, ChangHoon; Ko, HeeDong; Kim, TaiYun

2003-04-01

In this paper, we present a new framework NAVER for virtual reality application. The NAVER is based on a cluster of low-cost personal computers. The goal of NAVER is to provide flexible, extensible, scalable and re-configurable framework for the virtual environments defined as the integration of 3D virtual space and external modules. External modules are various input or output devices and applications on the remote hosts. From the view of system, personal computers are divided into three servers according to its specific functions: Render Server, Device Server and Control Server. While Device Server contains external modules requiring event-based communication for the integration, Control Server contains external modules requiring synchronous communication every frame. And, the Render Server consists of 5 managers: Scenario Manager, Event Manager, Command Manager, Interaction Manager and Sync Manager. These managers support the declaration and operation of virtual environment and the integration with external modules on remote servers.

High temperature material interactions of thermoelectric systems using silicon germanium.

NASA Technical Reports Server (NTRS)

Stapfer, G.; Truscello, V. C.

1973-01-01

The efficient use of silicon germanium thermoelectric material for radioisotope thermoelectric generators (RTG) is achieved by operation at relatively high temperatures. The insulation technique which is most appropriate for this application uses multiple layers of molybdenum foil and astroquartz. Even so, the long term operation of these materials at elevated temperatures can cause material interaction to occur within the system. To investigate these material interactions, the Jet Propulsion Laboratory is currently testing a number of thermoelectric modules which use four silicon germanium thermoelectric couples in conjunction with the multifoil thermal insulation. The paper discusses the results of the ongoing four-couple module test program and correlates test results with those of a basic material test program.

2D Materials for Optical Modulation: Challenges and Opportunities.

PubMed

Yu, Shaoliang; Wu, Xiaoqin; Wang, Yipei; Guo, Xin; Tong, Limin

2017-04-01

Owing to their atomic layer thickness, strong light-material interaction, high nonlinearity, broadband optical response, fast relaxation, controllable optoelectronic properties, and high compatibility with other photonic structures, 2D materials, including graphene, transition metal dichalcogenides and black phosphorus, have been attracting increasing attention for photonic applications. By tuning the carrier density via electrical or optical means that modifies their physical properties (e.g., Fermi level or nonlinear absorption), optical response of the 2D materials can be instantly changed, making them versatile nanostructures for optical modulation. Here, up-to-date 2D material-based optical modulation in three categories is reviewed: free-space, fiber-based, and on-chip configurations. By analysing cons and pros of different modulation approaches from material and mechanism aspects, the challenges faced by using these materials for device applications are presented. In addition, thermal effects (e.g., laser induced damage) in 2D materials, which are critical to practical applications, are also discussed. Finally, the outlook for future opportunities of these 2D materials for optical modulation is given. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dense module enumeration in biological networks

NASA Astrophysics Data System (ADS)

Tsuda, Koji; Georgii, Elisabeth

2009-12-01

Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

Interactive design and analysis of future large spacecraft concepts

NASA Technical Reports Server (NTRS)

Garrett, L. B.

1981-01-01

An interactive computer aided design program used to perform systems level design and analysis of large spacecraft concepts is presented. Emphasis is on rapid design, analysis of integrated spacecraft, and automatic spacecraft modeling for lattice structures. Capabilities and performance of multidiscipline applications modules, the executive and data management software, and graphics display features are reviewed. A single user at an interactive terminal create, design, analyze, and conduct parametric studies of Earth orbiting spacecraft with relative ease. Data generated in the design, analysis, and performance evaluation of an Earth-orbiting large diameter antenna satellite are used to illustrate current capabilities. Computer run time statistics for the individual modules quantify the speed at which modeling, analysis, and design evaluation of integrated spacecraft concepts is accomplished in a user interactive computing environment.

Interactive NMR: A Simulation Based Teaching Tool for Fundamentals to Applications with Tangible Analogies

NASA Astrophysics Data System (ADS)

Griesse-Nascimento, Sarah; Bridger, Joshua; Brown, Keith; Westervelt, Robert

2011-03-01

Interactive computer simulations increase students' understanding of difficult concepts and their ability to explain complex ideas. We created a module of eight interactive programs and accompanying lesson plans for teaching the fundamental concepts of Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) that we call interactive NMR (iNMR). We begin with an analogy between nuclear spins and metronomes to start to build intuition about the dynamics of spins in a magnetic field. We continue to explain T1, T2, and pulse sequences with the metronome analogy. The final three programs are used to introduce and explain the Magnetic Resonance Switch, a recent diagnostic technique based on NMR. A modern relevant application is useful to generate interest in the topic and confidence in the students' ability to apply their knowledge. The iNMR module was incorporated into a high school AP physics class. In a preliminary evaluation of implementation, students expressed enthusiasm and demonstrated enhanced understanding of the material relative to the previous year. Funded by NSF PHY-0646094 grant.

Intrinsic Sensing and Evolving Internal Model Control of Compact Elastic Module for a Lower Extremity Exoskeleton

PubMed Central

Wang, Likun; Du, Zhijiang; Dong, Wei; Shen, Yi; Zhao, Guangyu

2018-01-01

To achieve strength augmentation, endurance enhancement, and human assistance in a functional autonomous exoskeleton, control precision, back drivability, low output impedance, and mechanical compactness are desired. In our previous work, two elastic modules were designed for human–robot interaction sensing and compliant control, respectively. According to the intrinsic sensing properties of the elastic module, in this paper, only one compact elastic module is applied to realize both purposes. Thus, the corresponding control strategy is required and evolving internal model control is proposed to address this issue. Moreover, the input signal to the controller is derived from the deflection of the compact elastic module. The human–robot interaction is considered as the disturbance which is approximated by the output error between the exoskeleton control plant and evolving forward learning model. Finally, to verify our proposed control scheme, several experiments are conducted with our robotic exoskeleton system. The experiment shows a satisfying result and promising application feasibility. PMID:29562684

Intrinsic Sensing and Evolving Internal Model Control of Compact Elastic Module for a Lower Extremity Exoskeleton.

PubMed

Wang, Likun; Du, Zhijiang; Dong, Wei; Shen, Yi; Zhao, Guangyu

2018-03-19

To achieve strength augmentation, endurance enhancement, and human assistance in a functional autonomous exoskeleton, control precision, back drivability, low output impedance, and mechanical compactness are desired. In our previous work, two elastic modules were designed for human-robot interaction sensing and compliant control, respectively. According to the intrinsic sensing properties of the elastic module, in this paper, only one compact elastic module is applied to realize both purposes. Thus, the corresponding control strategy is required and evolving internal model control is proposed to address this issue. Moreover, the input signal to the controller is derived from the deflection of the compact elastic module. The human-robot interaction is considered as the disturbance which is approximated by the output error between the exoskeleton control plant and evolving forward learning model. Finally, to verify our proposed control scheme, several experiments are conducted with our robotic exoskeleton system. The experiment shows a satisfying result and promising application feasibility.

Periodically modulated single-photon transport in one-dimensional waveguide

NASA Astrophysics Data System (ADS)

Li, Xingmin; Wei, L. F.

2018-03-01

Single-photon transport along a one-dimension waveguide interacting with a quantum system (e.g., two-level atom) is a very useful and meaningful simplified model of the waveguide-based optical quantum devices. Thus, how to modulate the transport of the photons in the waveguide structures by adjusting certain external parameters should be particularly important. In this paper, we discuss how such a modulation could be implemented by periodically driving the energy splitting of the interacting atom and the atom-photon coupling strength. By generalizing the well developed time-independent full quantum mechanical theory in real space to the time-dependent one, we show that various sideband-transmission phenomena could be observed. This means that, with these modulations the photon has certain probabilities to transmit through the scattering atom in the other energy sidebands. Inversely, by controlling the sideband transmission the periodic modulations of the single photon waveguide devices could be designed for the future optical quantum information processing applications.

World Wide Web-based system for the calculation of substituent parameters and substituent similarity searches.

PubMed

Ertl, P

1998-02-01

Easy to use, interactive, and platform-independent WWW-based tools are ideal for development of chemical applications. By using the newly emerging Web technologies such as Java applets and sophisticated scripting, it is possible to deliver powerful molecular processing capabilities directly to the desk of synthetic organic chemists. In Novartis Crop Protection in Basel, a Web-based molecular modelling system has been in use since 1995. In this article two new modules of this system are presented: a program for interactive calculation of important hydrophobic, electronic, and steric properties of organic substituents, and a module for substituent similarity searches enabling the identification of bioisosteric functional groups. Various possible applications of calculated substituent parameters are also discussed, including automatic design of molecules with the desired properties and creation of targeted virtual combinatorial libraries.

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

PubMed

Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S

2015-07-14

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

"Cancer Cell Biology:" A Student-Centered Instructional Module Exploring the Use of Multimedia to Enrich Interactive, Constructivist Learning of Science

ERIC Educational Resources Information Center

Bockholt, Susanne M.; West, J. Paige; Bollenbacher, Walter E.

2003-01-01

Multimedia has the potential of providing bioscience education novel learning environments and pedagogy applications to foster student interest, involve students in the research process, advance critical thinking/problem-solving skills, and develop conceptual understanding of biological topics. "Cancer Cell Biology," an interactive, multimedia,…

Coherent population trapping with polarization modulation

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

Yun, Peter, E-mail: enxue.yun@obspm.fr; Guérandel, Stéphane; Clercq, Emeric de

Coherent population trapping (CPT) is extensively studied for future vapor cell clocks of high frequency stability. In the constructive polarization modulation CPT scheme, a bichromatic laser field with polarization and phase synchronously modulated is applied on an atomic medium. A high contrast CPT signal is observed in this so-called double-modulation configuration, due to the fact that the atomic population does not leak to the extreme Zeeman states, and that the two CPT dark states, which are produced successively by the alternate polarizations, add constructively. Here, we experimentally investigate CPT signal dynamics first in the usual configuration, a single circular polarization.more » The double-modulation scheme is then addressed in both cases: one pulse Rabi interaction and two pulses Ramsey interaction. The impact and the optimization of the experimental parameters involved in the time sequence are reviewed. We show that a simple seven-level model explains the experimental observations. The double-modulation scheme yields a high contrast similar to the one of other high contrast configurations like push-pull optical pumping or crossed linear polarization scheme, with a setup allowing a higher compactness. The constructive polarization modulation is attractive for atomic clock, atomic magnetometer, and high precision spectroscopy applications.« less

Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

PubMed

Xia, Hongwei; Fu, Hailin; Zhang, Yanfeng; Shih, Kuo-Chih; Ren, Yuan; Anuganti, Murali; Nieh, Mu-Ping; Cheng, Jianjun; Lin, Yao

2017-08-16

Supramolecular polymerization or assembly of proteins or large macromolecular units by a homogeneous nucleation mechanism can be quite slow and require specific solution conditions. In nature, protein assembly is often regulated by molecules that modulate the electrostatic interactions of the protein subunits for various association strengths. The key to this regulation is the coupling of the assembly process with a reversible or irreversible chemical reaction that occurs within the constituent subunits. However, realizing this complex process by the rational design of synthetic molecules or macromolecules remains a challenge. Herein, we use a synthetic polypeptide-grafted comb macromolecule to demonstrate how the in situ modulation of interactions between the charged macromolecules affects their resulting supramolecular structures. The kinetics of structural formation was studied and can be described by a generalized model of nucleated polymerization containing secondary pathways. Basic thermodynamic analysis indicated the delicate role of the electrostatic interactions between the charged subunits in the reaction-induced assembly process. This approach may be applicable for assembling a variety of ionic soft matters that are amenable to chemical reactions in situ.

Engineered Aptamers to Probe Molecular Interactions on the Cell Surface

PubMed Central

Batool, Sana; Bhandari, Sanam; George, Shanell; Okeoma, Precious; Van, Nabeela; Zümrüt, Hazan E.; Mallikaratchy, Prabodhika

2017-01-01

Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics. PMID:28850067

Chlorella vulgaris and Pseudomonas putida interaction modulates phosphate trafficking for reduced arsenic uptake in rice (Oryza sativa L.).

PubMed

Srivastava, Suchi; Srivastava, Sonal; Bist, Vidisha; Awasthi, Surabhi; Chauhan, Reshu; Chaudhry, Vasvi; Singh, Poonam C; Dwivedi, Sanjay; Niranjan, Abhishek; Agrawal, Lalit; Chauhan, Puneet Singh; Tripathi, Rudra Deo; Nautiyal, Chandra Shekhar

2018-06-05

Rice grown in arsenic (As) contaminated areas contributes to high dietary exposure of As inducing multiple adverse effects on human health. The As contamination and application of phosphate fertilizers during seedling stage creates a high P and As stress condition. The flooded paddy fields are also conducive for algal growth and microbial activity. The present study proposes potential role of microalgae, Chlorella vulgaris (CHL) and bacteria, Pseudomonas putida (RAR) on rice plant grown under excess As and phosphate (P) conditions. The results show synchronized interaction of CHL + RAR which, reduces As uptake through enhanced P:As and reduced As:biomass ratio by modulating P trafficking. Gene expression analysis of different phosphate transporters exhibited correlation with reduced As uptake and other essential metals. The balancing of reactive oxygen species (ROS), proline accumulation, hormone modulation, and As sequestration in microbial biomass were elucidated as possible mechanisms of As detoxification. The study concludes that RAR and CHL combination mitigates the As stress during P-enriched conditions in rice by: (i) reducing As availability, (ii) modulating the As uptake, and (iii) improving detoxification mechanism of the plant. The study will be important in assessing the role and applicability of P solubilizing biofertilizers in these conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

Introducing Scenario Based Learning interactive to postgraduates in UQ Orthodontic Program.

PubMed

Naser-ud-Din, S

2015-08-01

E-learning has gained momentum in health sciences and seems to have great potential in specialist dental education. Higher acceptability by learners is particularly associated with the surge of smart devices. Currently, there are limited number of e-learning modules available for dental education, particularly in Orthodontics. Scenario Based Learning interactive (SBLi(®)) software was used for the first time in Orthodontics Postgraduate training at the University of Queensland. Nine interactive modules were created embedded with clinical procedure videos, web-links, evidence-based literature, along with opportunity for self-assessment and evaluation. Qualitative data were collected before and after the administration of the SBLi(®) for Orthodontics. The purpose of this data was to investigate learning styles and the acceptance of e-modules as part of postgraduate training. Advantages of the package included high acceptance rate, greater confidence in the application of clinical skills covered in the modules and reduced contact time particularly with limited academic staff. E-modules demonstrated high compatibility with the learning styles of the participants and were considered engaging. It seems apparent that e-learning is most effective in a blended learning environment, supplemented with the traditional classroom approach, rather than as a sole mechanism for postgraduate training. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Development and application of the GIM code for the Cyber 203 computer

NASA Technical Reports Server (NTRS)

Stainaker, J. F.; Robinson, M. A.; Rawlinson, E. G.; Anderson, P. G.; Mayne, A. W.; Spradley, L. W.

1982-01-01

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented.

Supramolecularly Engineered Circular Bivalent Aptamer for Enhanced Functional Protein Delivery.

PubMed

Jiang, Ying; Pan, Xiaoshu; Chang, Jin; Niu, Weijia; Hou, Weijia; Kuai, Hailan; Zhao, Zilong; Liu, Ji; Wang, Ming; Tan, Weihong

2018-06-06

Circular bivalent aptamers (cb-apt) comprise an emerging class of chemically engineered aptamers with substantially improved stability and molecular recognition ability. Its therapeutic application, however, is challenged by the lack of functional modules to control the interactions of cb-apt with therapeutics. We present the design of a β-cyclodextrin-modified cb-apt (cb-apt-βCD) and its supramolecular interaction with molecular therapeutics via host-guest chemistry for targeted intracellular delivery. The supramolecular ensemble exhibits high serum stability and enhanced intracellular delivery efficiency compared to a monomeric aptamer. The cb-apt-βCD ensemble delivers green fluorescent protein into targeted cells with efficiency as high as 80%, or cytotoxic saporin to efficiently inhibit tumor cell growth. The strategy of conjugating βCD to cb-apt, and subsequently modulating the supramolecular chemistry of cb-apt-βCD, provides a general platform to expand and diversify the function of aptamers, enabling new biological and therapeutic applications.

CFD application to supersonic/hypersonic inlet airframe integration. [computational fluid dynamics (CFD)

NASA Technical Reports Server (NTRS)

Benson, Thomas J.

1988-01-01

Supersonic external compression inlets are introduced, and the computational fluid dynamics (CFD) codes and tests needed to study flow associated with these inlets are outlined. Normal shock wave turbulent boundary layer interaction is discussed. Boundary layer control is considered. Glancing sidewall shock interaction is treated. The CFD validation of hypersonic inlet configurations is explained. Scramjet inlet modules are shown.

Modulating interactions between ligand-coated nanoparticles and phase-separated lipid bilayers by varying the ligand density and the surface charge.

PubMed

Chen, Xiaojie; Tieleman, D Peter; Liang, Qing

2018-02-01

The interactions between nanoparticles and lipid bilayers are critical in applications of nanoparticles in nanomedicine, cell imaging, toxicology, and elsewhere. Here, we investigate the interactions between nanoparticles coated with neutral and/or charged ligands and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. Both penetration and adsorption processes as well as the final distribution of the nanoparticles can be readily modulated by varying the ligand density and the surface charge of the nanoparticles. Completely hydrophobic (neutral) nanoparticles with larger size initially preferentially penetrate into the liquid-disordered region of the lipid bilayer and finally transfer into the liquid-ordered region; partially hydrophilic nanoparticles with low or moderate surface charge tend to either distribute in the liquid-disordered region or be adsorbed on the surface of the lipid bilayer, while strongly hydrophilic nanoparticles with high surface charge always reside on the surface of the lipid bilayer. Interactions of the nanoparticles with the lipid bilayers are affected by the surface charge of nanoparticles, hydrophobic mismatch, bending of the ligands, and the packing state of the lipids. Insight in these factors can be used to improve the efficiency of designing nanoparticles for specific applications.

Augmenting reality in Direct View Optical (DVO) overlay applications

NASA Astrophysics Data System (ADS)

Hogan, Tim; Edwards, Tim

2014-06-01

The integration of overlay displays into rifle scopes can transform precision Direct View Optical (DVO) sights into intelligent interactive fire-control systems. Overlay displays can provide ballistic solutions within the sight for dramatically improved targeting, can fuse sensor video to extend targeting into nighttime or dirty battlefield conditions, and can overlay complex situational awareness information over the real-world scene. High brightness overlay solutions for dismounted soldier applications have previously been hindered by excessive power consumption, weight and bulk making them unsuitable for man-portable, battery powered applications. This paper describes the advancements and capabilities of a high brightness, ultra-low power text and graphics overlay display module developed specifically for integration into DVO weapon sight applications. Central to the overlay display module was the development of a new general purpose low power graphics controller and dual-path display driver electronics. The graphics controller interface is a simple 2-wire RS-232 serial interface compatible with existing weapon systems such as the IBEAM ballistic computer and the RULR and STORM laser rangefinders (LRF). The module features include multiple graphics layers, user configurable fonts and icons, and parameterized vector rendering, making it suitable for general purpose DVO overlay applications. The module is configured for graphics-only operation for daytime use and overlays graphics with video for nighttime applications. The miniature footprint and ultra-low power consumption of the module enables a new generation of intelligent DVO systems and has been implemented for resolutions from VGA to SXGA, in monochrome and color, and in graphics applications with and without sensor video.

Bayesian module identification from multiple noisy networks.

PubMed

Zamani Dadaneh, Siamak; Qian, Xiaoning

2016-12-01

Module identification has been studied extensively in order to gain deeper understanding of complex systems, such as social networks as well as biological networks. Modules are often defined as groups of vertices in these networks that are topologically cohesive with similar interaction patterns with the rest of the vertices. Most of the existing module identification algorithms assume that the given networks are faithfully measured without errors. However, in many real-world applications, for example, when analyzing protein-protein interaction networks from high-throughput profiling techniques, there is significant noise with both false positive and missing links between vertices. In this paper, we propose a new model for more robust module identification by taking advantage of multiple observed networks with significant noise so that signals in multiple networks can be strengthened and help improve the solution quality by combining information from various sources. We adopt a hierarchical Bayesian model to integrate multiple noisy snapshots that capture the underlying modular structure of the networks under study. By introducing a latent root assignment matrix and its relations to instantaneous module assignments in all the observed networks to capture the underlying modular structure and combine information across multiple networks, an efficient variational Bayes algorithm can be derived to accurately and robustly identify the underlying modules from multiple noisy networks. Experiments on synthetic and protein-protein interaction data sets show that our proposed model enhances both the accuracy and resolution in detecting cohesive modules, and it is less vulnerable to noise in the observed data. In addition, it shows higher power in predicting missing edges compared to individual-network methods.

Application programming in C# environment with recorded user software interactions and its application in autopilot of VMAT/IMRT treatment planning.

PubMed

Wang, Henry; Xing, Lei

2016-11-08

An autopilot scheme of volumetric-modulated arc therapy (VMAT)/intensity-modulated radiation therapy (IMRT) planning with the guidance of prior knowl-edge is established with recorded interactions between a planner and a commercial treatment planning system (TPS). Microsoft (MS) Visual Studio Coded UI is applied to record some common planner-TPS interactions as subroutines. The TPS used in this study is a Windows-based Eclipse system. The interactions of our application program with Eclipse TPS are realized through a series of subrou-tines obtained by prerecording the mouse clicks or keyboard strokes of a planner in operating the TPS. A strategy to autopilot Eclipse VMAT/IMRT plan selection process is developed as a specific example of the proposed "scripting" method. The autopiloted planning is navigated by a decision function constructed with a reference plan that has the same prescription and similar anatomy with the case at hand. The calculation proceeds by alternating between the Eclipse optimization and the outer-loop optimization independent of the Eclipse. In the C# program, the dosimetric characteristics of a reference treatment plan are used to assess and modify the Eclipse planning parameters and to guide the search for a clinically sensible treatment plan. The approach is applied to plan a head and neck (HN) VMAT case and a prostate IMRT case. Our study demonstrated the feasibility of application programming method in C# environment with recorded interactions of planner-TPS. The process mimics a planner's planning process and automatically provides clinically sensible treatment plans that would otherwise require a large amount of manual trial and error of a planner. The proposed technique enables us to harness a commercial TPS by application programming via the use of recorded human computer interactions and provides an effective tool to greatly facilitate the treatment planning process. © 2016 The Authors.

Application programming in C# environment with recorded user software interactions and its application in autopilot of VMAT/IMRT treatment planning

PubMed Central

Wang, Henry

2016-01-01

An autopilot scheme of volumetric‐modulated arc therapy (VMAT)/intensity‐modulated radiation therapy (IMRT) planning with the guidance of prior knowledge is established with recorded interactions between a planner and a commercial treatment planning system (TPS). Microsoft (MS) Visual Studio Coded UI is applied to record some common planner‐TPS interactions as subroutines. The TPS used in this study is a Windows‐based Eclipse system. The interactions of our application program with Eclipse TPS are realized through a series of subroutines obtained by prerecording the mouse clicks or keyboard strokes of a planner in operating the TPS. A strategy to autopilot Eclipse VMAT/IMRT plan selection process is developed as a specific example of the proposed “scripting” method. The autopiloted planning is navigated by a decision function constructed with a reference plan that has the same prescription and similar anatomy with the case at hand. The calculation proceeds by alternating between the Eclipse optimization and the outer‐loop optimization independent of the Eclipse. In the C# program, the dosimetric characteristics of a reference treatment plan are used to assess and modify the Eclipse planning parameters and to guide the search for a clinically sensible treatment plan. The approach is applied to plan a head and neck (HN) VMAT case and a prostate IMRT case. Our study demonstrated the feasibility of application programming method in C# environment with recorded interactions of planner‐TPS. The process mimics a planner's planning process and automatically provides clinically sensible treatment plans that would otherwise require a large amount of manual trial and error of a planner. The proposed technique enables us to harness a commercial TPS by application programming via the use of recorded human computer interactions and provides an effective tool to greatly facilitate the treatment planning process. PACS number(s): 87.55.D‐, 87.55.kd, 87.55.de PMID:27929493

Development of Wireless RFID Glove for Various Applications

NASA Astrophysics Data System (ADS)

Lee, Changwon; Kim, Minchul; Park, Jinwoo; Oh, Jeonghoon; Eom, Kihwan

Radio Frequency Identification is increasingly popular technology with many applications. The majority of applications of RFID are supply-chain management. In this paper, we proposed the development of wireless RFID Glove for various applications in real life. Proposed wireless RFID glove is composed of RFID reader of 13.56 MHz and RF wireless module. Proposed Gloves were applied to two applications. First is the interactive leaning and second is Meal aid system for blind people. The experimental results confirmed good performances.

First Principles based methods and applications for realistic simulations on complex soft materials to develop new materials for energy, health, and environmental sustainability

NASA Astrophysics Data System (ADS)

Goddard, William

2013-03-01

For soft materials applications it is essential to obtain accurate descriptions of the weak (London dispersion, electrostatic) interactions between nonbond units, to include interactions with and stabilization by solvent, and to obtain accurate free energies and entropic changes during chemical, physical, and thermal processing. We will describe some of the advances being made in first principles based methods for treating soft materials with applications selected from new organic electrodes and electrolytes for batteries and fuel cells, forward osmosis for water cleanup, extended matter stable at ambient conditions, and drugs for modulating activation of GCPR membrane proteins,

Using a network modularity analysis to inform management of a rare endemic plant in the northern Great Plains, USA

USGS Publications Warehouse

Larson, Diane L.; Droege, Sam; Rabie, Paul A.; Larson, Jennifer L.; Devalez, Jelle; Haar, Milton; McDermott-Kubeczko, Margaret

2014-01-01

1. Analyses of flower-visitor interaction networks allow application of community-level information to conservation problems, but management recommendations that ensue from such analyses are not well characterized. Results of modularity analyses, which detect groups of species (modules) that interact more with each other than with species outside their module, may be particularly applicable to management concerns. 2. We conducted modularity analyses of networks surrounding a rare endemic annual plant, Eriogonum visheri, at Badlands National Park, USA, in 2010 and 2011. Plant species visited were determined by pollen on insect bodies and by flower species upon which insects were captured. Roles within modules (network hub, module hub, connector and peripheral, in decreasing order of network structural importance) were determined for each species. 3. Relationships demonstrated by the modularity analysis, in concert with knowledge of pollen species carried by insects, allowed us to infer effects of two invasive species on E. visheri. Sharing a module increased risk of interspecific pollen transfer to E. visheri. Control of invasive Salsola tragus, which shared a module with E. visheri, is therefore a prudent management objective, but lack of control of invasive Melilotus officinalis, which occupied a different module, is unlikely to negatively affect pollination of E. visheri. Eriogonum pauciflorum may occupy a key position in this network, supporting insects from the E. visheri module when E. visheri is less abundant. 4. Year-to-year variation in species' roles suggests management decisions must be based on observations over several years. Information on pollen deposition on stigmas would greatly strengthen inferences made from the modularity analysis. 5. Synthesis and applications: Assessing the consequences of pollination, whether at the community or individual level, is inherently time-consuming. A trade-off exists: rather than an estimate of fitness effects, the network approach provides a broad understanding of the relationships among insect visitors and other plant species that may affect the focal rare plant. Knowledge of such relationships allows managers to detect, target and prioritize control of only the important subset of invasive species present and identify other species that may augment a rare species' population stability, such as E. pauciflorum in our study.

Vodcasts and active-learning exercises in a "flipped classroom" model of a renal pharmacotherapy module.

PubMed

Pierce, Richard; Fox, Jeremy

2012-12-12

To implement a "flipped classroom" model for a renal pharmacotherapy topic module and assess the impact on pharmacy students' performance and attitudes. Students viewed vodcasts (video podcasts) of lectures prior to the scheduled class and then discussed interactive cases of patients with end-stage renal disease in class. A process-oriented guided inquiry learning (POGIL) activity was developed and implemented that complemented, summarized, and allowed for application of the material contained in the previously viewed lectures. Students' performance on the final examination significantly improved compared to performance of students the previous year who completed the same module in a traditional classroom setting. Students' opinions of the POGIL activity and the flipped classroom instructional model were mostly positive. Implementing a flipped classroom model to teach a renal pharmacotherapy module resulted in improved student performance and favorable student perceptions about the instructional approach. Some of the factors that may have contributed to students' improved scores included: student mediated contact with the course material prior to classes, benchmark and formative assessments administered during the module, and the interactive class activities.

Integrating the Learning of Mathematics and Science Using Interactive Teaching and Learning Strategies

NASA Astrophysics Data System (ADS)

Holmes, Mark H.

2006-10-01

To help students grasp the intimate connections that exist between mathematics and its applications in other disciplines a library of interactive learning modules was developed. This library covers the mathematical areas normally studied by undergraduate students and is used in science courses at all levels. Moreover, the library is designed not just to provide critical connections across disciplines but to also provide longitudinal subject reinforcement as students progress in their studies. In the process of developing the modules a complete editing and publishing system was constructed that is optimized for automated maintenance and upgradeability of materials. The result is a single integrated production system for web-based educational materials. Included in this is a rigorous assessment program, involving both internal and external evaluations of each module. As will be seen, the formative evaluation obtained during the development of the library resulted in the modules successfully bridging multiple disciplines and breaking down the disciplinary barriers commonly found in their math and non-math courses.

Developing effective web-based regional anesthesia education: a randomized study evaluating case-based versus non-case-based module design.

PubMed

Kopp, Sandra L; Smith, Hugh M

2011-01-01

Little is known about the use of Web-based education in regional anesthesia training. Benefits of Web-based education include the ability to standardize learning material quality and content, build appropriate learning progressions, use interactive multimedia technologies, and individualize delivery of course materials. The goals of this investigation were (1) to determine whether module design influences regional anesthesia knowledge acquisition, (2) to characterize learner preference patterns among anesthesia residents, and (3) to determine whether learner preferences play a role in knowledge acquisition. Direct comparison of knowledge assessments, learning styles, and learner preferences will be made between an interactive case-based and a traditional textbook-style module design. Forty-three Mayo Clinic anesthesiology residents completed 2 online modules, a knowledge pretest, posttest, an Index of Learning Styles assessment, and a participant satisfaction survey. Interscalene and lumbar plexus regional techniques were selected as the learning content for 4 Web modules constructed using the Blackboard Vista coursework application. One traditional textbook-style module and 1 interactive case-based module were designed for each of the interscalene and lumbar plexus techniques. Participants scored higher on the postmodule knowledge assessment for both of the interscalene and lumbar plexus modules. Postmodule knowledge performance scores were independent of both module design (interactive case-based versus traditional textbook style) and learning style preferences. However, nearly all participants reported a preference for Web-based learning and believe that it should be used in anesthesia resident education. Participants did not feel that Web-base learning should replace the current lecture-based curriculum. All residents scored higher on the postmodule knowledge assessment, but this improvement was independent of the module design and individual learning styles. Although residents believe that online learning should be used in anesthesia training, the results of this study do not demonstrate improved learning or justify the time and expense of developing complex case-based training modules. While there may be practical benefits of Web-based education, educators in regional anesthesia should be cautious about developing curricula based on learner preference data.

Modulation in prototropism of the photosensitizer Harmane by host:guest interactions between β-cyclodextrin and surfactants.

PubMed

Paul, Bijan K; Ray, Debarati; Ganguly, Aniruddha; Guchhait, Nikhil

2013-12-01

The present contribution demonstrates the photophysics of a prospective cancer cell photosensitizer Harmane (HM) belonging to the family of β-carboline in mixed microheterogeneous environments of β-cyclodextrin (β-CD) and surfactants having varying surface charges using steady-state and time-resolved fluorescence spectroscopic techniques. The remarkable modulations in prototropic activities of the micelle-bound drug in the presence of β-CD evinces for disruption of the micellar structural integrity by β-CD. The results are meticulously discussed in relevance to the effect of a potential drug delivery vehicle (CD) on the membrane-mimetic micellar system. Further, application of an extrinsic fluorescence probe for monitoring such interactions is fraught by the possibilities of no less than three equilibria that can operate simultaneously viz., (i) surfactant-cyclodextrin, (ii) surfactant-fluorophore and (iii) cyclodextrin-fluorophore. This aspect highlights the enormous importance of the issue of suitability of the fluorescence probe to study such complicated systems and interaction phenomena. Also the varying interaction scenario of β-CD with the nature of the surfactant highlights the importance of precise knowledge of the strength and locus of drug binding in delineating such complex interactions. The results of the present investigation advocate for the potential applicability of the drug (HM) itself as a fluorescence reporter in study of such complex microheterogeneous interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Life sciences on-line: A study in hypermedia application

NASA Technical Reports Server (NTRS)

Christman, Linda A.; Hoang, Nam V.; Proctor, David R.

1990-01-01

The main objective was to determine the feasibility of using a computer-based interactive information recall module for the Life Sciences Project Division (LSPD) at NASA, Johnson Space Center. LSPD personnel prepare payload experiments to test and monitor physiological functions in zero gravity. Training refreshers and other types of online help are needed to support personnel in their tasks during mission testing and in flight. Results of a survey of other hypermedia and multimedia developers and lessons learned by the developer of the LSPD prototype module are presented. Related issues and future applications are also discussed and further hypermedia development within the LSPD is recommended.

Metal-graphene heterojunction modulation via H{sub 2} interaction

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

Cadore, A. R., E-mail: alissoncadore@gmail.com, E-mail: lccampos@fisica.ufmg.br; Mania, E.; Lacerda, R. G.

2016-07-18

Combining experiment and theory, we investigate how a naturally created heterojunction (pn junction) at a graphene and metallic contact interface is modulated via interaction with molecular hydrogen (H{sub 2}). Due to an electrostatic interaction, metallic electrodes induce pn junctions in graphene, leading to an asymmetrical resistance in electronic transport for electrons and holes. We report that the asymmetry in the resistance can be tuned in a reversible manner by exposing graphene devices to H{sub 2}. The interaction between the H{sub 2} and graphene occurs solely at the graphene-contact pn junction and induces a modification on the electrostatic interaction between graphenemore » and metallic contacts. We explain the experimental data with theory providing information concerning the length of the heterojunction and how it changes as a function of H{sub 2} adsorption. Our results are valuable for understanding the nature of the metal-graphene interfaces and have potential application for selective sensors of molecular hydrogen.« less

A reconfigurable multicarrier demodulator architecture

NASA Technical Reports Server (NTRS)

Kwatra, S. C.; Jamali, M. M.

1991-01-01

An architecture based on parallel and pipline design approaches has been developed for the Frequency Division Multiple Access/Time Domain Multiplexed (FDMA/TDM) conversion system. The architecture has two main modules namely the transmultiplexer and the demodulator. The transmultiplexer has two pipelined modules. These are the shared multiplexed polyphase filter and the Fast Fourier Transform (FFT). The demodulator consists of carrier, clock, and data recovery modules which are interactive. Progress on the design of the MultiCarrier Demodulator (MCD) using commercially available chips and Application Specific Integrated Circuits (ASIC) and simulation studies using Viewlogic software will be presented at the conference.

Pediatric trainees' engagement in the online nutrition curriculum: preliminary results.

PubMed

Lewis, Kadriye O; Frank, Graeme R; Nagel, Rollin; Turner, Teri L; Ferrell, Cynthia L; Sangvai, Shilpa G; Donthi, Rajesh; Mahan, John D

2014-09-16

The Pediatric Nutrition Series (PNS) consists of ten online, interactive modules and supplementary educational materials that have utilized web-based multimedia technologies to offer nutrition education for pediatric trainees and practicing physicians. The purpose of the study was to evaluate pediatric trainees' engagement, knowledge acquisition, and satisfaction with nutrition modules delivered online in interactive and non-interactive formats. From December 2010 through August 2011, pediatric trainees from seventy-three (73) different U.S. programs completed online nutrition modules designed to develop residents' knowledge of counseling around and management of nutritional issues in children. Data were analyzed using SPSS version 19. Both descriptive and inferential statistics were used in comparing interactive versus non-interactive modules. Pretest/posttest and module evaluations measured knowledge acquisition and satisfaction. Three hundred and twenty-two (322) pediatric trainees completed one or more of six modules for a total of four hundred and forty-two (442) accessions. All trainees who completed at least one module were included in the study. Two-way analyses of variance (ANOVA) with repeated measures (pre/posttest by interactive/non-interactive format) indicated significant knowledge gains from pretest to posttest (p < 0.002 for all six modules). Comparisons between interactive and non-interactive formats for Module 1 (N = 85 interactive, N = 95 non-interactive) and Module 5 (N = 5 interactive, N = 16 non-interactive) indicated a parallel improvement from the pretest to posttest, with the interactive format significantly higher than the non-interactive modules (p < .05). Both qualitative and quantitative data from module evaluations demonstrated that satisfaction with modules was high. However, there were lower ratings for whether learning objectives were met with Module 6 (p < 0.03) and lecturer rating (p < 0.004) compared to Module 1. Qualitative data also showed that completion of the interactive modules resulted in higher resident satisfaction. This initial assessment of the PNS modules shows that technology-mediated delivery of a nutrition curriculum in residency programs has great potential for providing rich learning environments for trainees while maintaining a high level of participant satisfaction.

Quantitative force measurements using frequency modulation atomic force microscopy—theoretical foundations

NASA Astrophysics Data System (ADS)

Sader, John E.; Uchihashi, Takayuki; Higgins, Michael J.; Farrell, Alan; Nakayama, Yoshikazu; Jarvis, Suzanne P.

2005-03-01

Use of the atomic force microscope (AFM) in quantitative force measurements inherently requires a theoretical framework enabling conversion of the observed deflection properties of the cantilever to an interaction force. In this paper, the theoretical foundations of using frequency modulation atomic force microscopy (FM-AFM) in quantitative force measurements are examined and rigorously elucidated, with consideration being given to both 'conservative' and 'dissipative' interactions. This includes a detailed discussion of the underlying assumptions involved in such quantitative force measurements, the presentation of globally valid explicit formulae for evaluation of so-called 'conservative' and 'dissipative' forces, discussion of the origin of these forces, and analysis of the applicability of FM-AFM to quantitative force measurements in liquid.

Engineering Breast Cancer Microenvironments and 3D Bioprinting

PubMed Central

Belgodere, Jorge A.; King, Connor T.; Bursavich, Jacob B.; Burow, Matthew E.; Martin, Elizabeth C.; Jung, Jangwook P.

2018-01-01

The extracellular matrix (ECM) is a critical cue to direct tumorigenesis and metastasis. Although two-dimensional (2D) culture models have been widely employed to understand breast cancer microenvironments over the past several decades, the 2D models still exhibit limited success. Overwhelming evidence supports that three dimensional (3D), physiologically relevant culture models are required to better understand cancer progression and develop more effective treatment. Such platforms should include cancer-specific architectures, relevant physicochemical signals, stromal–cancer cell interactions, immune components, vascular components, and cell-ECM interactions found in patient tumors. This review briefly summarizes how cancer microenvironments (stromal component, cell-ECM interactions, and molecular modulators) are defined and what emerging technologies (perfusable scaffold, tumor stiffness, supporting cells within tumors and complex patterning) can be utilized to better mimic native-like breast cancer microenvironments. Furthermore, this review emphasizes biophysical properties that differ between primary tumor ECM and tissue sites of metastatic lesions with a focus on matrix modulation of cancer stem cells, providing a rationale for investigation of underexplored ECM proteins that could alter patient prognosis. To engineer breast cancer microenvironments, we categorized technologies into two groups: (1) biochemical factors modulating breast cancer cell-ECM interactions and (2) 3D bioprinting methods and its applications to model breast cancer microenvironments. Biochemical factors include matrix-associated proteins, soluble factors, ECMs, and synthetic biomaterials. For the application of 3D bioprinting, we discuss the transition of 2D patterning to 3D scaffolding with various bioprinting technologies to implement biophysical cues to model breast cancer microenvironments. PMID:29881724

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. Copyright © 2017 Elsevier B.V. All rights reserved.

Coupled incompressible Smoothed Particle Hydrodynamics model for continuum-based modelling sediment transport

NASA Astrophysics Data System (ADS)

Pahar, Gourabananda; Dhar, Anirban

2017-04-01

A coupled solenoidal Incompressible Smoothed Particle Hydrodynamics (ISPH) model is presented for simulation of sediment displacement in erodible bed. The coupled framework consists of two separate incompressible modules: (a) granular module, (b) fluid module. The granular module considers a friction based rheology model to calculate deviatoric stress components from pressure. The module is validated for Bagnold flow profile and two standardized test cases of sediment avalanching. The fluid module resolves fluid flow inside and outside porous domain. An interaction force pair containing fluid pressure, viscous term and drag force acts as a bridge between two different flow modules. The coupled model is validated against three dambreak flow cases with different initial conditions of movable bed. The simulated results are in good agreement with experimental data. A demonstrative case considering effect of granular column failure under full/partial submergence highlights the capability of the coupled model for application in generalized scenario.

Design of Instrument Control Software for Solar Vector Magnetograph at Udaipur Solar Observatory

NASA Astrophysics Data System (ADS)

Gosain, Sanjay; Venkatakrishnan, P.; Venugopalan, K.

2004-04-01

A magnetograph is an instrument which makes measurement of solar magnetic field by measuring Zeeman induced polarization in solar spectral lines. In a typical filter based magnetograph there are three main modules namely, polarimeter, narrow-band spectrometer (filter), and imager(CCD camera). For a successful operation of magnetograph it is essential that these modules work in synchronization with each other. Here, we describe the design of instrument control system implemented for the Solar Vector Magnetograph under development at Udaipur Solar Observatory. The control software is written in Visual Basic and exploits the Component Object Model (COM) components for a fast and flexible application development. The user can interact with the instrument modules through a Graphical User Interface (GUI) and can program the sequence of magnetograph operations. The integration of Interactive Data Language (IDL) ActiveX components in the interface provides a powerful tool for online visualization, analysis and processing of images.

Millivolt Modulation of Plasmonic Metasurface Optical Response via Ionic Conductance.

PubMed

Thyagarajan, Krishnan; Sokhoyan, Ruzan; Zornberg, Leonardo; Atwater, Harry A

2017-08-01

A plasmonic metasurface with an electrically tunable optical response that operates at strikingly low modulation voltages is experimentally demonstrated. The fabricated metasurface shows up to 30% relative change in reflectance in the visible spectral range upon application of 5 mV and 78% absolute change in reflectance upon application of 100 mV of bias. The designed metasurface consists of nanostructured silver and indium tin oxide (ITO) electrodes which are separated by 5 nm thick alumina. The millivolt-scale optical modulation is attributed to a new modulation mechanism, in which transport of silver ions through alumina dielectric leads to bias-induced nucleation and growth of silver nanoparticles in the ITO counter-electrode, altering the optical extinction response. This transport mechanism, which occurs at applied electric fields of 1 mV nm -1 , provides a new approach to use of ionic transport for electrical control over light-matter interactions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generic Module for Collecting Data in Smart Cities

NASA Astrophysics Data System (ADS)

Martinez, A.; Ramirez, F.; Estrada, H.; Torres, L. A.

2017-09-01

The Future Internet brings new technologies to the common life of people, such as Internet of Things, Cloud Computing or Big Data. All this technologies have change the way people communicate and also the way the devices interact with the context, giving rise to new paradigms, as the case of smart cities. Currently, the mobile devices represent one of main sources of information for new applications that take into account the user context, such as apps for mobility, health, of security. Several platforms have been proposed that consider the development of Future Internet applications, however, no generic modules can be found that implement the collection of context data from smartphones. In this research work we present a generic module to collect data from different sensors of the mobile devices and also to send, in a standard manner, this data to the Open FIWARE Cloud to be stored or analyzed by software tools. The proposed module enables the human-as-a-sensor approach for FIWARE Platform.

Effect of curcumin analogs onα-synuclein aggregation and cytotoxicity

PubMed Central

Jha, Narendra Nath; Ghosh, Dhiman; Das, Subhadeep; Anoop, Arunagiri; Jacob, Reeba S.; Singh, Pradeep K.; Ayyagari, Narasimham; Namboothiri, Irishi N. N.; Maji, Samir K.

2016-01-01

Alpha-synuclein (α-Syn) aggregation into oligomers and fibrils is associated with dopaminergic neuron loss occurring in Parkinson’s disease (PD) pathogenesis. Compounds that modulate α-Syn aggregation and interact with preformed fibrils/oligomers and convert them to less toxic species could have promising applications in the drug development efforts against PD. Curcumin is one of the Asian food ingredient which showed promising role as therapeutic agent against many neurological disorders including PD. However, the instability and low solubility makes it less attractive for the drug development. In this work, we selected various curcumin analogs and studied their toxicity, stability and efficacy to interact with different α-Syn species and modulation of their toxicity. We found a subset of curcumin analogs with higher stability and showed that curcumin and its various analogs interact with preformed fibrils and oligomers and accelerate α-Syn aggregation to produce morphologically different amyloid fibrils in vitro. Furthermore, these curcumin analogs showed differential binding with the preformed α-Syn aggregates. The present data suggest the potential role of curcumin analogs in modulating α-Syn aggregation. PMID:27338805

Band structure of graphene modulated by Ti or N dopants and applications in gas sensoring.

PubMed

Zhang, Hong-Ping; Luo, Xue-Gang; Lin, Xiao-Yan; Zhang, Ya-Ping; Tang, Ping-Ping; Lu, Xiong; Tang, Youhong

2015-09-01

The exploration of novel sensors for NO2 detection is particularly important in material and environmental sciences. In this work, the HOMO-LUMO gap of graphene, Ti- or N-doped graphene is investigated by DFT methods. The adsorption of NO2, NO, and O2 on Ti- or N-doped graphene of different sizes is also explored. Results reveal that the interactions between gases (NO2, NO, and O2) and Ti- or N-doped graphenes is not affected by the size of graphene. The doped Ti greatly improves the interactions between gases and graphene whereas the doped N has no effect on those interactions. The HOMO- LUMO gap of Ti-doped graphene can be modulated by adsorption of the gases. The cross effect of the NO and O2 is also investigated, and it is demonstrated that Ti-doped graphene has specific interactions with NO2. Thus, Ti-doped graphene can be a candidate for NO2 sensor materials. Furthermore, doping the graphene with Ti or N improves the sensitivity of the sheets toward NO2, which can be trapped and detected by the intrinsic graphene. Efficient sensors are rationally designed to diversify their applications in environmental science and engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Mycoplasma fermentans and TNF-β interact to amplify immune-modulating cytokines in human lung fibroblasts

PubMed Central

Fabisiak, James P.; Gao, Fei; Thomson, Robyn G.; Strieter, Robert M.; Watkins, Simon C.; Dauber, James H.

2010-01-01

Mycoplasma can establish latent infections and are associated with arthritis, leukemia, and chronic lung disease. We developed an experimental model in which lung cells are deliberately infected with Mycoplasma fermentans. Human lung fibroblasts (HLF) were exposed to live M. fermentans and immune-modulating cytokine release was assessed with and without known inducers of cytokine production. M. fermentans increased IL-6, IL-8/CXCL8, MCP-1/CCL2, and Gro-α/CXCL1 production. M. fermentans interacted with TNF-β to release more IL-6, CXCL8, and CXCL1 than predicted by the responses to either stimulus alone. The effects of live infection were recapitulated by exposure to M. fermentans-derived macrophage-activating lipopeptide-2 (MALP-2), a Toll-like receptor-2- and receptor-6-specific ligand. The synergistic effect of combined stimuli was more pronounced with prolonged incubations. Preexposure to TNF-β sensitized the cells to subsequent MALP-2 challenge, but preexposure to MALP-2 did not alter the IL-6 response to TNF-β. Exposure to M. fermentans or MALP-2 did not enhance nuclear localization, DNA binding, or transcriptional activity of NF-κB and did not modulate early NF-κB activation in response to TNF-β. Application of specific inhibitors of various MAPKs suggested that p38 and JNK/stress-activated protein kinase were involved in early IL-6 release after exposure to TNF-β and M. fermentans, respectively. The combined response to M. fermentans and TNF-β, however, was uniquely sensitive to delayed application of SP-600125, suggesting that JNK/stress-activated protein kinase contributes to the amplification of IL-6 release. Thus M. fermentans interacts with stimuli such as TNF-β to amplify lung cell production of immune-modulating cytokines. The mechanisms accounting for this interaction can now be dissected with the use of this in vitro model. PMID:16751226

Controllable optical modulation of blue/green up-conversion fluorescence from Tm3+ (Er3+) single-doped glass ceramics upon two-step excitation of two-wavelengths

PubMed Central

Chen, Zhi; Kang, Shiliang; Zhang, Hang; Wang, Ting; Lv, Shichao; Chen, Qiuqun; Dong, Guoping; Qiu, Jianrong

2017-01-01

Optical modulation is a crucial operation in photonics for network data processing with the aim to overcome information bottleneck in terms of speed, energy consumption, dispersion and cross-talking from conventional electronic interconnection approach. However, due to the weak interactions between photons, a facile physical approach is required to efficiently manipulate photon-photon interactions. Herein, we demonstrate that transparent glass ceramics containing LaF3: Tm3+ (Er3+) nanocrystals can enable fast-slow optical modulation of blue/green up-conversion fluorescence upon two-step excitation of two-wavelengths at telecom windows (0.8–1.8 μm). We show an optical modulation of more than 1500% (800%) of the green (blue) up-conversion fluorescence intensity, and fast response of 280 μs (367 μs) as well as slow response of 5.82 ms (618 μs) in the green (blue) up-conversion fluorescence signal, respectively. The success of manipulating laser at telecom windows for fast-slow optical modulation from rear-earth single-doped glass ceramics may find application in all-optical fiber telecommunication areas. PMID:28368041

Implementation of a Parameterized Interacting Multiple Model Filter on an FPGA for Satellite Communications

NASA Technical Reports Server (NTRS)

Hackett, Timothy M.; Bilen, Sven G.; Ferreira, Paulo Victor R.; Wyglinski, Alexander M.; Reinhart, Richard C.

2016-01-01

In a communications channel, the space environment between a spacecraft and an Earth ground station can potentially cause the loss of a data link or at least degrade its performance due to atmospheric effects, shadowing, multipath, or other impairments. In adaptive and coded modulation, the signal power level at the receiver can be used in order to choose a modulation-coding technique that maximizes throughput while meeting bit error rate (BER) and other performance requirements. It is the goal of this research to implement a generalized interacting multiple model (IMM) filter based on Kalman filters for improved received power estimation on software-dened radio (SDR) technology for satellite communications applications. The IMM filter has been implemented in Verilog consisting of a customizable bank of Kalman filters for choosing between performance and resource utilization. Each Kalman filter can be implemented using either solely a Schur complement module (for high area efficiency) or with Schur complement, matrix multiplication, and matrix addition modules (for high performance). These modules were simulated and synthesized for the Virtex II platform on the JPL Radio Experimenter Development System (EDS) at NASA Glenn Research Center. The results for simulation, synthesis, and hardware testing are presented.

Vodcasts and Active-Learning Exercises in a “Flipped Classroom” Model of a Renal Pharmacotherapy Module

PubMed Central

Fox, Jeremy

2012-01-01

Objective. To implement a “flipped classroom” model for a renal pharmacotherapy topic module and assess the impact on pharmacy students’ performance and attitudes. Design. Students viewed vodcasts (video podcasts) of lectures prior to the scheduled class and then discussed interactive cases of patients with end-stage renal disease in class. A process-oriented guided inquiry learning (POGIL) activity was developed and implemented that complemented, summarized, and allowed for application of the material contained in the previously viewed lectures. Assessment. Students’ performance on the final examination significantly improved compared to performance of students the previous year who completed the same module in a traditional classroom setting. Students’ opinions of the POGIL activity and the flipped classroom instructional model were mostly positive. Conclusion. Implementing a flipped classroom model to teach a renal pharmacotherapy module resulted in improved student performance and favorable student perceptions about the instructional approach. Some of the factors that may have contributed to students’ improved scores included: student mediated contact with the course material prior to classes, benchmark and formative assessments administered during the module, and the interactive class activities. PMID:23275661

Three axis vector atomic magnetometer utilizing polarimetric technique

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

Pradhan, Swarupananda, E-mail: spradhan@barc.gov.in, E-mail: pradhans75@gmail.com

2016-09-15

The three axis vector magnetic field measurement based on the interaction of a single elliptically polarized light beam with an atomic system is described. The magnetic field direction dependent atomic responses are extracted by the polarimetric detection in combination with laser frequency modulation and magnetic field modulation techniques. The magnetometer geometry offers additional critical requirements like compact size and large dynamic range for space application. Further, the three axis magnetic field is measured using only the reflected signal (one polarization component) from the polarimeter and thus can be easily expanded to make spatial array of detectors and/or high sensitivity fieldmore » gradient measurement as required for biomedical application.« less

40 CFR 1042.205 - Application requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

...'s specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel fuel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1042.205 - Application requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

...'s specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel fuel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1042.205 - Application requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

...'s specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel fuel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1042.205 - Application requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

...'s specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel fuel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1042.205 - Application requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

...'s specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel fuel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

Program Helps Decompose Complex Design Systems

NASA Technical Reports Server (NTRS)

Rogers, James L., Jr.; Hall, Laura E.

1995-01-01

DeMAID (Design Manager's Aid for Intelligent Decomposition) computer program is knowledge-based software system for ordering sequence of modules and identifying possible multilevel structure for design problems such as large platforms in outer space. Groups modular subsystems on basis of interactions among them. Saves considerable amount of money and time in total design process, particularly in new design problem in which order of modules has not been defined. Originally written for design problems, also applicable to problems containing modules (processes) that take inputs and generate outputs. Available in three machine versions: Macintosh written in Symantec's Think C 3.01, Sun, and SGI IRIS in C language.

The molecular mechanism of flop-selectivity and subsite recognition for an AMPA receptor allosteric modulator: Structures of GluA2 and GluA3 complexed with PEPA

PubMed Central

Ahmed, Ahmed H.; Ptak, Christopher P.; Oswald, Robert E.

2011-01-01

Glutamate receptors are important potential drug targets for cognitive enhancement and the treatment of schizophrenia in part because they are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system. One approach to the application of therapeutic agents to the AMPA subtype of glutamate receptors is the use of allosteric modulators, which promote dimerization by binding to a dimer interface thereby reducing desensitization and deactivation. AMPA receptors exist in two alternatively spliced variants (flip and flop) that differ in desensitization and receptor activation profiles. Most of the structural information on modulators of the AMPA receptor target the flip subtype. We report here the crystal structure of the flop-selective allosteric modulator, PEPA, bound to the binding domains of the GluA2 and GluA3 flop isoforms of AMPA receptors. Specific hydrogen bonding patterns can explain the preference for the flop isoform. This includes a bidentate hydrogen bonding pattern between PEPA and N754 of the flop isoforms of GluA2 and GluA3 (the corresponding position in the flip isoform is S754). Comparison with other allosteric modulators provides a framework for the development of new allosteric modulators with preferences for either the flip or flop isoforms. In addition to interactions with N/S754, specific interactions of the sulfonamide with conserved residues in the binding site are characteristics of a number of allosteric modulators. These, in combination, with variable interactions with five subsites on the binding surface lead to different stoichiometries, orientations within the binding pockets, and functional outcomes. PMID:20199107

Solar dynamic power for the Space Station

NASA Technical Reports Server (NTRS)

Archer, J. S.; Diamant, E. S.

1986-01-01

This paper describes a computer code which provides a significant advance in the systems analysis capabilities of solar dynamic power modules. While the code can be used to advantage in the preliminary analysis of terrestrial solar dynamic modules its real value lies in the adaptions which make it particularly useful for the conceptualization of optimized power modules for space applications. In particular, as illustrated in the paper, the code can be used to establish optimum values of concentrator diameter, concentrator surface roughness, concentrator rim angle and receiver aperture corresponding to the main heat cycle options - Organic Rankine and Brayton - and for certain receiver design options. The code can also be used to establish system sizing margins to account for the loss of reflectivity in orbit or the seasonal variation of insolation. By the simulation of the interactions among the major components of a solar dynamic module and through simplified formulations of the major thermal-optic-thermodynamic interactions the code adds a powerful, efficient and economic analytical tool to the repertory of techniques available for the design of advanced space power systems.

Interactive Online Modules and Videos for Learning Geological Concepts at the University of Toronto Department of Earth Sciences

NASA Astrophysics Data System (ADS)

Veglio, E.; Graves, L. W.; Bank, C. G.

2014-12-01

We designed various computer-based applications and videos as educational resources for undergraduate courses at the University of Toronto in the Earth Science Department. These resources were developed in effort to enhance students' self-learning of key concepts as identified by educators at the department. The interactive learning modules and videos were created using the programs MATLAB and Adobe Creative Suite 5 (Photoshop and Premiere) and range from optical mineralogy (extinction and Becke line), petrology (equilibrium melting in 2-phase systems), crystallography (crystal systems), geophysics (gravity anomaly), and geologic history (evolution of Canada). These resources will be made available for students on internal course websites as well as through the University of Toronto Earth Science's website (www.es.utoronto.ca) where appropriate; the video platform YouTube.com may be used to reach a wide audience and promote the material. Usage of the material will be monitored and feedback will be collected over the next academic year in order to gage the use of these interactive learning tools and to assess if these computer-based applications and videos foster student engagement and active learning, and thus offer an enriched learning experience.

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells.

PubMed

Tan, Chris Soon Heng; Go, Ka Diam; Bisteau, Xavier; Dai, Lingyun; Yong, Chern Han; Prabhu, Nayana; Ozturk, Mert Burak; Lim, Yan Ting; Sreekumar, Lekshmy; Lengqvist, Johan; Tergaonkar, Vinay; Kaldis, Philipp; Sobota, Radoslaw M; Nordlund, Pär

2018-03-09

Proteins differentially interact with each other across cellular states and conditions, but an efficient proteome-wide strategy to monitor them is lacking. We report the application of thermal proximity coaggregation (TPCA) for high-throughput intracellular monitoring of protein complex dynamics. Significant TPCA signatures observed among well-validated protein-protein interactions correlate positively with interaction stoichiometry and are statistically observable in more than 350 annotated human protein complexes. Using TPCA, we identified many complexes without detectable differential protein expression, including chromatin-associated complexes, modulated in S phase of the cell cycle. Comparison of six cell lines by TPCA revealed cell-specific interactions even in fundamental cellular processes. TPCA constitutes an approach for system-wide studies of protein complexes in nonengineered cells and tissues and might be used to identify protein complexes that are modulated in diseases. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Frequency modulation atomic force microscopy: a dynamic measurement technique for biological systems

NASA Astrophysics Data System (ADS)

Higgins, Michael J.; Riener, Christian K.; Uchihashi, Takayuki; Sader, John E.; McKendry, Rachel; Jarvis, Suzanne P.

2005-03-01

Frequency modulation atomic force microscopy (FM-AFM) has been modified to operate in a liquid environment within an atomic force microscope specifically designed for investigating biological samples. We demonstrate the applicability of FM-AFM to biological samples using the spectroscopy mode to measure the unbinding forces of a single receptor-ligand (biotin-avidin) interaction. We show that quantitative adhesion force measurements can only be obtained provided certain modifications are made to the existing theory, which is used to convert the detected frequency shifts to an interaction force. Quantitative force measurements revealed that the unbinding forces for the biotin-avidin interaction were greater than those reported in previous studies. This finding was due to the use of high average tip velocities, which were calculated to be two orders of magnitude greater than those typically used in unbinding receptor-ligand experiments. This study therefore highlights the potential use of FM-AFM to study a range of biological systems, including living cells and/or single biomolecule interactions.

CyberMedVPS: visual programming for development of simulators.

PubMed

Morais, Aline M; Machado, Liliane S

2011-01-01

Computer applications based on Virtual Reality (VR) has been outstanding in training and teaching in the medical filed due to their ability to simulate realistic in which users can practice skills and decision making in different situations. But was realized in these frameworks a hard interaction of non-programmers users. Based on this problematic will be shown the CyberMedVPS, a graphical module which implement Visual Programming concepts to solve an interaction trouble. Frameworks to develop such simulators are available but their use demands knowledge of programming. Based on this problematic will be shown the CyberMedVPS, a graphical module for the CyberMed framework, which implements Visual Programming concepts to allow the development of simulators by non-programmers professionals of the medical field.

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

DOEpatents

Xavier, Patrick G [Albuquerque, NM; Gottlieb, Eric J [Corrales, NM; McDonald, Michael J [Albuquerque, NM; 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.

Self-propulsion and interactions of catalytic particles in a chemically active medium.

PubMed

Banigan, Edward J; Marko, John F

2016-01-01

Enzymatic "machines," such as catalytic rods or colloids, can self-propel and interact by generating gradients of their substrates. We theoretically investigate the behaviors of such machines in a chemically active environment where their catalytic substrates are continuously synthesized and destroyed, as occurs in living cells. We show how the kinetic properties of the medium modulate self-propulsion and pairwise interactions between machines, with the latter controlled by a tunable characteristic interaction range analogous to the Debye screening length in an electrolytic solution. Finally, we discuss the effective force arising between interacting machines and possible biological applications, such as partitioning of bacterial plasmids.

Partial Shade Stress Test for Thin-Film Photovoltaic Modules: Preprint

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

Silverman, Timothy J.; Deceglie, Michael G.; Deline, Chris

2015-09-02

Partial shade of monolithic thin-film PV modules can cause reverse-bias conditions leading to permanent damage. In this work, we propose a partial shade stress test for thin-film PV modules that quantifies permanent performance loss. We designed the test with the aid of a computer model that predicts the local voltage, current and temperature stress that result from partial shade. The model predicts the module-scale interactions among the illumination pattern, the electrical properties of the photovoltaic material and the thermal properties of the module package. The test reproduces shading and loading conditions that may occur in the field. It accounts formore » reversible light-induced performance changes and for additional stress that may be introduced by light-enhanced reverse breakdown. We present simulated and experimental results from the application of the proposed test.« less

Applications of GIFTS III to Structural Engineering Problems.

DTIC Science & Technology

The paper describes the latest version of the GIFTS SYSTEM (Graphics Oriented Interactive Finite Element Package for Time-Sharing), due for release...at the end of March 1976. The paper gives a description of the program modules available in the GIFTS library and the options available within its...framework. Examples are given to demonstrate the use of GIFTS in design-oriented applications. Some performance measurements are included. Amongst the

Application of spatial pedotransfer functions to understand soil modulation of vegetation response to climate

USDA-ARS?s Scientific Manuscript database

A fundamental knowledge gap in understanding land-atmosphere interactions is accurate, high resolution spatial representation of soil physical and hydraulic properties. We present a novel approach to predict hydraulic soil parameters by combining digital soil mapping techniques with pedotransfer fun...

Effect of counter ions of arginine as an additive for the solubilization of protein and aromatic compounds.

PubMed

Yoshizawa, Shunsuke; Arakawa, Tsutomu; Shiraki, Kentaro

2016-10-01

Arginine is widely used in biotechnological application, but mostly with chloride counter ion. Here, we examined the effects of various anions on solubilization of aromatic compounds and reduced lysozyme and on refolding of the lysozyme. All arginine salts tested increased the solubility of propyl gallate with acetate much more effectively than chloride. The effects of arginine salts were compared with those of sodium or guanidine salts, indicating that the ability of anions to modulate the propyl gallate solubility is independent of the cation. Comparison of transfer free energy of propyl gallate between sodium and arginine salts indicates that the interaction of propyl gallate is more favorable with arginine than sodium. On the contrary, the solubility of aromatic amino acids is only slightly modulated by anions, implying that there is specific interaction between acetic acid and propyl gallate. Unlike their effects on the solubility of small aromatic compounds, the solubility of reduced lysozyme was much higher in arginine chloride than in arginine acetate or sulfate. Consistent with high solubility, refolding of reduced lysozyme was most effective in arginine chloride. These results suggest potential broader applications of arginine modulated by different anions. Copyright © 2016 Elsevier B.V. All rights reserved.

A universal TagModule collection for parallel genetic analysis of microorganisms

PubMed Central

Oh, Julia; Fung, Eula; Price, Morgan N.; Dehal, Paramvir S.; Davis, Ronald W.; Giaever, Guri; Nislow, Corey; Arkin, Adam P.; Deutschbauer, Adam

2010-01-01

Systems-level analyses of non-model microorganisms are limited by the existence of numerous uncharacterized genes and a corresponding over-reliance on automated computational annotations. One solution to this challenge is to disrupt gene function using DNA tag technology, which has been highly successful in parallelizing reverse genetics in Saccharomyces cerevisiae and has led to discoveries in gene function, genetic interactions and drug mechanism of action. To extend the yeast DNA tag methodology to a wide variety of microorganisms and applications, we have created a universal, sequence-verified TagModule collection. A hallmark of the 4280 TagModules is that they are cloned into a Gateway entry vector, thus facilitating rapid transfer to any compatible genetic system. Here, we describe the application of the TagModules to rapidly generate tagged mutants by transposon mutagenesis in the metal-reducing bacterium Shewanella oneidensis MR-1 and the pathogenic yeast Candida albicans. Our results demonstrate the optimal hybridization properties of the TagModule collection, the flexibility in applying the strategy to diverse microorganisms and the biological insights that can be gained from fitness profiling tagged mutant collections. The publicly available TagModule collection is a platform-independent resource for the functional genomics of a wide range of microbial systems in the post-genome era. PMID:20494978

40 CFR 1039.205 - What must I include in my application?

Code of Federal Regulations, 2014 CFR

2014-07-01

... engine family's specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1039.205 - What must I include in my application?

Code of Federal Regulations, 2010 CFR

2010-07-01

... engine family's specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1039.205 - What must I include in my application?

Code of Federal Regulations, 2013 CFR

2013-07-01

... engine family's specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1039.205 - What must I include in my application?

Code of Federal Regulations, 2012 CFR

2012-07-01

... engine family's specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

40 CFR 1039.205 - What must I include in my application?

Code of Federal Regulations, 2011 CFR

2011-07-01

... engine family's specifications and other basic parameters of the engine's design and emission controls. List the fuel type on which your engines are designed to operate (for example, ultra low-sulfur diesel... or modulate the same parameter. Describe whether the strategies interact in a comparative or additive...

Meteorological Instrumentation and Measurements Open Resource Training Modules for Undergraduate and Graduate Education

NASA Astrophysics Data System (ADS)

Rockwell, A.; Clark, R. D.; Stevermer, A.

2017-12-01

The National Center for Atmospheric Research Earth Observing Laboratory, Millersville University and The COMET Program are collaborating to produce a series of nine online modules on the the topic of meteorological instrumentation and measurements. These interactive, multimedia educational modules can be integrated into undergraduate and graduate meteorology courses on instrumentation, measurement science, and observing systems to supplement traditional pedagogies and enhance blended instruction. These freely available and open-source training tools are designed to supplement traditional pedagogies and enhance blended instruction. Three of the modules are now available and address the theory and application of Instrument Performance Characteristics, Meteorological Temperature Instrumentation and Measurements, and Meteorological Pressure Instrumentation and Measurements. The content of these modules is of the highest caliber as it has been developed by scientists and engineers who are at the forefront of the field of observational science. Communicating the availability of these unique and influential educational resources with the community is of high priority. These modules will have a profound effect on the atmospheric observational sciences community by fulfilling a need for contemporary, interactive, multimedia guided education and training modules integrating the latest instructional design and assessment tools in observational science. Thousands of undergraduate and graduate students will benefit, while course instructors will value a set of high quality modules to use as supplements to their courses. The modules can serve as an alternative to observational research training and fill the void between field projects or assist those schools that lack the resources to stage a field- or laboratory-based instrumentation experience.

Reliability and engineering sciences area. Materials research: Single junction thin film

NASA Technical Reports Server (NTRS)

1986-01-01

A test bench was designed and fabricated for the purpose of improving control of hot-spot test accuracy. Electrochemical corrosion research focused on corrosion mechanisms to which both crystalline and a-Si modules may be subjected in central station applications. A variety of cells and several designs were subjected to accelerated stress tests. Humiditiy degradation rates were determined and key electrochemical failure mechanisms were identified. Software was developed for the prediction of power loss resulting from open circuits in an array field of a-Si modules. Failure analysis was continued on the four ARCO Solar Genesis modules. The interactions of water on the silicon module was examined. An autocatalytic photooxidation model was proposed. The reliability and durability of bonding materials and electrical insulation were also studied.

Programming Nanoparticles in Multiscale: Optically Modulated Assembly and Phase Switching of Silicon Nanoparticle Array.

PubMed

Wang, Letian; Rho, Yoonsoo; Shou, Wan; Hong, Sukjoon; Kato, Kimihiko; Eliceiri, Matthew; Shi, Meng; Grigoropoulos, Costas P; Pan, Heng; Carraro, Carlo; Qi, Dongfeng

2018-03-27

Manipulating and tuning nanoparticles by means of optical field interactions is of key interest for nanoscience and applications in electronics and photonics. We report scalable, direct, and optically modulated writing of nanoparticle patterns (size, number, and location) of high precision using a pulsed nanosecond laser. The complex nanoparticle arrangement is modulated by the laser pulse energy and polarization with the particle size ranging from 60 to 330 nm. Furthermore, we report fast cooling-rate induced phase switching of crystalline Si nanoparticles to the amorphous state. Such phase switching has usually been observed in compound phase change materials like GeSbTe. The ensuing modification of atomic structure leads to dielectric constant switching. Based on these effects, a multiscale laser-assisted method of fabricating Mie resonator arrays is proposed. The number of Mie resonators, as well as the resonance peaks and dielectric constants of selected resonators, can be programmed. The programmable light-matter interaction serves as a mechanism to fabricate optical metasurfaces, structural color, and multidimensional optical storage devices.

Temperature-responsive chromatography for the separation of biomolecules.

PubMed

Kanazawa, Hideko; Okano, Teruo

2011-12-09

Temperature-responsive chromatography for the separation of biomolecules utilizing poly(N-isopropylacrylamide) (PNIPAAm) and its copolymer-modified stationary phase is performed with an aqueous mobile phase without using organic solvent. The surface properties and function of the stationary phase are controlled by external temperature changes without changing the mobile-phase composition. This analytical system is based on nonspecific adsorption by the reversible transition of a hydrophilic-hydrophobic PNIPAAm-grafted surface. The driving force for retention is hydrophobic interaction between the solute molecules and the hydrophobized polymer chains on the stationary phase surface. The separation of the biomolecules, such as nucleotides and proteins was achieved by a dual temperature- and pH-responsive chromatography system. The electrostatic and hydrophobic interactions could be modulated simultaneously with the temperature in an aqueous mobile phase, thus the separation system would have potential applications in the separation of biomolecules. Additionally, chromatographic matrices prepared by a surface-initiated atom transfer radical polymerization (ATRP) exhibit a strong interaction with analytes, because the polymerization procedure forms a densely packed polymer, called a polymer brush, on the surfaces. The copolymer brush grafted surfaces prepared by ATRP was an effective tool for separating basic biomolecules by modulating the electrostatic and hydrophobic interactions. Applications of thermally responsive columns for the separations of biomolecules are reviewed here. Copyright © 2011 Elsevier B.V. All rights reserved.

PEG-coumarin based biocompatible self-assembled fluorescent nanoaggregates synthesized via click reactions and studies of aggregation behavior.

PubMed

Behl, Gautam; Sikka, Manisha; Chhikara, Aruna; Chopra, Madhu

2014-02-15

Click chemistry has found wide application in drug discovery, bioconjugation reactions, polymer chemistry and synthesis of amphiphilic materials with pharmaceutical and biomedical applications. Triazole substitution via a click reaction alters photophysical properties of coumarin. Both coumarin and triazole moieties participate in π-π stacking interactions. Hence it should be possible to prepare fluorescent self-assembly systems by conjugation of coumarin to poly (ethylene glycol) (PEG) via click reactions exhibiting hydrophilic, hydrophobic and π-π stacking interactions. Moreover, the materials can be suitable platforms to assess fluorescence modulation effect of triazole substitution on coumarins. PEG supported coumarin conjugates were synthesized and the fluorescence modulation effect of the formation of triazole on coumarin was assessed. Their aggregation properties were studied by surface tension measurements, dynamic light scattering (DLS), transmission electron microscopy (TEM), fluorescence and (1)H NMR spectroscopy. The conjugates were found to form nanoaggregates in the size range of 100-120 nm with a negative free energy of micellization (~-27 kJ mol(-1)) confirming aggregation and self-assembly. The Quantum yield of 4-methyl-7-propargylcoumarin (7P4MC) was enhanced after triazole formation with azide functionalized PEG (methoxy-PEG350 azide). The conjugates were found to exhibit π-π stacking interactions in addition to hydrophilic and hydrophobic interactions. They were found to be biocompatible with human pancreatic cancer cells. Copyright © 2013 Elsevier Inc. All rights reserved.

N-SCAN: new vibromodulation system for detection and monitoring of cracks and other contact-type defects

NASA Astrophysics Data System (ADS)

Donskoy, Dmitri; Ekimov, Alexander; Luzzato, Emile; Lottiaux, Jean-Louis; Stoupin, Stanislav; Zagrai, Andrei

2003-08-01

In recent years, innovative vibro-modulation technique has been introduced for detection of contact-type interfaces such as cracks, debondings, and delaminations. The technique utilizes the effect of nonlinear interaction of ultrasound and vibrations at the interface of the defect. Vibration varies on the contact area of the interface modulating passing through ultrasonic wave. The modulation manifests itself as additional side-band spectral components with the combination frequencies in the spectrum of the received signal. The presence of these components allows for detection and differentiation of the contact-type defects from other structural and material inhomogeneities. Vibro-modulation technique has been implemented in N-SCAN damage detection system. The system consists of a digital synthesizer, high and low frequency amplifiers, a magnetostrictive shaker, ultrasonic transducers and a PC-based data acquisition/processing station with N-SCAN software. The ability of the system to detect contact-type defects was experimentally verified using specimens of simple and complex geometries made of steel, aluminum, composites and other structural materials. N-SCAN proved to be very effective for nondestructive testing of full-scale structures ranging from 24 foot-long gun barrels to stainless steel pipes used in nuclear power plants. Among advantages of the system are applicability for the wide range of structural materials and for structures with complex geometries, real time data processing, convenient interface for system operation, simplicity of interpretation of results, no need for sensor scanning along structure, onsite inspection of large structures at a fraction of time as compared with conventional techniques. This paper describes the basic principles of nonlinear vibro-modulation NDE technique, some theoretical background for nonlinear interaction and justification of signal processing algorithm. It is also presents examples of practical implementation and application of the technique.

Innate immune humoral factors, C1q and factor H, with differential pattern recognition properties, alter macrophage response to carbon nanotubes.

PubMed

Pondman, Kirsten M; Pednekar, Lina; Paudyal, Basudev; Tsolaki, Anthony G; Kouser, Lubna; Khan, Haseeb A; Shamji, Mohamed H; Ten Haken, Bennie; Stenbeck, Gudrun; Sim, Robert B; Kishore, Uday

2015-11-01

Interaction between the complement system and carbon nanotubes (CNTs) can modify their intended biomedical applications. Pristine and derivatised CNTs can activate complement primarily via the classical pathway which enhances uptake of CNTs and suppresses pro-inflammatory response by immune cells. Here, we report that the interaction of C1q, the classical pathway recognition molecule, with CNTs involves charge pattern and classical pathway activation that is partly inhibited by factor H, a complement regulator. C1q and its globular modules, but not factor H, enhanced uptake of CNTs by macrophages and modulated the pro-inflammatory immune response. Thus, soluble complement factors can interact differentially with CNTs and alter the immune response even without complement activation. Coating CNTs with recombinant C1q globular heads offers a novel way of controlling classical pathway activation in nanotherapeutics. Surprisingly, the globular heads also enhance clearance by phagocytes and down-regulate inflammation, suggesting unexpected complexity in receptor interaction. Carbon nanotubes (CNTs) maybe useful in the clinical setting as targeting drug carriers. However, it is also well known that they can interact and activate the complement system, which may have a negative impact on the applicability of CNTs. In this study, the authors functionalized multi-walled CNT (MWNT), and investigated the interaction with the complement pathway. These studies are important so as to gain further understanding of the underlying mechanism in preparation for future use of CNTs in the clinical setting. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

DiME: A Scalable Disease Module Identification Algorithm with Application to Glioma Progression

PubMed Central

Liu, Yunpeng; Tennant, Daniel A.; Zhu, Zexuan; Heath, John K.; Yao, Xin; He, Shan

2014-01-01

Disease module is a group of molecular components that interact intensively in the disease specific biological network. Since the connectivity and activity of disease modules may shed light on the molecular mechanisms of pathogenesis and disease progression, their identification becomes one of the most important challenges in network medicine, an emerging paradigm to study complex human disease. This paper proposes a novel algorithm, DiME (Disease Module Extraction), to identify putative disease modules from biological networks. We have developed novel heuristics to optimise Community Extraction, a module criterion originally proposed for social network analysis, to extract topological core modules from biological networks as putative disease modules. In addition, we have incorporated a statistical significance measure, B-score, to evaluate the quality of extracted modules. As an application to complex diseases, we have employed DiME to investigate the molecular mechanisms that underpin the progression of glioma, the most common type of brain tumour. We have built low (grade II) - and high (GBM) - grade glioma co-expression networks from three independent datasets and then applied DiME to extract potential disease modules from both networks for comparison. Examination of the interconnectivity of the identified modules have revealed changes in topology and module activity (expression) between low- and high- grade tumours, which are characteristic of the major shifts in the constitution and physiology of tumour cells during glioma progression. Our results suggest that transcription factors E2F4, AR and ETS1 are potential key regulators in tumour progression. Our DiME compiled software, R/C++ source code, sample data and a tutorial are available at http://www.cs.bham.ac.uk/~szh/DiME. PMID:24523864

MO-DE-BRA-01: Enhancing Radiation Physics Instruction Through Gamification and E-Learning

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

Driewer, J; Lei, Y; Morgan, B

Purpose: This project sought to “gamify” the instruction of radiation interaction physics concepts for technology students. Gamification applies game mechanics and user interactions in active learning contexts. In one part of this project, a self-guided eModule was developed for conceptual radiation interaction instruction. In a second part, a web-based game, Particle Launch (http://particle-launcher.ist.unomaha.edu), was created to challenge students to quickly apply radiation interaction concepts in a way that is stimulating and motivating. Methods: The eModule, focused on conceptual interaction physics, was designed in Adobe Captivate and incorporates animation, web videos, and assessment questions in order to generate student interest. Navigatingmore » the whole module takes 40 minutes for beginners. Assessments after three main sections are comprised of 3–4 questions randomly selected from a question pool. In collaboration with the University of Nebraska at Omaha’s College of Information Science and Technology, the Particle Launch game was created with the Unity gaming engine and designed with a game-play look and feel. The object of the game is to utilize different particles, energies, and directions to destroy a target given a limited number of resources and time to complete the task. A rewards system encourages accurate shots. Results: The eModule part of the project encourages a flipped classroom model in which class time is devoted to application of concepts rather than information-based lectures. Currently, eModule assessments are not tracked but this feature could be incorporated to encourage participation. Furthermore, in a class of five technology students, the game was found to be fun and engaging and had the effect of reinforcing basic concepts from the eModule. Conclusion: Gamification has significant potential to alter medical physics instruction. Game-play feedback is an important part of the learning process. Students found Particle Launch inviting and challenging and further research could help game design. This project was generously supported by the Office of the Vice-Chancellor for Academic Affairs and the University of Nebraska Medical Center.« less

N-Scan®: New Vibro-Modulation System for Crack Detection, Monitoring and Characterization

NASA Astrophysics Data System (ADS)

Zagrai, Andrei; Donskoy, Dimitri; Lottiaux, Jean-Louis

2004-02-01

In recent years, an innovative vibro-modulation technique has been introduced for the detection of contact-type interfaces such as cracks, debondings, and delaminations. The technique utilizes the effect of nonlinear interaction of ultrasound and vibrations at the interface of the defect. Vibration varies the contact area of the interface, modulating a passing ultrasonic wave. The modulation manifests itself as additional side-band spectral components with the combination frequencies in the spectrum of the received signal. The presence of these components allows for the detection and differentiation of the contact-type defects from other structural and material inhomogeneities. The vibro-modulation technique has been implemented in the N-SCAN® damage detection system providing a cost effective solution for the complex NDT problems. N-SCAN® proved to be very effective for damage detection and characterization in structures and structural components of simple and complex geometries made of steel, aluminum, composites, and other materials. Examples include 24 foot-long gun barrels, stainless steel pipes used in nuclear power plants, aluminum automotive parts, steel train couplers, etc. This paper describes the basic principles of the nonlinear vibro-modulation NDE technique, some theoretical background for nonlinear interaction, and justification of signal processing algorithms. The laboratory experiment is presented for a set of specimens with the calibrated cracks and the quantitative characterization of fatigue damage is given in terms of a modulation index. The paper also discusses examples of practical implementation and application of the technique.

BioInt: an integrative biological object-oriented application framework and interpreter.

PubMed

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Application of ultrasound-tagged photons for measurement of amplitude of vibration of tissue caused by ultrasound: theory, simulation, and experiments.

PubMed

Devi, C Usha; Vasu, R M; Sood, A K

2006-01-01

We investigate the modulation of an optical field caused by its interaction with an ultrasound beam in a tissue mimicking phantom. This modulation appears as a modulation in the intensity autocorrelation, which is measured by a photon counting correlator. The factors contributing to the modulation are: 1. amplitude of vibration of the particles of the tissue, 2. refractive index modulation, and 3. absorption coefficient in the region of the tissue intercepted by the ultrasound beam and light. We show in this work that a significant part of the contribution to this modulation comes from displacement of the tissue particles, which in turn is governed by the elastic properties of the tissue. We establish, both through simulations and experiments using an optical elastography phantom, the effects of the elasticity and absorption coefficient variations on the modulation of intensity autocorrelation. In the case where there is no absorption coefficient variation, we suggest that the depth of modulation can be calibrated to measure the displacement of tissue particles that, in turn, can be used to measure the tissue elasticity.

Health Information System Simulation. Curriculum Improvement Project. Region II.

ERIC Educational Resources Information Center

Anderson, Beth H.; Lacobie, Kevin

This volume is one of three in a self-paced computer literacy course that gives allied health students a firm base of knowledge concerning computer usage in the hospital environment. It also develops skill in several applications software packages. This volume contains five self-paced modules that allow students to interact with a health…

Semantic integration to identify overlapping functional modules in protein interaction networks

PubMed Central

Cho, Young-Rae; Hwang, Woochang; Ramanathan, Murali; Zhang, Aidong

2007-01-01

Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification. PMID:17650343

Interaction between chitosan and its related enzymes: A review.

PubMed

Shinya, Shoko; Fukamizo, Tamo

2017-11-01

Chitosan-related enzymes including chitosanases, exo-β-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan polysaccharides. However, in GH8 chitosanases, several aromatic residues are also involved in substrate recognition through stacking interactions, and these enzymes consequently hydrolyze β-1,4-glucan as well as chitosan. The binding grooves of these chitosanases are extended and opened at both ends of the grooves, so that the enzymes can clamp a long chitosan polysaccharide. The association/dissociation of positively charged glucosamine residues to/from the binding pocket of a GH2 exo-β-glucosaminidase controls the p K a of the catalytic acid, thereby maintaining the high catalytic potency of the enzyme. In contrast to chitosanases, chitosan-binding modules only accommodate a couple of glucosamine residues, predominantly recognizing the non-reducing end glucosamine residue of chitosan by electrostatic interactions and a hydrogen-bonding network. These structural findings on chitosan-related enzymes may contribute to future applications for the efficient conversion of the chitin/chitosan biomass. Copyright © 2017 Elsevier B.V. All rights reserved.

Air-coupled laser vibrometry: analysis and applications.

PubMed

Solodov, Igor; Döring, Daniel; Busse, Gerd

2009-03-01

Acousto-optic interaction between a narrow laser beam and acoustic waves in air is analyzed theoretically. The photoelastic relation in air is used to derive the phase modulation of laser light in air-coupled reflection vibrometry induced by angular spatial spectral components comprising the acoustic beam. Maximum interaction was found for the zero spatial acoustic component propagating normal to the laser beam. The angular dependence of the imaging efficiency is determined for the axial and nonaxial acoustic components with the regard for the laser beam steering in the scanning mode. The sensitivity of air-coupled vibrometry is compared with conventional "Doppler" reflection vibrometry. Applications of the methodology for visualization of linear and nonlinear air-coupled fields are demonstrated.

Generation of high power sub millimeter radiation using free electron laser

NASA Astrophysics Data System (ADS)

Panwar, J.; Sharma, S. C.; Malik, P.; Yadav, M.; Sharma, R.

2018-03-01

We have developed an analytical formalism to study the emission of high power radiation lying in the sub millimetre range. A relativistic electron beam (REB) is velocity modulated by the pondermotive force exerted by the laser beams. After passing through the drift space, the beam gets density modulated which further interacts with the strong field wiggler and acquires a transverse velocity that couples with the modulated density of the beam in the presence of ion channel which contribute to the non-linear current density which further leads to the emission of the radiation. The output radiation can be modified by changing the wiggler parameters and the energy of the electron beam. The power of the output radiation is found to increase with the modulation. The obtained radiation can be employed for various applications.

Interactive Design and Development of Real Arm Movements for Application in Rehabilitation

NASA Astrophysics Data System (ADS)

Rosman, Rafidah; Hadi, Muhammad Zaidan Abdul; Abu Bakar, Nurulliyana

2018-03-01

An interactive real arm movements for application in rehabilitation is designed and developed. The aim is to encourage hand paralysis patients performing their physical therapy by introducing games application in replacing conventional hand therapy module and methods. In this project, the accelerometer is used for tracking the orientation of the arm. As the arm moves, the values from x, y and z axis from the accelerometer changes and are being read by the Analog Inputs of the Arduino Board. After being read by the Analog Inputs of the Arduino Board, the 3D model moves as well. Solidworks software was used to modeled the hand in which the data is then transferred to Matlab/Simulink using SimMechanicalLink from Mathworks. Lastly, the sensor glove was programmed to work as a controller of games application in hand rehabilitation thus makes it an enjoyable therapy process.

'Oncokompas', a web-based self-management application to support patient activation and optimal supportive care: a feasibility study among breast cancer survivors.

PubMed

Melissant, Heleen C; Verdonck-de Leeuw, Irma M; Lissenberg-Witte, Birgit I; Konings, Inge R; Cuijpers, Pim; Van Uden-Kraan, Cornelia F

2018-02-16

Cancer survivors have to deal with symptoms related to cancer and its treatment. In Oncokompas, cancer survivors monitor their quality of life by completing patient reported outcome measures (PROMs), followed by personalized feedback, self-care advice, and supportive care options to stimulate patient activation. The aim of this study was to investigate feasibility and pretest-posttest differences of Oncokompas including a newly developed breast cancer (BC) module among BC survivors. A pretest-posttest design was used. Feasibility was investigated by means of adoption, usage, and satisfaction rates. Several socio-demographic and clinical factors, and health-related quality of life (HRQOL) were explored that might be associated with patient satisfaction. Barriers and facilitators of Oncokompas feasibility were investigated by evaluating nurse consultation reports. Differences in patient activation (Patient Activation Measure) and patient-physician interaction (Perceived Efficacy in Patient-Physician Interactions) before and after Oncokompas use were investigated. In total, 101 BC survivors participated. Oncokompas had an adoption rate of 75%, a usage rate of 75-84%, a mean satisfaction score of 6.9 (range 0-10) and a Net Promoter Score (NPS) of -36 (range -100-100) (N = 68). The BC module had a mean satisfaction score of 7.6. BC survivors who received surgery including chemotherapy and/or radiotherapy were significantly more satisfied with Oncokompas than BC survivors with surgery alone (p = .013). Six facilitators and 10 barriers of Oncokompas feasibility were identified. After using Oncokompas, BC survivors scored significantly higher on patient activation (p = .007; r = .24), but not on patient-physician interaction (p = .75). Oncokompas including a BC module is considered feasible, but needs further optimization to increase user satisfaction. This study shows the value of tailoring eHealth applications for cancer survivors to their specific tumor type. Oncokompas including the BC module seems to improve patient activation among BC survivors.

Abscisic Acid-Cytokinin Antagonism Modulates Resistance Against Pseudomonas syringae in Tobacco.

PubMed

Großkinsky, Dominik K; van der Graaff, Eric; Roitsch, Thomas

2014-12-01

Phytohormones are known as essential regulators of plant defenses, with ethylene, jasmonic acid, and salicylic acid as the central immunity backbone, while other phytohormones have been demonstrated to interact with this. Only recently, a function of the classic phytohormone cytokinin in plant immunity has been described in Arabidopsis, rice, and tobacco. Although interactions of cytokinins with salicylic acid and auxin have been indicated, the complete network of cytokinin interactions with other immunity-relevant phytohormones is not yet understood. Therefore, we studied the interaction of kinetin and abscisic acid as a negative regulator of plant immunity to modulate resistance in tobacco against Pseudomonas syringae. By analyzing infection symptoms, pathogen proliferation, and accumulation of the phytoalexin scopoletin as a key mediator of kinetin-induced resistance in tobacco, antagonistic interaction of these phytohormones in plant immunity was identified. Kinetin reduced abscisic acid levels in tobacco, while increased abscisic acid levels by exogenous application or inhibition of abscisic acid catabolism by diniconazole neutralized kinetin-induced resistance. Based on these results, we conclude that reduction of abscisic acid levels by enhanced abscisic acid catabolism strongly contributes to cytokinin-mediated resistance effects. Thus, the identified cytokinin-abscisic acid antagonism is a novel regulatory mechanism in plant immunity.

Ionic Gel Modulation of RKKY Interactions in Synthetic Anti-Ferromagnetic Nanostructures for Low Power Wearable Spintronic Devices.

PubMed

Yang, Qu; Zhou, Ziyao; Wang, Liqian; Zhang, Hongjia; Cheng, Yuxin; Hu, Zhongqiang; Peng, Bin; Liu, Ming

2018-05-01

To meet the demand of developing compatible and energy-efficient flexible spintronics, voltage manipulation of magnetism on soft substrates is in demand. Here, a voltage tunable flexible field-effect transistor structure by ionic gel (IG) gating in perpendicular synthetic anti-ferromagnetic nanostructure is demonstrated. As a result, the interlayer Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction can be tuned electrically at room temperature. With a circuit gating voltage, anti-ferromagnetic (AFM) ordering is enhanced or converted into an AFM-ferromagnetic (FM) intermediate state, accompanying with the dynamic domain switching. This IG gating process can be repeated stably at different curvatures, confirming an excellent mechanical property. The IG-induced modification of interlayer exchange coupling is related to the change of Fermi level aroused by the disturbance of itinerant electrons. The voltage modulation of RKKY interaction with excellent flexibility proposes an application potential for wearable spintronic devices with energy efficiency and ultralow operation voltage. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A distributed analysis and visualization system for model and observational data

NASA Technical Reports Server (NTRS)

Wilhelmson, Robert B.

1994-01-01

Software was developed with NASA support to aid in the analysis and display of the massive amounts of data generated from satellites, observational field programs, and from model simulations. This software was developed in the context of the PATHFINDER (Probing ATmospHeric Flows in an Interactive and Distributed EnviRonment) Project. The overall aim of this project is to create a flexible, modular, and distributed environment for data handling, modeling simulations, data analysis, and visualization of atmospheric and fluid flows. Software completed with NASA support includes GEMPAK analysis, data handling, and display modules for which collaborators at NASA had primary responsibility, and prototype software modules for three-dimensional interactive and distributed control and display as well as data handling, for which NSCA was responsible. Overall process control was handled through a scientific and visualization application builder from Silicon Graphics known as the Iris Explorer. In addition, the GEMPAK related work (GEMVIS) was also ported to the Advanced Visualization System (AVS) application builder. Many modules were developed to enhance those already available in Iris Explorer including HDF file support, improved visualization and display, simple lattice math, and the handling of metadata through development of a new grid datatype. Complete source and runtime binaries along with on-line documentation is available via the World Wide Web at: http://redrock.ncsa.uiuc.edu/ PATHFINDER/pathre12/top/top.html.

Time-varying metamaterials based on graphene-wrapped microwires: Modeling and potential applications

NASA Astrophysics Data System (ADS)

Salary, Mohammad Mahdi; Jafar-Zanjani, Samad; Mosallaei, Hossein

2018-03-01

The successful realization of metamaterials and metasurfaces requires the judicious choice of constituent elements. In this paper, we demonstrate the implementation of time-varying metamaterials in the terahertz frequency regime by utilizing graphene-wrapped microwires as building blocks and modulation of graphene conductivity through exterior electrical gating. These elements enable enhancement of light-graphene interaction by utilizing optical resonances associated with Mie scattering, yielding a large tunability and modulation depth. We develop a semianalytical framework based on transition-matrix formulation for modeling and analysis of periodic and aperiodic arrays of such time-varying building blocks. The proposed method is validated against full-wave numerical results obtained using the finite-difference time-domain method. It provides an ideal tool for mathematical synthesis and analysis of space-time gradient metamaterials, eliminating the need for computationally expensive numerical models. Moreover, it allows for a wider exploration of exotic space-time scattering phenomena in time-modulated metamaterials. We apply the method to explore the role of modulation parameters in the generation of frequency harmonics and their emerging wavefronts. Several potential applications of such platforms are demonstrated, including frequency conversion, holographic generation of frequency harmonics, and spatiotemporal manipulation of light. The presented results provide key physical insights to design time-modulated functional metadevices using various building blocks and open up new directions in the emerging paradigm of time-modulated metamaterials.

Modulation Transfer Through Coherence and Its Application to Atomic Frequency Offset Locking

NASA Astrophysics Data System (ADS)

Jagatap, B. N.; Ray, Ayan; Kale, Y. B.; Singh, Niharika; Lawande, Q. V.

We discuss the process of modulation transfer in a coherently prepared three-level atomic medium and its prospective application to atomic frequency offset locking (AFOL). The issue of modulation transfer through coherence is treated in the framework of temporal evolution of dressed atomic system with externally superimposed deterministic flow. This dynamical description of the atom-field system offers distinctive advantage of using a single modulation source to dither passively the coherent phenomenon as probed by an independent laser system under pump-probe configuration. Modulation transfer is demonstrated experimentally using frequency modulation spectroscopy on a subnatural linewidth electromagnetically induced transparency (EIT) and a sub-Doppler linewidth Autler-Townes (AT) resonance in Doppler broadened alkali vapor medium, and AFOL is realized by stabilizing the probe laser on the first/third derivative signals. The stability of AFOL is discussed in terms of the frequency noise power spectral density and Allan variance. Analysis of AFOL schemes is carried out at the backdrop of closed loop active frequency control in a conventional master-slave scheme to point out the contrasting behavior of AFOL schemes based on EIT and AT resonances. This work adds up to the discussion on the subtle link between dressed state spectroscopy and AFOL, which is relevant for developing a master-slave type laser system in the domain of coherent photon-atom interaction.

The Design and Evaluation of "CAPTools"--A Computer Aided Parallelization Toolkit

NASA Technical Reports Server (NTRS)

Yan, Jerry; Frumkin, Michael; Hribar, Michelle; Jin, Haoqiang; Waheed, Abdul; Johnson, Steve; Cross, Jark; Evans, Emyr; Ierotheou, Constantinos; Leggett, Pete;

Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules

NASA Astrophysics Data System (ADS)

Menon, Govind; Krishnan, J.

2016-07-01

While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules.

PubMed

Menon, Govind; Krishnan, J

2016-07-21

While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

Approximate methods for the fast computation of EPR and ST-EPR spectra. V. Application of the perturbation approach to the problem of anisotropic motion

NASA Astrophysics Data System (ADS)

Robinson, B. H.; Dalton, L. R.

1981-01-01

The modulation perturbation treatment of Galloway and Dalton is applied to the solution of the stochastic Liouville equation for the spin density matrix which incorporates an anisotropic rotational diffusion operator. Pseudosecular and saturation terms of the spin hamiltonian are explicitly considered as is the interaction of the electron spins with the applied Zeeman modulation field. The modulation perturbation treatment results in a factor of four improvement in computational speed relative to inversion of the full supermatrix with little or no loss of computational accuracy. The theoretical simulations of EPR and ST-EPR spectra are in nearly quantitative agreement with experimental spectra taken under high resolution conditions.

Accumulation effects in modulation spectroscopy with high-repetition-rate pulses: Recursive solution of optical Bloch equations

NASA Astrophysics Data System (ADS)

Osipov, Vladimir Al.; Pullerits, Tõnu

2017-10-01

Application of the phase-modulated pulsed light for advance spectroscopic measurements is the area of growing interest. The phase modulation of the light causes modulation of the signal. Separation of the spectral components of the modulations allows to distinguish the contributions of various interaction pathways. The lasers with high repetition rate used in such experiments can lead to appearance of the accumulation effects, which become especially pronounced in systems with long-living excited states. Recently it was shown that such accumulation effects can be used to evaluate parameters of the dynamical processes in the material. In this work we demonstrate that the accumulation effects are also important in the quantum characteristics measurements provided by modulation spectroscopy. In particular, we consider a model of quantum two-level system driven by a train of phase-modulated light pulses, organized in analogy with the two-dimensional spectroscopy experiments. We evaluate the harmonics' amplitudes in the fluorescent signal and calculate corrections appearing from the accumulation effects. We show that the corrections can be significant and have to be taken into account at analysis of experimental data.

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…

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

Tuning spin-spin interactions in radical dendrimers.

PubMed

Vidal-Gancedo, José; Lloveras, Vega; Liko, Flonja; Pinto, Luiz F; Muñoz-Gómez, Jose L

2018-05-10

Two generations of phosphorous dendrimers were synthesized and fully functionalized with TEMPO radicals via acrylamido or imino group linkers to evaluate the impact of the linker substitution on the radical-radical interactions. A drastic change in the way that the radicals interacted among them was observed by EPR and CV studies: while radicals in Gn-imino-TEMPO dendrimers presented a strong spin-spin interaction, in the Gn-acrylamido-TEMPO ones they acted mainly as independent radicals. This shows that these interactions could be tuned by the solely substitution of the radical linker, opening the perspective of controlling and modulating the extension of these interactions depending on each application. The chemical properties of the linker strongly influence the spin-spin exchange between pendant radicals. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Q-controlled amplitude modulation atomic force microscopy in liquids: An analysis

NASA Astrophysics Data System (ADS)

Hölscher, H.; Schwarz, U. D.

2006-08-01

An analysis of amplitude modulation atomic force microscopy in liquids is presented with respect to the application of the Q-Control technique. The equation of motion is solved by numerical and analytic methods with and without Q-Control in the presence of a simple model interaction force adequate for many liquid environments. In addition, the authors give an explicit analytical formula for the tip-sample indentation showing that higher Q factors reduce the tip-sample force. It is found that Q-Control suppresses unwanted deformations of the sample surface, leading to the enhanced image quality reported in several experimental studies.

Remote Synchronization Reveals Network Symmetries and Functional Modules

NASA Astrophysics Data System (ADS)

Nicosia, Vincenzo; Valencia, Miguel; Chavez, Mario; Díaz-Guilera, Albert; Latora, Vito

2013-04-01

We study a Kuramoto model in which the oscillators are associated with the nodes of a complex network and the interactions include a phase frustration, thus preventing full synchronization. The system organizes into a regime of remote synchronization where pairs of nodes with the same network symmetry are fully synchronized, despite their distance on the graph. We provide analytical arguments to explain this result, and we show how the frustration parameter affects the distribution of phases. An application to brain networks suggests that anatomical symmetry plays a role in neural synchronization by determining correlated functional modules across distant locations.

High-Performance Tiled WMS and KML Web Server

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2007-01-01

This software is an Apache 2.0 module implementing a high-performance map server to support interactive map viewers and virtual planet client software. It can be used in applications that require access to very-high-resolution geolocated images, such as GIS, virtual planet applications, and flight simulators. It serves Web Map Service (WMS) requests that comply with a given request grid from an existing tile dataset. It also generates the KML super-overlay configuration files required to access the WMS image tiles.

Synthesis of base-modified 2'-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology.

PubMed

Hocek, Michal

2014-11-07

The synthesis of 2'-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined.

Dissemination and support of ARGUS for accelerator applications

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

Not Available

The ARGUS code is a three-dimensional code system for simulating for interactions between charged particles, electric and magnetic fields, and complex structure. It is a system of modules that share common utilities for grid and structure input, data handling, memory management, diagnostics, and other specialized functions. The code includes the fields due to the space charge and current density of the particles to achieve a self-consistent treatment of the particle dynamics. The physic modules in ARGUS include three-dimensional field solvers for electrostatics and electromagnetics, a three-dimensional electromagnetic frequency-domain module, a full particle-in-cell (PIC) simulation module, and a steady-state PIC model.more » These are described in the Appendix to this report. This project has a primary mission of developing the capabilities of ARGUS in accelerator modeling of release to the accelerator design community. Five major activities are being pursued in parallel during the first year of the project. To improve the code and/or add new modules that provide capabilities needed for accelerator design. To produce a User's Guide that documents the use of the code for all users. To release the code and the User's Guide to accelerator laboratories for their own use, and to obtain feed-back from the. To build an interactive user interface for setting up ARGUS calculations. To explore the use of ARGUS on high-power workstation platforms.« less

Detailed requirements document for common software of shuttle program information management system

NASA Technical Reports Server (NTRS)

Everette, J. M.; Bradfield, L. D.; Horton, C. L.

1975-01-01

Common software was investigated as a method for minimizing development and maintenance cost of the shuttle program information management system (SPIMS) applications while reducing the time-frame of their development. Those requirements satisfying these criteria are presented along with the stand-alone modules which may be used directly by applications. The SPIMS applications operating on the CYBER 74 computer, are specialized information management systems which use System 2000 as a data base manager. Common software provides the features to support user interactions on a CRT terminal using form input and command response capabilities. These features are available as subroutines to the applications.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Evaluation of a Gait Assessment Module Using 3D Motion Capture Technology

PubMed Central

Baskwill, Amanda J.; Belli, Patricia; Kelleher, Leila

2017-01-01

Background Gait analysis is the study of human locomotion. In massage therapy, this observation is part of an assessment process that informs treatment planning. Massage therapy students must apply the theory of gait assessment to simulated patients. At Humber College, the gait assessment module traditionally consists of a textbook reading and a three-hour, in-class session in which students perform gait assessment on each other. In 2015, Humber College acquired a three-dimensional motion capture system. Purpose The purpose was to evaluate the use of 3D motion capture in a gait assessment module compared to the traditional gait assessment module. Participants Semester 2 massage therapy students who were enrolled in Massage Theory 2 (n = 38). Research Design Quasi-experimental, wait-list comparison study. Intervention The intervention group participated in an in-class session with a Qualisys motion capture system. Main Outcome Measure(s) The outcomes included knowledge and application of gait assessment theory as measured by quizzes, and students’ satisfaction as measured through a questionnaire. Results There were no statistically significant differences in baseline and post-module knowledge between both groups (pre-module: p = .46; post-module: p = .63). There was also no difference between groups on the final application question (p = .13). The intervention group enjoyed the in-class session because they could visualize the content, whereas the comparison group enjoyed the interactivity of the session. The intervention group recommended adding the assessment of gait on their classmates to their experience. Both groups noted more time was needed for the gait assessment module. Conclusions Based on the results of this study, it is recommended that the gait assessment module combine both the traditional in-class session and the 3D motion capture system. PMID:28293329

Electro-optical modulator in a polymerinfiltrated silicon slotted photonic crystal waveguide heterostructure resonator.

PubMed

Wülbern, Jan Hendrik; Petrov, Alexander; Eich, Manfred

2009-01-05

We present a novel concept of a compact, ultra fast electro-optic modulator, based on photonic crystal resonator structures that can be realized in two dimensional photonic crystal slabs of silicon as core material employing a nonlinear optical polymer as infiltration and cladding material. The novel concept is to combine a photonic crystal heterostructure cavity with a slotted defect waveguide. The photonic crystal lattice can be used as a distributed electrode for the application of a modulation signal. An electrical contact is hence provided while the optical wave is kept isolated from the lossy metal electrodes. Thereby, well known disadvantages of segmented electrode designs such as excessive scattering are avoided. The optical field enhancement in the slotted region increases the nonlinear interaction with an external electric field resulting in an envisaged switching voltage of approximately 1 V at modulation speeds up to 100 GHz.

Generation of high-power, tunable terahertz radiation from laser interaction with a relativistic electron beam

DOE PAGES

Zhang, Zhen; Yan, Lixin; Du, Yingchao; ...

2017-05-01

We propose a method based on the slice energy spread modulation to generate strong subpicosecond density bunching in high-intensity relativistic electron beams. A laser pulse with periodic intensity envelope is used to modulate the slice energy spread of the electron beam, which can then be converted into density modulation after a dispersive section. It is found that the double-horn slice energy distribution of the electron beam induced by the laser modulation is very effective to increase the density bunching. Since the modulation is performed on a relativistic electron beam, the process does not suffer from strong space charge force ormore » coupling between phase spaces, so that it is straightforward to preserve the beam quality for terahertz (THz) radiation and other applications. We show in both theory and simulations that the tunable radiation from the beam can cover the frequency range of 1 - 10 THz with high power and narrow-band spectra.« less

An electromagnetic modulator based on electrically controllable metamaterial analogue to electromagnetically induced transparency.

PubMed

Fan, Yuancheng; Qiao, Tong; Zhang, Fuli; Fu, Quanhong; Dong, Jiajia; Kong, Botao; Li, Hongqiang

2017-01-16

Electromagnetically induced transparency (EIT) is a promising technology for the enhancement of light-matter interactions, and recent demonstrations of the EIT analogue realized in artificial micro-structured medium have remarkably reduced the extreme requirement for experimental observation of EIT spectrum. In this paper, we propose to electrically control the EIT-like spectrum in a metamaterial as an electromagnetic modulator. A diode acting as a tunable resistor is loaded in the gap of paired wires to inductively tune the magnetic resonance, which induces remarkable modulation on the EIT-like spectrum through the metamaterial sample. The experimental measurements confirmed that the prediction of electromagnetic modulation in three narrow bands on the EIT-like spectrum, and a modulation contrast of up to 31 dB was achieved on the transmission through the metamaterial. Our results may facilitate the study on active/dynamical technology in translational metamaterials, which connect extraordinary manipulations on the flow of light in metamaterials, e.g., the exotic EIT, and practical applications in industry.

The modular architecture of protein-protein binding interfaces.

PubMed

Reichmann, D; Rahat, O; Albeck, S; Meged, R; Dym, O; Schreiber, G

2005-01-04

Protein-protein interactions are essential for life. Yet, our understanding of the general principles governing binding is not complete. In the present study, we show that the interface between proteins is built in a modular fashion; each module is comprised of a number of closely interacting residues, with few interactions between the modules. The boundaries between modules are defined by clustering the contact map of the interface. We show that mutations in one module do not affect residues located in a neighboring module. As a result, the structural and energetic consequences of the deletion of entire modules are surprisingly small. To the contrary, within their module, mutations cause complex energetic and structural consequences. Experimentally, this phenomenon is shown on the interaction between TEM1-beta-lactamase and beta-lactamase inhibitor protein (BLIP) by using multiple-mutant analysis and x-ray crystallography. Replacing an entire module of five interface residues with Ala created a large cavity in the interface, with no effect on the detailed structure of the remaining interface. The modular architecture of binding sites, which resembles human engineering design, greatly simplifies the design of new protein interactions and provides a feasible view of how these interactions evolved.

Polyamines: naturally occurring small molecule modulators of electrostatic protein-protein interactions.

PubMed

Berwanger, Anja; Eyrisch, Susanne; Schuster, Inge; Helms, Volkhard; Bernhardt, Rita

2010-02-01

Modulations of protein-protein interactions are a key step in regulating protein function, especially in networks. Modulators of these interactions are supposed to be candidates for the development of novel drugs. Here, we describe the role of the small, polycationic and highly abundant natural polyamines that could efficiently bind to charged spots at protein interfaces as modulators of such protein-protein interactions. Using the mitochondrial cytochrome P45011A1 (CYP11A1) electron transfer system as a model, we have analyzed the capability of putrescine, spermidine, and spermine at physiologically relevant concentrations to affect the protein-protein interactions between adrenodoxin reductase (AdR), adrenodoxin (Adx), and CYP11A1. The actions of polyamines on the individual components, on their association/dissociation, on electron transfer, and on substrate conversion were examined. These studies revealed modulating effects of polyamines on distinct interactions and on the entire system in a complex way. Modulation via changed protein-protein interactions appeared plausible from docking experiments that suggested favourable high-affinity binding sites of polyamines (spermine>spermidine>putrescine) at the AdR-Adx interface. Our findings imply for the first time that small endogenous compounds are capable of interfering with distinct components of transient protein complexes and might control protein functions by modulating electrostatic protein-protein interactions.

Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers

PubMed Central

Hsiao, Tzu-Hung; Chiu, Yu-Chiao; Hsu, Pei-Yin; Lu, Tzu-Pin; Lai, Liang-Chuan; Tsai, Mong-Hsun; Huang, Tim H.-M.; Chuang, Eric Y.; Chen, Yidong

2016-01-01

Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC. PMID:26972162

Perfect absorption of modified-molybdenum-disulfide-based Tamm plasmonic structures

NASA Astrophysics Data System (ADS)

Wang, Xiaoyu; Wang, Jicheng; Hu, Zheng-Da; Sang, Tian; Feng, Yan

2018-06-01

The two-dimensional semiconductor materials of transition metal molybdenum disulfide display various special optical properties in the interaction of matter and light. In this work, we study the strong coupling between the two-dimensional materials’ excitons and Tamm plasmon polaritons (TPPs). To enhance the interaction between light and matter, we introduce the grating modulation in the traditional Tamm structure. By adjusting the structure parameters of the grating-modified Tamm system, we achieve perfect absorption in the visible region. Our research results will pave the way for the application of ultrathin polarization optical devices.

Time-resolved metabolomics reveals metabolic modulation in rice foliage

PubMed Central

Sato, Shigeru; Arita, Masanori; Soga, Tomoyoshi; Nishioka, Takaaki; Tomita, Masaru

2008-01-01

Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems. PMID:18564421

Rapid Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gribble, Adam; Alali, Sanaz; Vitkin, Alex

2016-03-01

Polarized light has many applications in biomedical imaging. The interaction of a biological sample with polarized light reveals information about its composition, both structural and functional. For example, the polarimetry-derived metric of linear retardance (birefringence) is dependent on tissue structural organization (anisotropy) and can be used to diagnose myocardial infarct; circular birefringence (optical rotation) can measure glucose concentrations. The most comprehensive type of polarimetry analysis is to measure the Mueller matrix, a polarization transfer function that completely describes how a sample interacts with polarized light. To derive this 4x4 matrix it is necessary to observe how a tissue interacts with different polarizations. A well-suited approach for tissue polarimetry is to use photoelastic modulators (PEMs), which dynamically modulate the polarization of light. Previously, we have demonstrated a rapid time-gated Stokes imaging system that is capable of characterizing the state of polarized light (the Stokes vector) over a large field, after interacting with any turbid media. This was accomplished by synchronizing CCD camera acquisition times relative to two PEMs using a field-programmable gate array (FPGA). Here, we extend this technology to four PEMs, yielding a polarimetry system that is capable of rapidly measuring the complete sample Mueller matrix over a large field of view, with no moving parts and no beam steering. We describe the calibration procedure and evaluate the accuracy of the measurements. Results are shown for tissue-mimicking phantoms, as well as initial biological samples.

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.

PubMed

Grapov, Dmitry; Newman, John W

2012-09-01

Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010).

NREL/industry interaction: Amorphous silicon alloy research team formation

NASA Astrophysics Data System (ADS)

Luft, Werner

1994-06-01

The low material cost and proven manufacturability of amorphous silicon (a-Si) alloy photovoltaic technology make it ideally suited for large-scale terrestrial applications. The present efficiency of a-Si alloy modules is, however, much lower than the 15% stable efficiency that would lead to significant penetration of the electric utility bulk-power market. The slow progress in achieving high stabilized a-Si alloy module efficiencies may in part be attributed to the fact that only in the last few years did we emphasize stable efficiencies. A mission-focused integrated effort among the a-Si PV industry, universities, and the National Renewable Energy Laboratory (NREL) would help. To foster research integration, NREL has established four research teams with significant industry participation. In the 11 months since the research team formation, a close interaction among the a-Si PV industry, universities, and NREL has been achieved and has resulted in mission-directed research.

NREL/industry interaction: Amorphous silicon alloy research team formation

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

Luft, W.

1994-06-30

The low material cost and proven manufacturability of amorphous silicon (a-Si) alloy photovoltaic technology make it ideally suited for large-scale terrestrial applications. The present efficiency of a-Si alloy modules is, however, much lower than the 15% stable efficiency that would lead to [ital significant] penetration of the electric utility bulk-power market. The slow progress in achieving high stabilized a-Si alloy module efficiencies may in part be attributed to the fact that only in the last few years did we emphasize stable efficiencies. A mission-focused integrated effort among the a-Si PV industry, universities, and the National Renewable Energy Laboratory (NREL) wouldmore » help. To foster research integration, NREL has established four research teams with significant industry participation. In the 11 months since the research team formation, a close interaction among the a-Si PV industry, universities, and NREL has been achieved and has resulted in mission-directed research.« less

Lasing from active optomechanical resonators

PubMed Central

Czerniuk, T.; Brüggemann, C.; Tepper, J.; Brodbeck, S.; Schneider, C.; Kamp, M.; Höfling, S.; Glavin, B. A.; Yakovlev, D. R.; Akimov, A. V.; Bayer, M.

2014-01-01

Planar microcavities with distributed Bragg reflectors (DBRs) host, besides confined optical modes, also mechanical resonances due to stop bands in the phonon dispersion relation of the DBRs. These resonances have frequencies in the 10- to 100-GHz range, depending on the resonator’s optical wavelength, with quality factors exceeding 1,000. The interaction of photons and phonons in such optomechanical systems can be drastically enhanced, opening a new route towards the manipulation of light. Here we implemented active semiconducting layers into the microcavity to obtain a vertical-cavity surface-emitting laser (VCSEL). Thereby, three resonant excitations—photons, phonons and electrons—can interact strongly with each other providing modulation of the VCSEL laser emission: a picosecond strain pulse injected into the VCSEL excites long-living mechanical resonances therein. As a result, modulation of the lasing intensity at frequencies up to 40 GHz is observed. From these findings, prospective applications of active optomechanical resonators integrated into nanophotonic circuits may emerge. PMID:25008784

Achieving nonlinear optical modulation via four-wave mixing in a four-level atomic system

NASA Astrophysics Data System (ADS)

Li, Hai-Chao; Ge, Guo-Qin; Zubairy, M. Suhail

2018-05-01

We propose an accessible scheme for implementing tunable nonlinear optical amplification and attenuation via a synergetic mechanism of four-wave mixing (FWM) and optical interference in a four-level ladder-type atomic system. By constructing a cyclic atom-field interaction, we show that two reverse FWM processes can coexist via optical transitions in different branches. In the suitable input-field conditions, strong interference effects between the input fields and the generated FWM fields can be induced and result in large amplification and deep attenuation of the output fields. Moreover, such an optical modulation from enhancement to suppression can be controlled by tuning the relative phase. The quantum system can be served as a switchable optical modulator with potential applications in quantum nonlinear optics.

The Electric Propulsion Interactions Code (EPIC)

NASA Technical Reports Server (NTRS)

Mikellides, I. G.; Mandell, M. J.; Kuharski, R. A.; Davis, V. A.; Gardner, B. M.; Minor, J.

2004-01-01

Science Applications International Corporation is currently developing the Electric Propulsion Interactions Code, EPIC, as part of a project sponsored by the Space Environments and Effects Program at the NASA Marshall Space Flight Center. Now in its second year of development, EPIC is an interactive computer tool that allows the construction of a 3-D spacecraft model, and the assessment of a variety of interactions between its subsystems and the plume from an electric thruster. These interactions may include erosion of surfaces due to sputtering and re-deposition of sputtered materials, surface heating, torque on the spacecraft, and changes in surface properties due to erosion and deposition. This paper describes the overall capability of EPIC and provides an outline of the physics and algorithms that comprise many of its computational modules.

Optical Properties of Gallium Arsenide and Indium Gallium Arsenide Quantum Wells and Their Applications to Opto-Electronic Devices.

NASA Astrophysics Data System (ADS)

Huang, Daming

1990-01-01

In this thesis we investigate the optical properties of modulation doped GaAs/AlGaAs and strained-layer undoped InGaAs/GaAs multiple quantum well structures (MQWS). The phenomena studied are the effects of carrier, strain, and the electric field on the absorption of excitons. For GaAs/AlGaAs modulation doped MQWS, the quenching of excitons by free carriers has been demonstrated. The comparison of the experimental results with calculations which consider phase space filling, screening, and exchange interaction showed the phase space filling to be the dominant mechanism responsible for the change of oscillator strength and binding energy of excitons associated with partially filled subband. On the other hand, the screening and exchange interaction are equally important to excitons associated with empty subbands. For InGaAs/GaAs strained-layer MQWS, we have demonstrated that the band edges are dramatically modified by strain. We determined the band discontinuities at InGaAs/GaAs interfaces using optical absorption, and showed that in this structure the heavy holes are confined in InGaAs layers while the light holes are in GaAs layers, in contrast to GaAs/AlGaAs MQWS. We also explore applications of GaAs/AlGaAs and InGaAs/GaAs MQWS to opto-electronic devices. The principle of devices investigated is mainly based on the electric field effect on the excitonic absorption in MQWS (the quantum confined Stark effect). Two examples presented in this thesis are the strained-layer InGaAs/GaAs MQWS electroabsorption modulators grown on GaAs substrates and the GaAs/AlGaAs MQWS reflection modulators grown on Si substrates. The large modulation observed in the absorption coefficient by an electric field is expected to facilitate opto-electronic integration.

The nicotinic receptor blocker hexamethonium alters neuronal responses to glutamate in the medial septal area of the brain of the ground squirrel in vitro.

PubMed

Karavaev, E N; Popova, I Yu; Kichigina, V F

2008-03-01

Despite extensive interest in studies of the medial septal area, the nature of the interactions of its various neurochemical systems remains largely unclear. The aim of the present work was to clarify the role of nicotinic receptors in mediating the interaction of the glutamatergic and cholinergic systems in this structure. Extracellular recording of neuron activity in living slices of ground squirrel brain was used to study the influences of L-glutamate (1 microM) during application of the nicotinic receptor blocker hexamethonium (1 mM). The responses of septal neurons to glutamate depended on the type of their initial activity and the presence of pacemaker properties. This study is the first to show that glutamate increases the frequency of volleys in rhythmic neurons in the septum. Hexamethonium induced changes in neuron activity similar to the influences of glutamate. After prior application of hexamethonium, the responses of neurons to glutamate changed: activatory responses were masked and inhibitory responses were enhanced. Cholinergic modulation of the responses of septal neurons to glutamate were shown to occur, as did modulation of the strength of the oscillatory properties of the septal network by nicotinic receptors.

Graph theory in brain-to-brain connectivity: A simulation study and an application to an EEG hyperscanning experiment.

PubMed

Toppi, J; Ciaramidaro, A; Vogel, P; Mattia, D; Babiloni, F; Siniatchkin, M; Astolfi, L

2015-08-01

Hyperscanning consists in the simultaneous recording of hemodynamic or neuroelectrical signals from two or more subjects acting in a social context. Well-established methodologies for connectivity estimation have already been adapted to hyperscanning purposes. The extension of graph theory approach to multi-subjects case is still a challenging issue. In the present work we aim to test the ability of the currently used graph theory global indices in describing the properties of a network given by two interacting subjects. The testing was conducted first on surrogate brain-to-brain networks reproducing typical social scenarios and then on real EEG hyperscanning data recorded during a Joint Action task. The results of the simulation study highlighted the ability of all the investigated indexes in modulating their values according to the level of interaction between subjects. However, only global efficiency and path length indexes demonstrated to be sensitive to an asymmetry in the communication between the two subjects. Such results were, then, confirmed by the application on real EEG data. Global efficiency modulated, in fact, their values according to the inter-brain density, assuming higher values in the social condition with respect to the non-social condition.

Septic safe interactions with smart glasses in health care.

PubMed

Czuszynski, K; Ruminski, J; Kocejko, T; Wtorek, J

2015-08-01

In this paper, septic safe methods of interaction with smart glasses, due to the health care environment applications consideration, are presented. The main focus is on capabilities of an optical, proximity-based gesture sensor and eye-tracker input systems. The design of both interfaces is being adapted to the open smart glasses platform that is being developed under the eGlasses project. Preliminary results obtained from the proximity sensor show that the recognition of different static and dynamic hand gestures is promising. The experiments performed for the eye-tracker module shown the possibility of interaction with simple Graphical User Interface provided by the near-to-eye display. Research leads to the conclusion of attractiveness of collaborative interfaces for interaction with smart glasses.

exVis: a visual analysis tool for wind tunnel data

NASA Astrophysics Data System (ADS)

Deardorff, D. G.; Keeley, Leslie E.; Uselton, Samuel P.

1998-05-01

exVis is a software tool created to support interactive display and analysis of data collected during wind tunnel experiments. It is a result of a continuing project to explore the uses of information technology in improving the effectiveness of aeronautical design professionals. The data analysis goals are accomplished by allowing aerodynamicists to display and query data collected by new data acquisition systems and to create traditional wind tunnel plots from this data by interactively interrogating these images. exVis was built as a collection of distinct modules to allow for rapid prototyping, to foster evolution of capabilities, and to facilitate object reuse within other applications being developed. It was implemented using C++ and Open Inventor, commercially available object-oriented tools. The initial version was composed of three main classes. Two of these modules are autonomous viewer objects intended to display the test images (ImageViewer) and the plots (GraphViewer). The third main class is the Application User Interface (AUI) which manages the passing of data and events between the viewers, as well as providing a user interface to certain features. User feedback was obtained on a regular basis, which allowed for quick revision cycles and appropriately enhanced feature sets. During the development process additional classes were added, including a color map editor and a data set manager. The ImageViewer module was substantially rewritten to add features and to use the data set manager. The use of an object-oriented design was successful in allowing rapid prototyping and easy feature addition.

The Interaction between Sytactic and Semantic Modules in Chinese Learners' English Spotaneous Speech

ERIC Educational Resources Information Center

Gang, Xu

2014-01-01

According to modular theory, there are interactive effects between the central modules and language modules. The central cognition may deploy and redeploy resources from language modules. Moreover, the language modules can activate the cognitive ability. So this paper studies the spontaneous speech of students who learn English as a foreign…

Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells.

PubMed

Kubota, Ryou; Hamachi, Itaru

2015-07-07

Chemical sensing of amino acids, peptides, and proteins provides fruitful information to understand their biological functions, as well as to develop the medical and technological applications. To detect amino acids, peptides, and proteins in vitro and in vivo, vast kinds of chemical sensors including small synthetic binders/sensors, genetically-encoded fluorescent proteins and protein-based semisynthetic biosensors have been intensely investigated. This review deals with concepts, strategies, and applications of protein recognition and sensing using small synthetic binders/sensors, which are now actively studied but still in the early stage of investigation. The recognition strategies for peptides and proteins can be divided into three categories: (i) recognition of protein substructures, (ii) protein surface recognition, and (iii) protein sensing through protein-ligand interaction. Here, we overview representative examples of protein recognition and sensing, and discuss biological or diagnostic applications such as potent inhibitors/modulators of protein-protein interactions.

Detection of protein complex from protein-protein interaction network using Markov clustering

NASA Astrophysics Data System (ADS)

Ochieng, P. J.; Kusuma, W. A.; Haryanto, T.

2017-05-01

Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks.

Oscillatory instability of a self-rewetting film driven by thermal modulation

NASA Astrophysics Data System (ADS)

Batson, William; Agnon, Yehuda; Oron, Alex

2016-11-01

Here we consider the self-rewetting fluids (SRWFs) that exhibit a well-defined minimum surface tension with respect to temperature, in contrast to those where surface tension decreases linearly. Utilization of SRWFs has grown significantly in the past decade, due to observations that heat transfer is enhanced in applications such as film boiling and pulsating heat pipes. With similar applications in mind, we investigate the dynamics of a thin SRWF film which is subjected to a temperature modulation in the bounding gas. A model is developed within the framework of the long-wave approximation, and a time-averaged thermocapillary driving force for destabilization is uncovered for SRWFs that results from the nonlinear surface tension. Linear analysis of the nonlinear PDE for the film thickness is used to determine the critical conditions at which this driving force destabilizes the film, and, numerical integration of this evolution equation reveals that linearly unstable perturbations saturate to regular periodic solutions (when the modulational frequency is set properly). Properties of these flows such as bifurcation and long-domain flows, where multiple unstable linear modes interact, will also be discussed.

Development and Impact Evaluation of an E-Learning Radiation Oncology Module

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

Alfieri, Joanne, E-mail: Joanne.alfieri@mail.mcgill.ca; Portelance, Lorraine; Souhami, Luis

Purpose: Radiation oncologists are faced with the challenge of irradiating tumors to a curative dose while limiting toxicity to healthy surrounding tissues. This can be achieved only with superior knowledge of radiologic anatomy and treatment planning. Educational resources designed to meet these specific needs are lacking. A web-based interactive module designed to improve residents' knowledge and application of key anatomy concepts pertinent to radiotherapy treatment planning was developed, and its effectiveness was assessed. Methods and Materials: The module, based on gynecologic malignancies, was developed in collaboration with a multidisciplinary team of subject matter experts. Subsequently, a multi-centre randomized controlled studymore » was conducted to test the module's effectiveness. Thirty-six radiation oncology residents participated in the study; 1920 were granted access to the module (intervention group), and 17 in the control group relied on traditional methods to acquire their knowledge. Pretests and posttests were administered to all participants. Statistical analysis was carried out using paired t test, analysis of variance, and post hoc tests. Results: The randomized control study revealed that the intervention group's pretest and posttest mean scores were 35% and 52%, respectively, and those of the control group were 37% and 42%, respectively. The mean improvement in test scores was 17% (p < 0.05) for the intervention group and 5% (p = not significant) for the control group. Retrospective pretest and posttest surveys showed a statistically significant change on all measured module objectives. Conclusions: The use of an interactive e-learning teaching module for radiation oncology is an effective method to improve the radiologic anatomy knowledge and treatment planning skills of radiation oncology residents.« less

All-optical modulation in Mid-Wavelength Infrared using porous Si membranes

PubMed Central

Park, Sung Jin; Zakar, Ammar; Zerova, Vera L.; Chekulaev, Dimitri; Canham, Leigh T.; Kaplan, Andre

2016-01-01

We demonstrate for the first time the possibility of all-optical modulation of self-standing porous Silicon (pSi) membrane in the Mid-Wavelength Infrared (MWIR) range using femtosecond pump-probe techniques. To study optical modulation, we used pulses of an 800 nm, 60 femtosecond for pump and a MWIR tunable probe in the spectral range between 3.5 and 4.4 μm. We show that pSi possesses a natural transparency window centred around 4 μm. Yet, about 55% of modulation contrast can be achieved by means of optical excitation at the pump power of 60 mW (4.8 mJ/cm2). Our analysis shows that the main mechanism of the modulation is interaction of the MWIR signal with the free charge carrier excited by the pump. The time-resolved measurements showed a sub-picosecond rise time and a recovery time of about 66 ps, which suggests a modulation speed performance of ~15 GHz. This optical modulation of pSi membrane in MWIR can be applied to a variety of applications such as thermal imaging and free space communications. PMID:27440224

Band gap modulation of graphene by metal substrate: A first principles study

NASA Astrophysics Data System (ADS)

Sahoo, Mihir Ranjan; Sahu, Sivabrata; Kushwaha, Anoop Kumar; Nayak, S. K.

2018-04-01

Due to high in-plane charge carrier mobility with high electron velocity and long spin diffusion length, graphene guarantees as a completely unique material for devices with various applications. Unaffected 2pz orbitals of carbon atoms in graphene can be highly influenced by substrates and leads to tuning in electronic properties. We report here a density functional calculation of graphene monolayer based on metallic substrate like nickel surfaces. Band-gap of graphene near K points opens due to interactions between 2pz and d-orbitals of nickel atoms and the gap modulation can be done with the increasing number of layers of substrates.

Expanding the therapeutic use of androgens via selective androgen receptor modulators (SARMs)

PubMed Central

Gao, Wenqing; Dalton, James T.

2007-01-01

Selective androgen receptor modulators (SARMs) are a novel class of androgen receptor (AR) ligands that might change the future of androgen therapy dramatically. With improved pharmacokinetic characteristics and tissue-selective pharmacological activities, SARMs are expected to greatly extend the clinical applications of androgens to osteoporosis, muscle wasting, male contraception and diseases of the prostate. Mechanistic studies with currently available SARMs will help to define the contributions of differential tissue distribution, tissue-specific expression of 5α-reductase, ligand-specific regulation of gene expression and AR interactions with tissue-specific coactivators to their observed tissue selectivity, and lead to even greater expansion of selective anabolic therapies. PMID:17331889

Electron spin-echo envelope modulation (ESEEM) reveals water and phosphate interactions with the KcsA potassium channel.

PubMed

Cieslak, John A; Focia, Pamela J; Gross, Adrian

2010-02-23

Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar water content, and water permeation profiles in membranes, among other applications. In the present study, we combine ESEEM spectroscopy with site-directed spin labeling (SDSL) and X-ray crystallography in order to evaluate the technique's potential as a structural tool to describe the native environment of membrane proteins. Using the KcsA potassium channel as a model system, we demonstrate that deuterium ESEEM can detect water permeation along the lipid-exposed surface of the KcsA outer helix. We further demonstrate that (31)P ESEEM is able to identify channel residues that interact with the phosphate headgroup of the lipid bilayer. In combination with X-ray crystallography, the (31)P data may be used to define the phosphate interaction surface of the protein. The results presented here establish ESEEM as a highly informative technique for SDSL studies of membrane proteins.

The iFlow modelling framework v2.4: a modular idealized process-based model for flow and transport in estuaries

NASA Astrophysics Data System (ADS)

Dijkstra, Yoeri M.; Brouwer, Ronald L.; Schuttelaars, Henk M.; Schramkowski, George P.

2017-07-01

The iFlow modelling framework is a width-averaged model for the systematic analysis of the water motion and sediment transport processes in estuaries and tidal rivers. The distinctive solution method, a mathematical perturbation method, used in the model allows for identification of the effect of individual physical processes on the water motion and sediment transport and study of the sensitivity of these processes to model parameters. This distinction between processes provides a unique tool for interpreting and explaining hydrodynamic interactions and sediment trapping. iFlow also includes a large number of options to configure the model geometry and multiple choices of turbulence and salinity models. Additionally, the model contains auxiliary components, including one that facilitates easy and fast sensitivity studies. iFlow has a modular structure, which makes it easy to include, exclude or change individual model components, called modules. Depending on the required functionality for the application at hand, modules can be selected to construct anything from very simple quasi-linear models to rather complex models involving multiple non-linear interactions. This way, the model complexity can be adjusted to the application. Once the modules containing the required functionality are selected, the underlying model structure automatically ensures modules are called in the correct order. The model inserts iteration loops over groups of modules that are mutually dependent. iFlow also ensures a smooth coupling of modules using analytical and numerical solution methods. This way the model combines the speed and accuracy of analytical solutions with the versatility of numerical solution methods. In this paper we present the modular structure, solution method and two examples of the use of iFlow. In the examples we present two case studies, of the Yangtze and Scheldt rivers, demonstrating how iFlow facilitates the analysis of model results, the understanding of the underlying physics and the testing of parameter sensitivity. A comparison of the model results to measurements shows a good qualitative agreement. iFlow is written in Python and is available as open source code under the LGPL license.

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

PubMed Central

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-01-01

Within the framework of ‘Network Physiology’, we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain–heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain–heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems. PMID:27044991

Quorum sensing is a language of chemical signals and plays an ecological role in algal-bacterial interactions

PubMed Central

Zhou, Jin; Lyu, Yihua; Richlen, Mindy; Anderson, Donald M.; Cai, Zhonghua

2017-01-01

Algae are ubiquitous in the marine environment, and the ways in which they interact with bacteria are of particular interest in marine ecology field. The interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape microbial diversity. Although algal-bacterial interactions are well known and studied, information regarding the chemical-ecological role of this relationship remains limited, particularly with respect to quorum sensing (QS), which is a system of stimuli and response correlated to population density. In the microbial biosphere, QS is pivotal in driving community structure and regulating behavioral ecology, including biofilm formation, virulence, antibiotic resistance, swarming motility, and secondary metabolite production. Many marine habitats, such as the phycosphere, harbour diverse populations of microorganisms and various signal languages (such as QS-based autoinducers). QS-mediated interactions widely influence algal-bacterial symbiotic relationships, which in turn determine community organization, population structure, and ecosystem functioning. Understanding infochemicals-mediated ecological processes may shed light on the symbiotic interactions between algae host and associated microbes. In this review, we summarize current achievements about how QS modulates microbial behavior, affects symbiotic relationships, and regulates phytoplankton chemical ecological processes. Additionally, we present an overview of QS-modulated co-evolutionary relationships between algae and bacterioplankton, and consider the potential applications and future perspectives of QS. PMID:28966438

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

NASA Astrophysics Data System (ADS)

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-05-01

Within the framework of `Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems.

'Bioengineered Bugs' - a patho-biotechnology approach to probiotic research and applications.

PubMed

Sleator, Roy D; Hill, Colin

2008-01-01

Given the increasing commercial and clinical relevance of probiotic cultures, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Pathogenic bacteria have evolved sophisticated strategies to overcome host defences, interact with the immune system and modulate essential host systems. The 'Patho-biotechnology' concept promotes the exploitation of these valuable traits for the design of more technologically robust and effective probiotic cultures with potentially improved biotechnological and clinical applications, as well as the development of novel vaccine and drug delivery platforms.

Dissemination and support of ARGUS for accelerator applications. Technical progress report, April 24, 1991--January 20, 1992

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

Not Available

The ARGUS code is a three-dimensional code system for simulating for interactions between charged particles, electric and magnetic fields, and complex structure. It is a system of modules that share common utilities for grid and structure input, data handling, memory management, diagnostics, and other specialized functions. The code includes the fields due to the space charge and current density of the particles to achieve a self-consistent treatment of the particle dynamics. The physic modules in ARGUS include three-dimensional field solvers for electrostatics and electromagnetics, a three-dimensional electromagnetic frequency-domain module, a full particle-in-cell (PIC) simulation module, and a steady-state PIC model.more » These are described in the Appendix to this report. This project has a primary mission of developing the capabilities of ARGUS in accelerator modeling of release to the accelerator design community. Five major activities are being pursued in parallel during the first year of the project. To improve the code and/or add new modules that provide capabilities needed for accelerator design. To produce a User`s Guide that documents the use of the code for all users. To release the code and the User`s Guide to accelerator laboratories for their own use, and to obtain feed-back from the. To build an interactive user interface for setting up ARGUS calculations. To explore the use of ARGUS on high-power workstation platforms.« less

Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments.

PubMed

Potapov, V; Reichmann, D; Abramovich, R; Filchtinski, D; Zohar, N; Ben Halevy, D; Edelman, M; Sobolev, V; Schreiber, G

2008-12-05

A new method is presented for the redesign of protein-protein interfaces, resulting in specificity of the designed pair while maintaining high affinity. The design is based on modular interface architecture and was carried out on the interaction between TEM1 beta-lactamase and its inhibitor protein, beta-lactamase inhibitor protein. The interface between these two proteins is composed of several mostly independent modules. We previously showed that it is possible to delete a complete module without affecting the overall structure of the interface. Here, we replace a complete module with structure fragments taken from nonrelated proteins. Nature-optimized fragments were chosen from 10(7) starting templates found in the Protein Data Bank. A procedure was then developed to identify sets of interacting template residues with a backbone arrangement mimicking the original module. This generated a final list of 361 putative replacement modules that were ranked using a novel scoring function based on grouped atom-atom contact surface areas. The top-ranked designed complex exhibited an affinity of at least the wild-type level and a mode of binding that was remarkably specific despite the absence of negative design in the procedure. In retrospect, the combined application of three factors led to the success of the design approach: utilizing the modular construction of the interface, capitalizing on native rather than artificial templates, and ranking with an accurate atom-atom contact surface scoring function.

Interharmonic modulation products as a means to quantify nonlinear D-region interactions

NASA Astrophysics Data System (ADS)

Moore, Robert

Experimental observations performed during dual beam ionospheric HF heating experiments at the High frequency Active Auroral Research Program (HAARP) HF transmitter in Gakona, Alaska are used to quantify the relative importance of specific nonlinear interactions that occur within the D region ionosphere. During these experiments, HAARP broadcast two amplitude modulated HF beams whose center frequencies were separated by less than 20 kHz. One beam was sinusoidally modulated at 500 Hz while the second beam was sinusoidally modulated using a 1-7 kHz linear frequency-time chirp. ELF/VLF observations performed at two different locations (3 and 98 km from HAARP) provide clear evidence of strong interactions between all field components of the two HF beams in the form of low and high order interharmonic modulation products. From a theoretical standpoint, the observed interharmonic modulation products could be produced by several different nonlinearities. The two primary nonlinearities take the form of wave-medium interactions (i.e., cross modulation), wherein the ionospheric conductivity modulation produced by one signal crosses onto the other signal via collision frequency modification, and wave-wave interactions, wherein the conduction current associated with one wave mixes with the electric field of the other wave to produce electron temperature oscillations. We are able to separate and quantify these two different nonlinearities, and we conclude that the wave-wave interactions dominate the wave-medium interactions by a factor of two. These results are of great importance for the modeling of transioinospheric radio wave propagation, in that both the wave-wave and the wave-medium interactions could be responsible for a significant amount of anomalous absorption.

Advanced composites structural concepts and materials technologies for primary aircraft structures: Structural response and failure analysis

NASA Technical Reports Server (NTRS)

Dorris, William J.; Hairr, John W.; Huang, Jui-Tien; Ingram, J. Edward; Shah, Bharat M.

1992-01-01

Non-linear analysis methods were adapted and incorporated in a finite element based DIAL code. These methods are necessary to evaluate the global response of a stiffened structure under combined in-plane and out-of-plane loading. These methods include the Arc Length method and target point analysis procedure. A new interface material model was implemented that can model elastic-plastic behavior of the bond adhesive. Direct application of this method is in skin/stiffener interface failure assessment. Addition of the AML (angle minus longitudinal or load) failure procedure and Hasin's failure criteria provides added capability in the failure predictions. Interactive Stiffened Panel Analysis modules were developed as interactive pre-and post-processors. Each module provides the means of performing self-initiated finite elements based analysis of primary structures such as a flat or curved stiffened panel; a corrugated flat sandwich panel; and a curved geodesic fuselage panel. This module brings finite element analysis into the design of composite structures without the requirement for the user to know much about the techniques and procedures needed to actually perform a finite element analysis from scratch. An interactive finite element code was developed to predict bolted joint strength considering material and geometrical non-linearity. The developed method conducts an ultimate strength failure analysis using a set of material degradation models.

The Impact of Interactive, Computerized Educational Modules on Preclinical Medical Education

ERIC Educational Resources Information Center

Bryner, Benjamin S.; Saddawi-Konefka, Daniel; Gest, Thomas R.

2008-01-01

Interactive computerized modules have been linked to improved retention of material in clinical medicine. This study examined the effects of a new series of interactive learning modules for preclinical medical education, specifically in the areas of quiz performance, perceived difficulty of concepts, study time, and perceived stress level. We…

Responsive nanoporous metals: recoverable modulations on strength and shape by watering

NASA Astrophysics Data System (ADS)

Ye, Xing-Long; Liu, Ling-Zhi; Jin, Hai-Jun

2016-08-01

Many biological materials can readily modulate their mechanical properties and shape by interacting with water in the surrounding environment, which is essential to their high performance in application. In contrast, typical inorganic materials (such as the metals) cannot change their strength and shape without involving thermal/mechanical treatments. By introducing nano-scale porous structure and exploiting a simple physical concept—the water-capillarity in nanopores, here we report that a ‘dead’ metal can be transformed into a ‘smart’ material with water-responsive properties. We demonstrate that the apparent strength, volume and shape of nanoporous Au and Au(Pt) can be modulated in situ, dramatically and recoverably, in response to water-dipping and partial-drying. The amplitude of strength-modulation reaches 20 MPa, which is nearly 50% of the yield strength at initial state. This approach also leads to reversible length change up to 1.3% in nanoporous Au and a large reversible bending motion of a bi-layer strip with tip displacement of ˜20 mm, which may be used for actuation. This method is simple and effective, occurring in situ under ambient conditions and requiring no external power, analogous to biological materials. The findings may open up novel applications in many areas such as micro-robotics and bio-medical devices.

Student Perceptions of a Flipped Pharmacotherapy Course

PubMed Central

Khanova, Julia; McLaughlin, Jacqueline E.; Rhoney, Denise H.; Roth, Mary T.

2015-01-01

Objective. To evaluate student perception of the flipped classroom redesign of a required pharmacotherapy course. Design. Key foundational content was packaged into interactive, text-based online modules for self-paced learning prior to class. Class time was used for active and applied—but primarily case-based—learning. Assessment. For students with a strong preference for traditional lecture learning, the perception of the learning experience was negatively affected by the flipped course design. Module length and time required to complete preclass preparation were the most frequently cited impediments to learning. Students desired instructor-directed reinforcement of independently acquired knowledge to connect foundational knowledge and its application. Conclusion. This study illustrates the challenges and highlights the importance of designing courses to effectively balance time requirements and connect preclass and in-class learning activities. It underscores the crucial role of the instructor in bridging the gap between material learned as independent study and its application. PMID:26839429

Modulation of Metabolic Detoxification Pathways Using Foods and Food-Derived Components: A Scientific Review with Clinical Application.

PubMed

Hodges, Romilly E; Minich, Deanna M

2015-01-01

Research into human biotransformation and elimination systems continues to evolve. Various clinical and in vivo studies have been undertaken to evaluate the effects of foods and food-derived components on the activity of detoxification pathways, including phase I cytochrome P450 enzymes, phase II conjugation enzymes, Nrf2 signaling, and metallothionein. This review summarizes the research in this area to date, highlighting the potential for foods and nutrients to support and/or modulate detoxification functions. Clinical applications to alter detoxification pathway activity and improve patient outcomes are considered, drawing on the growing understanding of the relationship between detoxification functions and different disease states, genetic polymorphisms, and drug-nutrient interactions. Some caution is recommended, however, due to the limitations of current research as well as indications that many nutrients exert biphasic, dose-dependent effects and that genetic polymorphisms may alter outcomes. A whole-foods approach may, therefore, be prudent.

Modulation of Metabolic Detoxification Pathways Using Foods and Food-Derived Components: A Scientific Review with Clinical Application

PubMed Central

Hodges, Romilly E.; Minich, Deanna M.

2015-01-01

Research into human biotransformation and elimination systems continues to evolve. Various clinical and in vivo studies have been undertaken to evaluate the effects of foods and food-derived components on the activity of detoxification pathways, including phase I cytochrome P450 enzymes, phase II conjugation enzymes, Nrf2 signaling, and metallothionein. This review summarizes the research in this area to date, highlighting the potential for foods and nutrients to support and/or modulate detoxification functions. Clinical applications to alter detoxification pathway activity and improve patient outcomes are considered, drawing on the growing understanding of the relationship between detoxification functions and different disease states, genetic polymorphisms, and drug-nutrient interactions. Some caution is recommended, however, due to the limitations of current research as well as indications that many nutrients exert biphasic, dose-dependent effects and that genetic polymorphisms may alter outcomes. A whole-foods approach may, therefore, be prudent. PMID:26167297

Large Advanced Space Systems (LASS) computer-aided design program additions

NASA Technical Reports Server (NTRS)

Farrell, C. E.

1982-01-01

The LSS preliminary and conceptual design requires extensive iteractive analysis because of the effects of structural, thermal, and control intercoupling. A computer aided design program that will permit integrating and interfacing of required large space system (LSS) analyses is discussed. The primary objective of this program is the implementation of modeling techniques and analysis algorithms that permit interactive design and tradeoff studies of LSS concepts. Eight software modules were added to the program. The existing rigid body controls module was modified to include solar pressure effects. The new model generator modules and appendage synthesizer module are integrated (interfaced) to permit interactive definition and generation of LSS concepts. The mass properties module permits interactive specification of discrete masses and their locations. The other modules permit interactive analysis of orbital transfer requirements, antenna primary beam n, and attitude control requirements.

WEB-GIS Decision Support System for CO2 storage

NASA Astrophysics Data System (ADS)

Gaitanaru, Dragos; Leonard, Anghel; Radu Gogu, Constantin; Le Guen, Yvi; Scradeanu, Daniel; Pagnejer, Mihaela

2013-04-01

Environmental decision support systems (DSS) paradigm evolves and changes as more knowledge and technology become available to the environmental community. Geographic Information Systems (GIS) can be used to extract, assess and disseminate some types of information, which are otherwise difficult to access by traditional methods. In the same time, with the help of the Internet and accompanying tools, creating and publishing online interactive maps has become easier and rich with options. The Decision Support System (MDSS) developed for the MUSTANG (A MUltiple Space and Time scale Approach for the quaNtification of deep saline formations for CO2 storaGe) project is a user friendly web based application that uses the GIS capabilities. MDSS can be exploited by the experts for CO2 injection and storage in deep saline aquifers. The main objective of the MDSS is to help the experts to take decisions based large structured types of data and information. In order to achieve this objective the MDSS has a geospatial objected-orientated database structure for a wide variety of data and information. The entire application is based on several principles leading to a series of capabilities and specific characteristics: (i) Open-Source - the entire platform (MDSS) is based on open-source technologies - (1) database engine, (2) application server, (3) geospatial server, (4) user interfaces, (5) add-ons, etc. (ii) Multiple database connections - MDSS is capable to connect to different databases that are located on different server machines. (iii)Desktop user experience - MDSS architecture and design follows the structure of a desktop software. (iv)Communication - the server side and the desktop are bound together by series functions that allows the user to upload, use, modify and download data within the application. The architecture of the system involves one database and a modular application composed by: (1) a visualization module, (2) an analysis module, (3) a guidelines module, and (4) a risk assessment module. The Database component is build by using the PostgreSQL and PostGIS open source technology. The visualization module allows the user to view data of CO2 injection sites in different ways: (1) geospatial visualization, (2) table view, (3) 3D visualization. The analysis module will allow the user to perform certain analysis like Injectivity, Containment and Capacity analysis. The Risk Assessment module focus on the site risk matrix approach. The Guidelines module contains the methodologies of CO2 injection and storage into deep saline aquifers guidelines.

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

PubMed Central

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

2012-01-01

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

Toward a convergence of regenerative medicine, rehabilitation, and neuroprosthetics.

PubMed

Aravamudhan, Shyam; Bellamkonda, Ravi V

2011-11-01

No effective therapeutic interventions exist for severe neural pathologies, despite significant advances in regenerative medicine, rehabilitation, and neuroprosthetics. Our current hypothesis is that a specific combination of tissue engineering, pharmacology, cell replacement, drug delivery, and electrical stimulation, together with plasticity-promoting and locomotor training (neurorehabilitation) is necessary to interact synergistically in order to activate and enable all damaged circuits. We postulate that various convergent themes exist among the different therapeutic fields. Therefore, the objective of this review is to highlight the convergent themes, which we believe have a common goal of restoring function after neural damage. The convergent themes discussed in this review include modulation of inflammation and secondary damage, encouraging endogenous repair/regeneration (using scaffolds, cell transplantation, and drug delivery), application of electrical fields to modulate healing and/or activity, and finally modulation of plasticity.

Modeling of Optoelectronic Devices

NASA Technical Reports Server (NTRS)

Li, Jian-Zhong; Woo, Alex C. (Technical Monitor)

2000-01-01

Ultrafast modulation of semiconductor quantum well (QW) laser is of technological importance for information technology. Improvement by order(s) of magnitude in data transfer rate is possible as terahertz (THz) radiation is available for heating the laser at picosecond time scale. Optical gain modulation in the QW is achieved via temperature modulation of electron-hole plasma (EHP). Applications include free-space THz communication, optical switching, and pulse generation. The EHP in the semiconductor QW is described with a two-band model. Semiconductor Bloch equations with many-body effects are used to derive a hydrodynamical model for the active QW region. Because of ultrafast carrier-carrier scatterings in the order of 50 fs, EHP follows quasiequilibrium Fermi-Dirac distributions and THz field interacts incoherently with it. Carrier-longitudinal optical (LO) phonon scatterings and coherent laser-EHP interaction are treated microscopically in our physical model. A set of hydrodynamical equations for plasma density, temperature, and laser envelop amplitude are derived and Runge-Kutta method is adopted for numerical simulation. A typical 8 nm GaAs/Al(0.3)Ga(0.7) As single QW at 300 K is used. Additional information is contained in the original extended abstract.

Fear conditioning is associated with dynamic directed functional interactions between and within the human amygdala, hippocampus, and frontal lobe.

PubMed

Liu, C C; Crone, N E; Franaszczuk, P J; Cheng, D T; Schretlen, D S; Lenz, F A

2011-08-25

The current model of fear conditioning suggests that it is mediated through modules involving the amygdala (AMY), hippocampus (HIP), and frontal lobe (FL). We now test the hypothesis that habituation and acquisition stages of a fear conditioning protocol are characterized by different event-related causal interactions (ERCs) within and between these modules. The protocol used the painful cutaneous laser as the unconditioned stimulus and ERC was estimated by analysis of local field potentials recorded through electrodes implanted for investigation of epilepsy. During the prestimulus interval of the habituation stage FL>AMY ERC interactions were common. For comparison, in the poststimulus interval of the habituation stage, only a subdivision of the FL (dorsolateral prefrontal cortex, dlPFC) still exerted the FL>AMY ERC interaction (dlFC>AMY). For a further comparison, during the poststimulus interval of the acquisition stage, the dlPFC>AMY interaction persisted and an AMY>FL interaction appeared. In addition to these ERC interactions between modules, the results also show ERC interactions within modules. During the poststimulus interval, HIP>HIP ERC interactions were more common during acquisition, and deep hippocampal contacts exerted causal interactions on superficial contacts, possibly explained by connectivity between the perihippocampal gyrus and the HIP. During the prestimulus interval of the habituation stage, AMY>AMY ERC interactions were commonly found, while interactions between the deep and superficial AMY (indirect pathway) were independent of intervals and stages. These results suggest that the network subserving fear includes distributed or widespread modules, some of which are themselves "local networks." ERC interactions between and within modules can be either static or change dynamically across intervals or stages of fear conditioning. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Cholinergic modulation of cognition: Insights from human pharmacological functional neuroimaging

PubMed Central

Bentley, Paul; Driver, Jon; Dolan, Raymond J.

2011-01-01

Evidence from lesion and cortical-slice studies implicate the neocortical cholinergic system in the modulation of sensory, attentional and memory processing. In this review we consider findings from sixty-three healthy human cholinergic functional neuroimaging studies that probe interactions of cholinergic drugs with brain activation profiles, and relate these to contemporary neurobiological models. Consistent patterns that emerge are: (1) the direction of cholinergic modulation of sensory cortex activations depends upon top-down influences; (2) cholinergic hyperstimulation reduces top-down selective modulation of sensory cortices; (3) cholinergic hyperstimulation interacts with task-specific frontoparietal activations according to one of several patterns, including: suppression of parietal-mediated reorienting; decreasing ‘effort’-associated activations in prefrontal regions; and deactivation of a ‘resting-state network’ in medial cortex, with reciprocal recruitment of dorsolateral frontoparietal regions during performance-challenging conditions; (4) encoding-related activations in both neocortical and hippocampal regions are disrupted by cholinergic blockade, or enhanced with cholinergic stimulation, while the opposite profile is observed during retrieval; (5) many examples exist of an ‘inverted-U shaped’ pattern of cholinergic influences by which the direction of functional neural activation (and performance) depends upon both task (e.g. relative difficulty) and subject (e.g. age) factors. Overall, human cholinergic functional neuroimaging studies both corroborate and extend physiological accounts of cholinergic function arising from other experimental contexts, while providing mechanistic insights into cholinergic-acting drugs and their potential clinical applications. PMID:21708219

Nonlinear Fano-Resonant Dielectric Metasurfaces

DOE PAGES

Yang, Yuanmu; Wang, Wenyi; Boulesbaa, Abdelaziz; ...

2015-10-26

Strong nonlinear light matter interaction is highly sought-after for a variety of applications including lasing and all-optical light modulation. Recently, resonant plasmonic structures have been considered promising candidates for enhancing nonlinear optical processes due to their ability to greatly enhance the optical near-field; however, their small mode volumes prevent the inherently large nonlinear susceptibility of the metal from being efficiently exploited. We present an alternative approach that utilizes a Fano-resonant silicon metasurface. The metasurface results in strong near-field enhancement within the volume of the silicon resonator while minimizing two photon absorption. Here, we measure a third harmonic generation enhancement factormore » of 1.5 105 with respect to an unpatterned silicon film and an absolute conversion efficiency of 1.2 10 6 with a peak pump intensity of 3.2 GW cm 2. The enhanced nonlinearity, combined with a sharp linear transmittance spectrum, results in transmission modulation with a modulation depth of 36%. Finally, the modulation mechanism is studied by pump probe experiments« less

Decoding telomere protein Rap1: Its telomeric and nontelomeric functions and potential implications in diabetic cardiomyopathy.

PubMed

Cai, Yin; Kandula, Vidya; Kosuru, Ramoji; Ye, Xiaodong; Irwin, Michael G; Xia, Zhengyuan

2017-10-02

Mammalian Rap1, the most conserved telomere-interacting protein, beyond its role within nucleus for the maintenance of telomeric functions, is also well known for its pleiotropic functions in various physiological and pathological conditions associated with metabolism, inflammation and oxidative stress. For all these, nowadays Rap1 is the subject of critical investigations aimed to unveil its molecular signaling pathways and to scrutinize the applicability of its modulation as a promising therapeutic strategy with clinical relevance. However, the underlying intimate mechanisms of Rap1 are not extensively studied, but any modulation of this protein level has been associated with pathologies like inflammation, oxidative stress and deregulated metabolism. This is considerably important in light of the recent discovery of Rap1 modulation in diseases like cancer and cardiac metabolic disorders. In this review, we focus on both the telomeric and nontelomeric functions of Rap1 and its modulation in various health risks, especially on the heart.

Electronic Module Design with Scientifically Character-Charged Approach on Kinematics Material Learning to Improve Holistic Competence of High School Students in 10th Grade

NASA Astrophysics Data System (ADS)

Anggraini, R.; Darvina, Y.; Amir, H.; Murtiani, M.; Yulkifli, Y.

2018-04-01

The availability of modules in schools is currently lacking. Learners have not used the module as a source in the learning process. In accordance with the demands of the 2013 curriculum, that learning should be conducted using a scientific approach and loaded with character values as well as learning using interactive learning resources. The solution of this problem is to create an interactive module with a scientifically charged character approach. This interactive module can be used by learners outside the classroom or in the classroom. This interactive module contains straight motion material, parabolic motion and circular motion of high school physics class X semester 1. The purpose of this research is to produce an interactive module with a scientific approach charged with character and determine the validity and practicality. The research is Research and Development. This study was conducted only until the validity test and practice test. The validity test was conducted by three lecturers of Physics of FMIPA UNP as experts. The instruments used in this research are validation sheet and worksheet sheet. Data analysis technique used is product validity analysis. The object of this research is electronic module, while the subject of this research is three validator.

Learning through student-authored interactive media: A mixed methods exploration

NASA Astrophysics Data System (ADS)

Sakai-Miller, Sharon (Sam)

2009-12-01

The purpose of this study was to improve student achievement in science and proficiency in information and communication technologies (ICT), which are vital 21st century workforce skills. Instead of isolating the issues, the study proposed an integrated solution that applied the constructivist approach to help students learn about a unit in biology using three software applications to create interactive, self-correcting eModules within a two-week period. Research questions focused on the effectiveness of the instructional strategy, the experience of students authoring eModules, obstacles they encountered, and the role of the teacher. Fifty-one out of the possible 55 eleventh and twelfth grade students in the two Advanced Biology classes consented to participate in the study. A comparison of pre and post-test scores showed an average 547% improvement. Students with low initial scores of 10% or less improved an average of 1229%. Ten students (20%) went from 20% or below on the pre-test to 80% or above on the post-test, and were analyzed as a subgroup called "big gainers." Student journals and exit surveys were explored to understand the process students followed to develop eModules. The majority of student responses in the exit survey (85%) described the overall experience as a positive one. Journals showed how students were able to follow the process of creating a concept map using Inspiration software, converting the outline into a PowerPoint slide show, editing the slides and importing them into Adobe Captivate files, inserting self-correcting questions, completing their eModules, and submitting them to their teacher. Students identified obstacles they encountered to help them to problem solve and provided data for improving the instructional strategy. Addressing technology learning objectives within the context and pacing of a content area class was accomplished, but it required providing a collaborative learning environment, an appropriate task, mediating tools, and assessment. The data analysis suggests that the instructional strategy of student-authored eModules had a positive impact on learning science content and ICT proficiencies. Historically students have been consumers of interactive media or producers of presentational media. This study suggests that they will learn more when they are the authors of interactive media.

Cross-Modulated Amplitudes and Frequencies Characterize Interacting Components in Complex Systems

NASA Astrophysics Data System (ADS)

Gans, Fabian; Schumann, Aicko Y.; Kantelhardt, Jan W.; Penzel, Thomas; Fietze, Ingo

2009-03-01

The dynamics of complex systems is characterized by oscillatory components on many time scales. To study the interactions between these components we analyze the cross modulation of their instantaneous amplitudes and frequencies, separating synchronous and antisynchronous modulation. We apply our novel technique to brain-wave oscillations in the human electroencephalogram and show that interactions between the α wave and the δ or β wave oscillators as well as spatial interactions can be quantified and related with physiological conditions (e.g., sleep stages). Our approach overcomes the limitation to oscillations with similar frequencies and enables us to quantify directly nonlinear effects such as positive or negative frequency modulation.

LAnd surface remote sensing Products VAlidation System (LAPVAS) and its preliminary application

NASA Astrophysics Data System (ADS)

Lin, Xingwen; Wen, Jianguang; Tang, Yong; Ma, Mingguo; Dou, Baocheng; Wu, Xiaodan; Meng, Lumin

2014-11-01

The long term record of remote sensing product shows the land surface parameters with spatial and temporal change to support regional and global scientific research widely. Remote sensing product with different sensors and different algorithms is necessary to be validated to ensure the high quality remote sensing product. Investigation about the remote sensing product validation shows that it is a complex processing both the quality of in-situ data requirement and method of precision assessment. A comprehensive validation should be needed with long time series and multiple land surface types. So a system named as land surface remote sensing product is designed in this paper to assess the uncertainty information of the remote sensing products based on a amount of in situ data and the validation techniques. The designed validation system platform consists of three parts: Validation databases Precision analysis subsystem, Inter-external interface of system. These three parts are built by some essential service modules, such as Data-Read service modules, Data-Insert service modules, Data-Associated service modules, Precision-Analysis service modules, Scale-Change service modules and so on. To run the validation system platform, users could order these service modules and choreograph them by the user interactive and then compete the validation tasks of remote sensing products (such as LAI ,ALBEDO ,VI etc.) . Taking SOA-based architecture as the framework of this system. The benefit of this architecture is the good service modules which could be independent of any development environment by standards such as the Web-Service Description Language(WSDL). The standard language: C++ and java will used as the primary programming language to create service modules. One of the key land surface parameter, albedo, is selected as an example of the system application. It is illustrated that the LAPVAS has a good performance to implement the land surface remote sensing product validation.

Interactive simulation system for artificial ventilation on the internet: virtual ventilator.

PubMed

Takeuchi, Akihiro; Abe, Tadashi; Hirose, Minoru; Kamioka, Koichi; Hamada, Atsushi; Ikeda, Noriaki

2004-12-01

To develop an interactive simulation system "virtual ventilator" that demonstrates the dynamics of pressure and flow in the respiratory system under the combination of spontaneous breathing, ventilation modes, and ventilator options. The simulation system was designed to be used by unexperienced health care professionals as a self-training tool. The system consists of a simulation controller and three modules: respiratory, spontaneous breath, and ventilator. The respiratory module models the respiratory system by three resistances representing the main airway, the right and left lungs, and two compliances also representing the right and left lungs. The spontaneous breath module generates inspiratory negative pressure produced by a patient. The ventilator module generates driving force of pressure or flow according to the combination of the ventilation mode and options. These forces are given to the respiratory module through the simulation controller. The simulation system was developed using HTML, VBScript (3000 lines, 100 kB) and ActiveX control (120 kB), and runs on Internet Explorer (5.5 or higher). The spontaneous breath is defined by a frequency, amplitude and inspiratory patterns in the spontaneous breath module. The user can construct a ventilation mode by setting a control variable, phase variables (trigger, limit, and cycle), and options. Available ventilation modes are: controlled mechanical ventilation (CMV), continuous positive airway pressure, synchronized intermittent mandatory ventilation (SIMV), pressure support ventilation (PSV), SIMV + PSV, pressure-controlled ventilation (PCV), pressure-regulated volume control (PRVC), proportional assisted ventilation, mandatory minute ventilation (MMV), bilevel positive airway pressure (BiPAP). The simulation system demonstrates in a graph and animation the airway pressure, flow, and volume of the respiratory system during mechanical ventilation both with and without spontaneous breathing. We developed a web application that demonstrated the respiratory mechanics and the basic theory of ventilation mode.

[The interactive neuroanatomical simulation and practical application of frontotemporal transsylvian exposure in neurosurgery].

PubMed

Balogh, Attila; Czigléczki, Gábor; Papal, Zsolt; Preul, Mark C; Banczerowski, Péter

2014-11-30

There is an increased need for new digital education tools in neurosurgical training. Illustrated textbooks offer anatomic and technical reference but do not substitute hands-on experience provided by surgery or cadaver dissection. Due to limited availability of cadaver dissections the need for development of simulation tools has been augmented. We explored simulation technology for producing virtual reality-like reconstructions of simulated surgical approaches on cadaver. Practical application of the simulation tool has been presented through frontotemporal transsylvian exposure. The dissections were performed on two cadaveric heads. Arteries and veins were prepared and injected with colorful silicon rubber. The heads were rigidly fixed in Mayfield headholder. A robotic microscope with two digital cameras in inverted cone method of image acquisition was used to capture images around a pivot point in several phases of dissections. Multilayered, high-resolution images have been built into interactive 4D environment by custom developed software. We have developed the simulation module of the frontotemporal transsylvian approach. The virtual specimens can be rotated or tilted to any selected angles and examined from different surgical perspectives at any stage of dissections. Important surgical issues such as appropriate head positioning or surgical maneuvers to expose deep situated neuroanatomic structures can be simulated and studied by using the module. The simulation module of the frontotemporal transsylvian exposure helps to examine effect of head positioning on the visibility of deep situated neuroanatomic structures and study surgical maneuvers required to achieve optimal exposure of deep situated anatomic structures. The simulation program is a powerful tool to study issues of preoperative planning and well suited for neurosurgical training.

Chemical Synthesis of Hydrocarbon-Stapled Peptides for Protein Interaction Research and Therapeutic Targeting

PubMed Central

Bird, Gregory H.; Crannell, W. Christian; Walensky, Loren D.

2016-01-01

The peptide alpha-helix represents one of Nature’s most featured protein shapes and is employed in a diversity of protein architectures, spanning the very cytoskeletal infrastructure of the cell to the most intimate contact points between crucial signaling proteins. By installing an all-hydrocarbon crosslink into native sequences, we recapitulate the shape and biological activity of natural peptide alpha-helices, yielding a chemical toolbox to both interrogate the protein interactome and modulate interaction networks for potential therapeutic benefit. Here, we describe our latest approach to synthesizing Stabilized Alpha-Helices (SAH) corresponding to key protein interaction domains. We emphasize a stepwise approach to the production of crosslinking non-natural amino acids, their incorporation into peptide templates, and the application of ruthenium-catalyzed ring closing metathesis to generate hydrocarbon-stapled peptides. Through facile derivatization and functionalization steps, SAHs can be tailored for a broad range of applications in biochemical, structural, proteomic, cellular and in vivo studies. PMID:23801563

The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide.

PubMed

Abramov, Y A; Volkov, A; Wu, G; Coppens, P

2000-11-01

A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods.

From systems biology to dynamical neuropharmacology: proposal for a new methodology.

PubMed

Erdi, P; Kiss, T; Tóth, J; Ujfalussy, B; Zalányi, L

2006-07-01

The concepts and methods of systems biology are extended to neuropharmacology in order to test and design drugs for the treatment of neurological and psychiatric disorders. Computational modelling by integrating compartmental neural modelling techniques and detailed kinetic descriptions of pharmacological modulation of transmitter-receptor interaction is offered as a method to test the electrophysiological and behavioural effects of putative drugs. Even more, an inverse method is suggested as a method for controlling a neural system to realise a prescribed temporal pattern. In particular, as an application of the proposed new methodology, a computational platform is offered to analyse the generation and pharmacological modulation of theta rhythm related to anxiety.

Modelface: an Application Programming Interface (API) for Homology Modeling Studies Using Modeller Software

PubMed Central

Sakhteman, Amirhossein; Zare, Bijan

2016-01-01

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures are also implemented inside Modelface. The API is a simple batch based application with no memory occupation and is free of charge for academic use. The application is also able to repair missing atom types in the PDB structures making it suitable for many molecular modeling studies such as docking and molecular dynamic simulation. Some successful instances of modeling studies using Modelface are also reported. PMID:28243276

Update 0.2 to "pysimm: A python package for simulation of molecular systems"

NASA Astrophysics Data System (ADS)

Demidov, Alexander G.; Fortunato, Michael E.; Colina, Coray M.

2018-01-01

An update to the pysimm Python molecular simulation API is presented. A major part of the update is the implementation of a new interface with CASSANDRA - a modern, versatile Monte Carlo molecular simulation program. Several significant improvements in the LAMMPS communication module that allow better and more versatile simulation setup are reported as well. An example of an application implementing iterative CASSANDRA-LAMMPS interaction is illustrated.

Identification of New Potential Scientific and Technology Areas for DoD Application. Summary of Activities

DTIC Science & Technology

1986-07-31

designer will be able to more rapid- ly assemble a total software package from perfected modules that can be easily de - bugged or replaced with more...antinuclear interactions e. gravitational effects of antimatter 2. possible machine parameters and lattice design 3. electron and stochastic cooling needs 4...implementation, reliability requirements; development of design environments and of experimental methodology; technology transfer methods from

ASTROS Enhancements. Volume I- ASTRO User’s Manual

DTIC Science & Technology

1993-03-01

alternative functions. The mechanisms by which these more advanced features are invoked are included in this manual but no attempt is made to provide... advanced topics are treated in the Programmer’s and Application Manuals which document the individual modules in the system and their interactions...of the more advanced features of the system without cluttering the discussion with details of the input structures. The detailed documentation of the

Web-4D-QSAR: A web-based application to generate 4D-QSAR descriptors.

PubMed

Ataide Martins, João Paulo; Rougeth de Oliveira, Marco Antônio; Oliveira de Queiroz, Mário Sérgio

2018-06-05

A web-based application is developed to generate 4D-QSAR descriptors using the LQTA-QSAR methodology, based on molecular dynamics (MD) trajectories and topology information retrieved from the GROMACS package. The LQTAGrid module calculates the intermolecular interaction energies at each grid point, considering probes and all aligned conformations resulting from MD simulations. These interaction energies are the independent variables or descriptors employed in a QSAR analysis. A friendly front end web interface, built using the Django framework and Python programming language, integrates all steps of the LQTA-QSAR methodology in a way that is transparent to the user, and in the backend, GROMACS and LQTAGrid are executed to generate 4D-QSAR descriptors to be used later in the process of QSAR model building. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

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

W. Lynn Watney; John H. Doveton

GEMINI (Geo-Engineering Modeling through Internet Informatics) is a public-domain web application focused on analysis and modeling of petroleum reservoirs and plays (http://www.kgs.ukans.edu/Gemini/index.html). GEMINI creates a virtual project by ''on-the-fly'' assembly and analysis of on-line data either from the Kansas Geological Survey or uploaded from the user. GEMINI's suite of geological and engineering web applications for reservoir analysis include: (1) petrofacies-based core and log modeling using an interactive relational rock catalog and log analysis modules; (2) a well profile module; (3) interactive cross sections to display ''marked'' wireline logs; (4) deterministic gridding and mapping of petrophysical data; (5) calculation and mappingmore » of layer volumetrics; (6) material balance calculations; (7) PVT calculator; (8) DST analyst, (9) automated hydrocarbon association navigator (KHAN) for database mining, and (10) tutorial and help functions. The Kansas Hydrocarbon Association Navigator (KHAN) utilizes petrophysical databases to estimate hydrocarbon pay or other constituent at a play- or field-scale. Databases analyzed and displayed include digital logs, core analysis and photos, DST, and production data. GEMINI accommodates distant collaborations using secure password protection and authorized access. Assembled data, analyses, charts, and maps can readily be moved to other applications. GEMINI's target audience includes small independents and consultants seeking to find, quantitatively characterize, and develop subtle and bypassed pays by leveraging the growing base of digital data resources. Participating companies involved in the testing and evaluation of GEMINI included Anadarko, BP, Conoco-Phillips, Lario, Mull, Murfin, and Pioneer Resources.« less

The Impact of an Interactive Statistics Module on Novices' Development of Scientific Process Skills and Attitudes in a First-Semester Research Foundations Course.

PubMed

Marsan, Lynnsay A; D'Arcy, Christina E; Olimpo, Jeffrey T

2016-12-01

Evidence suggests that incorporating quantitative reasoning exercises into existent curricular frameworks within the science, technology, engineering, and mathematics (STEM) disciplines is essential for novices' development of conceptual understanding and process skills in these domains. Despite this being the case, such studies acknowledge that students often experience difficulty in applying mathematics in the context of scientific problems. To address this concern, the present study sought to explore the impact of active demonstrations and critical reading exercises on novices' comprehension of basic statistical concepts, including hypothesis testing, experimental design, and interpretation of research findings. Students first engaged in a highly interactive height activity that served to intuitively illustrate normal distribution, mean, standard deviation, and sample selection criteria. To enforce practical applications of standard deviation and p -value, student teams were subsequently assigned a figure from a peer-reviewed primary research article and instructed to evaluate the trustworthiness of the data. At the conclusion of this exercise, students presented their evaluations to the class for open discussion and commentary. Quantitative assessment of pre- and post-module survey data indicated a statistically significant increase both in students' scientific reasoning and process skills and in their self-reported confidence in understanding the statistical concepts presented in the module. Furthermore, data indicated that the majority of students (>85%) found the module both interesting and helpful in nature. Future studies will seek to develop additional, novel exercises within this area and to evaluate the impact of such modules across a variety of STEM and non-STEM contexts.

The Impact of an Interactive Statistics Module on Novices’ Development of Scientific Process Skills and Attitudes in a First-Semester Research Foundations Course†

PubMed Central

Marsan, Lynnsay A.; D’Arcy, Christina E.; Olimpo, Jeffrey T.

2016-01-01

Evidence suggests that incorporating quantitative reasoning exercises into existent curricular frameworks within the science, technology, engineering, and mathematics (STEM) disciplines is essential for novices’ development of conceptual understanding and process skills in these domains. Despite this being the case, such studies acknowledge that students often experience difficulty in applying mathematics in the context of scientific problems. To address this concern, the present study sought to explore the impact of active demonstrations and critical reading exercises on novices’ comprehension of basic statistical concepts, including hypothesis testing, experimental design, and interpretation of research findings. Students first engaged in a highly interactive height activity that served to intuitively illustrate normal distribution, mean, standard deviation, and sample selection criteria. To enforce practical applications of standard deviation and p-value, student teams were subsequently assigned a figure from a peer-reviewed primary research article and instructed to evaluate the trustworthiness of the data. At the conclusion of this exercise, students presented their evaluations to the class for open discussion and commentary. Quantitative assessment of pre- and post-module survey data indicated a statistically significant increase both in students’ scientific reasoning and process skills and in their self-reported confidence in understanding the statistical concepts presented in the module. Furthermore, data indicated that the majority of students (>85%) found the module both interesting and helpful in nature. Future studies will seek to develop additional, novel exercises within this area and to evaluate the impact of such modules across a variety of STEM and non-STEM contexts. PMID:28101271

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

Kirschner, Matthew S.; Ding, Wendu; Li, Yuxiu

In this study, we demonstrate that coherent acoustic phonons derived from plasmonic nanoparticles can modulate electronic interactions with proximal excitonic molecular species. A series of gold bipyramids with systematically varied aspect ratios and corresponding localized surface plasmon resonance energies, functionalized with a J-aggregated thiacarbocyanine dye molecule, produce two hybridized states that exhibit clear anti-crossing behavior with a Rabi splitting energy of 120 meV. In metal nanoparticles, photoexcitation generates coherent acoustic phonons that cause oscillations in the plasmon resonance energy. In the coupled system, these photo-generated oscillations alter the metal nanoparticle’s energetic contribution to the hybridized system and, as a result,more » change the coupling between the plasmon and exciton. We demonstrate that such modulations in the hybridization is consistent across a wide range of bipyramid ensembles. We also use Finite-Difference Time Domain calculations to develop a simple model describing this behavior. Lastly, such oscillatory plasmonic-excitonic nanomaterials (OPENs) offer a route to manipulate and dynamically-tune the interactions of plasmonic/excitonic systems and unlock a range of potential applications.« less

imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel

PubMed Central

Grapov, Dmitry; Newman, John W.

2012-01-01

Summary: Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks. Availability and implementation: Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010). Contact: John.Newman@ars.usda.gov Supplementary Information: Installation instructions, tutorials and users manual are available at http://sourceforge.net/projects/imdev/. PMID:22815358

Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle

PubMed Central

2013-01-01

RNA–protein interactions are vital throughout the HIV-1 life cycle for the successful production of infectious virus particles. One such essential RNA–protein interaction occurs between the full-length genomic viral RNA and the major structural protein of the virus. The initial interaction is between the Gag polyprotein and the viral RNA packaging signal (psi or Ψ), a highly conserved RNA structural element within the 5′-UTR of the HIV-1 genome, which has gained attention as a potential therapeutic target. Here, we report the application of a target-based assay to identify small molecules, which modulate the interaction between Gag and Ψ. We then demonstrate that one such molecule exhibits potent inhibitory activity in a viral replication assay. The mode of binding of the lead molecules to the RNA target was characterized by 1H NMR spectroscopy. PMID:24358934

Abstract ID: 240 A probabilistic-based nuclear reaction model for Monte Carlo ion transport in particle therapy.

PubMed

Maria Jose, Gonzalez Torres; Jürgen, Henniger

2018-01-01

In order to expand the Monte Carlo transport program AMOS to particle therapy applications, the ion module is being developed in the radiation physics group (ASP) at the TU Dresden. This module simulates the three main interactions of ions in matter for the therapy energy range: elastic scattering, inelastic collisions and nuclear reactions. The simulation of the elastic scattering is based on the Binary Collision Approximation and the inelastic collisions on the Bethe-Bloch theory. The nuclear reactions, which are the focus of the module, are implemented according to a probabilistic-based model developed in the group. The developed model uses probability density functions to sample the occurrence of a nuclear reaction given the initial energy of the projectile particle as well as the energy at which this reaction will take place. The particle is transported until the reaction energy is reached and then the nuclear reaction is simulated. This approach allows a fast evaluation of the nuclear reactions. The theory and application of the proposed model will be addressed in this presentation. The results of the simulation of a proton beam colliding with tissue will also be presented. Copyright © 2017.

Scaling vectors of attoJoule per bit modulators

NASA Astrophysics Data System (ADS)

Sorger, Volker J.; Amin, Rubab; Khurgin, Jacob B.; Ma, Zhizhen; Dalir, Hamed; Khan, Sikandar

2018-01-01

Electro-optic modulation performs the conversion between the electrical and optical domain with applications in data communication for optical interconnects, but also for novel optical computing algorithms such as providing nonlinearity at the output stage of optical perceptrons in neuromorphic analog optical computing. While resembling an optical transistor, the weak light-matter-interaction makes modulators 105 times larger compared to their electronic counterparts. Since the clock frequency for photonics on-chip has a power-overhead sweet-spot around tens of GHz, ultrafast modulation may only be required in long-distance communication, not for short on-chip links. Hence, the search is open for power-efficient on-chip modulators beyond the solutions offered by foundries to date. Here, we show scaling vectors towards atto-Joule per bit efficient modulators on-chip as well as some experimental demonstrations of novel plasmonic modulators with sub-fJ/bit efficiencies. Our parametric study of placing different actively modulated materials into plasmonic versus photonic optical modes shows that 2D materials overcompensate their miniscule modal overlap by their unity-high index change. Furthermore, we reveal that the metal used in plasmonic-based modulators not only serves as an electrical contact, but also enables low electrical series resistances leading to near-ideal capacitors. We then discuss the first experimental demonstration of a photon-plasmon-hybrid graphene-based electro-absorption modulator on silicon. The device shows a sub-1 V steep switching enabled by near-ideal electrostatics delivering a high 0.05 dB V-1 μm-1 performance requiring only 110 aJ/bit. Improving on this demonstration, we discuss a plasmonic slot-based graphene modulator design, where the polarization of the plasmonic mode aligns with graphene’s in-plane dimension; where a push-pull dual-gating scheme enables 2 dB V-1 μm-1 efficient modulation allowing the device to be just 770 nm short for 3 dB small signal modulation. Lastly, comparing the switching energy of transistors to modulators shows that modulators based on emerging materials and plasmonic-silicon hybrid integration perform on-par relative to their electronic counter parts. This in turn allows for a device-enabled two orders-of-magnitude improvement of electrical-optical co-integrated network-on-chips over electronic-only architectures. The latter opens technological opportunities in cognitive computing, dynamic data-driven applications systems, and optical analog computer engines including neuromorphic photonic computing.

Production of bioproducts by endophytic fungi: chemical ecology, biotechnological applications, bottlenecks, and solutions.

PubMed

Yan, Lu; Zhao, Haobin; Zhao, Xixi; Xu, Xiaoguang; Di, Yichao; Jiang, Chunmei; Shi, Junling; Shao, Dongyan; Huang, Qingsheng; Yang, Hui; Jin, Mingliang

2018-05-29

Endophytes are microorganisms that colonize the interior of host plants without causing apparent disease. They have been widely studied for their ability to modulate relationships between plants and biotic/abiotic stresses, often producing valuable secondary metabolites that can affect host physiology. Owing to the advantages of microbial fermentation over plant/cell cultivation and chemical synthesis, endophytic fungi have received significant attention as a mean for secondary metabolite production. This article summarizes currently reported results on plant-endophyte interaction hypotheses and highlights the biotechnological applications of endophytic fungi and their metabolites in agriculture, environment, biomedicine, energy, and biocatalysts. Current bottlenecks in industrial development and commercial applications as well as possible solutions are also discussed.

Applications of systems approaches in the study of rheumatic diseases.

PubMed

Kim, Ki-Jo; Lee, Saseong; Kim, Wan-Uk

2015-03-01

The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.

Carboxysomes: metabolic modules for CO 2 fixation

DOE PAGES

Turmo, Aiko; Gonzalez-Esquer, Cesar Raul; Kerfeld, Cheryl A.

2017-08-14

The carboxysome is a bacterial microcompartment encapsulating the enzymes carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase. As the site of CO 2 fixation, it serves an essential role in the carbon dioxide concentrating mechanism of many chemoautotrophs and all cyanobacteria. Carboxysomes and other bacterial microcompartments self-assemble through specific protein–protein interactions that are typically mediated by conserved protein domains. In this review, we frame our current understanding of carboxysomes in the context of their component protein domains with their inherent function as the ‘building blocks’ of carboxysomes. These building blocks are organized in genetic modules (conserved chromosomal loci) that encode for carboxysomes andmore » ancillary proteins essential for the integration of the organelle with the rest of cellular metabolism. This conceptual framework provides the foundation for ‘plug-and-play’ engineering of carboxysomes as CO 2 fixation modules in a variety of biotechnological applications.« less

Virtual patient instruction for dental students: can it improve dental care access for persons with special needs?

PubMed

Sanders, Carla; Kleinert, Harold L; Boyd, Sara E; Herren, Chris; Theiss, Lynn; Mink, John

2008-01-01

An interactive, virtual-patient module was produced on compact disc (CD-ROM) in response to the critical need to increase dental students' clinical exposure to patients with developmental disabilities. A content development team consisting of dental faculty members, parents of children with developmental disabilities, an individual with a developmental disability, and educational specialists developed the interactive, virtual-patient module. The module focused on a young man with congenital deafblindness presenting as a new patient with a painful molar. Students were required to make decisions regarding clinical interactions throughout the module. Differences in both comfort and knowledge level were measured pre- and post-module completion, as well as the dental students' overall satisfaction with the learning experience. Significant results were obtained in students' perceived comfort and knowledge base. Participants reported overall satisfaction using the modules. This study demonstrated that an interactive, multi-media (CD-ROM), virtual patient learning module for dental students could be an effective tool in providing students needed clinical exposure to patients with developmental disabilities.

Cellulosome-based, Clostridium-derived multi-functional enzyme complexes for advanced biotechnology tool development: advances and applications.

PubMed

Hyeon, Jeong Eun; Jeon, Sang Duck; Han, Sung Ok

2013-11-01

The cellulosome is one of nature's most elegant and elaborate nanomachines and a key biological and biotechnological macromolecule that can be used as a multi-functional protein complex tool. Each protein module in the cellulosome system is potentially useful in an advanced biotechnology application. The high-affinity interactions between the cohesin and dockerin domains can be used in protein-based biosensors to improve both sensitivity and selectivity. The scaffolding protein includes a carbohydrate-binding module (CBM) that attaches strongly to cellulose substrates and facilitates the purification of proteins fused with the dockerin module through a one-step CBM purification method. Although the surface layer homology (SLH) domain of CbpA is not present in other strains, replacement of the cell surface anchoring domain allows a foreign protein to be displayed on the surface of other strains. The development of a hydrolysis enzyme complex is a useful strategy for consolidated bioprocessing (CBP), enabling microorganisms with biomass hydrolysis activity. Thus, the development of various configurations of multi-functional protein complexes for use as tools in whole-cell biocatalyst systems has drawn considerable attention as an attractive strategy for bioprocess applications. This review provides a detailed summary of the current achievements in Clostridium-derived multi-functional complex development and the impact of these complexes in various areas of biotechnology. Copyright © 2013 Elsevier Inc. All rights reserved.

Applied virtual reality at the Research Triangle Institute

NASA Technical Reports Server (NTRS)

Montoya, R. Jorge

1994-01-01

Virtual Reality (VR) is a way for humans to use computers in visualizing, manipulating and interacting with large geometric data bases. This paper describes a VR infrastructure and its application to marketing, modeling, architectural walk through, and training problems. VR integration techniques used in these applications are based on a uniform approach which promotes portability and reusability of developed modules. For each problem, a 3D object data base is created using data captured by hand or electronically. The object's realism is enhanced through either procedural or photo textures. The virtual environment is created and populated with the data base using software tools which also support interactions with and immersivity in the environment. These capabilities are augmented by other sensory channels such as voice recognition, 3D sound, and tracking. Four applications are presented: a virtual furniture showroom, virtual reality models of the North Carolina Global TransPark, a walk through the Dresden Fraunenkirche, and the maintenance training simulator for the National Guard.

BmP02 Atypically Delays Kv4.2 Inactivation: Implication for a Unique Interaction between Scorpion Toxin and Potassium Channel

PubMed Central

Wu, Bin; Zhu, Yan; Shi, Jian; Tao, Jie; Ji, Yonghua

2016-01-01

BmP02, a short-chain peptide with 28 residues from the venom of Chinese scorpion Buthus martensi Karsch, has been reported to inhibit the transient outward potassium currents (Ito) in rat ventricular muscle cells. However, it remains unclear whether BmP02 modulates the Kv4.2 channel, one of the main contributors to Ito. The present study investigated the effects of BmP02 on Kv4.2 kinetics and its underlying molecular mechanism. The electrophysiological recordings showed that the inactivation of Kv4.2 expressed in HEK293T cells was significantly delayed by BmP02 in a dose-response manner with EC50 of ~850 nM while the peak current, activation and voltage-dependent inactivation of Kv4.2 were not affected. Meanwhile, the recovery from inactivation of Kv4.2 was accelerated and the deactivation was slowed after the application of BmP02. The site-directed mutagenesis combined with computational modelling identified that K347 and K353, located in the turret motif of the Kv4.2, and E4/E5, D20/D21 in BmP02 are key residues to interact with BmP02 through electrostatic force. These findings not only reveal a novel interaction between Kv4.2 channel and its peptidyl modulator, but also provide valuable information for design of highly-selective Kv4.2 modulators. PMID:27690098

Quantum coherent optical phase modulation in an ultrafast transmission electron microscope.

PubMed

Feist, Armin; Echternkamp, Katharina E; Schauss, Jakob; Yalunin, Sergey V; Schäfer, Sascha; Ropers, Claus

2015-05-14

Coherent manipulation of quantum systems with light is expected to be a cornerstone of future information and communication technology, including quantum computation and cryptography. The transfer of an optical phase onto a quantum wavefunction is a defining aspect of coherent interactions and forms the basis of quantum state preparation, synchronization and metrology. Light-phase-modulated electron states near atoms and molecules are essential for the techniques of attosecond science, including the generation of extreme-ultraviolet pulses and orbital tomography. In contrast, the quantum-coherent phase-modulation of energetic free-electron beams has not been demonstrated, although it promises direct access to ultrafast imaging and spectroscopy with tailored electron pulses on the attosecond scale. Here we demonstrate the coherent quantum state manipulation of free-electron populations in an electron microscope beam. We employ the interaction of ultrashort electron pulses with optical near-fields to induce Rabi oscillations in the populations of electron momentum states, observed as a function of the optical driving field. Excellent agreement with the scaling of an equal-Rabi multilevel quantum ladder is obtained, representing the observation of a light-driven 'quantum walk' coherently reshaping electron density in momentum space. We note that, after the interaction, the optically generated superposition of momentum states evolves into a train of attosecond electron pulses. Our results reveal the potential of quantum control for the precision structuring of electron densities, with possible applications ranging from ultrafast electron spectroscopy and microscopy to accelerator science and free-electron lasers.

Quantum coherent optical phase modulation in an ultrafast transmission electron microscope

NASA Astrophysics Data System (ADS)

Feist, Armin; Echternkamp, Katharina E.; Schauss, Jakob; Yalunin, Sergey V.; Schäfer, Sascha; Ropers, Claus

2015-05-01

Coherent manipulation of quantum systems with light is expected to be a cornerstone of future information and communication technology, including quantum computation and cryptography. The transfer of an optical phase onto a quantum wavefunction is a defining aspect of coherent interactions and forms the basis of quantum state preparation, synchronization and metrology. Light-phase-modulated electron states near atoms and molecules are essential for the techniques of attosecond science, including the generation of extreme-ultraviolet pulses and orbital tomography. In contrast, the quantum-coherent phase-modulation of energetic free-electron beams has not been demonstrated, although it promises direct access to ultrafast imaging and spectroscopy with tailored electron pulses on the attosecond scale. Here we demonstrate the coherent quantum state manipulation of free-electron populations in an electron microscope beam. We employ the interaction of ultrashort electron pulses with optical near-fields to induce Rabi oscillations in the populations of electron momentum states, observed as a function of the optical driving field. Excellent agreement with the scaling of an equal-Rabi multilevel quantum ladder is obtained, representing the observation of a light-driven `quantum walk' coherently reshaping electron density in momentum space. We note that, after the interaction, the optically generated superposition of momentum states evolves into a train of attosecond electron pulses. Our results reveal the potential of quantum control for the precision structuring of electron densities, with possible applications ranging from ultrafast electron spectroscopy and microscopy to accelerator science and free-electron lasers.

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

PubMed

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

2017-07-13

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

Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes.

PubMed

Jagdale, Shounak S; Joshi, Rakesh S

2018-04-01

Viruses represent some of the deadliest pathogens known to science. Recently they have been reported to have mutualistic interactions with their hosts, providing them direct or indirect benefits. The mutualism and symbiogenesis of such viruses with lower eukaryotic partners such as fungi, yeast, and insects have been reported but the full mechanism of interaction often remains an enigma. In many instances, these viral interactions provide resistance against several biotic and abiotic stresses, which could be the prime reason for the ecological success and positive selection of the hosts. These viruses modulate host metabolism and behavior, so both can obtain maximum benefits from the environment. They bring about micro- and macro-level changes in the hosts, benefiting their adaptation, reproduction, development, and survival. These virus-host interactions can be bilateral or tripartite with a variety of interacting partners. Exploration of these interactions can shed light on one of the well-coordinated biological phenomena of co-evolution and can be highly utilized for various applications in agriculture, fermentation and the pharmaceutical industries.

Using Surface Enhanced Raman Scattering to Analyze the Interactions of Protein Receptors with Bacterial Quorum Sensing Modulators

PubMed Central

2015-01-01

Many members of the LuxR family of quorum sensing (QS) transcriptional activators, including LasR of Pseudomonas aeruginosa, are believed to require appropriate acyl-homoserine lactone (acyl-HSL) ligands to fold into an active conformation. The failure to purify ligand-free LuxR homologues in nonaggregated form at the high concentrations required for their structural characterization has limited the understanding of the mechanisms by which QS receptors are activated. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can be applied to study proteins at extremely low concentrations in their active state. The high sensitivity of SERS has allowed us to detect molecular interactions between the ligand-binding domain of LasR (LasRLBD) as a soluble apoprotein and modulators of P. aeruginosa QS. We found that QS activators and inhibitors produce differential SERS fingerprints in LasRLBD, and in combination with molecular docking analysis provide insight into the relevant interaction mechanism. This study reveals signal-specific structural changes in LasR upon ligand binding, thereby confirming the applicability of SERS to analyze ligand-induced conformational changes in proteins. PMID:25927541

Unexpected behavior of some nitric oxide modulators under cadmium excess in plant tissue.

PubMed

Kováčik, Jozef; Babula, Petr; Klejdus, Bořivoj; Hedbavny, Josef; Jarošová, Markéta

2014-01-01

Various nitric oxide modulators (NO donors--SNP, GSNO, DEA NONOate and scavengers--PTIO, cPTIO) were tested to highlight the role of NO under Cd excess in various ontogenetic stages of chamomile (Matricaria chamomilla). Surprisingly, compared to Cd alone, SNP and PTIO elevated Cd uptake (confirmed also by PhenGreen staining) but depleted glutathione (partially ascorbic acid) and phytochelatins PC2 and PC3 in both older plants (cultured hydroponically) and seedlings (cultured in deionised water). Despite these anomalous impacts, fluorescence staining of NO and ROS confirmed predictable assumptions and revealed reciprocal changes (decrease in NO but increase in ROS after PTIO addition and the opposite after SNP application). Subsequent tests using alternative modulators and seedlings confirmed changes to NO and ROS after application of GSNO and DEA NONOate as mentioned above for SNP while cPTIO altered only NO level (depletion). On the contrary to SNP and PTIO, GSNO, DEA NONOate and cPTIO did not elevate Cd content and phytochelatins (PC2, PC3) were rather elevated. These data provide evidence that various NO modulators are useful in terms of NO and ROS manipulation but interactions with intact plants affect metal uptake and must therefore be used with caution. In this view, cPTIO and DEA NONOate revealed the less pronounced side impacts and are recommended as suitable NO scavenger/donor in plant physiological studies under Cd excess.

Unexpected Behavior of Some Nitric Oxide Modulators under Cadmium Excess in Plant Tissue

PubMed Central

Kováčik, Jozef; Babula, Petr; Klejdus, Bořivoj; Hedbavny, Josef; Jarošová, Markéta

2014-01-01

Various nitric oxide modulators (NO donors - SNP, GSNO, DEA NONOate and scavengers – PTIO, cPTIO) were tested to highlight the role of NO under Cd excess in various ontogenetic stages of chamomile (Matricaria chamomilla). Surprisingly, compared to Cd alone, SNP and PTIO elevated Cd uptake (confirmed also by PhenGreen staining) but depleted glutathione (partially ascorbic acid) and phytochelatins PC2 and PC3 in both older plants (cultured hydroponically) and seedlings (cultured in deionised water). Despite these anomalous impacts, fluorescence staining of NO and ROS confirmed predictable assumptions and revealed reciprocal changes (decrease in NO but increase in ROS after PTIO addition and the opposite after SNP application). Subsequent tests using alternative modulators and seedlings confirmed changes to NO and ROS after application of GSNO and DEA NONOate as mentioned above for SNP while cPTIO altered only NO level (depletion). On the contrary to SNP and PTIO, GSNO, DEA NONOate and cPTIO did not elevate Cd content and phytochelatins (PC2, PC3) were rather elevated. These data provide evidence that various NO modulators are useful in terms of NO and ROS manipulation but interactions with intact plants affect metal uptake and must therefore be used with caution. In this view, cPTIO and DEA NONOate revealed the less pronounced side impacts and are recommended as suitable NO scavenger/donor in plant physiological studies under Cd excess. PMID:24626462

Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

PubMed

Kim, Inhae; Lee, Heetak; Han, Seong Kyu; Kim, Sanguk

2014-10-01

The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.

Modularity, pollination systems, and interaction turnover in plant-pollinator networks across space.

PubMed

Carstensen, Daniel W; Sabatino, Malena; Morellato, Leonor Patricia C

2016-05-01

Mutualistic interaction networks have been shown to be structurally conserved over space and time while pairwise interactions show high variability. In such networks, modularity is the division of species into compartments, or modules, where species within modules share more interactions with each other than they do with species from other modules. Such a modular structure is common in mutualistic networks and several evolutionary and ecological mechanisms have been proposed as underlying drivers. One prominent explanation is the existence of pollination syndromes where flowers tend to attract certain pollinators as determined by a set of traits. We investigate the modularity of seven community level plant-pollinator networks sampled in rupestrian grasslands, or campos rupestres, in SE Brazil. Defining pollination systems as corresponding groups of flower syndromes and pollinator functional groups, we test the two hypotheses that (1) interacting species from the same pollination system are more often assigned to the same module than interacting species from different pollination systems and; that (2) interactions between species from the same pollination system are more consistent across space than interactions between species from different pollination systems. Specifically we ask (1) whether networks are consistently modular across space; (2) whether interactions among species of the same pollination system occur more often inside modules, compared to interactions among species of different pollination systems, and finally; (3) whether the spatial variation in interaction identity, i.e., spatial interaction rewiring, is affected by trait complementarity among species as indicated by pollination systems. We confirm that networks are consistently modular across space and that interactions within pollination systems principally occur inside modules. Despite a strong tendency, we did not find a significant effect of pollination systems on the spatial consistency of pairwise interactions. These results indicate that the spatial rewiring of interactions could be constrained by pollination systems, resulting in conserved network structures in spite of high variation in pairwise interactions. Our findings suggest a relevant role of pollination systems in structuring plant-pollinator networks and we argue that structural patterns at the sub-network level can help us to fully understand how and why interactions vary across space and time.

Electric field effect on exchange interaction in ultrathin Co films with ionic liquids

NASA Astrophysics Data System (ADS)

Ishibashi, Mio; Yamada, Kihiro T.; Shiota, Yoichi; Ando, Fuyuki; Koyama, Tomohiro; Kakizakai, Haruka; Mizuno, Hayato; Miwa, Kazumoto; Ono, Shimpei; Moriyama, Takahiro; Chiba, Daichi; Ono, Teruo

2018-06-01

Electric-field modulations of magnetic properties have been extensively studied not only for practical applications but also for fundamental interest. In this study, we investigated the electric field effect on the exchange interaction in ultrathin Co films with ionic liquids. The exchange coupling J was characterized from the direct magnetization measurement as a function of temperature using Pt/ultrathin Co/MgO structures. The trend of the electric field effect on J is in good agreement with that of the theoretical prediction, and a large change in J by applying a gate voltage was observed by forming an electric double layer using ionic liquids.

Fluorescent polymer-based post-translational differentiation and subtyping of breast cancer cells.

PubMed

Scott, Michael D; Dutta, Rinku; Haldar, Manas K; Wagh, Anil; Gustad, Thomas R; Law, Benedict; Friesner, Daniel L; Mallik, Sanku

2012-12-07

Herein, we report the application of synthesized fluorescent, water soluble polymers for post-translational subtyping and differentiation of breast cancer cells in vitro. The fluorescence emission spectra from these polymers were modulated differently in the presence of conditioned cell culture media from various breast cancer cells. These polymers differentiate at a post-translation level possibly due to their ability to interact with extracellular enzymes that are over-expressed in cancerous conditions.

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

NASA Astrophysics Data System (ADS)

Deng, Li; Zhao, Yurong; Zhou, Peng; Xu, Hai; Wang, Yanting

2016-12-01

Not Available Project supported by the National Basic Research Program of China (Grant No. 2013CB932804), the National Natural Science Foundation of China (Grant Nos. 91227115, 11421063, 11504431, and 21503275), the Fundamental Research Funds for Central Universities of China (Grant No. 15CX02025A), and the Application Research Foundation for Post-doctoral Scientists of Qingdao City, China (Grant No. T1404096).

Local Application of Sodium Salicylate Enhances Auditory Responses in the Rat’s Dorsal Cortex of the Inferior Colliculus

PubMed Central

Patel, Chirag R.; Zhang, Huiming

2014-01-01

Sodium salicylate (SS) is a widely used medication with side effects on hearing. In order to understand these side effects, we recorded sound-driven local-field potentials in a neural structure, the dorsal cortex of the inferior colliculus (ICd). Using a microiontophoretic technique, we applied SS at sites of recording and studied how auditory responses were affected by the drug. Furthermore, we studied how the responses were affected by combined local application of SS and an agonists/antagonist of the type-A or type-B γ-aminobutyric acid receptor (GABAA or GABAB receptor). Results revealed that SS applied alone enhanced auditory responses in the ICd, indicating that the drug had local targets in the structure. Simultaneous application of the drug and a GABAergic receptor antagonist synergistically enhanced amplitudes of responses. The synergistic interaction between SS and a GABAA receptor antagonist had a relatively early start in reference to the onset of acoustic stimulation and the duration of this interaction was independent of sound intensity. The interaction between SS and a GABAB receptor antagonist had a relatively late start, and the duration of this interaction was dependent on sound intensity. Simultaneous application of the drug and a GABAergic receptor agonist produced an effect different from the sum of effects produced by the two drugs released individually. These differences between simultaneous and individual drug applications suggest that SS modified GABAergic inhibition in the ICd. Our results indicate that SS can affect sound-driven activity in the ICd by modulating local GABAergic inhibition. PMID:25452744

Development and Evaluation of an Interactive Internet-Based Pharmacokinetic Teaching Module.

ERIC Educational Resources Information Center

Hedaya, Mohsen A.

1998-01-01

Describes an Internet-based, interactive, learner-centered, asynchronous instructional module for pharmacokinetics that requires minimal computer knowledge to operate. Main components are concept presentation, a simulation exercise, and self-assessment questions. The module has been found effective in teaching the steady state concept at the…

Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way to Reversibly Concentrate Functionalized Nanoparticles

PubMed Central

Villarreal, Oscar D; Chen, Liao Y; Whetten, Robert L; Demeler, Borries

2015-01-01

Nanometer-sized gold particles (AuNPs) are of peculiar interest because their behaviors in an aqueous solution are sensitive to changes in environmental factors including the size and shape of the solute ions. In order to determine these important characteristics, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates (4-mercapto-benzoate, pMBA) in eight aqueous solutions having ions of varying sizes and shapes (Na+, K+, tetramethylamonium cation TMA+, trisamonium cation TRS+, Cl−, and OH−). For each solution, we computed the reversible work (potential of mean of force) to bring two nanoparticles together as a function of their separation distance. We found that the behavior of pMBA protected Au144 nanoparticles can be readily modulated by tuning their aqueous environmental factors (pH and solute ion combinations). We examined the atomistic details on how the sizes and shapes of solute ions quantitatively factor in the definitive characteristics of nanoparticle-environment and nanoparticle-nanoparticle interactions. We predict that tuning the concentrations of non-spherical composite ions such as TRS+ in an aqueous solution of AuNPs be an effective means to modulate the aggregation propensity desired in biomedical and other applications of small charged nanoparticles. PMID:26581232

Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles.

PubMed

Villarreal, Oscar D; Chen, Liao Y; Whetten, Robert L; Demeler, Borries

2015-12-17

Nanometer-sized gold particles (AuNPs) are of peculiar interest because their behaviors in an aqueous solution are sensitive to changes in environmental factors including the size and shape of the solute ions. In order to determine these important characteristics, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates (4-mercaptobenzoate, pMBA) in eight aqueous solutions having ions of varying sizes and shapes (Na(+), K(+), tetramethylamonium cation TMA(+), tris-ammonium cation TRS(+), Cl(-), and OH(-)). For each solution, we computed the reversible work (potential of mean of force) to bring two nanoparticles together as a function of their separation distance. We found that the behavior of pMBA protected Au144 nanoparticles can be readily modulated by tuning their aqueous environmental factors (pH and solute ion combinations). We examined the atomistic details on how the sizes and shapes of solute ions quantitatively factor in the definitive characteristics of nanoparticle-environment and nanoparticle-nanoparticle interactions. We predict that tuning the concentrations of nonspherical composite ions such as TRS(+) in an aqueous solution of AuNPs be an effective means to modulate the aggregation propensity desired in biomedical and other applications of small charged nanoparticles.

Interactions between nattokinase and heparin/GAGs

PubMed Central

Zhang, Fuming

2015-01-01

Nattokinase (NK) is a serine protease extracted from a traditional Japanese food called natto. Due to its strong fibrinolytic and thrombolytic activity, NK is regarded as a valuable dietary supplement or nutraceutical for the oral thrombolytic therapy. In addition, NK has been investigated for some other medical applications including treatment of hypertension, Alzheimer’s disease, and vitreoretinal disorders. The most widely used clinical anticoagulants are heparin and low molecular weight heparins. The interactions between heparin and proteins modulate a diverse patho-physiological processes and heparin modifies the activity of serine proteases. Indeed, heparin plays important roles in almost all of NK’s potential therapeutically applications. The current report relies on surface plasmon resonance spectroscopy to examine NK interacting with heparin as well as other glycosaminoglycans (GAGs). These studies showed that NK is a heparin binding protein with an affinity of ~250 nM. Examination with differently sized heparin oligosaccharides indicated that the interaction between NK and heparin is chain-length dependent and the minimum size for heparin binding is a hexasaccharide. Studies using chemically modified heparin showed the 6-O-sulfo as well as the N-sulfo groups but not the 2-O-sulfo groups within heparin, are essential for heparin’s interaction with NK. Other GAGs (including HS, DS, and CSE) displayed modest binding affinity to NK. NK also interfered with other heparin-protein interactions, including heparin’s interaction with antithrombin and fibroblast growth factors. PMID:26412225

Interactions between nattokinase and heparin/GAGs.

PubMed

Zhang, Fuming; Zhang, Jianhua; Linhardt, Robert J

2015-12-01

Nattokinase (NK) is a serine protease extracted from a traditional Japanese food called natto. Due to its strong fibrinolytic and thrombolytic activity, NK is regarded as a valuable dietary supplement or nutraceutical for the oral thrombolytic therapy. In addition, NK has been investigated for some other medical applications including treatment of hypertension, Alzheimer's disease, and vitreoretinal disorders. The most widely used clinical anticoagulants are heparin and low molecular weight heparins. The interactions between heparin and proteins modulate diverse patho-physiological processes and heparin modifies the activity of serine proteases. Indeed, heparin plays important roles in almost all of NK's potential therapeutically applications. The current report relies on surface plasmon resonance spectroscopy to examine NK interacting with heparin as well as other glycosaminoglycans (GAGs). These studies showed that NK is a heparin binding protein with an affinity of ~250 nM. Examination with differently sized heparin oligosaccharides indicated that the interaction between NK and heparin is chain-length dependent and the minimum size for heparin binding is a hexasaccharide. Studies using chemically modified heparin showed the 6-O-sulfo as well as the N-sulfo groups but not the 2-O-sulfo groups within heparin, are essential for heparin's interaction with NK. Other GAGs (including HS, DS, and CSE) displayed modest binding affinity to NK. NK also interfered with other heparin-protein interactions, including heparin's interaction with antithrombin and fibroblast growth factors.

Altered Protein Interactions of the Endogenous Interactome of PTPIP51 towards MAPK Signaling

PubMed Central

Brobeil, Alexander; Chehab, Rajaa; Dietel, Eric; Gattenlöhner, Stefan; Wimmer, Monika

2017-01-01

Protein–protein interactions play a pivotal role in normal cellular functions as well as in carcinogenesis. The protein–protein interactions form functional clusters during signal transduction. To elucidate the fine calibration of the protein–protein interactions of protein tyrosine phosphatase interacting protein 51 (PTPIP51) a small molecule drug, namely LDC-3, directly targeting PTPIP51 is now available. Therefore, LDC-3 allows for the studying of the regulation of the endogenous interactome by modulating PTPIP51 binding capacity. Small interfering ribonucleic acid (siRNA) experiments show that the modification in PTPIP51 binding capacity is induced by LDC-3. Application of LDC-3 annuls the known regulatory phosphorylation mechanisms for PTPIP51 and consequently, significantly alters the assembly of the PTPIP51 associated protein complexes. The treatment of human keratinocytes (HaCaT cells) with LDC-3 induces an altered protein–protein interaction profile of the endogenous interactome of PTPIP51. In addition, LDC-3 stabilizes PTPIP51 within a mitogen activated protein kinase (MAPK) complex composed of Raf-1 and the scaffold protein 14-3-3, independent of the phosphorylation status of PTPIP51. Of note, under LDC-3 treatment the regulatory function of the PTP1B on PTPIP51 fails to impact the PTPIP51 interaction characteristics, as reported for the HaCaT cell line. In summary, LDC-3 gives the unique opportunity to directly modulate PTPIP51 in malignant cells, thus targeting potential dysregulated signal transduction pathways such as the MAPK cascade. The provided data give critical insights in the therapeutic potential of PTPIP51 protein interactions and thus are basic for possible targeted therapy regimens. PMID:28754031

Dynamics of neuromodulatory feedback determines frequency modulation in a reduced respiratory network: a computational study.

PubMed

Toporikova, Natalia; Butera, Robert J

2013-02-01

Neuromodulators, such as amines and neuropeptides, alter the activity of neurons and neuronal networks. In this work, we investigate how neuromodulators, which activate G(q)-protein second messenger systems, can modulate the bursting frequency of neurons in a critical portion of the respiratory neural network, the pre-Bötzinger complex (preBötC). These neurons are a vital part of the ponto-medullary neuronal network, which generates a stable respiratory rhythm whose frequency is regulated by neuromodulator release from the nearby Raphe nucleus. Using a simulated 50-cell network of excitatory preBötC neurons with a heterogeneous distribution of persistent sodium conductance and Ca(2+), we determined conditions for frequency modulation in such a network by simulating interaction between Raphe and preBötC nuclei. We found that the positive feedback between the Raphe excitability and preBötC activity induces frequency modulation in the preBötC neurons. In addition, the frequency of the respiratory rhythm can be regulated via phasic release of excitatory neuromodulators from the Raphe nucleus. We predict that the application of a G(q) antagonist will eliminate this frequency modulation by the Raphe and keep the network frequency constant and low. In contrast, application of a G(q) agonist will result in a high frequency for all levels of Raphe stimulation. Our modeling results also suggest that high [K(+)] requirement in respiratory brain slice experiments may serve as a compensatory mechanism for low neuromodulatory tone. Copyright © 2012 Elsevier B.V. All rights reserved.

Ecological modules and roles of species in heathland plant-insect flower visitor networks.

PubMed

Dupont, Yoko L; Olesen, Jens M

2009-03-01

1. Co-existing plants and flower-visiting animals often form complex interaction networks. A long-standing question in ecology and evolutionary biology is how to detect nonrandom subsets (compartments, blocks, modules) of strongly interacting species within such networks. Here we use a network analytical approach to (i) detect modularity in pollination networks, (ii) investigate species composition of modules, and (iii) assess the stability of modules across sites. 2. Interactions between entomophilous plants and their flower-visitors were recorded throughout the flowering season at three heathland sites in Denmark, separated by >or= 10 km. Among sites, plant communities were similar, but composition of flower-visiting insect faunas differed. Visitation frequencies of visitor species were recorded as a measure of insect abundance. 3. Qualitative (presence-absence) interaction networks were tested for modularity. Modules were identified, and species classified into topological roles (peripherals, connectors, or hubs) using 'functional cartography by simulated annealing', a method recently developed by Guimerà & Amaral (2005a). 4. All networks were significantly modular. Each module consisted of 1-6 plant species and 18-54 insect species. Interactions aggregated around one or two hub plant species, which were largely identical at the three study sites. 5. Insect species were categorized in taxonomic groups, mostly at the level of orders. When weighted by visitation frequency, each module was dominated by one or few insect groups. This pattern was consistent across sites. 6. Our study adds support to the conclusion that certain plant species and flower-visitor groups are nonrandomly and repeatedly associated. Within a network, these strongly interacting subgroups of species may exert reciprocal selection pressures on each other. Thus, modules may be candidates for the long-sought key units of co-evolution.

Self-assembling peptide-based building blocks in medical applications

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

Acar, Handan; Srivastava, Samanvaya; Chung, Eun Ji

Peptides and peptide-conjugates, comprising natural and synthetic building blocks, are an increasingly popular class of biomaterials. Self-assembled nanostructures based on peptides and peptide-conjugates offer advantages such as precise selectivity and multifunctionality that can address challenges and limitations in the clinic. In this review article, we discuss recent developments in the design and self-assembly of various nanomaterials based on peptides and peptide-conjugates for medical applications, and categorize them into two themes based on the driving forces of molecular self-assembly. First, we present the self-assembled nanostructures driven by the supramolecular interactions between the peptides, with or without the presence of conjugates. Themore » studies where nanoassembly is driven by the interactions between the conjugates of peptide-conjugates are then presented. Particular emphasis is given to in vivo studies focusing on therapeutics, diagnostics, immune modulation and regenerative medicine. Finally, challenges and future perspectives are presented.« less

Peptide self-assembly: thermodynamics and kinetics.

PubMed

Wang, Juan; Liu, Kai; Xing, Ruirui; Yan, Xuehai

2016-10-21

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

In-vivo detection of binary PKA network interactions upon activation of endogenous GPCRs

PubMed Central

Röck, Ruth; Bachmann, Verena; Bhang, Hyo-eun C; Malleshaiah, Mohan; Raffeiner, Philipp; Mayrhofer, Johanna E; Tschaikner, Philipp M; Bister, Klaus; Aanstad, Pia; Pomper, Martin G; Michnick, Stephen W; Stefan, Eduard

2015-01-01

Membrane receptor-sensed input signals affect and modulate intracellular protein-protein interactions (PPIs). Consequent changes occur to the compositions of protein complexes, protein localization and intermolecular binding affinities. Alterations of compartmentalized PPIs emanating from certain deregulated kinases are implicated in the manifestation of diseases such as cancer. Here we describe the application of a genetically encoded Protein-fragment Complementation Assay (PCA) based on the Renilla Luciferase (Rluc) enzyme to compare binary PPIs of the spatially and temporally controlled protein kinase A (PKA) network in diverse eukaryotic model systems. The simplicity and sensitivity of this cell-based reporter allows for real-time recordings of mutually exclusive PPIs of PKA upon activation of selected endogenous G protein-coupled receptors (GPCRs) in cancer cells, xenografts of mice, budding yeast, and zebrafish embryos. This extends the application spectrum of Rluc PCA for the quantification of PPI-based receptor-effector relationships in physiological and pathological model systems. PMID:26099953

Computer-Assisted Learning Applications in Health Educational Informatics: A Review.

PubMed

Shaikh, Faiq; Inayat, Faisal; Awan, Omer; Santos, Marlise D; Choudhry, Adnan M; Waheed, Abdul; Kajal, Dilkash; Tuli, Sagun

2017-08-10

Computer-assisted learning (CAL) as a health informatics application is a useful tool for medical students in the era of expansive knowledge bases and the increasing need for and the consumption of automated and interactive systems. As the scope and breadth of medical knowledge expand, the need for additional learning outside of lecture hours is becoming increasingly important. CAL can be an impactful adjunct to conventional methods that currently exist in the halls of learning. There is an increasing body of literature that suggests that CAL should be a commonplace and the recommended method of learning for medical students. Factors such as technical issues that hinder the performance of CAL are also evaluated. We conclude by encouraging the use of CAL by medical students as a highly beneficial method of learning that complements and enhances lectures and provides intuitive, interactive modulation of a self-paced curriculum based on the individual's academic abilities.

Dynamic cross correlation studies of wave particle interactions in ULF phenomena

NASA Technical Reports Server (NTRS)

Mcpherron, R. L.

1979-01-01

Magnetic field observations made by satellites in the earth's magnetic field reveal a wide variety of ULF waves. These waves interact with the ambient particle populations in complex ways, causing modulation of the observed particle fluxes. This modulation is found to be a function of species, pitch angle, energy and time. The characteristics of this modulation provide information concerning the wave mode and interaction process. One important characteristic of wave-particle interactions is the phase of the particle flux modulation relative to the magnetic field variations. To display this phase as a function of time a dynamic cross spectrum program has been developed. The program produces contour maps in the frequency time plane of the cross correlation coefficient between any particle flux time series and the magnetic field vector. This program has been utilized in several studies of ULF wave-particle interactions at synchronous orbit.

Investigating local network interactions underlying first- and second-order processing.

PubMed

Ellemberg, Dave; Allen, Harriet A; Hess, Robert F

2004-01-01

We compared the spatial lateral interactions for first-order cues to those for second-order cues, and investigated spatial interactions between these two types of cues. We measured the apparent modulation depth of a target Gabor at fixation, in the presence and the absence of horizontally flanking Gabors. The Gabors' gratings were either added to (first-order) or multiplied with (second-order) binary 2-D noise. Apparent "contrast" or modulation depth (i.e., the perceived difference between the high and low luminance regions for the first-order stimulus, or between the high and low contrast regions for the second-order stimulus) was measured with a modulation depth-matching paradigm. For each observer, the first- and second-order Gabors were equated for apparent modulation depth without the flankers. Our results indicate that at the smallest inter-element spacing, the perceived reduction in modulation depth is significantly smaller for the second-order than for the first-order stimuli. Further, lateral interactions operate over shorter distances and the spatial frequency and orientation tuning of the suppression effect are broader for second- than first-order stimuli. Finally, first- and second-order information interact in an asymmetrical fashion; second-order flankers do not reduce the apparent modulation depth of the first-order target, whilst first-order flankers reduce the apparent modulation depth of the second-order target.

Identifying interactions between chemical entities in biomedical text.

PubMed

Lamurias, Andre; Ferreira, João D; Couto, Francisco M

2014-10-23

Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, \\"Identifying Interactions between Chemical Entities\\" (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to state-of-the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice.

Identifying interactions between chemical entities in biomedical text.

PubMed

Lamurias, Andre; Ferreira, João D; Couto, Francisco M

2014-12-01

Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, "Identifying Interactions between Chemical Entities" (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to stateof- the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice.

Neutron induced background in the COMPTEL detector on the Gamma Ray Observatory

NASA Technical Reports Server (NTRS)

Morris, D. J.; Aarts, H.; Bennett, K.; Busetta, M.; Byrd, R.; Collmar, W.; Connors, A.; Diehl, R.; Eymann, G.; Foster, C.

1992-01-01

Interactions of neutrons in a prototype of the Compton imaging telescope (COMPTEL) gamma ray detector for the Gamma Ray Observatory were studied to determine COMPTEL's sensitivity as a neutron telescope and to estimate the gamma ray background resulting from neutron interactions. The IUCF provided a pulsed neutron beam at five different energies between 18 and 120 MeV. These measurements showed that the gamma ray background from neutron interactions is greater than previously expected. It was thought that most such events would be due to interactions in the upper detector modules of COMPTEL and could be distinguished by pulse shape discrimination. Rather, the bulk of the gamma ray background appears to be due to interactions in passive material, primarily aluminum, surrounding the D1 modules. In a considerable fraction of these interactions, two or more gamma rays are produced simultaneously, with one interacting in the D1 module and the other interacting in the module of the lower (D2) detector. If the neutron interacts near the D1 module, the D1 D2 time of flight cannot distinguish such an event from a true gamma ray event. In order to assess the significance of this background, the flux of neutrons in orbit has been estimated based on observed events with neutron pulse shape signature in D1. The strength of this neutron induced background is estimated. This is compared with the rate expected from the isotropic cosmic gamma ray flux.

A Matlab/Simulink-Based Interactive Module for Servo Systems Learning

ERIC Educational Resources Information Center

Aliane, N.

2010-01-01

This paper presents an interactive module for learning both the fundamental and practical issues of servo systems. This module, developed using Simulink in conjunction with the Matlab graphical user interface (Matlab-GUI) tool, is used to supplement conventional lectures in control engineering and robotics subjects. First, the paper introduces the…

Wikis for a Collaborative Problem-Solving (CPS) Module for Secondary School Science

ERIC Educational Resources Information Center

DeWitt, Dorothy; Alias, Norlidah; Siraj, Saedah; Spector, Jonathan Michael

2017-01-01

Collaborative problem solving (CPS) can support online learning by enabling interactions for social and cognitive processes. Teachers may not have sufficient knowledge to support such interactions, so support needs to be designed into learning modules for this purpose. This study investigates to what extent an online module for teaching nutrition…

An improved land biosphere module for use in the DCESS Earth system model (version 1.1) with application to the last glacial termination

NASA Astrophysics Data System (ADS)

Eichinger, Roland; Shaffer, Gary; Albarrán, Nelson; Rojas, Maisa; Lambert, Fabrice

2017-09-01

Interactions between the land biosphere and the atmosphere play an important role for the Earth's carbon cycle and thus should be considered in studies of global carbon cycling and climate. Simple approaches are a useful first step in this direction but may not be applicable for certain climatic conditions. To improve the ability of the reduced-complexity Danish Center for Earth System Science (DCESS) Earth system model DCESS to address cold climate conditions, we reformulated the model's land biosphere module by extending it to include three dynamically varying vegetation zones as well as a permafrost component. The vegetation zones are formulated by emulating the behaviour of a complex land biosphere model. We show that with the new module, the size and timing of carbon exchanges between atmosphere and land are represented more realistically in cooling and warming experiments. In particular, we use the new module to address carbon cycling and climate change across the last glacial transition. Within the constraints provided by various proxy data records, we tune the DCESS model to a Last Glacial Maximum state and then conduct transient sensitivity experiments across the transition under the application of explicit transition functions for high-latitude ocean exchange, atmospheric dust, and the land ice sheet extent. We compare simulated time evolutions of global mean temperature, pCO2, atmospheric and oceanic carbon isotopes as well as ocean dissolved oxygen concentrations with proxy data records. In this way we estimate the importance of different processes across the transition with emphasis on the role of land biosphere variations and show that carbon outgassing from permafrost and uptake of carbon by the land biosphere broadly compensate for each other during the temperature rise of the early last deglaciation.

Development of a pyramidal wavefront sensor test-bench at INO

NASA Astrophysics Data System (ADS)

Turbide, Simon; Wang, Min; Gauvin, Jonny; Martin, Olivier; Savard, Maxime; Bourqui, Pascal; Veran, Jean-Pierre; Deschenes, William; Anctil, Genevieve; Chateauneuf, François

2013-12-01

The key technical element of the adaptive optics in astronomy is the wavefront sensing (WFS). One of the advantages of the pyramid wavefront sensor (P-WFS) over the widely used Shack-Hartmann wavefront sensor seems to be the increased sensitivity in closed-loop applications. A high-sensitivity and large dynamic-range WFS, such as P-WFS technology, still needs to be further investigated for proper justification in future Extremely Large Telescopes application. At INO, we have recently carried out the optical design, testing and performance evaluation of a P-WFS bench setup. The optical design of the bench setup mainly consists of the super-LED fiber source, source collimator, spatial light modulator (SLM), relay lenses, tip-tilt mirror, Fourier-transforming lens, and a four-faceted glass pyramid with a large vertex angle as well as pupil re-imaged optics. The phase-only SLM has been introduced in the bench setup to generate atmospheric turbulence with a maximum phase shift of more than 2π at each pixel (256 grey levels). Like a modified Foucault knife-edge test, the refractive pyramid element is used to produce four images of the entrance pupil on a CCD camera. The Fourier-transforming lens, which is used before the pyramid prism, is designed for telecentric output to allow dynamic modulation (rotation of the beam around the pyramid-prism center) from a tip-tilt mirror. Furthermore, a P-WFS diffraction-based model has been developed. This model includes most of the system limitations such as the SLM discrete voltage steps and the CCD pixel pitch. The pyramid effects (edges and tip) are considered as well. The modal wavefront reconstruction algorithm relies on the construction of an interaction matrix (one for each modulation's amplitude). Each column of the interaction matrix represents the combination of the four pupil images for a given wavefront aberration. The nice agreement between the data and the model suggest that the limitation of the system is not the P-WFS itself, but rather its environment such as source intensity fluctuation and vibration of the optical bench. Finally, the phase-reconstruction errors of the P-WFS have been compared to those of a Shack-Hartmann, showing the regions of interest of the former system. The bench setup will be focusing on the astronomy application as well as commercial applications, such as bio-medical application etc.

BioSIGHT: Interactive Visualization Modules for Science Education

NASA Technical Reports Server (NTRS)

Wong, Wee Ling

1998-01-01

Redefining science education to harness emerging integrated media technologies with innovative pedagogical goals represents a unique challenge. The Integrated Media Systems Center (IMSC) is the only engineering research center in the area of multimedia and creative technologies sponsored by the National Science Foundation. The research program at IMSC is focused on developing advanced technologies that address human-computer interfaces, database management, and high-speed network capabilities. The BioSIGHT project at is a demonstration technology project in the area of education that seeks to address how such emerging multimedia technologies can make an impact on science education. The scope of this project will help solidify NASA's commitment for the development of innovative educational resources that promotes science literacy for our students and the general population as well. These issues must be addressed as NASA marches toward the goal of enabling human space exploration that requires an understanding of life sciences in space. The IMSC BioSIGHT lab was established with the purpose of developing a novel methodology that will map a high school biology curriculum into a series of interactive visualization modules that can be easily incorporated into a space biology curriculum. Fundamental concepts in general biology must be mastered in order to allow a better understanding and application for space biology. Interactive visualization is a powerful component that can capture the students' imagination, facilitate their assimilation of complex ideas, and help them develop integrated views of biology. These modules will augment the role of the teacher and will establish the value of student-centered interactivity, both in an individual setting as well as in a collaborative learning environment. Students will be able to interact with the content material, explore new challenges, and perform virtual laboratory simulations. The BioSIGHT effort is truly cross-disciplinary in nature and requires expertise from many areas including Biology, Computer Science Electrical Engineering, Education, and the Cognitive Sciences. The BioSIGHT team includes a scientific illustrator, educational software designer, computer programmers as well as IMSC graduate and undergraduate students.

Combined effects of potassium chloride and ethanol as mobile phase modulators on hydrophobic interaction and reversed-phase chromatography of three insulin variants.

PubMed

Johansson, Karolina; Frederiksen, Søren S; Degerman, Marcus; Breil, Martin P; Mollerup, Jørgen M; Nilsson, Bernt

2015-02-13

The two main chromatographic modes based on hydrophobicity, hydrophobic interaction chromatography (HIC) and reversed-phase chromatography (RPC), are widely used for both analytical and preparative chromatography of proteins in the pharmaceutical industry. Despite the extensive application of these separation methods, and the vast amount of studies performed on HIC and RPC over the decades, the underlying phenomena remain elusive. As part of a systematic study of the influence of mobile phase modulators in hydrophobicity-based chromatography, we have investigated the effects of both KCl and ethanol on the retention of three insulin variants on two HIC adsorbents and two RPC adsorbents. The focus was on the linear adsorption range, separating the modulator effects from the capacity effects, but some complementary experiments at higher load were included to further investigate observed phenomena. The results show that the modulators have the same effect on the two RPC adsorbents in the linear range, indicating that the modulator concentration only affects the activity of the solute in the mobile phase, and not that of the solute-ligand complex, or that of the ligand. Unfortunately, the HIC adsorbents did not show the same behavior. However, the insulin variants displayed a strong tendency toward self-association on both HIC adsorbents; on one in particular. Since this causes peak fronting, the retention is affected, and this could probably explain the lack of congruity. This conclusion was supported by the results from the non-linear range experiments which were indicative of double-layer adsorption on the HIC adsorbents, while the RPC adsorbents gave the anticipated increased tailing at higher load. Copyright © 2015 Elsevier B.V. All rights reserved.

Creation and Global Deployment of a Mobile, Application-Based Cognitive Simulator for Cardiac Surgical Procedures.

PubMed

Brewer, Zachary E; Ogden, William David; Fann, James I; Burdon, Thomas A; Sheikh, Ahmad Y

Several modern learning frameworks (eg, cognitive apprenticeship, anchored instruction, and situated cognition) posit the utility of nontraditional methods for effective experiential learning. Thus, development of novel educational tools emphasizing the cognitive framework of operative sequences may be of benefit to surgical trainees. We propose the development and global deployment of an effective, mobile cognitive cardiac surgical simulator. In methods, 16 preclinical medical students were assessed. Overall, 4 separate surgical modules (sternotomy, cannulation, decannulation, and sternal closure) were created utilizing the Touch Surgery (London, UK) platform. Modules were made available to download free of charge for use on mobile devices. Usage data were collected over a 6-month period. Educational efficacy of the modules was evaluated by randomizing a cohort of medical students to either module usage or traditional, reading-based self-study, followed by a multiple-choice learning assessment tool. In results, downloads of the simulator achieved global penetrance, with highest usage in the USA, Brazil, Italy, UK, and India. Overall, 5368 unique users conducted a total of 1971 hours of simulation. Evaluation of the medical student cohort revealed significantly higher assessment scores in those randomized to module use versus traditional reading (75% ± 9% vs 61% ± 7%, respectively; P < 0.05). In conclusion, this study represents the first effort to create a mobile, interactive cognitive simulator for cardiac surgery. Simulators of this type may be effective for the training and assessment of surgical students. We investigated whether an interactive, mobile-computing-based cognitive task simulator for cardiac surgery could be developed, deployed, and validated. Our findings suggest that such simulators may be a useful learning tool. Copyright © 2016. Published by Elsevier Inc.

Perilipin polymorphism interacts with dietary carbohydrates to modulate anthropometric traits in Hispanics of Caribbean origin

USDA-ARS?s Scientific Manuscript database

Perilipin (PLIN) is the major protein surrounding lipid droplets in adipocytes and regulates adipocyte metabolism by modulating the interaction between lipases and triacylglycerol stores. Associations between PLIN gene polymorphisms and obesity risk have been described, but interactions with die...

A human functional protein interaction network and its application to cancer data analysis

PubMed Central

2010-01-01

Background One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. Results We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers. Conclusions We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases. PMID:20482850

Cell Adhesions: Actin-Based Modules that Mediate Cell-Extracellular Matrix and Cell-Cell Interactions

PubMed Central

Bachir, Alexia; Horwitz, Alan Rick; Nelson, W. James; Bianchini, Julie M.

2018-01-01

Cell adhesions link cells to the extracellular matrix (ECM) and to each other, and depend on interactions with the actin cytoskeleton. Both cell-ECM and cell-cell adhesion sites contain discrete, yet overlapping functional modules. These modules establish physical association with the actin cytoskeleton, locally modulate actin organization and dynamics, and trigger intracellular signaling pathways. Interplay between these modules generates distinct actin architectures that underlie different stages, types, and functions of cell-ECM and cell-cell adhesions. Actomyosin contractility is required to generate mature, stable adhesions, as well as sense and translate the mechanical properties of the cellular environment to changes in cell organization and behavior. In this chapter we discuss the organization and function of different adhesion modules and how they interact with the actin cytoskeleton. We highlight the molecular mechanisms of mechanotransduction in adhesions, and how adhesion molecules mediate crosstalk between cell-ECM and cell-cell adhesion sites. PMID:28679638

Interactive smart battery storage for a PV and wind hybrid energy management control based on conservative power theory

NASA Astrophysics Data System (ADS)

Godoy Simões, Marcelo; Davi Curi Busarello, Tiago; Saad Bubshait, Abdullah; Harirchi, Farnaz; Antenor Pomilio, José; Blaabjerg, Frede

2016-04-01

This paper presents interactive smart battery-based storage (BBS) for wind generator (WG) and photovoltaic (PV) systems. The BBS is composed of an asymmetric cascaded H-bridge multilevel inverter (ACMI) with staircase modulation. The structure is parallel to the WG and PV systems, allowing the ACMI to have a reduction in power losses compared to the usual solution for storage connected at the DC-link of the converter for WG or PV systems. Moreover, the BBS is embedded with a decision algorithm running real-time energy costs, plus a battery state-of-charge manager and power quality capabilities, making the described system in this paper very interactive, smart and multifunctional. The paper describes how BBS interacts with the WG and PV and how its performance is improved. Experimental results are presented showing the efficacy of this BBS for renewable energy applications.

Forbidden atomic transitions driven by an intensity-modulated laser trap.

PubMed

Moore, Kaitlin R; Anderson, Sarah E; Raithel, Georg

2015-01-20

Spectroscopy is an essential tool in understanding and manipulating quantum systems, such as atoms and molecules. The model describing spectroscopy includes the multipole-field interaction, which leads to established spectroscopic selection rules, and an interaction that is quadratic in the field, which is not often employed. However, spectroscopy using the quadratic (ponderomotive) interaction promises two significant advantages over spectroscopy using the multipole-field interaction: flexible transition rules and vastly improved spatial addressability of the quantum system. Here we demonstrate ponderomotive spectroscopy by using optical-lattice-trapped Rydberg atoms, pulsating the lattice light and driving a microwave atomic transition that would otherwise be forbidden by established spectroscopic selection rules. This ability to measure frequencies of previously inaccessible transitions makes possible improved determinations of atomic characteristics and constants underlying physics. The spatial resolution of ponderomotive spectroscopy is orders of magnitude better than the transition frequency would suggest, promising single-site addressability in dense particle arrays for quantum computing applications.

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

NASA Astrophysics Data System (ADS)

Wirkus, Lars; Strunck, Alexander

2013-04-01

War and violent conflict are omnipresent-be it war in the Middle East, violent conflicts in failed states or increasing military expenditures and exports/ imports of military goods. To understand certain conflicts or peace processes and their possible interrelation, to conduct a well-founded political discussion and to support or influence decision-making, one matter is of special importance: easily accessible and, in particular, reliable data and information. Against this background, the Bonn International Center for Conversion (BICC) in close cooperation with the German Federal Agency for Civic Education (bpb) has been developing a map-based information portal on war and peace with various thematic modules for the latter's online service (http://sicherheitspolitik.bpb.de). The portal will eventually offer nine of such modules that are intended to give various target groups, such as interested members of the public, teachers and learners, policymakers and representatives of the media access to the required information in form of an interactive and country-based global overview or a comparison of different issues. Five thematic modules have been completed so far: War and conflict, peace and demobilization, military capacities, resources and conflict, conventional weapons. The portal offers a broad spectrum of different data processing and visualization tools. Its central feature is an interactive mapping component based on WebGIS and a relational database. Content and data provided through thematic maps in the form of WebGIS layers are generally supplemented by info graphics, data tables and short articles providing deeper knowledge on the respective issue. All modules and their sub-chapters are introduced by background texts. They put all interactive maps of a module into an appropriate context and help the users to also understand the interrelation between various layers. If a layer is selected, all corresponding texts and graphics are shown automatically below the map. Data tables are offered if the copyright of datasets allows such use. All data of all thematic modules is presented in country profiles in a consolidated manner. The portal has been created with Open Source Software. PostgreSQL and PostGIS, MapServer, OpenLayers, MapProxy and cmsmadesimple are combined to manipulate and transform global data sets into interactive thematic maps. A purpose-programmed layer selection menu enables users to select single layers or to combine up to three matching layers from all possible pre-set layer combinations. This applies both to fields of topics within a module and across various modules. Due to the complexity of the structure and visualization constraints, no more than three layers can be combined. The WebGIS-based information portal on war and peace is an excellent example of how GIS technologies can be used for education and outreach. Not only can they play a crucial role in supporting the educational mandate and mission of certain institutions. They can also directly support various target groups in obtaining the knowledge needed by providing a collection of straight forward designed, ready-to-use data, info graphics and maps.

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.

PubMed

Bianco, Luca; Riccadonna, Samantha; Lavezzo, Enrico; Falda, Marco; Formentin, Elide; Cavalieri, Duccio; Toppo, Stefano; Fontana, Paolo

2017-02-01

Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. Contact:paolo.fontana@fmach.it

Application of digital interferogram evaluation techniques to the measurement of 3-D flow fields

NASA Technical Reports Server (NTRS)

Becker, Friedhelm; Yu, Yung H.

1987-01-01

A system for digitally evaluating interferograms, based on an image processing system connected to a host computer, was implemented. The system supports one- and two-dimensional interferogram evaluations. Interferograms are digitized, enhanced, and then segmented. The fringe coordinates are extracted, and the fringes are represented as polygonal data structures. Fringe numbering and fringe interpolation modules are implemented. The system supports editing and interactive features, as well as graphic visualization. An application of the system to the evaluation of double exposure interferograms from the transonic flow field around a helicopter blade and the reconstruction of the three dimensional flow field is given.

An Interactive Medical Knowledge Assistant

NASA Astrophysics Data System (ADS)

Czejdo, Bogdan D.; Baszun, Mikolaj

This paper describes an interactive medical knowledge assistant that can help a doctor or a patient in making important health related decisions. The system is Web based and consists of several modules, including a medical knowledge base, a doctor interface module, patient interface module and a the main module of the medical knowledge assistant. The medical assistant is designed to help interpret the fuzzy data using rough sets approach. The patient interface includes sub-system for real time monitoring of patients' health parameters and sending them to the main module of the medical knowledge assistant.

Transmission characteristics of a novel grating assisted microring

NASA Astrophysics Data System (ADS)

Lou, Fei; Zhang, Xinliang; Wosinski, Lech

2011-12-01

We propose a new type of grating-assisted microring (GAMR) structure with Bragg gratings placed on microring's arms. Two Fabry-Perot resonances interact with microring resonance, resulting in GAMR's unique amplitude and phase spectra. The structure's characteristics are analytically studied using coupled mode theory and numerically verified by 2D-FDTD. With proper cavity lengths, GAMR exhibits an electromagnetically induced transparency (EIT)-like spectrum. The ultra-narrow resonance can be used for sensing, modulation, and other applications.

Clinically oriented three-year medical physics curriculum: a new design for the future.

PubMed

Nachiappan, Arun C; Lee, Stephen R; Willis, Marc H; Galfione, Matthew R; Chinnappan, Raj R; Diaz-Marchan, Pedro J; Bushong, Stewart C

2012-09-01

Medical physics instruction for diagnostic radiology residency at our institution has been redesigned with an interactive and image-based approach that encourages clinical application. The new medical physics curriculum spans the first 3 years of radiology residency and is integrated with the core didactic curriculum. Salient features include clinical medical physics conferences, fundamentals of medical physics lectures, practicums, online modules, journal club, and a final review before the American Board of Radiology core examination.

Critical Analysis of an e-Learning and Interactive Teaching Module with Respect to the Interpretation of Emergency Computed Tomography of the Brain.

PubMed

Groth, Michael; Barthe, Käthe Greta; Riemer, Martin; Ernst, Marielle; Herrmann, Jochen; Fiehler, Jens; Buhk, Jan-Hendrik

2018-04-01

 To compare the learning benefit of three different teaching strategies on the interpretation of emergency cerebral computed tomography (CT) pathologies by medical students.  Three groups of students with different types of teaching (e-learning, interactive teaching, and standard curricular education in neuroradiology) were tested with respect to the detection of seven CT pathologies. The test results of each group were compared for each CT pathology using the chi-square test. A p-value ≤ 0.05 was considered to be significant.  Opposed to the results of the comparison group (curricular education), the e-learning group and interactive teaching tutorial group both showed a significantly better performance in detecting hyperdense middle cerebral artery sign (p = 0.001 and p < 0.0001) as well as subarachnoid hemorrhage (p = 0.03 and p = 0.001) on CT. Moreover, an increase in performance for the detection of subdural hematoma and skull fracture could be observed for both the interactive teaching group and the e-learning group, with statistical significance in the latter (p = 0.03 and p < 0.0001, respectively). No statistically significant differences were found for the detection of intracranial and epidural hemorrhage, as well as midline shift, among the groups studied.  Our study demonstrates potential learning benefits for both the interactive teaching tutorial and e-learning module group with respect to reading CT scans with slightly different advantages. Thus, the introduction of new learning methods in radiological education might be reasonable at an undergraduate stage but requires learning content-based considerations.   · E-learning can offer benefits regarding the reading of cerebral CT scans by students. · Interactive tutorial can offer benefits regarding the reading of cerebral CT scans by students. · E-learning and interactive tutorial feature different strengths for student learning in radiology. · Application of interactive teaching methods in radiology requires learning content-based considerations. · Groth M, Barthe KG, Riemer M et al. Critical Analysis of an e-Learning and Interactive Teaching Module with Respect to the Interpretation of Emergency Computed Tomography of the Brain. Fortschr Röntgenstr 2017; 190: 334 - 340. © Georg Thieme Verlag KG Stuttgart · New York.

Land Application of Wastes: An Educational Program - Introduction and Script.

ERIC Educational Resources Information Center

Clarkson, W. W.; And Others

This is the introductory module to the Land Application of Wastes educational program. The module contains information on the content, structure, and dynamics of the program. Also included with the module is a script to accompany a slide presentation. The Land Application of Wastes program consists of twenty-five modules and audio-visual…

Activation of Phosphoinositide Metabolism by Cholinergic Agents.

DTIC Science & Technology

1992-03-15

most notably calcium. Cholinergic agonist-induced seizures; Brain second messenger systems; Neurotransmitter/ Neuromodulator interactions; RAV; Lab...have been described: modulation by protein kinase C and modulation by neurotransmitter (or neuromodulator ) interactions. Agents which stimulate...phosphoinositide hydrolysis that has been identified consists of interactions among neurotransmitter systems or neuromodulators . Perhaps those most widely

Transitioning Communication Education to an Interactive Online Module Format.

PubMed

Williams, Kristine; Abd-Hamid, Nor Hashidah; Perkhounkova, Yelena

2017-07-01

The Changing Talk intervention improves nursing home staff communication by reducing elderspeak. To facilitate dissemination, interactive online modules were created, maintaining the original content. This article reports on the process of transitioning and the results of pilot testing the modules. Interactive online modules were developed, pilot tested, and the evaluated in comparison to outcomes from the classroom format training. Online participants (N = 9) demonstrated pre to posttest knowledge gain (scores improved from M = 82.4% to M = 91.2%). Rating of a staff-resident interaction showed improved recognition of elderspeak and person-centered communication after training. Online and original participants reported similar intentions to use learned skills and rated the program highly. Evidence-based interventions can be translated from traditional classroom to online format maintaining effects on increasing staff knowledge and intentions to use learned skills in practice. However, the modules should be tested in a larger and more representative sample. J Contin Educ Nurs. 2017;48(7):320-328. Copyright 2017, SLACK Incorporated.

EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments.

PubMed

Milewski, Marek C; Kamel, Karol; Kurzynska-Kokorniak, Anna; Chmielewski, Marcin K; Figlerowicz, Marek

2017-10-01

Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.

Infant Smiling during Social Interaction: Arousal Modulation or Activation Indicator?

ERIC Educational Resources Information Center

Ewy, Richard

In a study of infant smiling, 20 mother-infant dyads were videotaped in normal face-to-face interaction when the infants were 9 and 14 weeks of age. Videotapes were used to determine which of two classes of smiling behavior models, either arousal modulation or activation indicator, was most supported by empirical data. Arousal modulation models…

Antibody induced CD4 down-modulation of T cells is site-specifically mediated by CD64+ cells

PubMed Central

Vogel, Stephanie; Grabski, Elena; Buschjäger, Daniela; Klawonn, Frank; Döring, Marius; Wang, Junxi; Fletcher, Erika; Bechmann, Ingo; Witte, Torsten; Durisin, Martin; Schraven, Burkhart; Mangsbo, Sara M.; Schönfeld, Kurt; Czeloth, Niklas; Kalinke, Ulrich

2015-01-01

Treatment of PBMC with the CD4-specific mAb BT-061 induces CD4 down-modulation of T cells. Here we report that addition of BT-061 to purified T cells did not confer this effect, whereas incubation of T cells in BT-061 coated wells restored CD4 down-modulation. These results implied that Fcγ receptor mediated cell-cell interactions played a role. In consistence with this hypothesis PBMC depleted of CD64+ monocytes did not confer CD4 down-modulation of BT-061 decorated T cells. Strikingly, CD4 down-modulation was observed in BT-061 treated synovial fluid punctuated from patients’ inflamed joints that comprised enhanced numbers of CD64+ cells. In contrast, in a circulating whole blood system injection of BT-061 did not induce CD4 down-modulation, due to CD64 saturation by serum IgG. Similarly, tonsil derived mononuclear cells devoid of CD64+ cells did not show CD4 down-modulation, whereas addition of blood derived monocytes restored the effect. Thus, the interaction of BT-061 decorated T cells with CD64+ cells is needed for CD4 down-modulation, implying that in patients BT-061 would primarily induce CD4 down-modulation at inflammatory sites. These results highlight the need not only to examine the interaction of a given mAb with single FcγR, but also the immunological environment that is appropriate to support such interactions. PMID:26670584

Search for an Annual Modulation in a p-Type Point Contact Germanium Dark Matter Detector

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

Barbeau, P.S.; Collar, J.I.; Fields, N.

2011-01-01

Fifteen months of cumulative CoGeNT data are examined for indications of an annual modulation, a predicted signature of weakly interacting massive particle (WIMP) interactions. Presently available data support the presence of a modulated component of unknown origin, with parameters prima facie compatible with a galactic halo composed of light-mass WIMPs. Unoptimized estimators yield a statistical significance for a modulation of {approx}2.8{sigma}, limited by the short exposure.

Search for an Annual Modulation in a p-Type Point Contact Germanium Dark Matter Detector

NASA Astrophysics Data System (ADS)

Aalseth, C. E.; Barbeau, P. S.; Colaresi, J.; Collar, J. I.; Diaz Leon, J.; Fast, J. E.; Fields, N.; Hossbach, T. W.; Keillor, M. E.; Kephart, J. D.; Knecht, A.; Marino, M. G.; Miley, H. S.; Miller, M. L.; Orrell, J. L.; Radford, D. C.; Wilkerson, J. F.; Yocum, K. M.

2011-09-01

Fifteen months of cumulative CoGeNT data are examined for indications of an annual modulation, a predicted signature of weakly interacting massive particle (WIMP) interactions. Presently available data support the presence of a modulated component of unknown origin, with parameters prima facie compatible with a galactic halo composed of light-mass WIMPs. Unoptimized estimators yield a statistical significance for a modulation of ˜2.8σ, limited by the short exposure.

Leveraging retained physical capabilities to improve quality of life as assessed by persons with severe motor impairments.

PubMed

Felzer, Torsten; Beckerle, Philipp; Rinderknecht, Stephan; Nordmann, Rainer

2010-07-01

The main objective of this article is to present an alternative method of interacting with a computer which empowers persons with very severe motor impairments to leverage retained capabilities in order to independently control parts of their daily lives. The input strategy is based on tiny intentional contractions of a single muscle of choice (requiring a minimum of physical contribution only) which are used as selection markers in the context of scanning. To demonstrate the usefulness of the idea, two applications (combined in a single software system) have been implemented (initially): a module turning the PC into a Universal Remote Control and a Text-To-Speech module. The system has finally been supplemented by a third application offering to effortlessly make telephone calls. A simple experiment requesting the speed of the scanning scheme shows that the theoretical concept really works. Furthermore, the usability by novice users from the target population is proven in a user study focusing on the telephony application. It is concluded that the approach has a large potential for persons with severe physical disabilities, meaning that the resulting system is indeed able to improve its users' quality of life.

Automatic page layout using genetic algorithms for electronic albuming

NASA Astrophysics Data System (ADS)

Geigel, Joe; Loui, Alexander C. P.

2000-12-01

In this paper, we describe a flexible system for automatic page layout that makes use of genetic algorithms for albuming applications. The system is divided into two modules, a page creator module which is responsible for distributing images amongst various album pages, and an image placement module which positions images on individual pages. Final page layouts are specified in a textual form using XML for printing or viewing over the Internet. The system makes use of genetic algorithms, a class of search and optimization algorithms that are based on the concepts of biological evolution, for generating solutions with fitness based on graphic design preferences supplied by the user. The genetic page layout algorithm has been incorporated into a web-based prototype system for interactive page layout over the Internet. The prototype system is built using client-server architecture and is implemented in java. The system described in this paper has demonstrated the feasibility of using genetic algorithms for automated page layout in albuming and web-based imaging applications. We believe that the system adequately proves the validity of the concept, providing creative layouts in a reasonable number of iterations. By optimizing the layout parameters of the fitness function, we hope to further improve the quality of the final layout in terms of user preference and computation speed.

ISAC - A tool for aeroservoelastic modeling and analysis. [Interaction of Structures, Aerodynamics, and Control

NASA Technical Reports Server (NTRS)

Adams, William M., Jr.; Hoadley, Sherwood T.

1993-01-01

This paper discusses the capabilities of the Interaction of Structures, Aerodynamics, and Controls (ISAC) system of program modules. The major modeling, analysis, and data management components of ISAC are identified. Equations of motion are displayed for a Laplace-domain representation of the unsteady aerodynamic forces. Options for approximating a frequency-domain representation of unsteady aerodynamic forces with rational functions of the Laplace variable are shown. Linear time invariant state-space equations of motion that result are discussed. Model generation and analyses of stability and dynamic response characteristics are shown for an aeroelastic vehicle which illustrate some of the capabilities of ISAC as a modeling and analysis tool for aeroelastic applications.

Task modulated brain connectivity of the amygdala: a meta-analysis of psychophysiological interactions.

PubMed

Di, Xin; Huang, Jia; Biswal, Bharat B

2017-01-01

Understanding functional connectivity of the amygdala with other brain regions, especially task modulated connectivity, is a critical step toward understanding the role of the amygdala in emotional processes and the interactions between emotion and cognition. The present study performed coordinate-based meta-analysis on studies of task modulated connectivity of the amygdala which used psychophysiological interaction (PPI) analysis. We first analyzed 49 PPI studies on different types of tasks using activation likelihood estimation (ALE) meta-analysis. Widespread cortical and subcortical regions showed consistent task modulated connectivity with the amygdala, including the medial frontal cortex, bilateral insula, anterior cingulate, fusiform gyrus, parahippocampal gyrus, thalamus, and basal ganglia. These regions were in general overlapped with those showed coactivations with the amygdala, suggesting that these regions and amygdala are not only activated together, but also show different levels of interactions during tasks. Further analyses with subsets of PPI studies revealed task specific functional connectivities with the amygdala that were modulated by fear processing, face processing, and emotion regulation. These results suggest a dynamic modulation of connectivity upon task demands, and provide new insights on the functions of the amygdala in different affective and cognitive processes. The meta-analytic approach on PPI studies may offer a framework toward systematical examinations of task modulated connectivity.

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

NASA Astrophysics Data System (ADS)

Dror, Ron O.; Green, Hillary F.; Valant, Celine; Borhani, David W.; Valcourt, James R.; Pan, Albert C.; Arlow, Daniel H.; Canals, Meritxell; Lane, J. Robert; Rahmani, Raphaël; Baell, Jonathan B.; Sexton, Patrick M.; Christopoulos, Arthur; Shaw, David E.

2013-11-01

The design of G-protein-coupled receptor (GPCR) allosteric modulators, an active area of modern pharmaceutical research, has proved challenging because neither the binding modes nor the molecular mechanisms of such drugs are known. Here we determine binding sites, bound conformations and specific drug-receptor interactions for several allosteric modulators of the M2 muscarinic acetylcholine receptor (M2 receptor), a prototypical family A GPCR, using atomic-level simulations in which the modulators spontaneously associate with the receptor. Despite substantial structural diversity, all modulators form cation-π interactions with clusters of aromatic residues in the receptor extracellular vestibule, approximately 15Å from the classical, `orthosteric' ligand-binding site. We validate the observed modulator binding modes through radioligand binding experiments on receptor mutants designed, on the basis of our simulations, either to increase or to decrease modulator affinity. Simulations also revealed mechanisms that contribute to positive and negative allosteric modulation of classical ligand binding, including coupled conformational changes of the two binding sites and electrostatic interactions between ligands in these sites. These observations enabled the design of chemical modifications that substantially alter a modulator's allosteric effects. Our findings thus provide a structural basis for the rational design of allosteric modulators targeting muscarinic and possibly other GPCRs.

A web server for analysis, comparison and prediction of protein ligand binding sites.

PubMed

Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

2016-03-25

One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

Prior knowledge guided active modules identification: an integrated multi-objective approach.

PubMed

Chen, Weiqi; Liu, Jing; He, Shan

2017-03-14

Active module, defined as an area in biological network that shows striking changes in molecular activity or phenotypic signatures, is important to reveal dynamic and process-specific information that is correlated with cellular or disease states. A prior information guided active module identification approach is proposed to detect modules that are both active and enriched by prior knowledge. We formulate the active module identification problem as a multi-objective optimisation problem, which consists two conflicting objective functions of maximising the coverage of known biological pathways and the activity of the active module simultaneously. Network is constructed from protein-protein interaction database. A beta-uniform-mixture model is used to estimate the distribution of p-values and generate scores for activity measurement from microarray data. A multi-objective evolutionary algorithm is used to search for Pareto optimal solutions. We also incorporate a novel constraints based on algebraic connectivity to ensure the connectedness of the identified active modules. Application of proposed algorithm on a small yeast molecular network shows that it can identify modules with high activities and with more cross-talk nodes between related functional groups. The Pareto solutions generated by the algorithm provides solutions with different trade-off between prior knowledge and novel information from data. The approach is then applied on microarray data from diclofenac-treated yeast cells to build network and identify modules to elucidate the molecular mechanisms of diclofenac toxicity and resistance. Gene ontology analysis is applied to the identified modules for biological interpretation. Integrating knowledge of functional groups into the identification of active module is an effective method and provides a flexible control of balance between pure data-driven method and prior information guidance.

Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

PubMed Central

Bersanelli, Matteo; Mosca, Ettore; Remondini, Daniel; Castellani, Gastone; Milanesi, Luciano

2016-01-01

A relation exists between network proximity of molecular entities in interaction networks, functional similarity and association with diseases. The identification of network regions associated with biological functions and pathologies is a major goal in systems biology. We describe a network diffusion-based pipeline for the interpretation of different types of omics in the context of molecular interaction networks. We introduce the network smoothing index, a network-based quantity that allows to jointly quantify the amount of omics information in genes and in their network neighbourhood, using network diffusion to define network proximity. The approach is applicable to both descriptive and inferential statistics calculated on omics data. We also show that network resampling, applied to gene lists ranked by quantities derived from the network smoothing index, indicates the presence of significantly connected genes. As a proof of principle, we identified gene modules enriched in somatic mutations and transcriptional variations observed in samples of prostate adenocarcinoma (PRAD). In line with the local hypothesis, network smoothing index and network resampling underlined the existence of a connected component of genes harbouring molecular alterations in PRAD. PMID:27731320

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.

PubMed

Machiela, Mitchell J; Chanock, Stephen J

2015-11-01

Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci.nih.gov/LDlink/. mitchell.machiela@nih.gov. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling

PubMed Central

Li, Wenyuan; Dai, Chao; Liu, Chun-Chi

2012-01-01

Abstract Current network analysis methods all focus on one or multiple networks of the same type. However, cells are organized by multi-layer networks (e.g., transcriptional regulatory networks, splicing regulatory networks, protein-protein interaction networks), which interact and influence each other. Elucidating the coupling mechanisms among those different types of networks is essential in understanding the functions and mechanisms of cellular activities. In this article, we developed the first computational method for pattern mining across many two-layered graphs, with the two layers representing different types yet coupled biological networks. We formulated the problem of identifying frequent coupled clusters between the two layers of networks into a tensor-based computation problem, and proposed an efficient solution to solve the problem. We applied the method to 38 two-layered co-transcription and co-splicing networks, derived from 38 RNA-seq datasets. With the identified atlas of coupled transcription-splicing modules, we explored to what extent, for which cellular functions, and by what mechanisms transcription-splicing coupling takes place. PMID:22697243

Interactive Scene Analysis Module - A sensor-database fusion system for telerobotic environments

NASA Technical Reports Server (NTRS)

Cooper, Eric G.; Vazquez, Sixto L.; Goode, Plesent W.

1992-01-01

Accomplishing a task with telerobotics typically involves a combination of operator control/supervision and a 'script' of preprogrammed commands. These commands usually assume that the location of various objects in the task space conform to some internal representation (database) of that task space. The ability to quickly and accurately verify the task environment against the internal database would improve the robustness of these preprogrammed commands. In addition, the on-line initialization and maintenance of a task space database is difficult for operators using Cartesian coordinates alone. This paper describes the Interactive Scene' Analysis Module (ISAM) developed to provide taskspace database initialization and verification utilizing 3-D graphic overlay modelling, video imaging, and laser radar based range imaging. Through the fusion of taskspace database information and image sensor data, a verifiable taskspace model is generated providing location and orientation data for objects in a task space. This paper also describes applications of the ISAM in the Intelligent Systems Research Laboratory (ISRL) at NASA Langley Research Center, and discusses its performance relative to representation accuracy and operator interface efficiency.

Phonon-Driven Oscillatory Plasmonic Excitonic Nanomaterials

DOE PAGES

Kirschner, Matthew S.; Ding, Wendu; Li, Yuxiu; ...

2017-12-01

In this study, we demonstrate that coherent acoustic phonons derived from plasmonic nanoparticles can modulate electronic interactions with proximal excitonic molecular species. A series of gold bipyramids with systematically varied aspect ratios and corresponding localized surface plasmon resonance energies, functionalized with a J-aggregated thiacarbocyanine dye molecule, produce two hybridized states that exhibit clear anti-crossing behavior with a Rabi splitting energy of 120 meV. In metal nanoparticles, photoexcitation generates coherent acoustic phonons that cause oscillations in the plasmon resonance energy. In the coupled system, these photo-generated oscillations alter the metal nanoparticle’s energetic contribution to the hybridized system and, as a result,more » change the coupling between the plasmon and exciton. We demonstrate that such modulations in the hybridization is consistent across a wide range of bipyramid ensembles. We also use Finite-Difference Time Domain calculations to develop a simple model describing this behavior. Lastly, such oscillatory plasmonic-excitonic nanomaterials (OPENs) offer a route to manipulate and dynamically-tune the interactions of plasmonic/excitonic systems and unlock a range of potential applications.« less

User-centered design and usability testing of an innovative health-related quality of life module.

PubMed

Nagykaldi, Z J; Jordan, M; Quitoriano, J; Ciro, C A; Mold, J W

2014-01-01

Various computerized health risk appraisals (HRAs) are available, but few of them assess health-related quality of life (HRQoL) in a goal-directed framework. This study describes the user-centered development and usability testing of an innovative HRQoL module that extends a validated HRA tool in primary care settings. Systematic user-centered design, usability testing, and qualitative methods were used to develop the HRQoL module in primary care practices. Twenty two patients and 5 clinicians participated in two rounds of interactive technology think-out-loud sessions (TOLs) and semi-structured interviews (SSIs) to iteratively develop a four-step, computerized process that collects information on patient goals for meaningful life activities and current level of disability and presents a personalized and prioritized list of preventive recommendations linked to online resources. Analysis of TOLs and SSIs generated 5 categories and 11 sub-categories related to facilitators and barriers to usability and human-technology interaction. The categories included: Understanding the Purpose, Usability, Perceived Value, Literacy, and Participant Motivation. Some categories were inter-connected. The technology was continually and iteratively improved between sessions until saturation of positive feedback was achieved in 4 categories (addressing motivation will require more research). Usability of all screen units of the module was improved substantially. Clinician feedback emphasized the importance of the module's ability to translate the patient-centered HRQoL Report into actionable items for clinicians to facilitate shared decision-making. Complete integration of the HRQoL module into the existing HRA will require further development and testing. Systematic application of user-centered design and human factors principles in technology development and testing may significantly improve the usability and clinical value of health information systems. This more sophisticated approach helped us translate complex clinical concepts, goal-setting steps, and decision-support processes into an accepted and value-added technology.

An ensemble framework for clustering protein-protein interaction networks.

PubMed

Asur, Sitaram; Ucar, Duygu; Parthasarathy, Srinivasan

2007-07-01

Protein-Protein Interaction (PPI) networks are believed to be important sources of information related to biological processes and complex metabolic functions of the cell. The presence of biologically relevant functional modules in these networks has been theorized by many researchers. However, the application of traditional clustering algorithms for extracting these modules has not been successful, largely due to the presence of noisy false positive interactions as well as specific topological challenges in the network. In this article, we propose an ensemble clustering framework to address this problem. For base clustering, we introduce two topology-based distance metrics to counteract the effects of noise. We develop a PCA-based consensus clustering technique, designed to reduce the dimensionality of the consensus problem and yield informative clusters. We also develop a soft consensus clustering variant to assign multifaceted proteins to multiple functional groups. We conduct an empirical evaluation of different consensus techniques using topology-based, information theoretic and domain-specific validation metrics and show that our approaches can provide significant benefits over other state-of-the-art approaches. Our analysis of the consensus clusters obtained demonstrates that ensemble clustering can (a) produce improved biologically significant functional groupings; and (b) facilitate soft clustering by discovering multiple functional associations for proteins. Supplementary data are available at Bioinformatics online.

Defined surface immobilization of glycosaminoglycan molecules for probing and modulation of cell-material interactions.

PubMed

Wang, Kai; Luo, Ying

2013-07-08

As one important category of biological molecules on the cell surface and in the extracellular matrix (ECM), glycosaminoglycans (GAGs) have been widely studied for biomedical applications. With the understanding that the biological functions of GAGs are driven by the complex dynamics of physiological and pathological processes, methodologies are desired to allow the elucidation of cell-GAG interactions with molecular level precision. In this study, a microtiter plate-based system was devised through a new surface modification strategy involving polydopamine (PDA) and GAG molecules functionalized with hydrazide chemical groups. A small library of GAGs including hyaluronic acid (with different molecular weights), heparin, and chondroitin sulfate was successfully immobilized via defined binding sites onto the microtiter plate surface under facile aqueous conditions. The methodology then allowed parallel studies of the GAG-modified surfaces in a high-throughput format. The results show that immobilized GAGs possess distinct properties to mediate protein adsorption, cell adhesion, and inflammatory responses, with each property showing dependence on the type and molecular weight of specific GAG molecules. The PDA-assisted immobilization of hydrazide-functionalized GAGs allows biomimetic attachment of GAG molecules and retains their bioactivity, providing a new methodology to systematically probe fundamental cell-GAG interactions to modulate the bioactivity and biocompatibility of biomaterials.

On Electromagnetic Modulation of Flow Instabilities, Mixing and Heat Transfer in Conducting and Magnetized Fluids

NASA Astrophysics Data System (ADS)

Kenjeres, S.

2016-09-01

In the present paper we give a concise review of some recent highlights of our research dealing with electromagnetic control of flow, mixing and heat transfer of electrically conductive or magnetized fluids. We apply a combination of state-of-art numerical (DNS and LES) and experimental (PIV and LIF) techniques to provide fundamental insights into the complex phenomena of interactions between imposed (or induced) electromagnetic fields and underlying fluid flow. Our analysis covers an extensive range of working fluids, i.e. weakly- and highly-electrically-conductive, as well as magnetized fluids. These interactions are defined through the presence of different types of body forces acting per volume of fluid. A fully closed system of governing equations containing an extended set of the Navier-Stokes and a simplified set of the Maxwell equations is presented. The four characteristic examples are selected: the electromagnetic control of self-sustained jet oscillations, the electromagnetic enhancement of heat transfer in thermal convection, the wake interactions behind magnetic obstacles and finally, the thermo-magnetic convection in differentially heated cubical enclosure. The comparative assessment between experimental and numerical results is presented. It is concluded that generally good agreement between simulations and experiments is obtained for all cases considered, proving the concept of electromagnetic modulation, which can be used in numerous technological applications.

Search for an Annual Modulation in a p-Type Point Contact Germanium Dark Matter Detector

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

Aalseth, Craig E.; Barbeau, Phil; Colaresi, J.

2011-09-01

Fifteen months of cumulative CoGeNT data are examined for indications of an annual modulation, a predicted signature of Weakly Interacting Massive Particle (WIMP) interactions. Presently available data support the presence of a modulated component of unknown origin, with parameters prima facie compatible with a galactic halo composed of light-mass WIMPs.

“Beating speckles” via electrically-induced vibrations of Au nanorods embedded in sol-gel

PubMed Central

Ritenberg, Margarita; Beilis, Edith; Ilovitsh, Asaf; Barkai, Zehava; Shahmoon, Asaf; Richter, Shachar; Zalevsky, Zeev; Jelinek, Raz

2014-01-01

Generation of macroscopic phenomena through manipulating nano-scale properties of materials is among the most fundamental goals of nanotechnology research. We demonstrate cooperative “speckle beats” induced through electric-field modulation of gold (Au) nanorods embedded in a transparent sol-gel host. Specifically, we show that placing the Au nanorod/sol-gel matrix in an alternating current (AC) field gives rise to dramatic modulation of incident light scattered from the material. The speckle light patterns take form of “beats”, for which the amplitude and frequency are directly correlated with the voltage and frequency, respectively, of the applied AC field. The data indicate that the speckle beats arise from localized vibrations of the gel-embedded Au nanorods, induced through the interactions between the AC field and the electrostatically-charged nanorods. This phenomenon opens the way for new means of investigating nanoparticles in constrained environments. Applications in electro-optical devices, such as optical modulators, movable lenses, and others are also envisaged. PMID:24413086

Early bioelectric activities mediate redox-modulated regeneration

PubMed Central

Ferreira, Fernando; Luxardi, Guillaume; Reid, Brian

2016-01-01

Reactive oxygen species (ROS) and electric currents modulate regeneration; however, the interplay between biochemical and biophysical signals during regeneration remains poorly understood. We investigate the interactions between redox and bioelectric activities during tail regeneration in Xenopus laevis tadpoles. We show that inhibition of NADPH oxidase-mediated production of ROS, or scavenging or blocking their diffusion into cells, impairs regeneration and consistently regulates the dynamics of membrane potential, transepithelial potential (TEP) and electric current densities (JI) during regeneration. Depletion of ROS mimics the altered TEP and JI observed in the non-regenerative refractory period. Short-term application of hydrogen peroxide (H2O2) rescues (from depleted ROS) and induces (from the refractory period) regeneration, TEP increase and JI reversal. H2O2 is therefore necessary for and sufficient to induce regeneration and to regulate TEP and JI. Epistasis assays show that voltage-gated Na+ channels act downstream of H2O2 to modulate regeneration. Altogether, these results suggest a novel mechanism for regeneration via redox-bioelectric orchestration. PMID:27827821

Tribotronic Tuning Diode for Active Analog Signal Modulation.

PubMed

Zhou, Tao; Yang, Zhi Wei; Pang, Yaokun; Xu, Liang; Zhang, Chi; Wang, Zhong Lin

2017-01-24

Realizing active interaction with external environment/stimuli is a great challenge for current electronics. In this paper, a tribotronic tuning diode (TTD) is proposed by coupling a variable capacitance diode and a triboelectric nanogenerator in free-standing sliding mode. When the friction layer is sliding on the device surface for electrification, a reverse bias voltage is created and applied to the diode for tuning the junction capacitance. When the sliding distance increases from 0 to 25 mm, the capacitance of the TTD decreases from about 39 to 8 pF. The proposed TTD has been integrated into analog circuits and exhibited excellent performances in frequency modulation, phase shift, and filtering by sliding a finger. This work has demonstrated tunable diode and active analog signal modulation by tribotronics, which has great potential to replace ordinary variable capacitance diodes in various practical applications such as signal processing, electronic tuning circuits, precise tuning circuits, active sensor networks, electronic communications, remote controls, flexible electronics, etc.

A Comprehensive Electronic Health Record Based Patient Navigation Module Including Technology Driven Colorectal Cancer Outreach and Education.

PubMed

Ajeesh, Sunny; Luis, Rustveld

2018-06-01

The purpose of this concept paper is to propose an innovative multifaceted patient navigation module embedded in the Electronic Health Record (EHR) to address barriers to efficient and effective colorectal cancer (CRC) care. The EHR-based CRC patient navigation module will include several patient navigation features: (1) CRC screening registry; (2) patient navigation data, including CRC screening data, outcomes of patient navigation including navigation status (CRC screening referrals, fecal occult blood test (FOBT) completed, colonoscopy scheduled and completed, cancelations, reschedules, and no-shows); (3) CRC counseling aid; and 4) Web-based CRC education application including interactive features such as a standardized colonoscopy preparation guide, modifiable CRC risk factors, and links to existing resources. An essential component of health informatics is the use of EHR systems to not only provide a system for storing and retrieval of patient health data but can also be used to enhance patient decision-making both from a provider and patient perspective.

A Petri net synthesis theory for modeling flexible manufacturing systems.

PubMed

Jeng, M D

1997-01-01

A theory that synthesizes Petri nets for modeling flexible manufacturing systems is presented. The theory adopts a bottom-up or modular-composition approach to construct net models. Each module is modeled as a resource control net (RCN), which represents a subsystem that controls a resource type in a flexible manufacturing system. Interactions among the modules are described as the common transition and transition subnets. The net obtained by merging the modules with two minimal restrictions is shown to be conservative and thus bounded. An algorithm is developed to detect two sufficient conditions for structural liveness of the net. The algorithm examines only the net's structure and the initial marking, and appears to be more efficient than state enumeration techniques such as the reachability tree method. In this paper, the sufficient conditions for liveness are shown to be related to some structural objects called siphons. To demonstrate the applicability of the theory, a flexible manufacturing system of a moderate size is modeled and analyzed using the proposed theory.

"Flipping" the introductory clerkship in radiology: impact on medical student performance and perceptions.

PubMed

Belfi, Lily M; Bartolotta, Roger J; Giambrone, Ashley E; Davi, Caryn; Min, Robert J

2015-06-01

Among methods of "blended learning" (ie, combining online modules with in-class instruction), the "flipped classroom" involves student preclass review of material while reserving class time for interactive knowledge application. We integrated blended learning methodology in a "flipped" introductory clerkship in radiology, and assessed the impact of this approach on the student educational experience (performance and perception). In preparation for the "flipped clerkship," radiology faculty and residents created e-learning modules that were uploaded to an open-source website. The clerkship's 101 rising third-year medical students were exposed to different teaching methods during the course, such as blended learning, traditional lecture learning, and independent learning. Students completed precourse and postcourse knowledge assessments and surveys. Student knowledge improved overall as a result of taking the course. Blended learning achieved greater pretest to post-test improvement of high statistical significance (P value, .0060) compared to lecture learning alone. Blended learning also achieved greater pretest to post-test improvement of borderline statistical significance (P value, .0855) in comparison to independent learning alone. The difference in effectiveness of independent learning versus lecture learning was not statistically significant (P value, .2730). Student perceptions of the online modules used in blended learning portions of the course were very positive. They specifically enjoyed the self-paced interactivity and the ability to return to the modules in the future. Blended learning can be successfully applied to the introductory clerkship in radiology. This teaching method offers educators an innovative and efficient approach to medical student education in radiology. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Hierarchical cortical transcriptome disorganization in autism.

PubMed

Lombardo, Michael V; Courchesne, Eric; Lewis, Nathan E; Pramparo, Tiziano

2017-01-01

Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology. Two ASD cortical transcriptome datasets were re-analyzed using consensus weighted gene co-expression network analysis (WGCNA) to identify common co-expression modules across datasets. Linear mixed-effect models and Bayesian replication statistics were used to identify replicable differentially expressed modules. Eigengene network analysis was then utilized to identify between-group differences in how co-expression modules interact and cluster into hierarchical meta-modular organization. Protein-protein interaction analyses were also used to determine whether dysregulated co-expression modules show enhanced interactions. We find replicable evidence for 10 gene co-expression modules that are differentially expressed in ASD cortex. Rather than being independent non-interacting sources of pathology, these dysregulated co-expression modules work in synergy and physically interact at the protein level. These systems-level transcriptional signals are characterized by downregulation of synaptic processes coordinated with upregulation of immune/inflammation, response to other organism, catabolism, viral processes, translation, protein targeting and localization, cell proliferation, and vasculature development. Hierarchical organization of meta-modules (clusters of highly correlated modules) is also highly affected in ASD. These findings highlight that dysregulation of the ASD cortical transcriptome is characterized by the dysregulation of multiple coordinated transcriptional programs producing synergistic systems-level effects that cannot be fully appreciated by studying the individual component biological processes in isolation.

Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology

PubMed Central

2010-01-01

Background In the literature, there are fruitful algorithmic approaches for identification functional modules in protein-protein interactions (PPI) networks. Because of accumulation of large-scale interaction data on multiple organisms and non-recording interaction data in the existing PPI database, it is still emergent to design novel computational techniques that can be able to correctly and scalably analyze interaction data sets. Indeed there are a number of large scale biological data sets providing indirect evidence for protein-protein interaction relationships. Results The main aim of this paper is to present a prior knowledge based mining strategy to identify functional modules from PPI networks with the aid of Gene Ontology. Higher similarity value in Gene Ontology means that two gene products are more functionally related to each other, so it is better to group such gene products into one functional module. We study (i) to encode the functional pairs into the existing PPI networks; and (ii) to use these functional pairs as pairwise constraints to supervise the existing functional module identification algorithms. Topology-based modularity metric and complex annotation in MIPs will be used to evaluate the identified functional modules by these two approaches. Conclusions The experimental results on Yeast PPI networks and GO have shown that the prior knowledge based learning methods perform better than the existing algorithms. PMID:21172053

Dopamine acting at D1-like, D2-like and α1-adrenergic receptors differentially modulates theta and gamma oscillatory activity in primary motor cortex.

PubMed

Özkan, Mazhar; Johnson, Nicholas W; Sehirli, Umit S; Woodhall, Gavin L; Stanford, Ian M

2017-01-01

The loss of dopamine (DA) in Parkinson's is accompanied by the emergence of exaggerated theta and beta frequency neuronal oscillatory activity in the primary motor cortex (M1) and basal ganglia. DA replacement therapy or deep brain stimulation reduces the power of these oscillations and this is coincident with an improvement in motor performance implying a causal relationship. Here we provide in vitro evidence for the differential modulation of theta and gamma activity in M1 by DA acting at receptors exhibiting conventional and non-conventional DA pharmacology. Recording local field potentials in deep layer V of rat M1, co-application of carbachol (CCh, 5 μM) and kainic acid (KA, 150 nM) elicited simultaneous oscillations at a frequency of 6.49 ± 0.18 Hz (theta, n = 84) and 34.97 ± 0.39 Hz (gamma, n = 84). Bath application of DA resulted in a decrease in gamma power with no change in theta power. However, application of either the D1-like receptor agonist SKF38393 or the D2-like agonist quinpirole increased the power of both theta and gamma suggesting that the DA-mediated inhibition of oscillatory power is by action at other sites other than classical DA receptors. Application of amphetamine, which promotes endogenous amine neurotransmitter release, or the adrenergic α1-selective agonist phenylephrine mimicked the action of DA and reduced gamma power, a result unaffected by prior co-application of D1 and D2 receptor antagonists SCH23390 and sulpiride. Finally, application of the α1-adrenergic receptor antagonist prazosin blocked the action of DA on gamma power suggestive of interaction between α1 and DA receptors. These results show that DA mediates complex actions acting at dopamine D1-like and D2-like receptors, α1 adrenergic receptors and possibly DA/α1 heteromultimeric receptors to differentially modulate theta and gamma activity in M1.

General synthesis of inorganic single-walled nanotubes

PubMed Central

Ni, Bing; Liu, Huiling; Wang, Peng-peng; He, Jie; Wang, Xun

2015-01-01

The single-walled nanotube (SWNT) is an interesting nanostructure for fundamental research and potential applications. However, very few inorganic SWNTs are available to date due to the lack of efficient fabrication methods. Here we synthesize four types of SWNT: sulfide; hydroxide; phosphate; and polyoxometalate. Each type of SWNT possesses essentially uniform diameters. Detailed studies illustrate that the formation of SWNTs is initiated by the self-coiling of the corresponding ultrathin nanostructure embryo/building blocks on the base of weak interactions between them, which is not limited to specific compounds or crystal structures. The interactions between building blocks can be modulated by varying the solvents used, thus multi-walled tubes can also be obtained. Our results reveal that the generalized synthesis of inorganic SWNTs can be achieved by the self-coiling of ultrathin building blocks under the proper weak interactions. PMID:26510862

Convective cell generation by kinetic Alfven wave turbulence in the auroral ionosphere

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

Zhao, J. S.; Wu, D. J.; Yu, M. Y.

2012-06-15

Modulation of convective cells by kinetic Alfven wave (KAW) turbulence is investigated. The interaction is governed by a nonlinear dispersion relation for the convective cells. It is shown that KAW turbulence is disrupted by excitation of the large-scale convective motion through a resonant instability. Application of the results to the auroral ionosphere shows that cross-scale coupling of the KAW turbulence and convective cells plays an important role in the evolution of ionospheric plasma turbulence.

Nonlinear dynamics of cardiovascular ageing

PubMed Central

Shiogai, Y.; Stefanovska, A.; McClintock, P.V.E.

2010-01-01

The application of methods drawn from nonlinear and stochastic dynamics to the analysis of cardiovascular time series is reviewed, with particular reference to the identification of changes associated with ageing. The natural variability of the heart rate (HRV) is considered in detail, including the respiratory sinus arrhythmia (RSA) corresponding to modulation of the instantaneous cardiac frequency by the rhythm of respiration. HRV has been intensively studied using traditional spectral analyses, e.g. by Fourier transform or autoregressive methods, and, because of its complexity, has been used as a paradigm for testing several proposed new methods of complexity analysis. These methods are reviewed. The application of time–frequency methods to HRV is considered, including in particular the wavelet transform which can resolve the time-dependent spectral content of HRV. Attention is focused on the cardio-respiratory interaction by introduction of the respiratory frequency variability signal (RFV), which can be acquired simultaneously with HRV by use of a respiratory effort transducer. Current methods for the analysis of interacting oscillators are reviewed and applied to cardio-respiratory data, including those for the quantification of synchronization and direction of coupling. These reveal the effect of ageing on the cardio-respiratory interaction through changes in the mutual modulation of the instantaneous cardiac and respiratory frequencies. Analyses of blood flow signals recorded with laser Doppler flowmetry are reviewed and related to the current understanding of how endothelial-dependent oscillations evolve with age: the inner lining of the vessels (the endothelium) is shown to be of crucial importance to the emerging picture. It is concluded that analyses of the complex and nonlinear dynamics of the cardiovascular system can illuminate the mechanisms of blood circulation, and that the heart, the lungs and the vascular system function as a single entity in dynamical terms. Clear evidence is found for dynamical ageing. PMID:20396667

Nonlinear dynamics of cardiovascular ageing

NASA Astrophysics Data System (ADS)

Shiogai, Y.; Stefanovska, A.; McClintock, P. V. E.

2010-03-01

The application of methods drawn from nonlinear and stochastic dynamics to the analysis of cardiovascular time series is reviewed, with particular reference to the identification of changes associated with ageing. The natural variability of the heart rate (HRV) is considered in detail, including the respiratory sinus arrhythmia (RSA) corresponding to modulation of the instantaneous cardiac frequency by the rhythm of respiration. HRV has been intensively studied using traditional spectral analyses, e.g. by Fourier transform or autoregressive methods, and, because of its complexity, has been used as a paradigm for testing several proposed new methods of complexity analysis. These methods are reviewed. The application of time-frequency methods to HRV is considered, including in particular the wavelet transform which can resolve the time-dependent spectral content of HRV. Attention is focused on the cardio-respiratory interaction by introduction of the respiratory frequency variability signal (RFV), which can be acquired simultaneously with HRV by use of a respiratory effort transducer. Current methods for the analysis of interacting oscillators are reviewed and applied to cardio-respiratory data, including those for the quantification of synchronization and direction of coupling. These reveal the effect of ageing on the cardio-respiratory interaction through changes in the mutual modulation of the instantaneous cardiac and respiratory frequencies. Analyses of blood flow signals recorded with laser Doppler flowmetry are reviewed and related to the current understanding of how endothelial-dependent oscillations evolve with age: the inner lining of the vessels (the endothelium) is shown to be of crucial importance to the emerging picture. It is concluded that analyses of the complex and nonlinear dynamics of the cardiovascular system can illuminate the mechanisms of blood circulation, and that the heart, the lungs and the vascular system function as a single entity in dynamical terms. Clear evidence is found for dynamical ageing.

Inner-outer interactions in a turbulent boundary layer overlying complex roughness

NASA Astrophysics Data System (ADS)

Pathikonda, Gokul; Christensen, Kenneth T.

2017-04-01

Hot-wire measurements were performed in a zero-pressure-gradient turbulent boundary layer overlying both a smooth and a rough wall for the purpose of investigating the details of inner-outer flow interactions. The roughness considered embodies a broad range of topographical scales arranged in an irregular manner and reflects the topographical complexity often encountered in practical flow systems. Single-probe point-wise measurements with a traversing probe were made at two different regions of the rough-wall flow, which was previously shown to be heterogeneous in the spanwise direction, to investigate the distribution of streamwise turbulent kinetic energy and large scale-small scale interactions. In addition, two-probe simultaneous measurements were conducted enabling investigation of inner-outer interactions, wherein the large scales were independently sampled in the outer layer. Roughness-induced changes to the near-wall behavior were investigated, particularly by contrasting the amplitude and frequency modulation effects of inner-outer interactions in the rough-wall flow with well-established smooth-wall flow phenomena. It was observed that the rough-wall flow exhibits both amplitude and frequency modulation features close to the wall in a manner very similar to smooth-wall flow, though the correlated nature of these effects was found to be more intense in the rough-wall flow. In particular, frequency modulation was found to illuminate these enhanced modulation effects in the rough-wall flow. The two-probe measurements helped in evaluating the suitability of the interaction-schematic recently proposed by Baars et al., Exp. Fluids 56, 1 (2015), 10.1007/s00348-014-1876-4 for rough-wall flows. This model was found to be suitable for the rough-wall flow considered herein, and it was found that frequency modulation is a "cleaner" measure of the inner-outer modulation interactions for this rough-wall flow.

Actin-Based Adhesion Modules Mediate Cell Interactions with the Extracellular Matrix and Neighboring Cells.

PubMed

Bachir, Alexia I; Horwitz, Alan Rick; Nelson, W James; Bianchini, Julie M

2017-07-05

Cell adhesions link cells to the extracellular matrix (ECM) and to each other and depend on interactions with the actin cytoskeleton. Both cell-ECM and cell-cell adhesion sites contain discrete, yet overlapping, functional modules. These modules establish physical associations with the actin cytoskeleton, locally modulate actin organization and dynamics, and trigger intracellular signaling pathways. Interplay between these modules generates distinct actin architectures that underlie different stages, types, and functions of cell-ECM and cell-cell adhesions. Actomyosin contractility is required to generate mature, stable adhesions, as well as to sense and translate the mechanical properties of the cellular environment into changes in cell organization and behavior. Here, we review the organization and function of different adhesion modules and how they interact with the actin cytoskeleton. We highlight the molecular mechanisms of mechanotransduction in adhesions and how adhesion molecules mediate cross talk between cell-ECM and cell-cell adhesion sites. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

BinTree Seeking: A Novel Approach to Mine Both Bi-Sparse and Cohesive Modules in Protein Interaction Networks

PubMed Central

Shen, Hong-Bin

2011-01-01

Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between their components. Many methods were proposed to capture cohesive modules so that there is a higher density of edges within modules than those across them. Recent studies reveal that cohesively interacting modules of proteins is not a universal organizing principle in PINs, which has opened up new avenues for revisiting functional modules in PINs. In this paper, functional clusters in PINs are found to be able to form unorthodox structures defined as bi-sparse module. In contrast to the traditional cohesive module, the nodes in the bi-sparse module are sparsely connected internally and densely connected with other bi-sparse or cohesive modules. We present a novel protocol called the BinTree Seeking (BTS) for mining both bi-sparse and cohesive modules in PINs based on Edge Density of Module (EDM) and matrix theory. BTS detects modules by depicting links and nodes rather than nodes alone and its derivation procedure is totally performed on adjacency matrix of networks. The number of modules in a PIN can be automatically determined in the proposed BTS approach. BTS is tested on three real PINs and the results demonstrate that functional modules in PINs are not dominantly cohesive but can be sparse. BTS software and the supporting information are available at: www.csbio.sjtu.edu.cn/bioinf/BTS/. PMID:22140454

A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction

PubMed Central

Tsai, Kuang-Lei; Sato, Shigeo; Tomomori-Sato, Chieri; Conaway, Ronald C.; Conaway, Joan W.; Asturias, Francisco J.

2013-01-01

The CDK8 kinase module (CKM) is a conserved, dissociable Mediator subcomplex whose component subunits were genetically linked to the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and individually recognized as transcriptional repressors before Mediator was identified as a preeminent complex in eukaryotic transcription regulation. We used macromolecular electron microscopy and biochemistry to investigate the subunit organization, structure, and Mediator interaction of the Saccharomyces cerevisiae CKM. We found that interaction of the CKM with Mediator’s Middle module interferes with CTD-dependent RNAPII binding to a previously unknown Middle module CTD-binding site targeted early on in a multi-step holoenzyme formation process. Taken together, our results reveal the basis for CKM repression, clarify the origin of the connection between CKM subunits and the CTD, and suggest that a combination of competitive interactions and conformational changes that facilitate holoenzyme formation underlie the Mediator mechanism. PMID:23563140

A MASSive Laboratory Tour. An Interactive Mass Spectrometry Outreach Activity for Children

NASA Astrophysics Data System (ADS)

Jungmann, Julia H.; Mascini, Nadine E.; Kiss, Andras; Smith, Donald F.; Klinkert, Ivo; Eijkel, Gert B.; Duursma, Marc C.; Cillero Pastor, Berta; Chughtai, Kamila; Chughtai, Sanaullah; Heeren, Ron M. A.

2013-07-01

It is imperative to fascinate young children at an early stage in their education for the analytical sciences. The exposure of the public to mass spectrometry presently increases rapidly through the common media. Outreach activities can take advantage of this exposure and employ mass spectrometry as an exquisite example of an analytical science in which children can be fascinated. The presented teaching modules introduce children to mass spectrometry and give them the opportunity to experience a modern research laboratory. The modules are highly adaptable and can be applied to young children from the age of 6 to 14 y. In an interactive tour, the students explore three major scientific concepts related to mass spectrometry; the building blocks of matter, charged particle manipulation by electrostatic fields, and analyte identification by mass analysis. Also, the students carry out a mass spectrometry experiment and learn to interpret the resulting mass spectra. The multistage, inquiry-based tour contains flexible methods, which teach the students current-day research techniques and possible applications to real research topics. Besides the scientific concepts, laboratory safety and hygiene are stressed and the students are enthused for the analytical sciences by participating in "hands-on" work. The presented modules have repeatedly been successfully employed during laboratory open days. They are also found to be extremely suitable for (early) high school science classes during laboratory visit-focused field trips.

Eccentricity Evolution of Extrasolar Multiple Planetary Systems Due to the Depletion of Nascent Protostellar Disks

NASA Astrophysics Data System (ADS)

Nagasawa, M.; Lin, D. N. C.; Ida, S.

2003-04-01

Most extrasolar planets are observed to have eccentricities much larger than those in the solar system. Some of these planets have sibling planets, with comparable masses, orbiting around the same host stars. In these multiple planetary systems, eccentricity is modulated by the planets' mutual secular interaction as a consequence of angular momentum exchange between them. For mature planets, the eigenfrequencies of this modulation are determined by their mass and semimajor axis ratios. However, prior to the disk depletion, self-gravity of the planets' nascent disks dominates the precession eigenfrequencies. We examine here the initial evolution of young planets' eccentricity due to the apsidal libration or circulation induced by both the secular interaction between them and the self-gravity of their nascent disks. We show that as the latter effect declines adiabatically with disk depletion, the modulation amplitude of the planets' relative phase of periapsis is approximately invariant despite the time-asymmetrical exchange of angular momentum between planets. However, as the young planets' orbits pass through a state of secular resonance, their mean eccentricities undergo systematic quantitative changes. For applications, we analyze the eccentricity evolution of planets around υ Andromedae and HD 168443 during the epoch of protostellar disk depletion. We find that the disk depletion can change the planets' eccentricity ratio. However, the relatively large amplitude of the planets' eccentricity cannot be excited if all the planets had small initial eccentricities.

System and technique for retrieving depth information about a surface by projecting a composite image of modulated light patterns

NASA Technical Reports Server (NTRS)

Hassebrook, Laurence G. (Inventor); Lau, Daniel L. (Inventor); Guan, Chun (Inventor)

2010-01-01

A technique, associated system and program code, for retrieving depth information about at least one surface of an object, such as an anatomical feature. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the anatomical feature; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to produce a depth map/mapping thereof. Each signal waveform used for the modulation of a respective structured light pattern, is distinct from each of the other signal waveforms used for the modulation of other structured light patterns of a composite image; these signal waveforms may be selected from suitable types in any combination of distinct signal waveforms, provided the waveforms used are uncorrelated with respect to each other. The depth map/mapping to be utilized in a host of applications, for example: displaying a 3-D view of the object; virtual reality user-interaction interface with a computerized device; face--or other animal feature or inanimate object--recognition and comparison techniques for security or identification purposes; and 3-D video teleconferencing/telecollaboration.

System and technique for retrieving depth information about a surface by projecting a composite image of modulated light patterns

NASA Technical Reports Server (NTRS)

Guan, Chun (Inventor); Hassebrook, Laurence G. (Inventor); Lau, Daniel L. (Inventor)

2008-01-01

A technique, associated system and program code, for retrieving depth information about at least one surface of an object. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the object; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to produce a depth map/mapping thereof. Each signal waveform used for the modulation of a respective structured light pattern, is distinct from each of the other signal waveforms used for the modulation of other structured light patterns of a composite image; these signal waveforms may be selected from suitable types in any combination of distinct signal waveforms, provided the waveforms used are uncorrelated with respect to each other. The depth map/mapping to be utilized in a host of applications, for example: displaying a 3-D view of the object; virtual reality user-interaction interface with a computerized device; face--or other animal feature or inanimate object--recognition and comparison techniques for security or identification purposes; and 3-D video teleconferencing/telecollaboration.

Identification of Unstable Network Modules Reveals Disease Modules Associated with the Progression of Alzheimer’s Disease

PubMed Central

Kikuchi, Masataka; Ogishima, Soichi; Miyamoto, Tadashi; Miyashita, Akinori; Kuwano, Ryozo; Nakaya, Jun; Tanaka, Hiroshi

2013-01-01

Alzheimer’s disease (AD), the most common cause of dementia, is associated with aging, and it leads to neuron death. Deposits of amyloid β and aberrantly phosphorylated tau protein are known as pathological hallmarks of AD, but the underlying mechanisms have not yet been revealed. A high-throughput gene expression analysis previously showed that differentially expressed genes accompanying the progression of AD were more down-regulated than up-regulated in the later stages of AD. This suggested that the molecular networks and their constituent modules collapsed along with AD progression. In this study, by using gene expression profiles and protein interaction networks (PINs), we identified the PINs expressed in three brain regions: the entorhinal cortex (EC), hippocampus (HIP) and superior frontal gyrus (SFG). Dividing the expressed PINs into modules, we examined the stability of the modules with AD progression and with normal aging. We found that in the AD modules, the constituent proteins, interactions and cellular functions were not maintained between consecutive stages through all brain regions. Interestingly, the modules were collapsed with AD progression, specifically in the EC region. By identifying the modules that were affected by AD pathology, we found the transcriptional regulation-associated modules that interact with the proteasome-associated module via UCHL5 hub protein, which is a deubiquitinating enzyme. Considering PINs as a system made of network modules, we found that the modules relevant to the transcriptional regulation are disrupted in the EC region, which affects the ubiquitin-proteasome system. PMID:24348898

Development of a mobile borehole investigation software using augmented reality

NASA Astrophysics Data System (ADS)

Son, J.; Lee, S.; Oh, M.; Yun, D. E.; Kim, S.; Park, H. D.

2015-12-01

Augmented reality (AR) is one of the most developing technologies in smartphone and IT areas. While various applications have been developed using the AR, there are a few geological applications which adopt its advantages. In this study, a smartphone application to manage boreholes using AR has been developed. The application is consisted of three major modules, an AR module, a map module and a data management module. The AR module calculates the orientation of the device and displays nearby boreholes distributed in three dimensions using the orientation. This module shows the boreholes in a transparent layer on a live camera screen so the user can find and understand the overall characteristics of the underground geology. The map module displays the boreholes on a 2D map to show their distribution and the location of the user. The database module uses SQLite library which has proper characteristics for mobile platforms, and Binary XML is adopted to enable containing additional customized data. The application is able to provide underground information in an intuitive and refined forms and to decrease time and general equipment required for geological field investigations.

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…

A Unified Approach to Model-Based Planning and Execution

NASA Technical Reports Server (NTRS)

Muscettola, Nicola; Dorais, Gregory A.; Fry, Chuck; Levinson, Richard; Plaunt, Christian; Norvig, Peter (Technical Monitor)

2000-01-01

Writing autonomous software is complex, requiring the coordination of functionally and technologically diverse software modules. System and mission engineers must rely on specialists familiar with the different software modules to translate requirements into application software. Also, each module often encodes the same requirement in different forms. The results are high costs and reduced reliability due to the difficulty of tracking discrepancies in these encodings. In this paper we describe a unified approach to planning and execution that we believe provides a unified representational and computational framework for an autonomous agent. We identify the four main components whose interplay provides the basis for the agent's autonomous behavior: the domain model, the plan database, the plan running module, and the planner modules. This representational and problem solving approach can be applied at all levels of the architecture of a complex agent, such as Remote Agent. In the rest of the paper we briefly describe the Remote Agent architecture. The new agent architecture proposed here aims at achieving the full Remote Agent functionality. We then give the fundamental ideas behind the new agent architecture and point out some implication of the structure of the architecture, mainly in the area of reactivity and interaction between reactive and deliberative decision making. We conclude with related work and current status.

Propagation of modulated electron and X-ray beams through matter and interactions with radio-frequency structures

NASA Astrophysics Data System (ADS)

Harris, J. R.; Miller, R. B.

2018-02-01

The generation and evolution of modulated particle beams and their interactions with resonant radiofrequency (RF) structures are of fundamental interest for both particle accelerator and vacuum electronic systems. When the constraint of propagation in a vacuum is removed, the evolution of such beams can be greatly affected by interactions with matter including scattering, absorption, generation of atmospheric plasma, and the production of multiple generations of secondary particles. Here, we study the propagation of 21 MeV and 25 MeV electron beams produced in S-band and L-band linear accelerators, and their interaction with resonant RF structures, under a number of combinations of geometry, including transmission through both air and metal. Both resonant and nonresonant interactions were observed, with the resonant interactions indicating that the RF modulation on the electron beam is at least partially preserved as the beam propagates through air and metal. When significant thicknesses of metal are placed upstream of a resonant structure, preventing any primary beam electrons from reaching the structure, RF signals could still be induced in the structures. This indicated that the RF modulation present on the electron beam was also impressed onto the x-rays generated when the primary electrons were stopped in the metal, and that this RF modulation was also present on the secondary electrons generated when the x-rays struck the resonant structures. The nature of these interactions and their sensitivities to changes in system configurations will be discussed.

Fragment Impact Toolkit (FIT)

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

Shevitz, Daniel Wolf; Key, Brian P.; Garcia, Daniel B.

2017-09-05

The Fragment Impact Toolkit (FIT) is a software package used for probabilistic consequence evaluation of fragmenting sources. The typical use case for FIT is to simulate an exploding shell and evaluate the consequence on nearby objects. FIT is written in the programming language Python and is designed as a collection of interacting software modules. Each module has a function that interacts with the other modules to produce desired results.

Land Application of Wastes: An Educational Program. Legal Aspects - Module 16.

ERIC Educational Resources Information Center

Clarkson, W. W.; And Others

This module summarizes laws that are relevant to the land application of wastes, focusing on the applicable Federal laws and representative state regulations from different areas of the country. The module describes the 10 points of Public Law 92-500, the Federal Water Pollution Control Act Amendments of 1972, that relate to land application. It…

Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex

PubMed Central

Han, Yan; Luo, Jie; Ranish, Jeffrey; Hahn, Steven

2014-01-01

The conserved transcription coactivator SAGA is comprised of several modules that are involved in activator binding, TBP binding, histone acetylation (HAT) and deubiquitination (DUB). Crosslinking and mass spectrometry, together with genetic and biochemical analyses, were used to determine the molecular architecture of the SAGA-TBP complex. We find that the SAGA Taf and Taf-like subunits form a TFIID-like core complex at the center of SAGA that makes extensive interactions with all other SAGA modules. SAGA-TBP binding involves a network of interactions between subunits Spt3, Spt8, Spt20, and Spt7. The HAT and DUB modules are in close proximity, and the DUB module modestly stimulates HAT function. The large activator-binding subunit Tra1 primarily connects to the TFIID-like core via its FAT domain. These combined results were used to derive a model for the arrangement of the SAGA subunits and its interactions with TBP. Our results provide new insight into SAGA function in gene regulation, its structural similarity with TFIID, and functional interactions between the SAGA modules. PMID:25216679

Attention operates uniformly throughout the classical receptive field and the surround.

PubMed

Verhoef, Bram-Ernst; Maunsell, John Hr

2016-08-22

Shifting attention among visual stimuli at different locations modulates neuronal responses in heterogeneous ways, depending on where those stimuli lie within the receptive fields of neurons. Yet how attention interacts with the receptive-field structure of cortical neurons remains unclear. We measured neuronal responses in area V4 while monkeys shifted their attention among stimuli placed in different locations within and around neuronal receptive fields. We found that attention interacts uniformly with the spatially-varying excitation and suppression associated with the receptive field. This interaction explained the large variability in attention modulation across neurons, and a non-additive relationship among stimulus selectivity, stimulus-induced suppression and attention modulation that has not been previously described. A spatially-tuned normalization model precisely accounted for all observed attention modulations and for the spatial summation properties of neurons. These results provide a unified account of spatial summation and attention-related modulation across both the classical receptive field and the surround.

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms

PubMed Central

Bianco, Luca; Riccadonna, Samantha; Lavezzo, Enrico; Falda, Marco; Formentin, Elide; Cavalieri, Duccio; Toppo, Stefano

2017-01-01

Abstract Summary: Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. Availability and Implementation: Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. Contact: paolo.fontana@fmach.it PMID:28158604

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

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

Reinke, Aaron W.; Grant, Robert A.; Keating, Amy E.

2010-06-21

The versatile coiled-coil protein motif is widely used to induce and control macromolecular interactions in biology and materials science. Yet the types of interaction patterns that can be constructed using known coiled coils are limited. Here we greatly expand the coiled-coil toolkit by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coils using peptide microarrays. The resulting 55-member protein 'interactome' includes 27 pairs of interacting peptides that preferentially heteroassociate. The 27 pairs can be used in combinations to assemble sets of 3 to 6 proteins that compose networks of varying topologies. Of specialmore » interest are heterospecific peptide pairs that participate in mutually orthogonal interactions. Such pairs provide the opportunity to dimerize two separate molecular systems without undesired crosstalk. Solution and structural characterization of two such sets of orthogonal heterodimers provide details of their interaction geometries. The orthogonal pair, along with the many other network motifs discovered in our screen, provide new capabilities for synthetic biology and other applications.« less

Synchronous Oscillations in Van Der Pol Generator with Modulated Natural Frequency

NASA Astrophysics Data System (ADS)

Nimets, A. Yu.; Vavriv, D. M.

2015-12-01

The synchronous operation of Van Der Pole generator with the low-frequency modulated natural frequency has been investigated. The presence of low-frequency modulation is shown to lead to formation of additional synchronization regions. The appearance of such regions is found to be caused by threefrequency resonances resulted from the interaction between oscillations of the generator natural frequency, modulation frequency and synchronized signal frequency. Characteristics of synchronous oscillations due to the below mentioned three-frequency interaction are obtained and comparison with the case of synchronization of oscillator on the main mode made.

Block 4 solar cell module design and test specification for intermediate load center applications

NASA Technical Reports Server (NTRS)

1978-01-01

Requirements for performance of terrestrial solar cell modules intended for use in various test applications are established. During the 1979-80 time period, such applications are expected to be in the 20 to 500 kilowatt size range. A series of characterization and qualification tests necessary to certify the module design for production, and the necessary performance test for acceptance of modules are specified.

Finding Correlation between Protein Protein Interaction Modules Using Semantic Web Techniques

NASA Astrophysics Data System (ADS)

Kargar, Mehdi; Moaven, Shahrouz; Abolhassani, Hassan

Many complex networks such as social networks and computer show modular structures, where edges between nodes are much denser within modules than between modules. It is strongly believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. In this paper we used a human curated dataset. In this paper we consider each module in the PPI network as ontology. Using techniques in ontology alignment, we compare each pair of modules in the network. We want to see that is there a correlation between the structure of each module or they have totally different structures. Our results show that there is no correlation between proteins in a protein protein interaction network.

Interactions between the jasmonic and salicylic acid pathway modulate the plant metabolome and affect herbivores of different feeding types.

PubMed

Schweiger, R; Heise, A-M; Persicke, M; Müller, C

2014-07-01

The phytohormones jasmonic acid (JA) and salicylic acid (SA) mediate induced plant defences and the corresponding pathways interact in a complex manner as has been shown on the transcript and proteine level. Downstream, metabolic changes are important for plant-herbivore interactions. This study investigated metabolic changes in leaf tissue and phloem exudates of Plantago lanceolata after single and combined JA and SA applications as well as consequences on chewing-biting (Heliothis virescens) and piercing-sucking (Myzus persicae) herbivores. Targeted metabolite profiling and untargeted metabolic fingerprinting uncovered different categories of plant metabolites, which were influenced in a specific manner, indicating points of divergence, convergence, positive crosstalk and pronounced mutual antagonism between the signaling pathways. Phytohormone-specific decreases of primary metabolite pool sizes in the phloem exudates may indicate shifts in sink-source relations, resource allocation, nutrient uptake or photosynthesis. Survival of both herbivore species was significantly reduced by JA and SA treatments. However, the combined application of JA and SA attenuated the negative effects at least against H. virescens suggesting that mutual antagonism between the JA and SA pathway may be responsible. Pathway interactions provide a great regulatory potential for the plant that allows triggering of appropriate defences when attacked by different antagonist species. © 2013 John Wiley & Sons Ltd.

Essential attributes identified in the design of a Laboratory Information Management System for a high throughput siRNA screening laboratory.

PubMed

Grandjean, Geoffrey; Graham, Ryan; Bartholomeusz, Geoffrey

2011-11-01

In recent years high throughput screening operations have become a critical application in functional and translational research. Although a seemingly unmanageable amount of data is generated by these high-throughput, large-scale techniques, through careful planning, an effective Laboratory Information Management System (LIMS) can be developed and implemented in order to streamline all phases of a workflow. Just as important as data mining and analysis procedures at the end of complex processes is the tracking of individual steps of applications that generate such data. Ultimately, the use of a customized LIMS will enable users to extract meaningful results from large datasets while trusting the robustness of their assays. To illustrate the design of a custom LIMS, this practical example is provided to highlight the important aspects of the design of a LIMS to effectively modulate all aspects of an siRNA screening service. This system incorporates inventory management, control of workflow, data handling and interaction with investigators, statisticians and administrators. All these modules are regulated in a synchronous manner within the LIMS. © 2011 Bentham Science Publishers

Halo-independent determination of the unmodulated WIMP signal in DAMA: the isotropic case

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

Gondolo, Paolo; Scopel, Stefano, E-mail: paolo.gondolo@utah.edu, E-mail: scopel@sogang.ac.kr

2017-09-01

We present a halo-independent determination of the unmodulated signal corresponding to the DAMA modulation if interpreted as due to dark matter weakly interacting massive particles (WIMPs). First we show how a modulated signal gives information on the WIMP velocity distribution function in the Galactic rest frame from which the unmodulated signal descends. Then we describe a mathematically-sound profile likelihood analysis in which the likelihood is profiled over a continuum of nuisance parameters (namely, the WIMP velocity distribution). As a first application of the method, which is very general and valid for any class of velocity distributions, we restrict the analysismore » to velocity distributions that are isotropic in the Galactic frame. In this way we obtain halo-independent maximum-likelihood estimates and confidence intervals for the DAMA unmodulated signal. We find that the estimated unmodulated signal is in line with expectations for a WIMP-induced modulation and is compatible with the DAMA background+signal rate. Specifically, for the isotropic case we find that the modulated amplitude ranges between a few percent and about 25% of the unmodulated amplitude, depending on the WIMP mass.« less

Online Chemistry Modules: Interaction and Effective Faculty Facilitation

ERIC Educational Resources Information Center

Slocum, Laura E.; Towns Marcy Hamby; Zielinski, Theresa Julia

2004-01-01

Computer supported collaborative learning, cooperative learning combined with electronic communication, physical chemistry online modules, use of discussion boards, its advantages and limitations are experimented and discussed. The most important finding is the example of effective online faculty facilitation and interaction.

[The future of telepathology. An Internet "distributed system" with "open standards"].

PubMed

Brauchli, K; Helfrich, M; Christen, H; Jundt, G; Haroske, G; Mihatsch, M; Oberli, H; Oberholzer, M

2002-05-01

With the availability of Internet, the interest in the possibilities of telepathology has increased considerably. In the foreground is thereby the need of the non-expert to bring in the opinions of experts on morphological findings by means of a fast and simple procedure. The new telepathology system iPath is in compliance with these needs. The system is based on small, but when possible independently working modules. This concept allows a simple adaptation of the system to the individual environment of the user (e.g. for different cameras, frame-grabbers, microscope steering tables etc.) and for individual needs. iPath has been in use for 6 months with various working groups. In telepathology a distinction is made between "passive" and "active" consultations but for both forms a non-expert brings in the opinion of an expert. In an active consultation both are in direct connection with each other (orally or via a chat-function), this is however not the case with a passive consultation. An active consultation can include the interactive discussion of the expert with the non-expert on images in an image database or the direct interpretation of images from a microscope by the expert. Four software modules are available for a free and as fast as possible application: (1) the module "Microscope control", (2) the module "Connector" (insertion of images directly from the microscope without a motorized microscope), (3) the module "Client-application" via the web-browser and (4) the module "Server" with a database. The server is placed in the internet and not behind a firewall. The server permanently receives information from the periphery and returns the information to the periphery on request. The only thing which the expert, the non-expert and the microscope have to know is how contact can made with the server.

Teleoperated Modular Robots for Lunar Operations

NASA Technical Reports Server (NTRS)

Globus, Al; Hornby, Greg; Larchev, Greg; Hancher, Matt; Cannon, Howard; Lohn, Jason

2004-01-01

Solar system exploration is currently carried out by special purpose robots exquisitely designed for the anticipated tasks. However, all contingencies for in situ resource utilization (ISRU), human habitat preparation, and exploration will be difficult to anticipate. Furthermore, developing the necessary special purpose mechanisms for deployment and other capabilities is difficult and error prone. For example, the Galileo high gain antenna never opened, severely restricting the quantity of data returned by the spacecraft. Also, deployment hardware is used only once. To address these problems, we are developing teleoperated modular robots for lunar missions, including operations in transit from Earth. Teleoperation of lunar systems from Earth involves a three second speed-of-light delay, but experiment suggests that interactive operations are feasible.' Modular robots typically consist of many identical modules that pass power and data between them and can be reconfigured for different tasks providing great flexibility, inherent redundancy and graceful degradation as modules fail. Our design features a number of different hub, link, and joint modules to simplify the individual modules, lower structure cost, and provide specialized capabilities. Modular robots are well suited for space applications because of their extreme flexibility, inherent redundancy, high-density packing, and opportunities for mass production. Simple structural modules can be manufactured from lunar regolith in situ using molds or directed solar sintering. Software to direct and control modular robots is difficult to develop. We have used genetic algorithms to evolve both the morphology and control system for walking modular robots3 We are currently using evolvable system technology to evolve controllers for modular robots in the ISS glove box. Development of lunar modular robots will require software and physical simulators, including regolith simulation, to enable design and test of robot software and hardware, particularly automation software. Ready access to these simulators could provide opportunities for contest-driven development ala RoboCup (http://www.robocup.org/). Licensing of module designs could provide opportunities in the toy market and for spin-off applications.

A software architecture for multidisciplinary applications: Integrating task and data parallelism

NASA Technical Reports Server (NTRS)

Chapman, Barbara; Mehrotra, Piyush; Vanrosendale, John; Zima, Hans

1994-01-01

Data parallel languages such as Vienna Fortran and HPF can be successfully applied to a wide range of numerical applications. However, many advanced scientific and engineering applications are of a multidisciplinary and heterogeneous nature and thus do not fit well into the data parallel paradigm. In this paper we present new Fortran 90 language extensions to fill this gap. Tasks can be spawned as asynchronous activities in a homogeneous or heterogeneous computing environment; they interact by sharing access to Shared Data Abstractions (SDA's). SDA's are an extension of Fortran 90 modules, representing a pool of common data, together with a set of Methods for controlled access to these data and a mechanism for providing persistent storage. Our language supports the integration of data and task parallelism as well as nested task parallelism and thus can be used to express multidisciplinary applications in a natural and efficient way.

The Use of Simulation to Teach Suicide Risk Assessment to Health Profession Trainees-Rationale, Methodology, and a Proof of Concept Demonstration with a Virtual Patient.

PubMed

Foster, Adriana; Chaudhary, Neelam; Murphy, James; Lok, Benjamin; Waller, Jennifer; Buckley, Peter F

2015-12-01

There is increasing use of educational technologies in medical and surgical specialties. Described herein is the development and application of an interactive virtual patient (VP) to teach suicide risk assessment to health profession trainees. We studied the effect of the following: (1) an interaction with a bipolar VP who attempts suicide or (2) completion of a video-teaching module on interviewing a bipolar patient, on medical students' proficiency in assessing suicide risk in standardized patients. We hypothesized that students who interact with a bipolar VP will be at least as likely to assess suicide risk, as their peers who completed a video module. In a randomized, controlled study, we compared the frequency with which second-year students at the Medical College of Georgia asked suicide risk and bipolar symptoms questions by VP/video group. We recruited 67 students. The VP group inquired more frequently than the video group in 4 of 5 suicide risk areas and 11 of 14 other bipolar symptomatology areas. There were minimal to small effect sizes in favor of the VP technology. The students preferred the video over the VP as an educational tool (p = 0.007). Our study provides proof of concept that both VP and video module approaches are feasible for teaching students to assess suicide risk, and we present evidence about the role of active learning to improve communication skills. Depending on the learning context, interviewing a VP or observation of a videotaped interview can enhance the students' suicide risk assessment proficiency in an interview with a standardized patient. An interactive VP is a plausible modality to deliver basic concepts of suicide risk assessment to medical students, can facilitate individual preferences by providing easy access and portability, and has potential generalizability to other aspects of psychiatric training.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

PubMed Central

Gunner, MR; Baker, Nathan A.

2017-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. PMID:27497160

Mueller matrix polarimetry imaging for breast cancer analysis (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gribble, Adam; Vitkin, Alex

2017-02-01

Polarized light has many applications in biomedical imaging. The interaction of a biological sample with polarized light reveals information about its biological composition, both structural and functional. The most comprehensive type of polarimetry analysis is to measure the Mueller matrix, a polarization transfer function that completely describes how a sample interacts with polarized light. However, determination of the Mueller matrix requires tissue analysis under many different states of polarized light; a time consuming and measurement intensive process. Here we address this limitation with a new rapid polarimetry system, and use this polarimetry platform to investigate a variety of tissue changes associated with breast cancer. We have recently developed a rapid polarimetry imaging platform based on four photoelastic modulators (PEMs). The PEMs generate fast polarization modulations that allow the complete sample Mueller matrix to be imaged over a large field of view, with no moving parts. This polarimetry system is then demonstrated to be sensitive to a variety of tissue changes that are relevant to breast cancer. Specifically, we show that changes in depolarization can reveal tumor margins, and can differentiate between viable and necrotic breast cancer metastasized to the lymph nodes. Furthermore, the polarimetric property of linear retardance (related to birefringence) is dependent on collagen organization in the extracellular matrix. These findings indicate that our polarimetry platform may have future applications in fields such as breast cancer diagnosis, improving the speed and efficacy of intraoperative pathology, and providing prognostic information that may be beneficial for guiding treatment.

Intracellular signal modulation by nanomaterials.

PubMed

Hussain, Salik; Garantziotis, Stavros; Rodrigues-Lima, Fernando; Dupret, Jean-Marie; Baeza-Squiban, Armelle; Boland, Sonja

2014-01-01

A thorough understanding of the interactions of nanomaterials with biological systems and the resulting activation of signal transduction pathways is essential for the development of safe and consumer friendly nanotechnology. Here we present an overview of signaling pathways induced by nanomaterial exposures and describe the possible correlation of their physicochemical characteristics with biological outcomes. In addition to the hierarchical oxidative stress model and a review of the intrinsic and cell-mediated mechanisms of reactive oxygen species (ROS) generating capacities of nanomaterials, we also discuss other oxidative stress dependent and independent cellular signaling pathways. Induction of the inflammasome, calcium signaling, and endoplasmic reticulum stress are reviewed. Furthermore, the uptake mechanisms can be of crucial importance for the cytotoxicity of nanomaterials and membrane-dependent signaling pathways have also been shown to be responsible for cellular effects of nanomaterials. Epigenetic regulation by nanomaterials, effects of nanoparticle-protein interactions on cell signaling pathways, and the induction of various cell death modalities by nanomaterials are described. We describe the common trigger mechanisms shared by various nanomaterials to induce cell death pathways and describe the interplay of different modalities in orchestrating the final outcome after nanomaterial exposures. A better understanding of signal modulations induced by nanomaterials is not only essential for the synthesis and design of safer nanomaterials but will also help to discover potential nanomedical applications of these materials. Several biomedical applications based on the different signaling pathways induced by nanomaterials are already proposed and will certainly gain a great deal of attraction in the near future.

Intracellular Signal Modulation by Nanomaterials

PubMed Central

Hussain, Salik; Garantziotis, Stavros; Rodrigues-Lima, Fernando; Dupret, Jean-Marie; Baeza-Squiban, Armelle; Boland, Sonja

2016-01-01

A thorough understanding of the interactions of nanomaterials with biological systems and the resulting activation of signal transduction pathways is essential for the development of safe and consumer friendly nanotechnology. Here we present an overview of signaling pathways induced by nanomaterial exposures and describe the possible correlation of their physicochemical characteristics with biological outcomes. In addition to the hierarchical oxidative stress model and a review of the intrinsic and cell-mediated mechanisms of reactive Oxygen species (ROS) generating capacities of nanomaterials, we also discuss other oxidative stress dependent and independent cellular signaling pathways. Induction of the inflammasome, calcium signaling, and endoplasmic reticulum stress are reviewed. Furthermore, the uptake mechanisms can crucially affect the cytotoxicity of nanomaterials and membrane-dependent signaling pathways can be responsible for cellular effects of nanomaterials. Epigenetic regulation by nanomaterials effects of nanoparticle-protein interactions on cell signaling pathways, and the induction of various cell death modalities by nanomaterials are described. We describe the common trigger mechanisms shared by various nanomaterials to induce cell death pathways and describe the interplay of different modalities in orchestrating the final outcome after nanomaterial exposures. A better understanding of signal modulations induced by nanomaterials is not only essential for the synthesis and design of safer nanomaterials but will also help to discover potential nanomedical applications of these materials. Several biomedical applications based on the different signaling pathways induced by nanomaterials are already proposed and will certainly gain a great deal of attraction in the near future. PMID:24683030

Teaching Radiology Physics Interactively with Scientific Notebook Software.

PubMed

Richardson, Michael L; Amini, Behrang

2018-06-01

The goal of this study is to demonstrate how the teaching of radiology physics can be enhanced with the use of interactive scientific notebook software. We used the scientific notebook software known as Project Jupyter, which is free, open-source, and available for the Macintosh, Windows, and Linux operating systems. We have created a scientific notebook that demonstrates multiple interactive teaching modules we have written for our residents using the Jupyter notebook system. Scientific notebook software allows educators to create teaching modules in a form that combines text, graphics, images, data, interactive calculations, and image analysis within a single document. These notebooks can be used to build interactive teaching modules, which can help explain complex topics in imaging physics to residents. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

The interaction between thermodynamic stability and buried free cysteines in regulating the functional half-life of fibroblast growth factor-1.

PubMed

Lee, Jihun; Blaber, Michael

2009-10-16

Protein biopharmaceuticals are an important and growing area of human therapeutics; however, the intrinsic property of proteins to adopt alternative conformations (such as during protein unfolding and aggregation) presents numerous challenges, limiting their effective application as biopharmaceuticals. Using fibroblast growth factor-1 as model system, we describe a cooperative interaction between the intrinsic property of thermostability and the reactivity of buried free-cysteine residues that can substantially modulate protein functional half-life. A mutational strategy that combines elimination of buried free cysteines and secondary mutations that enhance thermostability to achieve a substantial gain in functional half-life is described. Furthermore, the implementation of this design strategy utilizing stabilizing mutations within the core region resulted in a mutant protein that is essentially indistinguishable from wild type as regard protein surface and solvent structure, thus minimizing the immunogenic potential of the mutations. This design strategy should be generally applicable to soluble globular proteins containing buried free-cysteine residues.

An overview of poly(lactic-co-glycolic) acid (PLGA)-based biomaterials for bone tissue engineering.

PubMed

Gentile, Piergiorgio; Chiono, Valeria; Carmagnola, Irene; Hatton, Paul V

2014-02-28

Poly(lactic-co-glycolic) acid (PLGA) has attracted considerable interest as a base material for biomedical applications due to its: (i) biocompatibility; (ii) tailored biodegradation rate (depending on the molecular weight and copolymer ratio); (iii) approval for clinical use in humans by the U.S. Food and Drug Administration (FDA); (iv) potential to modify surface properties to provide better interaction with biological materials; and (v) suitability for export to countries and cultures where implantation of animal-derived products is unpopular. This paper critically reviews the scientific challenge of manufacturing PLGA-based materials with suitable properties and shapes for specific biomedical applications, with special emphasis on bone tissue engineering. The analysis of the state of the art in the field reveals the presence of current innovative techniques for scaffolds and material manufacturing that are currently opening the way to prepare biomimetic PLGA substrates able to modulate cell interaction for improved substitution, restoration, or enhancement of bone tissue function.

Development, implementation and evaluation of a terminal and hospice care educational online module for preclinical students.

PubMed

Tse, Chung Sang; Ellman, Matthew S

2017-03-01

To explore the application of an online learning tool to teach preclinical medical students terminal and hospice care in a blended curricula. We created and evaluated a 30 min interactive online module at the Yale School of Medicine. Second-year medical students were randomly assigned to complete the online module or not (control group) prior to attending a required half-day hospice clinical experience. We assessed the students' knowledge and attitudes with a 23-item survey. 152 students (response rate 51%) participated in this study from 2012 to 2014. 56% (n=85) completed the online module, 37% (n=56) did not and 7% (n=11) did not indicate whether they had completed the module or not. Students who completed the online module prior to the hospice experience scored higher (p<0.05, two-way analysis of variance) on 5 out of 8 of the multiple choice questions pertaining to hospice and palliative care, but their attitudes were similar to those who did not complete the online module. Overall, the students felt somewhat uncomfortable caring for dying patients although they regarded it as a physician's duty and felt that palliative/hospice care education is important in medical school. When combined with a mentored clinical hospice experience, an online module appears to enhance the teaching of the dying process and terminal care for preclinical medical students. This online module may prove useful for other institutions. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Integrating Module - NEMS Documentation

EIA Publications

2014-01-01

Provides an overview of the complete National Energy Modeling System (NEMS) model, and includes brief descriptions of the modules with which the Integrating Module interacts. The emphasis and focus, however, is on the structure and function of the Integrating Module of NEMS.

Enhanced modulation rates via field modulation in spin torque nano-oscillators

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

Purbawati, A.; Garcia-Sanchez, F.; Buda-Prejbeanu, L. D.

Spin Transfer Nano-Oscillators (STNOs) are promising candidates for telecommunications applications due to their frequency tuning capabilities via either a dc current or an applied field. This frequency tuning is of interest for Frequency Shift Keying concepts to be used in wireless communication schemes or in read head applications. For these technological applications, one important parameter is the characterization of the maximum achievable rate at which an STNO can respond to a modulating signal, such as current or field. Previous studies of in-plane magnetized STNOs on frequency modulation via an rf current revealed that the maximum achievable rate is limited bymore » the amplitude relaxation rate Γ{sub p}, which gives the time scale over which amplitude fluctuations are damped out. This might be a limitation for applications. Here, we demonstrate via numerical simulation that application of an additional rf field is an alternative way for modulation of the in-plane magnetized STNO configuration, which has the advantage that frequency modulation is not limited by the amplitude relaxation rate, so that higher modulation rates above GHz are achievable. This occurs when the modulating rf field is oriented along the easy axis (longitudinal rf field). Tilting the direction of the modulating rf field in-plane and perpendicularly with respect to the easy axis (transverse rf field), the modulation is again limited by the amplitude relaxation rate similar to the response observed in current modulation.« less

Air-Coupled Vibrometry

NASA Astrophysics Data System (ADS)

Döring, D.; Solodov, I.; Busse, G.

Sound and ultrasound in air are the products of a multitude of different processes and thus can be favorable or undesirable phenomena. Development of experimental tools for non-invasive measurements and imaging of airborne sound fields is of importance for linear and nonlinear nondestructive material testing as well as noise control in industrial or civil engineering applications. One possible solution is based on acousto-optic interaction, like light diffraction imaging. The diffraction approach usually requires a sophisticated setup with fine optical alignment barely applicable in industrial environment. This paper focuses on the application of the robust experimental tool of scanning laser vibrometry, which utilizes commercial off-the-shelf equipment. The imaging technique of air-coupled vibrometry (ACV) is based on the modulation of the optical path length by the acoustic pressure of the sound wave. The theoretical considerations focus on the analysis of acousto-optical phase modulation. The sensitivity of the ACV in detecting vibration velocity was estimated as ~1 mm/s. The ACV applications to imaging of linear airborne fields are demonstrated for leaky wave propagation and measurements of ultrasonic air-coupled transducers. For higher-intensity ultrasound, the classical nonlinear effect of the second harmonic generation was measured in air. Another nonlinear application includes a direct observation of the nonlinear air-coupled emission (NACE) from the damaged areas in solid materials. The source of the NACE is shown to be strongly localized around the damage and proposed as a nonlinear "tag" to discern and image the defects.

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.

PubMed

Defoort, Jonas; Van de Peer, Yves; Vermeirssen, Vanessa

2018-06-05

Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein-protein, genetic and homologous interactions, and directed protein-DNA, regulatory and miRNA-mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.

High-throughput analysis of peptide binding modules

PubMed Central

Liu, Bernard A.; Engelmann, Brett; Nash, Piers D.

2014-01-01

Modular protein interaction domains that recognize linear peptide motifs are found in hundreds of proteins within the human genome. Some protein interaction domains such as SH2, 14-3-3, Chromo and Bromo domains serve to recognize post-translational modification of amino acids (such as phosphorylation, acetylation, methylation etc.) and translate these into discrete cellular responses. Other modules such as SH3 and PDZ domains recognize linear peptide epitopes and serve to organize protein complexes based on localization and regions of elevated concentration. In both cases, the ability to nucleate specific signaling complexes is in large part dependent on the selectivity of a given protein module for its cognate peptide ligand. High throughput analysis of peptide-binding domains by peptide or protein arrays, phage display, mass spectrometry or other HTP techniques provides new insight into the potential protein-protein interactions prescribed by individual or even whole families of modules. Systems level analyses have also promoted a deeper understanding of the underlying principles that govern selective protein-protein interactions and how selectivity evolves. Lastly, there is a growing appreciation for the limitations and potential pitfalls of high-throughput analysis of protein-peptide interactomes. This review will examine some of the common approaches utilized for large-scale studies of protein interaction domains and suggest a set of standards for the analysis and validation of datasets from large-scale studies of peptide-binding modules. We will also highlight how data from large-scale studies of modular interaction domain families can provide insight into systems level properties such as the linguistics of selective interactions. PMID:22610655

Semiconductor Devices and Applications. Electronics Module 5. Instructor's Guide.

ERIC Educational Resources Information Center

Chappell, John; And Others

This module is the fifth of 10 modules in the competency-based electronics series. Introductory materials include a listing of competencies addressed in the module, a parts/equipment list, and a cross-reference table of instructional materials. Sixteen instructional units cover: semiconductor materials; diodes; diode applications and…

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

PubMed

Colak, Recep; Moser, Flavia; Chu, Jeffrey Shih-Chieh; Schönhuth, Alexander; Chen, Nansheng; Ester, Martin

2010-10-25

Computational prediction of functionally related groups of genes (functional modules) from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense) regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented. We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB), by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples. We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely available large-scale datasets. Software and data sets are available at http://www.sfu.ca/~ester/software/DECOB.zip.

Self-synchronization of the modulation of energy-levels population with electrons in GaAs induced by picosecond pulses of probe radiation and intrinsic stimulated emission

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

Ageeva, N. N.; Bronevoi, I. L., E-mail: bil@cplire.ru; Zabegaev, D. N.

Picosecond optical pumping leads to the initiation of intrinsic picosecond stimulated emission in GaAs. As was established previously, due to the interaction of pulses of probe radiation with those of intrinsic emission, the dependence of the absorption α of the probe pulse on its delay τ with respect to the pump pulse is modulated with oscillations. It is found that the oscillatory dependences α(τ) have a similar shape only in the case of certain combinations of energies of the interacting pulses. As a result, it is assumed that the above interaction is, in fact, a synchronization of modulations (formed bymore » pulses) of charge-carrier populations at energy levels; this synchronization occurs in the direction of the reconstruction of detailed equilibrium. The real-time picosecond self-modulation of the absorption α is measured for the first time. The characteristics of this self-modulation as well as absorption α and intrinsic emission self-modulation characteristics measured previously by correlation methods are now accounted for by the concept of synchronization.« less

Ionization of Atoms by Slow Heavy Particles, Including Dark Matter.

PubMed

Roberts, B M; Flambaum, V V; Gribakin, G F

2016-01-15

Atoms and molecules can become ionized during the scattering of a slow, heavy particle off a bound electron. Such an interaction involving leptophilic weakly interacting massive particles (WIMPs) is a promising possible explanation for the anomalous 9σ annual modulation in the DAMA dark matter direct detection experiment [R. Bernabei et al., Eur. Phys. J. C 73, 2648 (2013)]. We demonstrate the applicability of the Born approximation for such an interaction by showing its equivalence to the semiclassical adiabatic treatment of atomic ionization by slow-moving WIMPs. Conventional wisdom has it that the ionization probability for such a process should be exponentially small. We show, however, that due to nonanalytic, cusplike behavior of Coulomb functions close to the nucleus this suppression is removed, leading to an effective atomic structure enhancement. We also show that electron relativistic effects actually give the dominant contribution to such a process, enhancing the differential cross section by up to 1000 times.

Interactive QR code beautification with full background image embedding

NASA Astrophysics Data System (ADS)

Lin, Lijian; Wu, Song; Liu, Sijiang; Jiang, Bo

2017-06-01

QR (Quick Response) code is a kind of two dimensional barcode that was first developed in automotive industry. Nowadays, QR code has been widely used in commercial applications like product promotion, mobile payment, product information management, etc. Traditional QR codes in accordance with the international standard are reliable and fast to decode, but are lack of aesthetic appearance to demonstrate visual information to customers. In this work, we present a novel interactive method to generate aesthetic QR code. By given information to be encoded and an image to be decorated as full QR code background, our method accepts interactive user's strokes as hints to remove undesired parts of QR code modules based on the support of QR code error correction mechanism and background color thresholds. Compared to previous approaches, our method follows the intention of the QR code designer, thus can achieve more user pleasant result, while keeping high machine readability.

CRPropa 3—a public astrophysical simulation framework for propagating extraterrestrial ultra-high energy particles

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

Batista, Rafael Alves; Dundovic, Andrej; Sigl, Guenter

2016-05-01

We present the simulation framework CRPropa version 3 designed for efficient development of astrophysical predictions for ultra-high energy particles. Users can assemble modules of the most relevant propagation effects in galactic and extragalactic space, include their own physics modules with new features, and receive on output primary and secondary cosmic messengers including nuclei, neutrinos and photons. In extension to the propagation physics contained in a previous CRPropa version, the new version facilitates high-performance computing and comprises new physical features such as an interface for galactic propagation using lensing techniques, an improved photonuclear interaction calculation, and propagation in time dependent environmentsmore » to take into account cosmic evolution effects in anisotropy studies and variable sources. First applications using highlighted features are presented as well.« less

Space Applications Industrial Laser System (SAILS)

NASA Technical Reports Server (NTRS)

Mccay, T. D.; Bible, J. B.; Mueller, R. E.

1993-01-01

A program is underway to develop a YAG laser based materials processing workstation to fly in the cargo bay of the Space Shuttle. This workstation, called Space Applications Industrial Laser System (SAILS), will be capable of cutting and welding steel, aluminum, and Inconel alloys of the type planned for use in constructing the Space Station Freedom. As well as demonstrating the ability of a YAG laser to perform remote (fiber-optic delivered) repair and fabrication operations in space, fundamental data will be collected on these interactions for comparison with terrestrial data and models. The flight system, scheduled to fly in 1996, will be constructed as three modules using standard Get-Away-Special (GAS) canisters. The first module holds the laser head and cooling system, while the second contains a high peak power electrical supply. The third module houses the materials processing workstation and the command and data acquisition subsystems. The laser head and workstation cansisters are linked by a fiber-optic cable to transmit the laser light. The team assembled to carry out this project includes Lumonics Industrial Products (laser), Tennessee Technological University (structural analysis and fabrication), Auburn University Center for Space Power (electrical engineering), University of Waterloo (low-g laser process consulting), and CSTAR/UTSI (data acquisition, control, software, integration, experiment design). This report describes the SAILS program and highlights recent activities undertaken at CSTAR.

The all-optical modulator in dielectric-loaded waveguide with graphene-silicon heterojunction structure

NASA Astrophysics Data System (ADS)

Sun, Feiying; Xia, Liangping; Nie, Changbin; Shen, Jun; Zou, Yixuan; Cheng, Guiyu; Wu, Hao; Zhang, Yong; Wei, Dongshan; Yin, Shaoyun; Du, Chunlei

2018-04-01

All-optical modulators based on graphene show great promise for on-chip optical interconnects. However, the modulation performance of all-optical modulators is usually based on the interaction between graphene and the fiber, limiting their potential in high integration. Based on this point, an all-optical modulator in a dielectric-loaded waveguide (DLW) with a graphene-silicon heterojunction structure (GSH) is proposed. The DLW raises the waveguide mode, which provides a strong light-graphene interaction. Sufficient tuning of the graphene Fermi energy beyond the Pauli blocking effect is obtained with the presented GSH structure. Under the modulation light with a wavelength of 532 nm and a power of 60 mW, a modulation efficiency of 0.0275 dB µm-1 is achieved for light with a communication wavelength of 1.55 µm in the experiment. This modulator has the advantage of having a compact footprint, which may make it a candidate for achieving a highly integrated all-optical modulator.

Transport and release of colloidal 3-mercaptopropionic acid-coated CdSe–CdS/ZnS core-multishell quantum dots in human umbilical vein endothelial cells

PubMed Central

Fontana, Jacopo M; Yin, Huijuan; Chen, Yun; Florez, Ricardo; Brismar, Hjalmar; Fu, Ying

2017-01-01

Colloidal semiconductor quantum dots (QDs) have been extensively researched and developed for biomedical applications, including drug delivery and biosensing assays. Hence, it is pivotal to understand their behavior in terms of intracellular transport and toxicological effects. In this study, we focused on 3-mercaptopropionic acid-coated CdSe-CdS/ZnS core-multishell quantum dots (3MPA-QDs) converted from the as-grown octadecylamine-coated quantum dots (ODA-QDs) and their direct and dynamic interactions with human umbilical vein endothelial cells (HUVECs). Live cell imaging using confocal fluorescence microscopy showed that 3MPA-QDs first attached to and subsequently aggregated on HUVEC plasma membrane ~25 min after QD deposition. The aggregated QDs started being internalized at ~2 h and reached their highest internalization degree at ~24 h. They were released from HUVECs after ~48 h. During the 48 h period, the HUVECs responded normally to external stimulations, grew, proliferated and wound healed without any perceptible apoptosis. Furthermore, 1) 3MPA-QDs were internalized in newly formed LysoTracker-stained early endosomes; 2) adenosine 5′-triphosphate-induced [Ca2+]i modulation caused a transient decrease in the fluorescence of 3MPA-QDs that were attached to the plasma membrane but a transient increase in the internalized 3MPA-QDs; and 3) fluorescence signal modulations of co-stained LysoTracker and QDs induced by the lysosomotropic agent Gly-Phe-β-naphthylamide were spatially co-localized and temporally synchronized. Our findings suggest that 3MPA-QDs converted from ODA-QDs are a potential nontoxic fluorescent probe for future use in clinical applications. Moreover, the photophysical strategy and techniques reported in this work are easily applicable to study of direct interactions between other nanoparticles and live cells; contributing to awareness and implementation of the safe applications of nanoparticles. PMID:29270011

Transport and release of colloidal 3-mercaptopropionic acid-coated CdSe-CdS/ZnS core-multishell quantum dots in human umbilical vein endothelial cells.

PubMed

Fontana, Jacopo M; Yin, Huijuan; Chen, Yun; Florez, Ricardo; Brismar, Hjalmar; Fu, Ying

2017-01-01

Colloidal semiconductor quantum dots (QDs) have been extensively researched and developed for biomedical applications, including drug delivery and biosensing assays. Hence, it is pivotal to understand their behavior in terms of intracellular transport and toxicological effects. In this study, we focused on 3-mercaptopropionic acid-coated CdSe-CdS/ZnS core-multishell quantum dots (3MPA-QDs) converted from the as-grown octadecylamine-coated quantum dots (ODA-QDs) and their direct and dynamic interactions with human umbilical vein endothelial cells (HUVECs). Live cell imaging using confocal fluorescence microscopy showed that 3MPA-QDs first attached to and subsequently aggregated on HUVEC plasma membrane ~25 min after QD deposition. The aggregated QDs started being internalized at ~2 h and reached their highest internalization degree at ~24 h. They were released from HUVECs after ~48 h. During the 48 h period, the HUVECs responded normally to external stimulations, grew, proliferated and wound healed without any perceptible apoptosis. Furthermore, 1) 3MPA-QDs were internalized in newly formed LysoTracker-stained early endosomes; 2) adenosine 5'-triphosphate-induced [Ca 2+ ] i modulation caused a transient decrease in the fluorescence of 3MPA-QDs that were attached to the plasma membrane but a transient increase in the internalized 3MPA-QDs; and 3) fluorescence signal modulations of co-stained LysoTracker and QDs induced by the lysosomotropic agent Gly-Phe-β-naphthylamide were spatially co-localized and temporally synchronized. Our findings suggest that 3MPA-QDs converted from ODA-QDs are a potential nontoxic fluorescent probe for future use in clinical applications. Moreover, the photophysical strategy and techniques reported in this work are easily applicable to study of direct interactions between other nanoparticles and live cells; contributing to awareness and implementation of the safe applications of nanoparticles.

GLADIATOR: a global approach for elucidating disease modules.

PubMed

Silberberg, Yael; Kupiec, Martin; Sharan, Roded

2017-05-26

Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based approaches for deciphering disease mechanisms. In particular, protein-protein interaction networks were successfully used to illuminate disease modules, i.e., interacting proteins working in concert to drive a disease. The identification of these modules can further our understanding of disease mechanisms. We devised a global method for the prediction of multiple disease modules simultaneously named GLADIATOR (GLobal Approach for DIsease AssociaTed mOdule Reconstruction). GLADIATOR relies on a gold-standard disease phenotypic similarity to obtain a pan-disease view of the underlying modules. To traverse the search space of potential disease modules, we applied a simulated annealing algorithm aimed at maximizing the correlation between module similarity and the gold-standard phenotypic similarity. Importantly, this optimization is employed over hundreds of diseases simultaneously. GLADIATOR's predicted modules highly agree with current knowledge about disease-related proteins. Furthermore, the modules exhibit high coherence with respect to functional annotations and are highly enriched with known curated pathways, outperforming previous methods. Examination of the predicted proteins shared by similar diseases demonstrates the diverse role of these proteins in mediating related processes across similar diseases. Last, we provide a detailed analysis of the suggested molecular mechanism predicted by GLADIATOR for hyperinsulinism, suggesting novel proteins involved in its pathology. GLADIATOR predicts disease modules by integrating knowledge of disease-related proteins and phenotypes across multiple diseases. The predicted modules are functionally coherent and are more in line with current biological knowledge compared to modules obtained using previous disease-centric methods. The source code for GLADIATOR can be downloaded from http://www.cs.tau.ac.il/~roded/GLADIATOR.zip .

Business/Marketing Education. Business Analysis/Business Computer Applications.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Div. of Occupational Education Programs.

This document contains 12 modules: 4 on business analysis and 8 on business computer applications. The business analysis modules are as follows: (1) the framework of business; (2) universal activities of business; (3) selected business subsystems; and (4) your place in business. Computer applications modules are on the following topics: (1)…

National Stormwater Calculator: Low Impact Development ...

EPA Pesticide Factsheets

The National Stormwater Calculator (NSC) makes it easy to estimate runoff reduction when planning a new development or redevelopment site with low impact development (LID) stormwater controls. The Calculator is currently deployed as a Windows desktop application. The Calculator is organized as a wizard style application that walks the user through the steps necessary to perform runoff calculations on a single urban sub-catchment of 10 acres or less in size. Using an interactive map, the user can select the sub-catchment location and the Calculator automatically acquires hydrologic data for the site.A new LID cost estimation module has been developed for the Calculator. This project involved programming cost curves into the existing Calculator desktop application. The integration of cost components of LID controls into the Calculator increases functionality and will promote greater use of the Calculator as a stormwater management and evaluation tool. The addition of the cost estimation module allows planners and managers to evaluate LID controls based on comparison of project cost estimates and predicted LID control performance. Cost estimation is accomplished based on user-identified size (or auto-sizing based on achieving volume control or treatment of a defined design storm), configuration of the LID control infrastructure, and other key project and site-specific variables, including whether the project is being applied as part of new development or redevelopm

Modulators of 14-3-3 Protein–Protein Interactions

PubMed Central

2017-01-01

Direct interactions between proteins are essential for the regulation of their functions in biological pathways. Targeting the complex network of protein–protein interactions (PPIs) has now been widely recognized as an attractive means to therapeutically intervene in disease states. Even though this is a challenging endeavor and PPIs have long been regarded as “undruggable” targets, the last two decades have seen an increasing number of successful examples of PPI modulators, resulting in growing interest in this field. PPI modulation requires novel approaches and the integrated efforts of multiple disciplines to be a fruitful strategy. This perspective focuses on the hub-protein 14-3-3, which has several hundred identified protein interaction partners, and is therefore involved in a wide range of cellular processes and diseases. Here, we aim to provide an integrated overview of the approaches explored for the modulation of 14-3-3 PPIs and review the examples resulting from these efforts in both inhibiting and stabilizing specific 14-3-3 protein complexes by small molecules, peptide mimetics, and natural products. PMID:28968506

Floating-Point Modules Targeted for Use with RC Compilation Tools

NASA Technical Reports Server (NTRS)

Sahin, Ibrahin; Gloster, Clay S.

2000-01-01

Reconfigurable Computing (RC) has emerged as a viable computing solution for computationally intensive applications. Several applications have been mapped to RC system and in most cases, they provided the smallest published execution time. Although RC systems offer significant performance advantages over general-purpose processors, they require more application development time than general-purpose processors. This increased development time of RC systems provides the motivation to develop an optimized module library with an assembly language instruction format interface for use with future RC system that will reduce development time significantly. In this paper, we present area/performance metrics for several different types of floating point (FP) modules that can be utilized to develop complex FP applications. These modules are highly pipelined and optimized for both speed and area. Using these modules, and example application, FP matrix multiplication, is also presented. Our results and experiences show, that with these modules, 8-10X speedup over general-purpose processors can be achieved.

Identification and functional analysis of a core gene module associated with hepatitis C virus-induced human hepatocellular carcinoma progression.

PubMed

Bai, Gaobo; Zheng, Wenling; Ma, Wenli

2018-05-01

Hepatitis C virus (HCV)-induced human hepatocellular carcinoma (HCC) progression may be due to a complex multi-step processes. The developmental mechanism of these processes is worth investigating for the prevention, diagnosis and therapy of HCC. The aim of the present study was to investigate the molecular mechanism underlying the progression of HCV-induced hepatocarcinogenesis. First, the dynamic gene module, consisting of key genes associated with progression between the normal stage and HCC, was identified using the Weighted Gene Co-expression Network Analysis tool from R language. By defining those genes in the module as seeds, the change of co-expression in differentially expressed gene sets in two consecutive stages of pathological progression was examined. Finally, interaction pairs of HCV viral proteins and their directly targeted proteins in the identified module were extracted from the literature and a comprehensive interaction dataset from yeast two-hybrid experiments. By combining the interactions between HCV and their targets, and protein-protein interactions in the Search Tool for the Retrieval of Interacting Genes database (STRING), the HCV-key genes interaction network was constructed and visualized using Cytoscape software 3.2. As a result, a module containing 44 key genes was identified to be associated with HCC progression, due to the dynamic features and functions of those genes in the module. Several important differentially co-expressed gene pairs were identified between non-HCC and HCC stages. In the key genes, cyclin dependent kinase 1 (CDK1), NDC80, cyclin A2 (CCNA2) and rac GTPase activating protein 1 (RACGAP1) were shown to be targeted by the HCV nonstructural proteins NS5A, NS3 and NS5B, respectively. The four genes perform an intermediary role between the HCV viral proteins and the dysfunctional module in the HCV key genes interaction network. These findings provided valuable information for understanding the mechanism of HCV-induced HCC progression and for seeking drug targets for the therapy and prevention of HCC.

Disentangling the co-structure of multilayer interaction networks: degree distribution and module composition in two-layer bipartite networks.

PubMed

Astegiano, Julia; Altermatt, Florian; Massol, François

2017-11-13

Species establish different interactions (e.g. antagonistic, mutualistic) with multiple species, forming multilayer ecological networks. Disentangling network co-structure in multilayer networks is crucial to predict how biodiversity loss may affect the persistence of multispecies assemblages. Existing methods to analyse multilayer networks often fail to consider network co-structure. We present a new method to evaluate the modular co-structure of multilayer networks through the assessment of species degree co-distribution and network module composition. We focus on modular structure because of its high prevalence among ecological networks. We apply our method to two Lepidoptera-plant networks, one describing caterpillar-plant herbivory interactions and one representing adult Lepidoptera nectaring on flowers, thereby possibly pollinating them. More than 50% of the species established either herbivory or visitation interactions, but not both. These species were over-represented among plants and lepidopterans, and were present in most modules in both networks. Similarity in module composition between networks was high but not different from random expectations. Our method clearly delineates the importance of interpreting multilayer module composition similarity in the light of the constraints imposed by network structure to predict the potential indirect effects of species loss through interconnected modular networks.

Administering an epoch initiated for remote memory access

DOEpatents

Blocksome, Michael A; Miller, Douglas R

2014-03-18

Methods, systems, and products are disclosed for administering an epoch initiated for remote memory access that include: initiating, by an origin application messaging module on an origin compute node, one or more data transfers to a target compute node for the epoch; initiating, by the origin application messaging module after initiating the data transfers, a closing stage for the epoch, including rejecting any new data transfers after initiating the closing stage for the epoch; determining, by the origin application messaging module, whether the data transfers have completed; and closing, by the origin application messaging module, the epoch if the data transfers have completed.

Efficient Parallel Engineering Computing on Linux Workstations

NASA Technical Reports Server (NTRS)

Lou, John Z.

2010-01-01

A C software module has been developed that creates lightweight processes (LWPs) dynamically to achieve parallel computing performance in a variety of engineering simulation and analysis applications to support NASA and DoD project tasks. The required interface between the module and the application it supports is simple, minimal and almost completely transparent to the user applications, and it can achieve nearly ideal computing speed-up on multi-CPU engineering workstations of all operating system platforms. The module can be integrated into an existing application (C, C++, Fortran and others) either as part of a compiled module or as a dynamically linked library (DLL).

Administering an epoch initiated for remote memory access

DOEpatents

Blocksome, Michael A; Miller, Douglas R

2012-10-23

Methods, systems, and products are disclosed for administering an epoch initiated for remote memory access that include: initiating, by an origin application messaging module on an origin compute node, one or more data transfers to a target compute node for the epoch; initiating, by the origin application messaging module after initiating the data transfers, a closing stage for the epoch, including rejecting any new data transfers after initiating the closing stage for the epoch; determining, by the origin application messaging module, whether the data transfers have completed; and closing, by the origin application messaging module, the epoch if the data transfers have completed.

Administering an epoch initiated for remote memory access

DOEpatents

Blocksome, Michael A.; Miller, Douglas R.

2013-01-01

Methods, systems, and products are disclosed for administering an epoch initiated for remote memory access that include: initiating, by an origin application messaging module on an origin compute node, one or more data transfers to a target compute node for the epoch; initiating, by the origin application messaging module after initiating the data transfers, a closing stage for the epoch, including rejecting any new data transfers after initiating the closing stage for the epoch; determining, by the origin application messaging module, whether the data transfers have completed; and closing, by the origin application messaging module, the epoch if the data transfers have completed.

"SURGENT" -- student e-learning for reality: the application of interactive visual images to problem-based learning in undergraduate surgery.

PubMed

Corrigan, Mark; Reardon, Michelle; Shields, Connor; Redmond, Henry

2008-01-01

Information technology has the potential to transform surgical education. Combining symbolic, iconic, and enactive teaching modalities to construct an authentic conceptual model potentially can transform a primarily didactic learning experience into an interactive Web-enhanced one. This study sought to assess the introduction of a Web-based module to complement traditional surgical undergraduate curricula. Adopting the clinical case as its fundamental educational approach, an online resource simulating surgical clinical decision making ("SURGENT," http://www.surgent.ie) was developed, which consists of the interpretation of clinical photographs, laboratory data, and X-rays as well as the formulation of a management plan. Evaluation was in both a qualitative and a quantitative fashion. An anonymous postcourse survey (73% response) of 117 final medical students was used to by researchers to evaluate access, process, and outcome criteria. SURGENT was used by 98% of students, with 69% spending more than 30 minutes per session on the program. First-class honors in the final surgical clinical examination improved from 11% to 20% (p = 0.01) as compared with the previous control year. A Web-enhanced interactive surgical module in an undergraduate course can convey successfully information and understanding beyond the textbook. It is intended that SURGENT will supplement textbooks and ward experience, allowing students to develop their clinical decision-making skills.

Modulated phases in a three-dimensional Maier-Saupe model with competing interactions

NASA Astrophysics Data System (ADS)

Bienzobaz, P. F.; Xu, Na; Sandvik, Anders W.

2017-07-01

This work is dedicated to the study of the discrete version of the Maier-Saupe model in the presence of competing interactions. The competition between interactions favoring different orientational ordering produces a rich phase diagram including modulated phases. Using a mean-field approach and Monte Carlo simulations, we show that the proposed model exhibits isotropic and nematic phases and also a series of modulated phases that meet at a multicritical point, a Lifshitz point. Though the Monte Carlo and mean-field phase diagrams show some quantitative disagreements, the Monte Carlo simulations corroborate the general behavior found within the mean-field approximation.

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

PubMed

Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

2017-06-01

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

The arguments for and against cannabinoids application in glaucomatous retinopathy.

PubMed

Panahi, Yunes; Manayi, Azadeh; Nikan, Marjan; Vazirian, Mahdi

2017-02-01

Glaucoma represents several optic neuropathies leading to irreversible blindness through progressive retinal ganglion cell (RGC) loss. Reduction of intraocular pressure (IOP) is known as the only modifiable factor in the treatment of this disorder. Application of exogenous cannabinoids to lower IOP has attracted attention of scientists as potential agents for the treatment of glaucoma. Accordingly, neuroprotective effect of these agents has been recently described through modulation of endocannabinoid system in the eye. In the present work, pertinent information regarding ocular endocannabinoid system, mechanism of exogenous cannabinoids interaction with the ocular endocannabinoid system to reduce IOP, and neuroprotection property of cannabinoids will be discussed according to current scientific literature. In addition to experimental studies, bioavailability of cannabinoids, clinical surveys, and adverse effects of application of cannabinoids in glaucoma will be reviewed. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Image-based electronic patient records for secured collaborative medical applications.

PubMed

Zhang, Jianguo; Sun, Jianyong; Yang, Yuanyuan; Liang, Chenwen; Yao, Yihong; Cai, Weihua; Jin, Jin; Zhang, Guozhen; Sun, Kun

2005-01-01

We developed a Web-based system to interactively display image-based electronic patient records (EPR) for secured intranet and Internet collaborative medical applications. The system consists of four major components: EPR DICOM gateway (EPR-GW), Image-based EPR repository server (EPR-Server), Web Server and EPR DICOM viewer (EPR-Viewer). In the EPR-GW and EPR-Viewer, the security modules of Digital Signature and Authentication are integrated to perform the security processing on the EPR data with integrity and authenticity. The privacy of EPR in data communication and exchanging is provided by SSL/TLS-based secure communication. This presentation gave a new approach to create and manage image-based EPR from actual patient records, and also presented a way to use Web technology and DICOM standard to build an open architecture for collaborative medical applications.

Hands-On Learning Modules for Interdisciplinary Environments: An Example with a Focus on Weather Radar Applications

ERIC Educational Resources Information Center

Chilson, P. B.; Yeary, M. B.

2012-01-01

Learning modules provide an effective means of encouraging cognition and active learning. This paper discusses several such modules that have been developed within a course on weather radar applications intended for students from Electrical Engineering and Meteorology. The modules were designed both to promote interdisciplinary exchange between…

Attention operates uniformly throughout the classical receptive field and the surround

PubMed Central

Verhoef, Bram-Ernst; Maunsell, John HR

2016-01-01

Shifting attention among visual stimuli at different locations modulates neuronal responses in heterogeneous ways, depending on where those stimuli lie within the receptive fields of neurons. Yet how attention interacts with the receptive-field structure of cortical neurons remains unclear. We measured neuronal responses in area V4 while monkeys shifted their attention among stimuli placed in different locations within and around neuronal receptive fields. We found that attention interacts uniformly with the spatially-varying excitation and suppression associated with the receptive field. This interaction explained the large variability in attention modulation across neurons, and a non-additive relationship among stimulus selectivity, stimulus-induced suppression and attention modulation that has not been previously described. A spatially-tuned normalization model precisely accounted for all observed attention modulations and for the spatial summation properties of neurons. These results provide a unified account of spatial summation and attention-related modulation across both the classical receptive field and the surround. DOI: http://dx.doi.org/10.7554/eLife.17256.001 PMID:27547989

BoreholeAR: A mobile tablet application for effective borehole database visualization using an augmented reality technology

NASA Astrophysics Data System (ADS)

Lee, Sangho; Suh, Jangwon; Park, Hyeong-Dong

2015-03-01

Boring logs are widely used in geological field studies since the data describes various attributes of underground and surface environments. However, it is difficult to manage multiple boring logs in the field as the conventional management and visualization methods are not suitable for integrating and combining large data sets. We developed an iPad application to enable its user to search the boring log rapidly and visualize them using the augmented reality (AR) technique. For the development of the application, a standard borehole database appropriate for a mobile-based borehole database management system was designed. The application consists of three modules: an AR module, a map module, and a database module. The AR module superimposes borehole data on camera imagery as viewed by the user and provides intuitive visualization of borehole locations. The map module shows the locations of corresponding borehole data on a 2D map with additional map layers. The database module provides data management functions for large borehole databases for other modules. Field survey was also carried out using more than 100,000 borehole data.

A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis

NASA Astrophysics Data System (ADS)

Ghosh, Eshan; Srivastava, Ashish; Baidya, Mithu; Kumari, Punita; Dwivedi, Hemlata; Nidhi, Kumari; Ranjan, Ravi; Dogra, Shalini; Koide, Akiko; Yadav, Prem N.; Sidhu, Sachdev S.; Koide, Shohei; Shukla, Arun K.

2017-12-01

Beta-arrestins (βarrs) critically mediate desensitization, endocytosis and signalling of G protein-coupled receptors (GPCRs), and they scaffold a large number of interaction partners. However, allosteric modulation of their scaffolding abilities and direct targeting of their interaction interfaces to modulate GPCR functions selectively have not been fully explored yet. Here we identified a series of synthetic antibody fragments (Fabs) against different conformations of βarrs from phage display libraries. Several of these Fabs allosterically and selectively modulated the interaction of βarrs with clathrin and ERK MAP kinase. Interestingly, one of these Fabs selectively disrupted βarr-clathrin interaction, and when expressed as an intrabody, it robustly inhibited agonist-induced endocytosis of a broad set of GPCRs without affecting ERK MAP kinase activation. Our data therefore demonstrate the feasibility of selectively targeting βarr interactions using intrabodies and provide a novel framework for fine-tuning GPCR functions with potential therapeutic implications.

Calcium accelerates SNARE-mediated lipid mixing through modulating α-synuclein membrane interaction.

PubMed

Zhang, Zeting; Jiang, Xin; Xu, Danrui; Zheng, Wenwen; Liu, Maili; Li, Conggang

2018-04-04

α-Synuclein is involved in Parkinson's disease, and its interaction with cell membrane is vital to its pathological and physiological functions. We have shown that Ca 2+ can regulate α-synuclein membrane interaction, but the physiological role of Ca 2+ in modulating α-synuclein membrane interaction is still unexplored. Based on the previous findings that α-synuclein inhibits membrane fusion and its inhibitory effect is highly related to its membrane binding, here we employed solution state Nuclear Magnetic Resonance (NMR) spectroscopy and the ensemble fluorescence fusion assay to show that Ca 2+ can modulate the inhibitory effect of α-synuclein on SNARE-mediated membrane fusion through disrupting α-synuclein membrane interaction, resulting in acceleration of SNARE-mediated membrane fusion. These results suggest a modulatory effect of Ca 2+ on membrane mediated normal function of α-synuclein, which of importance for the study of the Parkinson's disease. Copyright © 2018 Elsevier B.V. All rights reserved.

Hypertension module: an interactive learning tool in physiology.

PubMed

Işman, C A; Gülpinar, M A; Kurtel, H; Alican, I; Yeğen, B C

2003-12-01

The aim of the present study was to evaluate the strong or weak aspects of an interactive study module introduced during the "Cardiovascular and Respiratory Systems Subject Committee" in the second year of the medical program. Five study groups consisting of 25 students attended two-hour module sessions for six weeks with the same tutor. According to the module assessment questionnaire, the majority of the students assessed the module as excellent or good. The students reported that they had gained not only in knowledge but also in skills development. The general opinion of the students was that both the organization and the implementation of the module met their expectations. Nearly one-half of the students reported that their expectations with regard to the educational environment and the participation of students were fully met. The major weakness in this new educational trial appears to be assessment of the module.

Protein conformational modulation by photons: a mechanism for laser treatment effects.

PubMed

Liebert, Ann D; Bicknell, Brian T; Adams, Roger D

2014-03-01

Responsiveness to low-level laser treatment (LLTT) at a wavelength of 450-910 nm has established it as an effective treatment of medical, veterinary and dental chronic pain, chronic inflammation conditions (arthritis and macular degeneration), wound repair, and lymphoedema, yet the mechanisms underlying the effectiveness of LLLT remain unclear. However, there is now sufficient evidence from recent research to propose an integrated model of LLLT action. The hypothesis presented in this paper is that external applications of photons (through laser at an appropriate dose) modulates the nervous system through an integrated mechanism. This stimulated mechanism involves protein-to-protein interaction, where two or more proteins bind together to facilitate molecular processes, including modification of proteins by members of SUMO (small ubiquitin-related modifier proteins) and also protein phosphorylation and tyrosination. SUMO has been shown to have a role in multiple nuclear and perinuclear targets, including ion channels, and in the maintenance of telomeres and the post-translational modification of genes. The consequence of laser application in treatment, therefore, can be seen as influencing the transmission of neural information via an integrated and rapid modulation of ion channels, achieved through both direct action on photo-acceptors (such as cytochrome c-oxidase) and through indirect modulation via enzymes, including tyrosine hydroxylase (TH), tyrosine kinases and tyrosine kinase receptors. This exogenous action then facilitates an existing photonic biomodulation mechanism within the body, and initiates ion channel modulation both in the periphery and the central nervous system (CNS). Evidence indicates that the ion channel modulation functions predominately through the potassium channels, including two pore leak channels (K2P), which act as signal integrators from the periphery to the cortex. Photonic action also transforms SUMOylation processes at the cell membrane, nucleus and telomeres via signalling processes from the mitochondria (which is the main target of laser absorption) to these targets. Under the hypothesis, these observed biological effects would play a part in the bystander effect, the abscopal effect, and other systemic effects observed with the application of low level laser (LLLT). The implications of the hypothesis are important in that they point to mechanisms that can account for the effectiveness of laser in the treatment and prevention of inflammatory diseases, chronic pain and neurodegenerative disorders. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Design of Intelligent Robot as A Tool for Teaching Media Based on Computer Interactive Learning and Computer Assisted Learning to Improve the Skill of University Student

NASA Astrophysics Data System (ADS)

Zuhrie, M. S.; Basuki, I.; Asto B, I. G. P.; Anifah, L.

2018-01-01

The focus of the research is the teaching module which incorporates manufacturing, planning mechanical designing, controlling system through microprocessor technology and maneuverability of the robot. Computer interactive and computer-assisted learning is strategies that emphasize the use of computers and learning aids (computer assisted learning) in teaching and learning activity. This research applied the 4-D model research and development. The model is suggested by Thiagarajan, et.al (1974). 4-D Model consists of four stages: Define Stage, Design Stage, Develop Stage, and Disseminate Stage. This research was conducted by applying the research design development with an objective to produce a tool of learning in the form of intelligent robot modules and kit based on Computer Interactive Learning and Computer Assisted Learning. From the data of the Indonesia Robot Contest during the period of 2009-2015, it can be seen that the modules that have been developed confirm the fourth stage of the research methods of development; disseminate method. The modules which have been developed for students guide students to produce Intelligent Robot Tool for Teaching Based on Computer Interactive Learning and Computer Assisted Learning. Results of students’ responses also showed a positive feedback to relate to the module of robotics and computer-based interactive learning.

Tunable interactions between paramagnetic colloidal particles driven in a modulated ratchet potential.

PubMed

Straube, Arthur V; Tierno, Pietro

2014-06-14

We study experimentally and theoretically the interactions between paramagnetic particles dispersed in water and driven above the surface of a stripe patterned magnetic garnet film. An external rotating magnetic field modulates the stray field of the garnet film and generates a translating potential landscape which induces directed particle motion. By varying the ellipticity of the rotating field, we tune the inter-particle interactions from net repulsive to net attractive. For attractive interactions, we show that pairs of particles can approach each other and form stable doublets which afterwards travel along the modulated landscape at a constant mean speed. We measure the strength of the attractive force between the moving particles and propose an analytically tractable model that explains the observations and is in quantitative agreement with experiment.

ISPAN (Interactive Stiffened Panel Analysis): A tool for quick concept evaluation and design trade studies

NASA Technical Reports Server (NTRS)

Hairr, John W.; Dorris, William J.; Ingram, J. Edward; Shah, Bharat M.

1993-01-01

Interactive Stiffened Panel Analysis (ISPAN) modules, written in FORTRAN, were developed to provide an easy to use tool for creating finite element models of composite material stiffened panels. The modules allow the user to interactively construct, solve and post-process finite element models of four general types of structural panel configurations using only the panel dimensions and properties as input data. Linear, buckling and post-buckling solution capability is provided. This interactive input allows rapid model generation and solution by non finite element users. The results of a parametric study of a blade stiffened panel are presented to demonstrate the usefulness of the ISPAN modules. Also, a non-linear analysis of a test panel was conducted and the results compared to measured data and previous correlation analysis.

Fluorescent sensors based on boronic acids

NASA Astrophysics Data System (ADS)

Cooper, Christopher R.; James, Tony D.

1999-05-01

Sensor systems have long been needed for detecting the presence in solution of certain chemically or biologically important species. Sensors are used in a wide range of applications from simple litmus paper that shows a single color change in acidic or basic environments to complex biological assays that use enzymes, antibodies and antigens to display binding events. With this work the use of boronic acids in the design and synthesis of sensors for saccharides (diols) will be presented. The fluorescent sensory systems rely on photoinduced electron transfer (PET) to modulate the observed fluorescence. When saccharides form cyclic boronate esters with boronic acids, the Lewis acidity of the boronic acid is enhanced and therefore the Lewis acid-base interaction between the boronic acid and a neighboring amine is strengthened. The strength of this acid-base interaction modulates the PET from the amine (acting as a quencher) to anthracene (acting as a fluorophore). These compounds show increased fluorescence at neutral pH through suppression of the PET from nitrogen to anthracene on saccharide binding. The general strategy for the development of saccharide selective systems will be discussed. The potential of the boronic acid based systems will be illustrated using the development of glucose and glucosamine selective fluorescent sensors as examples.

Sirtuins and Their Roles in Brain Aging and Neurodegenerative Disorders.

PubMed

Jęśko, Henryk; Wencel, Przemysław; Strosznajder, Robert P; Strosznajder, Joanna B

2017-03-01

Sirtuins (SIRT1-SIRT7) are unique histone deacetylases (HDACs) whose activity depends on NAD + levels and thus on the cellular metabolic status. SIRTs regulate energy metabolism and mitochondrial function. They orchestrate the stress response and damage repair. Through these functions sirtuins modulate the course of aging and affect neurodegenerative diseases. SIRTSs interact with multiple signaling proteins, transcription factors (TFs) and poly(ADP-ribose) polymerases (PARPs) another class of NAD + -dependent post-translational protein modifiers. The cross-talk between SIRTs TFs and PARPs is a highly promising research target in a number of brain pathologies. This review describes updated results on sirtuins in brain aging/neurodegeneration. It focuses on SIRT1 but also on the roles of mitochondrial SIRTs (SIRT3, 4, 5) and on SIRT6 and SIRT2 localized in the nucleus and in cytosol, respectively. The involvement of SIRTs in regulation of insulin-like growth factor signaling in the brain during aging and in Alzheimer's disease was also focused. Moreover, we analyze the mechanism(s) and potential significance of interactions between SIRTs and several TFs in the regulation of cell survival and death. A critical view is given on the application of SIRT activators/modulators in therapy of neurodegenerative diseases.

Mesenchymal Stem Cells Modulate Differentiation of Myeloid Progenitor Cells During Inflammation.

PubMed

Amouzegar, Afsaneh; Mittal, Sharad K; Sahu, Anuradha; Sahu, Srikant K; Chauhan, Sunil K

2017-06-01

Mesenchymal stem cells (MSCs) possess distinct immunomodulatory properties and have tremendous potential for use in therapeutic applications in various inflammatory diseases. MSCs have been shown to regulate pathogenic functions of mature myeloid inflammatory cells, such as macrophages and neutrophils. Intriguingly, the capacity of MSCs to modulate differentiation of myeloid progenitors (MPs) to mature inflammatory cells remains unknown to date. Here, we report the novel finding that MSCs inhibit the expression of differentiation markers on MPs under inflammatory conditions. We demonstrate that the inhibitory effect of MSCs is dependent on direct cell-cell contact and that this intercellular contact is mediated through interaction of CD200 expressed by MSCs and CD200R1 expressed by MPs. Furthermore, using an injury model of sterile inflammation, we show that MSCs promote MP frequencies and suppress infiltration of inflammatory cells in the inflamed tissue. We also find that downregulation of CD200 in MSCs correlates with abrogation of their immunoregulatory function. Collectively, our study provides unequivocal evidence that MSCs inhibit differentiation of MPs in the inflammatory environment via CD200-CD200R1 interaction. Stem Cells 2017;35:1532-1541. © 2017 AlphaMed Press.

Voltage Control of Two-Magnon Scattering and Induced Anomalous Magnetoelectric Coupling in Ni-Zn Ferrite.

PubMed

Xue, Xu; Dong, Guohua; Zhou, Ziyao; Xian, Dan; Hu, Zhongqiang; Ren, Wei; Ye, Zuo-Guang; Chen, Wei; Jiang, Zhuang-De; Liu, Ming

2017-12-13

Controlling spin dynamics through modulation of spin interactions in a fast, compact, and energy-efficient way is compelling for its abundant physical phenomena and great application potential in next-generation voltage controllable spintronic devices. In this work, we report electric field manipulation of spin dynamics-the two-magnon scattering (TMS) effect in Ni 0.5 Zn 0.5 Fe 2 O 4 (NZFO)/Pb(Mg 2/3 Nb 1/3 )-PbTiO 3 (PMN-PT) multiferroic heterostructures, which breaks the bottleneck of magnetostatic interaction-based magnetoelectric (ME) coupling in multiferroics. An alternative approach allowing spin-wave damping to be controlled by external electric field accompanied by a significant enhancement of the ME effect has been demonstrated. A two-way modulation of the TMS effect with a large magnetic anisotropy change up to 688 Oe has been obtained, referring to a 24 times ME effect enhancement at the TMS critical angle at room temperature. Furthermore, the anisotropic spin-freezing behaviors of NZFO were first determined via identifying the spatial magnetic anisotropy fluctuations. A large spin-freezing temperature change of 160 K induced by the external electric field was precisely determined by electron spin resonance.

Voltage Control of Two-Magnon Scattering and Induced Anomalous Magnetoelectric Coupling in Ni–Zn Ferrite

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

Xue, Xu; Dong, Guohua; Zhou, Ziyao

2017-12-01

Controlling spin dynamics through modulation of spin interactions in a fast, compact, and energy-efficient way is compelling for its abundant physical phenomena and great application potential in next-generation voltage controllable spintronic devices. In this work, we report electric field manipulation of spin dynamics-the two-magnon scattering (TMS) effect in Ni0.5Zn0.5Fe2O4 (NZFO)/Pb(Mg2/3Nb1/3)-PbTiO3 (PMN-PT) multiferroic heterostructures, which breaks the bottleneck of magnetostatic interaction-based magnetoelectric (ME) coupling in multiferroics. An alternative approach allowing spin-wave damping to be controlled by external electric field accompanied by a significant enhancement of the ME effect has been demonstrated. A two-way modulation of the TMS effect with a largemore » magnetic anisotropy change up to 688 Oe has been obtained, referring to a 24 times ME effect enhancement at the TMS critical angle at room temperature. Furthermore, the anisotropic spin-freezing behaviors of NZFO were first determined via identifying the spatial magnetic anisotropy fluctuations. A large spin-freezing temperature change of 160 K induced by the external electric field was precisely determined by electron spin resonance.« less

Relaunch of the Interactive Plasma Physics Educational Experience (IPPEX)

NASA Astrophysics Data System (ADS)

Dominguez, A.; Rusaitis, L.; Zwicker, A.; Stotler, D. P.

2015-11-01

In the late 1990's PPPL's Science Education Department developed an innovative online site called the Interactive Plasma Physics Educational Experience (IPPEX). It featured (among other modules) two Java based applications which simulated tokamak physics: A steady state tokamak (SST) and a time dependent tokamak (TDT). The physics underlying the SST and the TDT are based on the ASPECT code which is a global power balance code developed to evaluate the performance of fusion reactor designs. We have relaunched the IPPEX site with updated modules and functionalities: The site itself is now dynamic on all platforms. The graphic design of the site has been modified to current standards. The virtual tokamak programming has been redone in Javascript, taking advantage of the speed and compactness of the code. The GUI of the tokamak has been completely redesigned, including more intuitive representations of changes in the plasma, e.g., particles moving along magnetic field lines. The use of GPU accelerated computation provides accurate and smooth visual representations of the plasma. We will present the current version of IPPEX as well near term plans of incorporating real time NSTX-U data into the simulation.

Multidimensional modulation for next-generation transmission systems

NASA Astrophysics Data System (ADS)

Millar, David S.; Koike-Akino, Toshiaki; Kojima, Keisuke; Parsons, Kieran

2017-01-01

Recent research in multidimensional modulation has shown great promise in long reach applications. In this work, we will investigate the origins of this gain, the different approaches to multidimensional constellation design, and different performance metrics for coded modulation. We will also discuss the reason that such coded modulation schemes seem to have limited application at shorter distances, and the potential for other coded modulation schemes in future transmission systems.

Interpersonal Biocybernetics: Connecting Through Social Psychophysiology

NASA Technical Reports Server (NTRS)

Pope, Alan T.; Stephens, Chad L.

2012-01-01

One embodiment of biocybernetic adaptation is a human-computer interaction system designed such that physiological signals modulate the effect that control of a task by other means, usually manual control, has on performance of the task. Such a modulation system enables a variety of human-human interactions based upon physiological self-regulation performance. These interpersonal interactions may be mixes of competition and cooperation for simulation training and/or videogame entertainment

International Conference on Infrared and Millimeter Waves, 13th, Honolulu, HI, Dec. 5-9, 1988, Conference Digest

NASA Astrophysics Data System (ADS)

Temkin, Richard J.

Recent advances in IR and mm-wave (MMW) physics, astrophysics, devices, and applications are examined in reviews and reports. Sections are devoted to MMW sources, MMW modulation of light, MMW antennas, FELs, MMW optical technology, astronomy, MMW systems, microwave-optical interactions, MMW waveguides, MMW detectors and mixers, plasma diagnostics, and atmospheric physics. Also considered are gyrotrons, guided propagation, high-Tc superconductors, sub-MMW detectors and related devices, ICs, near-MMW measurements and techniques, lasers, material characterization, semiconductors, and atmospheric propagation.

Tunable strength saddle-point contacts impact on quantum rings transmission

NASA Astrophysics Data System (ADS)

González, J. J.; Diago-Cisneros, L.

2016-09-01

A particular subject of investigation is the role of several sadle-point contact (QPC) parameters on the scattering properties of an Aharonov-Bohm-Aharonov-Casher quantum ring (QR) under Rashba-type spin orbit interaction. We discuss the interplay of the conductance with the confinement strengths and height of the QPC, which yields new and tunable harmonic and non-harmonics patterns, while one manipulates these constriction parameters. This phenomenology may be of utility to implement a novel way to modulate spin interference effects in semiconducting QRs, providing an appealing test-platform for spintronics applications.

Open Astronomy Catalogs API

NASA Astrophysics Data System (ADS)

Guillochon, James; Cowperthwaite, Philip S.

2018-05-01

We announce the public release of the application program interface (API) for the Open Astronomy Catalogs (OACs), the OACAPI. The OACs serve near-complete collections of supernova, tidal disruption, kilonova, and fast stars data (including photometry, spectra, radio, and X-ray observations) via a user-friendly web interface that displays the data interactively and offers full data downloads. The OACAPI, by contrast, enables users to specifically download particular pieces of the OAC dataset via a flexible programmatic syntax, either via URL GET requests, or via a module within the astroquery Python package.

Design of an Agent-Based Model to Examine Population-Environment Interactions in Nang Rong District, Thailand.

PubMed

Walsh, Stephen J; Malanson, George P; Entwisle, Barbara; Rindfuss, Ronald R; Mucha, Peter J; Heumann, Benjamin W; McDaniel, Philip M; Frizzelle, Brian G; Verdery, Ashton M; Williams, Nathalie; Xiaozheng, Yao; Ding, Deng

2013-05-01

The design of an Agent-Based Model (ABM) is described that integrates Social and Land Use Modules to examine population-environment interactions in a former agricultural frontier in Northeastern Thailand. The ABM is used to assess household income and wealth derived from agricultural production of lowland, rain-fed paddy rice and upland field crops in Nang Rong District as well as remittances returned to the household from family migrants who are engaged in off-farm employment in urban destinations. The ABM is supported by a longitudinal social survey of nearly 10,000 households, a deep satellite image time-series of land use change trajectories, multi-thematic social and ecological data organized within a GIS, and a suite of software modules that integrate data derived from an agricultural cropping system model (DSSAT - Decision Support for Agrotechnology Transfer) and a land suitability model (MAXENT - Maximum Entropy), in addition to multi-dimensional demographic survey data of individuals and households. The primary modules of the ABM are the Initialization Module, Migration Module, Assets Module, Land Suitability Module, Crop Yield Module, Fertilizer Module, and the Land Use Change Decision Module. The architecture of the ABM is described relative to module function and connectivity through uni-directional or bi-directional links. In general, the Social Modules simulate changes in human population and social networks, as well as changes in population migration and household assets, whereas the Land Use Modules simulate changes in land use types, land suitability, and crop yields. We emphasize the description of the Land Use Modules - the algorithms and interactions between the modules are described relative to the project goals of assessing household income and wealth relative to shifts in land use patterns, household demographics, population migration, social networks, and agricultural activities that collectively occur within a marginalized environment that is subjected to a suite of endogenous and exogenous dynamics.

Design of an Agent-Based Model to Examine Population-Environment Interactions in Nang Rong District, Thailand

PubMed Central

Walsh, Stephen J.; Malanson, George P.; Entwisle, Barbara; Rindfuss, Ronald R.; Mucha, Peter J.; Heumann, Benjamin W.; McDaniel, Philip M.; Frizzelle, Brian G.; Verdery, Ashton M.; Williams, Nathalie; Xiaozheng, Yao; Ding, Deng

2013-01-01

The design of an Agent-Based Model (ABM) is described that integrates Social and Land Use Modules to examine population-environment interactions in a former agricultural frontier in Northeastern Thailand. The ABM is used to assess household income and wealth derived from agricultural production of lowland, rain-fed paddy rice and upland field crops in Nang Rong District as well as remittances returned to the household from family migrants who are engaged in off-farm employment in urban destinations. The ABM is supported by a longitudinal social survey of nearly 10,000 households, a deep satellite image time-series of land use change trajectories, multi-thematic social and ecological data organized within a GIS, and a suite of software modules that integrate data derived from an agricultural cropping system model (DSSAT – Decision Support for Agrotechnology Transfer) and a land suitability model (MAXENT – Maximum Entropy), in addition to multi-dimensional demographic survey data of individuals and households. The primary modules of the ABM are the Initialization Module, Migration Module, Assets Module, Land Suitability Module, Crop Yield Module, Fertilizer Module, and the Land Use Change Decision Module. The architecture of the ABM is described relative to module function and connectivity through uni-directional or bi-directional links. In general, the Social Modules simulate changes in human population and social networks, as well as changes in population migration and household assets, whereas the Land Use Modules simulate changes in land use types, land suitability, and crop yields. We emphasize the description of the Land Use Modules – the algorithms and interactions between the modules are described relative to the project goals of assessing household income and wealth relative to shifts in land use patterns, household demographics, population migration, social networks, and agricultural activities that collectively occur within a marginalized environment that is subjected to a suite of endogenous and exogenous dynamics. PMID:24277975

Bacterial inclusion bodies as potential synthetic devices for pathogen recognition and a therapeutic substance release.

PubMed

Talafová, Klaudia; Hrabárová, Eva; Chorvát, Dušan; Nahálka, Jozef

2013-02-07

Adhesins of pathogens recognise the glycans on the host cell and mediate adherence. They are also crucial for determining the tissue preferences of pathogens. Currently, glyco-nanomaterials provide potential tool for antimicrobial therapy. We demonstrate that properly glyco-tailored inclusion bodies can specifically bind pathogen adhesins and release therapeutic substances. In this paper, we describe the preparation of tailored inclusion bodies via the conjugation of indicator protein aggregated to form inclusion bodies with soluble proteins. Whereas the indicator protein represents a remedy, the soluble proteins play a role in pathogen recognition. For conjugation, glutaraldehyde was used as linker. The treatment of conjugates with polar lysine, which was used to inactivate the residual glutaraldehyde, inhibited unwanted hydrophobic interactions between inclusion bodies. The tailored inclusion bodies specifically interacted with the SabA adhesin from Helicobacter pylori aggregated to form inclusion bodies that were bound to the sialic acids decorating the surface of human erythrocytes. We also tested the release of indicator proteins from the inclusion bodies using sortase A and Ssp DNAB intein self-cleaving modules, respectively. Sortase A released proteins in a relatively short period of time, whereas the intein cleavage took several weeks. The tailored inclusion bodies are promising "nanopills" for biomedical applications. They are able to specifically target the pathogen, while a self-cleaving module releases a soluble remedy. Various self-cleaving modules can be enabled to achieve the diverse pace of remedy release.

Bacterial inclusion bodies as potential synthetic devices for pathogen recognition and a therapeutic substance release

PubMed Central

2013-01-01

Background Adhesins of pathogens recognise the glycans on the host cell and mediate adherence. They are also crucial for determining the tissue preferences of pathogens. Currently, glyco-nanomaterials provide potential tool for antimicrobial therapy. We demonstrate that properly glyco-tailored inclusion bodies can specifically bind pathogen adhesins and release therapeutic substances. Results In this paper, we describe the preparation of tailored inclusion bodies via the conjugation of indicator protein aggregated to form inclusion bodies with soluble proteins. Whereas the indicator protein represents a remedy, the soluble proteins play a role in pathogen recognition. For conjugation, glutaraldehyde was used as linker. The treatment of conjugates with polar lysine, which was used to inactivate the residual glutaraldehyde, inhibited unwanted hydrophobic interactions between inclusion bodies. The tailored inclusion bodies specifically interacted with the SabA adhesin from Helicobacter pylori aggregated to form inclusion bodies that were bound to the sialic acids decorating the surface of human erythrocytes. We also tested the release of indicator proteins from the inclusion bodies using sortase A and Ssp DNAB intein self-cleaving modules, respectively. Sortase A released proteins in a relatively short period of time, whereas the intein cleavage took several weeks. Conclusions The tailored inclusion bodies are promising “nanopills” for biomedical applications. They are able to specifically target the pathogen, while a self-cleaving module releases a soluble remedy. Various self-cleaving modules can be enabled to achieve the diverse pace of remedy release. PMID:23391325

MetaboAnalyst 3.0--making metabolomics more meaningful.

PubMed

Xia, Jianguo; Sinelnikov, Igor V; Han, Beomsoo; Wishart, David S

2015-07-01

MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Laser intensity modulated real time monitoring cell growth sensor for bioprocess applications

NASA Astrophysics Data System (ADS)

Kishore, P.; Babu, P. Ravindra; Devi, V. Rama; Maunika, T.; Soujanya, P.; Kishore, P. V. N.; Dinakar, D.

2016-04-01

This article proposes an optical method for monitoring the growth of Escherichia coli in Luria Bertani medium and Saccharomyces cereviciae in YPD. Suitable light is selected which on interaction with the analyte under consideration, gets adsorption / scattered. Required electronic circuitry is designed to drive the laser source and to detect the intensity of light using Photo-detector. All these components are embedded and arranged in a proper way and monitored the growth of the microbs in real time. The sensors results are compared with standard techniques such as colorimeter, Nephelometer and hemocytometer. The experimental results are in good agreement with the existed techniques and well suitable for real time monitoring applications of the growth of the microbs.

Oasis: online analysis of small RNA deep sequencing data.

PubMed

Capece, Vincenzo; Garcia Vizcaino, Julio C; Vidal, Ramon; Rahman, Raza-Ur; Pena Centeno, Tonatiuh; Shomroni, Orr; Suberviola, Irantzu; Fischer, Andre; Bonn, Stefan

2015-07-01

Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data. Oasis is implemented in Python, R, Java, PHP, C++ and JavaScript. It is freely available at http://oasis.dzne.de. stefan.bonn@dzne.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Early bioelectric activities mediate redox-modulated regeneration.

PubMed

Ferreira, Fernando; Luxardi, Guillaume; Reid, Brian; Zhao, Min

2016-12-15

Reactive oxygen species (ROS) and electric currents modulate regeneration; however, the interplay between biochemical and biophysical signals during regeneration remains poorly understood. We investigate the interactions between redox and bioelectric activities during tail regeneration in Xenopus laevis tadpoles. We show that inhibition of NADPH oxidase-mediated production of ROS, or scavenging or blocking their diffusion into cells, impairs regeneration and consistently regulates the dynamics of membrane potential, transepithelial potential (TEP) and electric current densities (J I ) during regeneration. Depletion of ROS mimics the altered TEP and J I observed in the non-regenerative refractory period. Short-term application of hydrogen peroxide (H 2 O 2 ) rescues (from depleted ROS) and induces (from the refractory period) regeneration, TEP increase and J I reversal. H 2 O 2 is therefore necessary for and sufficient to induce regeneration and to regulate TEP and J I Epistasis assays show that voltage-gated Na + channels act downstream of H 2 O 2 to modulate regeneration. Altogether, these results suggest a novel mechanism for regeneration via redox-bioelectric orchestration. © 2016. Published by The Company of Biologists Ltd.

Peptide-coated gold nanoparticles for modulation of angiogenesis in vivo.

PubMed

Roma-Rodrigues, Catarina; Heuer-Jungemann, Amelie; Fernandes, Alexandra R; Kanaras, Antonios G; Baptista, Pedro V

2016-01-01

In this work, peptides designed to selectively interact with cellular receptors involved in the regulation of angiogenesis were anchored to oligo-ethylene glycol-capped gold nanoparticles (AuNPs) and used to evaluate the modulation of vascular development using an ex ovo chick chorioallantoic membrane assay. These nanoparticles alter the balance between naturally secreted pro- and antiangiogenic factors, under various biological conditions, without causing toxicity. Exposure of chorioallantoic membranes to AuNP-peptide activators of angiogenesis accelerated the formation of new arterioles when compared to scrambled peptide-coated nanoparticles. On the other hand, antiangiogenic AuNP-peptide conjugates were able to selectively inhibit angiogenesis in vivo. We demonstrated that AuNP vectorization is crucial for enhancing the effect of active peptides. Our data showed for the first time the effective control of activation or inhibition of blood vessel formation in chick embryo via AuNP-based formulations suitable for the selective modulation of angiogenesis, which is of paramount importance in applications where promotion of vascular growth is desirable (eg, wound healing) or ought to be contravened, as in cancer development.

Spacecraft Orbit Design and Analysis (SODA), version 1.0 user's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.; Davis, John S.

1989-01-01

The Spacecraft Orbit Design and Analysis (SODA) computer program, Version 1.0 is described. SODA is a spaceflight mission planning system which consists of five program modules integrated around a common database and user interface. SODA runs on a VAX/VMS computer with an EVANS & SUTHERLAND PS300 graphics workstation. BOEING RIM-Version 7 relational database management system performs transparent database services. In the current version three program modules produce an interactive three dimensional (3D) animation of one or more satellites in planetary orbit. Satellite visibility and sensor coverage capabilities are also provided. One module produces an interactive 3D animation of the solar system. Another module calculates cumulative satellite sensor coverage and revisit time for one or more satellites. Currently Earth, Moon, and Mars systems are supported for all modules except the solar system module.

Spacecraft Orbit Design and Analysis (SODA). Version 2.0: User's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.; Davis, John S.; Zsoldos, Jeffrey S.

1991-01-01

The Spacecraft Orbit Design and Analysis (SODA) computer program, Version 2.0, is discussed. SODA is a spaceflight mission planning system that consists of six program modules integrated around a common database and user interface. SODA runs on a VAX/VMS computer with an Evans and Sutherland PS300 graphics workstation. In the current version, three program modules produce an interactive three dimensional animation of one or more satellites in planetary orbit. Satellite visibility and sensor coverage capabilities are also provided. Circular and rectangular, off nadir, fixed and scanning sensors are supported. One module produces an interactive three dimensional animation of the solar system. Another module calculates cumulative satellite sensor coverage and revisit time for one or more satellites. Currently, Earth, Moon, and Mars systems are supported for all modules except the solar system module.

Reconfigurable Processing Module

NASA Technical Reports Server (NTRS)

Somervill, Kevin; Hodson, Robert; Jones, Robert; Williams, John

2005-01-01

To accommodate a wide spectrum of applications and technologies, NASA s Exploration System's Missions Directorate has called for reconfigurable and modular technologies to support future missions to the moon and Mars. In response, Langley Research Center is leading a program entitled Reconfigurable Scaleable Computing (RSC) that is centered on the development of FPGA-based computing resources in a stackable form factor. This paper details the architecture and implementation of the Reconfigurable Processing Module (RPM), which is the key element of the RSC system. The RPM is an FPGA-based, space-qualified printed circuit assembly leveraging terrestrial/commercial design standards into the space applications domain. The form factor is similar to, and backwards compatible with, the PCI-104 standard utilizing only the PCI interface. The size is expanded to accommodate the required functionality while still better than 30% smaller than a 3U CompactPCI(TradeMark)card and without the overhead of the backplane. The architecture is built around two FPGA devices, one hosting PCI and memory interfaces, and another hosting mission application resources; both of which are connected with a high-speed data bus. The PCI interface FPGA provides access via the PCI bus to onboard SDRAM, flash PROM, and the application resources; both configuration management as well as runtime interaction. The reconfigurable FPGA, referred to as the Application FPGA - or simply "the application" - is a radiation-tolerant Xilinx Virtex-4 FX60 hosting custom application specific logic or soft microprocessor IP. The RPM implements various SEE mitigation techniques including TMR, EDAC, and configuration scrubbing of the reconfigurable FPGA. Prototype hardware and formal modeling techniques are used to explore the performability trade space. These models provide a novel way to calculate quality-of-service performance measures while simultaneously considering fault-related behavior due to SEE soft errors.

A global interaction network maps a wiring diagram of cellular function

PubMed Central

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

2017-01-01

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

Effective connectivity of ascending and descending frontal-thalamic pathways during sustained attention: Complex brain network interactions in adolescence

PubMed Central

Jagtap, Pranav; Diwadkar, Vaibhav A.

2016-01-01

Frontal-thalamic interactions are crucial for bottom-up gating and top-down control, yet have not been well studied from brain network perspectives. We applied network modeling of fMRI signals (Dynamic Causal Modeling; DCM) to investigate frontal-thalamic interactions during an attention task with parametrically varying levels of demand. fMRI was collected while subjects participated in a sustained continuous performance task with low and high attention demands. 162 competing model architectures were employed in DCM to evaluate hypotheses on bilateral frontal-thalamic connections and their modulation by attention demand, selected at a second level using Bayesian Model Selection. The model architecture evinced significant contextual modulation by attention of ascending (thalamus → dPFC) and descending (dPFC → thalamus) pathways. However, modulation of these pathways was asymmetric: While positive modulation of the ascending pathway was comparable across attention demand, modulation of the descending pathway was significantly greater when attention demands were increased. Increased modulation of the (dPFC → thalamus) pathway in response to increased attention demand constitutes novel evidence of attention-related gain in the connectivity of the descending attention pathway. By comparison demand-independent modulation of the ascending (thalamus → dPFC) pathway suggests unbiased thalamic inputs to the cortex in the context of the paradigm. PMID:27145923

Residential photovoltaic module and array requirements study

NASA Technical Reports Server (NTRS)

Nearhoof, S. L.; Oster, J. R.

1979-01-01

Design requirements for photovoltaic modules and arrays used in residential applications were identified. Building codes and referenced standards were reviewed for their applicability to residential photovoltaic array installations. Four installation types were identified - integral (replaces roofing), direct (mounted on top of roofing), stand-off (mounted away from roofing), and rack (for flat or low slope roofs, or ground mounted). Installation costs were developed for these mounting types as a function of panel/module size. Studies were performed to identify optimum module shapes and sizes and operating voltage cost drivers. It is concluded that there are no perceived major obstacles to the use of photovoltaic modules in residential arrays. However, there is no applicable building code category for residential photovoltaic modules and arrays and additional work with standards writing organizations is needed to develop residential module and array requirements.

Autistic-like social behaviour in Shank2-mutant mice improved by restoring NMDA receptor function.

PubMed

Won, Hyejung; Lee, Hye-Ryeon; Gee, Heon Yung; Mah, Won; Kim, Jae-Ick; Lee, Jiseok; Ha, Seungmin; Chung, Changuk; Jung, Eun Suk; Cho, Yi Sul; Park, Sae-Geun; Lee, Jung-Soo; Lee, Kyungmin; Kim, Daesoo; Bae, Yong Chul; Kaang, Bong-Kiun; Lee, Min Goo; Kim, Eunjoon

2012-06-13

Autism spectrum disorder (ASD) is a group of conditions characterized by impaired social interaction and communication, and restricted and repetitive behaviours. ASD is a highly heritable disorder involving various genetic determinants. Shank2 (also known as ProSAP1) is a multi-domain scaffolding protein and signalling adaptor enriched at excitatory neuronal synapses, and mutations in the human SHANK2 gene have recently been associated with ASD and intellectual disability. Although ASD-associated genes are being increasingly identified and studied using various approaches, including mouse genetics, further efforts are required to delineate important causal mechanisms with the potential for therapeutic application. Here we show that Shank2-mutant (Shank2(-/-)) mice carrying a mutation identical to the ASD-associated microdeletion in the human SHANK2 gene exhibit ASD-like behaviours including reduced social interaction, reduced social communication by ultrasonic vocalizations, and repetitive jumping. These mice show a marked decrease in NMDA (N-methyl-D-aspartate) glutamate receptor (NMDAR) function. Direct stimulation of NMDARs with D-cycloserine, a partial agonist of NMDARs, normalizes NMDAR function and improves social interaction in Shank2(-/-) mice. Furthermore, treatment of Shank2(-/-) mice with a positive allosteric modulator of metabotropic glutamate receptor 5 (mGluR5), which enhances NMDAR function via mGluR5 activation, also normalizes NMDAR function and markedly enhances social interaction. These results suggest that reduced NMDAR function may contribute to the development of ASD-like phenotypes in Shank2(-/-) mice, and mGluR modulation of NMDARs offers a potential strategy to treat ASD.

Multimodal Neuroelectric Interface Development

NASA Technical Reports Server (NTRS)

Trejo, Leonard J.; Wheeler, Kevin R.; Jorgensen, Charles C.; Totah, Joseph (Technical Monitor)

2001-01-01

This project aims to improve performance of NASA missions by developing multimodal neuroelectric technologies for augmented human-system interaction. Neuroelectric technologies will add completely new modes of interaction that operate in parallel with keyboards, speech, or other manual controls, thereby increasing the bandwidth of human-system interaction. We recently demonstrated the feasibility of real-time electromyographic (EMG) pattern recognition for a direct neuroelectric human-computer interface. We recorded EMG signals from an elastic sleeve with dry electrodes, while a human subject performed a range of discrete gestures. A machine-teaming algorithm was trained to recognize the EMG patterns associated with the gestures and map them to control signals. Successful applications now include piloting two Class 4 aircraft simulations (F-15 and 757) and entering data with a "virtual" numeric keyboard. Current research focuses on on-line adaptation of EMG sensing and processing and recognition of continuous gestures. We are also extending this on-line pattern recognition methodology to electroencephalographic (EEG) signals. This will allow us to bypass muscle activity and draw control signals directly from the human brain. Our system can reliably detect P-rhythm (a periodic EEG signal from motor cortex in the 10 Hz range) with a lightweight headset containing saline-soaked sponge electrodes. The data show that EEG p-rhythm can be modulated by real and imaginary motions. Current research focuses on using biofeedback to train of human subjects to modulate EEG rhythms on demand, and to examine interactions of EEG-based control with EMG-based and manual control. Viewgraphs on these neuroelectric technologies are also included.

Protein-Protein Interactions, Not Substrate Recognition, Dominate the Turnover of Chimeric Assembly Line Polyketide Synthases*

PubMed Central

Klaus, Maja; Ostrowski, Matthew P.; Austerjost, Jonas; Robbins, Thomas; Lowry, Brian; Cane, David E.; Khosla, Chaitan

2016-01-01

The potential for recombining intact polyketide synthase (PKS) modules has been extensively explored. Both enzyme-substrate and protein-protein interactions influence chimeric PKS activity, but their relative contributions are unclear. We now address this issue by studying a library of 11 bimodular and 8 trimodular chimeric PKSs harboring modules from the erythromycin, rifamycin, and rapamycin synthases. Although many chimeras yielded detectable products, nearly all had specific activities below 10% of the reference natural PKSs. Analysis of selected bimodular chimeras, each with the same upstream module, revealed that turnover correlated with the efficiency of intermodular chain translocation. Mutation of the acyl carrier protein (ACP) domain of the upstream module in one chimera at a residue predicted to influence ketosynthase-ACP recognition led to improved turnover. In contrast, replacement of the ketoreductase domain of the upstream module by a paralog that produced the enantiomeric ACP-bound diketide caused no changes in processing rates for each of six heterologous downstream modules compared with those of the native diketide. Taken together, these results demonstrate that protein-protein interactions play a larger role than enzyme-substrate recognition in the evolution or design of catalytically efficient chimeric PKSs. PMID:27246853

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

PubMed

Gunner, M R; Baker, N A

2016-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. © 2016 Elsevier Inc. All rights reserved.

Multidrug evolutionary strategies to reverse antibiotic resistance

PubMed Central

Baym, Michael; Stone, Laura K.; Kishony, Roy

2017-01-01

Antibiotic treatment has two conflicting effects: the desired, immediate effect of inhibiting bacterial growth and the undesired, long-term effect of promoting the evolution of resistance. Although these contrasting outcomes seem inextricably linked, recent work has revealed several ways by which antibiotics can be combined to inhibit bacterial growth while, counterintuitively, selecting against resistant mutants. Decoupling treatment efficacy from the risk of resistance can be achieved by exploiting specific interactions between drugs, and the ways in which resistance mutations to a given drug can modulate these interactions or increase the sensitivity of the bacteria to other compounds. Although their practical application requires much further development and validation, and relies on advances in genomic diagnostics, these discoveries suggest novel paradigms that may restrict or even reverse the evolution of resistance. PMID:26722002

Complexation of C60 fullerene with aromatic drugs.

PubMed

Evstigneev, Maxim P; Buchelnikov, Anatoly S; Voronin, Dmitry P; Rubin, Yuriy V; Belous, Leonid F; Prylutskyy, Yuriy I; Ritter, Uwe

2013-02-25

The contributions of various physical factors to the energetics of complexation of aromatic drug molecules with C(60) fullerene are investigated in terms of the calculated magnitudes of equilibrium complexation constants and the components of the net Gibbs free energy. Models of complexation are developed taking into account the polydisperse nature of fullerene solutions in terms of the continuous or discrete (fractal) aggregation of C(60) molecules. Analysis of the energetics has shown that stabilization of the ligand-fullerene complexes in aqueous solution is mainly determined by intermolecular van der Waals interactions and, to lesser extent, by hydrophobic interactions. The results provide a physicochemical basis for a potentially new biotechnological application of fullerenes as modulators of biological activity of aromatic drugs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Turning Mechanics During Swimming by Oblate Hydromedusae

NASA Astrophysics Data System (ADS)

Costello, J.; Colin, S.; Sutherland, K.; Gemmell, B. J.

2016-02-01

Maneuverability is critical to the success of many species. Selective forces acting over millions of years have resulted in a range of capabilities currently unmatched by machines. Thus, understanding animal control of fluids for maneuvering has both biological and engineering applications. Medusae are radially symmetrical swimmers that must use asymmetric body motions to change direction during turning maneuvers. But what types of asymmetric motions are useful and how do they interact with surrounding fluids to generate rotational forces? We used high speed digital particle image velocimetry (DPIV) to investigate comparative swimming patterns of three hydromedusan species (Aequorea victoria, Clytia gregaria and Mitrocoma cellularia). We provide evidence for consistent animal-fluid interactions that underlie turning mechanics of oblate hydromedusae and provide new insights into the modulation and control of vorticity for low-speed animal maneuvering.

The Role of Heparan Sulfate in Inflammation, and the Development of Biomimetics as Anti-Inflammatory Strategies.

PubMed

Farrugia, Brooke L; Lord, Megan S; Melrose, James; Whitelock, John M

2018-04-01

Key events that occur during inflammation include the recruitment, adhesion, and transmigration of leukocytes from the circulation to the site of inflammation. These events are modulated by chemokines, integrins, and selectins and the interaction of these molecules with glycosaminoglycans, predominantly heparan sulfate (HS). The development of HS/heparin mimetics that interfere or inhibit the interactions that occur between glycosaminoglycans and modulators of inflammation holds great potential for use as anti-inflammatory therapeutics. This review will detail the role of HS in the events that occur during inflammation, their interaction and modulation of inflammatory mediators, and the current advances in the development of HS/heparin mimetics as anti-inflammatory biotherapeutics.

Structural and Functional Assessment of APOBEC3G Macromolecular Complexes

PubMed Central

Polevoda, Bogdan; McDougall, William M.; Bennett, Ryan P.; Salter, Jason D.; Smith, Harold C.

2016-01-01

There are eleven members in the human APOBEC family of proteins that are evolutionarily related through their zinc-dependent cytidine deaminase domains. The human APOBEC gene clusters arose on chromosome 6 and 22 through gene duplication and divergence to where current day APOBEC proteins are functionally diverse and broadly expressed in tissues. APOBEC serve enzymatic and non enzymatic functions in cells. In both cases, formation of higher-order structures driven by APOBEC protein-protein interactions and binding to RNA and/or single stranded DNA are integral to their function. In some circumstances, these interactions are regulatory and modulate APOBEC activities. We are just beginning to understand how macromolecular interactions drive processes such as APOBEC subcellular compartmentalization, formation of holoenzyme complexes, gene targeting, foreign DNA restriction, anti-retroviral activity, formation of ribonucleoprotein particles and APOBEC degradation. Protein-protein and protein-nucleic acid cross-linking methods coupled with mass spectrometry, electrophoretic mobility shift assays, glycerol gradient sedimentation, fluorescence anisotropy and APOBEC deaminase assays are enabling mapping of interacting surfaces that are essential for these functions. The goal of this methods review is through example of our research on APOBEC3G, describe the application of cross-linking methods to characterize and quantify macromolecular interactions and their functional implications. Given the homology in structure and function, it is proposed that these methods will be generally applicable to the discovery process for other APOBEC and RNA and DNA editing and modifying proteins. PMID:26988126

PLAID- A COMPUTER AIDED DESIGN SYSTEM

NASA Technical Reports Server (NTRS)

Brown, J. W.

1994-01-01

PLAID is a three-dimensional Computer Aided Design (CAD) system which enables the user to interactively construct, manipulate, and display sets of highly complex geometric models. PLAID was initially developed by NASA to assist in the design of Space Shuttle crewstation panels, and the detection of payload object collisions. It has evolved into a more general program for convenient use in many engineering applications. Special effort was made to incorporate CAD techniques and features which minimize the users workload in designing and managing PLAID models. PLAID consists of three major modules: the Primitive Object Generator (BUILD), the Composite Object Generator (COG), and the DISPLAY Processor. The BUILD module provides a means of constructing simple geometric objects called primitives. The primitives are created from polygons which are defined either explicitly by vertex coordinates, or graphically by use of terminal crosshairs or a digitizer. Solid objects are constructed by combining, rotating, or translating the polygons. Corner rounding, hole punching, milling, and contouring are special features available in BUILD. The COG module hierarchically organizes and manipulates primitives and other previously defined COG objects to form complex assemblies. The composite object is constructed by applying transformations to simpler objects. The transformations which can be applied are scalings, rotations, and translations. These transformations may be defined explicitly or defined graphically using the interactive COG commands. The DISPLAY module enables the user to view COG assemblies from arbitrary viewpoints (inside or outside the object) both in wireframe and hidden line renderings. The PLAID projection of a three-dimensional object can be either orthographic or with perspective. A conflict analysis option enables detection of spatial conflicts or collisions. DISPLAY provides camera functions to simulate a view of the model through different lenses. Other features include hardcopy plot generation, scaling and zoom options, distance tabulations, and descriptive text in different sizes and fonts. An object in the PLAID database is not just a collection of lines; rather, it is a true three-dimensional representation from which correct hidden line renditions can be computed for any specified eye point. The drawings produced in the various modules of PLAID can be stored in files for future use. The PLAID program product is available by license for a period of 10 years to domestic U.S. licensees. The licensed program product includes the PLAID source code, command procedures, sample applications, and one set of supporting documentation. Copies of the documentation may be purchased separately at the price indicated below. PLAID is written in FORTRAN 77 for single user interactive execution and has been implemented on a DEC VAX series computer operating under VMS with a recommended core memory of four megabytes. PLAID requires a Tektronix 4014 compatible graphics display terminal and optionally uses a Tektronix 4631 compatible graphics hardcopier. Plots of resulting PLAID displays may be produced using the Calcomp 960, HP 7221, or HP 7580 plotters. Digitizer tablets can also be supported. This program was developed in 1986.

Engaging Men in Prenatal Health Promotion: A Pilot Evaluation of Targeted e-Health Content

PubMed Central

Mackert, Michael; Guadagno, Marie; Lazard, Allison; Donovan, Erin; Rochlen, Aaron; Garcia, Alexandra; Damásio, Manuel José

2016-01-01

Pregnancy outcomes in the United States continue to rank among the worst in the developed world. Traditional maternal–child health promotion tends to focus exclusively on women, leaving men out of programs that can affect family health. Scholars advocate including men in prenatal health to reduce maternal and infant mortality and morbidity. This study explored the perceived role of men in prenatal health, the use of an e-health application, and participant-suggested ways of improving the application moving forward. This study interviewed men in a large Southwestern U.S. city with an average age of 26.0 years (N = 23). The sample was 52% White, 26% Hispanic, 9% Asian, 9% multiracial or other, and 4% Black. Participants were asked about pregnancy health and used a pregnancy-related e-health application on a tablet computer. Participants provided opinions on content, ease of use of tablets, and recommendations for a stronger application. Despite perceived barriers such as time constraints, financial burdens, and an unclear role, men believe it is important to be involved in pregnancy health. Most found the application to contain useful and interesting information. Participants recommended the addition of videos and interactive modules to make the application stronger. This study explored the use of a targeted e-health application to introduce men to prenatal health education. Results indicate men feel favorable to this type of intervention. Additional refinement of the application could include interactive tools or “push content” to further engage men in this important topic. PMID:27956587

The Scientific Filesystem.

PubMed

Sochat, Vanessa

2018-05-01

Here, we present the Scientific Filesystem (SCIF), an organizational format that supports exposure of executables and metadata for discoverability of scientific applications. The format includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within. SCIF makes it easy to expose metadata, multiple environments, installation steps, files, and entry points to render scientific applications consistent, modular, and discoverable. A SCIF can be installed on a traditional host or in a container technology such as Docker or Singularity. We start by reviewing the background and rationale for the SCIF, followed by an overview of the specification and the different levels of internal modules ("apps") that the organizational format affords. Finally, we demonstrate that SCIF is useful by implementing and discussing several use cases that improve user interaction and understanding of scientific applications. SCIF is released along with a client and integration in the Singularity 2.4 software to quickly install and interact with SCIF. When used inside of a reproducible container, a SCIF is a recipe for reproducibility and introspection of the functions and users that it serves. We use SCIF to evaluate container software, provide metrics, serve scientific workflows, and execute a primary function under different contexts. To encourage collaboration and sharing of applications, we developed tools along with an open source, version-controlled, tested, and programmatically accessible web infrastructure. SCIF and associated resources are available at https://sci-f.github.io. The ease of using SCIF, especially in the context of containers, offers promise for scientists' work to be self-documenting and programatically parseable for maximum reproducibility. SCIF opens up an abstraction from underlying programming languages and packaging logic to work with scientific applications, opening up new opportunities for scientific software development.

Predictive of the quantum capacitance effect on the excitation of plasma waves in graphene transistors with scaling limit

NASA Astrophysics Data System (ADS)

Wang, Lin; Chen, Xiaoshuang; Hu, Yibin; Wang, Shao-Wei; Lu, Wei

2015-04-01

Plasma waves in graphene field-effect transistors (FETs) and nano-patterned graphene sheets have emerged as very promising candidates for potential terahertz and infrared applications in myriad areas including remote sensing, biomedical science, military, and many other fields with their electrical tunability and strong interaction with light. In this work, we study the excitations and propagation properties of plasma waves in nanometric graphene FETs down to the scaling limit. Due to the quantum-capacitance effect, the plasma wave exhibits strong correlation with the distribution of density of states (DOS). It is indicated that the electrically tunable plasma resonance has a power-dependent V0.8TG relation on the gate voltage, which originates from the linear dependence of density of states (DOS) on the energy in pristine graphene, in striking difference to those dominated by classical capacitance with only V0.5TG dependence. The results of different transistor sizes indicate the potential application of nanometric graphene FETs in highly-efficient electro-optic modulation or detection of terahertz or infrared radiation. In addition, we highlight the perspectives of plasma resonance excitation in probing the many-body interaction and quantum matter state in strong correlation electron systems. This study reveals the key feature of plasma waves in decorated/nanometric graphene FETs, and paves the way to tailor plasma band-engineering and expand its application in both terahertz and mid-infrared regions.Plasma waves in graphene field-effect transistors (FETs) and nano-patterned graphene sheets have emerged as very promising candidates for potential terahertz and infrared applications in myriad areas including remote sensing, biomedical science, military, and many other fields with their electrical tunability and strong interaction with light. In this work, we study the excitations and propagation properties of plasma waves in nanometric graphene FETs down to the scaling limit. Due to the quantum-capacitance effect, the plasma wave exhibits strong correlation with the distribution of density of states (DOS). It is indicated that the electrically tunable plasma resonance has a power-dependent V0.8TG relation on the gate voltage, which originates from the linear dependence of density of states (DOS) on the energy in pristine graphene, in striking difference to those dominated by classical capacitance with only V0.5TG dependence. The results of different transistor sizes indicate the potential application of nanometric graphene FETs in highly-efficient electro-optic modulation or detection of terahertz or infrared radiation. In addition, we highlight the perspectives of plasma resonance excitation in probing the many-body interaction and quantum matter state in strong correlation electron systems. This study reveals the key feature of plasma waves in decorated/nanometric graphene FETs, and paves the way to tailor plasma band-engineering and expand its application in both terahertz and mid-infrared regions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07689c

Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules.

PubMed

Haburcak, Richard; Shi, Junfeng; Du, Xuewen; Yuan, Dan; Xu, Bing

2016-11-30

The concurrence of enzymatic reaction and ligand-receptor interactions is common for proteins, but rare for small molecules and has yet to be explored. Here we show that ligand-receptor interaction modulates the morphology of molecular assemblies formed by enzyme-instructed assembly of small molecules. While the absence of ligand-receptor interaction allows enzymatic dephosphorylation of a precursor to generate the hydrogelator that self-assembles to form long nanofibers, the presence of the ligand-receptor interaction biases the pathway to form precipitous aggregates containing short nanofibers. While the hydrogelators self-assemble to form nanofibers or nanoribbons that are unable to bind with the ligand (i.e., vancomycin), the addition of surfactant breaks up the assemblies to restore the ligand-receptor interaction. In addition, an excess amount of the ligands can disrupt the nanofibers and result in the precipitates. As the first example of the use of ligand-receptor interaction to modulate the kinetics of enzymatic self-assembly, this work not only provides a solution to evaluate the interaction between aggregates and target molecules but also offers new insight for understanding the emergent behavior of sophisticated molecular systems having multiple and parallel processes.

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

PubMed Central

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

2011-01-01

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

A computerized education module improves patient knowledge and attitudes about appropriate antibiotic use for acute respiratory tract infections.

PubMed

Price, Erika Leemann; Mackenzie, Thomas D; Metlay, Joshua P; Camargo, Carlos A; Gonzales, Ralph

2011-12-01

Over-use of antibiotics for acute respiratory infections (ARIs) increases antimicrobial resistance, treatment costs, and side effects. Patient desire for antibiotics contributes to over-use. To explore whether a point-of-care interactive computerized education module increases patient knowledge and decreases desire for antibiotics. Bilingual (English/Spanish) interactive kiosks were available in 8 emergency departments as part of a multidimensional intervention to reduce antibiotic prescribing for ARIs. The symptom-tailored module included assessment of symptoms, knowledge about ARIs (3 items), and desire for antibiotics on a 10-point visual analog scale. Multivariable analysis assessed predictors of change in desire for antibiotics. Of 686 adults with ARI symptoms, 63% initially thought antibiotics might help. The proportion of patients with low (1-3 on the scale) desire for antibiotics increased from 22% pre-module to 49% post-module (p<.001). Self-report of "learning something new" was associated with decreased desire for antibiotics, after adjusting for baseline characteristics (p=.001). An interactive educational kiosk improved knowledge about antibiotics and ARIs. Learning correlated with changes in personal desire for antibiotics. By reducing desire for antibiotics, point-of-care interactive educational computer technology may help decrease inappropriate use for antibiotics for ARIs. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

[Computers in nursing: development of free software application with care and management].

PubMed

dos Santos, Sérgio Ribeiro

2010-06-01

This study aimed at developing an information system in nursing with the implementation of nursing care and management of the service. The SisEnf--Information System in Nursing--is a free software module that comprises the care of nursing: history, clinical examination and care plan; the management module consists of: service shifts, personnel management, hospital indicators and other elements. The system was implemented at the Medical Clinic of the Lauro Wanderley University Hospital, at Universidade Federal da Paraiba. In view of the need to bring user and developer closer, in addition to the constant change of functional requirements during the interactive process, the method of unified process was used. The SisEnf was developed on a WEB platform and using free software. Hence, the work developed aimed at assisting in the working process of nursing, which will now have the opportunity to incorporate information technology in their work routine.

Immune signaling by RIG-I-like receptors

PubMed Central

Loo, Yueh-Ming; Gale, Michael

2011-01-01

The RIG-I-like receptors (RLRs) RIG-I, MDA5, and LGP2 play a major role in pathogen sensing of RNA virus infection to initiate and modulate antiviral immunity. The RLRs detect viral RNA ligands or processed self RNA in the cytoplasm to triggers innate immunity and inflammation and to impart gene expression that serves to control infection. Importantly, RLRs cooperate in signaling crosstalk networks with Toll-like receptors and other factors to impart innate immunity and to modulate the adaptive immune response. RLR regulation occurs at a variety of levels ranging from autoregulation to ligand and co-factor interactions and post-translational modifications. Abberant RLR signaling or dysregulation of RLR expression is now implicated in the development of autoimmune diseases. Understanding the processes of RLR signaling and response will provide insights to guide RLR-targeted therapeutics for antiviral and immune modifying applications. PMID:21616437

On-target diagnosing of few-cycle pulses by high-order-harmonic generation

NASA Astrophysics Data System (ADS)

Brambila, Danilo S.; Husakou, Anton; Ivanov, Misha; Zhavoronkov, Nickolai

2017-12-01

We propose an approach to determine the residual phase distortion directly in the interaction region of few-cycle laser radiation with a gaseous target. We describe how the spectra of the generated high harmonics measured as a function of externally introduced dispersion into the driving few-cycle laser pulse can be used to decode small amounts of second- and third-order spectral phase, including the sign. The diagnosis is based on the analysis of several key features in the high-harmonic spectrum: the depth of spectral modulation, the position of the cutoff, and the symmetry of the spectrum with respect to the introduced dispersion. The approach is applicable to pulses without carrier-envelope phase (CEP) stabilization. Surprisingly, we find that for nearly-single-cycle pulses with nonstabilized CEP, deep spectral modulations in the harmonic spectra emerge for positively rather than negatively chirped pulses, in contrast to the case of CEP-stabilized pulses.

Noncontact Viscoelastic Imaging of Living Cells Using a Long-Needle Atomic Force Microscope with Dual-Frequency Modulation

NASA Astrophysics Data System (ADS)

Guan, Dongshi; Charlaix, Elisabeth; Qi, Robert Z.; Tong, Penger

2017-10-01

Imaging of surface topography and elasticity of living cells can provide insight into the roles played by the cells' volumetric and mechanical properties and their response to external forces in regulating the essential cellular events and functions. Here, we report a unique technique of noncontact viscoelastic imaging of live cells using atomic force microscopy (AFM) with a long-needle glass probe. Because only the probe tip is placed in a liquid medium near the cell surface, the AFM cantilever in air functions well under dual-frequency modulation, retaining its high-quality resonant modes. The probe tip interacts with the cell surface through a minute hydrodynamic flow in the nanometer-thin gap region between them without physical contact. Quantitative measurements of the cell height, volume, and Young's modulus are conducted simultaneously. The experiment demonstrates that the long-needle AFM has a wide range of applications in the study of cell mechanics.

Electrospun nanofibers of polyCD/PMAA polymers and their potential application as drug delivery system.

PubMed

Oliveira, Michele F; Suarez, Diego; Rocha, Júlio Cézar Barbosa; de Carvalho Teixeira, Alvaro Vianna Novaes; Cortés, Maria E; De Sousa, Frederico B; Sinisterra, Rubén D

2015-09-01

Herein, we used an electrospinning process to develop highly efficacious and hydrophobic coaxial nanofibers based on poly-cyclodextrin (polyCD) associated with poly(methacrylic acid) (PMAA) that combines polymeric and supramolecular features for modulating the release of the hydrophilic drug, propranolol hydrochloride (PROP). For this purpose, polyCD was synthesized and characterized, and its biocompatibility was assessed using fibroblast cytotoxicity tests. Moreover, the interactions between the guest PROP molecule and both polyCD and βCD were found to be spontaneous. Subsequently, PROP was encapsulated in uniaxial and coaxial polyCD/PMAA nanofibers. A lower PROP burst effect (reduction of approximately 50%) and higher modulation were observed from the coaxial than from the uniaxial fibers. Thus, the coaxial nanofibers could potentially be a useful strategy for developing a controlled release system for hydrophilic molecules. Copyright © 2015 Elsevier B.V. All rights reserved.

Coherent control of an opsin in living brain tissue

NASA Astrophysics Data System (ADS)

Paul, Kush; Sengupta, Parijat; Ark, Eugene D.; Tu, Haohua; Zhao, Youbo; Boppart, Stephen A.

2017-11-01

Retinal-based opsins are light-sensitive proteins. The photoisomerization reaction of these proteins has been studied outside cellular environments using ultrashort tailored light pulses. However, how living cell functions can be modulated via opsins by modifying fundamental nonlinear optical properties of light interacting with the retinal chromophore has remained largely unexplored. We report the use of chirped ultrashort near-infrared pulses to modulate light-evoked ionic current from Channelrhodopsin-2 (ChR2) in brain tissue, and consequently the firing pattern of neurons, by manipulating the phase of the spectral components of the light. These results confirm that quantum coherence of the retinal-based protein system, even in a living neuron, can influence its current output, and open up the possibilities of using designer-tailored pulses for controlling molecular dynamics of opsins in living tissue to selectively enhance or suppress neuronal function for adaptive feedback-loop applications in the future.

Reversible Modulation of DNA-Based Hydrogel Shapes by Internal Stress Interactions.

PubMed

Hu, Yuwei; Kahn, Jason S; Guo, Weiwei; Huang, Fujian; Fadeev, Michael; Harries, Daniel; Willner, Itamar

2016-12-14

We present the assembly of asymmetric two-layer hybrid DNA-based hydrogels revealing stimuli-triggered reversibly modulated shape transitions. Asymmetric, linear hydrogels that include layer-selective switchable stimuli-responsive elements that control the hydrogel stiffness are designed. Trigger-induced stress in one of the layers results in the bending of the linear hybrid structure, thereby minimizing the elastic free energy of the systems. The removal of the stress by a counter-trigger restores the original linear bilayer hydrogel. The stiffness of the DNA hydrogel layers is controlled by thermal, pH (i-motif), K + ion/crown ether (G-quadruplexes), chemical (pH-doped polyaniline), or biocatalytic (glucose oxidase/urease) triggers. A theoretical model relating the experimental bending radius of curvatures of the hydrogels with the Young's moduli and geometrical parameters of the hydrogels is provided. Promising applications of shape-regulated stimuli-responsive asymmetric hydrogels include their use as valves, actuators, sensors, and drug delivery devices.

Engineering Cell-Cell Signaling

PubMed Central

Milano, Daniel F.; Natividad, Robert J.; Asthagiri, Anand R.

2014-01-01

Juxtacrine cell-cell signaling mediated by the direct interaction of adjoining mammalian cells is arguably the mode of cell communication that is most recalcitrant to engineering. Overcoming this challenge is crucial for progress in biomedical applications, such as tissue engineering, regenerative medicine, immune system engineering and therapeutic design. Here, we describe the significant advances that have been made in developing synthetic platforms (materials and devices) and synthetic cells (cell surface engineering and synthetic gene circuits) to modulate juxtacrine cell-cell signaling. In addition, significant progress has been made in elucidating design rules and strategies to modulate juxtacrine signaling based on quantitative, engineering analysis of the mechanical and regulatory role of juxtacrine signals in the context of other cues and physical constraints in the microenvironment. These advances in engineering juxtacrine signaling lay a strong foundation for an integrative approach to utilizing synthetic cells, advanced ‘chassis’ and predictive modeling to engineer the form and function of living tissues. PMID:23856592

General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

PubMed

Teif, Vladimir B

2007-01-01

The transfer matrix methodology is proposed as a systematic tool for the statistical-mechanical description of DNA-protein-drug binding involved in gene regulation. We show that a genetic system of several cis-regulatory modules is calculable using this method, considering explicitly the site-overlapping, competitive, cooperative binding of regulatory proteins, their multilayer assembly and DNA looping. In the methodological section, the matrix models are solved for the basic types of short- and long-range interactions between DNA-bound proteins, drugs and nucleosomes. We apply the matrix method to gene regulation at the O(R) operator of phage lambda. The transfer matrix formalism allowed the description of the lambda-switch at a single-nucleotide resolution, taking into account the effects of a range of inter-protein distances. Our calculations confirm previously established roles of the contact CI-Cro-RNAP interactions. Concerning long-range interactions, we show that while the DNA loop between the O(R) and O(L) operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters P(R) and P(RM) becomes more important at small CI concentrations. A large change in the expression pattern may arise in this regime due to anticooperative interactions between DNA-bound RNA polymerases. The applicability of the matrix method to more complex systems is discussed.

General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to OR operator of phage λ

PubMed Central

Teif, Vladimir B.

2007-01-01

The transfer matrix methodology is proposed as a systematic tool for the statistical–mechanical description of DNA–protein–drug binding involved in gene regulation. We show that a genetic system of several cis-regulatory modules is calculable using this method, considering explicitly the site-overlapping, competitive, cooperative binding of regulatory proteins, their multilayer assembly and DNA looping. In the methodological section, the matrix models are solved for the basic types of short- and long-range interactions between DNA-bound proteins, drugs and nucleosomes. We apply the matrix method to gene regulation at the OR operator of phage λ. The transfer matrix formalism allowed the description of the λ-switch at a single-nucleotide resolution, taking into account the effects of a range of inter-protein distances. Our calculations confirm previously established roles of the contact CI–Cro–RNAP interactions. Concerning long-range interactions, we show that while the DNA loop between the OR and OL operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters PR and PRM becomes more important at small CI concentrations. A large change in the expression pattern may arise in this regime due to anticooperative interactions between DNA-bound RNA polymerases. The applicability of the matrix method to more complex systems is discussed. PMID:17526526

The FLUKA code for space applications: recent developments

NASA Technical Reports Server (NTRS)

Andersen, V.; Ballarini, F.; Battistoni, G.; Campanella, M.; Carboni, M.; Cerutti, F.; Empl, A.; Fasso, A.; Ferrari, A.; Gadioli, E.;

Spectroscopic and viscometric elucidation of the interaction between a potential chloride channel blocker and calf-thymus DNA: the effect of medium ionic strength on the binding mode.

PubMed

Ganguly, Aniruddha; Ghosh, Soumen; Guchhait, Nikhil

2015-01-07

The present study demonstrates a detailed characterization of the binding interaction of a potential chloride channel blocker 9-methyl anthroate (9-MA) with calf-thymus DNA. The modulated photophysical properties of the emissive molecule within the microheterogeneous bio-assembly have been spectroscopically exploited to monitor the drug-DNA binding interaction. Experimental results based on fluorescence and absorption spectroscopy aided with DNA-melting, viscometric and circular dichroism studies unambiguously establish the binding mode between the drug and DNA to be principally intercalative. Concomitantly, a discernible dependence of the mode of binding between the concerned moieties on the ionic strength of the medium is noteworthy. A dip-and-rise characteristic of the rotational relaxation profile of the drug within the DNA environment has been argued to be originating from a substantial difference in the lifetime as well as amplitude of the free and DNA bound drug molecule. In view of the prospective biological applications of the drug, the issue of facile dissociation of the intercalated drug from the DNA helix via a simple detergent-sequestration technique has also been unveiled. The utility of the present work resides in exploring the potential applicability of the fluorescence properties of 9-MA for studying its interactions with other relevant biological or biomimicking targets.

Optical modulation techniques for analog signal processing and CMOS compatible electro-optic modulation

NASA Astrophysics Data System (ADS)

Gill, Douglas M.; Rasras, Mahmoud; Tu, Kun-Yii; Chen, Young-Kai; White, Alice E.; Patel, Sanjay S.; Carothers, Daniel; Pomerene, Andrew; Kamocsai, Robert; Beattie, James; Kopa, Anthony; Apsel, Alyssa; Beals, Mark; Mitchel, Jurgen; Liu, Jifeng; Kimerling, Lionel C.

2008-02-01

Integrating electronic and photonic functions onto a single silicon-based chip using techniques compatible with mass-production CMOS electronics will enable new design paradigms for existing system architectures and open new opportunities for electro-optic applications with the potential to dramatically change the management, cost, footprint, weight, and power consumption of today's communication systems. While broadband analog system applications represent a smaller volume market than that for digital data transmission, there are significant deployments of analog electro-optic systems for commercial and military applications. Broadband linear modulation is a critical building block in optical analog signal processing and also could have significant applications in digital communication systems. Recently, broadband electro-optic modulators on a silicon platform have been demonstrated based on the plasma dispersion effect. The use of the plasma dispersion effect within a CMOS compatible waveguide creates new challenges and opportunities for analog signal processing since the index and propagation loss change within the waveguide during modulation. We will review the current status of silicon-based electrooptic modulators and also linearization techniques for optical modulation.

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…

Apollo program soil mechanics experiment. [interaction of the lunar module with the lunar surface

NASA Technical Reports Server (NTRS)

Scott, R. F.

1975-01-01

The soil mechanics investigation was conducted to obtain information relating to the landing interaction of the lunar module (LM) with the lunar surface, and lunar soil erosion caused by the spacecraft engine exhaust. Results obtained by study of LM landing performance on each Apollo mission are summarized.

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond.

PubMed

Stajdohar, Miha; Rosengarten, Rafael D; Kokosar, Janez; Jeran, Luka; Blenkus, Domen; Shaulsky, Gad; Zupan, Blaz

2017-06-02

Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of next-generation sequencing for genomics and transcriptomics. Dictyostelium biologists now face the widespread challenges of analyzing and exploring high dimensional data sets to generate hypotheses and discovering novel insights. We present dictyExpress (2.0), a web application designed for exploratory analysis of gene expression data, as well as data from related experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq). The application features visualization modules that include time course expression profiles, clustering, gene ontology enrichment analysis, differential expression analysis and comparison of experiments. All visualizations are interactive and interconnected, such that the selection of genes in one module propagates instantly to visualizations in other modules. dictyExpress currently stores the data from over 800 Dictyostelium experiments and is embedded within a general-purpose software framework for management of next-generation sequencing data. dictyExpress allows users to explore their data in a broader context by reciprocal linking with dictyBase-a repository of Dictyostelium genomic data. In addition, we introduce a companion application called GenBoard, an intuitive graphic user interface for data management and bioinformatics analysis. dictyExpress and GenBoard enable broad adoption of next generation sequencing based inquiries by the Dictyostelium research community. Labs without the means to undertake deep sequencing projects can mine the data available to the public. The entire information flow, from raw sequence data to hypothesis testing, can be accomplished in an efficient workspace. The software framework is generalizable and represents a useful approach for any research community. To encourage more wide usage, the backend is open-source, available for extension and further development by bioinformaticians and data scientists.

LiNbO3 Cylinder Fiber

NASA Technical Reports Server (NTRS)

2004-01-01

We have successfully fabricate optical fiber with a thin layer of LiNbO3 at the boundary of the glass core and dear glass cladding. The construction of this fiber is based on our successful Semiconductor Cylinder Fibers (SCF). A schematic representation of a LiNbO3 Cylinder Fiber is shown. These fibers can be used as light modulators, sonar detectors and in other applications. The core diameter of the fiber is sufficiently small compared to the light wavelength and the indices of refraction of the core and cladding glasses are sufficiently close in value so that there is sufficient light at the core cladding boundary to interact with the LiNbO3 layer. This fiber functions best when just a single light mode propagates through the fiber. The idea for a LiNbO3 Cylinder Fiber came from Dr. Tracee Jamison of NASA. The optical properties of LiNbO3 can be changed with strain or the application of an electric field. Thus these fibers can be used as acoustic sensors as for example in a sonar. They can also be used as electric field operated light modulators. However, for this application the fibers would be made with a cross section in the form of a 'D'. The core with its surrounding LiNbO, layer would be close to the flat portion of the 'D' shaped fiber. Two metal contacts would be deposited on the flat portion of the fiber on either side of the core. A voltage applied across these contacts will result in an electric field in the core region that can be used for modulating the optical properties of the LiNbO, layer. To our knowledge this is the first ever LiNbO, Cylinder Fiber made.

LiNbO3 Cylinder Fiber

NASA Technical Reports Server (NTRS)

Kornreich, Philip

2004-01-01

We have successfully fabricate optical fiber with a thin layer of LiNbO3 at the boundary of the glass core and clear glass cladding. The construction of this fiber is based on our successful Semiconductor Cylinder Fibers (SCF). A schematic representation of a LiN bo, Cylinder Fiber. These fibers can be used as light modulators, sonar detectors and in other applications. The core diameter of the fiber is sufficiently small compared to the light wavelength and the indices of refraction of the core and cladding glasses are sufficiently close in value so that there is sufficient light at the core cladding boundary to interact with the LiNbO3 layer. This fiber functions best when just a single light mode propagates through the fiber. The idea for a LiNbO3 Cylinder Fiber came from Dr. Tracee Jamison of NASA. The optical properties of LiNbO3 can be changed with strain or the application of an electric field. Thus these fibers can be used as acoustic sensors as for example in a sonar. They can also be used as electric field operated light modulators. However, for this application the fibers would be made with a cross section in the form of a "D". The core with its surrounding LiNbO, layer would be close to the flat portion of the "D" shaped fiber. Two metal contacts would be deposited on the flat portion of the fiber on either side of the core. A voltage applied across these contacts will result in an electric field in the core region that can be used for modulating the optical properties of the LiNbO3 layer. To our knowledge this is the first ever LiNbO3 Cylinder Fiber made.

Functional modules by relating protein interaction networks and gene expression.

PubMed

Tornow, Sabine; Mewes, H W

2003-11-01

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships.

Functional modules by relating protein interaction networks and gene expression

PubMed Central

Tornow, Sabine; Mewes, H. W.

2003-01-01

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships. PMID:14576317

Land Application of Wastes: An Educational Program. Design Procedures for Land Application of Wastes - Module 6, Objectives, Script and Figures.

ERIC Educational Resources Information Center

Clarkson, W. W.; And Others

The purpose of this module is to develop a general procedure to decide the feasibility of land application as a waste management alternative, given a specific problem situation. This information provides a framework within which to apply the information presented in all other modules in the program. An outline of the general procedure followed in…

Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography

PubMed Central

Koirala, Deepak; Shelke, Sandip A; Dupont, Marcel; Ruiz, Stormy; DasGupta, Saurja; Bailey, Lucas J; Benner, Steven A; Piccirilli, Joseph A

2018-01-01

Abstract Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3–6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5′-GNGACCC-3′ consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab–RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography. PMID:29309709

Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions

PubMed Central

Basu, Mahashweta; Bhattacharyya, Nitai P.; Mohanty, Pradeep K.

2013-01-01

Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched () GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins. PMID:23741403

Ultrafast Modulation and Switching of Quantum-Well Lasers using Terahertz Fields

NASA Technical Reports Server (NTRS)

Ning, Cun-Zheng; Hughes, S.; Citrin, D.; Saini, Subhash (Technical Monitor)

1998-01-01

Modulation and switching of semiconductor lasers are important for laser-based information technology. Typically the speed of modulation and switching is limited by interband processes such as stimulated and spontaneous recombinations which occur on a nanosecond time scale. This is why the diode laser modulation has been restricted to tens of GHz. Modulation at higher speed is highly desirable as the information technology enters into the so-called tera-era. In this paper, we study the possibility of utilizing THz-field-induced plasma heating to modulate quantum-well lasers. This is a timely study since, with the advancement of THz solid-state sources and free-electron lasers, THz physics and related technology is currently coming out of its infancy. The investigation of interplaying THz and optical fields is also of intruiging fundamental interest. First, we introduce theoretical plasma heating results for the quantum-well optical amplifier in the presense of an intense half-cycle THz pulse. The heated carrier distributions are then utilized to calculate the THz-pulse-induced change in refractive index and gain profile. Since the electron-hole-plasma is heated using intraband transitions, we circumvent the usual complications due to an overall change in density, and the nonlinear recovery is governed solely by the carrier-LO-phonon interactions, typically 5 ps for a complete recovery. This procedure implies THz and sub-THz switching and recovery rates, respectively; using either gain modulation or index modulation. Plasma heating via steady-state THz fields is also studied. Finally, numerical simulation of a coupled set of equations to investigate the THz modulation based on a simplified model for quantum-well lasers is presented. Our results show that a semiconductor laser can be modulated at up to 1 THz with little distortion with a THz field amplitude at the order of a few kV/cm. Laser responses to a change in THz frequency will be shown. Constraints, practicalities, and applications will be discussed.

Test Waveform Applications for JPL STRS Operating Environment

NASA Technical Reports Server (NTRS)

Lux, James P.; Peters, Kenneth J.; Taylor, Gregory H.; Lang, Minh; Stern, Ryan A.; Duncan, Courtney B.

2013-01-01

This software demonstrates use of the JPL Space Telecommunications Radio System (STRS) Operating Environment (OE), tests APIs (application programming interfaces) presented by JPL STRS OE, and allows for basic testing of the underlying hardware platform. This software uses the JPL STRS Operating Environment ["JPL Space Tele com - munications Rad io System Operating Environment,"(NPO-4776) NASA Tech Briefs, commercial edition, Vol. 37, No. 1 (January 2013), p. 47] to interact with the JPL-SDR Software Defined Radio developed for the CoNNeCT (COmmunications, Navigation, and Networking rEconfigurable Testbed) Project as part of the SCaN Testbed installed on the International Space Station (ISS). These are the first applications that are compliant with the new NASA STRS Architecture Standard. Several example waveform applications are provided to demonstrate use of the JPL STRS OE for the JPL-SDR platform used for the CoNNeCT Project. The waveforms provide a simple digitizer and playback capability for the SBand RF slice, and a simple digitizer for the GPS slice [CoNNeCT Global Positioning System RF Module, (NPO-47764) NASA Tech Briefs, commercial edition, Vol. 36, No. 3 (March 2012), p. 36]. These waveforms may be used for hardware test, as well as for on-orbit or laboratory checkout. Additional example waveforms implement SpaceWire and timer modules, which can be used for time transfer and demonstration of communication between the two Xilinx FPGAs in the JPLSDR. The waveforms are also compatible with ground-based use of the JPL STRS OE on radio breadboards and Linux.

The Arctic Research Mapping Application (ARMAP): a Geoportal for Visualizing Project-level Information About U.S. Funded Research in the Arctic

NASA Astrophysics Data System (ADS)

Kassin, A.; Cody, R. P.; Barba, M.; Gaylord, A. G.; Manley, W. F.; Score, R.; Escarzaga, S. M.; Tweedie, C. E.

2016-12-01

The Arctic Research Mapping Application (ARMAP; http://armap.org/) is a suite of online applications and data services that support Arctic science by providing project tracking information (who's doing what, when and where in the region) for United States Government funded projects. In collaboration with 17 research agencies, project locations are displayed in a visually enhanced web mapping application. Key information about each project is presented along with links to web pages that provide additional information, including links to data where possible. The latest ARMAP iteration has i) reworked the search user interface (UI) to enable multiple filters to be applied in user-driven queries and ii) implemented ArcGIS Javascript API 4.0 to allow for deployment of 3D maps directly into a users web-browser and enhanced customization of popups. Module additions include i) a dashboard UI powered by a back-end Apache SOLR engine to visualize data in intuitive and interactive charts; and ii) a printing module that allows users to customize maps and export these to different formats (pdf, ppt, gif and jpg). New reference layers and an updated ship tracks layer have also been added. These improvements have been made to improve discoverability, enhance logistics coordination, identify geographic gaps in research/observation effort, and foster enhanced collaboration among the research community. Additionally, ARMAP can be used to demonstrate past, present, and future research effort supported by the U.S. Government.

ANABOLIC STEROIDS ALTER THE PHYSIOLOGICAL ACTIVITY OF AGGRESSION CIRCUITS IN THE LATERAL ANTERIOR HYPOTHALAMUS

PubMed Central

Morrison, Thomas R.; Sikes, Robert W.; Melloni, Richard H.

2016-01-01

Syrian hamsters exposed to anabolic/androgenic steroids (AAS) during adolescence consistently show increased aggressive behavior across studies. Although the behavioral and anatomical profiles of AAS-induced alterations have been well characterized, there is a lack of data describing physiological changes that accompany these alterations. For instance, behavioral pharmacology and neuroanatomical studies show that AAS-induced changes in the vasopressin (AVP) neural system within the latero-anterior hypothalamus (LAH) interact with the serotonin (5HT) and dopamine (DA) systems to modulate aggression. To characterize the electrophysiological profile of the AAS aggression circuit, we recorded LAH neurons in adolescent male hamsters in vivo and microiontophoretically applied agonists and antagonists of aggressive behavior. The interspike interval (ISI) of neurons from AAS-treated animals correlated positively with aggressive behaviors, and adolescent AAS exposure altered parameters of activity in regular firing neurons while also changing the proportion of neuron types (i.e., bursting, regular, irregular). AAS treated animals had more responsive neurons that were excited by AVP application, while cells from control animals showed the opposite effect and were predominantly inhibited by AVP. Both DA D2 antagonists and 5HT increased the firing frequency of AVP responsive cells from AAS animals and dual application of AVP and D2 antagonists doubled the excitatory effect of AVP or D2 antagonist administration alone. These data suggest that multiple DA circuits in the LAH modulate AAS-induced aggressive responding. More broadly, these data show that multiple neurochemical interactions at the neurophysiological level are altered by adolescent AAS exposure. PMID:26691962

[Virtual educational proposal in cardiopulmonary resuscitation for the neonate care].

PubMed

Gonçalves, Gilciane Ribeiro; Peres, Heloisa Helena Ciqueto; Rodrigues, Rita de Cássia; Tronchin, Daisy Maria Rizatto; Pereira, Irene Mari

2010-06-01

The purpose of this study was to develop an educational proposal using virtual multimedia resources, to innovate, stimulate and diversify areas of communication and interaction, facilitating nurses' autonomous and reflexive process of teaching and learning. This is an applied research, following the cyclical and interactive phases of designing, planning, developing and implementing. The educational proposal was developed on the TelEduc platform, using specific tools for content organization and communication between students and administrator. The teaching modules were on the following themes: Module 1--Fundamentals of the heart anatomy and physiology in newborns; Module 2--Risk factors for the occurrence of cardiorespiratory arrest in newborns; Module 3--Planning nursing care; Module 4--Medications used in cardiopulmonary arrests in newborns; and Module 5--Cardiorespiratory arrest care in newborns. This study may contribute to innovating teaching in nursing from a virtual educational proposal on the important issue of newborn cardiopulmonary resuscitation care.

RM-SORN: a reward-modulated self-organizing recurrent neural network.

PubMed

Aswolinskiy, Witali; Pipa, Gordon

2015-01-01

Neural plasticity plays an important role in learning and memory. Reward-modulation of plasticity offers an explanation for the ability of the brain to adapt its neural activity to achieve a rewarded goal. Here, we define a neural network model that learns through the interaction of Intrinsic Plasticity (IP) and reward-modulated Spike-Timing-Dependent Plasticity (STDP). IP enables the network to explore possible output sequences and STDP, modulated by reward, reinforces the creation of the rewarded output sequences. The model is tested on tasks for prediction, recall, non-linear computation, pattern recognition, and sequence generation. It achieves performance comparable to networks trained with supervised learning, while using simple, biologically motivated plasticity rules, and rewarding strategies. The results confirm the importance of investigating the interaction of several plasticity rules in the context of reward-modulated learning and whether reward-modulated self-organization can explain the amazing capabilities of the brain.

A theoretical model for the Gla-TSR-EGF-1 region of the anticoagulant cofactor protein S: From biostructural pathology to specie

NASA Astrophysics Data System (ADS)

Villoutreix, Bruno O.; Teleman, Olle; Dahlbäck, Björn

1997-05-01

Protein S (PS), which functions as a species-specific anticoagulant cofactor to activated protein C (APC), is a mosaic protein that interacts with the phospholipid membrane via its γ-carboxyglutamate-rich (Gla) module. This module is followed by the thrombin-sensitive region (TSR), sensitive to thrombin cleavage, four epidermal growth factor (EGF)-like modules and a last region referred to as the sex hormone binding globulin (SHBG) domain. Of these, the TSR and the first EGF-like regions have been shown to be important for the species-specific interaction with APC. Difficulties in crystallising PS have so far hindered its study at the atomic level. Here, we report theoretical models for the Gla and EGF-1 modules of human PS constructed using prothrombin and factor X experimental structures. The TSR was built interactively. Analysis of the model linked with the large body of biochemical literature on PS and related proteins leads to suggestions that (i) the TSR stabilises the calcium-loaded Gla module through hydrophobic and ionic interactions and its conformation depends on the presence of the Gla module; (ii) the TSR does not form a calcium binding site but is protected from thrombin cleavage in the calcium-loaded form owing to short secondary structure elements and close contact with the Gla module; (iii) the PS missense mutations in this region are consistent with the structural data, except in one case which needs further investigation; and (iv) the two PS `faces' involving regions of residues Arg49-Gln52-Lys97 (TSR-EGF-1) and Thr103-Pro106 (EGF-1) may be involved in species-specific interactions with APC as they are richer in nonconservative substitution when comparing human and bovine protein S. This preliminary model helps to plan future experiments and the resulting data will be used to further validate and optimise the present structure.

MINE: Module Identification in Networks

PubMed Central

2011-01-01

Background Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules are insufficient when applied to dense networks of experimentally derived interaction data. To address this problem, we have developed an agglomerative clustering method that is able to identify highly modular sets of gene products within highly interconnected molecular interaction networks. Results MINE outperforms MCODE, CFinder, NEMO, SPICi, and MCL in identifying non-exclusive, high modularity clusters when applied to the C. elegans protein-protein interaction network. The algorithm generally achieves superior geometric accuracy and modularity for annotated functional categories. In comparison with the most closely related algorithm, MCODE, the top clusters identified by MINE are consistently of higher density and MINE is less likely to designate overlapping modules as a single unit. MINE offers a high level of granularity with a small number of adjustable parameters, enabling users to fine-tune cluster results for input networks with differing topological properties. Conclusions MINE was created in response to the challenge of discovering high quality modules of gene products within highly interconnected biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters. MINE outperforms several popular clustering algorithms in identifying modules with high modularity and obtains good overall recall and precision of functional annotations in protein-protein interaction networks from both S. cerevisiae and C. elegans. PMID:21605434

AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

PubMed

Wang, Yi; Thilmony, Roger; Zhao, Yunjun; Chen, Guoping; Gu, Yong Q

2014-01-01

Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw.usda.gov/AIM Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Maximizing the Production of Biogas in an Instructional Manipulative Designed to Teach Energy Concepts to High School Students

NASA Astrophysics Data System (ADS)

McCall, Shakira Renee

In an effort to stress the benefits of the application of renewable energy to the next generation of science, technology, engineering, arts, and mathematics (STEAM) professionals, instructional modules on energy and biogas were integrated into a summer camp curriculum that challenged students to apply STEAM concepts in the design and development of chain reaction machines. Each module comprised an interactive presentations and a hands-on component where students operated a manipulative relevant to the content. During summer 2013, this camp was implemented at two high schools in Arizona and one in Trinidad and Tobago. Assessments showed that the overall modules were effective in helping students learn and retain the information presented on energy and biogas production. To improve future implementations of these modules, specifically the module on biogas production, the anaerobic digester was redesigned. In addition, a designed experiment was conducted to determine how to optimize the influent and operational environment that is available in an average high school classroom to generate maximum biogas yield. Eight plug-flow anaerobic digesters made of PVC piping and fixtures were used in a 2x3 factorial design assessing: co-digestion (20mL or 50mL) used cooking oil, temperature (25°C or 40°C), and addition of inoculum (0mL or 200mL). Biogas production was captured at two intervals over a 30-day period, and the experiments were replicated three times. Results showed that temperature at 40°C significantly increased biogas production and should be used over 25°C when using anaerobic digesters. Other factors that may potentially increase biogas production are combination of temperature at 40°C and 50mL of used cooking oil. In the future, the improvements made in the design of the anaerobic digester, and the applications of the finding from the experimental design, are expected to lead to an improved manipulative for teaching students about biogas production.

E-learning tools for education: regulatory aspects, current applications in radiology and future prospects.

PubMed

Pinto, A; Selvaggi, S; Sicignano, G; Vollono, E; Iervolino, L; Amato, F; Molinari, A; Grassi, R

2008-02-01

E-learning, an abbreviation of electronic learning, indicates the provision of education and training on the Internet or the World Wide Web. The impact of networks and the Internet on radiology is undoubtedly important, as it is for medicine as a whole. The Internet offers numerous advantages compared with other mass media: it provides access to a large amount of information previously known only to individual specialists; it is flexible, permitting the use of images or video; and it allows linking to Web sites on a specific subject, thus contributing to further expand knowledge. Our purpose is to illustrate the regulatory aspects (including Internet copyright laws), current radiological applications and future prospects of e-learning. Our experience with the installation of an e-learning platform is also presented. We performed a PubMed search on the published literature (without time limits) dealing with e-learning tools and applications in the health sector with specific reference to radiology. The search included all study types in the English language with the following key words: e-learning, education, teaching, online exam, radiology and radiologists. The Fiaso study was referred to for the regulatory aspects of e-learning. The application of e-learning to radiology requires the development of a model that involves selecting and creating e-learning platforms, creating and technologically adapting multimedia teaching modules, creating and managing a unified catalogue of teaching modules, planning training actions, defining training pathways and Continuing Education in Medicine (CME) credits, identifying levels of teaching and technological complexity of support tools, sharing an organisational and methodological model, training the trainers, operators' participation and relational devices, providing training, monitoring progress of the activities, and measuring the effectiveness of training. Since 2004, a platform--LiveLearning--has been used at our university: this is a Web-oriented application, that is, an Internet software solution that users can access through a Web browser. The pages displayed by the browser are dynamically generated through interaction with a database that collects both data required for the application to work and data related to the courses provided. There are different approaches to developing applications that use databases to store information. The selected approach is based on a modular three-level architecture divided into presentation level, intermediate level, and data level. The LiveLearning platform includes modules to manage multimedia contents and to interface with the streaming server so that the student can access the training contents directly from the platform interfaces. Furthermore, the platform offers its users different modules: Teaching Units, Documents, Forums, and Chats. By appropriately combining these modules, customised training can be devised based on specific requirements. The increasing diffusion of continuous education will reduce the costs of e-learning and make this training method, which helps keep pace with technological progress, more attractive, with significant professional gains for radiologists.

Advanced space system analysis software. Technical, user, and programmer guide

NASA Technical Reports Server (NTRS)

Farrell, C. E.; Zimbelman, H. F.

1981-01-01

The LASS computer program provides a tool for interactive preliminary and conceptual design of LSS. Eight program modules were developed, including four automated model geometry generators, an associated mass properties module, an appendage synthesizer module, an rf analysis module, and an orbital transfer analysis module. The existing rigid body controls analysis module was modified to permit analysis of effects of solar pressure on orbital performance. A description of each module, user instructions, and programmer information are included.

Application of epigenetic markers in molecular breeding of the swine.

PubMed

Zhang, Ke; Feng, Guang-de; Zhang, Bao-yun; Xiang, Wei; Chen, Long; Yang, Fang; Chu, Ming-xing; Wang, Ping-qing

2016-07-20

Livestock phenotypes are determined by the interaction of a variety of factors, including the genome, the epigenome and the environment. Epigenetics refers to gene expression changes without DNA sequence alterations. Epigenetic markers mainly include DNA methylation, histone modifications, non-coding RNAs, and imprinting genes. More and more researches show that epigenetic markers play an important role in the traits of pigs by modulating phenotype changes via gene expression. However, the role of epigenetic markers has caught little attention in swine breeding. The mechanism that influences important traits of swine has not been analyzed in detail, and it still lacks adequate scientific basis for practical applications. From the aspects of nutrition, diseases, important economic traits and trans-generational inheritance, we summarize the research, application prospects and challenges in the field of utilizing epigenetic markers in molecular breeding of pigs, thus providing a more comprehensive theoretical basis to promote more rapid research development in this field.

Thin film lithium niobate electro-optic modulator with terahertz operating bandwidth.

PubMed

Mercante, Andrew J; Shi, Shouyuan; Yao, Peng; Xie, Linli; Weikle, Robert M; Prather, Dennis W

2018-05-28

We present a thin film crystal ion sliced (CIS) LiNbO 3 phase modulator that demonstrates an unprecedented measured electro-optic (EO) response up to 500 GHz. Shallow rib waveguides are utilized for guiding a single transverse electric (TE) optical mode, and Au coplanar waveguides (CPWs) support the modulating radio frequency (RF) mode. Precise index matching between the co-propagating RF and optical modes is responsible for the device's broadband response, which is estimated to extend even beyond 500 GHz. Matching the velocities of these co-propagating RF and optical modes is realized by cladding the modulator's interaction region in a thin UV15 polymer layer, which increases the RF modal index. The fabricated modulator possesses a tightly confined optical mode, which lends itself to a strong interaction between the modulating RF field and the guided optical carrier; resulting in a measured DC half-wave voltage of 3.8 V·cm -1 . The design, fabrication, and characterization of our broadband modulator is presented in this work.

Macrogenomic engineering via modulation of the scaling of chromatin packing density.

PubMed

Almassalha, Luay M; Bauer, Greta M; Wu, Wenli; Cherkezyan, Lusik; Zhang, Di; Kendra, Alexis; Gladstein, Scott; Chandler, John E; VanDerway, David; Seagle, Brandon-Luke L; Ugolkov, Andrey; Billadeau, Daniel D; O'Halloran, Thomas V; Mazar, Andrew P; Roy, Hemant K; Szleifer, Igal; Shahabi, Shohreh; Backman, Vadim

2017-11-01

Many human diseases result from the dysregulation of the complex interactions between tens to thousands of genes. However, approaches for the transcriptional modulation of many genes simultaneously in a predictive manner are lacking. Here, through the combination of simulations, systems modelling and in vitro experiments, we provide a physical regulatory framework based on chromatin packing-density heterogeneity for modulating the genomic information space. Because transcriptional interactions are essentially chemical reactions, they depend largely on the local physical nanoenvironment. We show that the regulation of the chromatin nanoenvironment allows for the predictable modulation of global patterns in gene expression. In particular, we show that the rational modulation of chromatin density fluctuations can lead to a decrease in global transcriptional activity and intercellular transcriptional heterogeneity in cancer cells during chemotherapeutic responses to achieve near-complete cancer cell killing in vitro. Our findings represent a 'macrogenomic engineering' approach to modulating the physical structure of chromatin for whole-scale transcriptional modulation.

Modelling of Rainfall Induced Landslides in Puerto Rico

NASA Astrophysics Data System (ADS)

Lepore, C.; Arnone, E.; Sivandran, G.; Noto, L. V.; Bras, R. L.

2010-12-01

We performed an island-wide determination of static landslide susceptibility and hazard assessment as well as dynamic modeling of rainfall-induced shallow landslides in a particular hydrologic basin. Based on statistical analysis of past landslides, we determined that reliable prediction of the susceptibility to landslides is strongly dependent on the resolution of the digital elevation model (DEM) employed and the reliability of the rainfall data. A distributed hydrology model, Triangulated Irregular Network (TIN)-based Real-time Integrated Basin Simulator with VEGetation Generator for Interactive Evolution (tRIBS-VEGGIE), tRIBS-VEGGIE, has been implemented for the first time in a humid tropical environment like Puerto Rico and validated against in-situ measurements. A slope-failure module has been added to tRIBS-VEGGIE’s framework, after analyzing several failure criterions to identify the most suitable for our application; the module is used to predict the location and timing of landsliding events. The Mameyes basin, located in the Luquillo Experimental Forest in Puerto Rico, was selected for modeling based on the availability of soil, vegetation, topographical, meteorological and historic landslide data. Application of the model yields a temporal and spatial distribution of predicted rainfall-induced landslides.

Development and in vitro evaluation of potential electromodulated transdermal drug delivery systems based on carbon nanotube buckypapers.

PubMed

Schwengber, Alex; Prado, Héctor J; Bonelli, Pablo R; Cukierman, Ana L

2017-07-01

Buckypapers based on different types of carbon nanotubes with and without the addition of four model drugs, two of basic nature (clonidine hydrochloride, selegiline hydrochloride) and the others of acidic character (flurbiprofen, ketorolac tromethamine) were prepared and characterized. The influence of the conditions employed in the preparation of the buckypapers (dispersion time and solvents used in the preparation, as well as the type of carbon nanotubes used and the characteristics of the drug involved) on their conductivity was especially examined. The in vitro performance of the drug loaded buckypapers as passive and active transdermal drug release systems, the latter being modulated by means of the application of electric voltages, was studied. Passive drug loaded buckypapers presented characteristic release profiles, also depending on the drug used, which indicate differences in the drug-carbon nanotubes non-covalent interactions. Application of electrical biases of appropriate polarities enabled the modulation of the drug release profiles in any desired direction. Different mathematical models were fitted to passive and electromodulated experimental release data for the four model drugs. Among these models, the most appropriate for data description was a two-compartment pseudo-second-order one. Copyright © 2017 Elsevier B.V. All rights reserved.

Adaptive Plasticity in the Healthy Language Network: Implications for Language Recovery after Stroke

PubMed Central

2016-01-01

Across the last three decades, the application of noninvasive brain stimulation (NIBS) has substantially increased the current knowledge of the brain's potential to undergo rapid short-term reorganization on the systems level. A large number of studies applied transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS) in the healthy brain to probe the functional relevance and interaction of specific areas for different cognitive processes. NIBS is also increasingly being used to induce adaptive plasticity in motor and cognitive networks and shape cognitive functions. Recently, NIBS has been combined with electrophysiological techniques to modulate neural oscillations of specific cortical networks. In this review, we will discuss recent advances in the use of NIBS to modulate neural activity and effective connectivity in the healthy language network, with a special focus on the combination of NIBS and neuroimaging or electrophysiological approaches. Moreover, we outline how these results can be transferred to the lesioned brain to unravel the dynamics of reorganization processes in poststroke aphasia. We conclude with a critical discussion on the potential of NIBS to facilitate language recovery after stroke and propose a phase-specific model for the application of NIBS in language rehabilitation. PMID:27830094

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

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Experience with specifications applicable to certification. [of photovoltaic modules for large-scale application

NASA Technical Reports Server (NTRS)

Ross, R. G., Jr.

1982-01-01

The Jet Propulsion Laboratory has developed a number of photovoltaic test and measurement specifications to guide the development of modules toward the requirements of future large-scale applications. Experience with these specifications and the extensive module measurement and testing that has accompanied their use is examined. Conclusions are drawn relative to three aspects of product certification: performance measurement, endurance testing and safety evaluation.

Dynamic coupled metal transport-speciation model: application to assess a zinc-contaminated lake.

PubMed

Bhavsar, Satyendra P; Diamond, Miriam L; Gandhi, Nilima; Nilsen, Joel

2004-10-01

A coupled metal transport and speciation/complexation model (TRANSPEC) has been developed to estimate the speciation and fate of multiple interconverting species in surface aquatic systems. Dynamic-TRANSPEC loosely, sequentially couples the speciation/complexation and fate modules that, for the unsteady state formulation, run alternatively at every time step. The speciation module first estimates species abundance using, in this version, MINEQL+ considering time-dependent changes in water and pore-water chemistry. The fate module is based on the quantitative water air sediment interaction (QWASI) model and fugacity/aquivalence formulation, with the option of using a pseudo-steady state solution to account for past discharges. Similarly to the QWASI model for organic contaminants, TRANSPEC assumes the instantaneous equilibrium distribution of metal species among dissolved, colloidal, and particulate phases based on ambient chemistry parameters that can be collected through conventional field methods. The model is illustrated with its application to Ross Lake (Manitoba, Canada) that has elevated Zn concentrations due to discharges over 70 years from a mining operation. Using measurements from field studies, the model reproduces year-round variations in Zn water concentrations. A 10-year projection for current conditions suggests decreasing Zn remobilization and export from the lake. Decreasing Zn loadings increases sediment-to-water transport but decreases water concentrations, and vice versa. Species distribution is affected by pH such that a decrease in pH increases metal export from the lake and vice versa.

ANSL-V: ENDF/B-V based multigroup cross-section libraries for Advanced Neutron Source (ANS) reactor studies. Supplement 1

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

Wright, R.Q.; Renier, J.P.; Bucholz, J.A.

1995-08-01

The original ANSL-V cross-section libraries (ORNL-6618) were developed over a period of several years for the physics analysis of the ANS reactor, with little thought toward including the materials commonly needed for shielding applications. Materials commonly used for shielding applications include calcium barium, sulfur, phosphorous, and bismuth. These materials, as well as {sup 6}Li, {sup 7}Li, and the naturally occurring isotopes of hafnium, have been added to the ANSL-V libraries. The gamma-ray production and gamma-ray interaction cross sections were completely regenerated for the ANSL-V 99n/44g library which did not exist previously. The MALOCS module was used to collapse the 99n/44gmore » coupled library to the 39n/44g broad- group library. COMET was used to renormalize the two-dimensional (2- D) neutron matrix sums to agree with the one-dimensional (1-D) averaged values. The FRESH module was used to adjust the thermal scattering matrices on the 99n/44g and 39n/44g ANSL-V libraries. PERFUME was used to correct the original XLACS Legendre polynomial fits to produce acceptable distributions. The final ANSL-V 99n/44g and 39n/44g cross-section libraries were both checked by running RADE. The AIM module was used to convert the master cross-section libraries from binary coded decimal to binary format (or vice versa).« less

Client/server approach to image capturing

NASA Astrophysics Data System (ADS)

Tuijn, Chris; Stokes, Earle

1998-01-01

The diversity of the digital image capturing devices on the market today is quite astonishing and ranges from low-cost CCD scanners to digital cameras (for both action and stand-still scenes), mid-end CCD scanners for desktop publishing and pre- press applications and high-end CCD flatbed scanners and drum- scanners with photo multiplier technology. Each device and market segment has its own specific needs which explains the diversity of the associated scanner applications. What all those applications have in common is the need to communicate with a particular device to import the digital images; after the import, additional image processing might be needed as well as color management operations. Although the specific requirements for all of these applications might differ considerably, a number of image capturing and color management facilities as well as other services are needed which can be shared. In this paper, we propose a client/server architecture for scanning and image editing applications which can be used as a common component for all these applications. One of the principal components of the scan server is the input capturing module. The specification of the input jobs is based on a generic input device model. Through this model we make abstraction of the specific scanner parameters and define the scan job definitions by a number of absolute parameters. As a result, scan job definitions will be less dependent on a particular scanner and have a more universal meaning. In this context, we also elaborate on the interaction of the generic parameters and the color characterization (i.e., the ICC profile). Other topics that are covered are the scheduling and parallel processing capabilities of the server, the image processing facilities, the interaction with the ICC engine, the communication facilities (both in-memory and over the network) and the different client architectures (stand-alone applications, TWAIN servers, plug-ins, OLE or Apple-event driven applications). This paper is structured as follows. In the introduction, we further motive the need for a scan server-based architecture. In the second section, we give a brief architectural overview of the scan server and the other components it is connected to. The third chapter exposes the generic model for input devices as well as the image processing model; the fourth chapter reveals the different shapes the scanning applications (or modules) can have. In the last section, we briefly summarize the presented material and point out trends for future development.

MCT IR detection modules with 15 µm pitch for high-reliability applications

NASA Astrophysics Data System (ADS)

Breiter, R.; Ihle, T.; Wendler, J.; Lutz, H.; Rutzinger, S.; Schallenberg, T.; Hofmann, K.; Ziegler, J.

2010-04-01

Additional to the development of 3rd Gen IR modules like dual-band and dual-color devices AIM is focused on IR FPAs with reduced pitch. These FPAs allow manufacturing of compact low cost IR modules with minimum power consumption for state-of-the-art high performance IR systems. AIM has realized full TV format MCT 640x512 mid-wave and long-wave IR detection modules with a 15 μm pitch to meet the requirements of critical military applications like thermal weapon sights or thermal imagers in UAV applications. In typical configurations like a F/4.6 cold shield for the 640x512 MWIR module an NETD < 25 mK @ 5 ms integration time is achieved, while the LWIR modules achieve an NETD < 38 mK @ F/2 and 180 μs integration time. For the LWIR modules FPAs with a cut-off of 9 and 10 μm have been realized. The modules are available either with different integral rotary cooler configurations for portable applications which require minimum cooling power or a new split linear cooler providing long lifetime with a MTTF > 20,000 h as required e.g. for warning sensors in 24/7 operation. The modules are available with an optional image processing electronics providing non-uniformity correction and further image processing for a complete IR imaging solution. A double field of view FLIR for an upgrade of the German Army UAV LUNA has been developed by AIM using the MCT 640x512 MWIR 15μm pitch engine. The latest results and performance of those modules and their applications are presented.

Fault Tolerance Middleware for a Multi-Core System

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Springer, Paul L.; Zima, Hans P.; James, Mark; Wagner, David A.

2012-01-01

Fault Tolerance Middleware (FTM) provides a framework to run on a dedicated core of a multi-core system and handles detection of single-event upsets (SEUs), and the responses to those SEUs, occurring in an application running on multiple cores of the processor. This software was written expressly for a multi-core system and can support different kinds of fault strategies, such as introspection, algorithm-based fault tolerance (ABFT), and triple modular redundancy (TMR). It focuses on providing fault tolerance for the application code, and represents the first step in a plan to eventually include fault tolerance in message passing and the FTM itself. In the multi-core system, the FTM resides on a single, dedicated core, separate from the cores used by the application. This is done in order to isolate the FTM from application faults and to allow it to swap out any application core for a substitute. The structure of the FTM consists of an interface to a fault tolerant strategy module, a responder module, a fault manager module, an error factory, and an error mapper that determines the severity of the error. In the present reference implementation, the only fault tolerant strategy implemented is introspection. The introspection code waits for an application node to send an error notification to it. It then uses the error factory to create an error object, and at this time, a severity level is assigned to the error. The introspection code uses its built-in knowledge base to generate a recommended response to the error. Responses might include ignoring the error, logging it, rolling back the application to a previously saved checkpoint, swapping in a new node to replace a bad one, or restarting the application. The original error and recommended response are passed to the top-level fault manager module, which invokes the response. The responder module also notifies the introspection module of the generated response. This provides additional information to the introspection module that it can use in generating its next response. For example, if the responder triggers an application rollback and errors are still occurring, the introspection module may decide to recommend an application restart.

Supporting High School Student Accomplishment of Biology Content Using Interactive Computer-Based Curricular Case Studies

NASA Astrophysics Data System (ADS)

Oliver, Joseph Steve; Hodges, Georgia W.; Moore, James N.; Cohen, Allan; Jang, Yoonsun; Brown, Scott A.; Kwon, Kyung A.; Jeong, Sophia; Raven, Sara P.; Jurkiewicz, Melissa; Robertson, Tom P.

2017-11-01

Research into the efficacy of modules featuring dynamic visualizations, case studies, and interactive learning environments is reported here. This quasi-experimental 2-year study examined the implementation of three interactive computer-based instructional modules within a curricular unit covering cellular biology concepts in an introductory high school biology course. The modules featured dynamic visualizations and focused on three processes that underlie much of cellular biology: diffusion, osmosis, and filtration. Pre-tests and post-tests were used to assess knowledge growth across the unit. A mixture Rasch model analysis of the post-test data revealed two groups of students. In both years of the study, a large proportion of the students were classified as low-achieving based on their pre-test scores. The use of the modules in the Cell Unit in year 2 was associated with a much larger proportion of the students having transitioned to the high-achieving group than in year 1. In year 2, the same teachers taught the same concepts as year 1 but incorporated the interactive computer-based modules into the cell biology unit of the curriculum. In year 2, 67% of students initially classified as low-achieving were classified as high-achieving at the end of the unit. Examination of responses to assessments embedded within the modules as well as post-test items linked transition to the high-achieving group with correct responses to items that both referenced the visualization and the contextualization of that visualization within the module. This study points to the importance of dynamic visualization within contextualized case studies as a means to support student knowledge acquisition in biology.

Interaction between total body gamma-irradiation and choline deficiency triggers immediate modulation of choline and choline-containing moieties.

PubMed

Batra, Vipen; Kislay, Binita; Devasagayam, Thomas Paul Asir

2011-12-01

The objective of this study was to examine the effect of 60Co-gamma (γ) radiation on acute phase modulation, if any, of choline and choline-containing moieties in choline-deficient subjects. Corresponding results could provide information that might be useful in the management of adverse effects of γ-radiation. Male Swiss mice maintained on a choline-sufficient diet (CSD) and choline-free diet (CFD) based on AIN-93M formula, were subjected to whole body γ-irradiation (2-6 Gy). Liver, serum and brain samples from each group were then tested for: (i) Alterations in choline and choline-containing moieties such as phosphatidylcholine (PC) and sphingomyeline (SM); and (ii) modulation of choline profile modulating enzymes such as phospholipase D (PLD) and total sphingomyelinase (t-SMase). Liver and brain samples were also subjected to histo-pathological examinations. No significant changes were observed in folate, choline, choline-containing moieties and choline-modulating enzymes in choline-sufficient mice. In contrast, interaction between cytotoxic effects of γ-radiation and choline deficiency modulated choline and choline-containing moieties. Feeding CFD reduced hepatic concentrations of choline, PC and SM whereas PLD and t-SMase activities were significantly raised. The decrease in liver choline and choline-containing moieties was accompanied by an increase in blood choline concentration. Despite choline deficiency, the level of choline and acetylcholine synthesizing enzyme choline acetyltransfease (ChAT) significantly increased in the brain. We propose that choline deprivation and γ-radiation interact to modulate choline reserves of hepatic tissue, which might release choline to blood. Our studies also clearly showed that interaction between choline deficiency and γ-radiation might substantially enhance liver adipogenesis.

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

Allosteric Modulation of Chemoattractant Receptors

PubMed Central

Allegretti, Marcello; Cesta, Maria Candida; Locati, Massimo

2016-01-01

Chemoattractants control selective leukocyte homing via interactions with a dedicated family of related G protein-coupled receptor (GPCR). Emerging evidence indicates that the signaling activity of these receptors, as for other GPCR, is influenced by allosteric modulators, which interact with the receptor in a binding site distinct from the binding site of the agonist and modulate the receptor signaling activity in response to the orthosteric ligand. Allosteric modulators have a number of potential advantages over orthosteric agonists/antagonists as therapeutic agents and offer unprecedented opportunities to identify extremely selective drug leads. Here, we resume evidence of allosterism in the context of chemoattractant receptors, discussing in particular its functional impact on functional selectivity and probe/concentration dependence of orthosteric ligands activities. PMID:27199992

Simultaneous exposure of nematophagous fungi, entomopathogenic nematodes and entomopathogenic fungi can modulate belowground insect pest control.

PubMed

Bueno-Pallero, Francisco Ángel; Blanco-Pérez, Rubén; Dionísio, Lídia; Campos-Herrera, Raquel

2018-05-01

Entomopathogenic nematodes (EPNs) and fungi (EPF) are well known biological control agents (BCAs) against insect pests. Similarly, the nematophagous fungi (NF) are considered good BCA candidates for controlling plant parasitic nematodes. Because NF can employ EPNs as food and interact with EPF, we speculate that the simultaneous application of EPNs and EPF might result in higher insect mortality, whereas the triple species combination with NF will reduce the EPN and EPF activity by predation or inhibition. Here we evaluated single, dual (EPN + EPF, EPF + NF, EPN + NF) and triple (EPN + EPF + NF) combinations of one EPN, Steinernema feltiae (Rhabditida: Steinernematidae), one EPF, Beauveria bassiana (Hypocreales: Clavicipitaceae), and two NF, Arthrobotrys musiformis (Orbiliales: Orbiliaceae) and Purpureocillium lilacinum (Hypocreales: Ophiocordycipitaceae) under laboratory conditions. First, we showed that EPF reduced the growth rate of NF and vice versa when combined in both rich and limiting media, suggesting a negative interaction when combining both fungi. Three different fungal applications (contact with mycelia-conidia, immersion in conidial suspension, and injection of conidial suspension) were tested in single, dual and triple species combinations, evaluating Galleria mellonella (Lepidoptera: Pyralidae) larval mortality and time to kill. When mycelia was presented, the EPF appeared to be the dominant in combined treatments, whereas in immersion exposure was the EPN. In both types of exposure, NF alone did not produce any effect on larvae. However, when A. musiformis was injected, it produced larval mortalities >70% in the same time span as EPN. Overall, additive effects dominated the dual and triple combinations, with the exception of injection method, where synergisms occurred for both NF species combined with EPN + EPF. This study illustrates how differences in species combination and timing of fungal arrival can modulate the action of BCAs when augmented in the soil. Further studies are required to fine-tune these multitrophic interactions to provide successful, sustainable and resilient pest management in agroecosystems. Copyright © 2018 Elsevier Inc. All rights reserved.

Vitamin D Status and the Host Resistance to Infections: What It Is Currently (Not) Understood.

PubMed

Lang, Pierre Olivier; Aspinall, Richard

2017-05-01

Vitamin D is increasingly thought to play a role in regulating immunity. This comprehensive review updates the current understanding regarding ways in which we believe that vitamin D regulates responsiveness of the immune system and how serum status modulates the host defense against pathogens. The literature was searched by using PubMed and Scopus with the following key words: vitamin D, immunity, innate and adaptive immunity, infectious disease, and vaccine response. Vitamin D deficiency remains a major public health concern worldwide. The overall body of evidence confirms that vitamin D plays an important role in modulating the immune response to infections. Epidemiologic studies suggest a clear association between vitamin D deficiency and susceptibility to various pathogens. However, translation of vitamin D use into the clinic as a means of controlling infections is fraught with methodologic and epidemiologic challenges. The recent discovery of alternative activation pathways, different active forms of vitamin D, and possible interaction with non-vitamin D receptors provide further complications to an already complex interaction between vitamin D and the immune system. Moreover, it has become apparent that the individual responsiveness to supplementation is more dynamic than presumed from the static assessment of 25-hydroxy vitamin D status. Furthermore, the epigenetic response at the level of the individual to environmental changes and lifestyle or health conditions provides greater variation than those resulting from vitamin D receptor polymorphisms. To understand the future of vitamin D with respect to clinical applications in the prevention and better control of infectious diseases, it is necessary to determine all aspects of vitamin D metabolism, as well as the mechanisms by which active forms interact with the immune system globally. For the most part, we are unable to identify tissue-specific applications of supplementation except for those subjects at high risk of osteomalacia and osteoporosis. Copyright © 2017 Elsevier HS Journals, Inc. All rights reserved.

IAEA programs in empowering the nuclear medicine profession through online educational resources.

PubMed

Pascual, Thomas Nb; Dondi, Maurizio; Paez, Diana; Kashyap, Ravi; Nunez-Miller, Rodolfo

2013-05-01

The International Atomic Energy Agency's (IAEA) programme in human health aims to enhance the capabilities in Member States to address needs related to the prevention, diagnosis, and treatment of diseases through the application of nuclear techniques. It has the specific mission of fostering the application of nuclear medicine techniques as part of the clinical management of certain types of diseases. Attuned to the continuous evolution of this specialty as well as to the advancement and diversity of methods in delivering capacity building efforts in this digital age, the section of nuclear medicine of the IAEA has enhanced its program by incorporating online educational resources for nuclear medicine professionals into its repertoire of projects to further its commitment in addressing the needs of its Member States in the field of nuclear medicine. Through online educational resources such as the Human Health Campus website, e-learning modules, and scheduled interactive webinars, a validation of the commitment by the IAEA in addressing the needs of its Member States in the field of nuclear medicine is strengthened while utilizing the advanced internet and communications technology which is progressively becoming available worldwide. The Human Health Campus (www.humanhealth.iaea.org) is the online educational resources initiative of the Division of Human Health of the IAEA geared toward enhancing professional knowledge of health professionals in radiation medicine (nuclear medicine and diagnostic imaging, radiation oncology, and medical radiation physics), and nutrition. E-learning modules provide an interactive learning environment to its users while providing immediate feedback for each task accomplished. Webinars, unlike webcasts, offer the opportunity of enhanced interaction with the learners facilitated through slide shows where the presenter guides and engages the audience using video and live streaming. This paper explores the IAEA's available online educational resources programs geared toward the enhancement of the nuclear medicine profession as delivered by the section of nuclear medicine of the IAEA. Copyright © 2013 Elsevier Inc. All rights reserved.

An Interactive Computer Lab of the Galvanic Cell for Students in Biochemistry

ERIC Educational Resources Information Center

Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

2018-01-01

We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as ?rG, ?rH, and ?rS that are calculated but not directly…

An Essay on Interactive Investigations of the Zeeman Effect in the Interstellar Medium

ERIC Educational Resources Information Center

Woolsey, Lauren

2015-01-01

The paper presents an interactive module created through the Wolfram Demonstrations Project that visualizes the Zeeman effect for the small magnetic field strengths present in the interstellar medium. The paper provides an overview of spectral lines and a few examples of strong and weak Zeeman splitting before discussing the module in depth.…