A Laboratory-Based Nonlinear Dynamics Course for Science and Engineering Students.

ERIC Educational Resources Information Center

Sungar, N.; Sharpe, J. P.; Moelter, M. J.; Fleishon, N.; Morrison, K.; McDill, J.; Schoonover, R.

2001-01-01

Describes the implementation of a new laboratory-based, interdisciplinary undergraduate course on linear dynamical systems. Focuses on geometrical methods and data visualization techniques. (Contains 20 references.) (Author/YDS)

Visualization of Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Gerald-Yamasaki, Michael; Hultquist, Jeff; Bryson, Steve; Kenwright, David; Lane, David; Walatka, Pamela; Clucas, Jean; Watson, Velvin; Lasinski, T. A. (Technical Monitor)

1995-01-01

Scientific visualization serves the dual purpose of exploration and exposition of the results of numerical simulations of fluid flow. Along with the basic visualization process which transforms source data into images, there are four additional components to a complete visualization system: Source Data Processing, User Interface and Control, Presentation, and Information Management. The requirements imposed by the desired mode of operation (i.e. real-time, interactive, or batch) and the source data have their effect on each of these visualization system components. The special requirements imposed by the wide variety and size of the source data provided by the numerical simulation of fluid flow presents an enormous challenge to the visualization system designer. We describe the visualization system components including specific visualization techniques and how the mode of operation and source data requirements effect the construction of computational fluid dynamics visualization systems.

Dynamic visual noise reduces confidence in short-term memory for visual information.

PubMed

Kemps, Eva; Andrade, Jackie

2012-05-01

Previous research has shown effects of the visual interference technique, dynamic visual noise (DVN), on visual imagery, but not on visual short-term memory, unless retention of precise visual detail is required. This study tested the prediction that DVN does also affect retention of gross visual information, specifically by reducing confidence. Participants performed a matrix pattern memory task with three retention interval interference conditions (DVN, static visual noise and no interference control) that varied from trial to trial. At recall, participants indicated whether or not they were sure of their responses. As in previous research, DVN did not impair recall accuracy or latency on the task, but it did reduce recall confidence relative to static visual noise and no interference. We conclude that DVN does distort visual representations in short-term memory, but standard coarse-grained recall measures are insensitive to these distortions.

Single-molecule imaging of cytoplasmic dynein in vivo.

PubMed

Ananthanarayanan, Vaishnavi; Tolić, Iva M

2015-01-01

While early fluorescence microscopy experiments employing fluorescent probes afforded snapshots of the cell, the power of live-cell microscopy is required to understand complex dynamics in biological processes. The first successful cloning of green fluorescent protein in the 1990s paved the way for development of approaches that we now utilize for visualization in a living cell. In this chapter, we discuss a technique to observe fluorescently tagged single molecules in fission yeast. With a few simple modifications to the established total internal reflection fluorescence microscopy, cytoplasmic dynein molecules in the cytoplasm and on the microtubules can be visualized and their intracellular dynamics can be studied. We illustrate a technique to study motor behavior, which is not apparent in conventional ensemble studies of motors. In general, this technique can be employed to study single-molecule dynamics of fluorescently tagged proteins in the cell interior. Copyright © 2015 Elsevier Inc. All rights reserved.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

StreamSqueeze: a dynamic stream visualization for monitoring of event data

NASA Astrophysics Data System (ADS)

Mansmann, Florian; Krstajic, Milos; Fischer, Fabian; Bertini, Enrico

2012-01-01

While in clear-cut situations automated analytical solution for data streams are already in place, only few visual approaches have been proposed in the literature for exploratory analysis tasks on dynamic information. However, due to the competitive or security-related advantages that real-time information gives in domains such as finance, business or networking, we are convinced that there is a need for exploratory visualization tools for data streams. Under the conditions that new events have higher relevance and that smooth transitions enable traceability of items, we propose a novel dynamic stream visualization called StreamSqueeze. In this technique the degree of interest of recent items is expressed through an increase in size and thus recent events can be shown with more details. The technique has two main benefits: First, the layout algorithm arranges items in several lists of various sizes and optimizes the positions within each list so that the transition of an item from one list to the other triggers least visual changes. Second, the animation scheme ensures that for 50 percent of the time an item has a static screen position where reading is most effective and then continuously shrinks and moves to the its next static position in the subsequent list. To demonstrate the capability of our technique, we apply it to large and high-frequency news and syslog streams and show how it maintains optimal stability of the layout under the conditions given above.

Interactive visualization of vegetation dynamics

USGS Publications Warehouse

Reed, B.C.; Swets, D.; Bard, L.; Brown, J.; Rowland, James

2001-01-01

Satellite imagery provides a mechanism for observing seasonal dynamics of the landscape that have implications for near real-time monitoring of agriculture, forest, and range resources. This study illustrates a technique for visualizing timely information on key events during the growing season (e.g., onset, peak, duration, and end of growing season), as well as the status of the current growing season with respect to the recent historical average. Using time-series analysis of normalized difference vegetation index (NDVI) data from the advanced very high resolution radiometer (AVHRR) satellite sensor, seasonal dynamics can be derived. We have developed a set of Java-based visualization and analysis tools to make comparisons between the seasonal dynamics of the current year with those from the past twelve years. In addition, the visualization tools allow the user to query underlying databases such as land cover or administrative boundaries to analyze the seasonal dynamics of areas of their own interest. The Java-based tools (data exploration and visualization analysis or DEVA) use a Web-based client-server model for processing the data. The resulting visualization and analysis, available via the Internet, is of value to those responsible for land management decisions, resource allocation, and at-risk population targeting.

Multivariate spatiotemporal visualizations for mobile devices in Flyover Country

NASA Astrophysics Data System (ADS)

Loeffler, S.; Thorn, R.; Myrbo, A.; Roth, R.; Goring, S. J.; Williams, J.

2017-12-01

Visualizing and interacting with complex multivariate and spatiotemporal datasets on mobile devices is challenging due to their smaller screens, reduced processing power, and limited data connectivity. Pollen data require visualizing pollen assemblages spatially, temporally, and across multiple taxa to understand plant community dynamics through time. Drawing from cartography, information visualization, and paleoecology, we have created new mobile-first visualization techniques that represent multiple taxa across many sites and enable user interaction. Using pollen datasets from the Neotoma Paleoecology Database as a case study, the visualization techniques allow ecological patterns and trends to be quickly understood on a mobile device compared to traditional pollen diagrams and maps. This flexible visualization system can be used for datasets beyond pollen, with the only requirements being point-based localities and multiple variables changing through time or depth.

Development of High Speed Imaging and Analysis Techniques Compressible Dynamics Stall

NASA Technical Reports Server (NTRS)

Chandrasekhara, M. S.; Carr, L. W.; Wilder, M. C.; Davis, Sanford S. (Technical Monitor)

1996-01-01

Dynamic stall has limited the flight envelope of helicopters for many years. The problem has been studied in the laboratory as well as in flight, but most research, even in the laboratory, has been restricted to surface measurement techniques such as pressure transducers or skin friction gauges, except at low speed. From this research, it became apparent that flow visualization tests performed at Mach numbers representing actual flight conditions were needed if the complex physics associated with dynamic stall was to be properly understood. However, visualization of the flow field during compressible conditions required carefully aligned and meticulously reconstructed holographic interferometry. As part of a long-range effort focused on exposing of the physics of compressible dynamic stall, a research wind tunnel was developed at NASA Ames Research Center which permits visual access to the full flow field surrounding an oscillating airfoil during compressible dynamic stall. Initially, a stroboscopic schlieren technique was used for visualization of the stall process, but the primary research tool has been point diffraction interferometry(PDI), a technique carefully optimized for use in th is project. A review of the process of development of PDI will be presented in the full paper. One of the most valuable aspects of PDI is the fact that interferograms are produced in real time on a continuous basis. The use of a rapidly-pulsed laser makes this practical; a discussion of this approach will be presented in the full paper. This rapid pulsing(up to 40,000 pulses/sec) produces interferograms of the rapidly developing dynamic stall field in sufficient resolution(both in space and time) that the fluid physics of the compressible dynamic stall flowfield can be quantitatively determined, including the gradients of pressure in space and time. This permits analysis of the influence of the effect of pitch rate, Mach number, Reynolds number, amplitude of oscillation, and other parameters on the dynamic stall process. When interferograms can be captured in real time, the potential for real-time mapping of a developing unsteady flow such as dynamic stall becomes a possibility. This has been achieved in the present case through the use of a high-speed drum camera combined with electronic circuitry which has resulted in a series of interferograms obtained during a single cycle of dynamic stall; images obtained at the rate of 20 KHz will be presented as a part of the formal presentation. Interferometry has been available for a long time; however, most of its use has been limited to visualization. The present research has focused on use of interferograms for quantitative mapping of the flow over oscillating airfoils. Instantaneous pressure distributions can now be obtained semi-automatically, making practical the analysis of the thousands of interferograms that are produced in this research. A review of the techniques that have been developed as part of this research effort will be presented in the final paper.

Dynamic Visualization of Co-expression in Systems Genetics Data

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

New, Joshua Ryan; Huang, Jian; Chesler, Elissa J

2008-01-01

Biologists hope to address grand scientific challenges by exploring the abundance of data made available through modern microarray technology and other high-throughput techniques. The impact of this data, however, is limited unless researchers can effectively assimilate such complex information and integrate it into their daily research; interactive visualization tools are called for to support the effort. Specifically, typical studies of gene co-expression require novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These tools should allow biologists to develop an intuitive understanding of the structure of biologicalmore » networks and discover genes which reside in critical positions in networks and pathways. By using a graph as a universal data representation of correlation in gene expression data, our novel visualization tool employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene co-expression data integrates techniques such as: graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by querying an optimized b-tree, dynamic level-of-detail graph abstraction, and template-based fuzzy classification using neural networks. We demonstrate our system using a real-world workflow from a large-scale, systems genetics study of mammalian gene co-expression.« less

CollaborationViz: Interactive Visual Exploration of Biomedical Research Collaboration Networks

PubMed Central

Bian, Jiang; Xie, Mengjun; Hudson, Teresa J.; Eswaran, Hari; Brochhausen, Mathias; Hanna, Josh; Hogan, William R.

2014-01-01

Social network analysis (SNA) helps us understand patterns of interaction between social entities. A number of SNA studies have shed light on the characteristics of research collaboration networks (RCNs). Especially, in the Clinical Translational Science Award (CTSA) community, SNA provides us a set of effective tools to quantitatively assess research collaborations and the impact of CTSA. However, descriptive network statistics are difficult for non-experts to understand. In this article, we present our experiences of building meaningful network visualizations to facilitate a series of visual analysis tasks. The basis of our design is multidimensional, visual aggregation of network dynamics. The resulting visualizations can help uncover hidden structures in the networks, elicit new observations of the network dynamics, compare different investigators and investigator groups, determine critical factors to the network evolution, and help direct further analyses. We applied our visualization techniques to explore the biomedical RCNs at the University of Arkansas for Medical Sciences – a CTSA institution. And, we created CollaborationViz, an open-source visual analytical tool to help network researchers and administration apprehend the network dynamics of research collaborations through interactive visualization. PMID:25405477

Innovative application of virtual display technique in virtual museum

NASA Astrophysics Data System (ADS)

Zhang, Jiankang

2017-09-01

Virtual museum refers to display and simulate the functions of real museum on the Internet in the form of 3 Dimensions virtual reality by applying interactive programs. Based on Virtual Reality Modeling Language, virtual museum building and its effective interaction with the offline museum lie in making full use of 3 Dimensions panorama technique, virtual reality technique and augmented reality technique, and innovatively taking advantages of dynamic environment modeling technique, real-time 3 Dimensions graphics generating technique, system integration technique and other key virtual reality techniques to make sure the overall design of virtual museum.3 Dimensions panorama technique, also known as panoramic photography or virtual reality, is a technique based on static images of the reality. Virtual reality technique is a kind of computer simulation system which can create and experience the interactive 3 Dimensions dynamic visual world. Augmented reality, also known as mixed reality, is a technique which simulates and mixes the information (visual, sound, taste, touch, etc.) that is difficult for human to experience in reality. These technologies make virtual museum come true. It will not only bring better experience and convenience to the public, but also be conducive to improve the influence and cultural functions of the real museum.

3D Feature Extraction for Unstructured Grids

NASA Technical Reports Server (NTRS)

Silver, Deborah

1996-01-01

Visualization techniques provide tools that help scientists identify observed phenomena in scientific simulation. To be useful, these tools must allow the user to extract regions, classify and visualize them, abstract them for simplified representations, and track their evolution. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This article explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and those from Finite Element Analysis.

Rotational dynamics of cargos at pauses during axonal transport.

PubMed

Gu, Yan; Sun, Wei; Wang, Gufeng; Jeftinija, Ksenija; Jeftinija, Srdija; Fang, Ning

2012-01-01

Direct visualization of axonal transport in live neurons is essential for our understanding of the neuronal functions and the working mechanisms of microtubule-based motor proteins. Here we use the high-speed single particle orientation and rotational tracking technique to directly visualize the rotational dynamics of cargos in both active directional transport and pausing stages of axonal transport, with a temporal resolution of 2 ms. Both long and short pauses are imaged, and the correlations between the pause duration, the rotational behaviour of the cargo at the pause, and the moving direction after the pause are established. Furthermore, the rotational dynamics leading to switching tracks are visualized in detail. These first-time observations of cargo's rotational dynamics provide new insights on how kinesin and dynein motors take the cargo through the alternating stages of active directional transport and pause.

Segmentation of Unstructured Datasets

NASA Technical Reports Server (NTRS)

Bhat, Smitha

1996-01-01

Datasets generated by computer simulations and experiments in Computational Fluid Dynamics tend to be extremely large and complex. It is difficult to visualize these datasets using standard techniques like Volume Rendering and Ray Casting. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This thesis explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and from Finite Element Analysis.

Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

PubMed

Rajendiran, Nivedita; Durrant, Jacob D

2018-05-05

Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Netgram: Visualizing Communities in Evolving Networks

PubMed Central

Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

2015-01-01

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems. PMID:26356538

Dynamic lens and monovision 3D displays to improve viewer comfort.

PubMed

Johnson, Paul V; Parnell, Jared Aq; Kim, Joohwan; Saunter, Christopher D; Love, Gordon D; Banks, Martin S

2016-05-30

Stereoscopic 3D (S3D) displays provide an additional sense of depth compared to non-stereoscopic displays by sending slightly different images to the two eyes. But conventional S3D displays do not reproduce all natural depth cues. In particular, focus cues are incorrect causing mismatches between accommodation and vergence: The eyes must accommodate to the display screen to create sharp retinal images even when binocular disparity drives the eyes to converge to other distances. This mismatch causes visual discomfort and reduces visual performance. We propose and assess two new techniques that are designed to reduce the vergence-accommodation conflict and thereby decrease discomfort and increase visual performance. These techniques are much simpler to implement than previous conflict-reducing techniques. The first proposed technique uses variable-focus lenses between the display and the viewer's eyes. The power of the lenses is yoked to the expected vergence distance thereby reducing the mismatch between vergence and accommodation. The second proposed technique uses a fixed lens in front of one eye and relies on the binocularly fused percept being determined by one eye and then the other, depending on simulated distance. We conducted performance tests and discomfort assessments with both techniques and compared the results to those of a conventional S3D display. The first proposed technique, but not the second, yielded clear improvements in performance and reductions in discomfort. This dynamic-lens technique therefore offers an easily implemented technique for reducing the vergence-accommodation conflict and thereby improving viewer experience.

Visualization of stratospheric ozone depletion and the polar vortex

NASA Technical Reports Server (NTRS)

Treinish, Lloyd A.

1995-01-01

Direct analysis of spacecraft observations of stratospheric ozone yields information about the morphology of annual austral depletion. Visual correlation of ozone with other atmospheric data illustrates the diurnal dynamics of the polar vortex and contributions from the upper troposphere, including the formation and breakup of the depletion region each spring. These data require care in their presentation to minimize the introduction of visualization artifacts that are erroneously interpreted as data features. Non geographically registered data of differing mesh structures can be visually correlated via cartographic warping of base geometries without interpolation. Because this approach is independent of the realization technique, it provides a framework for experimenting with many visualization strategies. This methodology preserves the fidelity of the original data sets in a coordinate system suitable for three-dimensional, dynamic examination of atmospheric phenomena.

Optimization of Visual Information Presentation for Visual Prosthesis.

PubMed

Guo, Fei; Yang, Yuan; Gao, Yong

2018-01-01

Visual prosthesis applying electrical stimulation to restore visual function for the blind has promising prospects. However, due to the low resolution, limited visual field, and the low dynamic range of the visual perception, huge loss of information occurred when presenting daily scenes. The ability of object recognition in real-life scenarios is severely restricted for prosthetic users. To overcome the limitations, optimizing the visual information in the simulated prosthetic vision has been the focus of research. This paper proposes two image processing strategies based on a salient object detection technique. The two processing strategies enable the prosthetic implants to focus on the object of interest and suppress the background clutter. Psychophysical experiments show that techniques such as foreground zooming with background clutter removal and foreground edge detection with background reduction have positive impacts on the task of object recognition in simulated prosthetic vision. By using edge detection and zooming technique, the two processing strategies significantly improve the recognition accuracy of objects. We can conclude that the visual prosthesis using our proposed strategy can assist the blind to improve their ability to recognize objects. The results will provide effective solutions for the further development of visual prosthesis.

Optimization of Visual Information Presentation for Visual Prosthesis

PubMed Central

Gao, Yong

2018-01-01

Visual prosthesis applying electrical stimulation to restore visual function for the blind has promising prospects. However, due to the low resolution, limited visual field, and the low dynamic range of the visual perception, huge loss of information occurred when presenting daily scenes. The ability of object recognition in real-life scenarios is severely restricted for prosthetic users. To overcome the limitations, optimizing the visual information in the simulated prosthetic vision has been the focus of research. This paper proposes two image processing strategies based on a salient object detection technique. The two processing strategies enable the prosthetic implants to focus on the object of interest and suppress the background clutter. Psychophysical experiments show that techniques such as foreground zooming with background clutter removal and foreground edge detection with background reduction have positive impacts on the task of object recognition in simulated prosthetic vision. By using edge detection and zooming technique, the two processing strategies significantly improve the recognition accuracy of objects. We can conclude that the visual prosthesis using our proposed strategy can assist the blind to improve their ability to recognize objects. The results will provide effective solutions for the further development of visual prosthesis. PMID:29731769

Computer animation challenges for computational fluid dynamics

NASA Astrophysics Data System (ADS)

Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine

2012-07-01

Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.

Development of bimolecular fluorescence complementation using rsEGFP2 for detection and super-resolution imaging of protein-protein interactions in live cells

PubMed Central

Wang, Sheng; Ding, Miao; Chen, Xuanze; Chang, Lei; Sun, Yujie

2017-01-01

Direct visualization of protein-protein interactions (PPIs) at high spatial and temporal resolution in live cells is crucial for understanding the intricate and dynamic behaviors of signaling protein complexes. Recently, bimolecular fluorescence complementation (BiFC) assays have been combined with super-resolution imaging techniques including PALM and SOFI to visualize PPIs at the nanometer spatial resolution. RESOLFT nanoscopy has been proven as a powerful live-cell super-resolution imaging technique. With regard to the detection and visualization of PPIs in live cells with high temporal and spatial resolution, here we developed a BiFC assay using split rsEGFP2, a highly photostable and reversibly photoswitchable fluorescent protein previously developed for RESOLFT nanoscopy. Combined with parallelized RESOLFT microscopy, we demonstrated the high spatiotemporal resolving capability of a rsEGFP2-based BiFC assay by detecting and visualizing specifically the heterodimerization interactions between Bcl-xL and Bak as well as the dynamics of the complex on mitochondria membrane in live cells. PMID:28663931

Information visualization of the minority game

NASA Astrophysics Data System (ADS)

Jiang, W.; Herbert, R. D.; Webber, R.

2008-02-01

Many dynamical systems produce large quantities of data. How can the system be understood from the output data? Often people are simply overwhelmed by the data. Traditional tools such as tables and plots are often not adequate, and new techniques are needed to help people to analyze the system. In this paper, we propose the use of two spacefilling visualization tools to examine the output from a complex agent-based financial model. We measure the effectiveness and performance of these tools through usability experiments. Based on the experimental results, we develop two new visualization techniques that combine the advantages and discard the disadvantages of the information visualization tools. The model we use is an evolutionary version of the Minority Game which simulates a financial market.

Oscillatory flow in the cochlea visualized by a magnetic resonance imaging technique.

PubMed

Denk, W; Keolian, R M; Ogawa, S; Jelinski, L W

1993-02-15

We report a magnetic resonance imaging technique that directly measures motion of cochlear fluids. It uses oscillating magnetic field gradients phase-locked to an external stimulus to selectively visualize and quantify oscillatory fluid motion. It is not invasive, and it does not require optical line-of-sight access to the inner ear. It permits the detection of displacements far smaller than the spatial resolution. The method is demonstrated on a phantom and on living rats. It is projected to have applications for auditory research, for the visualization of vocal tract dynamics during speech and singing, and for determination of the spatial distribution of mechanical relaxations in materials.

[Homeostasis and Disorder of Musculoskeletal System.Cellular dynamics in musculoskeletal system visualized by intravital imaging techniques.

PubMed

Kikuta, Junichi; Ishii, Masaru

Bone is continually remodeled by bone-resorbing osteoclasts and bone-forming osteoblasts. Although it has long been believed that bone homeostasis is tightly regulated by communication between osteoclasts and osteoblasts, the fundamental process and dynamics have remained elusive. We originally established an advanced imaging system to visualize living bone tissues using intravital two-photon microscopy. By means of this system, we revealed the in vivo behavior of bone-resorbing osteoclasts and bone-forming osteoblasts in bone tissues. This approach facilitates investigation of cellular dynamics in the pathogenesis of musculoskeletal disorders, and would thus be useful for evaluating the efficacy of novel therapeutic agents.

Correlated and uncorrelated heart rate fluctuations during relaxing visualization

NASA Astrophysics Data System (ADS)

Papasimakis, N.; Pallikari, F.

2010-05-01

The heart rate variability (HRV) of healthy subjects practicing relaxing visualization is studied by use of three multiscale analysis techniques: the detrended fluctuation analysis (DFA), the entropy in natural time (ENT) and the average wavelet (AWC) coefficient. The scaling exponent of normal interbeat interval increments exhibits characteristics of the presence of long-range correlations. During relaxing visualization the HRV dynamics change in the sense that two new features emerge independent of each other: a respiration-induced periodicity that often dominates the HRV at short scales (<40 interbeat intervals) and the decrease of the scaling exponent at longer scales (40-512 interbeat intervals). In certain cases, the scaling exponent during relaxing visualization indicates the breakdown of long-range correlations. These characteristics have been previously seen in the HRV dynamics during non-REM sleep.

Visualizing statistical significance of disease clusters using cartograms.

PubMed

Kronenfeld, Barry J; Wong, David W S

2017-05-15

Health officials and epidemiological researchers often use maps of disease rates to identify potential disease clusters. Because these maps exaggerate the prominence of low-density districts and hide potential clusters in urban (high-density) areas, many researchers have used density-equalizing maps (cartograms) as a basis for epidemiological mapping. However, we do not have existing guidelines for visual assessment of statistical uncertainty. To address this shortcoming, we develop techniques for visual determination of statistical significance of clusters spanning one or more districts on a cartogram. We developed the techniques within a geovisual analytics framework that does not rely on automated significance testing, and can therefore facilitate visual analysis to detect clusters that automated techniques might miss. On a cartogram of the at-risk population, the statistical significance of a disease cluster is determinate from the rate, area and shape of the cluster under standard hypothesis testing scenarios. We develop formulae to determine, for a given rate, the area required for statistical significance of a priori and a posteriori designated regions under certain test assumptions. Uniquely, our approach enables dynamic inference of aggregate regions formed by combining individual districts. The method is implemented in interactive tools that provide choropleth mapping, automated legend construction and dynamic search tools to facilitate cluster detection and assessment of the validity of tested assumptions. A case study of leukemia incidence analysis in California demonstrates the ability to visually distinguish between statistically significant and insignificant regions. The proposed geovisual analytics approach enables intuitive visual assessment of statistical significance of arbitrarily defined regions on a cartogram. Our research prompts a broader discussion of the role of geovisual exploratory analyses in disease mapping and the appropriate framework for visually assessing the statistical significance of spatial clusters.

Visuo-Vestibular Interactions

NASA Technical Reports Server (NTRS)

1997-01-01

Session TA3 includes short reports covering: (1) Vestibulo-Oculomotor Interaction in Long-Term Microgravity; (2) Effects of Weightlessness on the Spatial Orientation of Visually Induced Eye Movements; (3) Adaptive Modification of the Three-Dimensional Vestibulo-Ocular Reflex during Prolonged Microgravity; (4) The Dynamic Change of Brain Potential Related to Selective Attention to Visual Signals from Left and Right Visual Fields; (5) Locomotor Errors Caused by Vestibular Suppression; and (6) A Novel, Image-Based Technique for Three-Dimensional Eye Measurement.

Flow visualization of CFD using graphics workstations

NASA Technical Reports Server (NTRS)

Lasinski, Thomas; Buning, Pieter; Choi, Diana; Rogers, Stuart; Bancroft, Gordon

1987-01-01

High performance graphics workstations are used to visualize the fluid flow dynamics obtained from supercomputer solutions of computational fluid dynamic programs. The visualizations can be done independently on the workstation or while the workstation is connected to the supercomputer in a distributed computing mode. In the distributed mode, the supercomputer interactively performs the computationally intensive graphics rendering tasks while the workstation performs the viewing tasks. A major advantage of the workstations is that the viewers can interactively change their viewing position while watching the dynamics of the flow fields. An overview of the computer hardware and software required to create these displays is presented. For complex scenes the workstation cannot create the displays fast enough for good motion analysis. For these cases, the animation sequences are recorded on video tape or 16 mm film a frame at a time and played back at the desired speed. The additional software and hardware required to create these video tapes or 16 mm movies are also described. Photographs illustrating current visualization techniques are discussed. Examples of the use of the workstations for flow visualization through animation are available on video tape.

Real-time application of advanced three-dimensional graphic techniques for research aircraft simulation

NASA Technical Reports Server (NTRS)

Davis, Steven B.

1990-01-01

Visual aids are valuable assets to engineers for design, demonstration, and evaluation. Discussed here are a variety of advanced three-dimensional graphic techniques used to enhance the displays of test aircraft dynamics. The new software's capabilities are examined and possible future uses are considered.

Active microrheology and simultaneous visualization of sheared phospholipid monolayers

PubMed Central

Choi, S.Q.; Steltenkamp, S.; Zasadzinski, J.A.; Squires, T.M.

2011-01-01

Two-dimensional films of surface-active agents—from phospholipids and proteins to nanoparticles and colloids—stabilize fluid interfaces, which are essential to the science, technology and engineering of everyday life. The 2D nature of interfaces present unique challenges and opportunities: coupling between the 2D films and the bulk fluids complicates the measurement of surface dynamic properties, but allows the interfacial microstructure to be directly visualized during deformation. Here we present a novel technique that combines active microrheology with fluorescence microscopy to visualize fluid interfaces as they deform under applied stress, allowing structure and rheology to be correlated on the micron-scale in monolayer films. We show that even simple, single-component lipid monolayers can exhibit viscoelasticity, history dependence, a yield stress and hours-long time scales for elastic recoil and aging. Simultaneous visualization of the monolayer under stress shows that the rich dynamical response results from the cooperative dynamics and deformation of liquid-crystalline domains and their boundaries. PMID:21587229

A new technique of deploying dynamic y stent using flexible bronchoscope, video laryngoscope, and laryngeal mask airway.

PubMed

Obeidat, Shadi; Badin, Shadi; Khawaja, Imran

2010-04-01

Dynamic Y stents are used in tracheobronchial obstruction, tracheal stenosis, and tracheomalacia. Placement may be difficult and is usually accomplished using a rigid grasping forceps (under fluoroscopic guidance) or a rigid bronchoscope. We report using a new stent placement technique on an elderly patient with a central tracheobronchial tumor. It included using a flexible bronchoscope, video laryngoscope, and laryngeal mask airway. The new technique we used has the advantages of continuous direct endoscopic visualization during stent advancement and manipulation, and securing the airways with a laryngeal mask airway at the same time. This technique eliminates the need for intraoperative fluoroscopy.

Airway mechanics and methods used to visualize smooth muscle dynamics in vitro.

PubMed

Cooper, P R; McParland, B E; Mitchell, H W; Noble, P B; Politi, A Z; Ressmeyer, A R; West, A R

2009-10-01

Contraction of airway smooth muscle (ASM) is regulated by the physiological, structural and mechanical environment in the lung. We review two in vitro techniques, lung slices and airway segment preparations, that enable in situ ASM contraction and airway narrowing to be visualized. Lung slices and airway segment approaches bridge a gap between cell culture and isolated ASM, and whole animal studies. Imaging techniques enable key upstream events involved in airway narrowing, such as ASM cell signalling and structural and mechanical events impinging on ASM, to be investigated.

Resolving the neural dynamics of visual and auditory scene processing in the human brain: a methodological approach

PubMed Central

Teng, Santani

2017-01-01

In natural environments, visual and auditory stimulation elicit responses across a large set of brain regions in a fraction of a second, yielding representations of the multimodal scene and its properties. The rapid and complex neural dynamics underlying visual and auditory information processing pose major challenges to human cognitive neuroscience. Brain signals measured non-invasively are inherently noisy, the format of neural representations is unknown, and transformations between representations are complex and often nonlinear. Further, no single non-invasive brain measurement technique provides a spatio-temporally integrated view. In this opinion piece, we argue that progress can be made by a concerted effort based on three pillars of recent methodological development: (i) sensitive analysis techniques such as decoding and cross-classification, (ii) complex computational modelling using models such as deep neural networks, and (iii) integration across imaging methods (magnetoencephalography/electroencephalography, functional magnetic resonance imaging) and models, e.g. using representational similarity analysis. We showcase two recent efforts that have been undertaken in this spirit and provide novel results about visual and auditory scene analysis. Finally, we discuss the limits of this perspective and sketch a concrete roadmap for future research. This article is part of the themed issue ‘Auditory and visual scene analysis’. PMID:28044019

Resolving the neural dynamics of visual and auditory scene processing in the human brain: a methodological approach.

PubMed

Cichy, Radoslaw Martin; Teng, Santani

2017-02-19

In natural environments, visual and auditory stimulation elicit responses across a large set of brain regions in a fraction of a second, yielding representations of the multimodal scene and its properties. The rapid and complex neural dynamics underlying visual and auditory information processing pose major challenges to human cognitive neuroscience. Brain signals measured non-invasively are inherently noisy, the format of neural representations is unknown, and transformations between representations are complex and often nonlinear. Further, no single non-invasive brain measurement technique provides a spatio-temporally integrated view. In this opinion piece, we argue that progress can be made by a concerted effort based on three pillars of recent methodological development: (i) sensitive analysis techniques such as decoding and cross-classification, (ii) complex computational modelling using models such as deep neural networks, and (iii) integration across imaging methods (magnetoencephalography/electroencephalography, functional magnetic resonance imaging) and models, e.g. using representational similarity analysis. We showcase two recent efforts that have been undertaken in this spirit and provide novel results about visual and auditory scene analysis. Finally, we discuss the limits of this perspective and sketch a concrete roadmap for future research.This article is part of the themed issue 'Auditory and visual scene analysis'. © 2017 The Authors.

3D Visualization of Global Ocean Circulation

NASA Astrophysics Data System (ADS)

Nelson, V. G.; Sharma, R.; Zhang, E.; Schmittner, A.; Jenny, B.

2015-12-01

Advanced 3D visualization techniques are seldom used to explore the dynamic behavior of ocean circulation. Streamlines are an effective method for visualization of flow, and they can be designed to clearly show the dynamic behavior of a fluidic system. We employ vector field editing and extraction software to examine the topology of velocity vector fields generated by a 3D global circulation model coupled to a one-layer atmosphere model simulating preindustrial and last glacial maximum (LGM) conditions. This results in a streamline-based visualization along multiple density isosurfaces on which we visualize points of vertical exchange and the distribution of properties such as temperature and biogeochemical tracers. Previous work involving this model examined the change in the energetics driving overturning circulation and mixing between simulations of LGM and preindustrial conditions. This visualization elucidates the relationship between locations of vertical exchange and mixing, as well as demonstrates the effects of circulation and mixing on the distribution of tracers such as carbon isotopes.

Vector Flow Visualization of Urinary Flow Dynamics in a Bladder Outlet Obstruction Model.

PubMed

Ishii, Takuro; Yiu, Billy Y S; Yu, Alfred C H

2017-11-01

Voiding dysfunction that results from bladder outlet (BO) obstruction is known to alter significantly the dynamics of urine passage through the urinary tract. To non-invasively image this phenomenon on a time-resolved basis, we pursued the first application of a recently developed flow visualization technique called vector projectile imaging (VPI) that can track the spatiotemporal dynamics of flow vector fields at a frame rate of 10,000 fps (based on plane wave excitation and least-squares Doppler vector estimation principles). For this investigation, we designed a new anthropomorphic urethral tract phantom to reconstruct urinary flow dynamics under controlled conditions (300 mm H 2 O inlet pressure and atmospheric outlet pressure). Both a normal model and a diseased model with BO obstruction were developed for experimentation. VPI cine loops were derived from these urinary flow phantoms. Results show that VPI is capable of depicting differences in the flow dynamics of normal and diseased urinary tracts. In the case with BO obstruction, VPI depicted the presence of BO flow jet and vortices in the prostatic urethra. The corresponding spatial-maximum flow velocity magnitude was estimated to be 2.43 m/s, and it is significantly faster than that for the normal model (1.52 m/s) and is in line with values derived from computational fluid dynamics simulations. Overall, this investigation demonstrates the feasibility of using vector flow visualization techniques to non-invasively examine internal flow characteristics related to voiding dysfunction in the urethral tract. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Live-cell CRISPR imaging in plants reveals dynamic telomere movements.

PubMed

Dreissig, Steven; Schiml, Simon; Schindele, Patrick; Weiss, Oda; Rutten, Twan; Schubert, Veit; Gladilin, Evgeny; Mette, Michael F; Puchta, Holger; Houben, Andreas

2017-08-01

Elucidating the spatiotemporal organization of the genome inside the nucleus is imperative to our understanding of the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies, which reveal genomic information, and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9). By fusing eGFP/mRuby2 to catalytically inactive versions of Streptococcus pyogenes and Staphylococcus aureus Cas9, we show robust visualization of telomere repeats in live leaf cells of Nicotiana benthamiana. By tracking the dynamics of telomeres visualized by CRISPR-dCas9, we reveal dynamic telomere movements of up to 2 μm over 30 min during interphase. Furthermore, we show that CRISPR-dCas9 can be combined with fluorescence-labelled proteins to visualize DNA-protein interactions in vivo. By simultaneously using two dCas9 orthologues, we pave the way for the imaging of multiple genomic loci in live plants cells. CRISPR imaging bears the potential to significantly improve our understanding of the dynamics of chromosomes in live plant cells. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

High-Speed Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Ando, Toshio; Uchihashi, Takayuki; Kodera, Noriyuki

2012-08-01

The technology of high-speed atomic force microscopy (HS-AFM) has reached maturity. HS-AFM enables us to directly visualize the structure and dynamics of biological molecules in physiological solutions at subsecond to sub-100 ms temporal resolution. By this microscopy, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. High-resolution molecular movies reveal the dynamic behavior of molecules in action in great detail. Inferences no longer have to be made from static snapshots of molecular structures and from the dynamic behavior of optical markers attached to biomolecules. In this review, we first describe theoretical considerations for the highest possible imaging rate, then summarize techniques involved in HS-AFM and highlight recent imaging studies. Finally, we briefly discuss future challenges to explore.

Changing Libraries: Facilitating Self-Reflection and Action Research on Organizational Change in Academic Libraries

ERIC Educational Resources Information Center

Whitworth, Andrew; Torras I Calvo, Maria Carme; Moss, Bodil; Amlesom Kifle, Nazareth; Blåsternes, Terje

2014-01-01

Visualization and mapping techniques can build a dynamic picture of information practices, including action research, within libraries, raising awareness of how the information landscape at each library may both support and retard research into the library's information practices. These techniques have implications for researchers as they generate…

Interactive Visualization of Large-Scale Hydrological Data using Emerging Technologies in Web Systems and Parallel Programming

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2013-12-01

As geoscientists are confronted with increasingly massive datasets from environmental observations to simulations, one of the biggest challenges is having the right tools to gain scientific insight from the data and communicate the understanding to stakeholders. Recent developments in web technologies make it easy to manage, visualize and share large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to interact with data, and modify the parameters to create custom views of the data to gain insight from simulations and environmental observations. This requires developing new data models and intelligent knowledge discovery techniques to explore and extract information from complex computational simulations or large data repositories. Scientific visualization will be an increasingly important component to build comprehensive environmental information platforms. This presentation provides an overview of the trends and challenges in the field of scientific visualization, and demonstrates information visualization and communication tools developed within the light of these challenges.

Understanding neurodynamical systems via Fuzzy Symbolic Dynamics.

PubMed

Dobosz, Krzysztof; Duch, Włodzisław

2010-05-01

Neurodynamical systems are characterized by a large number of signal streams, measuring activity of individual neurons, local field potentials, aggregated electrical (EEG) or magnetic potentials (MEG), oxygen use (fMRI) or activity of simulated neurons. Various basis set decomposition techniques are used to analyze such signals, trying to discover components that carry meaningful information, but these techniques tell us little about the global activity of the whole system. A novel technique called Fuzzy Symbolic Dynamics (FSD) is introduced to help in understanding of the multidimensional dynamical system's behavior. It is based on a fuzzy partitioning of the signal space that defines a non-linear mapping of the system's trajectory to the low-dimensional space of membership function activations. This allows for visualization of the trajectory showing various aspects of observed signals that may be difficult to discover looking at individual components, or to notice otherwise. FSD mapping can be applied to raw signals, transformed signals (for example, ICA components), or to signals defined in the time-frequency domain. To illustrate the method two FSD visualizations are presented: a model system with artificial radial oscillatory sources, and the output layer (50 neurons) of Respiratory Rhythm Generator (RRG) composed of 300 spiking neurons. 2009 Elsevier Ltd. All rights reserved.

A graph algebra for scalable visual analytics.

PubMed

Shaverdian, Anna A; Zhou, Hao; Michailidis, George; Jagadish, Hosagrahar V

2012-01-01

Visual analytics (VA), which combines analytical techniques with advanced visualization features, is fast becoming a standard tool for extracting information from graph data. Researchers have developed many tools for this purpose, suggesting a need for formal methods to guide these tools' creation. Increased data demands on computing requires redesigning VA tools to consider performance and reliability in the context of analysis of exascale datasets. Furthermore, visual analysts need a way to document their analyses for reuse and results justification. A VA graph framework encapsulated in a graph algebra helps address these needs. Its atomic operators include selection and aggregation. The framework employs a visual operator and supports dynamic attributes of data to enable scalable visual exploration of data.

Visualization of spatial-temporal data based on 3D virtual scene

NASA Astrophysics Data System (ADS)

Wang, Xianghong; Liu, Jiping; Wang, Yong; Bi, Junfang

2009-10-01

The main purpose of this paper is to realize the expression of the three-dimensional dynamic visualization of spatialtemporal data based on three-dimensional virtual scene, using three-dimensional visualization technology, and combining with GIS so that the people's abilities of cognizing time and space are enhanced and improved by designing dynamic symbol and interactive expression. Using particle systems, three-dimensional simulation, virtual reality and other visual means, we can simulate the situations produced by changing the spatial location and property information of geographical entities over time, then explore and analyze its movement and transformation rules by changing the interactive manner, and also replay history and forecast of future. In this paper, the main research object is the vehicle track and the typhoon path and spatial-temporal data, through three-dimensional dynamic simulation of its track, and realize its timely monitoring its trends and historical track replaying; according to visualization techniques of spatialtemporal data in Three-dimensional virtual scene, providing us with excellent spatial-temporal information cognitive instrument not only can add clarity to show spatial-temporal information of the changes and developments in the situation, but also be used for future development and changes in the prediction and deduction.

Spatial Paradigm for Information Retrieval and Exploration

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

The SPIRE system consists of software for visual analysis of primarily text based information sources. This technology enables the content analysis of text documents without reading all the documents. It employs several algorithms for text and word proximity analysis. It identifies the key themes within the text documents. From this analysis, it projects the results onto a visual spatial proximity display (Galaxies or Themescape) where items (documents and/or themes) visually close to each other are known to have content which is close to each other. Innovative interaction techniques then allow for dynamic visual analysis of large text based information spaces.

SPIRE1.03. Spatial Paradigm for Information Retrieval and Exploration

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

Adams, K.J.; Bohn, S.; Crow, V.

The SPIRE system consists of software for visual analysis of primarily text based information sources. This technology enables the content analysis of text documents without reading all the documents. It employs several algorithms for text and word proximity analysis. It identifies the key themes within the text documents. From this analysis, it projects the results onto a visual spatial proximity display (Galaxies or Themescape) where items (documents and/or themes) visually close to each other are known to have content which is close to each other. Innovative interaction techniques then allow for dynamic visual analysis of large text based information spaces.

ESTEEM: A Novel Framework for Qualitatively Evaluating and Visualizing Spatiotemporal Embeddings in Social Media

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

Arendt, Dustin L.; Volkova, Svitlana

Analyzing and visualizing large amounts of social media communications and contrasting short-term conversation changes over time and geo-locations is extremely important for commercial and government applications. Earlier approaches for large-scale text stream summarization used dynamic topic models and trending words. Instead, we rely on text embeddings – low-dimensional word representations in a continuous vector space where similar words are embedded nearby each other. This paper presents ESTEEM,1 a novel tool for visualizing and evaluating spatiotemporal embeddings learned from streaming social media texts. Our tool allows users to monitor and analyze query words and their closest neighbors with an interactive interface.more » We used state-of- the-art techniques to learn embeddings and developed a visualization to represent dynamically changing relations between words in social media over time and other dimensions. This is the first interactive visualization of streaming text representations learned from social media texts that also allows users to contrast differences across multiple dimensions of the data.« less

Software-based stacking techniques to enhance depth of field and dynamic range in digital photomicrography.

PubMed

Piper, Jörg

2010-01-01

Several software solutions are powerful tools to enhance the depth of field and improve focus in digital photomicrography. By these means, the focal depth can be fundamentally optimized so that three-dimensional structures within specimens can be documented with superior quality. Thus, images can be created in light microscopy which will be comparable with scanning electron micrographs. The remaining sharpness will no longer be dependent on the specimen's vertical dimension or its range in regional thickness. Moreover, any potential lack of definition associated with loss of planarity and unsteadiness in the visual accommodation can be mitigated or eliminated so that the contour sharpness and resolution can be strongly enhanced.Through the use of complementary software, ultrahigh ranges in brightness and contrast (the so-called high-dynamic range) can be corrected so that the final images will also be free from locally over- or underexposed zones. Furthermore, fine detail in low natural contrast can be visualized in much higher clarity. Fundamental enhancements of the global visual information will result from both techniques.

Studies of human dynamic space orientation using techniques of control theory

NASA Technical Reports Server (NTRS)

Young, L. R.

1974-01-01

Studies of human orientation and manual control in high order systems are summarized. Data cover techniques for measuring and altering orientation perception, role of non-visual motion sensors, particularly the vestibular and tactile sensors, use of motion cues in closed loop control of simple stable and unstable systems, and advanced computer controlled display systems.

Distal airways in humans: dynamic hyperpolarized 3He MR imaging--feasibility

NASA Technical Reports Server (NTRS)

Tooker, Angela C.; Hong, Kwan Soo; McKinstry, Erin L.; Costello, Philip; Jolesz, Ferenc A.; Albert, Mitchell S.

2003-01-01

Dynamic hyperpolarized helium 3 (3He) magnetic resonance (MR) imaging of the human airways is achieved by using a fast gradient-echo pulse sequence during inhalation. The resulting dynamic images show differential contrast enhancement of both distal airways and the lung periphery, unlike static hyperpolarized 3He MR images on which only the lung periphery is seen. With this technique, up to seventh-generation airway branching can be visualized. Copyright RSNA, 2003.

Static and dynamic views of visual cortical organization.

PubMed

Casagrande, Vivien A; Xu, Xiangmin; Sáry, Gyula

2002-01-01

Without the aid of modern techniques Cajal speculated that cells in the visual cortex were connected in circuits. From Cajal's time until fairly recently, the flow of information within the cells and circuits of visual cortex has been described as progressing from input to output, from sensation to action. In this chapter we argue that a paradigm shift in our concept of the visual cortical neuron is under way. The most important change in our view concerns the neuron's functional role. Visual cortical neurons do not have static functional signatures but instead function dynamically depending on the ongoing activity of the networks to which they belong. These networks are not merely top-down or bottom-up unidirectional transmission lines, but rather represent machinery that uses recurrent information and is dynamic and highly adaptable. With the advancement of technology for analyzing the conversations of multiple neurons at many levels in the visual system and higher resolution imaging, we predict that the paradigm shift will progress to the point where neurons are no longer viewed as independent processing units but as members of subsets of networks where their role is mapped in space-time coordinates in relationship to the other neuronal members. This view moves us far from Cajal's original views of the neuron. Nevertheless, we believe that understanding the basic morphology and wiring of networks will continue to contribute to our overall understanding of the visual cortex.

Synchronization trigger control system for flow visualization

NASA Technical Reports Server (NTRS)

Chun, K. S.

1987-01-01

The use of cinematography or holographic interferometry for dynamic flow visualization in an internal combustion engine requires a control device that globally synchronizes camera and light source timing at a predefined shaft encoder angle. The device is capable of 0.35 deg resolution for rotational speeds of up to 73 240 rpm. This was achieved by implementing the shaft encoder signal addressed look-up table (LUT) and appropriate latches. The developed digital signal processing technique achieves 25 nsec of high speed triggering angle detection by using direct parallel bit comparison of the shaft encoder digital code with a simulated angle reference code, instead of using angle value comparison which involves more complicated computation steps. In order to establish synchronization to an AC reference signal whose magnitude is variant with the rotating speed, a dynamic peak followup synchronization technique has been devised. This method scrutinizes the reference signal and provides the right timing within 40 nsec. Two application examples are described.

Direct visualization of hemolymph flow in the heart of a grasshopper (Schistocerca americana)

PubMed Central

Lee, Wah-Keat; Socha, John J

2009-01-01

Background Hemolymph flow patterns in opaque insects have never been directly visualized due to the lack of an appropriate imaging technique. The required spatial and temporal resolutions, together with the lack of contrast between the hemolymph and the surrounding soft tissue, are major challenges. Previously, indirect techniques have been used to infer insect heart motion and hemolymph flow, but such methods fail to reveal fine-scale kinematics of heartbeat and details of intra-heart flow patterns. Results With the use of microbubbles as high contrast tracer particles, we directly visualized hemolymph flow in a grasshopper (Schistocerca americana) using synchrotron x-ray phase-contrast imaging. In-vivo intra-heart flow patterns and the relationship between respiratory (tracheae and air sacs) and circulatory (heart) systems were directly observed for the first time. Conclusion Synchrotron x-ray phase contrast imaging is the only generally applicable technique that has the necessary spatial, temporal resolutions and sensitivity to directly visualize heart dynamics and flow patterns inside opaque animals. This technique has the potential to illuminate many long-standing questions regarding small animal circulation, encompassing topics such as retrograde heart flow in some insects and the development of flow in embryonic vertebrates. PMID:19272159

Real-Time Visualization of Network Behaviors for Situational Awareness

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

Best, Daniel M.; Bohn, Shawn J.; Love, Douglas V.

Plentiful, complex, and dynamic data make understanding the state of an enterprise network difficult. Although visualization can help analysts understand baseline behaviors in network traffic and identify off-normal events, visual analysis systems often do not scale well to operational data volumes (in the hundreds of millions to billions of transactions per day) nor to analysis of emergent trends in real-time data. We present a system that combines multiple, complementary visualization techniques coupled with in-stream analytics, behavioral modeling of network actors, and a high-throughput processing platform called MeDICi. This system provides situational understanding of real-time network activity to help analysts takemore » proactive response steps. We have developed these techniques using requirements gathered from the government users for which the tools are being developed. By linking multiple visualization tools to a streaming analytic pipeline, and designing each tool to support a particular kind of analysis (from high-level awareness to detailed investigation), analysts can understand the behavior of a network across multiple levels of abstraction.« less

Using the technique of computed tomography for nondestructive analysis of pharmaceutical dosage forms

NASA Astrophysics Data System (ADS)

de Oliveira, José Martins, Jr.; Mangini, F. Salvador; Carvalho Vila, Marta Maria Duarte; ViníciusChaud, Marco

2013-05-01

This work presents an alternative and non-conventional technique for evaluatingof physic-chemical properties of pharmaceutical dosage forms, i.e. we used computed tomography (CT) technique as a nondestructive technique to visualize internal structures of pharmaceuticals dosage forms and to conduct static and dynamical studies. The studies were conducted involving static and dynamic situations through the use of tomographic images, generated by the scanner at University of Sorocaba - Uniso. We have shown that through the use of tomographic images it is possible to conduct studies of porosity, densities, analysis of morphological parameters and performing studies of dissolution. Our results are in agreement with the literature, showing that CT is a powerful tool for use in the pharmaceutical sciences.

Visualization of spiral and scroll waves in simulated and experimental cardiac tissue

NASA Astrophysics Data System (ADS)

Cherry, E. M.; Fenton, F. H.

2008-12-01

The heart is a nonlinear biological system that can exhibit complex electrical dynamics, complete with period-doubling bifurcations and spiral and scroll waves that can lead to fibrillatory states that compromise the heart's ability to contract and pump blood efficiently. Despite the importance of understanding the range of cardiac dynamics, studying how spiral and scroll waves can initiate, evolve, and be terminated is challenging because of the complicated electrophysiology and anatomy of the heart. Nevertheless, over the last two decades advances in experimental techniques have improved access to experimental data and have made it possible to visualize the electrical state of the heart in more detail than ever before. During the same time, progress in mathematical modeling and computational techniques has facilitated using simulations as a tool for investigating cardiac dynamics. In this paper, we present data from experimental and simulated cardiac tissue and discuss visualization techniques that facilitate understanding of the behavior of electrical spiral and scroll waves in the context of the heart. The paper contains many interactive media, including movies and interactive two- and three-dimensional Java appletsDisclaimer: IOP Publishing was not involved in the programming of this software and does not accept any responsibility for it. You download and run the software at your own risk. If you experience any problems with the software, please contact the author directly. To the fullest extent permitted by law, IOP Publishing Ltd accepts no responsibility for any loss, damage and/or other adverse effect on your computer system caused by your downloading and running this software. IOP Publishing Ltd accepts no responsibility for consequential loss..

Hierarchical tone mapping for high dynamic range image visualization

NASA Astrophysics Data System (ADS)

Qiu, Guoping; Duan, Jiang

2005-07-01

In this paper, we present a computationally efficient, practically easy to use tone mapping techniques for the visualization of high dynamic range (HDR) images in low dynamic range (LDR) reproduction devices. The new method, termed hierarchical nonlinear linear (HNL) tone-mapping operator maps the pixels in two hierarchical steps. The first step allocates appropriate numbers of LDR display levels to different HDR intensity intervals according to the pixel densities of the intervals. The second step linearly maps the HDR intensity intervals to theirs allocated LDR display levels. In the developed HNL scheme, the assignment of LDR display levels to HDR intensity intervals is controlled by a very simple and flexible formula with a single adjustable parameter. We also show that our new operators can be used for the effective enhancement of ordinary images.

Flow Visualization in Evaporating Liquid Drops and Measurement of Dynamic Contact Angles and Spreading Rate

NASA Technical Reports Server (NTRS)

Zhang, Neng-Li; Chao, David F.

2001-01-01

A new hybrid optical system, consisting of reflection-refracted shadowgraphy and top-view photography, is used to visualize flow phenomena and simultaneously measure the spreading and instant dynamic contact angle in a volatile-liquid drop on a nontransparent substrate. Thermocapillary convection in the drop, induced by evaporation, and the drop real-time profile data are synchronously recorded by video recording systems. Experimental results obtained from this unique technique clearly reveal that thermocapillary convection strongly affects the spreading process and the characteristics of dynamic contact angle of the drop. Comprehensive information of a sessile drop, including the local contact angle along the periphery, the instability of the three-phase contact line, and the deformation of the drop shape is obtained and analyzed.

Particle dynamics during nanoparticle synthesis by laser ablation in a background gas

NASA Astrophysics Data System (ADS)

Nakata, Yoshiki; Muramoto, Junichi; Okada, Tatsuo; Maeda, Mitsuo

2002-02-01

Particle dynamics during Si nanoparticle synthesis in a laser-ablation plume in different background gases were investigated by laser-spectroscopic imaging techniques. Two-dimensional laser induced fluorescence and ultraviolet Rayleigh scattering techniques were used to visualize the spatial distribution of the Si atoms and nanoparticles grown, respectively. We have developed a visualization technique called re-decomposition laser-induced fluorescence to observe small nanoparticles (hereafter called clusters) which are difficult to observe by the conventional imaging techniques. In this article, the whole process of nanoparticle synthesis in different background gases of He, Ne, Ar, N2 and O2 was investigated by these techniques. In He, Ne, Ar and N2 background gases at 10 Torr, the clustering of the Si atoms started 200, 250, 300 and 800 μs after ablation, respectively. The growth rate of the clusters in He background gas was much larger than that in the other gases. The spatial distributions of the Si nanoparticles were mushroom like in He, N2 and O2, and column like in Ne and Ar. It is thought that the difference in distribution was caused by differences in the flow characteristics of the background gases, which would imply that the viscosity of the background gas is one of the main governing parameters.

Network visualization of conformational sampling during molecular dynamics simulation.

PubMed

Ahlstrom, Logan S; Baker, Joseph Lee; Ehrlich, Kent; Campbell, Zachary T; Patel, Sunita; Vorontsov, Ivan I; Tama, Florence; Miyashita, Osamu

2013-11-01

Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions. Copyright © 2013 Elsevier Inc. All rights reserved.

Real-Time High-Dynamic Range Texture Mapping

DTIC Science & Technology

2001-01-01

the renderings produced by radiosity and global illumination algorithms. As a particular example, Greg Ward’s RADIANCE synthetic imaging system [32...in soft- ware only. [26] presented a technique for performing Ward’s tone reproduction algo- rithm interactively to visualize radiosity solutions

The Effective Dynamic Ranges for Glaucomatous Visual Field Progression With Standard Automated Perimetry and Stimulus Sizes III and V.

PubMed

Wall, Michael; Zamba, Gideon K D; Artes, Paul H

2018-01-01

It has been shown that threshold estimates below approximately 20 dB have little effect on the ability to detect visual field progression in glaucoma. We aimed to compare stimulus size V to stimulus size III, in areas of visual damage, to confirm these findings by using (1) a different dataset, (2) different techniques of progression analysis, and (3) an analysis to evaluate the effect of censoring on mean deviation (MD). In the Iowa Variability in Perimetry Study, 120 glaucoma subjects were tested every 6 months for 4 years with size III SITA Standard and size V Full Threshold. Progression was determined with three complementary techniques: pointwise linear regression (PLR), permutation of PLR, and linear regression of the MD index. All analyses were repeated on "censored'' datasets in which threshold estimates below a given criterion value were set to equal the criterion value. Our analyses confirmed previous observations that threshold estimates below 20 dB contribute much less to visual field progression than estimates above this range. These findings were broadly similar with stimulus sizes III and V. Censoring of threshold values < 20 dB has relatively little impact on the rates of visual field progression in patients with mild to moderate glaucoma. Size V, which has lower retest variability, performs at least as well as size III for longitudinal glaucoma progression analysis and appears to have a larger useful dynamic range owing to the upper sensitivity limit being higher.

Visualizing protein interactions and dynamics: evolving a visual language for molecular animation.

PubMed

Jenkinson, Jodie; McGill, Gaël

2012-01-01

Undergraduate biology education provides students with a number of learning challenges. Subject areas that are particularly difficult to understand include protein conformational change and stability, diffusion and random molecular motion, and molecular crowding. In this study, we examined the relative effectiveness of three-dimensional visualization techniques for learning about protein conformation and molecular motion in association with a ligand-receptor binding event. Increasingly complex versions of the same binding event were depicted in each of four animated treatments. Students (n = 131) were recruited from the undergraduate biology program at University of Toronto, Mississauga. Visualization media were developed in the Center for Molecular and Cellular Dynamics at Harvard Medical School. Stem cell factor ligand and cKit receptor tyrosine kinase were used as a classical example of a ligand-induced receptor dimerization and activation event. Each group completed a pretest, viewed one of four variants of the animation, and completed a posttest and, at 2 wk following the assessment, a delayed posttest. Overall, the most complex animation was the most effective at fostering students' understanding of the events depicted. These results suggest that, in select learning contexts, increasingly complex representations may be more desirable for conveying the dynamic nature of cell binding events.

A tone mapping operator based on neural and psychophysical models of visual perception

NASA Astrophysics Data System (ADS)

Cyriac, Praveen; Bertalmio, Marcelo; Kane, David; Vazquez-Corral, Javier

2015-03-01

High dynamic range imaging techniques involve capturing and storing real world radiance values that span many orders of magnitude. However, common display devices can usually reproduce intensity ranges only up to two to three orders of magnitude. Therefore, in order to display a high dynamic range image on a low dynamic range screen, the dynamic range of the image needs to be compressed without losing details or introducing artefacts, and this process is called tone mapping. A good tone mapping operator must be able to produce a low dynamic range image that matches as much as possible the perception of the real world scene. We propose a two stage tone mapping approach, in which the first stage is a global method for range compression based on a gamma curve that equalizes the lightness histogram the best, and the second stage performs local contrast enhancement and color induction using neural activity models for the visual cortex.

Imaging of Chromosome Dynamics in Mouse Testis Tissue by Immuno-FISH.

PubMed

Scherthan, Harry

2017-01-01

The mouse (Mus musculus) represents the central mammalian genetic model system for biomedical and developmental research. Mutant mouse models have provided important insights into chromosome dynamics during the complex meiotic differentiation program that compensates for the genome doubling at fertilization. Homologous chromosomes (homologues) undergo dynamic pairing and recombine during first meiotic prophase before they become partitioned into four haploid sets by two consecutive meiotic divisions that lack an intervening S-phase. Fluorescence in situ hybridization (FISH) has been instrumental in the visualization and imaging of the dynamic reshaping of chromosome territories and mobility during prophase I, in which meiotic telomeres were found to act as pacemakers for the chromosome pairing dance. FISH combined with immunofluorescence (IF) co-staining of nuclear proteins has been instrumental for the visualization and imaging of mammalian meiotic chromosome behavior. This chapter describes FISH and IF methods for the analysis of chromosome dynamics in nuclei of paraffin-embedded mouse testes. The techniques have proven useful for fresh and archived paraffin testis material of several mammalian species.

Seminar in Flow Visualization at Lafayette College: Variations on the Hertzberg Effect

NASA Astrophysics Data System (ADS)

Rossmann, Jenn Stroud

2013-11-01

Flow visualization reveals an invisible world of fluid dynamics, blending scientific investigation and artistic exploration. The resulting images have inspired, and in some cases themselves become appreciated as, art. At Lafayette College, a sophomore-level seminar in The Art and Science of Flow Visualization exposes students to these techniques and the science of fluid mechanics, and to the photographic methods needed to create effective images that are successful both scientifically and artistically. Unlike other courses in flow visualization, this course assumes no a priori familiarity with fluid flow or with photography. The fundamentals of both are taught and practiced in a studio setting. Students are engaged in an interdisciplinary discourse about fluids and physics, photography, scientific ethics, and historical societal responses to science and art. Relevant texts from several disciplines are read, discussed, and responded to in student writing. This seminar approach makes flow visualization and fluid dynamics a natural part of a liberal education. The development, implementation, and assessment of this team-taught course at Lafayette College will be discussed. Support provided by National Science Foundation.

Model–Free Visualization of Suspicious Lesions in Breast MRI Based on Supervised and Unsupervised Learning

PubMed Central

Twellmann, Thorsten; Meyer-Baese, Anke; Lange, Oliver; Foo, Simon; Nattkemper, Tim W.

2008-01-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has become an important tool in breast cancer diagnosis, but evaluation of multitemporal 3D image data holds new challenges for human observers. To aid the image analysis process, we apply supervised and unsupervised pattern recognition techniques for computing enhanced visualizations of suspicious lesions in breast MRI data. These techniques represent an important component of future sophisticated computer-aided diagnosis (CAD) systems and support the visual exploration of spatial and temporal features of DCE-MRI data stemming from patients with confirmed lesion diagnosis. By taking into account the heterogeneity of cancerous tissue, these techniques reveal signals with malignant, benign and normal kinetics. They also provide a regional subclassification of pathological breast tissue, which is the basis for pseudo-color presentations of the image data. Intelligent medical systems are expected to have substantial implications in healthcare politics by contributing to the diagnosis of indeterminate breast lesions by non-invasive imaging. PMID:19255616

6D Visualization of Multidimensional Data by Means of Cognitive Technology

NASA Astrophysics Data System (ADS)

Vitkovskiy, V.; Gorohov, V.; Komarinskiy, S.

2010-12-01

On the basis of the cognitive graphics concept, we worked out the SW-system for visualization and analysis. It allows to train and to aggravate intuition of researcher, to raise his interest and motivation to the creative, scientific cognition, to realize process of dialogue with the very problems simultaneously. The Space Hedgehog system is the next step in the cognitive means of the multidimensional data analyze. The technique and technology cognitive 6D visualization of the multidimensional data is developed on the basis of the cognitive visualization research and technology development. The Space Hedgehog system allows direct dynamic visualization of 6D objects. It is developed with use of experience of the program Space Walker creation and its applications.

Distributed augmented reality with 3-D lung dynamics--a planning tool concept.

PubMed

Hamza-Lup, Felix G; Santhanam, Anand P; Imielińska, Celina; Meeks, Sanford L; Rolland, Jannick P

2007-01-01

Augmented reality (AR) systems add visual information to the world by using advanced display techniques. The advances in miniaturization and reduced hardware costs make some of these systems feasible for applications in a wide set of fields. We present a potential component of the cyber infrastructure for the operating room of the future: a distributed AR-based software-hardware system that allows real-time visualization of three-dimensional (3-D) lung dynamics superimposed directly on the patient's body. Several emergency events (e.g., closed and tension pneumothorax) and surgical procedures related to lung (e.g., lung transplantation, lung volume reduction surgery, surgical treatment of lung infections, lung cancer surgery) could benefit from the proposed prototype.

Innovative Visualization Techniques applied to a Flood Scenario

NASA Astrophysics Data System (ADS)

Falcão, António; Ho, Quan; Lopes, Pedro; Malamud, Bruce D.; Ribeiro, Rita; Jern, Mikael

2013-04-01

The large and ever-increasing amounts of multi-dimensional, time-varying and geospatial digital information from multiple sources represent a major challenge for today's analysts. We present a set of visualization techniques that can be used for the interactive analysis of geo-referenced and time sampled data sets, providing an integrated mechanism and that aids the user to collaboratively explore, present and communicate visually complex and dynamic data. Here we present these concepts in the context of a 4 hour flood scenario from Lisbon in 2010, with data that includes measures of water column (flood height) every 10 minutes at a 4.5 m x 4.5 m resolution, topography, building damage, building information, and online base maps. Techniques we use include web-based linked views, multiple charts, map layers and storytelling. We explain two of these in more detail that are not currently in common use for visualization of data: storytelling and web-based linked views. Visual storytelling is a method for providing a guided but interactive process of visualizing data, allowing more engaging data exploration through interactive web-enabled visualizations. Within storytelling, a snapshot mechanism helps the author of a story to highlight data views of particular interest and subsequently share or guide others within the data analysis process. This allows a particular person to select relevant attributes for a snapshot, such as highlighted regions for comparisons, time step, class values for colour legend, etc. and provide a snapshot of the current application state, which can then be provided as a hyperlink and recreated by someone else. Since data can be embedded within this snapshot, it is possible to interactively visualize and manipulate it. The second technique, web-based linked views, includes multiple windows which interactively respond to the user selections, so that when selecting an object and changing it one window, it will automatically update in all the other windows. These concepts can be part of a collaborative platform, where multiple people share and work together on the data, via online access, which also allows its remote usage from a mobile platform. Storytelling augments analysis and decision-making capabilities allowing to assimilate complex situations and reach informed decisions, in addition to helping the public visualize information. In our visualization scenario, developed in the context of the VA-4D project for the European Space Agency (see http://www.ca3-uninova.org/project_va4d), we make use of the GAV (GeoAnalytics Visualization) framework, a web-oriented visual analytics application based on multiple interactive views. The final visualization that we produce includes multiple interactive views, including a dynamic multi-layer map surrounded by other visualizations such as bar charts, time graphs and scatter plots. The map provides flood and building information, on top of a base city map (street maps and/or satellite imagery provided by online map services such as Google Maps, Bing Maps etc.). Damage over time for selected buildings, damage for all buildings at a chosen time period, correlation between damage and water depth can be analysed in the other views. This interactive web-based visualization that incorporates the ideas of storytelling, web-based linked views, and other visualization techniques, for a 4 hour flood event in Lisbon in 2010, can be found online at http://www.ncomva.se/flash/projects/esa/flooding/.

Spatiotemporal Visualization of Time-Series Satellite-Derived CO2 Flux Data Using Volume Rendering and Gpu-Based Interpolation on a Cloud-Driven Digital Earth

NASA Astrophysics Data System (ADS)

Wu, S.; Yan, Y.; Du, Z.; Zhang, F.; Liu, R.

2017-10-01

The ocean carbon cycle has a significant influence on global climate, and is commonly evaluated using time-series satellite-derived CO2 flux data. Location-aware and globe-based visualization is an important technique for analyzing and presenting the evolution of climate change. To achieve realistic simulation of the spatiotemporal dynamics of ocean carbon, a cloud-driven digital earth platform is developed to support the interactive analysis and display of multi-geospatial data, and an original visualization method based on our digital earth is proposed to demonstrate the spatiotemporal variations of carbon sinks and sources using time-series satellite data. Specifically, a volume rendering technique using half-angle slicing and particle system is implemented to dynamically display the released or absorbed CO2 gas. To enable location-aware visualization within the virtual globe, we present a 3D particlemapping algorithm to render particle-slicing textures onto geospace. In addition, a GPU-based interpolation framework using CUDA during real-time rendering is designed to obtain smooth effects in both spatial and temporal dimensions. To demonstrate the capabilities of the proposed method, a series of satellite data is applied to simulate the air-sea carbon cycle in the China Sea. The results show that the suggested strategies provide realistic simulation effects and acceptable interactive performance on the digital earth.

Computer-aided light sheet flow visualization using photogrammetry

NASA Technical Reports Server (NTRS)

Stacy, Kathryn; Severance, Kurt; Childers, Brooks A.

1994-01-01

A computer-aided flow visualization process has been developed to analyze video images acquired from rotating and translating light sheet visualization systems. The computer process integrates a mathematical model for image reconstruction, advanced computer graphics concepts, and digital image processing to provide a quantitative and a visual analysis capability. The image reconstruction model, based on photogrammetry, uses knowledge of the camera and light sheet locations and orientations to project two-dimensional light sheet video images into three-dimensional space. A sophisticated computer visualization package, commonly used to analyze computational fluid dynamics (CFD) results, was chosen to interactively display the reconstructed light sheet images with the numerical surface geometry for the model or aircraft under study. The photogrammetric reconstruction technique and the image processing and computer graphics techniques and equipment are described. Results of the computer-aided process applied to both a wind tunnel translating light sheet experiment and an in-flight rotating light sheet experiment are presented. The capability to compare reconstructed experimental light sheet images with CFD solutions in the same graphics environment is also demonstrated.

Computer-Aided Light Sheet Flow Visualization

NASA Technical Reports Server (NTRS)

Stacy, Kathryn; Severance, Kurt; Childers, Brooks A.

1993-01-01

A computer-aided flow visualization process has been developed to analyze video images acquired from rotating and translating light sheet visualization systems. The computer process integrates a mathematical model for image reconstruction, advanced computer graphics concepts, and digital image processing to provide a quantitative and visual analysis capability. The image reconstruction model, based on photogrammetry, uses knowledge of the camera and light sheet locations and orientations to project two-dimensional light sheet video images into three-dimensional space. A sophisticated computer visualization package, commonly used to analyze computational fluid dynamics (CFD) data sets, was chosen to interactively display the reconstructed light sheet images, along with the numerical surface geometry for the model or aircraft under study. A description is provided of the photogrammetric reconstruction technique, and the image processing and computer graphics techniques and equipment. Results of the computer aided process applied to both a wind tunnel translating light sheet experiment and an in-flight rotating light sheet experiment are presented. The capability to compare reconstructed experimental light sheet images and CFD solutions in the same graphics environment is also demonstrated.

Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data

DOE PAGES

Murugesan, Sugeerth; Bouchard, Kristofer; Chang, Edward; ...

2016-10-02

Here, we present ECoG ClusterFlow, a novel interactive visual analysis tool for the exploration of high-resolution Electrocorticography (ECoG) data. Our system detects and visualizes dynamic high-level structures, such as communities, using the time-varying spatial connectivity network derived from the high-resolution ECoG data. ECoG ClusterFlow provides a multi-scale visualization of the spatio-temporal patterns underlying the time-varying communities using two views: 1) an overview summarizing the evolution of clusters over time and 2) a hierarchical glyph-based technique that uses data aggregation and small multiples techniques to visualize the propagation of clusters in their spatial domain. ECoG ClusterFlow makes it possible 1) tomore » compare the spatio-temporal evolution patterns across various time intervals, 2) to compare the temporal information at varying levels of granularity, and 3) to investigate the evolution of spatial patterns without occluding the spatial context information. Lastly, we present case studies done in collaboration with neuroscientists on our team for both simulated and real epileptic seizure data aimed at evaluating the effectiveness of our approach.« less

Computer-aided light sheet flow visualization

NASA Technical Reports Server (NTRS)

Stacy, Kathryn; Severance, Kurt; Childers, Brooks A.

1993-01-01

A computer-aided flow visualization process has been developed to analyze video images acquired from rotating and translating light sheet visualization systems. The computer process integrates a mathematical model for image reconstruction, advanced computer graphics concepts, and digital image processing to provide a quantitative and visual analysis capability. The image reconstruction model, based on photogrammetry, uses knowledge of the camera and light sheet locations and orientations to project two-dimensional light sheet video images into three-dimensional space. A sophisticated computer visualization package, commonly used to analyze computational fluid dynamics (CFD) data sets, was chosen to interactively display the reconstructed light sheet images, along with the numerical surface geometry for the model or aircraft under study. A description is provided of the photogrammetric reconstruction technique, and the image processing and computer graphics techniques and equipment. Results of the computer aided process applied to both a wind tunnel translating light sheet experiment and an in-flight rotating light sheet experiment are presented. The capability to compare reconstructed experimental light sheet images and CFD solutions in the same graphics environment is also demonstrated.

Chronological protein synthesis in regenerating rat liver.

PubMed

He, Jinjun; Hao, Shuai; Zhang, Hao; Guo, Fuzheng; Huang, Lingyun; Xiao, Xueyuan; He, Dacheng

2015-07-01

Liver regeneration has been studied for decades; however, its regulation remains unclear. In this study, we report a dynamic tracing of protein synthesis in rat regenerating liver with a new proteomic technique, (35) S in vivo labeling analysis for dynamic proteomics (SiLAD). Conventional proteomic techniques typically measure protein alteration in accumulated amounts. The SiLAD technique specifically detects protein synthesis velocity instead of accumulated amounts of protein through (35) S pulse labeling of newly synthesized proteins, providing a direct way for analyzing protein synthesis variations. Consequently, protein synthesis within short as 30 min was visualized and protein regulations in the first 8 h of regenerating liver were dynamically traced. Further, the 3.5-5 h post partial hepatectomy (PHx) was shown to be an important regulatory turning point by acute regulation of many proteins in the initiation of liver regeneration. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-Time Single Molecule Visualization of SH2 Domain Membrane Recruitment in Growth Factor Stimulated Cells.

PubMed

Oh, Dongmyung

2017-01-01

In the last decade, single molecule tracking (SMT) techniques have emerged as a versatile tool for molecular cell biology research. This approach allows researchers to monitor the real-time behavior of individual molecules in living cells with nanometer and millisecond resolution. As a result, it is possible to visualize biological processes as they occur at a molecular level in real time. Here we describe a method for the real-time visualization of SH2 domain membrane recruitment from the cytoplasm to epidermal growth factor (EGF) induced phosphotyrosine sites on the EGF receptor. Further, we describe methods that utilize SMT data to define SH2 domain membrane dynamics parameters such as binding (τ), dissociation (k d ), and diffusion (D) rates. Together these methods may allow us to gain greater understanding of signal transduction dynamics and the molecular basis of disease-related aberrant pathways.

SnapShot: Visualization to Propel Ice Hockey Analytics.

PubMed

Pileggi, H; Stolper, C D; Boyle, J M; Stasko, J T

2012-12-01

Sports analysts live in a world of dynamic games flattened into tables of numbers, divorced from the rinks, pitches, and courts where they were generated. Currently, these professional analysts use R, Stata, SAS, and other statistical software packages for uncovering insights from game data. Quantitative sports consultants seek a competitive advantage both for their clients and for themselves as analytics becomes increasingly valued by teams, clubs, and squads. In order for the information visualization community to support the members of this blossoming industry, it must recognize where and how visualization can enhance the existing analytical workflow. In this paper, we identify three primary stages of today's sports analyst's routine where visualization can be beneficially integrated: 1) exploring a dataspace; 2) sharing hypotheses with internal colleagues; and 3) communicating findings to stakeholders.Working closely with professional ice hockey analysts, we designed and built SnapShot, a system to integrate visualization into the hockey intelligence gathering process. SnapShot employs a variety of information visualization techniques to display shot data, yet given the importance of a specific hockey statistic, shot length, we introduce a technique, the radial heat map. Through a user study, we received encouraging feedback from several professional analysts, both independent consultants and professional team personnel.

Wetlands for Wastewater: a Visual Approach to Microbial Dynamics

NASA Astrophysics Data System (ADS)

Joubert, L.; Wolfaardt, G.; Du Plessis, K.

2007-12-01

The complex character of distillery wastewater comprises high concentrations of sugars, lignins, hemicelluloses, dextrans, resins, polyphenols and organic acids which are recalcitrant to biodegradation. Microorganisms play a key role in the production and degradation of organic matter, environmental pollutants, and cycling of nutrients and metals. Due to their short life cycles microbes respond rapidly to external nutrient loading, with major consequences for the stability of biological systems. We evaluated the feasibility of wetlands to treat winery and distillery effluents in experimental systems based on constructed wetlands, including down-scaled on-site distillery wetlands, small-scale controlled greenhouse systems, and bench-scale mesocosms. Chemical, visual and molecular fingerprinting (t-RFLP) techniques were applied to study the dynamics of planktonic and attached (biofilm) communities at various points in wetlands of different size, retention time and geological substrate, and under influence of shock nutrient loadings. Variable- Pressure Scanning Electron Microscopy (VP-SEM) was applied to visualize microbial colonization, morphotype diversity and distribution, and 3D biofilm architecture. Cross-taxon and predator-prey interactions were markedly influenced by organic loading, while the presence of algae affected microbial community composition and biofilm structure. COD removal varied with geological substrate, and was positively correlated with retention time in gravel wetlands. Planktonic and biofilm communities varied markedly in different regions of the wetland and over time, as indicated by whole-community t-RFLP and VP-SEM. An integrative visual approach to community dynamics enhanced data retrieval not afforded by molecular techniques alone. The high microbial diversity along spatial and temporal gradients, and responsiveness to the physico-chemical environment, suggest that microbial communities maintain metabolic function by modifying species composition in response to fluctuations in their environment. It seems apparent that microbial community plasticity may indeed be the distinguishing characteristic of a successful wetland system.

Accelerating Large Data Analysis By Exploiting Regularities

NASA Technical Reports Server (NTRS)

Moran, Patrick J.; Ellsworth, David

2003-01-01

We present techniques for discovering and exploiting regularity in large curvilinear data sets. The data can be based on a single mesh or a mesh composed of multiple submeshes (also known as zones). Multi-zone data are typical to Computational Fluid Dynamics (CFD) simulations. Regularities include axis-aligned rectilinear and cylindrical meshes as well as cases where one zone is equivalent to a rigid-body transformation of another. Our algorithms can also discover rigid-body motion of meshes in time-series data. Next, we describe a data model where we can utilize the results from the discovery process in order to accelerate large data visualizations. Where possible, we replace general curvilinear zones with rectilinear or cylindrical zones. In rigid-body motion cases we replace a time-series of meshes with a transformed mesh object where a reference mesh is dynamically transformed based on a given time value in order to satisfy geometry requests, on demand. The data model enables us to make these substitutions and dynamic transformations transparently with respect to the visualization algorithms. We present results with large data sets where we combine our mesh replacement and transformation techniques with out-of-core paging in order to achieve significant speed-ups in analysis.

The practice of agent-based model visualization.

PubMed

Dorin, Alan; Geard, Nicholas

2014-01-01

We discuss approaches to agent-based model visualization. Agent-based modeling has its own requirements for visualization, some shared with other forms of simulation software, and some unique to this approach. In particular, agent-based models are typified by complexity, dynamism, nonequilibrium and transient behavior, heterogeneity, and a researcher's interest in both individual- and aggregate-level behavior. These are all traits requiring careful consideration in the design, experimentation, and communication of results. In the case of all but final communication for dissemination, researchers may not make their visualizations public. Hence, the knowledge of how to visualize during these earlier stages is unavailable to the research community in a readily accessible form. Here we explore means by which all phases of agent-based modeling can benefit from visualization, and we provide examples from the available literature and online sources to illustrate key stages and techniques.

General visual robot controller networks via artificial evolution

NASA Astrophysics Data System (ADS)

Cliff, David; Harvey, Inman; Husbands, Philip

1993-08-01

We discuss recent results from our ongoing research concerning the application of artificial evolution techniques (i.e., an extended form of genetic algorithm) to the problem of developing `neural' network controllers for visually guided robots. The robot is a small autonomous vehicle with extremely low-resolution vision, employing visual sensors which could readily be constructed from discrete analog components. In addition to visual sensing, the robot is equipped with a small number of mechanical tactile sensors. Activity from the sensors is fed to a recurrent dynamical artificial `neural' network, which acts as the robot controller, providing signals to motors governing the robot's motion. Prior to presentation of new results, this paper summarizes our rationale and past work, which has demonstrated that visually guided control networks can arise without any explicit specification that visual processing should be employed: the evolutionary process opportunistically makes use of visual information if it is available.

Visualizing Mobility of Public Transportation System.

PubMed

Zeng, Wei; Fu, Chi-Wing; Arisona, Stefan Müller; Erath, Alexander; Qu, Huamin

2014-12-01

Public transportation systems (PTSs) play an important role in modern cities, providing shared/massive transportation services that are essential for the general public. However, due to their increasing complexity, designing effective methods to visualize and explore PTS is highly challenging. Most existing techniques employ network visualization methods and focus on showing the network topology across stops while ignoring various mobility-related factors such as riding time, transfer time, waiting time, and round-the-clock patterns. This work aims to visualize and explore passenger mobility in a PTS with a family of analytical tasks based on inputs from transportation researchers. After exploring different design alternatives, we come up with an integrated solution with three visualization modules: isochrone map view for geographical information, isotime flow map view for effective temporal information comparison and manipulation, and OD-pair journey view for detailed visual analysis of mobility factors along routes between specific origin-destination pairs. The isotime flow map linearizes a flow map into a parallel isoline representation, maximizing the visualization of mobility information along the horizontal time axis while presenting clear and smooth pathways from origin to destinations. Moreover, we devise several interactive visual query methods for users to easily explore the dynamics of PTS mobility over space and time. Lastly, we also construct a PTS mobility model from millions of real passenger trajectories, and evaluate our visualization techniques with assorted case studies with the transportation researchers.

Human Factors in Streaming Data Analysis: Challenges and Opportunities for Information Visualization

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

Dasgupta, Aritra; Arendt, Dustin L.; Franklin, Lyndsey

State-of-the-art visual analytics models and frameworks mostly assume a static snapshot of the data, while in many cases it is a stream with constant updates and changes. Exploration of streaming data poses unique challenges as machine-level computations and abstractions need to be synchronized with the visual representation of the data and the temporally evolving human insights. In the visual analytics literature, we lack a thorough characterization of streaming data and analysis of the challenges associated with task abstraction, visualization design, and adaptation of the role of human-in-the-loop for exploration of data streams. We aim to fill this gap by conductingmore » a survey of the state-of-the-art in visual analytics of streaming data for systematically describing the contributions and shortcomings of current techniques and analyzing the research gaps that need to be addressed in the future. Our contributions are: i) problem characterization for identifying challenges that are unique to streaming data analysis tasks, ii) a survey and analysis of the state-of-the-art in streaming data visualization research with a focus on the visualization design space for dynamic data and the role of the human-in-the-loop, and iii) reflections on the design-trade-offs for streaming visual analytics techniques and their practical applicability in real-world application scenarios.« less

Py-SPHViewer: Cosmological simulations using Smoothed Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Benítez-Llambay, Alejandro

2017-12-01

Py-SPHViewer visualizes and explores N-body + Hydrodynamics simulations. The code interpolates the underlying density field (or any other property) traced by a set of particles, using the Smoothed Particle Hydrodynamics (SPH) interpolation scheme, thus producing not only beautiful but also useful scientific images. Py-SPHViewer enables the user to explore simulated volumes using different projections. Py-SPHViewer also provides a natural way to visualize (in a self-consistent fashion) gas dynamical simulations, which use the same technique to compute the interactions between particles.

Infrared imaging - A validation technique for computational fluid dynamics codes used in STOVL applications

NASA Technical Reports Server (NTRS)

Hardman, R. R.; Mahan, J. R.; Smith, M. H.; Gelhausen, P. A.; Van Dalsem, W. R.

1991-01-01

The need for a validation technique for computational fluid dynamics (CFD) codes in STOVL applications has led to research efforts to apply infrared thermal imaging techniques to visualize gaseous flow fields. Specifically, a heated, free-jet test facility was constructed. The gaseous flow field of the jet exhaust was characterized using an infrared imaging technique in the 2 to 5.6 micron wavelength band as well as conventional pitot tube and thermocouple methods. These infrared images are compared to computer-generated images using the equations of radiative exchange based on the temperature distribution in the jet exhaust measured with the thermocouple traverses. Temperature and velocity measurement techniques, infrared imaging, and the computer model of the infrared imaging technique are presented and discussed. From the study, it is concluded that infrared imaging techniques coupled with the radiative exchange equations applied to CFD models are a valid method to qualitatively verify CFD codes used in STOVL applications.

Scientific Visualization and Simulation for Multi-dimensional Marine Environment Data

NASA Astrophysics Data System (ADS)

Su, T.; Liu, H.; Wang, W.; Song, Z.; Jia, Z.

2017-12-01

As higher attention on the ocean and rapid development of marine detection, there are increasingly demands for realistic simulation and interactive visualization of marine environment in real time. Based on advanced technology such as GPU rendering, CUDA parallel computing and rapid grid oriented strategy, a series of efficient and high-quality visualization methods, which can deal with large-scale and multi-dimensional marine data in different environmental circumstances, has been proposed in this paper. Firstly, a high-quality seawater simulation is realized by FFT algorithm, bump mapping and texture animation technology. Secondly, large-scale multi-dimensional marine hydrological environmental data is virtualized by 3d interactive technologies and volume rendering techniques. Thirdly, seabed terrain data is simulated with improved Delaunay algorithm, surface reconstruction algorithm, dynamic LOD algorithm and GPU programming techniques. Fourthly, seamless modelling in real time for both ocean and land based on digital globe is achieved by the WebGL technique to meet the requirement of web-based application. The experiments suggest that these methods can not only have a satisfying marine environment simulation effect, but also meet the rendering requirements of global multi-dimension marine data. Additionally, a simulation system for underwater oil spill is established by OSG 3D-rendering engine. It is integrated with the marine visualization method mentioned above, which shows movement processes, physical parameters, current velocity and direction for different types of deep water oil spill particle (oil spill particles, hydrates particles, gas particles, etc.) dynamically and simultaneously in multi-dimension. With such application, valuable reference and decision-making information can be provided for understanding the progress of oil spill in deep water, which is helpful for ocean disaster forecasting, warning and emergency response.

Flow Visualization at Cryogenic Conditions Using a Modified Pressure Sensitive Paint Approach

NASA Technical Reports Server (NTRS)

Watkins, A. Neal; Goad, William K.; Obara, Clifford J.; Sprinkle, Danny R.; Campbell, Richard L.; Carter, Melissa B.; Pendergraft, Odis C., Jr.; Bell, James H.; Ingram, JoAnne L.; Oglesby, Donald M.

2005-01-01

A modification to the Pressure Sensitive Paint (PSP) method was used to visualize streamlines on a Blended Wing Body (BWB) model at full-scale flight Reynolds numbers. In order to achieve these conditions, the tests were carried out in the National Transonic Facility operating under cryogenic conditions in a nitrogen environment. Oxygen is required for conventional PSP measurements, and several tests have been successfully completed in nitrogen environments by injecting small amounts (typically < 3000 ppm) of oxygen into the flow. A similar technique was employed here, except that air was purged through pressure tap orifices already existent on the model surface, resulting in changes in the PSP wherever oxygen was present. The results agree quite well with predicted results obtained through computational fluid dynamics analysis (CFD), which show this to be a viable technique for visualizing flows without resorting to more invasive procedures such as oil flow or minitufts.

Dynamic simulation of the effect of soft toric contact lenses movement on retinal image quality.

PubMed

Niu, Yafei; Sarver, Edwin J; Stevenson, Scott B; Marsack, Jason D; Parker, Katrina E; Applegate, Raymond A

2008-04-01

To report the development of a tool designed to dynamically simulate the effect of soft toric contact lens movement on retinal image quality, initial findings on three eyes, and the next steps to be taken to improve the utility of the tool. Three eyes of two subjects wearing soft toric contact lenses were cyclopleged with 1% cyclopentolate and 2.5% phenylephrine. Four hundred wavefront aberration measurements over a 5-mm pupil were recorded during soft contact lens wear at 30 Hz using a complete ophthalmic analysis system aberrometer. Each wavefront error measurement was input into Visual Optics Laboratory (version 7.15, Sarver and Associates, Inc.) to generate a retinal simulation of a high contrast log MAR visual acuity chart. The individual simulations were combined into a single dynamic movie using a custom MatLab PsychToolbox program. Visual acuity was measured for each eye reading the movie with best cycloplegic spectacle correction through a 3-mm artificial pupil to minimize the influence of the eyes' uncorrected aberrations. Comparison of the simulated acuity was made to values recorded while the subject read unaberrated charts with contact lenses through a 5-mm artificial pupil. For one study eye, average acuity was the same as the natural contact lens viewing condition. For the other two study eyes visual acuity of the best simulation was more than one line worse than natural viewing conditions. Dynamic simulation of retinal image quality, although not yet perfect, is a promising technique for visually illustrating the optical effects on image quality because of the movements of alignment-sensitive corrections.

The Effective Dynamic Ranges for Glaucomatous Visual Field Progression With Standard Automated Perimetry and Stimulus Sizes III and V

PubMed Central

Zamba, Gideon K. D.; Artes, Paul H.

2018-01-01

Purpose It has been shown that threshold estimates below approximately 20 dB have little effect on the ability to detect visual field progression in glaucoma. We aimed to compare stimulus size V to stimulus size III, in areas of visual damage, to confirm these findings by using (1) a different dataset, (2) different techniques of progression analysis, and (3) an analysis to evaluate the effect of censoring on mean deviation (MD). Methods In the Iowa Variability in Perimetry Study, 120 glaucoma subjects were tested every 6 months for 4 years with size III SITA Standard and size V Full Threshold. Progression was determined with three complementary techniques: pointwise linear regression (PLR), permutation of PLR, and linear regression of the MD index. All analyses were repeated on “censored'' datasets in which threshold estimates below a given criterion value were set to equal the criterion value. Results Our analyses confirmed previous observations that threshold estimates below 20 dB contribute much less to visual field progression than estimates above this range. These findings were broadly similar with stimulus sizes III and V. Conclusions Censoring of threshold values < 20 dB has relatively little impact on the rates of visual field progression in patients with mild to moderate glaucoma. Size V, which has lower retest variability, performs at least as well as size III for longitudinal glaucoma progression analysis and appears to have a larger useful dynamic range owing to the upper sensitivity limit being higher. PMID:29356822

High-speed atomic force microscopy coming of age

NASA Astrophysics Data System (ADS)

Ando, Toshio

2012-02-01

High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

Dynamical Analysis and Visualization of Tornadoes Time Series

PubMed Central

2015-01-01

In this paper we analyze the behavior of tornado time-series in the U.S. from the perspective of dynamical systems. A tornado is a violently rotating column of air extending from a cumulonimbus cloud down to the ground. Such phenomena reveal features that are well described by power law functions and unveil characteristics found in systems with long range memory effects. Tornado time series are viewed as the output of a complex system and are interpreted as a manifestation of its dynamics. Tornadoes are modeled as sequences of Dirac impulses with amplitude proportional to the events size. First, a collection of time series involving 64 years is analyzed in the frequency domain by means of the Fourier transform. The amplitude spectra are approximated by power law functions and their parameters are read as an underlying signature of the system dynamics. Second, it is adopted the concept of circular time and the collective behavior of tornadoes analyzed. Clustering techniques are then adopted to identify and visualize the emerging patterns. PMID:25790281

Dynamical analysis and visualization of tornadoes time series.

PubMed

Lopes, António M; Tenreiro Machado, J A

2015-01-01

In this paper we analyze the behavior of tornado time-series in the U.S. from the perspective of dynamical systems. A tornado is a violently rotating column of air extending from a cumulonimbus cloud down to the ground. Such phenomena reveal features that are well described by power law functions and unveil characteristics found in systems with long range memory effects. Tornado time series are viewed as the output of a complex system and are interpreted as a manifestation of its dynamics. Tornadoes are modeled as sequences of Dirac impulses with amplitude proportional to the events size. First, a collection of time series involving 64 years is analyzed in the frequency domain by means of the Fourier transform. The amplitude spectra are approximated by power law functions and their parameters are read as an underlying signature of the system dynamics. Second, it is adopted the concept of circular time and the collective behavior of tornadoes analyzed. Clustering techniques are then adopted to identify and visualize the emerging patterns.

Similarity-Based Fusion of MEG and fMRI Reveals Spatio-Temporal Dynamics in Human Cortex During Visual Object Recognition

PubMed Central

Cichy, Radoslaw Martin; Pantazis, Dimitrios; Oliva, Aude

2016-01-01

Every human cognitive function, such as visual object recognition, is realized in a complex spatio-temporal activity pattern in the brain. Current brain imaging techniques in isolation cannot resolve the brain's spatio-temporal dynamics, because they provide either high spatial or temporal resolution but not both. To overcome this limitation, we developed an integration approach that uses representational similarities to combine measurements of magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) to yield a spatially and temporally integrated characterization of neuronal activation. Applying this approach to 2 independent MEG–fMRI data sets, we observed that neural activity first emerged in the occipital pole at 50–80 ms, before spreading rapidly and progressively in the anterior direction along the ventral and dorsal visual streams. Further region-of-interest analyses established that dorsal and ventral regions showed MEG–fMRI correspondence in representations later than early visual cortex. Together, these results provide a novel and comprehensive, spatio-temporally resolved view of the rapid neural dynamics during the first few hundred milliseconds of object vision. They further demonstrate the feasibility of spatially unbiased representational similarity-based fusion of MEG and fMRI, promising new insights into how the brain computes complex cognitive functions. PMID:27235099

Visualizing Protein Interactions and Dynamics: Evolving a Visual Language for Molecular Animation

PubMed Central

Jenkinson, Jodie; McGill, Gaël

2012-01-01

Undergraduate biology education provides students with a number of learning challenges. Subject areas that are particularly difficult to understand include protein conformational change and stability, diffusion and random molecular motion, and molecular crowding. In this study, we examined the relative effectiveness of three-dimensional visualization techniques for learning about protein conformation and molecular motion in association with a ligand–receptor binding event. Increasingly complex versions of the same binding event were depicted in each of four animated treatments. Students (n = 131) were recruited from the undergraduate biology program at University of Toronto, Mississauga. Visualization media were developed in the Center for Molecular and Cellular Dynamics at Harvard Medical School. Stem cell factor ligand and cKit receptor tyrosine kinase were used as a classical example of a ligand-induced receptor dimerization and activation event. Each group completed a pretest, viewed one of four variants of the animation, and completed a posttest and, at 2 wk following the assessment, a delayed posttest. Overall, the most complex animation was the most effective at fostering students' understanding of the events depicted. These results suggest that, in select learning contexts, increasingly complex representations may be more desirable for conveying the dynamic nature of cell binding events. PMID:22383622

Review of fluorescence guided surgery visualization and overlay techniques

PubMed Central

Elliott, Jonathan T.; Dsouza, Alisha V.; Davis, Scott C.; Olson, Jonathan D.; Paulsen, Keith D.; Roberts, David W.; Pogue, Brian W.

2015-01-01

In fluorescence guided surgery, data visualization represents a critical step between signal capture and display needed for clinical decisions informed by that signal. The diversity of methods for displaying surgical images are reviewed, and a particular focus is placed on electronically detected and visualized signals, as required for near-infrared or low concentration tracers. Factors driving the choices such as human perception, the need for rapid decision making in a surgical environment, and biases induced by display choices are outlined. Five practical suggestions are outlined for optimal display orientation, color map, transparency/alpha function, dynamic range compression, and color perception check. PMID:26504628

Google-Earth Based Visualizations for Environmental Flows and Pollutant Dispersion in Urban Areas

PubMed Central

Liu, Daoming; Kenjeres, Sasa

2017-01-01

In the present study, we address the development and application of an efficient tool for conversion of results obtained by an integrated computational fluid dynamics (CFD) and computational reaction dynamics (CRD) approach and their visualization in the Google Earth. We focus on results typical for environmental fluid mechanics studies at a city scale that include characteristic wind flow patterns and dispersion of reactive scalars. This is achieved by developing a code based on the Java language, which converts the typical four-dimensional structure (spatial and temporal dependency) of data results in the Keyhole Markup Language (KML) format. The visualization techniques most often used are revisited and implemented into the conversion tool. The potential of the tool is demonstrated in a case study of smog formation due to an intense traffic emission in Rotterdam (The Netherlands). It is shown that the Google Earth can provide a computationally efficient and user-friendly means of data representation. This feature can be very useful for visualization of pollution at street levels, which is of great importance for the city residents. Various meteorological and traffic emissions can be easily visualized and analyzed, providing a powerful, user-friendly tool for traffic regulations and urban climate adaptations. PMID:28257078

Connecting Swath Satellite Data With Imagery in Mapping Applications

NASA Astrophysics Data System (ADS)

Thompson, C. K.; Hall, J. R.; Penteado, P. F.; Roberts, J. T.; Zhou, A. Y.

2016-12-01

Visualizations of gridded science data products (referred to as Level 3 or Level 4) typically provide a straightforward correlation between image pixels and the source science data. This direct relationship allows users to make initial inferences based on imagery values, facilitating additional operations on the underlying data values, such as data subsetting and analysis. However, that same pixel-to-data relationship for ungridded science data products (referred to as Level 2) is significantly more challenging. These products, also referred to as "swath products", are in orbital "instrument space" and raster visualization pixels do not directly correlate to science data values. Interpolation algorithms are often employed during the gridding or projection of a science dataset prior to image generation, introducing intermediary values that separate the image from the source data values. NASA's Global Imagery Browse Services (GIBS) is researching techniques for efficiently serving "image-ready" data allowing client-side dynamic visualization and analysis capabilities. This presentation will cover some GIBS prototyping work designed to maintain connectivity between Level 2 swath data and its corresponding raster visualizations. Specifically, we discuss the DAta-to-Image-SYstem (DAISY), an indexing approach for Level 2 swath data, and the mechanisms whereby a client may dynamically visualize the data in raster form.

3D Flow Visualization Using Texture Advection

NASA Technical Reports Server (NTRS)

Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)

2001-01-01

Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.

Technology Resources: Mathematics Accessibility for All Not Accommodation for Some

ERIC Educational Resources Information Center

Duranczyk, Irene M.

2009-01-01

When faculty and learning assistance staff create teaching documents and web pages envisioning the widest range of users they can save time while achieving access for all. There are tools and techniques available to make mathematics visual, orally, and dynamically more accessible through multimodal presentation forms. Resources from Design…

Visualizing and Understanding Probability and Statistics: Graphical Simulations Using Excel

ERIC Educational Resources Information Center

Gordon, Sheldon P.; Gordon, Florence S.

2009-01-01

The authors describe a collection of dynamic interactive simulations for teaching and learning most of the important ideas and techniques of introductory statistics and probability. The modules cover such topics as randomness, simulations of probability experiments such as coin flipping, dice rolling and general binomial experiments, a simulation…

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Spatio-temporal visualization of air-sea CO2 flux and carbon budget using volume rendering

NASA Astrophysics Data System (ADS)

Du, Zhenhong; Fang, Lei; Bai, Yan; Zhang, Feng; Liu, Renyi

2015-04-01

This paper presents a novel visualization method to show the spatio-temporal dynamics of carbon sinks and sources, and carbon fluxes in the ocean carbon cycle. The air-sea carbon budget and its process of accumulation are demonstrated in the spatial dimension, while the distribution pattern and variation of CO2 flux are expressed by color changes. In this way, we unite spatial and temporal characteristics of satellite data through visualization. A GPU-based direct volume rendering technique using half-angle slicing is adopted to dynamically visualize the released or absorbed CO2 gas with shadow effects. A data model is designed to generate four-dimensional (4D) data from satellite-derived air-sea CO2 flux products, and an out-of-core scheduling strategy is also proposed for on-the-fly rendering of time series of satellite data. The presented 4D visualization method is implemented on graphics cards with vertex, geometry and fragment shaders. It provides a visually realistic simulation and user interaction for real-time rendering. This approach has been integrated into the Information System of Ocean Satellite Monitoring for Air-sea CO2 Flux (IssCO2) for the research and assessment of air-sea CO2 flux in the China Seas.

Active visual search in non-stationary scenes: coping with temporal variability and uncertainty

NASA Astrophysics Data System (ADS)

Ušćumlić, Marija; Blankertz, Benjamin

2016-02-01

Objective. State-of-the-art experiments for studying neural processes underlying visual cognition often constrain sensory inputs (e.g., static images) and our behavior (e.g., fixed eye-gaze, long eye fixations), isolating or simplifying the interaction of neural processes. Motivated by the non-stationarity of our natural visual environment, we investigated the electroencephalography (EEG) correlates of visual recognition while participants overtly performed visual search in non-stationary scenes. We hypothesized that visual effects (such as those typically used in human-computer interfaces) may increase temporal uncertainty (with reference to fixation onset) of cognition-related EEG activity in an active search task and therefore require novel techniques for single-trial detection. Approach. We addressed fixation-related EEG activity in an active search task with respect to stimulus-appearance styles and dynamics. Alongside popping-up stimuli, our experimental study embraces two composite appearance styles based on fading-in, enlarging, and motion effects. Additionally, we explored whether the knowledge obtained in the pop-up experimental setting can be exploited to boost the EEG-based intention-decoding performance when facing transitional changes of visual content. Main results. The results confirmed our initial hypothesis that the dynamic of visual content can increase temporal uncertainty of the cognition-related EEG activity in active search with respect to fixation onset. This temporal uncertainty challenges the pivotal aim to keep the decoding performance constant irrespective of visual effects. Importantly, the proposed approach for EEG decoding based on knowledge transfer between the different experimental settings gave a promising performance. Significance. Our study demonstrates that the non-stationarity of visual scenes is an important factor in the evolution of cognitive processes, as well as in the dynamic of ocular behavior (i.e., dwell time and fixation duration) in an active search task. In addition, our method to improve single-trial detection performance in this adverse scenario is an important step in making brain-computer interfacing technology available for human-computer interaction applications.

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

Li, Song

CFD (Computational Fluid Dynamics) is a widely used technique in engineering design field. It uses mathematical methods to simulate and predict flow characteristics in a certain physical space. Since the numerical result of CFD computation is very hard to understand, VR (virtual reality) and data visualization techniques are introduced into CFD post-processing to improve the understandability and functionality of CFD computation. In many cases CFD datasets are very large (multi-gigabytes), and more and more interactions between user and the datasets are required. For the traditional VR application, the limitation of computing power is a major factor to prevent visualizing largemore » dataset effectively. This thesis presents a new system designing to speed up the traditional VR application by using parallel computing and distributed computing, and the idea of using hand held device to enhance the interaction between a user and VR CFD application as well. Techniques in different research areas including scientific visualization, parallel computing, distributed computing and graphical user interface designing are used in the development of the final system. As the result, the new system can flexibly be built on heterogeneous computing environment, dramatically shorten the computation time.« less

Real-time dynamic display of registered 4D cardiac MR and ultrasound images using a GPU

NASA Astrophysics Data System (ADS)

Zhang, Q.; Huang, X.; Eagleson, R.; Guiraudon, G.; Peters, T. M.

2007-03-01

In minimally invasive image-guided surgical interventions, different imaging modalities, such as magnetic resonance imaging (MRI), computed tomography (CT), and real-time three-dimensional (3D) ultrasound (US), can provide complementary, multi-spectral image information. Multimodality dynamic image registration is a well-established approach that permits real-time diagnostic information to be enhanced by placing lower-quality real-time images within a high quality anatomical context. For the guidance of cardiac procedures, it would be valuable to register dynamic MRI or CT with intraoperative US. However, in practice, either the high computational cost prohibits such real-time visualization of volumetric multimodal images in a real-world medical environment, or else the resulting image quality is not satisfactory for accurate guidance during the intervention. Modern graphics processing units (GPUs) provide the programmability, parallelism and increased computational precision to begin to address this problem. In this work, we first outline our research on dynamic 3D cardiac MR and US image acquisition, real-time dual-modality registration and US tracking. Then we describe image processing and optimization techniques for 4D (3D + time) cardiac image real-time rendering. We also present our multimodality 4D medical image visualization engine, which directly runs on a GPU in real-time by exploiting the advantages of the graphics hardware. In addition, techniques such as multiple transfer functions for different imaging modalities, dynamic texture binding, advanced texture sampling and multimodality image compositing are employed to facilitate the real-time display and manipulation of the registered dual-modality dynamic 3D MR and US cardiac datasets.

Scientific Visualization in High Speed Network Environments

NASA Technical Reports Server (NTRS)

Vaziri, Arsi; Kutler, Paul (Technical Monitor)

1997-01-01

In several cases, new visualization techniques have vastly increased the researcher's ability to analyze and comprehend data. Similarly, the role of networks in providing an efficient supercomputing environment have become more critical and continue to grow at a faster rate than the increase in the processing capabilities of supercomputers. A close relationship between scientific visualization and high-speed networks in providing an important link to support efficient supercomputing is identified. The two technologies are driven by the increasing complexities and volume of supercomputer data. The interaction of scientific visualization and high-speed networks in a Computational Fluid Dynamics simulation/visualization environment are given. Current capabilities supported by high speed networks, supercomputers, and high-performance graphics workstations at the Numerical Aerodynamic Simulation Facility (NAS) at NASA Ames Research Center are described. Applied research in providing a supercomputer visualization environment to support future computational requirements are summarized.

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

Tools for 3D scientific visualization in computational aerodynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

Visual Reconciliation of Alternative Similarity Spaces in Climate Modeling.

PubMed

Poco, Jorge; Dasgupta, Aritra; Wei, Yaxing; Hargrove, William; Schwalm, Christopher R; Huntzinger, Deborah N; Cook, Robert; Bertini, Enrico; Silva, Claudio T

2014-12-01

Visual data analysis often requires grouping of data objects based on their similarity. In many application domains researchers use algorithms and techniques like clustering and multidimensional scaling to extract groupings from data. While extracting these groups using a single similarity criteria is relatively straightforward, comparing alternative criteria poses additional challenges. In this paper we define visual reconciliation as the problem of reconciling multiple alternative similarity spaces through visualization and interaction. We derive this problem from our work on model comparison in climate science where climate modelers are faced with the challenge of making sense of alternative ways to describe their models: one through the output they generate, another through the large set of properties that describe them. Ideally, they want to understand whether groups of models with similar spatio-temporal behaviors share similar sets of criteria or, conversely, whether similar criteria lead to similar behaviors. We propose a visual analytics solution based on linked views, that addresses this problem by allowing the user to dynamically create, modify and observe the interaction among groupings, thereby making the potential explanations apparent. We present case studies that demonstrate the usefulness of our technique in the area of climate science.

Visualization of particle interactions in granular media.

PubMed

Meier, Holger A; Schlemmer, Michael; Wagner, Christian; Kerren, Andreas; Hagen, Hans; Kuhl, Ellen; Steinmann, Paul

2008-01-01

Interaction between particles in so-called granular media, such as soil and sand, plays an important role in the context of geomechanical phenomena and numerous industrial applications. A two scale homogenization approach based on a micro and a macro scale level is briefly introduced in this paper. Computation of granular material in such a way gives a deeper insight into the context of discontinuous materials and at the same time reduces the computational costs. However, the description and the understanding of the phenomena in granular materials are not yet satisfactory. A sophisticated problem-specific visualization technique would significantly help to illustrate failure phenomena on the microscopic level. As main contribution, we present a novel 2D approach for the visualization of simulation data, based on the above outlined homogenization technique. Our visualization tool supports visualization on micro scale level as well as on macro scale level. The tool shows both aspects closely arranged in form of multiple coordinated views to give users the possibility to analyze the particle behavior effectively. A novel type of interactive rose diagrams was developed to represent the dynamic contact networks on the micro scale level in a condensed and efficient way.

Applying projective techniques to formative research in health communication development.

PubMed

Wiehagen, Theresa; Caito, Nicole M; Thompson, Vetta Sanders; Casey, Christopher M; Weaver, Nancy L; Jupka, Keri; Kreuter, Matthew W

2007-04-01

This article describes a new approach to formative research in which projective techniques commonly used in psychological assessment were adapted for use in focus groups to help design colorectal-cancer screening materials for African American men and women. Participants (N = 20) were divided into six "design teams." Each team was given a selection of design supplies and asked to create and discuss a visual layout for screening materials. Participants chose design elements that reflected visual preferences that they felt would connect meaningfully with other African Americans. The dynamics within the design teams were different than in traditional focus groups, with participants having more control over the group's direction. Using projective techniques helped draw out unique information from participants by allowing them to "project" their opinions onto objects. This approach may be a valuable tool for health-promotion and health-communication practitioners seeking insight on the implicit values of a priority population.

Liquid Microjunction Surface Sampling Probe Fluid Dynamics: Computational and Experimental Analysis of Coaxial Intercapillary Positioning Effects on Sample Manipulation

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

ElNaggar, Mariam S; Barbier, Charlotte N; Van Berkel, Gary J

A coaxial geometry liquid microjunction surface sampling probe (LMJ-SSP) enables direct extraction of analytes from surfaces for subsequent analysis by techniques like mass spectrometry. Solution dynamics at the probe-to-sample surface interface in the LMJ-SSP has been suspected to influence sampling efficiency and dispersion but has not been rigorously investigated. The effect on flow dynamics and analyte transport to the mass spectrometer caused by coaxial retraction of the inner and outer capillaries from each other and the surface during sampling with a LMJ-SSP was investigated using computational fluid dynamics and experimentation. A transparent LMJ-SSP was constructed to provide the means formore » visual observation of the dynamics of the surface sampling process. Visual observation, computational fluid dynamics (CFD) analysis, and experimental results revealed that inner capillary axial retraction from the flush position relative to the outer capillary transitioned the probe from a continuous sampling and injection mode through an intermediate regime to sample plug formationmode caused by eddy currents at the sampling end of the probe. The potential for analytical implementation of these newly discovered probe operational modes is discussed.« less

Imaging multi-scale dynamics in vivo with spiral volumetric optoacoustic tomography

NASA Astrophysics Data System (ADS)

Deán-Ben, X. Luís.; Fehm, Thomas F.; Ford, Steven J.; Gottschalk, Sven; Razansky, Daniel

2017-03-01

Imaging dynamics in living organisms is essential for the understanding of biological complexity. While multiple imaging modalities are often required to cover both microscopic and macroscopic spatial scales, dynamic phenomena may also extend over different temporal scales, necessitating the use of different imaging technologies based on the trade-off between temporal resolution and effective field of view. Optoacoustic (photoacoustic) imaging has been shown to offer the exclusive capability to link multiple spatial scales ranging from organelles to entire organs of small animals. Yet, efficient visualization of multi-scale dynamics remained difficult with state-of-the-art systems due to inefficient trade-offs between image acquisition and effective field of view. Herein, we introduce a spiral volumetric optoacoustic tomography (SVOT) technique that provides spectrally-enriched high-resolution optical absorption contrast across multiple spatio-temporal scales. We demonstrate that SVOT can be used to monitor various in vivo dynamics, from video-rate volumetric visualization of cardiac-associated motion in whole organs to high-resolution imaging of pharmacokinetics in larger regions. The multi-scale dynamic imaging capability thus emerges as a powerful and unique feature of the optoacoustic technology that adds to the multiple advantages of this technology for structural, functional and molecular imaging.

Visualizing and quantifying the in vivo structure and dynamics of the Arabidopsis cortical cytoskeleton using CLSM and VAEM.

PubMed

Rosero, Amparo; Zárský, Viktor; Cvrčková, Fatima

2014-01-01

The cortical microtubules, and to some extent also the actin meshwork, play a central role in the shaping of plant cells. Transgenic plants expressing fluorescent protein markers specifically tagging the two main cytoskeletal systems are available, allowing noninvasive in vivo studies. Advanced microscopy techniques, in particular confocal laser scanning microscopy (CLSM) and variable angle epifluorescence microscopy (VAEM), can be nowadays used for imaging the cortical cytoskeleton of living cells with unprecedented spatial and temporal resolution. With the aid of suitable computing techniques, quantitative information can be extracted from microscopic images and video sequences, providing insight into both architecture and dynamics of the cortical cytoskeleton.

Real-time colouring and filtering with graphics shaders

NASA Astrophysics Data System (ADS)

Vohl, D.; Fluke, C. J.; Barnes, D. G.; Hassan, A. H.

2017-11-01

Despite the popularity of the Graphics Processing Unit (GPU) for general purpose computing, one should not forget about the practicality of the GPU for fast scientific visualization. As astronomers have increasing access to three-dimensional (3D) data from instruments and facilities like integral field units and radio interferometers, visualization techniques such as volume rendering offer means to quickly explore spectral cubes as a whole. As most 3D visualization techniques have been developed in fields of research like medical imaging and fluid dynamics, many transfer functions are not optimal for astronomical data. We demonstrate how transfer functions and graphics shaders can be exploited to provide new astronomy-specific explorative colouring methods. We present 12 shaders, including four novel transfer functions specifically designed to produce intuitive and informative 3D visualizations of spectral cube data. We compare their utility to classic colour mapping. The remaining shaders highlight how common computation like filtering, smoothing and line ratio algorithms can be integrated as part of the graphics pipeline. We discuss how this can be achieved by utilizing the parallelism of modern GPUs along with a shading language, letting astronomers apply these new techniques at interactive frame rates. All shaders investigated in this work are included in the open source software shwirl (Vohl 2017).

Kalman filter techniques for accelerated Cartesian dynamic cardiac imaging.

PubMed

Feng, Xue; Salerno, Michael; Kramer, Christopher M; Meyer, Craig H

2013-05-01

In dynamic MRI, spatial and temporal parallel imaging can be exploited to reduce scan time. Real-time reconstruction enables immediate visualization during the scan. Commonly used view-sharing techniques suffer from limited temporal resolution, and many of the more advanced reconstruction methods are either retrospective, time-consuming, or both. A Kalman filter model capable of real-time reconstruction can be used to increase the spatial and temporal resolution in dynamic MRI reconstruction. The original study describing the use of the Kalman filter in dynamic MRI was limited to non-Cartesian trajectories because of a limitation intrinsic to the dynamic model used in that study. Here the limitation is overcome, and the model is applied to the more commonly used Cartesian trajectory with fast reconstruction. Furthermore, a combination of the Kalman filter model with Cartesian parallel imaging is presented to further increase the spatial and temporal resolution and signal-to-noise ratio. Simulations and experiments were conducted to demonstrate that the Kalman filter model can increase the temporal resolution of the image series compared with view-sharing techniques and decrease the spatial aliasing compared with TGRAPPA. The method requires relatively little computation, and thus is suitable for real-time reconstruction. Copyright © 2012 Wiley Periodicals, Inc.

Kalman Filter Techniques for Accelerated Cartesian Dynamic Cardiac Imaging

PubMed Central

Feng, Xue; Salerno, Michael; Kramer, Christopher M.; Meyer, Craig H.

2012-01-01

In dynamic MRI, spatial and temporal parallel imaging can be exploited to reduce scan time. Real-time reconstruction enables immediate visualization during the scan. Commonly used view-sharing techniques suffer from limited temporal resolution, and many of the more advanced reconstruction methods are either retrospective, time-consuming, or both. A Kalman filter model capable of real-time reconstruction can be used to increase the spatial and temporal resolution in dynamic MRI reconstruction. The original study describing the use of the Kalman filter in dynamic MRI was limited to non-Cartesian trajectories, because of a limitation intrinsic to the dynamic model used in that study. Here the limitation is overcome and the model is applied to the more commonly used Cartesian trajectory with fast reconstruction. Furthermore, a combination of the Kalman filter model with Cartesian parallel imaging is presented to further increase the spatial and temporal resolution and SNR. Simulations and experiments were conducted to demonstrate that the Kalman filter model can increase the temporal resolution of the image series compared with view sharing techniques and decrease the spatial aliasing compared with TGRAPPA. The method requires relatively little computation, and thus is suitable for real-time reconstruction. PMID:22926804

Visual Outcome in Meningiomas Around Anterior Visual Pathways Treated With Linear Accelerator Fractionated Stereotactic Radiotherapy

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

Stiebel-Kalish, Hadas, E-mail: kalishhadas@gmail.com; Sackler School of Medicine, Tel Aviv University, Tel Aviv; Reich, Ehud

Purpose: Meningiomas threatening the anterior visual pathways (AVPs) and not amenable for surgery are currently treated with multisession stereotactic radiotherapy. Stereotactic radiotherapy is available with a number of devices. The most ubiquitous include the gamma knife, CyberKnife, tomotherapy, and isocentric linear accelerator systems. The purpose of our study was to describe a case series of AVP meningiomas treated with linear accelerator fractionated stereotactic radiotherapy (FSRT) using the multiple, noncoplanar, dynamic conformal rotation paradigm and to compare the success and complication rates with those reported for other techniques. Patients and Methods: We included all patients with AVP meningiomas followed up atmore » our neuro-ophthalmology unit for a minimum of 12 months after FSRT. We compared the details of the neuro-ophthalmologic examinations and tumor size before and after FSRT and at the end of follow-up. Results: Of 87 patients with AVP meningiomas, 17 had been referred for FSRT. Of the 17 patients, 16 completed >12 months of follow-up (mean 39). Of the 16 patients, 11 had undergone surgery before FSRT and 5 had undergone FSRT as first-line management. Tumor control was achieved in 14 of the 16 patients, with three meningiomas shrinking in size after RT. Two meningiomas progressed, one in an area that was outside the radiation field. The visual function had improved in 6 or stabilized in 8 of the 16 patients (88%) and worsened in 2 (12%). Conclusions: Linear accelerator fractionated RT using the multiple noncoplanar dynamic rotation conformal paradigm can be offered to patients with meningiomas that threaten the anterior visual pathways as an adjunct to surgery or as first-line treatment, with results comparable to those reported for other stereotactic RT techniques.« less

Volumetric visualization of 3D data

NASA Technical Reports Server (NTRS)

Russell, Gregory; Miles, Richard

1989-01-01

In recent years, there has been a rapid growth in the ability to obtain detailed data on large complex structures in three dimensions. This development occurred first in the medical field, with CAT (computer aided tomography) scans and now magnetic resonance imaging, and in seismological exploration. With the advances in supercomputing and computational fluid dynamics, and in experimental techniques in fluid dynamics, there is now the ability to produce similar large data fields representing 3D structures and phenomena in these disciplines. These developments have produced a situation in which currently there is access to data which is too complex to be understood using the tools available for data reduction and presentation. Researchers in these areas are becoming limited by their ability to visualize and comprehend the 3D systems they are measuring and simulating.

Integration of Dynamic Models in Range Operations

NASA Technical Reports Server (NTRS)

Bardina, Jorge; Thirumalainambi, Rajkumar

2004-01-01

This work addresses the various model interactions in real-time to make an efficient internet based decision making tool for Shuttle launch. The decision making tool depends on the launch commit criteria coupled with physical models. Dynamic interaction between a wide variety of simulation applications and techniques, embedded algorithms, and data visualizations are needed to exploit the full potential of modeling and simulation. This paper also discusses in depth details of web based 3-D graphics and applications to range safety. The advantages of this dynamic model integration are secure accessibility and distribution of real time information to other NASA centers.

Lensless microscopy technique for static and dynamic colloidal systems.

PubMed

Alvarez-Palacio, D C; Garcia-Sucerquia, J

2010-09-15

We present the application of a lensless microscopy technique known as digital in-line holographic microscopy (DIHM) to image dynamic and static colloidal systems of microspheres. DIHM has been perfected up to the point that submicrometer lateral resolution with several hundreds of micrometers depth of field is achieved with visible light; it is shown that the lateral resolution of DIHM is enough to resolve self-assembled colloidal monolayers built up from polystyrene spheres with submicrometer diameters. The time resolution of DIHM is of the order of 4 frames/s at 2048 x 2048 pixels, which represents an overall improvement of 16 times the time resolution of confocal scanning microscopy. This feature is applied to the visualization of the migration of dewetting fronts in dynamic colloidal systems and the formation of front-like arrangements of particles. Copyright 2010 Elsevier Inc. All rights reserved.

Dynamic two-photon imaging of the immune response to Toxoplasma gondii infection.

PubMed

Luu, L; Coombes, J L

2015-03-01

Toxoplasma gondii is a highly successful parasite that can manipulate host immune responses to optimize its persistence and spread. As a result, a highly complex relationship exists between T. gondii and the immune system of the host. Advances in imaging techniques, and in particular, the application of two-photon microscopy to mouse infection models, have made it possible to directly visualize interactions between parasites and the host immune system as they occur in living tissues. Here, we will discuss how dynamic imaging techniques have provided unexpected new insight into (i) how immune responses are dynamically regulated by cells and structures in the local tissue environment, (ii) how protective responses to T. gondii are generated and (iii) how the parasite exploits the immune system for its own benefit. © 2014 John Wiley & Sons Ltd.

When Art Moves the Eyes: A Behavioral and Eye-Tracking Study

PubMed Central

Massaro, Davide; Savazzi, Federica; Di Dio, Cinzia; Freedberg, David; Gallese, Vittorio; Gilli, Gabriella; Marchetti, Antonella

2012-01-01

The aim of this study was to investigate, using eye-tracking technique, the influence of bottom-up and top-down processes on visual behavior while subjects, naïve to art criticism, were presented with representational paintings. Forty-two subjects viewed color and black and white paintings (Color) categorized as dynamic or static (Dynamism) (bottom-up processes). Half of the images represented natural environments and half human subjects (Content); all stimuli were displayed under aesthetic and movement judgment conditions (Task) (top-down processes). Results on gazing behavior showed that content-related top-down processes prevailed over low-level visually-driven bottom-up processes when a human subject is represented in the painting. On the contrary, bottom-up processes, mediated by low-level visual features, particularly affected gazing behavior when looking at nature-content images. We discuss our results proposing a reconsideration of the definition of content-related top-down processes in accordance with the concept of embodied simulation in art perception. PMID:22624007

Spray visualization of alternative fuels at hot ambient conditions

NASA Astrophysics Data System (ADS)

Kannaiyan, Kumaran; Sadr, Reza

2017-11-01

Gas-to-Liquid (GTL) has gained significant interest as drop-in alternative jet fuel owing to its cleaner combustion characteristics. The physical and evaporation properties of GTL fuels are different from those of the conventional jet fuels. Those differences will have an effect on the spray, and in turn, the combustion performance. In this study, the non-reacting near nozzle spray dynamics such as spray cone angle, liquid sheet breakup and liquid velocity of GTL fuel will be investigated and compared with those of the conventional jet fuel. This work is a follow up of the preliminary study performed at atmospheric ambient conditions where differences were observed in the near nozzle spray characteristics between the fuels. Whereas, in this study the spray visualization will be performed in a hot and inert environment to account for the difference in evaporation characteristics of the fuels. The spray visualization images will be captured using the shadowgraph technique. A rigorous statistical analysis of the images will be performed to compare the spray dynamics between the fuels.

When art moves the eyes: a behavioral and eye-tracking study.

PubMed

Massaro, Davide; Savazzi, Federica; Di Dio, Cinzia; Freedberg, David; Gallese, Vittorio; Gilli, Gabriella; Marchetti, Antonella

2012-01-01

The aim of this study was to investigate, using eye-tracking technique, the influence of bottom-up and top-down processes on visual behavior while subjects, naïve to art criticism, were presented with representational paintings. Forty-two subjects viewed color and black and white paintings (Color) categorized as dynamic or static (Dynamism) (bottom-up processes). Half of the images represented natural environments and half human subjects (Content); all stimuli were displayed under aesthetic and movement judgment conditions (Task) (top-down processes). Results on gazing behavior showed that content-related top-down processes prevailed over low-level visually-driven bottom-up processes when a human subject is represented in the painting. On the contrary, bottom-up processes, mediated by low-level visual features, particularly affected gazing behavior when looking at nature-content images. We discuss our results proposing a reconsideration of the definition of content-related top-down processes in accordance with the concept of embodied simulation in art perception.

Visualization of the wake behind a sliding bubble

NASA Astrophysics Data System (ADS)

O'Reilly Meehan, R.; Grennan, K.; Davis, I.; Nolan, K.; Murray, D. B.

2017-10-01

In this work, Schlieren measurements are presented for the wake of an air bubble sliding under a heated, inclined surface in quiescent water to provide new insights into the intricate sliding bubble wake structure and the associated convective cooling process. This is a two-phase flow configuration that is pertinent to thermal management solutions, where the fundamental flow physics have yet to be fully described. In this work, we present an experimental apparatus that enables high-quality Schlieren images for different bubble sizes and measurement planes. By combining these visualizations with an advanced bubble tracking technique, we can simultaneously quantify the symbiotic relationship that exists between the sliding bubble dynamics and its associated wake. An unstable, dynamic wake structure is revealed, consisting of multiple hairpin-shaped vortex structures interacting within the macroscopic area affected by the bubble. As vorticity is generated in the near wake, the bubble shape is observed to recoil and rebound. This also occurs normal to the surface and is particularly noticeable for larger bubble sizes, with a periodic ejection of material from the near wake corresponding to significant shape changes. These findings, along with their implications from a thermal management perspective, provide information on the rich dynamics of this natural flow that cannot be obtained using alternate experimental techniques.

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering

PubMed Central

Stone, John E.; Sherman, William R.; Schulten, Klaus

2016-01-01

Immersive molecular visualization provides the viewer with intuitive perception of complex structures and spatial relationships that are of critical interest to structural biologists. The recent availability of commodity head mounted displays (HMDs) provides a compelling opportunity for widespread adoption of immersive visualization by molecular scientists, but HMDs pose additional challenges due to the need for low-latency, high-frame-rate rendering. State-of-the-art molecular dynamics simulations produce terabytes of data that can be impractical to transfer from remote supercomputers, necessitating routine use of remote visualization. Hardware-accelerated video encoding has profoundly increased frame rates and image resolution for remote visualization, however round-trip network latencies would cause simulator sickness when using HMDs. We present a novel two-phase rendering approach that overcomes network latencies with the combination of omnidirectional stereoscopic progressive ray tracing and high performance rasterization, and its implementation within VMD, a widely used molecular visualization and analysis tool. The new rendering approach enables immersive molecular visualization with rendering techniques such as shadows, ambient occlusion lighting, depth-of-field, and high quality transparency, that are particularly helpful for the study of large biomolecular complexes. We describe ray tracing algorithms that are used to optimize interactivity and quality, and we report key performance metrics of the system. The new techniques can also benefit many other application domains. PMID:27747138

Live-cell imaging of migrating cells expressing fluorescently-tagged proteins in a three-dimensional matrix.

PubMed

Shih, Wenting; Yamada, Soichiro

2011-12-22

Traditionally, cell migration has been studied on two-dimensional, stiff plastic surfaces. However, during important biological processes such as wound healing, tissue regeneration, and cancer metastasis, cells must navigate through complex, three-dimensional extracellular tissue. To better understand the mechanisms behind these biological processes, it is important to examine the roles of the proteins responsible for driving cell migration. Here, we outline a protocol to study the mechanisms of cell migration using the epithelial cell line (MDCK), and a three-dimensional, fibrous, self-polymerizing matrix as a model system. This optically clear extracellular matrix is easily amenable to live-cell imaging studies and better mimics the physiological, soft tissue environment. This report demonstrates a technique for directly visualizing protein localization and dynamics, and deformation of the surrounding three-dimensional matrix. Examination of protein localization and dynamics during cellular processes provides key insight into protein functions. Genetically encoded fluorescent tags provide a unique method for observing protein localization and dynamics. Using this technique, we can analyze the subcellular accumulation of key, force-generating cytoskeletal components in real-time as the cell maneuvers through the matrix. In addition, using multiple fluorescent tags with different wavelengths, we can examine the localization of multiple proteins simultaneously, thus allowing us to test, for example, whether different proteins have similar or divergent roles. Furthermore, the dynamics of fluorescently tagged proteins can be quantified using Fluorescent Recovery After Photobleaching (FRAP) analysis. This measurement assays the protein mobility and how stably bound the proteins are to the cytoskeletal network. By combining live-cell imaging with the treatment of protein function inhibitors, we can examine in real-time the changes in the distribution of proteins and morphology of migrating cells. Furthermore, we also combine live-cell imaging with the use of fluorescent tracer particles embedded within the matrix to visualize the matrix deformation during cell migration. Thus, we can visualize how a migrating cell distributes force-generating proteins, and where the traction forces are exerted to the surrounding matrix. Through these techniques, we can gain valuable insight into the roles of specific proteins and their contributions to the mechanisms of cell migration.

Introduction to Vector Field Visualization

NASA Technical Reports Server (NTRS)

Kao, David; Shen, Han-Wei

2010-01-01

Vector field visualization techniques are essential to help us understand the complex dynamics of flow fields. These can be found in a wide range of applications such as study of flows around an aircraft, the blood flow in our heart chambers, ocean circulation models, and severe weather predictions. The vector fields from these various applications can be visually depicted using a number of techniques such as particle traces and advecting textures. In this tutorial, we present several fundamental algorithms in flow visualization including particle integration, particle tracking in time-dependent flows, and seeding strategies. For flows near surfaces, a wide variety of synthetic texture-based algorithms have been developed to depict near-body flow features. The most common approach is based on the Line Integral Convolution (LIC) algorithm. There also exist extensions of LIC to support more flexible texture generations for 3D flow data. This tutorial reviews these algorithms. Tensor fields are found in several real-world applications and also require the aid of visualization to help users understand their data sets. Examples where one can find tensor fields include mechanics to see how material respond to external forces, civil engineering and geomechanics of roads and bridges, and the study of neural pathway via diffusion tensor imaging. This tutorial will provide an overview of the different tensor field visualization techniques, discuss basic tensor decompositions, and go into detail on glyph based methods, deformation based methods, and streamline based methods. Practical examples will be used when presenting the methods; and applications from some case studies will be used as part of the motivation.

3D visualization of unsteady 2D airplane wake vortices

NASA Technical Reports Server (NTRS)

Ma, Kwan-Liu; Zheng, Z. C.

1994-01-01

Air flowing around the wing tips of an airplane forms horizontal tornado-like vortices that can be dangerous to following aircraft. The dynamics of such vortices, including ground and atmospheric effects, can be predicted by numerical simulation, allowing the safety and capacity of airports to be improved. In this paper, we introduce three-dimensional techniques for visualizing time-dependent, two-dimensional wake vortex computations, and the hazard strength of such vortices near the ground. We describe a vortex core tracing algorithm and a local tiling method to visualize the vortex evolution. The tiling method converts time-dependent, two-dimensional vortex cores into three-dimensional vortex tubes. Finally, a novel approach calculates the induced rolling moment on the following airplane at each grid point within a region near the vortex tubes and thus allows three-dimensional visualization of the hazard strength of the vortices. We also suggest ways of combining multiple visualization methods to present more information simultaneously.

Visualization of airflow growing soap bubbles

NASA Astrophysics Data System (ADS)

Al Rahbi, Hamood; Bock, Matthew; Ryu, Sangjin

2016-11-01

Visualizing airflow inside growing soap bubbles can answer questions regarding the fluid dynamics of soap bubble blowing, which is a model system for flows with a gas-liquid-gas interface. Also, understanding the soap bubble blowing process is practical because it can contribute to controlling industrial processes similar to soap bubble blowing. In this study, we visualized airflow which grows soap bubbles using the smoke wire technique to understand how airflow blows soap bubbles. The soap bubble blower setup was built to mimic the human blowing process of soap bubbles, which consists of a blower, a nozzle and a bubble ring. The smoke wire was placed between the nozzle and the bubble ring, and smoke-visualized airflow was captured using a high speed camera. Our visualization shows how air jet flows into the growing soap bubble on the ring and how the airflow interacts with the soap film of growing bubble.

A comparison of neural network and fuzzy clustering techniques in segmenting magnetic resonance images of the brain

NASA Technical Reports Server (NTRS)

Hall, Lawrence O.; Bensaid, Amine M.; Clarke, Laurence P.; Velthuizen, Robert P.; Silbiger, Martin S.; Bezdek, James C.

1992-01-01

Magnetic resonance (MR) brain section images are segmented and then synthetically colored to give visual representations of the original data with three approaches: the literal and approximate fuzzy c-means unsupervised clustering algorithms and a supervised computational neural network, a dynamic multilayered perception trained with the cascade correlation learning algorithm. Initial clinical results are presented on both normal volunteers and selected patients with brain tumors surrounded by edema. Supervised and unsupervised segmentation techniques provide broadly similar results. Unsupervised fuzzy algorithms were visually observed to show better segmentation when compared with raw image data for volunteer studies. However, for a more complex segmentation problem with tumor/edema or cerebrospinal fluid boundary, where the tissues have similar MR relaxation behavior, inconsistency in rating among experts was observed.

Interactive Web-based Floodplain Simulation System for Realistic Experiments of Flooding and Flood Damage

NASA Astrophysics Data System (ADS)

Demir, I.

2013-12-01

Recent developments in web technologies make it easy to manage and visualize large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The floodplain simulation system is a web-based 3D interactive flood simulation environment to create real world flooding scenarios. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create and modify predefined scenarios, control environmental parameters, and evaluate flood mitigation techniques. The web-based simulation system provides an environment to children and adults learn about the flooding, flood damage, and effects of development and human activity in the floodplain. The system provides various scenarios customized to fit the age and education level of the users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various flooding and land use scenarios.

Dynamic visualization techniques for high consequence software

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

Pollock, G.M.

1998-02-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification. The prototype tool is described along with the requirements constraint language after a brief literature review is presented. Examples of howmore » the tool can be used are also presented. In conclusion, the most significant advantage of this tool is to provide a first step in evaluating specification completeness, and to provide a more productive method for program comprehension and debugging. The expected payoff is increased software surety confidence, increased program comprehension, and reduced development and debugging time.« less

Coupled auralization and virtual video for immersive multimedia displays

NASA Astrophysics Data System (ADS)

Henderson, Paul D.; Torres, Rendell R.; Shimizu, Yasushi; Radke, Richard; Lonsway, Brian

2003-04-01

The implementation of maximally-immersive interactive multimedia in exhibit spaces requires not only the presentation of realistic visual imagery but also the creation of a perceptually accurate aural experience. While conventional implementations treat audio and video problems as essentially independent, this research seeks to couple the visual sensory information with dynamic auralization in order to enhance perceptual accuracy. An implemented system has been developed for integrating accurate auralizations with virtual video techniques for both interactive presentation and multi-way communication. The current system utilizes a multi-channel loudspeaker array and real-time signal processing techniques for synthesizing the direct sound, early reflections, and reverberant field excited by a moving sound source whose path may be interactively defined in real-time or derived from coupled video tracking data. In this implementation, any virtual acoustic environment may be synthesized and presented in a perceptually-accurate fashion to many participants over a large listening and viewing area. Subject tests support the hypothesis that the cross-modal coupling of aural and visual displays significantly affects perceptual localization accuracy.

Application of chaos theory to the particle dynamics of asymmetry-induced transport

NASA Astrophysics Data System (ADS)

Eggleston, D. L.

2018-03-01

The techniques of chaos theory are employed in an effort to better understand the complex single-particle dynamics of asymmetry-induced transport in non-neutral plasmas. The dynamical equations are re-conceptualized as describing time-independent trajectories in a four-dimensional space consisting of the radius r, rotating frame angle ψ, axial position z, and axial velocity v. Results include the identification of an integral of the motion, fixed-point analysis of the dynamical equations, the construction and interpretation of Poincaré sections to visualize the dynamics, and, for the case of chaotic motion, numerical calculation of the largest Lyapunov exponent. Chaotic cases are shown to be associated with the overlap of resonance islands formed by the applied asymmetry.

The Use of Spinning-Disk Confocal Microscopy for the Intravital Analysis of Platelet Dynamics in Response to Systemic and Local Inflammation

PubMed Central

Jenne, Craig N.; Wong, Connie H. Y.; Petri, Björn; Kubes, Paul

2011-01-01

Platelets are central players in inflammation and are an important component of the innate immune response. The ability to visualize platelets within the live host is essential to understanding their role in these processes. Past approaches have involved adoptive transfer of labelled platelets, non-specific dyes, or the use of fluorescent antibodies to tag platelets in vivo. Often, these techniques result in either the activation of the platelet, or blockade of specific platelet receptors. In this report, we describe two new methods for intravital visualization of platelet biology, intravenous administration of labelled anti-CD49b, which labels all platelets, and CD41-YFP transgenic mice, in which a percentage of platelets express YFP. Both approaches label endogenous platelets and allow for their visualization using spinning-disk confocal fluorescent microscopy. Following LPS-induced inflammation, we were able to measure a significant increase in both the number and size of platelet aggregates observed within the vasculature of a number of different tissues. Real-time observation of these platelet aggregates reveals them to be large, dynamic structures that are continually expanding and sloughing-off into circulation. Using these techniques, we describe for the first time, platelet recruitment to, and behaviour within numerous tissues of the mouse, both under control conditions and following LPS induced inflammation. PMID:21949865

Conductor gestures influence evaluations of ensemble performance

PubMed Central

Morrison, Steven J.; Price, Harry E.; Smedley, Eric M.; Meals, Cory D.

2014-01-01

Previous research has found that listener evaluations of ensemble performances vary depending on the expressivity of the conductor’s gestures, even when performances are otherwise identical. It was the purpose of the present study to test whether this effect of visual information was evident in the evaluation of specific aspects of ensemble performance: articulation and dynamics. We constructed a set of 32 music performances that combined auditory and visual information and were designed to feature a high degree of contrast along one of two target characteristics: articulation and dynamics. We paired each of four music excerpts recorded by a chamber ensemble in both a high- and low-contrast condition with video of four conductors demonstrating high- and low-contrast gesture specifically appropriate to either articulation or dynamics. Using one of two equivalent test forms, college music majors and non-majors (N = 285) viewed sixteen 30 s performances and evaluated the quality of the ensemble’s articulation, dynamics, technique, and tempo along with overall expressivity. Results showed significantly higher evaluations for performances featuring high rather than low conducting expressivity regardless of the ensemble’s performance quality. Evaluations for both articulation and dynamics were strongly and positively correlated with evaluations of overall ensemble expressivity. PMID:25104944

Visual saliency in MPEG-4 AVC video stream

NASA Astrophysics Data System (ADS)

Ammar, M.; Mitrea, M.; Hasnaoui, M.; Le Callet, P.

2015-03-01

Visual saliency maps already proved their efficiency in a large variety of image/video communication application fields, covering from selective compression and channel coding to watermarking. Such saliency maps are generally based on different visual characteristics (like color, intensity, orientation, motion,…) computed from the pixel representation of the visual content. This paper resumes and extends our previous work devoted to the definition of a saliency map solely extracted from the MPEG-4 AVC stream syntax elements. The MPEG-4 AVC saliency map thus defined is a fusion of static and dynamic map. The static saliency map is in its turn a combination of intensity, color and orientation features maps. Despite the particular way in which all these elementary maps are computed, the fusion techniques allowing their combination plays a critical role in the final result and makes the object of the proposed study. A total of 48 fusion formulas (6 for combining static features and, for each of them, 8 to combine static to dynamic features) are investigated. The performances of the obtained maps are evaluated on a public database organized at IRCCyN, by computing two objective metrics: the Kullback-Leibler divergence and the area under curve.

Visual analysis of fluid dynamics at NASA's numerical aerodynamic simulation facility

NASA Technical Reports Server (NTRS)

Watson, Velvin R.

1991-01-01

A study aimed at describing and illustrating visualization tools used in Computational Fluid Dynamics (CFD) and indicating how these tools are likely to change by showing a projected resolution of the human computer interface is presented. The following are outlined using a graphically based test format: the revolution of human computer environments for CFD research; comparison of current environments; current environments with the ideal; predictions for the future CFD environments; what can be done to accelerate the improvements. The following comments are given: when acquiring visualization tools, potential rapid changes must be considered; environmental changes over the next ten years due to human computer interface cannot be fathomed; data flow packages such as AVS, apE, Explorer and Data Explorer are easy to learn and use for small problems, excellent for prototyping, but not so efficient for large problems; the approximation techniques used in visualization software must be appropriate for the data; it has become more cost effective to move jobs that fit on workstations and run only memory intensive jobs on the supercomputer; use of three dimensional skills will be maximized when the three dimensional environment is built in from the start.

Real time visualization of dynamic magnetic fields with a nanomagnetic ferrolens

NASA Astrophysics Data System (ADS)

Markoulakis, Emmanouil; Rigakis, Iraklis; Chatzakis, John; Konstantaras, Antonios; Antonidakis, Emmanuel

2018-04-01

Due to advancements in nanomagnetism and latest nanomagnetic materials and devices, a new potential field has been opened up for research and applications which was not possible before. We herein propose a new research field and application for nanomagnetism for the visualization of dynamic magnetic fields in real-time. In short, Nano Magnetic Vision. A new methodology, technique and apparatus were invented and prototyped in order to demonstrate and test this new application. As an application example the visualization of the dynamic magnetic field on a transmitting antenna was chosen. Never seen before high-resolution, photos and real-time color video revealing the actual dynamic magnetic field inside a transmitting radio antenna rod has been captured for the first time. The antenna rod is fed with six hundred volts, orthogonal pulses. This unipolar signal is in the very low frequency (i.e. VLF) range. The signal combined with an extremely short electrical length of the rod, ensures the generation of a relatively strong fluctuating magnetic field, analogue to the signal transmitted, along and inside the antenna. This field is induced into a ferrolens and becomes visible in real-time within the normal human eyes frequency spectrum. The name we have given to the new observation apparatus is, SPIONs Superparamagnetic Ferrolens Microscope (SSFM), a powerful passive scientific observation tool with many other potential applications in the near future.

Dynamic contrast optical coherence tomography images transit time and quantifies microvascular plasma volume and flow in the retina and choriocapillaris

PubMed Central

Merkle, Conrad W.; Leahy, Conor; Srinivasan, Vivek J.

2016-01-01

Despite the prevalence of optical imaging techniques to measure hemodynamics in large retinal vessels, quantitative measurements of retinal capillary and choroidal hemodynamics have traditionally been challenging. Here, a new imaging technique called dynamic contrast optical coherence tomography (DyC-OCT) is applied in the rat eye to study microvascular blood flow in individual retinal and choroidal layers in vivo. DyC-OCT is based on imaging the transit of an intravascular tracer dynamically as it passes through the field-of-view. Hemodynamic parameters can be determined through quantitative analysis of tracer kinetics. In addition to enabling depth-resolved transit time, volume, and flow measurements, the injected tracer also enhances OCT angiograms and enables clear visualization of the choriocapillaris, particularly when combined with a post-processing method for vessel enhancement. DyC-OCT complements conventional OCT angiography through quantification of tracer dynamics, similar to fluorescence angiography, but with the important added benefit of laminar resolution. PMID:27867732

Dynamic contrast optical coherence tomography images transit time and quantifies microvascular plasma volume and flow in the retina and choriocapillaris.

PubMed

Merkle, Conrad W; Leahy, Conor; Srinivasan, Vivek J

2016-10-01

Despite the prevalence of optical imaging techniques to measure hemodynamics in large retinal vessels, quantitative measurements of retinal capillary and choroidal hemodynamics have traditionally been challenging. Here, a new imaging technique called dynamic contrast optical coherence tomography (DyC-OCT) is applied in the rat eye to study microvascular blood flow in individual retinal and choroidal layers in vivo . DyC-OCT is based on imaging the transit of an intravascular tracer dynamically as it passes through the field-of-view. Hemodynamic parameters can be determined through quantitative analysis of tracer kinetics. In addition to enabling depth-resolved transit time, volume, and flow measurements, the injected tracer also enhances OCT angiograms and enables clear visualization of the choriocapillaris, particularly when combined with a post-processing method for vessel enhancement. DyC-OCT complements conventional OCT angiography through quantification of tracer dynamics, similar to fluorescence angiography, but with the important added benefit of laminar resolution.

Exploring the Micro-Social Geography of Children's Interactions in Preschool: A Long-Term Observational Study and Analysis Using Geographic Information Technologies

ERIC Educational Resources Information Center

Torrens, Paul M.; Griffin, William A.

2013-01-01

The authors describe an observational and analytic methodology for recording and interpreting dynamic microprocesses that occur during social interaction, making use of space--time data collection techniques, spatial-statistical analysis, and visualization. The scheme has three investigative foci: Structure, Activity Composition, and Clustering.…

Computational Technique for Teaching Mathematics (CTTM): Visualizing the Polynomial's Resultant

ERIC Educational Resources Information Center

Alves, Francisco Regis Vieira

2015-01-01

We find several applications of the Dynamic System Geogebra--DSG related predominantly to the basic mathematical concepts at the context of the learning and teaching in Brasil. However, all these works were developed in the basic level of Mathematics. On the other hand, we discuss and explore, with DSG's help, some applications of the polynomial's…

Insensitivity of visual short-term memory to irrelevant visual information.

PubMed

Andrade, Jackie; Kemps, Eva; Werniers, Yves; May, Jon; Szmalec, Arnaud

2002-07-01

Several authors have hypothesized that visuo-spatial working memory is functionally analogous to verbal working memory. Irrelevant background speech impairs verbal short-term memory. We investigated whether irrelevant visual information has an analogous effect on visual short-term memory, using a dynamic visual noise (DVN) technique known to disrupt visual imagery (Quinn & McConnell, 1996b). Experiment I replicated the effect of DVN on pegword imagery. Experiments 2 and 3 showed no effect of DVN on recall of static matrix patterns, despite a significant effect of a concurrent spatial tapping task. Experiment 4 showed no effect of DVN on encoding or maintenance of arrays of matrix patterns, despite testing memory by a recognition procedure to encourage visual rather than spatial processing. Serial position curves showed a one-item recency effect typical of visual short-term memory. Experiment 5 showed no effect of DVN on short-term recognition of Chinese characters, despite effects of visual similarity and a concurrent colour memory task that confirmed visual processing of the characters. We conclude that irrelevant visual noise does not impair visual short-term memory. Visual working memory may not be functionally analogous to verbal working memory, and different cognitive processes may underlie visual short-term memory and visual imagery.

Creating executable architectures using Visual Simulation Objects (VSO)

NASA Astrophysics Data System (ADS)

Woodring, John W.; Comiskey, John B.; Petrov, Orlin M.; Woodring, Brian L.

2005-05-01

Investigations have been performed to identify a methodology for creating executable models of architectures and simulations of architecture that lead to an understanding of their dynamic properties. Colored Petri Nets (CPNs) are used to describe architecture because of their strong mathematical foundations, the existence of techniques for their verification and graph theory"s well-established history of success in modern science. CPNs have been extended to interoperate with legacy simulations via a High Level Architecture (HLA) compliant interface. It has also been demonstrated that an architecture created as a CPN can be integrated with Department of Defense Architecture Framework products to ensure consistency between static and dynamic descriptions. A computer-aided tool, Visual Simulation Objects (VSO), which aids analysts in specifying, composing and executing architectures, has been developed to verify the methodology and as a prototype commercial product.

Visualizing the BEC-BCS crossover in a two-dimensional Fermi gas: Pairing gaps and dynamical response functions from ab initio computations

NASA Astrophysics Data System (ADS)

Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei

2017-12-01

Experiments with ultracold atoms provide a highly controllable laboratory setting with many unique opportunities for precision exploration of quantum many-body phenomena. The nature of such systems, with strong interaction and quantum entanglement, makes reliable theoretical calculations challenging. Especially difficult are excitation and dynamical properties, which are often the most directly relevant to experiment. We carry out exact numerical calculations, by Monte Carlo sampling of imaginary-time propagation of Slater determinants, to compute the pairing gap in the two-dimensional Fermi gas from first principles. Applying state-of-the-art analytic continuation techniques, we obtain the spectral function and the density and spin structure factors providing unique tools to visualize the BEC-BCS crossover. These quantities will allow for a direct comparison with experiments.

Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics.

PubMed

Mullen, Anna; Hall, Jenny; Diegel, Janika; Hassan, Isa; Fey, Adam; MacMillan, Fraser

2016-06-15

During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Techniques for extracting single-trial activity patterns from large-scale neural recordings

PubMed Central

Churchland, Mark M; Yu, Byron M; Sahani, Maneesh; Shenoy, Krishna V

2008-01-01

Summary Large, chronically-implanted arrays of microelectrodes are an increasingly common tool for recording from primate cortex, and can provide extracellular recordings from many (order of 100) neurons. While the desire for cortically-based motor prostheses has helped drive their development, such arrays also offer great potential to advance basic neuroscience research. Here we discuss the utility of array recording for the study of neural dynamics. Neural activity often has dynamics beyond that driven directly by the stimulus. While governed by those dynamics, neural responses may nevertheless unfold differently for nominally identical trials, rendering many traditional analysis methods ineffective. We review recent studies – some employing simultaneous recording, some not – indicating that such variability is indeed present both during movement generation, and during the preceding premotor computations. In such cases, large-scale simultaneous recordings have the potential to provide an unprecedented view of neural dynamics at the level of single trials. However, this enterprise will depend not only on techniques for simultaneous recording, but also on the use and further development of analysis techniques that can appropriately reduce the dimensionality of the data, and allow visualization of single-trial neural behavior. PMID:18093826

Visualizing biological reaction intermediates with DNA curtains

NASA Astrophysics Data System (ADS)

Zhao, Yiling; Jiang, Yanzhou; Qi, Zhi

2017-04-01

Single-molecule approaches have tremendous potential analyzing dynamic biological reaction with heterogeneity that cannot be effectively accessed via traditional ensemble-level biochemical approaches. The approach of deoxyribonucleic acid (DNA) curtains developed by Dr Eric Greene and his research team at Columbia University is a high-throughput single-molecule technique that utilizes fluorescent imaging to visualize protein-DNA interactions directly and allows the acquisition of statistically relevant information from hundreds or even thousands of individual reactions. This review aims to summarize the past, present, and future of DNA curtains, with an emphasis on its applications to solve important biological questions.

MR imaging of the fetal musculoskeletal system.

PubMed

Nemec, Stefan Franz; Nemec, Ursula; Brugger, Peter C; Bettelheim, Dieter; Rotmensch, Siegfried; Graham, John M; Rimoin, David L; Prayer, Daniela

2012-03-01

Magnetic resonance imaging (MRI) appears to be increasingly used, in addition to standard ultrasonography for the diagnosis of abnormalities in utero. Previous studies have recently drawn attention to the technical refinement of MRI to visualize the fetal bones and muscles. Beyond commonly used T2-weighted MRI, echoplanar, thick-slab T2-weighted and dynamic sequences, and three-dimensional MRI techniques, are about to provide new imaging insights into the normal and the pathological musculoskeletal system of the fetus. This review emphasizes the potential significance of MRI in the visualization of the fetal musculoskeletal system. © 2012 John Wiley & Sons, Ltd.

Toward dynamic magnetic resonance imaging of the vocal tract during speech production.

PubMed

Ventura, Sandra M Rua; Freitas, Diamantino Rui S; Tavares, João Manuel R S

2011-07-01

The most recent and significant magnetic resonance imaging (MRI) improvements allow for the visualization of the vocal tract during speech production, which has been revealed to be a powerful tool in dynamic speech research. However, a synchronization technique with enhanced temporal resolution is still required. The study design was transversal in nature. Throughout this work, a technique for the dynamic study of the vocal tract with MRI by using the heart's signal to synchronize and trigger the imaging-acquisition process is presented and described. The technique in question is then used in the measurement of four speech articulatory parameters to assess three different syllables (articulatory gestures) of European Portuguese Language. The acquired MR images are automatically reconstructed so as to result in a variable sequence of images (slices) of different vocal tract shapes in articulatory positions associated with Portuguese speech sounds. The knowledge obtained as a result of the proposed technique represents a direct contribution to the improvement of speech synthesis algorithms, thereby allowing for novel perceptions in coarticulation studies, in addition to providing further efficient clinical guidelines in the pursuit of more proficient speech rehabilitation processes. Copyright © 2011 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Dynamic Chest Image Analysis: Evaluation of Model-Based Pulmonary Perfusion Analysis With Pyramid Images

DTIC Science & Technology

2001-10-25

Image Analysis aims to develop model-based computer analysis and visualization methods for showing focal and general abnormalities of lung ventilation and perfusion based on a sequence of digital chest fluoroscopy frames collected with the Dynamic Pulmonary Imaging technique 18,5,17,6. We have proposed and evaluated a multiresolutional method with an explicit ventilation model based on pyramid images for ventilation analysis. We have further extended the method for ventilation analysis to pulmonary perfusion. This paper focuses on the clinical evaluation of our method for

Surface mapping of spike potential fields: experienced EEGers vs. computerized analysis.

PubMed

Koszer, S; Moshé, S L; Legatt, A D; Shinnar, S; Goldensohn, E S

1996-03-01

An EEG epileptiform spike focus recorded with scalp electrodes is clinically localized by visual estimation of the point of maximal voltage and the distribution of its surrounding voltages. We compared such estimated voltage maps, drawn by experienced electroencephalographers (EEGers), with a computerized spline interpolation technique employed in the commercially available software package FOCUS. Twenty-two spikes were recorded from 15 patients during long-term continuous EEG monitoring. Maps of voltage distribution from the 28 electrodes surrounding the points of maximum change in slope (the spike maximum) were constructed by the EEGer. The same points of maximum spike and voltage distributions at the 29 electrodes were mapped by computerized spline interpolation and a comparison between the two methods was made. The findings indicate that the computerized spline mapping techniques employed in FOCUS construct voltage maps with similar maxima and distributions as the maps created by experienced EEGers. The dynamics of spike activity, including correlations, are better visualized using the computerized technique than by manual interpretation alone. Its use as a technique for spike localization is accurate and adds information of potential clinical value.

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

Kiss, L.I.; Bui, R.T.; Charette, A.

The flow structure inside round furnaces with various numbers of burners, burner arrangement, and exit conditions has been studied experimentally with the purpose of improving the flow conditions and the resulting heat transfer. Small-scale transparent models were built according to the laws of geometric and dynamic similarity. Various visualization and experimental techniques were applied. The flow pattern in the near-surface regions was visualized by the fluorescent minituft and popcorn techniques; the flow structure in the bulk was analyzed by smoke injection and laser sheet illumination. For the study of the transient effects, high-speed video photography was applied. The effects ofmore » the various flow patterns, like axisymmetric and rotational flow, on the magnitude and uniformity of the residence time, as well as on the formation of stagnation zones, were discussed. Conclusions were drawn and have since been applied for the improvement of furnace performance.« less

Application of Deep Learning in Automated Analysis of Molecular Images in Cancer: A Survey

PubMed Central

Xue, Yong; Chen, Shihui; Liu, Yong

2017-01-01

Molecular imaging enables the visualization and quantitative analysis of the alterations of biological procedures at molecular and/or cellular level, which is of great significance for early detection of cancer. In recent years, deep leaning has been widely used in medical imaging analysis, as it overcomes the limitations of visual assessment and traditional machine learning techniques by extracting hierarchical features with powerful representation capability. Research on cancer molecular images using deep learning techniques is also increasing dynamically. Hence, in this paper, we review the applications of deep learning in molecular imaging in terms of tumor lesion segmentation, tumor classification, and survival prediction. We also outline some future directions in which researchers may develop more powerful deep learning models for better performance in the applications in cancer molecular imaging. PMID:29114182

Multiparametric optical coherence tomography imaging of the inner retinal hemodynamic response to visual stimulation

NASA Astrophysics Data System (ADS)

Radhakrishnan, Harsha; Srinivasan, Vivek J.

2013-08-01

The hemodynamic response to neuronal activation is a well-studied phenomenon in the brain, due to the prevalence of functional magnetic resonance imaging. The retina represents an optically accessible platform for studying lamina-specific neurovascular coupling in the central nervous system; however, due to methodological limitations, this has been challenging to date. We demonstrate techniques for the imaging of visual stimulus-evoked hyperemia in the rat inner retina using Doppler optical coherence tomography (OCT) and OCT angiography. Volumetric imaging with three-dimensional motion correction, en face flow calculation, and normalization of dynamic signal to static signal are techniques that reduce spurious changes caused by motion. We anticipate that OCT imaging of retinal functional hyperemia may yield viable biomarkers in diseases, such as diabetic retinopathy, where the neurovascular unit may be impaired.

Real-time phase-contrast x-ray imaging: a new technique for the study of animal form and function

PubMed Central

Socha, John J; Westneat, Mark W; Harrison, Jon F; Waters, James S; Lee, Wah-Keat

2007-01-01

Background Despite advances in imaging techniques, real-time visualization of the structure and dynamics of tissues and organs inside small living animals has remained elusive. Recently, we have been using synchrotron x-rays to visualize the internal anatomy of millimeter-sized opaque, living animals. This technique takes advantage of partially-coherent x-rays and diffraction to enable clear visualization of internal soft tissue not viewable via conventional absorption radiography. However, because higher quality images require greater x-ray fluxes, there exists an inherent tradeoff between image quality and tissue damage. Results We evaluated the tradeoff between image quality and harm to the animal by determining the impact of targeted synchrotron x-rays on insect physiology, behavior and survival. Using 25 keV x-rays at a flux density of 80 μW/mm-2, high quality video-rate images can be obtained without major detrimental effects on the insects for multiple minutes, a duration sufficient for many physiological studies. At this setting, insects do not heat up. Additionally, we demonstrate the range of uses of synchrotron phase-contrast imaging by showing high-resolution images of internal anatomy and observations of labeled food movement during ingestion and digestion. Conclusion Synchrotron x-ray phase contrast imaging has the potential to revolutionize the study of physiology and internal biomechanics in small animals. This is the only generally applicable technique that has the necessary spatial and temporal resolutions, penetrating power, and sensitivity to soft tissue that is required to visualize the internal physiology of living animals on the scale from millimeters to microns. PMID:17331247

Damage of composite structures: Detection technique, dynamic response and residual strength

NASA Astrophysics Data System (ADS)

Lestari, Wahyu

2001-10-01

Reliable and accurate health monitoring techniques can prevent catastrophic failures of structures. Conventional damage detection methods are based on visual or localized experimental methods and very often require prior information concerning the vicinity of the damage or defect. The structure must also be readily accessible for inspections. The techniques are also labor intensive. In comparison to these methods, health-monitoring techniques that are based on the structural dynamic response offers unique information on failure of structures. However, systematic relations between the experimental data and the defect are not available and frequently, the number of vibration modes needed for an accurate identification of defects is much higher than the number of modes that can be readily identified in the experiment. These motivated us to develop an experimental data based detection method with systematic relationships between the experimentally identified information and the analytical or mathematical model representing the defective structures. The developed technique use changes in vibrational curvature modes and natural frequencies. To avoid misinterpretation of the identified information, we also need to understand the effects of defects on the structural dynamic response prior to developing health-monitoring techniques. In this thesis work we focus on two type of defects in composite structures, namely delamination and edge notch like defect. Effects of nonlinearity due to the presence of defect and due to the axial stretching are studied for beams with delamination. Once defects are detected in a structure, next concern is determining the effects of the defects on the strength of the structure and its residual stiffness under dynamic loading. In this thesis, energy release rate due to dynamic loading in a delaminated structure is studied, which will be a foundation toward determining the residual strength of the structure.

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

Visualizing cellulase activity.

PubMed

Bubner, Patricia; Plank, Harald; Nidetzky, Bernd

2013-06-01

Commercial exploitation of lignocellulose for biotechnological production of fuels and commodity chemicals requires efficient-usually enzymatic-saccharification of the highly recalcitrant insoluble substrate. A key characteristic of cellulose conversion is that the actual hydrolysis of the polysaccharide chains is intrinsically entangled with physical disruption of substrate morphology and structure. This "substrate deconstruction" by cellulase activity is a slow, yet markedly dynamic process that occurs at different length scales from and above the nanometer range. Little is currently known about the role of progressive substrate deconstruction on hydrolysis efficiency. Application of advanced visualization techniques to the characterization of enzymatic degradation of different celluloses has provided important new insights, at the requisite nano-scale resolution and down to the level of single enzyme molecules, into cellulase activity on the cellulose surface. Using true in situ imaging, dynamic features of enzyme action and substrate deconstruction were portrayed at different morphological levels of the cellulose, thus providing new suggestions and interpretations of rate-determining factors. Here, we review the milestones achieved through visualization, the methods which significantly promoted the field, compare suitable (model) substrates, and identify limiting factors, challenges and future tasks. Copyright © 2013 Wiley Periodicals, Inc.

Malware analysis using visualized image matrices.

PubMed

Han, KyoungSoo; Kang, BooJoong; Im, Eul Gyu

2014-01-01

This paper proposes a novel malware visual analysis method that contains not only a visualization method to convert binary files into images, but also a similarity calculation method between these images. The proposed method generates RGB-colored pixels on image matrices using the opcode sequences extracted from malware samples and calculates the similarities for the image matrices. Particularly, our proposed methods are available for packed malware samples by applying them to the execution traces extracted through dynamic analysis. When the images are generated, we can reduce the overheads by extracting the opcode sequences only from the blocks that include the instructions related to staple behaviors such as functions and application programming interface (API) calls. In addition, we propose a technique that generates a representative image for each malware family in order to reduce the number of comparisons for the classification of unknown samples and the colored pixel information in the image matrices is used to calculate the similarities between the images. Our experimental results show that the image matrices of malware can effectively be used to classify malware families both statically and dynamically with accuracy of 0.9896 and 0.9732, respectively.

Design and Development of Low-Cost Water Tunnel for Educational Purpose

NASA Astrophysics Data System (ADS)

Zahari, M.; Dol, S. S.

2015-04-01

The hydrodynamic behaviour of immersed body is essential in fluid dynamics study. Water tunnel is an example of facility required to provide a controlled condition for fluid flow research. The operational principle of water tunnel is quite similar to the wind tunnel but with different working fluid and higher flow-pumping capacity. Flow visualization in wind tunnel is more difficult to conduct as turbulent flows in wind dissipate quickly whilst water tunnel is more suitable for such purpose due to higher fluid viscosity and wide variety of visualization techniques can be employed. The present work focusses on the design and development of open flow water tunnel for the purpose of studying vortex-induced vibration from turbulent vortex shedding phenomenon. The water tunnel is designed to provide a steady and uniform flow speed within the test section area. Construction details are discussed for development of low-cost water tunnel for quantitative and qualitative fluid flow measurements. The water tunnel can also be used for educational purpose such as fluid dynamics class activity to provide quick access to visualization medium for better understanding of various turbulence motion learnt in class.

Manipulating and Visualizing Molecular Interactions in Customized Nanoscale Spaces

NASA Astrophysics Data System (ADS)

Stabile, Francis; Henkin, Gil; Berard, Daniel; Shayegan, Marjan; Leith, Jason; Leslie, Sabrina

We present a dynamically adjustable nanofluidic platform for formatting the conformations of and visualizing the interaction kinetics between biomolecules in solution, offering new time resolution and control of the reaction processes. This platform extends convex lens-induced confinement (CLiC), a technique for imaging molecules under confinement, by introducing a system for in situ modification of the chemical environment; this system uses a deep microchannel to diffusively exchange reagents within the nanoscale imaging region, whose height is fixed by a nanopost array. To illustrate, we visualize and manipulate salt-induced, surfactant-induced, and enzyme-induced reactions between small-molecule reagents and DNA molecules, where the conformations of the DNA molecules are formatted by the imposed nanoscale confinement. By using nanofabricated, nonabsorbing, low-background glass walls to confine biomolecules, our nanofluidic platform facilitates quantitative exploration of physiologically and biotechnologically relevant processes at the nanoscale. This device provides new kinetic information about dynamic chemical processes at the single-molecule level, using advancements in the CLiC design including a microchannel-based diffuser and postarray-based dialysis slit.

Dynamic Imaging of the Eye, Optic Nerve, and Extraocular Muscles With Golden Angle Radial MRI

PubMed Central

Smith, David S.; Smith, Alex K.; Welch, E. Brian; Smith, Seth A.

2017-01-01

Purpose The eye and its accessory structures, the optic nerve and the extraocular muscles, form a complex dynamic system. In vivo magnetic resonance imaging (MRI) of this system in motion can have substantial benefits in understanding oculomotor functioning in health and disease, but has been restricted to date to imaging of static gazes only. The purpose of this work was to develop a technique to image the eye and its accessory visual structures in motion. Methods Dynamic imaging of the eye was developed on a 3-Tesla MRI scanner, based on a golden angle radial sequence that allows freely selectable frame-rate and temporal-span image reconstructions from the same acquired data set. Retrospective image reconstructions at a chosen frame rate of 57 ms per image yielded high-quality in vivo movies of various eye motion tasks performed in the scanner. Motion analysis was performed for a left–right version task where motion paths, lengths, and strains/globe angle of the medial and lateral extraocular muscles and the optic nerves were estimated. Results Offline image reconstructions resulted in dynamic images of bilateral visual structures of healthy adults in only ∼15-s imaging time. Qualitative and quantitative analyses of the motion enabled estimation of trajectories, lengths, and strains on the optic nerves and extraocular muscles at very high frame rates of ∼18 frames/s. Conclusions This work presents an MRI technique that enables high-frame-rate dynamic imaging of the eyes and orbital structures. The presented sequence has the potential to be used in furthering the understanding of oculomotor mechanics in vivo, both in health and disease. PMID:28813574

Visualization of MMP-2 Activity Using Dual-Probe Nanoparticles to Detect Potential Metastatic Cancer Cells

PubMed Central

Kim, Sung Hoon; Lee, Hyun; Kim, Bohee; Kim, Yoon Suk; Key, Jaehong

2018-01-01

Matrix metalloproteinases (MMPs) are a family of zinc-dependent enzymes capable of degrading extracellular matrix components. Previous studies have shown that the upregulation of MMP-2 is closely related to metastatic cancers. While Western blotting, zymography, and Enzyme-Linked Immunosorbent Assays (ELISA) can be used to measure the amount of MMP-2 activity, it is not possible to visualize the dynamic MMP-2 activities of cancer cells using these techniques. In this study, MMP-2-activated poly(lactic-co-glycolic acid) with polyethylenimine (MMP-2-PLGA-PEI) nanoparticles were developed to visualize time-dependent MMP-2 activities. The MMP-2-PLGA-PEI nanoparticles contain MMP-2-activated probes that were detectable via fluorescence microscopy only in the presence of MMP-2 activity, while the Rhodamine-based probes in the nanoparticles were used to continuously visualize the location of the nanoparticles. This approach allowed us to visualize MMP-2 activities in cancer cells and their microenvironment. Our results showed that the MMP-2-PLGA-PEI nanoparticles were able to distinguish between MMP-2-positive (HaCat) and MMP-2-negative (MCF-7) cells. While the MMP-2-PLGA-PEI nanoparticles gave fluorescent signals recovered by active recombinant MMP-2, there was no signal recovery in the presence of an MMP-2 inhibitor. In conclusion, MMP-2-PLGA-PEI nanoparticles are an effective tool to visualize dynamic MMP-2 activities of potential metastatic cancer cells. PMID:29466303

Principles and biophysical applications of single particle super-localization and rotational tracking

NASA Astrophysics Data System (ADS)

Gu, Yan

While conventional Single Particle Tracking (SPT) techniques acquire 2D or 3D trajectories of particle probes, we have developed Single Particle Orientation and Rotational Tracking (SPORT) techniques to extract orientation and rotational information. Combined with DIC microscopy, the SPORT technique has been applied in biophysical studies, including membrane diffusion and intracellular transport. The rotational dynamics of nanoparticle vectors on live cell membranes was recorded and its influence on the fate of these nanoparticle vectors was elucidated. The rotational motions of gold nanorods with various surface modifiers were tracked continuously at a temporal resolution of 5 ms under a DIC microscope. We found that the rotational behaviors of gold nanorod vectors are strongly related to their surface charge, specific surface functional groups, and the availability of receptors on cell membranes. The study of rotational Brownian motion of nanoparticles on cell membranes will lead to a better understanding of the mechanisms of drug delivery and provide guidance in designing surface modification strategies for drug delivery vectors under various circumstances. To characterize the rotation mode of surface functionalized gold nanorods on cell membranes, the SPORT technique is combined with the correlation analysis of the bright and dark DIC intensities. The unique capabilities of visualizing and understanding rotational motions of functionalized nanoparticles on live cell membranes allow us to correlate rotational and translational dynamics in unprecedented detail and provide new insights for complex membrane processes, including electrostatic interactions, ligand-receptor binding, and lateral (confined and hopping) diffusion of membrane receptors. Surface-functionalized nanoparticles interact with the membrane in fundamentally different ways and exhibit distinct rotational modes. The early events of particle-membrane approach and attachment are directly visualized for the first time. The rotational dynamics of cargos in both active directional transport and pausing stages of axonal transport was also visualized using high-speed SPORT with a temporal resolution of 2 ms. Both long and short pauses are imaged, and the correlations between the pause duration, the rotational behaviour of the cargo at the pause, and the moving direction after the pause are established. Furthermore, the rotational dynamics leading to switching tracks are visualized in detail. These first-time observations of cargo's rotational dynamics provide new insights on how kinesin and dynein motors take the cargo through the alternating stages of active directional transport and pause. To improve the localization precision of the SPT technique with DIC microscopy, a precise three-dimensional (3D) localization method of spherical gold nanoparticle probes using model-based correlation coefficient mapping was introduced. To accomplish this, a stack of sample images at different z-positions are acquired, and a 3D intensity profile of the probe serving as the model is used to map out the positions of nanoparticles in the sample. By using this model-based correlation imaging method, precise localization can be achieved in imaging techniques with complicated point spread functions (PSF) such as differential interference contrast (DIC) microscopy. The 3D superlocalization method was applied to tracking gold nanospheres during live endocytosis events. Finally, a novel dual-modality imaging technique has been developed to super-localize a single gold nanorod while providing its orientation and rotational information. The super-localization of the gold nanorod can be accomplished by curve fitting the modified bright-field images generated by one of the two beams laterally shifted by the first Nomarski prism in a DIC microscope. The orientation and rotational information is derived from the DIC images of gold nanorods. The new imaging setup has been applied to study the steric hindrance induced by relatively large cargos in the microtubule gliding assay and to track nanocargos in the crowded cellular environment.

Principles and biophysical applications of single particle super-localization and rotational tracking

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

Gu, Yan

While conventional Single Particle Tracking (SPT) techniques acquire 2D or 3D trajectories of particle probes, we have developed Single Particle Orientation and Rotational Tracking (SPORT) techniques to extract orientation and rotational information. Combined with DIC microscopy, the SPORT technique has been applied in biophysical studies, including membrane diffusion and intracellular transport. The rotational dynamics of nanoparticle vectors on live cell membranes was recorded and its influence on the fate of these nanoparticle vectors was elucidated. The rotational motions of gold nanorods with various surface modifiers were tracked continuously at a temporal resolution of 5 ms under a DIC microscope. Wemore » found that the rotational behaviors of gold nanorod vectors are strongly related to their surface charge, specific surface functional groups, and the availability of receptors on cell membranes. The study of rotational Brownian motion of nanoparticles on cell membranes will lead to a better understanding of the mechanisms of drug delivery and provide guidance in designing surface modification strategies for drug delivery vectors under various circumstances. To characterize the rotation mode of surface functionalized gold nanorods on cell membranes, the SPORT technique is combined with the correlation analysis of the bright and dark DIC intensities. The unique capabilities of visualizing and understanding rotational motions of functionalized nanoparticles on live cell membranes allow us to correlate rotational and translational dynamics in unprecedented detail and provide new insights for complex membrane processes, including electrostatic interactions, ligand-receptor binding, and lateral (confined and hopping) diffusion of membrane receptors. Surface-functionalized nanoparticles interact with the membrane in fundamentally different ways and exhibit distinct rotational modes. The early events of particle-membrane approach and attachment are directly visualized for the first time. The rotational dynamics of cargos in both active directional transport and pausing stages of axonal transport was also visualized using high-speed SPORT with a temporal resolution of 2 ms. Both long and short pauses are imaged, and the correlations between the pause duration, the rotational behaviour of the cargo at the pause, and the moving direction after the pause are established. Furthermore, the rotational dynamics leading to switching tracks are visualized in detail. These first-time observations of cargo's rotational dynamics provide new insights on how kinesin and dynein motors take the cargo through the alternating stages of active directional transport and pause. To improve the localization precision of the SPT technique with DIC microscopy, a precise three-dimensional (3D) localization method of spherical gold nanoparticle probes using model-based correlation coefficient mapping was introduced. To accomplish this, a stack of sample images at different z-positions are acquired, and a 3D intensity profile of the probe serving as the model is used to map out the positions of nanoparticles in the sample. By using this model-based correlation imaging method, precise localization can be achieved in imaging techniques with complicated point spread functions (PSF) such as differential interference contrast (DIC) microscopy. The 3D superlocalization method was applied to tracking gold nanospheres during live endocytosis events. Finally, a novel dual-modality imaging technique has been developed to super-localize a single gold nanorod while providing its orientation and rotational information. The super-localization of the gold nanorod can be accomplished by curve fitting the modified bright-field images generated by one of the two beams laterally shifted by the first Nomarski prism in a DIC microscope. The orientation and rotational information is derived from the DIC images of gold nanorods. The new imaging setup has been applied to study the steric hindrance induced by relatively large cargos in the microtubule gliding assay and to track nanocargos in the crowded cellular environment.« less

Road boundary detection

NASA Technical Reports Server (NTRS)

Sowers, J.; Mehrotra, R.; Sethi, I. K.

1989-01-01

A method for extracting road boundaries using the monochrome image of a visual road scene is presented. The statistical information regarding the intensity levels present in the image along with some geometrical constraints concerning the road are the basics of this approach. Results and advantages of this technique compared to others are discussed. The major advantages of this technique, when compared to others, are its ability to process the image in only one pass, to limit the area searched in the image using only knowledge concerning the road geometry and previous boundary information, and dynamically adjust for inconsistencies in the located boundary information, all of which helps to increase the efficacy of this technique.

Visualization of nanocrystal breathing modes at extreme strains

NASA Astrophysics Data System (ADS)

Szilagyi, Erzsi; Wittenberg, Joshua S.; Miller, Timothy A.; Lutker, Katie; Quirin, Florian; Lemke, Henrik; Zhu, Diling; Chollet, Matthieu; Robinson, Joseph; Wen, Haidan; Sokolowski-Tinten, Klaus; Lindenberg, Aaron M.

2015-03-01

Nanoscale dimensions in materials lead to unique electronic and structural properties with applications ranging from site-specific drug delivery to anodes for lithium-ion batteries. These functional properties often involve large-amplitude strains and structural modifications, and thus require an understanding of the dynamics of these processes. Here we use femtosecond X-ray scattering techniques to visualize, in real time and with atomic-scale resolution, light-induced anisotropic strains in nanocrystal spheres and rods. Strains at the percent level are observed in CdS and CdSe samples, associated with a rapid expansion followed by contraction along the nanosphere or nanorod radial direction driven by a transient carrier-induced stress. These morphological changes occur simultaneously with the first steps in the melting transition on hundreds of femtosecond timescales. This work represents the first direct real-time probe of the dynamics of these large-amplitude strains and shape changes in few-nanometre-scale particles.

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

Hartmann, Anja, E-mail: hartmann@ipk-gatersleben.de; Schreiber, Falk; Martin-Luther-University Halle-Wittenberg, Halle

The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the contextmore » of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM{sup 2} – Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.« less

A habituation based approach for detection of visual changes in surveillance camera

NASA Astrophysics Data System (ADS)

Sha'abani, M. N. A. H.; Adan, N. F.; Sabani, M. S. M.; Abdullah, F.; Nadira, J. H. S.; Yasin, M. S. M.

2017-09-01

This paper investigates a habituation based approach in detecting visual changes using video surveillance systems in a passive environment. Various techniques have been introduced for dynamic environment such as motion detection, object classification and behaviour analysis. However, in a passive environment, most of the scenes recorded by the surveillance system are normal. Therefore, implementing a complex analysis all the time in the passive environment resulting on computationally expensive, especially when using a high video resolution. Thus, a mechanism of attention is required, where the system only responds to an abnormal event. This paper proposed a novelty detection mechanism in detecting visual changes and a habituation based approach to measure the level of novelty. The objective of the paper is to investigate the feasibility of the habituation based approach in detecting visual changes. Experiment results show that the approach are able to accurately detect the presence of novelty as deviations from the learned knowledge.

Electron microscopy approach for the visualization of the epithelial and endothelial glycocalyx.

PubMed

Chevalier, L; Selim, J; Genty, D; Baste, J M; Piton, N; Boukhalfa, I; Hamzaoui, M; Pareige, P; Richard, V

2017-06-01

This study presents a methodological approach for the visualization of the glycocalyx by electron microscopy. The glycocalyx is a three dimensional network mainly composed of glycolipids, glycoproteins and proteoglycans associated with the plasma membrane. Since less than a decade, the epithelial and endothelial glycocalyx proved to play an important role in physiology and pathology, increasing its research interest especially in vascular functions. Therefore, visualization of the glycocalyx requires reliable techniques and its preservation remains challenging due to its fragile and dynamic organization, which is highly sensitive to the different process steps for electron microscopy sampling. In this study, chemical fixation was performed by perfusion as a good alternative to conventional fixation. Additional lanthanum nitrate in the fixative enhances staining of the glycocalyx in transmission electron microscopy bright field and improves its visualization by detecting the elastic scattered electrons, thus providing a chemical contrast. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Visual display aid for orbital maneuvering - Design considerations

NASA Technical Reports Server (NTRS)

Grunwald, Arthur J.; Ellis, Stephen R.

1993-01-01

This paper describes the development of an interactive proximity operations planning system that allows on-site planning of fuel-efficient multiburn maneuvers in a potential multispacecraft environment. Although this display system most directly assists planning by providing visual feedback to aid visualization of the trajectories and constraints, its most significant features include: (1) the use of an 'inverse dynamics' algorithm that removes control nonlinearities facing the operator, and (2) a trajectory planning technique that separates, through a 'geometric spreadsheet', the normally coupled complex problems of planning orbital maneuvers and allows solution by an iterative sequence of simple independent actions. The visual feedback of trajectory shapes and operational constraints, provided by user-transparent and continuously active background computations, allows the operator to make fast, iterative design changes that rapidly converge to fuel-efficient solutions. The planning tool provides an example of operator-assisted optimization of nonlinear cost functions.

Multi-scale volumetric cell and tissue imaging based on optical projection tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ban, Sungbea; Cho, Nam Hyun; Ryu, Yongjae; Jung, Sunwoo; Vavilin, Andrey; Min, Eunjung; Jung, Woonggyu

2016-04-01

Optical projection tomography is a new optical imaging method for visualizing small biological specimens in three dimension. The most important advantage of OPT is to fill the gap between MRI and confocal microscope for the specimen having the range of 1-10 mm. Thus, it has been mainly used for whole-mount small animals and developmental study since this imaging modality was developed. The ability of OPT delivering anatomical and functional information of relatively large tissue in 3D has made it a promising platform in biomedical research. Recently, the potential of OPT spans its coverage to cellular scale. Even though there are increasing demand to obtain better understanding of cellular dynamics, only few studies to visualize cellular structure, shape, size and functional morphology over tissue has been investigated in existing OPT system due to its limited field of view. In this study, we develop a novel optical imaging system for 3D cellular imaging with OPT integrated with dynamic focusing technique. Our tomographic setup has great potential to be used for identifying cell characteristic in tissue because it can provide selective contrast on dynamic focal plane allowing for fluorescence as well as absorption. While the dominant contrast of optical imaging technique is to use the fluorescence for detecting certain target only, the newly developed OPT system will offer considerable advantages over currently available method when imaging cellar molecular dynamics by permitting contrast variation. By achieving multi-contrast, it is expected for this new imaging system to play an important role in delivering better cytological information to pathologist.

Modeling and visualizing cell type switching.

PubMed

Ghaffarizadeh, Ahmadreza; Podgorski, Gregory J; Flann, Nicholas S

2014-01-01

Understanding cellular differentiation is critical in explaining development and for taming diseases such as cancer. Differentiation is conventionally represented using bifurcating lineage trees. However, these lineage trees cannot readily capture or quantify all the types of transitions now known to occur between cell types, including transdifferentiation or differentiation off standard paths. This work introduces a new analysis and visualization technique that is capable of representing all possible transitions between cell states compactly, quantitatively, and intuitively. This method considers the regulatory network of transcription factors that control cell type determination and then performs an analysis of network dynamics to identify stable expression profiles and the potential cell types that they represent. A visualization tool called CellDiff3D creates an intuitive three-dimensional graph that shows the overall direction and probability of transitions between all pairs of cell types within a lineage. In this study, the influence of gene expression noise and mutational changes during myeloid cell differentiation are presented as a demonstration of the CellDiff3D technique, a new approach to quantify and envision all possible cell state transitions in any lineage network.

Identification of visual evoked response parameters sensitive to pilot mental state

NASA Technical Reports Server (NTRS)

Zacharias, G. L.

1988-01-01

Systems analysis techniques were developed and demonstrated for modeling the electroencephalographic (EEG) steady state visual evoked response (ssVER), for use in EEG data compression and as an indicator of mental workload. The study focused on steady state frequency domain stimulation and response analysis, implemented with a sum-of-sines (SOS) stimulus generator and an off-line describing function response analyzer. Three major tasks were conducted: (1) VER related systems identification material was reviewed; (2) Software for experiment control and data analysis was developed and implemented; and (3) ssVER identification and modeling was demonstrated, via a mental loading experiment. It was found that a systems approach to ssVER functional modeling can serve as the basis for eventual development of a mental workload indicator. The review showed how transient visual evoked response (tVER) and ssVER research are related at the functional level, the software development showed how systems techniques can be used for ssVER characterization, and the pilot experiment showed how a simple model can be used to capture the basic dynamic response of the ssVER, under varying loads.

Seeing the Song: Left Auditory Structures May Track Auditory-Visual Dynamic Alignment

PubMed Central

Mossbridge, Julia A.; Grabowecky, Marcia; Suzuki, Satoru

2013-01-01

Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements), it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization) across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR) was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment. PMID:24194873

Evaluation of Static vs. Dynamic Visualizations for Engineering Technology Students and Implications on Spatial Visualization Ability: A Quasi-Experimental Study

ERIC Educational Resources Information Center

Katsioloudis, Petros; Dickerson, Daniel; Jovanovic, Vukica; Jones, Mildred

2015-01-01

The benefit of using static versus dynamic visualizations is a controversial one. Few studies have explored the effectiveness of static visualizations to those of dynamic visualizations, and the current state of the literature remains somewhat unclear. During the last decade there has been a lengthy debate about the opportunities for using…

Visualizing the spinal neuronal dynamics of locomotion

NASA Astrophysics Data System (ADS)

Subramanian, Kalpathi R.; Bashor, D. P.; Miller, M. T.; Foster, J. A.

2004-06-01

Modern imaging and simulation techniques have enhanced system-level understanding of neural function. In this article, we present an application of interactive visualization to understanding neuronal dynamics causing locomotion of a single hip joint, based on pattern generator output of the spinal cord. Our earlier work visualized cell-level responses of multiple neuronal populations. However, the spatial relationships were abstract, making communication with colleagues difficult. We propose two approaches to overcome this: (1) building a 3D anatomical model of the spinal cord with neurons distributed inside, animated by the simulation and (2) adding limb movements predicted by neuronal activity. The new system was tested using a cat walking central pattern generator driving a pair of opposed spinal motoneuron pools. Output of opposing motoneuron pools was combined into a single metric, called "Net Neural Drive", which generated angular limb movement in proportion to its magnitude. Net neural drive constitutes a new description of limb movement control. The combination of spatial and temporal information in the visualizations elegantly conveys the neural activity of the output elements (motoneurons), as well as the resulting movement. The new system encompasses five biological levels of organization from ion channels to observed behavior. The system is easily scalable, and provides an efficient interactive platform for rapid hypothesis testing.

Visualization of DNA molecules in time during electrophoresis

NASA Technical Reports Server (NTRS)

Lubega, Seth

1991-01-01

For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.

Visual exploration and analysis of human-robot interaction rules

NASA Astrophysics Data System (ADS)

Zhang, Hui; Boyles, Michael J.

2013-01-01

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

Design and implementation of a PC-based image-guided surgical system.

PubMed

Stefansic, James D; Bass, W Andrew; Hartmann, Steven L; Beasley, Ryan A; Sinha, Tuhin K; Cash, David M; Herline, Alan J; Galloway, Robert L

2002-11-01

In interactive, image-guided surgery, current physical space position in the operating room is displayed on various sets of medical images used for surgical navigation. We have developed a PC-based surgical guidance system (ORION) which synchronously displays surgical position on up to four image sets and updates them in real time. There are three essential components which must be developed for this system: (1) accurately tracked instruments; (2) accurate registration techniques to map physical space to image space; and (3) methods to display and update the image sets on a computer monitor. For each of these components, we have developed a set of dynamic link libraries in MS Visual C++ 6.0 supporting various hardware tools and software techniques. Surgical instruments are tracked in physical space using an active optical tracking system. Several of the different registration algorithms were developed with a library of robust math kernel functions, and the accuracy of all registration techniques was thoroughly investigated. Our display was developed using the Win32 API for windows management and tomographic visualization, a frame grabber for live video capture, and OpenGL for visualization of surface renderings. We have begun to use this current implementation of our system for several surgical procedures, including open and minimally invasive liver surgery.

How Temporal and Spatial Aspects of Presenting Visualizations Affect Learning about Locomotion Patterns

ERIC Educational Resources Information Center

Imhof, Birgit; Scheiter, Katharina; Edelmann, Jorg; Gerjets, Peter

2012-01-01

Two studies investigated the effectiveness of dynamic and static visualizations for a perceptual learning task (locomotion pattern classification). In Study 1, seventy-five students viewed either dynamic, static-sequential, or static-simultaneous visualizations. For tasks of intermediate difficulty, dynamic visualizations led to better…

Cardiovascular cine imaging and flow evaluation using Fast Interrupted Steady-State (FISS) magnetic resonance.

PubMed

Edelman, Robert R; Serhal, Ali; Pursnani, Amit; Pang, Jianing; Koktzoglou, Ioannis

2018-02-19

Existing cine imaging techniques rely on balanced steady-state free precession (bSSFP) or spoiled gradient-echo readouts, each of which has limitations. For instance, with bSSFP, artifacts occur from rapid through-plane flow and off-resonance effects. We hypothesized that a prototype cine technique, radial fast interrupted steady-state (FISS), could overcome these limitations. The technique was compared with standard cine bSSFP for cardiac function, coronary artery conspicuity, and aortic valve morphology. Given its advantageous properties, we further hypothesized that the cine FISS technique, in combination with arterial spin labeling (ASL), could provide an alternative to phase contrast for visualizing in-plane flow patterns within the aorta and branch vessels. The study was IRB-approved and subjects provided consent. Breath-hold cine FISS and bSSFP were acquired using similar imaging parameters. There was no significant difference in biplane left ventricular ejection fraction or cardiac image quality between the two techniques. Compared with cine bSSFP, cine FISS demonstrated a marked decrease in fat signal which improved conspicuity of the coronary arteries, while suppression of through-plane flow artifact on thin-slice cine FISS images improved visualization of the aortic valve. Banding artifacts in the subcutaneous tissues were reduced. In healthy subjects, dynamic flow patterns were well visualized in the aorta, coronary and renal arteries using cine FISS ASL, even when the slice was substantially thicker than the vessel diameter. Cine FISS demonstrates several benefits for cardiovascular imaging compared with cine bSSFP, including better suppression of fat signal and reduced artifacts from through-plane flow and off-resonance effects. The main drawback is a slight (~ 20%) decrease in temporal resolution. In addition, preliminary results suggest that cine FISS ASL provides a potential alternative to phase contrast techniques for in-plane flow quantification, while enabling an efficient, visually-appealing, semi-projective display of blood flow patterns throughout the course of an artery and its branches.

Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

PubMed

Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

2015-12-01

Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

An Advanced Framework for Improving Situational Awareness in Electric Power Grid Operation

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

Chen, Yousu; Huang, Zhenyu; Zhou, Ning

With the deployment of new smart grid technologies and the penetration of renewable energy in power systems, significant uncertainty and variability is being introduced into power grid operation. Traditionally, the Energy Management System (EMS) operates the power grid in a deterministic mode, and thus will not be sufficient for the future control center in a stochastic environment with faster dynamics. One of the main challenges is to improve situational awareness. This paper reviews the current status of power grid operation and presents a vision of improving wide-area situational awareness for a future control center. An advanced framework, consisting of parallelmore » state estimation, state prediction, parallel contingency selection, parallel contingency analysis, and advanced visual analytics, is proposed to provide capabilities needed for better decision support by utilizing high performance computing (HPC) techniques and advanced visual analytic techniques. Research results are presented to support the proposed vision and framework.« less

Exciplex Fluorescence Systems for Two-Phase Visualization.

NASA Astrophysics Data System (ADS)

Kim, J.-U.; Golding, B.; Schock, H. J.; Nocera, D. G.; Keller, P.

1996-03-01

We report the development of diagnostic chemical systems for vapor-liquid visualization based on an exciplex (excited state complex) formed between dimethyl- or diethyl-substituted aniline and trimethyl-substituted naphthalenes. Quantum yields of individual monomers were measured and the exciplex emission spectra as well as fluorescence quenching mechanisms were analyzed. Quenching occurs by both static and dynamic mechanisms. Among the many formulations investigated in this study, a system consisting of 7% 1,4,6-trimethylnaphthalene (1,4,6-TMN) and 5% N,N-dimethylaniline (DMA) in 88% isooctane exciplex was found to be useful for the laser- induced fluorescence technique. The technique is expected to find application in observing mixture formation in diesel or spark ignition engines with spectrally well-separated fluorescence images obtained from the monomer and exciplex constituents dissolved in the gasoline fuel. *Supported by NSF MRSEC DMR-9400417 and the Center for Fundamental Materials Research.

Ultrasound-assisted endoscopic partial plantar fascia release.

PubMed

Ohuchi, Hiroshi; Ichikawa, Ken; Shinga, Kotaro; Hattori, Soichi; Yamada, Shin; Takahashi, Kazuhisa

2013-01-01

Various surgical treatment procedures for plantar fasciitis, such as open surgery, percutaneous release, and endoscopic surgery, exist. Skin trouble, nerve disturbance, infection, and persistent pain associated with prolonged recovery time are complications of open surgery. Endoscopic partial plantar fascia release offers the surgeon clear visualization of the anatomy at the surgical site. However, the primary medial portal and portal tract used for this technique have been shown to be in close proximity to the posterior tibial nerves and their branches, and there is always the risk of nerve damage by introducing the endoscope deep to the plantar fascia. By performing endoscopic partial plantar fascia release under ultrasound assistance, we could dynamically visualize the direction of the endoscope and instrument introduction, thus preventing nerve damage from inadvertent insertion deep to the fascia. Full-thickness release of the plantar fascia at the ideal position could also be confirmed under ultrasound imaging. We discuss the technique for this new procedure.

Ultrasound-Assisted Endoscopic Partial Plantar Fascia Release

PubMed Central

Ohuchi, Hiroshi; Ichikawa, Ken; Shinga, Kotaro; Hattori, Soichi; Yamada, Shin; Takahashi, Kazuhisa

2013-01-01

Various surgical treatment procedures for plantar fasciitis, such as open surgery, percutaneous release, and endoscopic surgery, exist. Skin trouble, nerve disturbance, infection, and persistent pain associated with prolonged recovery time are complications of open surgery. Endoscopic partial plantar fascia release offers the surgeon clear visualization of the anatomy at the surgical site. However, the primary medial portal and portal tract used for this technique have been shown to be in close proximity to the posterior tibial nerves and their branches, and there is always the risk of nerve damage by introducing the endoscope deep to the plantar fascia. By performing endoscopic partial plantar fascia release under ultrasound assistance, we could dynamically visualize the direction of the endoscope and instrument introduction, thus preventing nerve damage from inadvertent insertion deep to the fascia. Full-thickness release of the plantar fascia at the ideal position could also be confirmed under ultrasound imaging. We discuss the technique for this new procedure. PMID:24265989

Development and Application of PIV in Supersonic flows

NASA Astrophysics Data System (ADS)

Rong, Z.; Liu, H.; Chen, F.

2011-09-01

This paper presents PIV measurements obtained in Mach 4.0 flowfields performed in the SJTU Hypersonic wind tunnel (HWT). In order to certificate this technique, PIV experiments were conducted to the empty test section to provide uniform flow data for comparison with analysis data. Dynamical properties of particle tracers were investigated to measure the particle response across an oblique shock wave. The flow over a sharp cone at Ma = 4.0 were tested in comparasion with the CFD and schlieren visualization. It is shown that shock wave angles measured with PIV are in good agreement with theory and schlieren visualization, in addition the overall flow is consistent with the CFD results.

Visualizing Breath using Digital Holography

NASA Astrophysics Data System (ADS)

Hobson, P. R.; Reid, I. D.; Wilton, J. B.

2013-02-01

Artist Jayne Wilton and physicists Peter Hobson and Ivan Reid of Brunel University are collaborating at Brunel University on a project which aims to use a range of techniques to make visible the normally invisible dynamics of the breath and the verbal and non-verbal communication it facilitates. The breath is a source of a wide range of chemical, auditory and physical exchanges with the direct environment. Digital Holography is being investigated to enable a visually stimulating articulation of the physical trajectory of the breath as it leaves the mouth. Initial findings of this research are presented. Real time digital hologram replay allows the audience to move through holographs of breath-born particles.

The role of visual representation in physics learning: dynamic versus static visualization

NASA Astrophysics Data System (ADS)

Suyatna, Agus; Anggraini, Dian; Agustina, Dina; Widyastuti, Dini

2017-11-01

This study aims to examine the role of visual representation in physics learning and to compare the learning outcomes of using dynamic and static visualization media. The study was conducted using quasi-experiment with Pretest-Posttest Control Group Design. The samples of this research are students of six classes at State Senior High School in Lampung Province. The experimental class received a learning using dynamic visualization and control class using static visualization media. Both classes are given pre-test and post-test with the same instruments. Data were tested with N-gain analysis, normality test, homogeneity test and mean difference test. The results showed that there was a significant increase of mean (N-Gain) learning outcomes (p <0.05) in both experimental and control classes. The averages of students’ learning outcomes who are using dynamic visualization media are significantly higher than the class that obtains learning by using static visualization media. It can be seen from the characteristics of visual representation; each visualization provides different understanding support for the students. Dynamic visual media is more suitable for explaining material related to movement or describing a process, whereas static visual media is appropriately used for non-moving physical phenomena and requires long-term observation.

Hypervelocity Technology Escape System Concepts. Volume 1. Development and Evaluation

DTIC Science & Technology

1988-07-01

airplane escape systems. These include separation at high dynamic pressure, stability, impact attenuation , crew member accelerations, adequate...changes (TTS; 0 Shock attenuator design PTS) 0 Restraint system design * Limb flail * Non-auditory changes (gag, dec. visual acuity) * Reduced psycho-motor...detected by ultrasonic technique. The DCS symptoms may not appear until at slightly lower total pressures (8 N psia - 9 pals). Since the pressurization

Polymer physics experiments with single DNA molecules

NASA Astrophysics Data System (ADS)

Smith, Douglas E.

1999-11-01

Bacteriophage DNA molecules were taken as a model flexible polymer chain for the experimental study of polymer dynamics at the single molecule level. Video fluorescence microscopy was used to directly observe the conformational dynamics of fluorescently labeled molecules, optical tweezers were used to manipulate individual molecules, and micro-fabricated flow cells were used to apply controlled hydrodynamic strain to molecules. These techniques constitute a powerful new experimental approach in the study of basic polymer physics questions. I have used these techniques to study the diffusion and relaxation of isolated and entangled polymer molecules and the hydrodynamic deformation of polymers in elongational and shear flows. These studies revealed a rich, and previously unobserved, ``molecular individualism'' in the dynamical behavior of single molecules. Individual measurements on ensembles of identical molecules allowed the average conformation to be determined as well as the underlying probability distributions for molecular conformation. Scaling laws, that predict the dependence of properties on chain length and concentration, were also tested. The basic assumptions of the reptation model were directly confirmed by visualizing the dynamics of entangled chains.

Nanoscale live cell optical imaging of the dynamics of intracellular microvesicles in neural cells.

PubMed

Lee, Sohee; Heo, Chaejeong; Suh, Minah; Lee, Young Hee

2013-11-01

Recent advances in biotechnology and imaging technology have provided great opportunities to investigate cellular dynamics. Conventional imaging methods such as transmission electron microscopy, scanning electron microscopy, and atomic force microscopy are powerful techniques for cellular imaging, even at the nanoscale level. However, these techniques have limitations applications in live cell imaging because of the experimental preparation required, namely cell fixation, and the innately small field of view. In this study, we developed a nanoscale optical imaging (NOI) system that combines a conventional optical microscope with a high resolution dark-field condenser (Cytoviva, Inc.) and halogen illuminator. The NOI system's maximum resolution for live cell imaging is around 100 nm. We utilized NOI to investigate the dynamics of intracellular microvesicles of neural cells without immunocytological analysis. In particular, we studied direct, active random, and moderate random dynamic motions of intracellular microvesicles and visualized lysosomal vesicle changes after treatment of cells with a lysosomal inhibitor (NH4Cl). Our results indicate that the NOI system is a feasible, high-resolution optical imaging system for live small organelles that does not require complicated optics or immunocytological staining processes.

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport.

PubMed

Kaplan, Luke; Ierokomos, Athena; Chowdary, Praveen; Bryant, Zev; Cui, Bianxiao

2018-03-01

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors.

Dynamic Load Balancing Based on Constrained K-D Tree Decomposition for Parallel Particle Tracing

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

Zhang, Jiang; Guo, Hanqi; Yuan, Xiaoru

Particle tracing is a fundamental technique in flow field data visualization. In this work, we present a novel dynamic load balancing method for parallel particle tracing. Specifically, we employ a constrained k-d tree decomposition approach to dynamically redistribute tasks among processes. Each process is initially assigned a regularly partitioned block along with duplicated ghost layer under the memory limit. During particle tracing, the k-d tree decomposition is dynamically performed by constraining the cutting planes in the overlap range of duplicated data. This ensures that each process is reassigned particles as even as possible, and on the other hand the newmore » assigned particles for a process always locate in its block. Result shows good load balance and high efficiency of our method.« less

The NASA Langley Isolator Dynamics Research Lab

NASA Technical Reports Server (NTRS)

Middleton, Troy F.; Balla, Robert J.; Baurle, Robert A.; Humphreys, William M.; Wilson, Lloyd G.

2010-01-01

The Isolator Dynamics Research Lab (IDRL) is under construction at the NASA Langley Research Center in Hampton, Virginia. A unique test apparatus is being fabricated to support both wall and in-stream measurements for investigating the internal flow of a dual-mode scramjet isolator model. The test section is 24 inches long with a 1-inch by 2-inch cross sectional area and is supplied with unheated, dry air through a Mach 2.5 converging-diverging nozzle. The test section is being fabricated with two sets (glass and metallic) of interchangeable sidewalls to support flow visualization and laser-based measurement techniques as well as static pressure, wall temperature, and high frequency pressure measurements. During 2010, a CFD code validation experiment will be conducted in the lab in support of NASA s Fundamental Aerodynamics Program. This paper describes the mechanical design of the Isolator Dynamics Research Lab test apparatus and presents a summary of the measurement techniques planned for investigating the internal flow field of a scramjet isolator model.

Real-time intravital microscopy of individual nanoparticle dynamics in liver and tumors of live mice

PubMed Central

van de Ven, Anne L; Kim, Pilhan; Ferrari, Mauro; Yun, Seok Hyun

2013-01-01

Intravital microscopy is emerging as an important experimental tool for the research and development of multi-functional therapeutic nanoconstructs. The direct visualization of nanoparticle dynamics within live animals provides invaluable insights into the mechanisms that regulate nanotherapeutics transport and cell-particle interactions. Here we present a protocol to image the dynamics of nanoparticles within the liver and tumors of live mice immediately following systemic injection using a high-speed (30-400 fps) confocal or multi-photon laser-scanning fluorescence microscope. Techniques for quantifying the real-time accumulation and cellular association of individual particles with a size ranging from several tens of nanometers to micrometers are described, as well as an experimental strategy for labeling Kupffer cells in the liver in vivo. Experimental design considerations and controls are provided, as well as minimum equipment requirements. The entire protocol takes approximately 4-8 hours and yields quantitative information. These techniques can serve to study a wide range of kinetic parameters that drive nanotherapeutics delivery, uptake, and treatment response. PMID:25383179

Intravascular perfusion of carbon black ink allows reliable visualization of cerebral vessels.

PubMed

Hasan, Mohammad R; Herz, Josephine; Hermann, Dirk M; Doeppner, Thorsten R

2013-01-04

The anatomical structure of cerebral vessels is a key determinant for brain hemodynamics as well as the severity of injury following ischemic insults. The cerebral vasculature dynamically responds to various pathophysiological states and it exhibits considerable differences between strains and under conditions of genetic manipulations. Essentially, a reliable technique for intracranial vessel staining is essential in order to study the pathogenesis of ischemic stroke. Until recently, a set of different techniques has been employed to visualize the cerebral vasculature including injection of low viscosity resin, araldite F, gelatin mixed with various dyes (i.e. carmine red, India ink) or latex with or without carbon black. Perfusion of white latex compound through the ascending aorta has been first reported by Coyle and Jokelainen. Maeda et al. have modified the protocol by adding carbon black ink to the latex compound for improved contrast visualization of the vessels after saline perfusion of the brain. However, inefficient perfusion and inadequate filling of the vessels are frequently experienced due to high viscosity of the latex compound. Therefore, we have described a simple and cost-effective technique using a mixture of two commercially available carbon black inks (CB1 and CB2) to visualize the cerebral vasculature in a reproducible manner. We have shown that perfusion with CB1+CB2 in mice results in staining of significantly smaller cerebral vessels at a higher density in comparison to latex perfusion. Here, we describe our protocol to identify the anastomotic points between the anterior (ACA) and middle cerebral arteries (MCA) to study vessel variations in mice with different genetic backgrounds. Finally, we demonstrate the feasibility of our technique in a transient focal cerebral ischemia model in mice by combining CB1+CB2-mediated vessel staining with TTC staining in various degrees of ischemic injuries.

Visual Vestibular Interaction in the Dynamic Visual Acuity Test during Voluntary Head Rotation

NASA Technical Reports Server (NTRS)

Lee, Moo Hoon; Durnford, Simon; Crowley, John; Rupert, Angus

1996-01-01

Although intact vestibular function is essential in maintaining spatial orientation, no good screening tests of vestibular function are available to the aviation community. High frequency voluntary head rotation was selected as a vestibular stimulus to isolate the vestibulo-ocular reflex (VOR) from visual influence. A dynamic visual acuity test that incorporates voluntary head rotation was evaluated as a potential vestibular function screening tool. Twenty-seven normal subjects performed voluntary sinusoidal head rotation at frequencies from 0.7-4.0 Hz under three different visual conditions: visually-enhanced VOR, normal VOR, and visually suppressed VOR. Standardized Baily-Lovie chart letters were presented on a computer monitor in front of the subject, who then was asked to read the letters while rotating his head horizontally. The electro-oculogram and dynamic visual acuity score were recorded and analyzed. There were no significant differences in gain or phase shift among three visual conditions in the frequency range of 2.8 to 4.0 Hz. The dynamic visual acuity score shifted less than 0.3 logMAR at frequencies under 2.0 Hz. The dynamic visual acuity test at frequencies a round 2.0 Hz can be recommended for evaluating vestibular function.

Additional helmet and pack loading reduce situational awareness during the establishment of marksmanship posture.

PubMed

Lim, Jongil; Palmer, Christopher J; Busa, Michael A; Amado, Avelino; Rosado, Luis D; Ducharme, Scott W; Simon, Darnell; Van Emmerik, Richard E A

2017-06-01

The pickup of visual information is critical for controlling movement and maintaining situational awareness in dangerous situations. Altered coordination while wearing protective equipment may impact the likelihood of injury or death. This investigation examined the consequences of load magnitude and distribution on situational awareness, segmental coordination and head gaze in several protective equipment ensembles. Twelve soldiers stepped down onto force plates and were instructed to quickly and accurately identify visual information while establishing marksmanship posture in protective equipment. Time to discriminate visual information was extended when additional pack and helmet loads were added, with the small increase in helmet load having the largest effect. Greater head-leading and in-phase trunk-head coordination were found with lighter pack loads, while trunk-leading coordination increased and head gaze dynamics were more disrupted in heavier pack loads. Additional armour load in the vest had no consequences for Time to discriminate, coordination or head dynamics. This suggests that the addition of head borne load be carefully considered when integrating new technology and that up-armouring does not necessarily have negative consequences for marksmanship performance. Practitioner Summary: Understanding the trade-space between protection and reductions in task performance continue to challenge those developing personal protective equipment. These methods provide an approach that can help optimise equipment design and loading techniques by quantifying changes in task performance and the emergent coordination dynamics that underlie that performance.

Top-down influences on visual attention during listening are modulated by observer sex.

PubMed

Shen, John; Itti, Laurent

2012-07-15

In conversation, women have a small advantage in decoding non-verbal communication compared to men. In light of these findings, we sought to determine whether sex differences also existed in visual attention during a related listening task, and if so, if the differences existed among attention to high-level aspects of the scene or to conspicuous visual features. Using eye-tracking and computational techniques, we present direct evidence that men and women orient attention differently during conversational listening. We tracked the eyes of 15 men and 19 women who watched and listened to 84 clips featuring 12 different speakers in various outdoor settings. At the fixation following each saccadic eye movement, we analyzed the type of object that was fixated. Men gazed more often at the mouth and women at the eyes of the speaker. Women more often exhibited "distracted" saccades directed away from the speaker and towards a background scene element. Examining the multi-scale center-surround variation in low-level visual features (static: color, intensity, orientation, and dynamic: motion energy), we found that men consistently selected regions which expressed more variation in dynamic features, which can be attributed to a male preference for motion and a female preference for areas that may contain nonverbal information about the speaker. In sum, significant differences were observed, which we speculate arise from different integration strategies of visual cues in selecting the final target of attention. Our findings have implications for studies of sex in nonverbal communication, as well as for more predictive models of visual attention. Published by Elsevier Ltd.

Semantics by analogy for illustrative volume visualization☆

PubMed Central

Gerl, Moritz; Rautek, Peter; Isenberg, Tobias; Gröller, Eduard

2012-01-01

We present an interactive graphical approach for the explicit specification of semantics for volume visualization. This explicit and graphical specification of semantics for volumetric features allows us to visually assign meaning to both input and output parameters of the visualization mapping. This is in contrast to the implicit way of specifying semantics using transfer functions. In particular, we demonstrate how to realize a dynamic specification of semantics which allows to flexibly explore a wide range of mappings. Our approach is based on three concepts. First, we use semantic shader augmentation to automatically add rule-based rendering functionality to static visualization mappings in a shader program, while preserving the visual abstraction that the initial shader encodes. With this technique we extend recent developments that define a mapping between data attributes and visual attributes with rules, which are evaluated using fuzzy logic. Second, we let users define the semantics by analogy through brushing on renderings of the data attributes of interest. Third, the rules are specified graphically in an interface that provides visual clues for potential modifications. Together, the presented methods offer a high degree of freedom in the specification and exploration of rule-based mappings and avoid the limitations of a linguistic rule formulation. PMID:23576827

GLO-STIX: Graph-Level Operations for Specifying Techniques and Interactive eXploration

PubMed Central

Stolper, Charles D.; Kahng, Minsuk; Lin, Zhiyuan; Foerster, Florian; Goel, Aakash; Stasko, John; Chau, Duen Horng

2015-01-01

The field of graph visualization has produced a wealth of visualization techniques for accomplishing a variety of analysis tasks. Therefore analysts often rely on a suite of different techniques, and visual graph analysis application builders strive to provide this breadth of techniques. To provide a holistic model for specifying network visualization techniques (as opposed to considering each technique in isolation) we present the Graph-Level Operations (GLO) model. We describe a method for identifying GLOs and apply it to identify five classes of GLOs, which can be flexibly combined to re-create six canonical graph visualization techniques. We discuss advantages of the GLO model, including potentially discovering new, effective network visualization techniques and easing the engineering challenges of building multi-technique graph visualization applications. Finally, we implement the GLOs that we identified into the GLO-STIX prototype system that enables an analyst to interactively explore a graph by applying GLOs. PMID:26005315

Bandwidth and SIMDUCE as simulator fidelity criteria

NASA Technical Reports Server (NTRS)

Key, David

1992-01-01

The potential application of two concepts from the new Handling Qualities Specification for Military Rotorcraft was discussed. The first concept is bandwidth, a measure of the dynamic response to control. The second is a qualitative technique developed for assessing the visual cue environment the pilot has in bad weather and at night. Simulated Day Usable Cue Environment (SIMDUCE) applies this concept to assessing the day cuing fidelity in the simulator.

Visualization Techniques Applied to 155-mm Projectile Analysis

DTIC Science & Technology

2014-11-01

semi-infinite Riemann problems are used in CFD++ to provide upwind flux information to the underlying transport scheme. Approximate Riemann solvers ...characteristics-based inflow/outflow boundary condition, which is based on solving a Riemann problem at the boundary. 2.3 Numerics Rolling/spinning is the...the solution files generated by the computational fluid dynamics (CFD) solver for the time-accurate rolling simulations at each timestep for the Mach

Expressive facial animation synthesis by learning speech coarticulation and expression spaces.

PubMed

Deng, Zhigang; Neumann, Ulrich; Lewis, J P; Kim, Tae-Yong; Bulut, Murtaza; Narayanan, Shrikanth

2006-01-01

Synthesizing expressive facial animation is a very challenging topic within the graphics community. In this paper, we present an expressive facial animation synthesis system enabled by automated learning from facial motion capture data. Accurate 3D motions of the markers on the face of a human subject are captured while he/she recites a predesigned corpus, with specific spoken and visual expressions. We present a novel motion capture mining technique that "learns" speech coarticulation models for diphones and triphones from the recorded data. A Phoneme-Independent Expression Eigenspace (PIEES) that encloses the dynamic expression signals is constructed by motion signal processing (phoneme-based time-warping and subtraction) and Principal Component Analysis (PCA) reduction. New expressive facial animations are synthesized as follows: First, the learned coarticulation models are concatenated to synthesize neutral visual speech according to novel speech input, then a texture-synthesis-based approach is used to generate a novel dynamic expression signal from the PIEES model, and finally the synthesized expression signal is blended with the synthesized neutral visual speech to create the final expressive facial animation. Our experiments demonstrate that the system can effectively synthesize realistic expressive facial animation.

Malware Analysis Using Visualized Image Matrices

PubMed Central

Im, Eul Gyu

2014-01-01

This paper proposes a novel malware visual analysis method that contains not only a visualization method to convert binary files into images, but also a similarity calculation method between these images. The proposed method generates RGB-colored pixels on image matrices using the opcode sequences extracted from malware samples and calculates the similarities for the image matrices. Particularly, our proposed methods are available for packed malware samples by applying them to the execution traces extracted through dynamic analysis. When the images are generated, we can reduce the overheads by extracting the opcode sequences only from the blocks that include the instructions related to staple behaviors such as functions and application programming interface (API) calls. In addition, we propose a technique that generates a representative image for each malware family in order to reduce the number of comparisons for the classification of unknown samples and the colored pixel information in the image matrices is used to calculate the similarities between the images. Our experimental results show that the image matrices of malware can effectively be used to classify malware families both statically and dynamically with accuracy of 0.9896 and 0.9732, respectively. PMID:25133202

Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos.

PubMed

Zhao, Ziqing W; White, Melanie D; Bissiere, Stephanie; Levi, Valeria; Plachta, Nicolas

2016-12-23

Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.

Voltage-sensitive dye imaging of transcranial magnetic stimulation-induced intracortical dynamics

PubMed Central

Kozyrev, Vladislav; Eysel, Ulf T.; Jancke, Dirk

2014-01-01

Transcranial magnetic stimulation (TMS) is widely used in clinical interventions and basic neuroscience. Additionally, it has become a powerful tool to drive plastic changes in neuronal networks. However, highly resolved recordings of the immediate TMS effects have remained scarce, because existing recording techniques are limited in spatial or temporal resolution or are interfered with by the strong TMS-induced electric field. To circumvent these constraints, we performed optical imaging with voltage-sensitive dye (VSD) in an animal experimental setting using anaesthetized cats. The dye signals reflect gradual changes in the cells' membrane potential across several square millimeters of cortical tissue, thus enabling direct visualization of TMS-induced neuronal population dynamics. After application of a single TMS pulse across visual cortex, brief focal activation was immediately followed by synchronous suppression of a large pool of neurons. With consecutive magnetic pulses (10 Hz), widespread activity within this “basin of suppression” increased stepwise to suprathreshold levels and spontaneous activity was enhanced. Visual stimulation after repetitive TMS revealed long-term potentiation of evoked activity. Furthermore, loss of the “deceleration–acceleration” notch during the rising phase of the response, as a signature of fast intracortical inhibition detectable with VSD imaging, indicated weakened inhibition as an important driving force of increasing cortical excitability. In summary, our data show that high-frequency TMS changes the balance between excitation and inhibition in favor of an excitatory cortical state. VSD imaging may thus be a promising technique to trace TMS-induced changes in excitability and resulting plastic processes across cortical maps with high spatial and temporal resolutions. PMID:25187557

EDITORIAL: Focus on Visualization in Physics FOCUS ON VISUALIZATION IN PHYSICS

NASA Astrophysics Data System (ADS)

Sanders, Barry C.; Senden, Tim; Springel, Volker

2008-12-01

Advances in physics are intimately connected with developments in a new technology, the telescope, precision clocks, even the computer all have heralded a shift in thinking. These landmark developments open new opportunities accelerating research and in turn new scientific directions. These technological drivers often correspond to new instruments, but equally might just as well flag a new mathematical tool, an algorithm or even means to visualize physics in a new way. Early on in this twenty-first century, scientific communities are just starting to explore the potential of digital visualization. Whether visualization is used to represent and communicate complex concepts, or to understand and interpret experimental data, or to visualize solutions to complex dynamical equations, the basic tools of visualization are shared in each of these applications and implementations. High-performance computing exemplifies the integration of visualization with leading research. Visualization is an indispensable tool for analyzing and interpreting complex three-dimensional dynamics as well as to diagnose numerical problems in intricate parallel calculation algorithms. The effectiveness of visualization arises by exploiting the unmatched capability of the human eye and visual cortex to process the large information content of images. In a brief glance, we recognize patterns or identify subtle features even in noisy data, something that is difficult or impossible to achieve with more traditional forms of data analysis. Importantly, visualizations guide the intuition of researchers and help to comprehend physical phenomena that lie far outside of direct experience. In fact, visualizations literally allow us to see what would otherwise remain completely invisible. For example, artificial imagery created to visualize the distribution of dark matter in the Universe has been instrumental to develop the notion of a cosmic web, and for helping to establish the current standard model of cosmology wherein this (in principle invisible) dark matter dominates the cosmic matter content. The advantages of visualization found for simulated data also hold for real world data as well. With the application of computerized acquisition many scientific disciplines are witnessing exponential growth rates of the volume of accumulated raw data, which often makes it daunting to condense the information into a manageable form, a challenge that can be addressed by modern visualization techniques. Such visualizations are also often an enticing way to communicate scientific results to the general public. This need for visualization is especially true in basic science, with its reliance on a benevolent and interested general public that drives the need for high-quality visualizations. Despite the widespread use of visualization, this technology has suffered from a lack of the unifying influence of shared common experiences. As with any emerging technology practitioners have often independently found solutions to similar problems. It is the aim of this focus issue to celebrate the importance of visualization, report on its growing use by the broad community of physicists, including biophysics, chemical physics, geophysics, astrophysics, and medical physics, and provide an opportunity for the diverse community of scientists using visualization to share work in one issue of a journal that itself is in the vanguard of supporting visualization and multimedia. A remarkable breadth and diversity of visualization in physics is to be found in this issue spanning fundamental aspects of relativity theory to computational fluid dynamics. The topics span length scales that are as small as quantum phenomena to the entire observable Universe. We have been impressed by the quality of the submissions and hope that this snap-shot will introduce, inform, motivate and maybe even help to unify visualization in physics. Readers are also directed to the December issue of Physics World which includes the following features highlighting work in this collection and other novel uses of visualization techniques: 'A feast of visualization' Physics World December 2008 pp 20 23 'Seeing the quantum world' by Barry Sanders Physics World December 2008 pp 24 27 'A picture of the cosmos' by Mark SubbaRao and Miguel Aragon-Calvo Physics World December 2008 pp 29 32 'Thinking outside the cube' by César A Hidalgo Physics World December 2008 pp 34 37 Focus on Visualization in Physics Contents Visualization of spiral and scroll waves in simulated and experimental cardiac tissue E M Cherry and F H Fenton Visualization of large scale structure from the Sloan Digital Sky Survey M U SubbaRao, M A Aragón-Calvo, H W Chen, J M Quashnock, A S Szalay and D G York How computers can help us in creating an intuitive access to relativity Hanns Ruder, Daniel Weiskopf, Hans-Peter Nollert and Thomas Müller Lagrangian particle tracking in three dimensions via single-camera in-line digital holography Jiang Lu, Jacob P Fugal, Hansen Nordsiek, Ewe Wei Saw, Raymond A Shaw and Weidong Yang Quantifying spatial heterogeneity from images Andrew E Pomerantz and Yi-Qiao Song Disaggregation and scientific visualization of earthscapes considering trends and spatial dependence structures S Grunwald Strength through structure: visualization and local assessment of the trabecular bone structure C Räth, R Monetti, J Bauer, I Sidorenko, D Müller, M Matsuura, E-M Lochmüller, P Zysset and F Eckstein Thermonuclear supernovae: a multi-scale astrophysical problem challenging numerical simulations and visualization F K Röpke and R Bruckschen Visualization needs and techniques for astrophysical simulations W Kapferer and T Riser Flow visualization and field line advection in computational fluid dynamics: application to magnetic fields and turbulent flows Pablo Mininni, Ed Lee, Alan Norton and John Clyne Splotch: visualizing cosmological simulations K Dolag, M Reinecke, C Gheller and S Imboden Visualizing a silicon quantum computer Barry C Sanders, Lloyd C L Hollenberg, Darran Edmundson and Andrew Edmundson Colliding galaxies, rotating neutron stars and merging black holes—visualizing high dimensional datasets on arbitrary meshes Werner Benger A low complexity visualization tool that helps to perform complex systems analysis M G Beiró, J I Alvarez-Hamelin and J R Busch Visualizing astrophysical N-body systems John Dubinski

Supporting Students' Knowledge Integration with Technology-Enhanced Inquiry Curricula

ERIC Educational Resources Information Center

Chiu, Jennifer Lopseen

2010-01-01

Dynamic visualizations of scientific phenomena have the potential to transform how students learn and understand science. Dynamic visualizations enable interaction and experimentation with unobservable atomic-level phenomena. A series of studies clarify the conditions under which embedding dynamic visualizations in technology-enhanced inquiry…

Flow visualization and modeling for education and outreach in low-income countries

NASA Astrophysics Data System (ADS)

Motanated, K.

2016-12-01

Being able to visualize the dynamic interaction between the movement of water and sediment flux is undeniably a profound tool for students and novices to understand complicated earth surface processes. In a laser-sheet flow visualization technique, a light source that is thin and monochromatic is required to illuminate sediments or tracers in the flow. However, an ideal laser sheet generator is rather expensive, especially for schools and universities residing in low-income countries. This project is proposing less-expensive options for a laser-sheet source and flow visualization experiment configuration for qualitative observation and quantitative analysis of the interaction between fluid media and sediments. Here, Fresnel lens is used to convert from point laser into sheet laser. Multiple combinations of laser diodes of various wavelength (nanometer) and power (milliwatt) and Fresnel lenses of various dimensions are analyzed. The pair that is able to produce the thinnest and brightest light sheet is not only effective but also affordable. The motion of sediments in a flow can be observed by illuminating the laser-sheet in an interested flow region. The particle motion is recorded by a video camera that is capable of taking multiple frames per second and having a narrow depth of view. The recorded video file can be played in a slow-motion mode so students can visually observe and qualitatively analyze the particle motion. An open source software package for Particle Imaging Velocimetry (PIV) can calculate the local velocity of particles from still images extracted from the video and create a vector map depicting particle motion. This flow visualization experiment is inexpensive and the configuration is simple to setup. Most importantly, this flow visualization technique serves as a fundamental tool for earth surface process education and can further be applied to sedimentary process modeling.

A combined static-dynamic single-dose imaging protocol to compare quantitative dynamic SPECT with static conventional SPECT.

PubMed

Sciammarella, Maria; Shrestha, Uttam M; Seo, Youngho; Gullberg, Grant T; Botvinick, Elias H

2017-08-03

SPECT myocardial perfusion imaging (MPI) is a clinical mainstay that is typically performed with static imaging protocols and visually or semi-quantitatively assessed for perfusion defects based upon the relative intensity of myocardial regions. Dynamic cardiac SPECT presents a new imaging technique based on time-varying information of radiotracer distribution, which permits the evaluation of regional myocardial blood flow (MBF) and coronary flow reserve (CFR). In this work, a preliminary feasibility study was conducted in a small patient sample designed to implement a unique combined static-dynamic single-dose one-day visit imaging protocol to compare quantitative dynamic SPECT with static conventional SPECT for improving the diagnosis of coronary artery disease (CAD). Fifteen patients (11 males, four females, mean age 71 ± 9 years) were enrolled for a combined dynamic and static SPECT (Infinia Hawkeye 4, GE Healthcare) imaging protocol with a single dose of 99m Tc-tetrofosmin administered at rest and a single dose administered at stress in a one-day visit. Out of 15 patients, eleven had selective coronary angiography (SCA), 8 within 6 months and the rest within 24 months of SPECT imaging, without intervening symptoms or interventions. The extent and severity of perfusion defects in each myocardial region was graded visually. Dynamically acquired data were also used to estimate the MBF and CFR. Both visually graded images and estimated CFR were tested against SCA as a reference to evaluate the validity of the methods. Overall, conventional static SPECT was normal in ten patients and abnormal in five patients, dynamic SPECT was normal in 12 patients and abnormal in three patients, and CFR from dynamic SPECT was normal in nine patients and abnormal in six patients. Among those 11 patients with SCA, conventional SPECT was normal in 5, 3 with documented CAD on SCA with an overall accuracy of 64%, sensitivity of 40% and specificity of 83%. Dynamic SPECT image analysis also produced a similar accuracy, sensitivity, and specificity. CFR was normal in 6, each with CAD on SCA with an overall accuracy of 91%, sensitivity of 80%, and specificity of 100%. The mean CFR was significantly lower for SCA detected abnormal than for normal patients (3.86±1.06 vs 1.94±0. 0.67, P < 0.001). The visually assessed image findings in static and dynamic SPECT are subjective, and may not reflect direct physiologic measures of coronary lesion based on SCA. The CFR measured with dynamic SPECT is fully objective, with better sensitivity and specificity, available only with the data generated from the dynamic SPECT method.

Closure technique after carotid endarterectomy influences local hemodynamics.

PubMed

Harrison, Gareth J; How, Thien V; Poole, Robert J; Brennan, John A; Naik, Jagjeeth B; Vallabhaneni, S Rao; Fisher, Robert K

2014-08-01

Meta-analysis supports patch angioplasty after carotid endarterectomy (CEA); however, studies indicate considerable variation in practice. The hemodynamic effect of a patch is unclear and this study attempted to elucidate this and guide patch width selection. Four groups were selected: healthy volunteers and patients undergoing CEA with primary closure, trimmed patch (5 mm), or 8-mm patch angioplasty. Computer-generated three-dimensional models of carotid bifurcations were produced from transverse ultrasound images recorded at 1-mm intervals. Rapid prototyping generated models for flow visualization studies. Computational fluid dynamic studies were performed for each model and validated by flow visualization. Mean wall shear stress (WSS) and oscillatory shear index (OSI) maps were created for each model using pulsatile inflow at 300 mL/min. WSS of <0.4 Pa and OSI >0.3 were considered pathological, predisposing to accretion of intimal hyperplasia. The resultant WSS and OSI maps were compared. The four groups comprised 8 normal carotid arteries, 6 primary closures, 6 trimmed patches, and seven 8-mm patches. Flow visualization identified flow separation and recirculation at the bifurcation increased with a patch and was related to the patch width. Computational fluid dynamic identified that primary closure had the fewest areas of low WSS or elevated OSI but did have mild common carotid artery stenoses at the proximal arteriotomy that caused turbulence. Trimmed patches had more regions of abnormal WSS and OSI at the bifurcation, but 8-mm patches had the largest areas of deleteriously low WSS and high OSI. Qualitative comparison among the four groups confirmed that incorporation of a patch increased areas of low WSS and high OSI at the bifurcation and that this was related to patch width. Closure technique after CEA influences the hemodynamic profile. Patching does not appear to generate favorable flow dynamics. However, a trimmed 5-mm patch may offer hemodynamic benefits over an 8-mm patch and may be the preferred option. Copyright © 2014 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

Health diagnosis of arch bridge suspender by acoustic emission technique

NASA Astrophysics Data System (ADS)

Li, Dongsheng; Ou, Jinping

2007-01-01

Conventional non-destructive methods can't be dynamically monitored the suspenders' damage levels and types, so acoustic emission (AE) technique is proposed to monitor its activity. The validity signals are determined by the relationship with risetime and duration. The ambient noise is eliminated using float threshold value and placing a guard sensor. The cement mortar and steel strand damage level is analyzed by AE parameter method and damage types are judged by waveform analyzing technique. Based on these methods, all the suspenders of Sichuan Ebian Dadu river arch bridge have been monitored using AE techniques. The monitoring results show that AE signal amplitude, energy, counts can visually display the suspenders' damage levels, the difference of waveform and frequency range express different damage type. The testing results are well coincide with the practical situation.

Visualizing Energy on Target: Molecular Dynamics Simulations

DTIC Science & Technology

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

Multimodal Neuroimaging: Basic Concepts and Classification of Neuropsychiatric Diseases.

PubMed

Tulay, Emine Elif; Metin, Barış; Tarhan, Nevzat; Arıkan, Mehmet Kemal

2018-06-01

Neuroimaging techniques are widely used in neuroscience to visualize neural activity, to improve our understanding of brain mechanisms, and to identify biomarkers-especially for psychiatric diseases; however, each neuroimaging technique has several limitations. These limitations led to the development of multimodal neuroimaging (MN), which combines data obtained from multiple neuroimaging techniques, such as electroencephalography, functional magnetic resonance imaging, and yields more detailed information about brain dynamics. There are several types of MN, including visual inspection, data integration, and data fusion. This literature review aimed to provide a brief summary and basic information about MN techniques (data fusion approaches in particular) and classification approaches. Data fusion approaches are generally categorized as asymmetric and symmetric. The present review focused exclusively on studies based on symmetric data fusion methods (data-driven methods), such as independent component analysis and principal component analysis. Machine learning techniques have recently been introduced for use in identifying diseases and biomarkers of disease. The machine learning technique most widely used by neuroscientists is classification-especially support vector machine classification. Several studies differentiated patients with psychiatric diseases and healthy controls with using combined datasets. The common conclusion among these studies is that the prediction of diseases increases when combining data via MN techniques; however, there remain a few challenges associated with MN, such as sample size. Perhaps in the future N-way fusion can be used to combine multiple neuroimaging techniques or nonimaging predictors (eg, cognitive ability) to overcome the limitations of MN.

Global Skin-Friction Measurements Using Particle Image Surface FLow Visualization and a Luminescent Oil-Film

NASA Technical Reports Server (NTRS)

Husen, Nicholas; Roozeboom, Nettie; Liu, Tianshu; Sullivan, John P.

2015-01-01

A quantitative global skin-friction measurement technique is proposed. An oil-film is doped with a luminescent molecule and thereby made to fluoresce in order to resolve oil-film thickness, and Particle Image Surface Flow Visualization is used to resolve the velocity field of the surface of the oil-film. Skin-friction is then calculated at location x as (x )xh, where x is the displacement of the surface of the oil-film and is the dynamic viscosity of the oil. The data collection procedure and data analysis procedures are explained, and preliminary experimental skin-friction results for flow over the wing of the CRM are presented.

Visualization of suspicious lesions in breast MRI based on intelligent neural systems

NASA Astrophysics Data System (ADS)

Twellmann, Thorsten; Lange, Oliver; Nattkemper, Tim Wilhelm; Meyer-Bäse, Anke

2006-05-01

Intelligent medical systems based on supervised and unsupervised artificial neural networks are applied to the automatic visualization and classification of suspicious lesions in breast MRI. These systems represent an important component of future sophisticated computer-aided diagnosis systems and enable the extraction of spatial and temporal features of dynamic MRI data stemming from patients with confirmed lesion diagnosis. By taking into account the heterogenity of the cancerous tissue, these techniques reveal the malignant, benign and normal kinetic signals and and provide a regional subclassification of pathological breast tissue. Intelligent medical systems are expected to have substantial implications in healthcare politics by contributing to the diagnosis of indeterminate breast lesions by non-invasive imaging.

Hemodynamic flow visualization of early embryonic great vessels using μPIV.

PubMed

Goktas, Selda; Chen, Chia-Yuan; Kowalski, William J; Pekkan, Kerem

2015-01-01

Microparticle image velocimetry (μPIV) is an evolving quantitative methodology to closely and accurately monitor the cardiac flow dynamics and mechanotransduction during vascular morphogenesis. While PIV technique has a long history, contemporary developments in advanced microscopy have significantly expanded its power. This chapter includes three new methods for μPIV acquisition in selected embryonic structures achieved through advanced optical imaging: (1) high-speed confocal scanning of transgenic zebrafish embryos, where the transgenic erythrocytes act as the tracing particles; (2) microinjection of artificial seeding particles in chick embryos visualized with stereomicroscopy; and (3) real-time, time-resolved optical coherence tomography acquisition of vitelline vessel flow profiles in chick embryos, tracking the erythrocytes.

Visualization of gas flow and diffusion in porous media

PubMed Central

Kaiser, Lana G.; Meersmann, Thomas; Logan, John W.; Pines, Alexander

2000-01-01

The transport of gases in porous materials is a crucial component of many important processes in science and technology. In the present work, we demonstrate how magnetic resonance microscopy with continuous flow laser-polarized noble gases makes it possible to “light up” and thereby visualize, with unprecedented sensitivity and resolution, the dynamics of gases in samples of silica aerogels and zeolite molecular sieve particles. The “polarization-weighted” images of gas transport in aerogel fragments are correlated to the diffusion coefficient of xenon obtained from NMR pulsed-field gradient experiments. The technique provides a unique means of studying the combined effects of flow and diffusion in systems with macroscopic dimensions and microscopic internal pore structure. PMID:10706617

Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

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

Cheng, Xiaofei; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036; Deng, Ping

Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings themore » split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.« less

Software Aids Visualization of Computed Unsteady Flow

NASA Technical Reports Server (NTRS)

Kao, David; Kenwright, David

2003-01-01

Unsteady Flow Analysis Toolkit (UFAT) is a computer program that synthesizes motions of time-dependent flows represented by very large sets of data generated in computational fluid dynamics simulations. Prior to the development of UFAT, it was necessary to rely on static, single-snapshot depictions of time-dependent flows generated by flow-visualization software designed for steady flows. Whereas it typically takes weeks to analyze the results of a largescale unsteady-flow simulation by use of steady-flow visualization software, the analysis time is reduced to hours when UFAT is used. UFAT can be used to generate graphical objects of flow visualization results using multi-block curvilinear grids in the format of a previously developed NASA data-visualization program, PLOT3D. These graphical objects can be rendered using FAST, another popular flow visualization software developed at NASA. Flow-visualization techniques that can be exploited by use of UFAT include time-dependent tracking of particles, detection of vortex cores, extractions of stream ribbons and surfaces, and tetrahedral decomposition for optimal particle tracking. Unique computational features of UFAT include capabilities for automatic (batch) processing, restart, memory mapping, and parallel processing. These capabilities significantly reduce analysis time and storage requirements, relative to those of prior flow-visualization software. UFAT can be executed on a variety of supercomputers.

Live-cell imaging combined with immunofluorescence, RNA, or DNA FISH to study the nuclear dynamics and expression of the X-inactivation center.

PubMed

Pollex, Tim; Piolot, Tristan; Heard, Edith

2013-01-01

Differentiation of embryonic stem cells is accompanied by changes of gene expression and chromatin and chromosome dynamics. One of the most impressive examples for these changes is inactivation of one of the two X chromosomes occurring upon differentiation of mouse female embryonic stem cells. With a few exceptions, these events have been mainly studied in fixed cells. In order to better understand the dynamics, kinetics, and order of events during differentiation, one needs to employ live-cell imaging techniques. Here, we describe a combination of live-cell imaging with techniques that can be used in fixed cells (e.g., RNA FISH) to correlate locus dynamics or subnuclear localization with, e.g., gene expression. To study locus dynamics in female ES cells, we generated cell lines containing TetO arrays in the X-inactivation center, the locus on the X chromosome regulating X-inactivation, which can be visualized upon expression of TetR fused to fluorescent proteins. We will use this system to elaborate on how to generate ES cell lines for live-cell imaging of locus dynamics, how to culture ES cells prior to live-cell imaging, and to describe typical live-cell imaging conditions for ES cells using different microscopes. Furthermore, we will explain how RNA, DNA FISH, or immunofluorescence can be applied following live-cell imaging to correlate gene expression with locus dynamics.

Human image tracking technique applied to remote collaborative environments

NASA Astrophysics Data System (ADS)

Nagashima, Yoshio; Suzuki, Gen

1993-10-01

To support various kinds of collaborations over long distances by using visual telecommunication, it is necessary to transmit visual information related to the participants and topical materials. When people collaborate in the same workspace, they use visual cues such as facial expressions and eye movement. The realization of coexistence in a collaborative workspace requires the support of these visual cues. Therefore, it is important that the facial images be large enough to be useful. During collaborations, especially dynamic collaborative activities such as equipment operation or lectures, the participants often move within the workspace. When the people move frequently or over a wide area, the necessity for automatic human tracking increases. Using the movement area of the human being or the resolution of the extracted area, we have developed a memory tracking method and a camera tracking method for automatic human tracking. Experimental results using a real-time tracking system show that the extracted area fairly moves according to the movement of the human head.

Development of closed-loop neural interface technology in a rat model: combining motor cortex operant conditioning with visual cortex microstimulation.

PubMed

Marzullo, Timothy Charles; Lehmkuhle, Mark J; Gage, Gregory J; Kipke, Daryl R

2010-04-01

Closed-loop neural interface technology that combines neural ensemble decoding with simultaneous electrical microstimulation feedback is hypothesized to improve deep brain stimulation techniques, neuromotor prosthetic applications, and epilepsy treatment. Here we describe our iterative results in a rat model of a sensory and motor neurophysiological feedback control system. Three rats were chronically implanted with microelectrode arrays in both the motor and visual cortices. The rats were subsequently trained over a period of weeks to modulate their motor cortex ensemble unit activity upon delivery of intra-cortical microstimulation (ICMS) of the visual cortex in order to receive a food reward. Rats were given continuous feedback via visual cortex ICMS during the response periods that was representative of the motor cortex ensemble dynamics. Analysis revealed that the feedback provided the animals with indicators of the behavioral trials. At the hardware level, this preparation provides a tractable test model for improving the technology of closed-loop neural devices.

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Kelaita, Paul G.; Mccabe, R. Kevin; Merritt, Fergus J.; Plessel, Todd C.; Sandstrom, Timothy A.; West, John T.

1993-01-01

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described.

Geometric Optimization for Non-Thrombogenicity of a Centrifugal Blood Pump through Flow Visualization

NASA Astrophysics Data System (ADS)

Toyoda, Masahiro; Nishida, Masahiro; Maruyama, Osamu; Yamane, Takashi; Tsutsui, Tatsuo; Sankai, Yoshiyuki

A monopivot centrifugal blood pump, whose impeller is supported with a pivot bearing and a passive magnetic bearing, is under development for implantable artificial heart. The hemolysis level is less than that of commercial centrifugal pumps and the pump size is as small as 160 mL in volume. To solve a problem of thrombus caused by fluid dynamics, flow visualization experiments and animal experiments have been undertaken. For flow visualization a three-fold scale-up model, high-speed video system, and particle tracking velocimetry software were used. To verify non-thrombogenicity one-week animal experiments were conducted with sheep. The initially observed thrombus around the pivot was removed through unifying the separate washout holes to a small centered hole to induce high shear around the pivot. It was found that the thrombus contours corresponded to the shear rate of 300s-1 for red thrombus and 1300-1700s-1 for white thrombus, respectively. Thus flow visualization technique was found to be a useful tool to predict thrombus location.

Cardiac-driven Pulsatile Motion of Intracranial Cerebrospinal Fluid Visualized Based on a Correlation Mapping Technique.

PubMed

Yatsushiro, Satoshi; Sunohara, Saeko; Hayashi, Naokazu; Hirayama, Akihiro; Matsumae, Mitsunori; Atsumi, Hideki; Kuroda, Kagayaki

2018-04-10

A correlation mapping technique delineating delay time and maximum correlation for characterizing pulsatile cerebrospinal fluid (CSF) propagation was proposed. After proofing its technical concept, this technique was applied to healthy volunteers and idiopathic normal pressure hydrocephalus (iNPH) patients. A time-resolved three dimensional-phase contrast (3D-PC) sampled the cardiac-driven CSF velocity at 32 temporal points per cardiac period at each spatial location using retrospective cardiac gating. The proposed technique visualized distributions of propagation delay and correlation coefficient of the PC-based CSF velocity waveform with reference to a waveform at a particular point in the CSF space. The delay time was obtained as the amount of time-shift, giving the maximum correlation for the velocity waveform at an arbitrary location with that at the reference location. The validity and accuracy of the technique were confirmed in a flow phantom equipped with a cardiovascular pump. The technique was then applied to evaluate the intracranial CSF motions in young, healthy (N = 13), and elderly, healthy (N = 13) volunteers and iNPH patients (N = 13). The phantom study demonstrated that root mean square error of the delay time was 2.27%, which was less than the temporal resolution of PC measurement used in this study (3.13% of a cardiac cycle). The human studies showed a significant difference (P < 0.01) in the mean correlation coefficient between the young, healthy group and the other two groups. A significant difference (P < 0.05) was also recognized in standard deviation of the correlation coefficients in intracranial CSF space among all groups. The result suggests that the CSF space compliance of iNPH patients was lower than that of healthy volunteers. The correlation mapping technique allowed us to visualize pulsatile CSF velocity wave propagations as still images. The technique may help to classify diseases related to CSF dynamics, such as iNPH.

Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells.

PubMed

Spahn, Christoph; Glaesmann, Mathilda; Gao, Yunfeng; Foo, Yong Hwee; Lampe, Marko; Kenney, Linda J; Heilemann, Mike

2017-01-01

Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.

Laparoscopic surgical skills training: an investigation of the potential of using surgeons' visual search behaviour as a performance indicator

NASA Astrophysics Data System (ADS)

Chen, Yan; Dong, Leng; Gale, Alastair G.; Rees, Benjamin; Maxwell-Armstrong, Charles

2014-03-01

Laparoscopic surgery is a difficult perceptual-motor task and effective and efficient training in the technique is important. Viewing previously recorded laparoscopic operations is a possible available training technique for surgeons to increase their knowledge of such minimal access surgery (MAS). It is not well known whether this is a useful technique, how effective it is or what effect it has on the surgeon watching the recorded video. As part of an on-going series of studies into laparoscopic surgery, an experiment was conducted to examine whether surgical skill level has an effect on the visual search behaviour of individuals of different surgical experience when they examine such imagery. Medically naive observers, medical students, junior surgeons and experienced surgeons viewed a laparoscopic recording of a recent operation. Initial examination of the recorded eye movement data indicated commonalities between all observers, largely irrespective of surgical experience. This, it is argued, is due to visual search in this situation largely being driven by the dynamic nature of the images. The data were then examined in terms of surgical steps and also in terms of interventions when differences were found related to surgical experience. Consequently, it is argued that monitoring the eye movements of trainee surgeons whilst they watch pre-recorded operations is a potential useful adjunct to existing training regimes.

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL.

PubMed

Stone, John E; Messmer, Peter; Sisneros, Robert; Schulten, Klaus

2016-05-01

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications.

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL

PubMed Central

Stone, John E.; Messmer, Peter; Sisneros, Robert; Schulten, Klaus

2016-01-01

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications. PMID:27747137

In Situ Distribution Guided Analysis and Visualization of Transonic Jet Engine Simulations.

PubMed

Dutta, Soumya; Chen, Chun-Ming; Heinlein, Gregory; Shen, Han-Wei; Chen, Jen-Ping

2017-01-01

Study of flow instability in turbine engine compressors is crucial to understand the inception and evolution of engine stall. Aerodynamics experts have been working on detecting the early signs of stall in order to devise novel stall suppression technologies. A state-of-the-art Navier-Stokes based, time-accurate computational fluid dynamics simulator, TURBO, has been developed in NASA to enhance the understanding of flow phenomena undergoing rotating stall. Despite the proven high modeling accuracy of TURBO, the excessive simulation data prohibits post-hoc analysis in both storage and I/O time. To address these issues and allow the expert to perform scalable stall analysis, we have designed an in situ distribution guided stall analysis technique. Our method summarizes statistics of important properties of the simulation data in situ using a probabilistic data modeling scheme. This data summarization enables statistical anomaly detection for flow instability in post analysis, which reveals the spatiotemporal trends of rotating stall for the expert to conceive new hypotheses. Furthermore, the verification of the hypotheses and exploratory visualization using the summarized data are realized using probabilistic visualization techniques such as uncertain isocontouring. Positive feedback from the domain scientist has indicated the efficacy of our system in exploratory stall analysis.

Direct Visualization of Exciton Reequilibration in the LH1 and LH2 Complexes of Rhodobacter sphaeroides by Multipulse Spectroscopy

PubMed Central

Cohen Stuart, Thomas A.; Vengris, Mikas; Novoderezhkin, Vladimir I.; Cogdell, Richard J.; Hunter, C. Neil; van Grondelle, Rienk

2011-01-01

The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ∼150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas. PMID:21539791

Direct visualization of exciton reequilibration in the LH1 and LH2 complexes of Rhodobacter sphaeroides by multipulse spectroscopy.

PubMed

Cohen Stuart, Thomas A; Vengris, Mikas; Novoderezhkin, Vladimir I; Cogdell, Richard J; Hunter, C Neil; van Grondelle, Rienk

2011-05-04

The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ∼150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

PubMed Central

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin-ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

2015-01-01

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined. PMID:25727920

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

DOE PAGES

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; ...

2015-03-02

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances.more » Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.« less

A reconfigurable visual-programming library for real-time closed-loop cellular electrophysiology

PubMed Central

Biró, István; Giugliano, Michele

2015-01-01

Most of the software platforms for cellular electrophysiology are limited in terms of flexibility, hardware support, ease of use, or re-configuration and adaptation for non-expert users. Moreover, advanced experimental protocols requiring real-time closed-loop operation to investigate excitability, plasticity, dynamics, are largely inaccessible to users without moderate to substantial computer proficiency. Here we present an approach based on MATLAB/Simulink, exploiting the benefits of LEGO-like visual programming and configuration, combined to a small, but easily extendible library of functional software components. We provide and validate several examples, implementing conventional and more sophisticated experimental protocols such as dynamic-clamp or the combined use of intracellular and extracellular methods, involving closed-loop real-time control. The functionality of each of these examples is demonstrated with relevant experiments. These can be used as a starting point to create and support a larger variety of electrophysiological tools and methods, hopefully extending the range of default techniques and protocols currently employed in experimental labs across the world. PMID:26157385

Micro/nano-computed tomography technology for quantitative dynamic, multi-scale imaging of morphogenesis.

PubMed

Gregg, Chelsea L; Recknagel, Andrew K; Butcher, Jonathan T

2015-01-01

Tissue morphogenesis and embryonic development are dynamic events challenging to quantify, especially considering the intricate events that happen simultaneously in different locations and time. Micro- and more recently nano-computed tomography (micro/nanoCT) has been used for the past 15 years to characterize large 3D fields of tortuous geometries at high spatial resolution. We and others have advanced micro/nanoCT imaging strategies for quantifying tissue- and organ-level fate changes throughout morphogenesis. Exogenous soft tissue contrast media enables visualization of vascular lumens and tissues via extravasation. Furthermore, the emergence of antigen-specific tissue contrast enables direct quantitative visualization of protein and mRNA expression. Micro-CT X-ray doses appear to be non-embryotoxic, enabling longitudinal imaging studies in live embryos. In this chapter we present established soft tissue contrast protocols for obtaining high-quality micro/nanoCT images and the image processing techniques useful for quantifying anatomical and physiological information from the data sets.

Efficient Usage of Dense GNSS Networks in Central Europe for the Visualization and Investigation of Ionospheric TEC Variations

PubMed Central

Zanimonskiy, Yevgen M.; Yampolski, Yuri M.; Figurski, Mariusz

2017-01-01

The technique of the orthogonal projection of ionosphere electronic content variations for mapping total electron content (TEC) allows us to visualize ionospheric irregularities. For the reconstruction of global ionospheric characteristics, numerous global navigation satellite system (GNSS) receivers located in different regions of the Earth are used as sensors. We used dense GNSS networks in central Europe to detect and investigate a special type of plasma inhomogeneities, called travelling ionospheric disturbances (TID). Such use of GNSS sensors allows us to reconstruct the main TID parameters, such as spatial dimensions, velocities, and directions of their movement. The paper gives examples of the restoration of dynamic characteristics of ionospheric irregularities for quiet and disturbed geophysical conditions. Special attention is paid to the dynamics of ionospheric disturbances stimulated by the magnetic storms of two St. Patrick’s Days (17 March 2013 and 2015). Additional opportunities for the remote sensing of the ionosphere with the use of dense regional networks of GNSS receiving sensors have been noted too. PMID:28994718

Europium-doped aluminum oxide phosphors as indicators for frontal polymerization dynamics

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

Carranza, Arturo; Gewin, Mariah; Pojman, John A., E-mail: japojman@lsu.edu

2014-06-15

In this study, we present an inexpensive and practical method that allows the monitoring and visualization of front polymerization, propagation, and dynamics. Commercially available europium-doped aluminum oxide powders were combined with video imaging to visualize free-radical propagating polymer fronts. In order to demonstrate the applicability of this method, frontal copolymerization reactions of propoxylated glycerin triacrylate (EB53), pentaerythritol triacrylate (PETA), and pentaerythritol tetra-acrylate (PETEA) with 1,1-Bis(tert-butylperoxy)-3,3,5-trimethylcyclohexane (Luperox 231®) as an initiator were studied and compared to the results obtained by IR imaging. Systems exhibiting higher filler loading, higher EB53 content, and less acrylated monomers showed a marked decrease in front velocity,more » while those with more acrylated monomers and higher crosslinking density showed a marked increase in front velocity. Finally, in order to show the potential of the imaging technique, we studied fronts propagating in planar and spherical geometries.« less

Efficient Usage of Dense GNSS Networks in Central Europe for the Visualization and Investigation of Ionospheric TEC Variations.

PubMed

Nykiel, Grzegorz; Zanimonskiy, Yevgen M; Yampolski, Yuri M; Figurski, Mariusz

2017-10-10

The technique of the orthogonal projection of ionosphere electronic content variations for mapping total electron content (TEC) allows us to visualize ionospheric irregularities. For the reconstruction of global ionospheric characteristics, numerous global navigation satellite system (GNSS) receivers located in different regions of the Earth are used as sensors. We used dense GNSS networks in central Europe to detect and investigate a special type of plasma inhomogeneities, called travelling ionospheric disturbances (TID). Such use of GNSS sensors allows us to reconstruct the main TID parameters, such as spatial dimensions, velocities, and directions of their movement. The paper gives examples of the restoration of dynamic characteristics of ionospheric irregularities for quiet and disturbed geophysical conditions. Special attention is paid to the dynamics of ionospheric disturbances stimulated by the magnetic storms of two St. Patrick's Days (17 March 2013 and 2015). Additional opportunities for the remote sensing of the ionosphere with the use of dense regional networks of GNSS receiving sensors have been noted too.

RP and RQA Analysis for Floating Potential Fluctuations in a DC Magnetron Sputtering Plasma

NASA Astrophysics Data System (ADS)

Sabavath, Gopikishan; Banerjee, I.; Mahapatra, S. K.

2016-04-01

The nonlinear dynamics of a direct current magnetron sputtering plasma is visualized using recurrence plot (RP) technique. RP comprises the recurrence quantification analysis (RQA) which is an efficient method to observe critical regime transitions in dynamics. Further, RQA provides insight information about the system’s behavior. We observed the floating potential fluctuations of the plasma as a function of discharge voltage by using Langmuir probe. The system exhibits quasi-periodic-chaotic-quasi-periodic-chaotic transitions. These transitions are quantified from determinism, Lmax, and entropy of RQA. Statistical investigations like kurtosis and skewness also studied for these transitions which are in well agreement with RQA results.

Remote Visualization and Remote Collaboration On Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

A new technology has been developed for remote visualization that provides remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as fluid dynamics simulations or measurements). Based on this technology, some World Wide Web sites on the Internet are providing fluid dynamics data for educational or testing purposes. This technology is also being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics and wind tunnel testing. Previously, remote visualization of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit).

Can Dynamic Visualizations Improve Middle School Students' Understanding of Energy in Photosynthesis?

ERIC Educational Resources Information Center

Ryoo, Kihyun; Linn, Marcia C.

2012-01-01

Dynamic visualizations have the potential to make abstract scientific phenomena more accessible and visible to students, but they can also be confusing and difficult to comprehend. This research investigates how dynamic visualizations, compared to static illustrations, can support middle school students in developing an integrated understanding of…

How Dynamic Visualization Technology Can Support Molecular Reasoning

ERIC Educational Resources Information Center

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Molecular expressions: exploring the world of optics and microscopy. http://microscopy.fsu.edu.

PubMed

Eliceiri, Kevin W

2004-08-01

Our knowledge of the structure, dynamics and physiology of a cell has increased significantly in the last ten years through the emergence of new optical imaging modalities such as optical sectioning microscopy, computer- enhanced video microscopy and laser-scanning microscopy. These techniques together with the use of genetically engineered fluorophores have helped scientists visualize the 3-dimensional dynamic processes of living cells. However as powerful as these imaging tools are, they can often be difficult to understand and fully utilize. Below I will discuss my favorite website: The Molecular Expressions Web Site that endeavors to present the power of microscopy to its visitors. The Molecular Expressions group does a remarkable job of not only clearly presenting the principles behind these techniques in a manner approachable by lay and scientific audiences alike but also provides representative data from each as well.

A novel data hiding scheme for block truncation coding compressed images using dynamic programming strategy

NASA Astrophysics Data System (ADS)

Chang, Ching-Chun; Liu, Yanjun; Nguyen, Son T.

2015-03-01

Data hiding is a technique that embeds information into digital cover data. This technique has been concentrated on the spatial uncompressed domain, and it is considered more challenging to perform in the compressed domain, i.e., vector quantization, JPEG, and block truncation coding (BTC). In this paper, we propose a new data hiding scheme for BTC-compressed images. In the proposed scheme, a dynamic programming strategy was used to search for the optimal solution of the bijective mapping function for LSB substitution. Then, according to the optimal solution, each mean value embeds three secret bits to obtain high hiding capacity with low distortion. The experimental results indicated that the proposed scheme obtained both higher hiding capacity and hiding efficiency than the other four existing schemes, while ensuring good visual quality of the stego-image. In addition, the proposed scheme achieved a low bit rate as original BTC algorithm.

Visualizing Time-Varying Phenomena In Numerical Simulations Of Unsteady Flows

NASA Technical Reports Server (NTRS)

Lane, David A.

1996-01-01

Streamlines, contour lines, vector plots, and volume slices (cutting planes) are commonly used for flow visualization. These techniques are sometimes referred to as instantaneous flow visualization techniques because calculations are based on an instant of the flowfield in time. Although instantaneous flow visualization techniques are effective for depicting phenomena in steady flows,they sometimes do not adequately depict time-varying phenomena in unsteady flows. Streaklines and timelines are effective visualization techniques for depicting vortex shedding, vortex breakdown, and shock waves in unsteady flows. These techniques are examples of time-dependent flow visualization techniques, which are based on many instants of the flowfields in time. This paper describes the algorithms for computing streaklines and timelines. Using numerically simulated unsteady flows, streaklines and timelines are compared with streamlines, contour lines, and vector plots. It is shown that streaklines and timelines reveal vortex shedding and vortex breakdown more clearly than instantaneous flow visualization techniques.

Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio)

PubMed Central

Shang, Chunfeng; Yang, Wenbin; Bai, Lu; Du, Jiulin

2017-01-01

The internal brain dynamics that link sensation and action are arguably better studied during natural animal behaviors. Here, we report on a novel volume imaging and 3D tracking technique that monitors whole brain neural activity in freely swimming larval zebrafish (Danio rerio). We demonstrated the capability of our system through functional imaging of neural activity during visually evoked and prey capture behaviors in larval zebrafish. PMID:28930070

Virtualized Traffic: reconstructing traffic flows from discrete spatiotemporal data.

PubMed

Sewall, Jason; van den Berg, Jur; Lin, Ming C; Manocha, Dinesh

2011-01-01

We present a novel concept, Virtualized Traffic, to reconstruct and visualize continuous traffic flows from discrete spatiotemporal data provided by traffic sensors or generated artificially to enhance a sense of immersion in a dynamic virtual world. Given the positions of each car at two recorded locations on a highway and the corresponding time instances, our approach can reconstruct the traffic flows (i.e., the dynamic motions of multiple cars over time) between the two locations along the highway for immersive visualization of virtual cities or other environments. Our algorithm is applicable to high-density traffic on highways with an arbitrary number of lanes and takes into account the geometric, kinematic, and dynamic constraints on the cars. Our method reconstructs the car motion that automatically minimizes the number of lane changes, respects safety distance to other cars, and computes the acceleration necessary to obtain a smooth traffic flow subject to the given constraints. Furthermore, our framework can process a continuous stream of input data in real time, enabling the users to view virtualized traffic events in a virtual world as they occur. We demonstrate our reconstruction technique with both synthetic and real-world input. © 2011 IEEE Published by the IEEE Computer Society

Percutaneous Ultrasound-Guided TOPAZ Radiofrequency Coblation: A Novel Coaxial Technique for the Treatment of Recalcitrant Plantar Fasciitis-Our Experience.

PubMed

Shah, Amit; Best, Alistair J; Rennie, Winston J

2016-06-01

Various therapeutic options are available for treatment of recalcitrant plantar fasciitis. Studies using TOPAZ coblation (ArthroCare, Sunnyvale, CA) have had good early results. The current coblation technique involves a surgical incision or breach of the highly specialized plantar fat pad, which can be associated with risks. We describe a novel technique of ultrasound-guided percutaneous coblation with a lateral heel approach. Advantages include precise targeting of the plantar fascia by direct dynamic visualization of the coblation tip, a true percutaneous approach with a needle skin puncture (<5 mm), and preservation of the plantar fat pad by using a lateral heel approach. © 2016 by the American Institute of Ultrasound in Medicine.

cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets

PubMed Central

Le Muzic, Mathieu; Autin, Ludovic; Parulek, Julius; Viola, Ivan

2017-01-01

In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend. PMID:29291131

To speak or not to speak - A multiple resource perspective

NASA Technical Reports Server (NTRS)

Tsang, P. S.; Hartzell, E. J.; Rothschild, R. A.

1985-01-01

The desirability of employing speech response in a dynamic dual task situation was discussed from a multiple resource perspective. A secondary task technique was employed to examine the time-sharing performance of five dual tasks with various degrees of resource overlap according to the structure-specific resource model of Wickens (1980). The primary task was a visual/manual tracking task which required spatial processing. The secondary task was either another tracking task or a spatial transformation task with one of four input (visual or auditory) and output (manual or speech) configurations. The results show that the dual task performance was best when the primary tracking task was paired with the visual/speech transformation task. This finding was explained by an interaction of the stimulus-central processing-response compatibility of the transformation task and the degree of resource competition between the time-shared tasks. Implications on the utility of speech response were discussed.

Interactive Terascale Particle Visualization

NASA Technical Reports Server (NTRS)

Ellsworth, David; Green, Bryan; Moran, Patrick

2004-01-01

This paper describes the methods used to produce an interactive visualization of a 2 TB computational fluid dynamics (CFD) data set using particle tracing (streaklines). We use the method introduced by Bruckschen et al. [2001] that pre-computes a large number of particles, stores them on disk using a space-filling curve ordering that minimizes seeks, and then retrieves and displays the particles according to the user's command. We describe how the particle computation can be performed using a PC cluster, how the algorithm can be adapted to work with a multi-block curvilinear mesh, and how the out-of-core visualization can be scaled to 296 billion particles while still achieving interactive performance on PG hardware. Compared to the earlier work, our data set size and total number of particles are an order of magnitude larger. We also describe a new compression technique that allows the lossless compression of the particles by 41% and speeds the particle retrieval by about 30%.

In vivo dynamic analysis of water refilling in embolized xylem vessels of intact Zea mays leaves

PubMed Central

Ryu, Jeongeun; Hwang, Bae Geun; Lee, Sang Joon

2016-01-01

Background and Aims The refilling of embolized xylem vessels under tension is a major issue in water transport among vascular plants. However, xylem embolism and refilling remain poorly understood because of technical limitations. Direct observation of embolism repair in intact plants is essential to understand the biophysical aspects of water refilling in embolized xylem vessels. This paper reports on details of the water refilling process in leaves of the intact herbaceous monocot plant Zea mays and its refilling kinetics obtained by a direct visualization technique. Methods A synchrotron X-ray micro-imaging technique was used to monitor water refilling in embolized xylem vessels of intact maize leaves. Xylem embolism was artificially induced by using a glass capillary; real-time images of water refilling dynamics were consecutively captured at a frame rate of 50 f.p.s. Key Results Water supply in the radial direction initiates droplet formation on the wall of embolized xylem vessels. Each droplet grows into a water column; this phenomenon shows translation motion or continuous increase in water column volume. In some instances, water columns merge and form one large water column. Water refilling in the radial direction causes rapid recovery from embolism in several minutes. The average water refilling velocity is approx. 1 μm s−1. Conclusions Non-destructive visualization of embolized xylem vessels demonstrates rapid water refilling and gas bubble removal as key elements of embolism repair in a herbaceous monocot species. The refilling kinetics provides new insights into the dynamic mechanism of water refilling phenomena. PMID:27539601

2D-Visualization of metabolic activity with planar optical chemical sensors (optodes)

NASA Astrophysics Data System (ADS)

Meier, R. J.; Liebsch, G.

2015-12-01

Microbia plays an outstandingly important role in many hydrologic compartments, such as e.g. the benthic community in sediments, or biologically active microorganisms in the capillary fringe, in ground water, or soil. Oxygen, pH, and CO2 are key factors and indicators for microbial activity. They can be measured using optical chemical sensors. These sensors record changing fluorescence properties of specific indicator dyes. The signals can be measured in a non-contact mode, even through transparent walls, which is important for many lab-experiments. They can measure in closed (transparent) systems, without sampling or intruding into the sample. They do not consume the analytes while measuring, are fully reversible and able to measure in non-stirred solutions. These sensors can be applied as high precision fiberoptic sensors (for profiling), robust sensor spots, or as planar sensors for 2D visualization (imaging). Imaging enables to detect thousands of measurement spots at the same time and generate 2D analyte maps over a region of interest. It allows for comparing different regions within one recorded image, visualizing spatial analyte gradients, or more important to identify hot spots of metabolic activity. We present ready-to-use portable imaging systems for the analytes oxygen, pH, and CO2. They consist of a detector unit, planar sensor foils and a software for easy data recording and evaluation. Sensors foils for various analytes and measurement ranges enable visualizing metabolic activity or analyte changes in the desired range. Dynamics of metabolic activity can be detected in one shot or over long time periods. We demonstrate the potential of this analytical technique by presenting experiments on benthic disturbance-recovery dynamics in sediments and microbial degradation of organic material in the capillary fringe. We think this technique is a new tool to further understand how microbial and geochemical processes are linked in (not solely) hydrologic systems.

Perceptual suppression revealed by adaptive multi-scale entropy analysis of local field potential in monkey visual cortex.

PubMed

Hu, Meng; Liang, Hualou

2013-04-01

Generalized flash suppression (GFS), in which a salient visual stimulus can be rendered invisible despite continuous retinal input, provides a rare opportunity to directly study the neural mechanism of visual perception. Previous work based on linear methods, such as spectral analysis, on local field potential (LFP) during GFS has shown that the LFP power at distinctive frequency bands are differentially modulated by perceptual suppression. Yet, the linear method alone may be insufficient for the full assessment of neural dynamic due to the fundamentally nonlinear nature of neural signals. In this study, we set forth to analyze the LFP data collected from multiple visual areas in V1, V2 and V4 of macaque monkeys while performing the GFS task using a nonlinear method - adaptive multi-scale entropy (AME) - to reveal the neural dynamic of perceptual suppression. In addition, we propose a new cross-entropy measure at multiple scales, namely adaptive multi-scale cross-entropy (AMCE), to assess the nonlinear functional connectivity between two cortical areas. We show that: (1) multi-scale entropy exhibits percept-related changes in all three areas, with higher entropy observed during perceptual suppression; (2) the magnitude of the perception-related entropy changes increases systematically over successive hierarchical stages (i.e. from lower areas V1 to V2, up to higher area V4); and (3) cross-entropy between any two cortical areas reveals higher degree of asynchrony or dissimilarity during perceptual suppression, indicating a decreased functional connectivity between cortical areas. These results, taken together, suggest that perceptual suppression is related to a reduced functional connectivity and increased uncertainty of neural responses, and the modulation of perceptual suppression is more effective at higher visual cortical areas. AME is demonstrated to be a useful technique in revealing the underlying dynamic of nonlinear/nonstationary neural signal.

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport

PubMed Central

Kaplan, Luke; Ierokomos, Athena; Chowdary, Praveen; Bryant, Zev; Cui, Bianxiao

2018-01-01

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors. PMID:29536037

Supporting students' knowledge integration with technology-enhanced inquiry curricula

NASA Astrophysics Data System (ADS)

Chiu, Jennifer Lopseen

Dynamic visualizations of scientific phenomena have the potential to transform how students learn and understand science. Dynamic visualizations enable interaction and experimentation with unobservable atomic-level phenomena. A series of studies clarify the conditions under which embedding dynamic visualizations in technology-enhanced inquiry instruction can help students develop robust and durable chemistry knowledge. Using the knowledge integration perspective, I designed Chemical Reactions, a technology-enhanced curriculum unit, with a partnership of teachers, educational researchers, and chemists. This unit guides students in an exploration of how energy and chemical reactions relate to climate change. It uses powerful dynamic visualizations to connect atomic level interactions to the accumulation of greenhouse gases. The series of studies were conducted in typical classrooms in eleven high schools across the country. This dissertation describes four studies that contribute to understanding of how visualizations can be used to transform chemistry learning. The efficacy study investigated the impact of the Chemical Reactions unit compared to traditional instruction using pre-, post- and delayed posttest assessments. The self-monitoring study used self-ratings in combination with embedded assessments to explore how explanation prompts help students learn from dynamic visualizations. The self-regulation study used log files of students' interactions with the learning environment to investigate how external feedback and explanation prompts influence students' exploration of dynamic visualizations. The explanation study compared specific and general explanation prompts to explore the processes by which explanations benefit learning with dynamic visualizations. These studies delineate the conditions under which dynamic visualizations embedded in inquiry instruction can enhance student outcomes. The studies reveal that visualizations can be deceptively clear, deterring learners from exploring details. Asking students to generate explanations helps them realize what they don't understand and can spur students to revisit visualizations to remedy gaps in their knowledge. The studies demonstrate that science instruction focused on complex topics can succeed by combining visualizations with generative activities to encourage knowledge integration. Students are more successful at monitoring their progress and remedying gaps in knowledge when required to distinguish among alternative explanations. The results inform the design of technology-enhanced science instruction for typical classrooms.

Dynamic Visualizations: How Attraction, Motivation and Communication Affect Streaming Video Tutorial Implementation

ERIC Educational Resources Information Center

Boger, Claire

2011-01-01

The rapid advancement in the capabilities of computer technologies has made it easier to design and deploy dynamic visualizations in web-based learning environments; yet, the implementation of these dynamic visuals has been met with mixed results. While many guidelines exist to assist instructional designers in the design and application of…

Ultra-high contrast retinal display system for single photoreceptor psychophysics

PubMed Central

Domdei, Niklas; Domdei, Lennart; Reiniger, Jenny L.; Linden, Michael; Holz, Frank G.; Roorda, Austin; Harmening, Wolf M.

2017-01-01

Due to the enormous dynamic range of human photoreceptors in response to light, studying their visual function in the intact retina challenges the stimulation hardware, specifically with regard to the displayable luminance contrast. The adaptive optics scanning laser ophthalmoscope (AOSLO) is an optical platform that focuses light to extremely small retinal extents, approaching the size of single photoreceptor cells. However, the current light modulation techniques produce spurious visible backgrounds which fundamentally limit experimental options. To remove unwanted background light and to improve contrast for high dynamic range visual stimulation in an AOSLO, we cascaded two commercial fiber-coupled acousto-optic modulators (AOMs) and measured their combined optical contrast. By compensating for zero-point differences in the individual AOMs, we demonstrate a multiplicative extinction ratio in the cascade that was in accordance with the extinction ratios of both single AOMs. When latency differences in the AOM response functions were individually corrected, single switch events as short as 50 ns with radiant power contrasts up to 1:1010 were achieved. This is the highest visual contrast reported for any display system so far. We show psychophysically that this contrast ratio is sufficient to stimulate single foveal photoreceptor cells with small and bright enough visible targets that do not contain a detectable background. Background-free stimulation will enable photoreceptor testing with custom adaptation lights. Furthermore, a larger dynamic range in displayable light levels can drive photoreceptor responses in cones as well as in rods. PMID:29359094

A study of the laminar separation bubble on an airfoil at low Reynolds numbers using flow visualization techniques

NASA Technical Reports Server (NTRS)

Schmidt, Gordon S.; Mueller, Thomas J.

1987-01-01

The use of flow visualization to study separation bubbles is evaluated. The wind tunnel, two NACA 66(3)-018 airfoil models, and kerosene vapor, titanium tetrachloride, and surface flow visualizations techniques are described. The application of the three visualization techniques to the two airfoil models reveals that the smoke and vapor techniques provide data on the location of laminar separation and the onset of transition, and the surface method produces information about the location of turbulent boundary layer separation. The data obtained with the three flow visualization techniques are compared to pressure distribution data and good correlation is detected. It is noted that flow visualization is an effective technique for examining separation bubbles.

High-Speed Photographic Study of Wave Propagation and Impact Damage in Fused Silica and AlON Using the Edge-On Impact (EOI) Method

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

Strassburger, E.; Patel, P.; McCauley, J. W.

An Edge-on Impact (EOI) technique, developed at the Ernst-Mach-Institute (EMI), coupled with a Cranz-Schardin high-speed camera, has been successfully utilized to visualize dynamic fracture in many brittle materials. In a typical test, the projectile strikes one edge of a specimen and damage formation and fracture propagation is recorded during the first 20 {mu}s after impact. In the present study, stress waves and damage propagation in fused silica and AlON were examined by means of two modified Edge-on Impact arrangements. In one arrangement, fracture propagation was observed simultaneously in side and top views of the specimens by means of two Cranz-Schardinmore » cameras. In another arrangement, the photographic technique was modified by placing the specimen between crossed polarizers and using the photo-elastic effect to visualize the stress waves. Pairs of impact tests at approximately equivalent velocities were carried out in transmitted plane (shadowgraphs) and crossed polarized light.« less

Reversible conformational switching of i-motif DNA studied by fluorescence spectroscopy.

PubMed

Choi, Jungkweon; Majima, Tetsuro

2013-01-01

Non-B DNAs, which can form unique structures other than double helix of B-DNA, have attracted considerable attention from scientists in various fields including biology, chemistry and physics etc. Among them, i-motif DNA, which is formed from cytosine (C)-rich sequences found in telomeric DNA and the promoter region of oncogenes, has been extensively investigated as a signpost and controller for the oncogene expression at the transcription level and as a promising material in nanotechnology. Fluorescence techniques such as fluorescence resonance energy transfer (FRET) and the fluorescence quenching are important for studying DNA and in particular for the visualization of reversible conformational switching of i-motif DNA that is triggered by the protonation. Here, we review the latest studies on the conformational dynamics of i-motif DNA as well as the application of FRET and fluorescence quenching techniques to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology. © 2013 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2013 The American Society of Photobiology.

Visualizing Molecular Diffusion through Passive Permeability Barriers in Cells: Conventional and Novel Approaches

PubMed Central

Lin, Yu-Chun; Phua, Siew Cheng; Lin, Benjamin; Inoue, Takanari

2013-01-01

Diffusion barriers are universal solutions for cells to achieve distinct organizations, compositions, and activities within a limited space. The influence of diffusion barriers on the spatiotemporal dynamics of signaling molecules often determines cellular physiology and functions. Over the years, the passive permeability barriers in various subcellular locales have been characterized using elaborate analytical techniques. In this review, we will summarize the current state of knowledge on the various passive permeability barriers present in mammalian cells. We will conclude with a description of several conventional techniques and one new approach based on chemically-inducible diffusion trap (C-IDT) for probing permeable barriers. PMID:23731778

The Effects of Realism in Learning with Dynamic Visualizations

ERIC Educational Resources Information Center

Scheiter, Katharina; Gerjets, Peter; Huk, Thomas; Imhof, Birgit; Kammerer, Yvonne

2009-01-01

Two experiments are reported that investigated the relative effectiveness of a realistic dynamic visualization as opposed to a schematic visualization for learning about cell replication (mitosis). In Experiment 1, 37 university students watched either realistic or schematic visualizations. Students' subjective task demands ratings as well as…

Pulse Phase Dynamic Thermal Tomography Investigation on the Defects of the Solid-Propellant Missile Engine Cladding Layer

NASA Astrophysics Data System (ADS)

Peng, Wei; Wang, Fei; Liu, Jun-yan; Xiao, Peng; Wang, Yang; Dai, Jing-min

2018-04-01

Pulse phase dynamic thermal tomography (PP-DTT) was introduced as a nondestructive inspection technique to detect the defects of the solid-propellant missile engine cladding layer. One-dimensional thermal wave mathematical model stimulated by pulse signal was developed and employed to investigate the thermal wave transmission characteristics. The pulse phase algorithm was used to extract the thermal wave characteristic of thermal radiation. Depth calibration curve was obtained by fuzzy c-means algorithm. Moreover, PP-DTT, a depth-resolved photothermal imaging modality, was employed to enable three-dimensional (3D) visualization of cladding layer defects. The comparison experiment between PP-DTT and classical dynamic thermal tomography was investigated. The results showed that PP-DTT can reconstruct the 3D topography of defects in a high quality.

Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping

NASA Astrophysics Data System (ADS)

Frasinski, L. J.; Zhaunerchyk, V.; Mucke, M.; Squibb, R. J.; Siano, M.; Eland, J. H. D.; Linusson, P.; v. d. Meulen, P.; Salén, P.; Thomas, R. D.; Larsson, M.; Foucar, L.; Ullrich, J.; Motomura, K.; Mondal, S.; Ueda, K.; Osipov, T.; Fang, L.; Murphy, B. F.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Schorb, S.; Messerschmidt, M.; Glownia, J. M.; Cryan, J. P.; Coffee, R. N.; Takahashi, O.; Wada, S.; Piancastelli, M. N.; Richter, R.; Prince, K. C.; Feifel, R.

2013-08-01

When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called “partial covariance mapping” to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.

How to identify dislocations in molecular dynamics simulations?

NASA Astrophysics Data System (ADS)

Li, Duo; Wang, FengChao; Yang, ZhenYu; Zhao, YaPu

2014-12-01

Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

NASA Astrophysics Data System (ADS)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-09-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

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

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlapmore » with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.« less

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

PubMed Central

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-01-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space. PMID:25240340

Learning about Locomotion Patterns from Visualizations: Effects of Presentation Format and Realism

ERIC Educational Resources Information Center

Imhof, Birgit; Scheiter, Katharina; Gerjets, Peter

2011-01-01

The rapid development of computer graphics technology has made possible an easy integration of dynamic visualizations into computer-based learning environments. This study examines the relative effectiveness of dynamic visualizations, compared either to sequentially or simultaneously presented static visualizations. Moreover, the degree of realism…

Perceptual upright: the relative effectiveness of dynamic and static images under different gravity States.

PubMed

Jenkin, Michael R; Dyde, Richard T; Jenkin, Heather L; Zacher, James E; Harris, Laurence R

2011-01-01

The perceived direction of up depends on both gravity and visual cues to orientation. Static visual cues to orientation have been shown to be less effective in influencing the perception of upright (PU) under microgravity conditions than they are on earth (Dyde et al., 2009). Here we introduce dynamic orientation cues into the visual background to ascertain whether they might increase the effectiveness of visual cues in defining the PU under different gravity conditions. Brief periods of microgravity and hypergravity were created using parabolic flight. Observers viewed a polarized, natural scene presented at various orientations on a laptop viewed through a hood which occluded all other visual cues. The visual background was either an animated video clip in which actors moved along the visual ground plane or an individual static frame taken from the same clip. We measured the perceptual upright using the oriented character recognition test (OCHART). Dynamic visual cues significantly enhance the effectiveness of vision in determining the perceptual upright under normal gravity conditions. Strong trends were found for dynamic visual cues to produce an increase in the visual effect under both microgravity and hypergravity conditions.

Dynamic motion analysis of dart throwers motion visualized through computerized tomography and calculation of the axis of rotation.

PubMed

Edirisinghe, Y; Troupis, J M; Patel, M; Smith, J; Crossett, M

2014-05-01

We used a dynamic three-dimensional (3D) mapping method to model the wrist in dynamic unrestricted dart throwers motion in three men and four women. With the aid of precision landmark identification, a 3D coordinate system was applied to the distal radius and the movement of the carpus was described. Subsequently, with dynamic 3D reconstructions and freedom to position the camera viewpoint anywhere in space, we observed the motion pathways of all carpal bones in dart throwers motion and calculated its axis of rotation. This was calculated to lie in 27° of anteversion from the coronal plane and 44° of varus angulation relative to the transverse plane. This technique is a safe and a feasible carpal imaging method to gain key information for decision making in future hand surgical and rehabilitative practices.

A rain pixel recovery algorithm for videos with highly dynamic scenes.

PubMed

Jie Chen; Lap-Pui Chau

2014-03-01

Rain removal is a very useful and important technique in applications such as security surveillance and movie editing. Several rain removal algorithms have been proposed these years, where photometric, chromatic, and probabilistic properties of the rain have been exploited to detect and remove the rainy effect. Current methods generally work well with light rain and relatively static scenes, when dealing with heavier rainfall in dynamic scenes, these methods give very poor visual results. The proposed algorithm is based on motion segmentation of dynamic scene. After applying photometric and chromatic constraints for rain detection, rain removal filters are applied on pixels such that their dynamic property as well as motion occlusion clue are considered; both spatial and temporal informations are then adaptively exploited during rain pixel recovery. Results show that the proposed algorithm has a much better performance for rainy scenes with large motion than existing algorithms.

Infant Attention to Dynamic Audiovisual Stimuli: Look Duration from 3 to 9 Months of Age

ERIC Educational Resources Information Center

Reynolds, Greg D.; Zhang, Dantong; Guy, Maggie W.

2013-01-01

The goal of this study was to examine developmental change in visual attention to dynamic visual and audiovisual stimuli in 3-, 6-, and 9-month-old infants. Infant look duration was measured during exposure to dynamic geometric patterns and Sesame Street video clips under three different stimulus modality conditions: unimodal visual, synchronous…

Visual Design Guidelines for Improving Learning from Dynamic and Interactive Digital Text

ERIC Educational Resources Information Center

Jin, Sung-Hee

2013-01-01

Despite the dynamic and interactive features of digital text, the visual design guidelines for digital text are similar to those for printed text. The purpose of this study was to develop visual design guidelines for improving learning from dynamic and interactive digital text and to validate them by controlled testing. Two structure design…

Enhancing Learning from Dynamic and Static Visualizations by Means of Cueing

ERIC Educational Resources Information Center

Kuhl, Tim; Scheiter, Katharina; Gerjets, Peter

2012-01-01

The current study investigated whether learning from dynamic and two presentation formats for static visualizations can be enhanced by means of cueing. One hundred and fifty university students were randomly assigned to six conditions, resulting from a 2x3-design, with cueing (with/without) and type of visualization (dynamic, static-sequential,…

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Fundamental considerations in dynamic fracture in nuclear materials

NASA Astrophysics Data System (ADS)

Cady, Carl; Eastwood, David; Bourne, Neil; Pei, Ruizhi; Mummery, Paul; Rau, Christoph

2017-06-01

The structural integrity of components used in nuclear power plants is the biggest concern of operators. A diverse range of materials, loading, prior histories and environmental conditions, leads to a complex operating environment. An experimental technique has been developed to characterize brittle materials and using linear elastic fracture mechanics, has given accurate measurements of the fracture toughness of materials. X-ray measurements were used to track the crack front as a function of loading parameters as well as determine the crack surface area as loads increased. This X-ray tomographic study of dynamic fracture in beryllium indicates the onset of damage within the target as load is increased. Similarly, measurements on nuclear graphite were conducted to evaluate the technique. This new, quantitative information obtained using the X-ray techniques has shown application in other materials. These materials exhibited a range of brittle and ductile responses that will test our modelling schemes for fracture. Further visualization of crack front advance and the correlated strain fields that are generated during the experiment for the two distinct deformation processes provide a vital step in validating new multiscale predicative modelling.

Visual-area coding technique (VACT): optical parallel implementation of fuzzy logic and its visualization with the digital-halftoning process

NASA Astrophysics Data System (ADS)

Konishi, Tsuyoshi; Tanida, Jun; Ichioka, Yoshiki

1995-06-01

A novel technique, the visual-area coding technique (VACT), for the optical implementation of fuzzy logic with the capability of visualization of the results is presented. This technique is based on the microfont method and is considered to be an instance of digitized analog optical computing. Huge amounts of data can be processed in fuzzy logic with the VACT. In addition, real-time visualization of the processed result can be accomplished.

Visualizing the chain-flipping mechanism in fatty-acid biosynthesis

DOE PAGES

Beld, Joris; Cang, Hu; Burkart, Michael D.

2014-10-29

The acyl carrier protein (ACP) from fatty acid synthases sequesters elongating products within its hydrophobic core, but this dynamic mechanism remains poorly understood. In this paper, we exploited solvatochromic pantetheine probes attached to ACP that fluoresce when sequestered. The addition of a catalytic partner lures the cargo out of the ACP and into the active site of the enzyme, thus enhancing fluorescence to reveal the elusive chain-flipping mechanism. This activity was confirmed by the use of a dual solvatochromic cross-linking probe and solution-phase NMR spectroscopy. Finally, the chain-flipping mechanism was visualized by single-molecule fluorescence techniques, thus demonstrating specificity between themore » Escherichia coli ACP and its ketoacyl synthase catalytic partner KASII.« less

Virtual reality in radiology: virtual intervention

NASA Astrophysics Data System (ADS)

Harreld, Michael R.; Valentino, Daniel J.; Duckwiler, Gary R.; Lufkin, Robert B.; Karplus, Walter J.

1995-04-01

Intracranial aneurysms are the primary cause of non-traumatic subarachnoid hemorrhage. Morbidity and mortality remain high even with current endovascular intervention techniques. It is presently impossible to identify which aneurysms will grow and rupture, however hemodynamics are thought to play an important role in aneurysm development. With this in mind, we have simulated blood flow in laboratory animals using three dimensional computational fluid dynamics software. The data output from these simulations is three dimensional, complex and transient. Visualization of 3D flow structures with standard 2D display is cumbersome, and may be better performed using a virtual reality system. We are developing a VR-based system for visualization of the computed blood flow and stress fields. This paper presents the progress to date and future plans for our clinical VR-based intervention simulator. The ultimate goal is to develop a software system that will be able to accurately model an aneurysm detected on clinical angiography, visualize this model in virtual reality, predict its future behavior, and give insight into the type of treatment necessary. An associated database will give historical and outcome information on prior aneurysms (including dynamic, structural, and categorical data) that will be matched to any current case, and assist in treatment planning (e.g., natural history vs. treatment risk, surgical vs. endovascular treatment risks, cure prediction, complication rates).

3D MRI Modeling of Thin and Spatially Complex Soft Tissue Structures without Shrinkage: Lamprey Myosepta as an Example.

PubMed

Wood, Bradley M; Jia, Guang; Carmichael, Owen; McKlveen, Kevin; Homberger, Dominique G

2018-05-12

3D imaging techniques enable the non-destructive analysis and modeling of complex structures. Among these, MRI exhibits good soft tissue contrast, but is currently less commonly used for non-clinical research than x-ray CT, even though the latter requires contrast-staining that shrinks and distorts soft tissues. When the objective is the creation of a realistic and complete 3D model of soft tissue structures, MRI data are more demanding to acquire and visualize and require extensive post-processing because they comprise non-cubic voxels with dimensions that represent a trade-off between tissue contrast and image resolution. Therefore, thin soft tissue structures with complex spatial configurations are not always visible in a single MRI dataset, so that standard segmentation techniques are not sufficient for their complete visualization. By using the example of the thin and spatially complex connective tissue myosepta in lampreys, we developed a workflow protocol for the selection of the appropriate parameters for the acquisition of MRI data and for the visualization and 3D modeling of soft tissue structures. This protocol includes a novel recursive segmentation technique for supplementing missing data in one dataset with data from another dataset to produce realistic and complete 3D models. Such 3D models are needed for the modeling of dynamic processes, such as the biomechanics of fish locomotion. However, our methodology is applicable to the visualization of any thin soft tissue structures with complex spatial configurations, such as fasciae, aponeuroses, and small blood vessels and nerves, for clinical research and the further exploration of tensegrity. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Virtual 3D Modeling of Airways in Congenital Heart Defects

PubMed Central

Speggiorin, Simone; Durairaj, Saravanan; Mimic, Branko; Corno, Antonio F.

2016-01-01

The involvement of the airway is not uncommon in the presence of complex cardiovascular malformations. In these cases, a careful inspection of the relationship between the airway and the vasculature is paramount to plan the surgical procedure. Three-dimensional printing enhanced the visualization of the cardiovascular structure. Unfortunately, IT does not allow to remove selected anatomy to improve the visualization of the surrounding ones. Computerized modeling has the potential to fill this gap by allowing a dynamic handling of different anatomies, increasing the exposure of vessels or bronchi to show their relationship. We started to use this technique to plan the surgical repair in these complex cases where the airway is affected. This technique is routinely used in our Institution as an additional tool in the presurgical assessment. We report four cases in which the airways were compressed by vascular structures – ascending aorta in one, left pulmonary artery sling in one, patent ductus arteriosus in one, and major aorto-pulmonary collateral artery in one. We believe this technique can enhance the understanding of the causes of airway involvement and facilitate the creation of an appropriate surgical plan. PMID:27833903

Visualizing Structure and Dynamics of Disaccharide Simulations

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

Matthews, J. F.; Beckham, G. T.; Himmel, M. E.

2012-01-01

We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

Improving resolution of dynamic communities in human brain networks through targeted node removal

PubMed Central

Turner, Benjamin O.; Miller, Michael B.; Carlson, Jean M.

2017-01-01

Current approaches to dynamic community detection in complex networks can fail to identify multi-scale community structure, or to resolve key features of community dynamics. We propose a targeted node removal technique to improve the resolution of community detection. Using synthetic oscillator networks with well-defined “ground truth” communities, we quantify the community detection performance of a common modularity maximization algorithm. We show that the performance of the algorithm on communities of a given size deteriorates when these communities are embedded in multi-scale networks with communities of different sizes, compared to the performance in a single-scale network. We demonstrate that targeted node removal during community detection improves performance on multi-scale networks, particularly when removing the most functionally cohesive nodes. Applying this approach to network neuroscience, we compare dynamic functional brain networks derived from fMRI data taken during both repetitive single-task and varied multi-task experiments. After the removal of regions in visual cortex, the most coherent functional brain area during the tasks, community detection is better able to resolve known functional brain systems into communities. In addition, node removal enables the algorithm to distinguish clear differences in brain network dynamics between these experiments, revealing task-switching behavior that was not identified with the visual regions present in the network. These results indicate that targeted node removal can improve spatial and temporal resolution in community detection, and they demonstrate a promising approach for comparison of network dynamics between neuroscientific data sets with different resolution parameters. PMID:29261662

Moving to higher ground: The dynamic field theory and the dynamics of visual cognition

PubMed Central

Johnson, Jeffrey S.; Spencer, John P.; Schöner, Gregor

2009-01-01

In the present report, we describe a new dynamic field theory that captures the dynamics of visuo-spatial cognition. This theory grew out of the dynamic systems approach to motor control and development, and is grounded in neural principles. The initial application of dynamic field theory to issues in visuo-spatial cognition extended concepts of the motor approach to decision making in a sensori-motor context, and, more recently, to the dynamics of spatial cognition. Here we extend these concepts still further to address topics in visual cognition, including visual working memory for non-spatial object properties, the processes that underlie change detection, and the ‘binding problem’ in vision. In each case, we demonstrate that the general principles of the dynamic field approach can unify findings in the literature and generate novel predictions. We contend that the application of these concepts to visual cognition avoids the pitfalls of reductionist approaches in cognitive science, and points toward a formal integration of brains, bodies, and behavior. PMID:19173013

VMD DisRg: New User-Friendly Implement for calculation distance and radius of gyration in VMD program

PubMed Central

Falsafi-Zadeh, Sajad; Karimi, Zahra; Galehdari, Hamid

2012-01-01

Molecular dynamic simulation is a practical and powerful technique for analysis of protein structure. Several programs have been developed to facilitate the mentioned investigation, under them the visual molecular dynamic or VMD is the most frequently used programs. One of the beneficial properties of the VMD is its ability to be extendable by designing new plug-in. We introduce here a new facility of the VMD for distance analysis and radius of gyration of biopolymers such as protein and DNA. Availability The database is available for free at http://trc.ajums.ac.ir/HomePage.aspx/?TabID/=12618/&Site/=trc.ajums.ac/&Lang/=fa-IR PMID:22553393

Surface nanobubble nucleation dynamics during water-ethanol exchange

NASA Astrophysics Data System (ADS)

Chan, Chon U.; Ohl, Claus-Dieter

2015-11-01

Water-ethanol exchange has been a promising nucleation method for surface attached nanobubbles since their discovery. In this process, water and ethanol displace each other sequentially on a substrate. As the gas solubility is 36 times higher in ethanol than water, it was suggested that the exchange process leads to transient supersaturation and is responsible for the nanobubble nucleation. In this work, we visualize the nucleation dynamics by controllably mixing water and ethanol. It depicts the temporal evolution of the conventional exchange in a single field of view, detailing the conditions for surface nanobubble nucleation and the flow field that influences their spatial organization. This technique can also pattern surface nanobubbles with variable size distribution.

Tissue structure characterization of biotissue phantom by use of the speckle-correlometric technique

NASA Astrophysics Data System (ADS)

Isaeva, A. A.; Isaeva, E. A.; Zimnyakov, D. A.; Pantyukov, A. V.; Agapova, Y. V.; Macheyev, M. A.

2017-03-01

Speckle correlometry gives the possibilities to visualize tissue scattering structure analyzing the correlation characteristics of speckle-modulated images. In this work, the inhomogeneous multiple scattering medium with the "dynamic" long inclusions was investigated like a blood vessels in living tissue. The scattering media is 0.28% weight fraction of gelatin dissolved in water and 1 gram per liter (gL-1) and 100 mg per liter (gL-1) of TiO2 for optical scattering. The movement of fluid (distilled water) in the cylindrical hole with given radius simulate a blood motion in the vessel. It was shown the possibility to determinate the depth location of dynamic inhomogeneities inside a scattering medium.

Minimizing Retraction by Pia-Arachnoidal 10-0 Sutures in Intrasulcal Dissection.

PubMed

Uluc, Kutluay; Cikla, Ulas; Morkan, Deniz B; Sirin, Alperen; Ahmed, Azam S; Swanson, Kyle; Baskaya, Mustafa K

2018-07-01

In contemporary microneurosurgery reducing retraction-induced injury to the brain is essential. Self-retaining retractor systems are commonly used to improve visualization and decrease the repetitive microtrauma, but sometimes self-retaining retractor systems can be cumbersome and the force applied can cause focal ischemia or contusions. This may increase the morbidity and mortality. Here, we describe a technique of retraction using 10-0 sutures in the arachnoid. To evaluate the imaging and clinical results in patients where 10-0 suture retraction was used to aid the surgical procedure. Adjacent cortex was retracted by placing 10-0 nylon suture in the arachnoid of the bank or banks of the sulcus. The suture was secured to the adjacent dural edge by using aneurysm clips, allowing for easy adjustability of the amount of retraction. We retrospectively analyzed the neurological outcome, signal changes in postoperative imaging, and ease of performing surgery in 31 patients with various intracranial lesions including intracranial aneurysms, intra- and extra-axial tumors, and cerebral ischemia requiring arterial bypass. Clinically, there were no injuries, vascular events, or neurological deficits referable to the relevant cortex. Postoperative imaging did not show changes consistent with ischemia or contusion due to the retraction. This technique improved the visualization and illumination of the surgical field in all cases. Retraction of the arachnoid can be used safely in cases where trans-sulcal dissection is required. This technique may improve initial visualization and decrease the need for dynamic or static retraction.

Principal component analysis of indocyanine green fluorescence dynamics for diagnosis of vascular diseases

NASA Astrophysics Data System (ADS)

Seo, Jihye; An, Yuri; Lee, Jungsul; Choi, Chulhee

2015-03-01

Indocyanine green (ICG), a near-infrared fluorophore, has been used in visualization of vascular structure and non-invasive diagnosis of vascular disease. Although many imaging techniques have been developed, there are still limitations in diagnosis of vascular diseases. We have recently developed a minimally invasive diagnostics system based on ICG fluorescence imaging for sensitive detection of vascular insufficiency. In this study, we used principal component analysis (PCA) to examine ICG spatiotemporal profile and to obtain pathophysiological information from ICG dynamics. Here we demonstrated that principal components of ICG dynamics in both feet showed significant differences between normal control and diabetic patients with vascula complications. We extracted the PCA time courses of the first three components and found distinct pattern in diabetic patient. We propose that PCA of ICG dynamics reveal better classification performance compared to fluorescence intensity analysis. We anticipate that specific feature of spatiotemporal ICG dynamics can be useful in diagnosis of various vascular diseases.

The Elicitation Interview Technique: Capturing People's Experiences of Data Representations.

PubMed

Hogan, Trevor; Hinrichs, Uta; Hornecker, Eva

2016-12-01

Information visualization has become a popular tool to facilitate sense-making, discovery and communication in a large range of professional and casual contexts. However, evaluating visualizations is still a challenge. In particular, we lack techniques to help understand how visualizations are experienced by people. In this paper we discuss the potential of the Elicitation Interview technique to be applied in the context of visualization. The Elicitation Interview is a method for gathering detailed and precise accounts of human experience. We argue that it can be applied to help understand how people experience and interpret visualizations as part of exploration and data analysis processes. We describe the key characteristics of this interview technique and present a study we conducted to exemplify how it can be applied to evaluate data representations. Our study illustrates the types of insights this technique can bring to the fore, for example, evidence for deep interpretation of visual representations and the formation of interpretations and stories beyond the represented data. We discuss general visualization evaluation scenarios where the Elicitation Interview technique may be beneficial and specify what needs to be considered when applying this technique in a visualization context specifically.

Dynamic single photon emission computed tomography—basic principles and cardiac applications

PubMed Central

Gullberg, Grant T; Reutter, Bryan W; Sitek, Arkadiusz; Maltz, Jonathan S; Budinger, Thomas F

2011-01-01

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time–activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time–activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging, especially in light of new developments that enable measurement of dynamic processes directly from projection measurements. PMID:20858925

TOPICAL REVIEW: Dynamic single photon emission computed tomography—basic principles and cardiac applications

NASA Astrophysics Data System (ADS)

Gullberg, Grant T.; Reutter, Bryan W.; Sitek, Arkadiusz; Maltz, Jonathan S.; Budinger, Thomas F.

2010-10-01

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time-activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time-activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging, especially in light of new developments that enable measurement of dynamic processes directly from projection measurements.

TopicLens: Efficient Multi-Level Visual Topic Exploration of Large-Scale Document Collections.

PubMed

Kim, Minjeong; Kang, Kyeongpil; Park, Deokgun; Choo, Jaegul; Elmqvist, Niklas

2017-01-01

Topic modeling, which reveals underlying topics of a document corpus, has been actively adopted in visual analytics for large-scale document collections. However, due to its significant processing time and non-interactive nature, topic modeling has so far not been tightly integrated into a visual analytics workflow. Instead, most such systems are limited to utilizing a fixed, initial set of topics. Motivated by this gap in the literature, we propose a novel interaction technique called TopicLens that allows a user to dynamically explore data through a lens interface where topic modeling and the corresponding 2D embedding are efficiently computed on the fly. To support this interaction in real time while maintaining view consistency, we propose a novel efficient topic modeling method and a semi-supervised 2D embedding algorithm. Our work is based on improving state-of-the-art methods such as nonnegative matrix factorization and t-distributed stochastic neighbor embedding. Furthermore, we have built a web-based visual analytics system integrated with TopicLens. We use this system to measure the performance and the visualization quality of our proposed methods. We provide several scenarios showcasing the capability of TopicLens using real-world datasets.

Visual Iconic Patterns of Instant Messaging: Steps Towards Understanding Visual Conversations

NASA Astrophysics Data System (ADS)

Bays, Hillary

An Instant Messaging (IM) conversation is a dynamic communication register made up of text, images, animation and sound played out on a screen with potentially several parallel conversations and activities all within a physical environment. This article first examines how best to capture this unique gestalt using in situ recording techniques (video, screen capture, XML logs) which highlight the micro-phenomenal level of the exchange and the macro-social level of the interaction. Of particular interest are smileys first as cultural artifacts in CMC in general then as linguistic markers. A brief taxonomy of these markers is proposed in an attempt to clarify their frequency and patterns of their use. Then, focus is placed on their importance as perceptual cues which facilitate communication, while also serving as emotive and emphatic functional markers. We try to demonstrate that the use of smileys and animation is not arbitrary but an organized interactional and structured practice. Finally, we discuss how the study of visual markers in IM could inform the study of other visual conversation codes, such as sign languages, which also have co-produced, physical behavior, suggesting the possibility of a visual phonology.

Regional cerebral blood flow measurement with intravenous ( sup 15 O)water bolus and ( sup 18 F)fluoromethane inhalation

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

Herholz, K.; Pietrzyk, U.; Wienhard, K.

1989-09-01

In 20 patients with ischemic cerebrovascular disease, classic migraine, or angiomas, we compared paired dynamic positron emission tomographic measurements of regional cerebral blood flow using both ({sup 15}O)water and ({sup 18}F)fluoromethane as tracers. Cerebral blood flow was also determined according to the autoradiographic technique with a bolus injection of ({sup 15}O)water. There were reasonable overall correlations between dynamic ({sup 15}O)water and ({sup 18}F)fluoromethane values for cerebral blood flow (r = 0.82) and between dynamic and autoradiographic ({sup 15}O)water values for cerebral blood flow (r = 0.83). We found a close correspondence between abnormal pathologic findings and visually evaluated cerebral bloodmore » flow tomograms obtained with the two tracers. On average, dynamic ({sup 15}O)water cerebral blood flow was 6% lower than that measured with ({sup 18}F)fluoromethane. There also was a general trend toward a greater underestimation with ({sup 15}O)water in high-flow areas, particularly in hyperemic areas, probably due to incomplete first-pass extraction of ({sup 15}O)water. Underestimation was not detected in low-flow areas or in the cerebellum. Absolute cerebral blood flow values were less closely correlated between tracers and techniques than cerebral blood flow patterns. The variability of the relation between absolute flow values was probably caused by confounding effects of the variation in the circulatory delay time. The autoradiographic technique was most sensitive to this type error.« less

Neonatal hemodynamic response to visual cortex activity: high-density near-infrared spectroscopy study

NASA Astrophysics Data System (ADS)

Liao, Steve M.; Gregg, Nick M.; White, Brian R.; Zeff, Benjamin W.; Bjerkaas, Katelin A.; Inder, Terrie E.; Culver, Joseph P.

2010-03-01

The neurodevelopmental outcome of neonatal intensive care unit (NICU) infants is a major clinical concern with many infants displaying neurobehavioral deficits in childhood. Functional neuroimaging may provide early recognition of neural deficits in high-risk infants. Near-infrared spectroscopy (NIRS) has the advantage of providing functional neuroimaging in infants at the bedside. However, limitations in traditional NIRS have included contamination from superficial vascular dynamics in the scalp. Furthermore, controversy exists over the nature of normal vascular, responses in infants. To address these issues, we extend the use of novel high-density NIRS arrays with multiple source-detector distances and a superficial signal regression technique to infants. Evaluations of healthy term-born infants within the first three days of life are performed without sedation using a visual stimulus. We find that the regression technique significantly improves brain activation signal quality. Furthermore, in six out of eight infants, both oxy- and total hemoglobin increases while deoxyhemoglobin decreases, suggesting that, at term, the neurovascular coupling in the visual cortex is similar to that found in healthy adults. These results demonstrate the feasibility of using high-density NIRS arrays in infants to improve signal quality through superficial signal regression, and provide a foundation for further development of high-density NIRS as a clinical tool.

Clinical application of photodynamic medicine technology using light-emitting fluorescence imaging based on a specialized luminous source.

PubMed

Namikawa, Tsutomu; Fujisawa, Kazune; Munekage, Eri; Iwabu, Jun; Uemura, Sunao; Tsujii, Shigehiro; Maeda, Hiromichi; Kitagawa, Hiroyuki; Fukuhara, Hideo; Inoue, Keiji; Sato, Takayuki; Kobayashi, Michiya; Hanazaki, Kazuhiro

2018-04-04

The natural amino acid 5-aminolevulinic acid (ALA) is a protoporphyrin IX (PpIX) precursor and a new-generation photosensitive substance that accumulates specifically in cancer cells. When indocyanine green (ICG) is irradiated with near-infrared (NIR) light, it shifts to a higher energy state and emits infrared light with a longer wavelength than the irradiated NIR light. Photodynamic diagnosis (PDD) using ALA and ICG-based NIR fluorescence imaging has emerged as a new diagnostic technique. Specifically, in laparoscopic examinations for serosa-invading advanced gastric cancer, peritoneal metastases could be detected by ALA-PDD, but not by conventional visible-light imaging. The HyperEye Medical System (HEMS) can visualize ICG fluorescence as color images simultaneously projected with visible light in real time. This ICG fluorescence method is widely applicable, including for intraoperative identification of sentinel lymph nodes, visualization of blood vessels in organ resection, and blood flow evaluation during surgery. Fluorescence navigation by ALA-PDD and NIR using ICG imaging provides good visualization and detection of the target lesions that is not possible with the naked eye. We propose that this technique should be used in fundamental research on the relationship among cellular dynamics, metabolic enzymes, and tumor tissues, and to evaluate clinical efficacy and safety in multicenter cooperative clinical trials.

Implications on visual apperception: energy, duration, structure and synchronization.

PubMed

Bókkon, I; Vimal, Ram Lakhan Pandey

2010-07-01

Although primary visual cortex (V1 or striate) activity per se is not sufficient for visual apperception (normal conscious visual experiences and conscious functions such as detection, discrimination, and recognition), the same is also true for extrastriate visual areas (such as V2, V3, V4/V8/VO, V5/M5/MST, IT, and GF). In the lack of V1 area, visual signals can still reach several extrastriate parts but appear incapable of generating normal conscious visual experiences. It is scarcely emphasized in the scientific literature that conscious perceptions and representations must have also essential energetic conditions. These energetic conditions are achieved by spatiotemporal networks of dynamic mitochondrial distributions inside neurons. However, the highest density of neurons in neocortex (number of neurons per degree of visual angle) devoted to representing the visual field is found in retinotopic V1. It means that the highest mitochondrial (energetic) activity can be achieved in mitochondrial cytochrome oxidase-rich V1 areas. Thus, V1 bear the highest energy allocation for visual representation. In addition, the conscious perceptions also demand structural conditions, presence of adequate duration of information representation, and synchronized neural processes and/or 'interactive hierarchical structuralism.' For visual apperception, various visual areas are involved depending on context such as stimulus characteristics such as color, form/shape, motion, and other features. Here, we focus primarily on V1 where specific mitochondrial-rich retinotopic structures are found; we will concisely discuss V2 where smaller riches of these structures are found. We also point out that residual brain states are not fully reflected in active neural patterns after visual perception. Namely, after visual perception, subliminal residual states are not being reflected in passive neural recording techniques, but require active stimulation to be revealed.

Pinch-off dynamics, extensional viscosity and relaxation time of dilute and ultradilute aqueous polymer solutions

NASA Astrophysics Data System (ADS)

Biagioli, Madeleine; Dinic, Jelena; Jimenez, Leidy Nallely; Sharma, Vivek

Free surface flows and drop formation processes present in printing, jetting, spraying, and coating involve the development of columnar necks that undergo spontaneous surface-tension driven instability, thinning, and pinch-off. Stream-wise velocity gradients that arise within the thinning neck create and extensional flow field, which induces micro-structural changes within complex fluids that contribute elastic stresses, changing the thinning and pinch-off dynamics. In this contribution, we use dripping-onto-substrate (DoS) extensional rheometry technique for visualization and analysis of the pinch-off dynamics of dilute and ultra-dilute aqueous polyethylene oxide (PEO) solutions. Using a range of molecular weights, we study the effect of both elasticity and finite extensibility. Both effective relaxation time and the transient extensional viscosity are found to be strongly concentration-dependent even for highly dilute solutions.

Dynamic acousto-elastic testing of concrete with a coda-wave probe: comparison with standard linear and nonlinear ultrasonic techniques.

PubMed

Shokouhi, Parisa; Rivière, Jacques; Lake, Colton R; Le Bas, Pierre-Yves; Ulrich, T J

2017-11-01

The use of nonlinear acoustic techniques in solids consists in measuring wave distortion arising from compliant features such as cracks, soft intergrain bonds and dislocations. As such, they provide very powerful nondestructive tools to monitor the onset of damage within materials. In particular, a recent technique called dynamic acousto-elasticity testing (DAET) gives unprecedented details on the nonlinear elastic response of materials (classical and non-classical nonlinear features including hysteresis, transient elastic softening and slow relaxation). Here, we provide a comprehensive set of linear and nonlinear acoustic responses on two prismatic concrete specimens; one intact and one pre-compressed to about 70% of its ultimate strength. The two linear techniques used are Ultrasonic Pulse Velocity (UPV) and Resonance Ultrasound Spectroscopy (RUS), while the nonlinear ones include DAET (fast and slow dynamics) as well as Nonlinear Resonance Ultrasound Spectroscopy (NRUS). In addition, the DAET results correspond to a configuration where the (incoherent) coda portion of the ultrasonic record is used to probe the samples, as opposed to a (coherent) first arrival wave in standard DAET tests. We find that the two visually identical specimens are indistinguishable based on parameters measured by linear techniques (UPV and RUS). On the contrary, the extracted nonlinear parameters from NRUS and DAET are consistent and orders of magnitude greater for the damaged specimen than those for the intact one. This compiled set of linear and nonlinear ultrasonic testing data including the most advanced technique (DAET) provides a benchmark comparison for their use in the field of material characterization. Copyright © 2017 Elsevier B.V. All rights reserved.

Review of Static Approaches to Surgical Correction of Presbyopia

PubMed Central

Zare Mehrjerdi, Mohammad Ali; Mohebbi, Masomeh; Zandian, Mehdi

2017-01-01

Presbyopia is the primary cause of reduction in the quality of life of people in their 40s, due to dependence on spectacles. Therefore, presbyopia correction has become an evolving and rapidly progressive field in refractive surgery. There are two primary options for presbyopia correction: the dynamic approach uses the residual accommodative capacity of the eye, and the static approach attempts to enhance the depth of focus of the optical system. The dynamic approach attempts to reverse suspected pathophysiologic changes. Dynamic approaches such as accommodative intraocular lenses (IOLs), scleral expansion techniques, refilling, and photodisruption of the crystalline lens have attracted less clinical interest due to inconsistent results and the complexity of the techniques. We have reviewed the most popular static techniques in presbyopia surgery, including multifocal IOLs, PresbyLASIK, and corneal inlays, but we should emphasize that these techniques are very different from the physiologic status of an untouched eye. A systematic PubMed search for the keywords “presbylasik”, “multifocal IOL”, and “presbyopic corneal inlay” revealed 634 articles; 124 were controlled clinical trials, 95 were published in the previous 10 years, and 78 were English with available full text. We reviewed the abstracts and rejected the unrelated articles; other references were included as needed. This narrative review compares different treatments according to available information on the optical basis of each treatment modality, including the clinical outcomes such as near, intermediate, and far visual acuity, spectacles independence, quality of vision, and dysphotopic phenomena. PMID:29090052

Visualization of conserved structures by fusing highly variable datasets.

PubMed

Silverstein, Jonathan C; Chhadia, Ankur; Dech, Fred

2002-01-01

Skill, effort, and time are required to identify and visualize anatomic structures in three-dimensions from radiological data. Fundamentally, automating these processes requires a technique that uses symbolic information not in the dynamic range of the voxel data. We were developing such a technique based on mutual information for automatic multi-modality image fusion (MIAMI Fuse, University of Michigan). This system previously demonstrated facility at fusing one voxel dataset with integrated symbolic structure information to a CT dataset (different scale and resolution) from the same person. The next step of development of our technique was aimed at accommodating the variability of anatomy from patient to patient by using warping to fuse our standard dataset to arbitrary patient CT datasets. A standard symbolic information dataset was created from the full color Visible Human Female by segmenting the liver parenchyma, portal veins, and hepatic veins and overwriting each set of voxels with a fixed color. Two arbitrarily selected patient CT scans of the abdomen were used for reference datasets. We used the warping functions in MIAMI Fuse to align the standard structure data to each patient scan. The key to successful fusion was the focused use of multiple warping control points that place themselves around the structure of interest automatically. The user assigns only a few initial control points to align the scans. Fusion 1 and 2 transformed the atlas with 27 points around the liver to CT1 and CT2 respectively. Fusion 3 transformed the atlas with 45 control points around the liver to CT1 and Fusion 4 transformed the atlas with 5 control points around the portal vein. The CT dataset is augmented with the transformed standard structure dataset, such that the warped structure masks are visualized in combination with the original patient dataset. This combined volume visualization is then rendered interactively in stereo on the ImmersaDesk in an immersive Virtual Reality (VR) environment. The accuracy of the fusions was determined qualitatively by comparing the transformed atlas overlaid on the appropriate CT. It was examined for where the transformed structure atlas was incorrectly overlaid (false positive) and where it was incorrectly not overlaid (false negative). According to this method, fusions 1 and 2 were correct roughly 50-75% of the time, while fusions 3 and 4 were correct roughly 75-100%. The CT dataset augmented with transformed dataset was viewed arbitrarily in user-centered perspective stereo taking advantage of features such as scaling, windowing and volumetric region of interest selection. This process of auto-coloring conserved structures in variable datasets is a step toward the goal of a broader, standardized automatic structure visualization method for radiological data. If successful it would permit identification, visualization or deletion of structures in radiological data by semi-automatically applying canonical structure information to the radiological data (not just processing and visualization of the data's intrinsic dynamic range). More sophisticated selection of control points and patterns of warping may allow for more accurate transforms, and thus advances in visualization, simulation, education, diagnostics, and treatment planning.

Variability of normal vocal fold dynamics for different vocal loading in one healthy subject investigated by phonovibrograms.

PubMed

Doellinger, Michael; Lohscheller, Joerg; McWhorter, Andrew; Kunduk, Melda

2009-03-01

We investigate the potential of high-speed digital imaging technique (HSI) and the phonovibrogram (PVG) analysis in normal vocal fold dynamics by studying the effects of continuous voice use (vocal loading) during the workday. One healthy subject was recorded at sustained phonation 13 times within 2 consecutive days in the morning before and in the afternoon after vocal loading, respectively. Vocal fold dynamics were extracted and visualized by PVGs. The characteristic PVG patterns were extracted representing vocal fold vibration types. The parameter values were then analyzed by statistics regarding vocal load, left-right PVG asymmetries, anterior-posterior PVG asymmetries, and opening-closing differences. For the first time, the direct impact of vocal load could be determined by analyzing vocal fold dynamics. For same vocal loading conditions, equal dynamical behavior of the vocal folds were confirmed. Comparison of recordings performed in the morning with the recordings after work revealed significant changes in vibration behavior, indicating impact of occurring vocal load. Left-right asymmetries in vocal fold dynamics were found confirming earlier assumptions. Different dynamics between opening and closing procedure as well as for anterior and posterior parts were found. Constant voice usage stresses the vocal folds even in healthy subjects and can be detected by applying the PVG technique. Furthermore, left-right PVG asymmetries do occur in healthy voice to a certain extent. HSI in combination with PVG analysis seems to be a promising tool for investigation of vocal fold fatigue and pathologies resulting in small forms of dynamical changes.

Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

PubMed

Roberts, Christopher C; Chang, Chia-En A

2016-08-25

We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering, and enzymology in both predictive and explanatory roles.

Dynamic three-dimensional display of common congenital cardiac defects from reconstruction of two-dimensional echocardiographic images.

PubMed

Hsieh, K S; Lin, C C; Liu, W S; Chen, F L

1996-01-01

Two-dimensional echocardiography had long been a standard diagnostic modality for congenital heart disease. Further attempts of three-dimensional reconstruction using two-dimensional echocardiographic images to visualize stereotypic structure of cardiac lesions have been successful only recently. So far only very few studies have been done to display three-dimensional anatomy of the heart through two-dimensional image acquisition because such complex procedures were involved. This study introduced a recently developed image acquisition and processing system for dynamic three-dimensional visualization of various congenital cardiac lesions. From December 1994 to April 1995, 35 cases were selected in the Echo Laboratory here from about 3000 Echo examinations completed. Each image was acquired on-line with specially designed high resolution image grazmber with EKG and respiratory gating technique. Off-line image processing using a window-architectured interactive software package includes construction of 2-D ehcocardiographic pixel to 3-D "voxel" with conversion of orthogonal to rotatory axial system, interpolation, extraction of region of interest, segmentation, shading and, finally, 3D rendering. Three-dimensional anatomy of various congenital cardiac defects was shown, including four cases with ventricular septal defects, two cases with atrial septal defects, and two cases with aortic stenosis. Dynamic reconstruction of a "beating heart" is recorded as vedio tape with video interface. The potential application of 3D display of the reconstruction from 2D echocardiographic images for the diagnosis of various congenital heart defects has been shown. The 3D display was able to improve the diagnostic ability of echocardiography, and clear-cut display of the various congenital cardiac defects and vavular stenosis could be demonstrated. Reinforcement of current techniques will expand future application of 3D display of conventional 2D images.

Damage characterization in engineering materials using a combination of optical, acoustic, and thermal techniques

NASA Astrophysics Data System (ADS)

Tragazikis, I. K.; Exarchos, D. A.; Dalla, P. T.; Matikas, T. E.

2016-04-01

This paper deals with the use of complimentary nondestructive methods for the evaluation of damage in engineering materials. The application of digital image correlation (DIC) to engineering materials is a useful tool for accurate, noncontact strain measurement. DIC is a 2D, full-field optical analysis technique based on gray-value digital images to measure deformation, vibration and strain a vast variety of materials. In addition, this technique can be applied from very small to large testing areas and can be used for various tests such as tensile, torsion and bending under static or dynamic loading. In this study, DIC results are benchmarked with other nondestructive techniques such as acoustic emission for damage localization and fracture mode evaluation, and IR thermography for stress field visualization and assessment. The combined use of these three nondestructive methods enables the characterization and classification of damage in materials and structures.

Application of Thinned-Skull Cranial Window to Mouse Cerebral Blood Flow Imaging Using Optical Microangiography

PubMed Central

Wang, Ruikang K.

2014-01-01

In vivo imaging of mouse brain vasculature typically requires applying skull window opening techniques: open-skull cranial window or thinned-skull cranial window. We report non-invasive 3D in vivo cerebral blood flow imaging of C57/BL mouse by the use of ultra-high sensitive optical microangiography (UHS-OMAG) and Doppler optical microangiography (DOMAG) techniques to evaluate two cranial window types based on their procedures and ability to visualize surface pial vessel dynamics. Application of the thinned-skull technique is found to be effective in achieving high quality images for pial vessels for short-term imaging, and has advantages over the open-skull technique in available imaging area, surgical efficiency, and cerebral environment preservation. In summary, thinned-skull cranial window serves as a promising tool in studying hemodynamics in pial microvasculature using OMAG or other OCT blood flow imaging modalities. PMID:25426632

A multi-resolution approach for optimal mass transport

NASA Astrophysics Data System (ADS)

Dominitz, Ayelet; Angenent, Sigurd; Tannenbaum, Allen

2007-09-01

Optimal mass transport is an important technique with numerous applications in econometrics, fluid dynamics, automatic control, statistical physics, shape optimization, expert systems, and meteorology. Motivated by certain problems in image registration and medical image visualization, in this note, we describe a simple gradient descent methodology for computing the optimal L2 transport mapping which may be easily implemented using a multiresolution scheme. We also indicate how the optimal transport map may be computed on the sphere. A numerical example is presented illustrating our ideas.

Detection and tracking of dual-labeled HIV particles using wide-field live cell imaging to follow viral core integrity

PubMed Central

Mamede, Joao I.; Hope, Thomas J.

2016-01-01

Summary Live cell imaging is a valuable technique that allows the characterization of the dynamic processes of the HIV-1 life-cycle. Here, we present a method of production and imaging of dual-labeled HIV viral particles that allows the visualization of two events. Varying release of the intravirion fluid phase marker reveals virion fusion and the loss of the integrity of HIV viral cores with the use of live wide-field fluorescent microscopy. PMID:26714704

DNA molecule stretching through thermo-electrophoresis and thermal convection in a heated converging-diverging microchannel.

PubMed

Hsieh, Shou-Shing; Chen, Jyun-Hong; Tsai, Cheng-Fung

2013-02-18

A novel DNA molecule stretching technique is developed and tested herein. Through a heated converging-diverging microchannel, thermal convection and thermophoresis induced by regional heating are shown to significantly elongate single DNA molecules; they are visualized via a confocal laser scanning microscopy. In addition, electrophoretic stretching is also implemented to examine the hybrid effect on the conformation and dynamics of single DNA molecules. The physical properties of the DNA molecules are secured via experimental measurements.

Innovative Visualizations Shed Light on Avian Nocturnal Migration

PubMed Central

Farnsworth, Andrew; Aelterman, Bart; Alves, Jose A.; Azijn, Kevin; Bernstein, Garrett; Branco, Sérgio; Desmet, Peter; Dokter, Adriaan M.; Horton, Kyle; Kelling, Steve; Kelly, Jeffrey F.; Leijnse, Hidde; Rong, Jingjing; Sheldon, Daniel; Van den Broeck, Wouter; Van Den Meersche, Jan Klaas; Van Doren, Benjamin Mark; van Gasteren, Hans

2016-01-01

Globally, billions of flying animals undergo seasonal migrations, many of which occur at night. The temporal and spatial scales at which migrations occur and our inability to directly observe these nocturnal movements makes monitoring and characterizing this critical period in migratory animals’ life cycles difficult. Remote sensing, therefore, has played an important role in our understanding of large-scale nocturnal bird migrations. Weather surveillance radar networks in Europe and North America have great potential for long-term low-cost monitoring of bird migration at scales that have previously been impossible to achieve. Such long-term monitoring, however, poses a number of challenges for the ornithological and ecological communities: how does one take advantage of this vast data resource, integrate information across multiple sensors and large spatial and temporal scales, and visually represent the data for interpretation and dissemination, considering the dynamic nature of migration? We assembled an interdisciplinary team of ecologists, meteorologists, computer scientists, and graphic designers to develop two different flow visualizations, which are interactive and open source, in order to create novel representations of broad-front nocturnal bird migration to address a primary impediment to long-term, large-scale nocturnal migration monitoring. We have applied these visualization techniques to mass bird migration events recorded by two different weather surveillance radar networks covering regions in Europe and North America. These applications show the flexibility and portability of such an approach. The visualizations provide an intuitive representation of the scale and dynamics of these complex systems, are easily accessible for a broad interest group, and are biologically insightful. Additionally, they facilitate fundamental ecological research, conservation, mitigation of human–wildlife conflicts, improvement of meteorological products, and public outreach, education, and engagement. PMID:27557096

Innovative Visualizations Shed Light on Avian Nocturnal Migration.

PubMed

Shamoun-Baranes, Judy; Farnsworth, Andrew; Aelterman, Bart; Alves, Jose A; Azijn, Kevin; Bernstein, Garrett; Branco, Sérgio; Desmet, Peter; Dokter, Adriaan M; Horton, Kyle; Kelling, Steve; Kelly, Jeffrey F; Leijnse, Hidde; Rong, Jingjing; Sheldon, Daniel; Van den Broeck, Wouter; Van Den Meersche, Jan Klaas; Van Doren, Benjamin Mark; van Gasteren, Hans

2016-01-01

Globally, billions of flying animals undergo seasonal migrations, many of which occur at night. The temporal and spatial scales at which migrations occur and our inability to directly observe these nocturnal movements makes monitoring and characterizing this critical period in migratory animals' life cycles difficult. Remote sensing, therefore, has played an important role in our understanding of large-scale nocturnal bird migrations. Weather surveillance radar networks in Europe and North America have great potential for long-term low-cost monitoring of bird migration at scales that have previously been impossible to achieve. Such long-term monitoring, however, poses a number of challenges for the ornithological and ecological communities: how does one take advantage of this vast data resource, integrate information across multiple sensors and large spatial and temporal scales, and visually represent the data for interpretation and dissemination, considering the dynamic nature of migration? We assembled an interdisciplinary team of ecologists, meteorologists, computer scientists, and graphic designers to develop two different flow visualizations, which are interactive and open source, in order to create novel representations of broad-front nocturnal bird migration to address a primary impediment to long-term, large-scale nocturnal migration monitoring. We have applied these visualization techniques to mass bird migration events recorded by two different weather surveillance radar networks covering regions in Europe and North America. These applications show the flexibility and portability of such an approach. The visualizations provide an intuitive representation of the scale and dynamics of these complex systems, are easily accessible for a broad interest group, and are biologically insightful. Additionally, they facilitate fundamental ecological research, conservation, mitigation of human-wildlife conflicts, improvement of meteorological products, and public outreach, education, and engagement.

Advecting Procedural Textures for 2D Flow Animation

NASA Technical Reports Server (NTRS)

Kao, David; Pang, Alex; Moran, Pat (Technical Monitor)

2001-01-01

This paper proposes the use of specially generated 3D procedural textures for visualizing steady state 2D flow fields. We use the flow field to advect and animate the texture over time. However, using standard texture advection techniques and arbitrary textures will introduce some undesirable effects such as: (a) expanding texture from a critical source point, (b) streaking pattern from the boundary of the flowfield, (c) crowding of advected textures near an attracting spiral or sink, and (d) absent or lack of textures in some regions of the flow. This paper proposes a number of strategies to solve these problems. We demonstrate how the technique works using both synthetic data and computational fluid dynamics data.

Visualizing molecular diffusion through passive permeability barriers in cells: conventional and novel approaches.

PubMed

Lin, Yu-Chun; Phua, Siew Cheng; Lin, Benjamin; Inoue, Takanari

2013-08-01

Diffusion barriers are universal solutions for cells to achieve distinct organizations, compositions, and activities within a limited space. The influence of diffusion barriers on the spatiotemporal dynamics of signaling molecules often determines cellular physiology and functions. Over the years, the passive permeability barriers in various subcellular locales have been characterized using elaborate analytical techniques. In this review, we will summarize the current state of knowledge on the various passive permeability barriers present in mammalian cells. We will conclude with a description of several conventional techniques and one new approach based on chemically inducible diffusion trap (CIDT) for probing permeable barriers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Topological characterization versus synchronization for assessing (or not) dynamical equivalence

NASA Astrophysics Data System (ADS)

Letellier, Christophe; Mangiarotti, Sylvain; Sendiña-Nadal, Irene; Rössler, Otto E.

2018-04-01

Model validation from experimental data is an important and not trivial topic which is too often reduced to a simple visual inspection of the state portrait spanned by the variables of the system. Synchronization was suggested as a possible technique for model validation. By means of a topological analysis, we revisited this concept with the help of an abstract chemical reaction system and data from two electrodissolution experiments conducted by Jack Hudson's group. The fact that it was possible to synchronize topologically different global models led us to conclude that synchronization is not a recommendable technique for model validation. A short historical preamble evokes Jack Hudson's early career in interaction with Otto E. Rössler.

Laboratory investigations of earthquake dynamics

NASA Astrophysics Data System (ADS)

Xia, Kaiwen

In this thesis this will be attempted through controlled laboratory experiments that are designed to mimic natural earthquake scenarios. The earthquake dynamic rupturing process itself is a complicated phenomenon, involving dynamic friction, wave propagation, and heat production. Because controlled experiments can produce results without assumptions needed in theoretical and numerical analysis, the experimental method is thus advantageous over theoretical and numerical methods. Our laboratory fault is composed of carefully cut photoelastic polymer plates (Homahte-100, Polycarbonate) held together by uniaxial compression. As a unique unit of the experimental design, a controlled exploding wire technique provides the triggering mechanism of laboratory earthquakes. Three important components of real earthquakes (i.e., pre-existing fault, tectonic loading, and triggering mechanism) correspond to and are simulated by frictional contact, uniaxial compression, and the exploding wire technique. Dynamic rupturing processes are visualized using the photoelastic method and are recorded via a high-speed camera. Our experimental methodology, which is full-field, in situ, and non-intrusive, has better control and diagnostic capacity compared to other existing experimental methods. Using this experimental approach, we have investigated several problems: dynamics of earthquake faulting occurring along homogeneous faults separating identical materials, earthquake faulting along inhomogeneous faults separating materials with different wave speeds, and earthquake faulting along faults with a finite low wave speed fault core. We have observed supershear ruptures, subRayleigh to supershear rupture transition, crack-like to pulse-like rupture transition, self-healing (Heaton) pulse, and rupture directionality.

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

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

Arthroscopic Release of Flexor Hallucis Longus Tendon Sheath in Female Ballet Dancers: Dynamic Pathology, Surgical Technique, and Return to Dancing Performance.

PubMed

Funasaki, Hiroki; Hayashi, Hiroteru; Sakamoto, Kanako; Tsuruga, Rei; Marumo, Keishi

2015-12-01

Stenosing tenosynovitis of the flexor hallucis longus (FHL) tendon is known as a major overuse lesion in female dancers. We describe arthroscopic surgical techniques in relation to the dynamic pathology of the disease. Crepitus and pain on moving the great toe with the ankle in plantar flexion on preoperative examination confirm the diagnosis of FHL stenosing tenosynovitis even if the os trigonum is not evident. The ankle is approached through standard posterolateral and posteromedial portals. A 4.0-mm-diameter 30° arthroscope is used. Soft tissues around the talus are cleared with a motorized shaver and a radiofrequency device. The posterior aspects of the talus, os trigonum, and FHL tendon surrounded by the tendon sheath are visualized. The dynamic pathology of the FHL tendon is well observed on passive motion of the great toe. The prominent bone fragment of the talus is removed and the tendon sheath is cut with a retrograde knife and a motorized shaver from the superior border down to the entrance of the fibro-osseous tunnel. Arthroscopic release of the FHL tendon sheath is a useful and easy method to directly approach the dynamic pathology of FHL tenosynovitis in female ballet dancers.

Visualization of Air Particle Dynamics in an Engine Inertial Particle Separator

NASA Astrophysics Data System (ADS)

Wolf, Jason; Zhang, Wei

2015-11-01

Unmanned Aerial Vehicles (UAVs) are regularly deployed around the world in support of military, civilian and humanitarian efforts. Due to their unique mission profiles, these advanced UAVs utilize various internal combustion engines, which consume large quantities of air. Operating these UAVs in areas with high concentrations of sand and dust can be hazardous to the engines, especially during takeoff and landing. In such events, engine intake filters quickly become saturated and clogged with dust particles, causing a substantial decrease in the UAVs' engine performance and service life. Development of an Engine Air Particle Separator (EAPS) with high particle separation efficiency is necessary for maintaining satisfactory performance of the UAVs. Inertial Particle Separators (IPS) have been one common effective method but they experience complex internal particle-laden flows that are challenging to understand and model. This research employs an IPS test rig to simulate dust particle separation under different flow conditions. Soda lime glass spheres with a mean diameter of 35-45 microns are used in experiments as a surrogate for airborne particulates encountered during flight. We will present measurements of turbulent flow and particle dynamics using flow visualization techniques to understand the multiphase fluid dynamics in the IPS device. This knowledge can contribute to design better performing IPS systems for UAVs. Cleveland State University, Cleveland, Ohio, 44115.

Dynamics and control of gold-encapped gallium arsenide nanowires imaged by 4D electron microscopy

PubMed Central

Chen, Bin; Fu, Xuewen; Tang, Jau; Lysevych, Mykhaylo; Tan, Hark Hoe; Jagadish, Chennupati; Zewail, Ahmed H.

2017-01-01

Eutectic-related reaction is a special chemical/physical reaction involving multiple phases, solid and liquid. Visualization of a phase reaction of composite nanomaterials with high spatial and temporal resolution provides a key understanding of alloy growth with important industrial applications. However, it has been a rather challenging task. Here, we report the direct imaging and control of the phase reaction dynamics of a single, as-grown free-standing gallium arsenide nanowire encapped with a gold nanoparticle, free from environmental confinement or disturbance, using four-dimensional (4D) electron microscopy. The nondestructive preparation of as-grown free-standing nanowires without supporting films allows us to study their anisotropic properties in their native environment with better statistical character. A laser heating pulse initiates the eutectic-related reaction at a temperature much lower than the melting points of the composite materials, followed by a precisely time-delayed electron pulse to visualize the irreversible transient states of nucleation, growth, and solidification of the complex. Combined with theoretical modeling, useful thermodynamic parameters of the newly formed alloy phases and their crystal structures could be determined. This technique of dynamical control aided by 4D imaging of phase reaction processes on the nanometer-ultrafast time scale opens new venues for engineering various reactions in a wide variety of other systems. PMID:29158393

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

Unraveling Cell Processes: Interference Imaging Interwoven with Data Analysis

PubMed Central

Brazhe, A. R.; Pavlov, A. N.; Erokhova, L. A.; Yusipovich, A. I.; Maksimov, G. V.; Mosekilde, E.; Sosnovtseva, O. V.

2006-01-01

The paper presents results on the application of interference microscopy and wavelet-analysis for cell visualization and studies of cell dynamics. We demonstrate that interference imaging of erythrocytes can reveal reorganization of the cytoskeleton and inhomogenity in the distribution of hemoglobin, and that interference imaging of neurons can show intracellular compartmentalization and submembrane structures. We investigate temporal and spatial variations of the refractive index for different cell types: isolated neurons, mast cells and erythrocytes. We show that the refractive dynamical properties differ from cell type to cell type and depend on the cellular compartment. Our results suggest that low frequency variations (0.1–0.6 Hz) result from plasma membrane processes and that higher frequency variations (20–26 Hz) are related to the movement of vesicles. Using double-wavelet analysis, we study the modulation of the 1 Hz rhythm in neurons and reveal its changes under depolarization and hyperpolarization of the plasma membrane. We conclude that interference microscopy combined with wavelet analysis is a useful technique for non-invasive cell studies, cell visualization, and investigation of plasma membrane properties. PMID:19669463

Real Time Data Acquisition and Online Signal Processing for Magnetoencephalography

NASA Astrophysics Data System (ADS)

Rongen, H.; Hadamschek, V.; Schiek, M.

2006-06-01

To establish improved therapies for patients suffering from severe neurological and psychiatric diseases, a demand controlled and desynchronizing brain-pacemaker has been developed with techniques from statistical physics and nonlinear dynamics. To optimize the novel therapeutic approach, brain activity is investigated with a Magnetoencephalography (MEG) system prior to surgery. For this, a real time data acquisition system for a 148 channel MEG and online signal processing for artifact rejection, filtering, cross trial phase resetting analysis and three-dimensional (3-D) reconstruction of the cerebral current sources was developed. The developed PCI bus hardware is based on a FPGA and DSP design, using the benefits from both architectures. The reconstruction and visualization of the 3-D volume data is done by the PC which hosts the real time DAQ and pre-processing board. The framework of the MEG-online system is introduced and the architecture of the real time DAQ board and online reconstruction is described. In addition we show first results with the MEG-Online system for the investigation of dynamic brain activities in relation to external visual stimulation, based on test data sets.

Aurally aided visual search performance in a dynamic environment

NASA Astrophysics Data System (ADS)

McIntire, John P.; Havig, Paul R.; Watamaniuk, Scott N. J.; Gilkey, Robert H.

2008-04-01

Previous research has repeatedly shown that people can find a visual target significantly faster if spatial (3D) auditory displays direct attention to the corresponding spatial location. However, previous research has only examined searches for static (non-moving) targets in static visual environments. Since motion has been shown to affect visual acuity, auditory acuity, and visual search performance, it is important to characterize aurally-aided search performance in environments that contain dynamic (moving) stimuli. In the present study, visual search performance in both static and dynamic environments is investigated with and without 3D auditory cues. Eight participants searched for a single visual target hidden among 15 distracting stimuli. In the baseline audio condition, no auditory cues were provided. In the 3D audio condition, a virtual 3D sound cue originated from the same spatial location as the target. In the static search condition, the target and distractors did not move. In the dynamic search condition, all stimuli moved on various trajectories at 10 deg/s. The results showed a clear benefit of 3D audio that was present in both static and dynamic environments, suggesting that spatial auditory displays continue to be an attractive option for a variety of aircraft, motor vehicle, and command & control applications.

Presentation-Oriented Visualization Techniques.

PubMed

Kosara, Robert

2016-01-01

Data visualization research focuses on data exploration and analysis, yet the vast majority of visualizations people see were created for a different purpose: presentation. Whether we are talking about charts showing data to help make a presenter's point, data visuals created to accompany a news story, or the ubiquitous infographics, many more people consume charts than make them. Traditional visualization techniques treat presentation as an afterthought, but are there techniques uniquely suited to data presentation but not necessarily ideal for exploration and analysis? This article focuses on presentation-oriented techniques, considering their usefulness for presentation first and any other purposes as secondary.

Development Of A Dynamic Radiographic Capability Using High-Speed Video

NASA Astrophysics Data System (ADS)

Bryant, Lawrence E.

1985-02-01

High-speed video equipment can be used to optically image up to 2,000 full frames per second or 12,000 partial frames per second. X-ray image intensifiers have historically been used to image radiographic images at 30 frames per second. By combining these two types of equipment, it is possible to perform dynamic x-ray imaging of up to 2,000 full frames per second. The technique has been demonstrated using conventional, industrial x-ray sources such as 150 Kv and 300 Kv constant potential x-ray generators, 2.5 MeV Van de Graaffs, and linear accelerators. A crude form of this high-speed radiographic imaging has been shown to be possible with a cobalt 60 source. Use of a maximum aperture lens makes best use of the available light output from the image intensifier. The x-ray image intensifier input and output fluors decay rapidly enough to allow the high frame rate imaging. Data are presented on the maximum possible video frame rates versus x-ray penetration of various thicknesses of aluminum and steel. Photographs illustrate typical radiographic setups using the high speed imaging method. Video recordings show several demonstrations of this technique with the played-back x-ray images slowed down up to 100 times as compared to the actual event speed. Typical applications include boiling type action of liquids in metal containers, compressor operation with visualization of crankshaft, connecting rod and piston movement and thermal battery operation. An interesting aspect of this technique combines both the optical and x-ray capabilities to observe an object or event with both external and internal details with one camera in a visual mode and the other camera in an x-ray mode. This allows both kinds of video images to appear side by side in a synchronized presentation.

Estimating Starch Content in Roots of Deciduous Trees--A Visual Technique

Treesearch

Philip M. Wargo; Philip M. Wargo

1975-01-01

A visual technique for determining starch content in roots of forest trees, based onz iodine-staining of starch granules, was compared with a chemical method. Although the chemical method was more precise, roots could be sorted with the visual method into groups that are probably biologically important. The visual technique is simple and can be adapted for use in the...

Integration of Scale Invariant Generator Technique and S-A Technique for Characterizing 2-D Patterns for Information Retrieve

NASA Astrophysics Data System (ADS)

Cao, L.; Cheng, Q.

2004-12-01

The scale invariant generator technique (SIG) and spectrum-area analysis technique (S-A) were developed independently relevant to the concept of the generalized scale invariance (GSI). The former was developed for characterizing the parameters involved in the GSI for characterizing and simulating multifractal measures whereas the latter was for identifying scaling breaks for decomposition of superimposed multifractal measures caused by multiple geophysical processes. A natural integration of these two techniques may yield a new technique to serve two purposes, on the one hand, that can enrich the power of S-A by increasing the interpretability of decomposed patterns in some applications of S-A and, on the other hand, that can provide a mean to test the uniqueness of multifractality of measures which is essential for application of SIG technique in more complicated environment. The implementation of the proposed technique has been done as a Dynamic Link Library (DLL) in Visual C++. The program can be friendly used for method validation and application in different fields.

Visual Environments for CFD Research

NASA Technical Reports Server (NTRS)

Watson, Val; George, Michael W. (Technical Monitor)

1994-01-01

This viewgraph presentation gives an overview of the visual environments for computational fluid dynamics (CFD) research. It includes details on critical needs from the future computer environment, features needed to attain this environment, prospects for changes in and the impact of the visualization revolution on the human-computer interface, human processing capabilities, limits of personal environment and the extension of that environment with computers. Information is given on the need for more 'visual' thinking (including instances of visual thinking), an evaluation of the alternate approaches for and levels of interactive computer graphics, a visual analysis of computational fluid dynamics, and an analysis of visualization software.

Emergent 1d Ising Behavior in AN Elementary Cellular Automaton Model

NASA Astrophysics Data System (ADS)

Kassebaum, Paul G.; Iannacchione, Germano S.

The fundamental nature of an evolving one-dimensional (1D) Ising model is investigated with an elementary cellular automaton (CA) simulation. The emergent CA simulation employs an ensemble of cells in one spatial dimension, each cell capable of two microstates interacting with simple nearest-neighbor rules and incorporating an external field. The behavior of the CA model provides insight into the dynamics of coupled two-state systems not expressible by exact analytical solutions. For instance, state progression graphs show the causal dynamics of a system through time in relation to the system's entropy. Unique graphical analysis techniques are introduced through difference patterns, diffusion patterns, and state progression graphs of the 1D ensemble visualizing the evolution. All analyses are consistent with the known behavior of the 1D Ising system. The CA simulation and new pattern recognition techniques are scalable (in both dimension, complexity, and size) and have many potential applications such as complex design of materials, control of agent systems, and evolutionary mechanism design.

High-pressure microscopy for tracking dynamic properties of molecular machines.

PubMed

Nishiyama, Masayoshi

2017-12-01

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli. Copyright © 2017 Elsevier B.V. All rights reserved.

V-DRASTIC: Using visualization to engage policymakers in groundwater vulnerability assessment

NASA Astrophysics Data System (ADS)

Bojórquez-Tapia, Luis A.; Cruz-Bello, Gustavo M.; Luna-González, Laura; Juárez, Lourdes; Ortiz-Pérez, Mario A.

2009-06-01

SummaryGroundwater vulnerability mapping is increasingly being used to design aquifer protection and management strategies. This paper presents a dynamic visualization method to groundwater vulnerability mapping. This method—called V-DRASTIC—extends the capacities of DRASTIC, an overlay/index technique that has been applied worldwide to evaluate the condition of hydrogeological factors and determine groundwater vulnerability at regional scales. V-DRASTIC is based upon psychophysics' principles (a theory that describes the people's response to a stimulus) to generate alternative groundwater vulnerability categorization schemes. These are used as inputs in a fuzzy pattern recognition procedure to enable planners, decision makers and stakeholders identify which scheme conveys meaningful information regarding groundwater vulnerability across a territory. V-DRASTIC was applied in the groundwater vulnerability assessment of two urban watersheds in Mexico.

Impulse processing: A dynamical systems model of incremental eye movements in the visual world paradigm

PubMed Central

Kukona, Anuenue; Tabor, Whitney

2011-01-01

The visual world paradigm presents listeners with a challenging problem: they must integrate two disparate signals, the spoken language and the visual context, in support of action (e.g., complex movements of the eyes across a scene). We present Impulse Processing, a dynamical systems approach to incremental eye movements in the visual world that suggests a framework for integrating language, vision, and action generally. Our approach assumes that impulses driven by the language and the visual context impinge minutely on a dynamical landscape of attractors corresponding to the potential eye-movement behaviors of the system. We test three unique predictions of our approach in an empirical study in the visual world paradigm, and describe an implementation in an artificial neural network. We discuss the Impulse Processing framework in relation to other models of the visual world paradigm. PMID:21609355

Differential temporal dynamics during visual imagery and perception.

PubMed

Dijkstra, Nadine; Mostert, Pim; Lange, Floris P de; Bosch, Sander; van Gerven, Marcel Aj

2018-05-29

Visual perception and imagery rely on similar representations in the visual cortex. During perception, visual activity is characterized by distinct processing stages, but the temporal dynamics underlying imagery remain unclear. Here, we investigated the dynamics of visual imagery in human participants using magnetoencephalography. Firstly, we show that, compared to perception, imagery decoding becomes significant later and representations at the start of imagery already overlap with later time points. This suggests that during imagery, the entire visual representation is activated at once or that there are large differences in the timing of imagery between trials. Secondly, we found consistent overlap between imagery and perceptual processing around 160 ms and from 300 ms after stimulus onset. This indicates that the N170 gets reactivated during imagery and that imagery does not rely on early perceptual representations. Together, these results provide important insights for our understanding of the neural mechanisms of visual imagery. © 2018, Dijkstra et al.

Are Covert Saccade Functionally Relevant in Vestibular Hypofunction?

PubMed

Hermann, R; Pelisson, D; Dumas, O; Urquizar, Ch; Truy, E; Tilikete, C

2018-06-01

The vestibulo-ocular reflex maintains gaze stabilization during angular or linear head accelerations, allowing adequate dynamic visual acuity. In case of bilateral vestibular hypofunction, patients use saccades to compensate for the reduced vestibulo-ocular reflex function, with covert saccades occurring even during the head displacement. In this study, we questioned whether covert saccades help maintain dynamic visual acuity, and evaluated which characteristic of these saccades are the most relevant to improve visual function. We prospectively included 18 patients with chronic bilateral vestibular hypofunction. Subjects underwent evaluation of dynamic visual acuity in the horizontal plane as well as video recording of their head and eye positions during horizontal head impulse tests in both directions (36 ears tested). Frequency, latency, consistency of covert saccade initiation, and gain of covert saccades as well as residual vestibulo-ocular reflex gain were calculated. We found no correlation between residual vestibulo-ocular reflex gain and dynamic visual acuity. Dynamic visual acuity performance was however positively correlated with the frequency and gain of covert saccades and negatively correlated with covert saccade latency. There was no correlation between consistency of covert saccade initiation and dynamic visual acuity. Even though gaze stabilization in space during covert saccades might be of very short duration, these refixation saccades seem to improve vision in patients with bilateral vestibular hypofunction during angular head impulses. These findings emphasize the need for specific rehabilitation technics that favor the triggering of covert saccades. The physiological origin of covert saccades is discussed.

Dynamic frame resizing with convolutional neural network for efficient video compression

NASA Astrophysics Data System (ADS)

Kim, Jaehwan; Park, Youngo; Choi, Kwang Pyo; Lee, JongSeok; Jeon, Sunyoung; Park, JeongHoon

2017-09-01

In the past, video codecs such as vc-1 and H.263 used a technique to encode reduced-resolution video and restore original resolution from the decoder for improvement of coding efficiency. The techniques of vc-1 and H.263 Annex Q are called dynamic frame resizing and reduced-resolution update mode, respectively. However, these techniques have not been widely used due to limited performance improvements that operate well only under specific conditions. In this paper, video frame resizing (reduced/restore) technique based on machine learning is proposed for improvement of coding efficiency. The proposed method features video of low resolution made by convolutional neural network (CNN) in encoder and reconstruction of original resolution using CNN in decoder. The proposed method shows improved subjective performance over all the high resolution videos which are dominantly consumed recently. In order to assess subjective quality of the proposed method, Video Multi-method Assessment Fusion (VMAF) which showed high reliability among many subjective measurement tools was used as subjective metric. Moreover, to assess general performance, diverse bitrates are tested. Experimental results showed that BD-rate based on VMAF was improved by about 51% compare to conventional HEVC. Especially, VMAF values were significantly improved in low bitrate. Also, when the method is subjectively tested, it had better subjective visual quality in similar bit rate.

Machine Detection of Enhanced Electromechanical Energy Conversion in PbZr 0.2Ti 0.8O 3 Thin Films

DOE PAGES

Agar, Joshua C.; Cao, Ye; Naul, Brett; ...

2018-05-28

Many energy conversion, sensing, and microelectronic applications based on ferroic materials are determined by the domain structure evolution under applied stimuli. New hyperspectral, multidimensional spectroscopic techniques now probe dynamic responses at relevant length and time scales to provide an understanding of how these nanoscale domain structures impact macroscopic properties. Such approaches, however, remain limited in use because of the difficulties that exist in extracting and visualizing scientific insights from these complex datasets. Using multidimensional band-excitation scanning probe spectroscopy and adapting tools from both computer vision and machine learning, an automated workflow is developed to featurize, detect, and classify signatures ofmore » ferroelectric/ferroelastic switching processes in complex ferroelectric domain structures. This approach enables the identification and nanoscale visualization of varied modes of response and a pathway to statistically meaningful quantification of the differences between those modes. Lastly, among other things, the importance of domain geometry is spatially visualized for enhancing nanoscale electromechanical energy conversion.« less

Virtual reality training and assessment in laparoscopic rectum surgery.

PubMed

Pan, Jun J; Chang, Jian; Yang, Xiaosong; Liang, Hui; Zhang, Jian J; Qureshi, Tahseen; Howell, Robert; Hickish, Tamas

2015-06-01

Virtual-reality (VR) based simulation techniques offer an efficient and low cost alternative to conventional surgery training. This article describes a VR training and assessment system in laparoscopic rectum surgery. To give a realistic visual performance of interaction between membrane tissue and surgery tools, a generalized cylinder based collision detection and a multi-layer mass-spring model are presented. A dynamic assessment model is also designed for hierarchy training evaluation. With this simulator, trainees can operate on the virtual rectum with both visual and haptic sensation feedback simultaneously. The system also offers surgeons instructions in real time when improper manipulation happens. The simulator has been tested and evaluated by ten subjects. This prototype system has been verified by colorectal surgeons through a pilot study. They believe the visual performance and the tactile feedback are realistic. It exhibits the potential to effectively improve the surgical skills of trainee surgeons and significantly shorten their learning curve. Copyright © 2014 John Wiley & Sons, Ltd.

Nanohybrids with Magnetic and Persistent Luminescence Properties for Cell Labeling, Tracking, In Vivo Real-Time Imaging, and Magnetic Vectorization.

PubMed

Teston, Eliott; Maldiney, Thomas; Marangon, Iris; Volatron, Jeanne; Lalatonne, Yoann; Motte, Laurence; Boisson-Vidal, Catherine; Autret, Gwennhael; Clément, Olivier; Scherman, Daniel; Gazeau, Florence; Richard, Cyrille

2018-04-01

Once injected into a living organism, cells diffuse or migrate around the initial injection point and become impossible to be visualized and tracked in vivo. The present work concerns the development of a new technique for therapeutic cell labeling and subsequent in vivo visualization and magnetic retention. It is hypothesized and subsequently demonstrated that nanohybrids made of persistent luminescence nanoparticles and ultrasmall superparamagnetic iron oxide nanoparticles incorporated into a silica matrix can be used as an effective nanoplatform to label therapeutic cells in a nontoxic way in order to dynamically track them in real-time in vitro and in living mice. As a proof-of-concept, it is shown that once injected, these labeled cells can be visualized and attracted in vivo using a magnet. This first step suggests that these nanohybrids represent efficient multifunctional nanoprobes for further imaging guided cell therapies development. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Visualization of electrochemically driven solid-state phase transformations using operando hard X-ray spectro-imaging

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

Li, Linsen; Chen-Wiegart, Yu-chen Karen; Wang, Jiajun

In situ techniques with high temporal, spatial and chemical resolution are key to understand ubiquitous solid-state phase transformations, which are crucial to many technological applications. Hard X-ray spectro-imaging can visualize electrochemically driven phase transformations but demands considerably large samples with strong absorption signal so far. Here we show a conceptually new data analysis method to enable operando visualization of mechanistically relevant weakly absorbing samples at the nanoscale and study electrochemical reaction dynamics of iron fluoride, a promising high-capacity conversion cathode material. In two specially designed samples with distinctive microstructure and porosity, we observe homogeneous phase transformations during both discharge andmore » charge, faster and more complete Li-storage occurring in porous polycrystalline iron fluoride, and further, incomplete charge reaction following a pathway different from conventional belief. In conclusion, these mechanistic insights provide guidelines for designing better conversion cathode materials to realize the promise of high-capacity lithium-ion batteries.« less

Machine Detection of Enhanced Electromechanical Energy Conversion in PbZr 0.2Ti 0.8O 3 Thin Films

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

Agar, Joshua C.; Cao, Ye; Naul, Brett

Many energy conversion, sensing, and microelectronic applications based on ferroic materials are determined by the domain structure evolution under applied stimuli. New hyperspectral, multidimensional spectroscopic techniques now probe dynamic responses at relevant length and time scales to provide an understanding of how these nanoscale domain structures impact macroscopic properties. Such approaches, however, remain limited in use because of the difficulties that exist in extracting and visualizing scientific insights from these complex datasets. Using multidimensional band-excitation scanning probe spectroscopy and adapting tools from both computer vision and machine learning, an automated workflow is developed to featurize, detect, and classify signatures ofmore » ferroelectric/ferroelastic switching processes in complex ferroelectric domain structures. This approach enables the identification and nanoscale visualization of varied modes of response and a pathway to statistically meaningful quantification of the differences between those modes. Lastly, among other things, the importance of domain geometry is spatially visualized for enhancing nanoscale electromechanical energy conversion.« less

Projection-type see-through holographic three-dimensional display

NASA Astrophysics Data System (ADS)

Wakunami, Koki; Hsieh, Po-Yuan; Oi, Ryutaro; Senoh, Takanori; Sasaki, Hisayuki; Ichihashi, Yasuyuki; Okui, Makoto; Huang, Yi-Pai; Yamamoto, Kenji

2016-10-01

Owing to the limited spatio-temporal resolution of display devices, dynamic holographic three-dimensional displays suffer from a critical trade-off between the display size and the visual angle. Here we show a projection-type holographic three-dimensional display, in which a digitally designed holographic optical element and a digital holographic projection technique are combined to increase both factors at the same time. In the experiment, the enlarged holographic image, which is twice as large as the original display device, projected on the screen of the digitally designed holographic optical element was concentrated at the target observation area so as to increase the visual angle, which is six times as large as that for a general holographic display. Because the display size and the visual angle can be designed independently, the proposed system will accelerate the adoption of holographic three-dimensional displays in industrial applications, such as digital signage, in-car head-up displays, smart-glasses and head-mounted displays.

Visualization of electrochemically driven solid-state phase transformations using operando hard X-ray spectro-imaging

DOE PAGES

Li, Linsen; Chen-Wiegart, Yu-chen Karen; Wang, Jiajun; ...

2015-04-20

In situ techniques with high temporal, spatial and chemical resolution are key to understand ubiquitous solid-state phase transformations, which are crucial to many technological applications. Hard X-ray spectro-imaging can visualize electrochemically driven phase transformations but demands considerably large samples with strong absorption signal so far. Here we show a conceptually new data analysis method to enable operando visualization of mechanistically relevant weakly absorbing samples at the nanoscale and study electrochemical reaction dynamics of iron fluoride, a promising high-capacity conversion cathode material. In two specially designed samples with distinctive microstructure and porosity, we observe homogeneous phase transformations during both discharge andmore » charge, faster and more complete Li-storage occurring in porous polycrystalline iron fluoride, and further, incomplete charge reaction following a pathway different from conventional belief. In conclusion, these mechanistic insights provide guidelines for designing better conversion cathode materials to realize the promise of high-capacity lithium-ion batteries.« less

Interactive Visual Analysis within Dynamic Ocean Models

NASA Astrophysics Data System (ADS)

Butkiewicz, T.

2012-12-01

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

Visually Evoked Spiking Evolves While Spontaneous Ongoing Dynamics Persist

PubMed Central

Huys, Raoul; Jirsa, Viktor K.; Darokhan, Ziauddin; Valentiniene, Sonata; Roland, Per E.

2016-01-01

Neurons in the primary visual cortex spontaneously spike even when there are no visual stimuli. It is unknown whether the spiking evoked by visual stimuli is just a modification of the spontaneous ongoing cortical spiking dynamics or whether the spontaneous spiking state disappears and is replaced by evoked spiking. This study of laminar recordings of spontaneous spiking and visually evoked spiking of neurons in the ferret primary visual cortex shows that the spiking dynamics does not change: the spontaneous spiking as well as evoked spiking is controlled by a stable and persisting fixed point attractor. Its existence guarantees that evoked spiking return to the spontaneous state. However, the spontaneous ongoing spiking state and the visual evoked spiking states are qualitatively different and are separated by a threshold (separatrix). The functional advantage of this organization is that it avoids the need for a system reorganization following visual stimulation, and impedes the transition of spontaneous spiking to evoked spiking and the propagation of spontaneous spiking from layer 4 to layers 2–3. PMID:26778982

Factors influencing real time internal structural visualization and dynamic process monitoring in plants using synchrotron-based phase contrast X-ray imaging

PubMed Central

Karunakaran, Chithra; Lahlali, Rachid; Zhu, Ning; Webb, Adam M.; Schmidt, Marina; Fransishyn, Kyle; Belev, George; Wysokinski, Tomasz; Olson, Jeremy; Cooper, David M. L.; Hallin, Emil

2015-01-01

Minimally invasive investigation of plant parts (root, stem, leaves, and flower) has good potential to elucidate the dynamics of plant growth, morphology, physiology, and root-rhizosphere interactions. Laboratory based absorption X-ray imaging and computed tomography (CT) systems are extensively used for in situ feasibility studies of plants grown in natural and artificial soil. These techniques have challenges such as low contrast between soil pore space and roots, long X-ray imaging time, and low spatial resolution. In this study, the use of synchrotron (SR) based phase contrast X-ray imaging (PCI) has been demonstrated as a minimally invasive technique for imaging plants. Above ground plant parts and roots of 10 day old canola and wheat seedlings grown in sandy clay loam soil were successfully scanned and reconstructed. Results confirmed that SR-PCI can deliver good quality images to study dynamic and real time processes such as cavitation and water-refilling in plants. The advantages of SR-PCI, effect of X-ray energy, and effective pixel size to study plant samples have been demonstrated. The use of contrast agents to monitor physiological processes in plants was also investigated and discussed. PMID:26183486

Measurement of the Dynamic Shear Modulus of Mouse Brain Tissue In Vivo By Magnetic Resonance Elastography

PubMed Central

Atay, Stefan M.; Kroenke, Christopher D.; Sabet, Arash; Bayly, Philip V.

2008-01-01

In this study, the magnetic resonance elastography (MRE) technique was used to estimate the dynamic shear modulus of mouse brain tissue in vivo. The technique allows visualization and measurement of mechanical shear waves excited by lateral vibration of the skull. Quantitative measurements of displacement in three dimensions (3-D) during vibration at 1200 Hz were obtained by applying oscillatory magnetic field gradients at the same frequency during an MR imaging sequence. Contrast in the resulting phase images of the mouse brain is proportional to displacement. To obtain estimates of shear modulus, measured displacement fields were fitted to the shear wave equation. Validation of the procedure was performed on gel characterized by independent rheometry tests and on data from finite element simulations. Brain tissue is, in reality, viscoelastic and nonlinear. The current estimates of dynamic shear modulus are strictly relevant only to small oscillations at a specific frequency, but these estimates may be obtained at high frequencies (and thus high deformation rates), non-invasively throughout the brain. These data complement measurements of nonlinear viscoelastic properties obtained by others at slower rates, either ex vivo or invasively. PMID:18412500

Learning from Chemical Visualizations: Comparing Generation and Selection

ERIC Educational Resources Information Center

Zhang, Zhihui Helen; Linn, Marcia C.

2013-01-01

Dynamic visualizations can make unseen phenomena such as chemical reactions visible but students need guidance to benefit from them. This study explores the value of generating drawings versus selecting among alternatives to guide students to learn chemical reactions from a dynamic visualization of hydrogen combustion as part of an online inquiry…

EMG-Torque Dynamics Change With Contraction Bandwidth.

PubMed

Golkar, Mahsa A; Jalaleddini, Kian; Kearney, Robert E

2018-04-01

An accurate model for ElectroMyoGram (EMG)-torque dynamics has many uses. One of its applications which has gained high attention among researchers is its use, in estimating the muscle contraction level for the efficient control of prosthesis. In this paper, the dynamic relationship between the surface EMG and torque during isometric contractions at the human ankle was studied using system identification techniques. Subjects voluntarily modulated their ankle torque in dorsiflexion direction, by activating their tibialis anterior muscle, while tracking a pseudo-random binary sequence in a torque matching task. The effects of contraction bandwidth, described by torque spectrum, on EMG-torque dynamics were evaluated by varying the visual command switching time. Nonparametric impulse response functions (IRF) were estimated between the processed surface EMG and torque. It was demonstrated that: 1) at low contraction bandwidths, the identified IRFs had unphysiological anticipatory (i.e., non-causal) components, whose amplitude decreased as the contraction bandwidth increased. We hypothesized that this non-causal behavior arose, because the EMG input contained a component due to feedback from the output torque, i.e., it was recorded from within a closed-loop. Vision was not the feedback source since the non-causal behavior persisted when visual feedback was removed. Repeating the identification using a nonparametric closed-loop identification algorithm yielded causal IRFs at all bandwidths, supporting this hypothesis. 2) EMG-torque dynamics became faster and the bandwidth of system increased as contraction modulation rate increased. Thus, accurate prediction of torque from EMG signals must take into account the contraction bandwidth sensitivity of this system.

Decoding information about dynamically occluded objects in visual cortex

PubMed Central

Erlikhman, Gennady; Caplovitz, Gideon P.

2016-01-01

During dynamic occlusion, an object passes behind an occluding surface and then later reappears. Even when completely occluded from view, such objects are experienced as continuing to exist or persist behind the occluder, even though they are no longer visible. The contents and neural basis of this persistent representation remain poorly understood. Questions remain as to whether there is information maintained about the object itself (i.e. its shape or identity) or, non-object-specific information such as its position or velocity as it is tracked behind an occluder as well as which areas of visual cortex represent such information. Recent studies have found that early visual cortex is activated by “invisible” objects during visual imagery and by unstimulated regions along the path of apparent motion, suggesting that some properties of dynamically occluded objects may also be neurally represented in early visual cortex. We applied functional magnetic resonance imaging in human subjects to examine the representation of information within visual cortex during dynamic occlusion. For gradually occluded, but not for instantly disappearing objects, there was an increase in activity in early visual cortex (V1, V2, and V3). This activity was spatially-specific, corresponding to the occluded location in the visual field. However, the activity did not encode enough information about object identity to discriminate between different kinds of occluded objects (circles vs. stars) using MVPA. In contrast, object identity could be decoded in spatially-specific subregions of higher-order, topographically organized areas such as ventral, lateral, and temporal occipital areas (VO, LO, and TO) as well as the functionally defined LOC and hMT+. These results suggest that early visual cortex may represent the dynamically occluded object’s position or motion path, while later visual areas represent object-specific information. PMID:27663987

Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences

PubMed Central

Jung, Minju; Hwang, Jungsik; Tani, Jun

2015-01-01

It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns. PMID:26147887

Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences.

PubMed

Jung, Minju; Hwang, Jungsik; Tani, Jun

2015-01-01

It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns.

A Microplate Reader-Based System for Visualizing Transcriptional Activity During in vivo Microbial Interactions in Space and Time.

PubMed

Hennessy, Rosanna C; Stougaard, Peter; Olsson, Stefan

2017-03-21

Here, we report the development of a microplate reader-based system for visualizing gene expression dynamics in living bacterial cells in response to a fungus in space and real-time. A bacterium expressing the red fluorescent protein mCherry fused to the promoter region of a regulator gene nunF indicating activation of an antifungal secondary metabolite gene cluster was used as a reporter system. Time-lapse image recordings of the reporter red signal and a green signal from fluorescent metabolites combined with microbial growth measurements showed that nunF-regulated gene transcription is switched on when the bacterium enters the deceleration growth phase and upon physical encounter with fungal hyphae. This novel technique enables real-time live imaging of samples by time-series multi-channel automatic recordings using a microplate reader as both an incubator and image recorder of general use to researchers. The technique can aid in deciding when to destructively sample for other methods e.g. transcriptomics and mass spectrometry imaging to study gene expression and metabolites exchanged during the interaction.

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

NASA Astrophysics Data System (ADS)

Hamprecht, Fred A.; Peter, Christine; Daura, Xavier; Thiel, Walter; van Gunsteren, Wilfred F.

2001-02-01

We propose an approach for summarizing the output of long simulations of complex systems, affording a rapid overview and interpretation. First, multidimensional scaling techniques are used in conjunction with dimension reduction methods to obtain a low-dimensional representation of the configuration space explored by the system. A nonparametric estimate of the density of states in this subspace is then obtained using kernel methods. The free energy surface is calculated from that density, and the configurations produced in the simulation are then clustered according to the topography of that surface, such that all configurations belonging to one local free energy minimum form one class. This topographical cluster analysis is performed using basin spanning trees which we introduce as subgraphs of Delaunay triangulations. Free energy surfaces obtained in dimensions lower than four can be visualized directly using iso-contours and -surfaces. Basin spanning trees also afford a glimpse of higher-dimensional topographies. The procedure is illustrated using molecular dynamics simulations on the reversible folding of peptide analoga. Finally, we emphasize the intimate relation of density estimation techniques to modern enhanced sampling algorithms.

Visualization of Secondary Flow Development in High Aspect Ratio Channels with Curvature

NASA Technical Reports Server (NTRS)

Meyer, Michael L.; Giuliani, James E.

1994-01-01

The results of an experimental project to visually examine the secondary flow structure that develops in curved, high aspect-ratio rectangular channels are presented. The results provide insight into the fluid dynamics within high aspect ratio channels. A water flow test rig constructed out of plexiglass, with an adjustable aspect ratio, was used for these experiments. Results were obtained for a channel geometry with a hydraulic diameter of 10.6 mm (0.417 in.), an aspect ratio of 5.0, and a hydraulic radius to curvature radius ratio of 0.0417. Flow conditions were varied to achieve Reynolds numbers up to 5,100. A new particle imaging velocimetry technique was developed which could resolve velocity information from particles entering and leaving the field of view. Time averaged secondary flow velocity vectors, obtained using this velocimetry technique, are presented for 30 degrees, 60 degrees, and 90 degrees into a 180 degrees bend and at a Reynolds number of 5,100. The secondary flow results suggest the coexistence of both the classical curvature induced vortex pair flow structure and the eddies seen in straight turbulent channel flow.

Exploratory visualization software for reporting environmental survey results.

PubMed

Fisher, P; Arnot, C; Bastin, L; Dykes, J

2001-08-01

Environmental surveys yield three principal products: maps, a set of data tables, and a textual report. The relationships between these three elements, however, are often cumbersome to present, making full use of all the information in an integrated and systematic sense difficult. The published paper report is only a partial solution. Modern developments in computing, particularly in cartography, GIS, and hypertext, mean that it is increasingly possible to conceive of an easier and more interactive approach to the presentation of such survey results. Here, we present such an approach which links map and tabular datasets arising from a vegetation survey, allowing users ready access to a complex dataset using dynamic mapping techniques. Multimedia datasets equipped with software like this provide an exciting means of quick and easy visual data exploration and comparison. These techniques are gaining popularity across the sciences as scientists and decision-makers are presented with increasing amounts of diverse digital data. We believe that the software environment actively encourages users to make complex interrogations of the survey information, providing a new vehicle for the reader of an environmental survey report.

High dynamic range adaptive real-time smart camera: an overview of the HDR-ARTiST project

NASA Astrophysics Data System (ADS)

Lapray, Pierre-Jean; Heyrman, Barthélémy; Ginhac, Dominique

2015-04-01

Standard cameras capture only a fraction of the information that is visible to the human visual system. This is specifically true for natural scenes including areas of low and high illumination due to transitions between sunlit and shaded areas. When capturing such a scene, many cameras are unable to store the full Dynamic Range (DR) resulting in low quality video where details are concealed in shadows or washed out by sunlight. The imaging technique that can overcome this problem is called HDR (High Dynamic Range) imaging. This paper describes a complete smart camera built around a standard off-the-shelf LDR (Low Dynamic Range) sensor and a Virtex-6 FPGA board. This smart camera called HDR-ARtiSt (High Dynamic Range Adaptive Real-time Smart camera) is able to produce a real-time HDR live video color stream by recording and combining multiple acquisitions of the same scene while varying the exposure time. This technique appears as one of the most appropriate and cheapest solution to enhance the dynamic range of real-life environments. HDR-ARtiSt embeds real-time multiple captures, HDR processing, data display and transfer of a HDR color video for a full sensor resolution (1280 1024 pixels) at 60 frames per second. The main contributions of this work are: (1) Multiple Exposure Control (MEC) dedicated to the smart image capture with alternating three exposure times that are dynamically evaluated from frame to frame, (2) Multi-streaming Memory Management Unit (MMMU) dedicated to the memory read/write operations of the three parallel video streams, corresponding to the different exposure times, (3) HRD creating by combining the video streams using a specific hardware version of the Devebecs technique, and (4) Global Tone Mapping (GTM) of the HDR scene for display on a standard LCD monitor.

Bubble Dynamics on a Heated Surface

NASA Technical Reports Server (NTRS)

Kassemi, M.; Rashidnia, N.

1999-01-01

In this work, we study steady and oscillatory thermocapillary and natural convective flows generated by a bubble on a heated solid surface. The interaction between gas and vapor bubbles with the surrounding fluid is of interest for both space and ground-based processing. A combined numerical-experimental approach is adopted here. The temperature field is visualized using Mach-Zehnder and/or Wollaston Prism Interferometry and the flow field is observed by a laser sheet flow visualization technique. A finite element numerical model is developed which solves the transient two-dimensional continuity, momentum, and energy equations and includes the effects of temperature-dependent surface tension and bubble surface deformation. Below the critical Marangoni number, the steady state low-g and 1-g temperature and velocity fields predicted by the finite element model are in excellent agreement with both the visualization experiments in our laboratory and recently published experimental results in the literature. Above the critical Marangoni number, the model predicts an oscillatory flow which is also closely confirmed by experiments. It is shown that the dynamics of the oscillatory flow are directly controlled by the thermal and hydrodynamic interactions brought about by combined natural and thermocapillary convection. Therefore, as numerical simulations show, there are considerable differences between the 1-g and low-g temperature and flow fields at both low and high Marangoni numbers. This has serious implications for both materials processing and fluid management in space.

Comparison of KTP, Thulium, and CO2 laser in stapedotomy using specialized visualization techniques: thermal effects.

PubMed

Kamalski, Digna M A; Verdaasdonk, Rudolf M; de Boorder, Tjeerd; Vincent, Robert; Trabelzini, Franco; Grolman, Wilko

2014-06-01

High-speed thermal imaging enables visualization of heating of the vestibule during laser-assisted stapedotomy, comparing KTP, CO2, and Thulium laser light. Perforation of the stapes footplate with laser bears the risk of heating of the inner ear fluids. The amount of heating depends on absorption of the laser light and subsequent tissue ablation. The ablation of the footplate is driven by strong water absorption for the CO2 and Thulium laser. For the KTP laser wavelength, ablation is driven by carbonization of the footplate and it might penetrate deep into the inner ear without absorption in water. The thermal effects were visualized in an inner ear model, using two new techniques: (1) high-speed Schlieren imaging shows relative dynamic changes of temperatures up to 2 ms resolution in the perilymph. (2) Thermo imaging provides absolute temperature measurements around the footplate up to 40 ms resolution. The high-speed Schlieren imaging showed minimal heating using the KTP laser. Both CO2 and Thulium laser showed heating below the footplate. Thulium laser wavelength generated heating up to 0.6 mm depth. This was confirmed with thermal imaging, showing a rise of temperature of 4.7 (±3.5) °C for KTP and 9.4 (±6.9) for Thulium in the area of 2 mm below the footplate. For stapedotomy, the Thulium and CO2 laser show more extended thermal effects compared to KTP. High-speed Schlieren imaging and thermal imaging are complimentary techniques to study lasers thermal effects in tissue.

Technical note: real-time web-based wireless visual guidance system for radiotherapy.

PubMed

Lee, Danny; Kim, Siyong; Palta, Jatinder R; Kim, Taeho

2017-06-01

Describe a Web-based wireless visual guidance system that mitigates issues associated with hard-wired audio-visual aided patient interactive motion management systems that are cumbersome to use in routine clinical practice. Web-based wireless visual display duplicates an existing visual display of a respiratory-motion management system for visual guidance. The visual display of the existing system is sent to legacy Web clients over a private wireless network, thereby allowing a wireless setting for real-time visual guidance. In this study, active breathing coordinator (ABC) trace was used as an input for visual display, which captured and transmitted to Web clients. Virtual reality goggles require two (left and right eye view) images for visual display. We investigated the performance of Web-based wireless visual guidance by quantifying (1) the network latency of visual displays between an ABC computer display and Web clients of a laptop, an iPad mini 2 and an iPhone 6, and (2) the frame rate of visual display on the Web clients in frames per second (fps). The network latency of visual display between the ABC computer and Web clients was about 100 ms and the frame rate was 14.0 fps (laptop), 9.2 fps (iPad mini 2) and 11.2 fps (iPhone 6). In addition, visual display for virtual reality goggles was successfully shown on the iPhone 6 with 100 ms and 11.2 fps. A high network security was maintained by utilizing the private network configuration. This study demonstrated that a Web-based wireless visual guidance can be a promising technique for clinical motion management systems, which require real-time visual display of their outputs. Based on the results of this study, our approach has the potential to reduce clutter associated with wired-systems, reduce space requirements, and extend the use of medical devices from static usage to interactive and dynamic usage in a radiotherapy treatment vault.

MD Simulations of P-Type ATPases in a Lipid Bilayer System.

PubMed

Autzen, Henriette Elisabeth; Musgaard, Maria

2016-01-01

Molecular dynamics (MD) simulation is a computational method which provides insight on protein dynamics with high resolution in both space and time, in contrast to many experimental techniques. MD simulations can be used as a stand-alone method to study P-type ATPases as well as a complementary method aiding experimental studies. In particular, MD simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of P-type ATPases. In the following, we describe a detailed practical procedure on how to set up and run a MD simulation of a P-type ATPase embedded in a lipid bilayer using software free of use for academics. We emphasize general considerations and problems typically encountered when setting up simulations. While full coverage of all possible procedures is beyond the scope of this chapter, we have chosen to illustrate the MD procedure with the Nanoscale Molecular Dynamics (NAMD) and the Visual Molecular Dynamics (VMD) software suites.

Granular dynamics during impact.

PubMed

Nordstrom, K N; Lim, E; Harrington, M; Losert, W

2014-06-06

We study the impact of a projectile onto a bed of 3 mm grains immersed in an index-matched fluid. We vary the amount of prestrain on the sample, strengthening the force chains within the system. We find this affects only the prefactor of the linear depth-dependent term in the stopping force. We propose a simple model to account for the strain dependence of this term, owing to increased pressure in the pile. Interestingly, we find that the presence of the fluid does not affect the impact dynamics, suggesting that dynamic friction is not a factor. Using a laser sheet scanning technique to visualize internal grain motion, we measure the trajectory of each grain throughout an impact. Microscopically, our results indicate that weaker initial force chains result in more irreversible, plastic rearrangements, suggesting static friction between grains does play a substantial role in the energy dissipation.

Beyond the G-spot: clitourethrovaginal complex anatomy in female orgasm.

PubMed

Jannini, Emmanuele A; Buisson, Odile; Rubio-Casillas, Alberto

2014-09-01

The search for the legendary, highly erogenous vaginal region, the Gräfenberg spot (G-spot), has produced important data, substantially improving understanding of the complex anatomy and physiology of sexual responses in women. Modern imaging techniques have enabled visualization of dynamic interactions of female genitals during self-sexual stimulation or coitus. Although no single structure consistent with a distinct G-spot has been identified, the vagina is not a passive organ but a highly dynamic structure with an active role in sexual arousal and intercourse. The anatomical relationships and dynamic interactions between the clitoris, urethra, and anterior vaginal wall have led to the concept of a clitourethrovaginal (CUV) complex, defining a variable, multifaceted morphofunctional area that, when properly stimulated during penetration, could induce orgasmic responses. Knowledge of the anatomy and physiology of the CUV complex might help to avoid damage to its neural, muscular, and vascular components during urological and gynaecological surgical procedures.

Domain and rim growth kinetics in stratifying foam films

NASA Astrophysics Data System (ADS)

Zhang, Yiran; Yilixiati, Subinuer; Sharma, Vivek

Foam films are freely standing thin liquid films that typically consist of two surfactant-laden surfaces that are ~5 nm - 10 micron apart. Sandwiched between these interfacial layers is a fluid that drains primarily under the influence of viscous and interfacial forces, including disjoining pressure. Interestingly, a layered ordering of micelles inside the foam films (thickness <100 nm) leads to a stepwise thinning phenomena called stratification, which results in a thickness-dependent variation in reflected light intensity, visualized as progressively darker shades of gray. Thinner, darker domains spontaneously grow within foam films. During the initial expansion, a rim forms near the contact line between the growing thinner domain and the surrounding region, which influences the dynamics of domain growth as well as stratification Using newly developed interferometry digitial imaging optical microscopy (IDIOM) technique, we capture the rim evolution dynamics. Finally, we also develop a theoretical model to describe both rim evolution and domain growth dynamics.

Cardiovascular and pulmonary dynamics by quantitative imaging

NASA Technical Reports Server (NTRS)

Wood, E. H.

1976-01-01

The accuracy and range of studies on cardiovascular and pulmonary functions can be greatly facilitated if the motions of the underlying organ systems throughout individual cycles can be directly visualized and readily measured with minimum or preferably no effect on these motions. Achievement of this objective requires development of techniques for quantitative noninvasive or minimally invasive dynamic and stop-action imaging of the organ systems. A review of advances in dynamic quantitative imaging of moving organs reveals that the revolutionary value of cross-sectional and three-dimensional images produced by various types of radiant energy such as X-rays and gamma rays, positrons, electrons, protons, light, and ultrasound for clinical diagnostic and biomedical research applications is just beginning to be realized. The fabrication of a clinically useful cross-section reconstruction device with sensing capabilities for both anatomical structural composition and chemical composition may be possible and awaits future development.

Oculometric Assessment of Dynamic Visual Processing

NASA Technical Reports Server (NTRS)

Liston, Dorion Bryce; Stone, Lee

2014-01-01

Eye movements are the most frequent (3 per second), shortest-latency (150-250 ms), and biomechanically simplest (1 joint, no inertial complexities) voluntary motor behavior in primates, providing a model system to assess sensorimotor disturbances arising from trauma, fatigue, aging, or disease states (e.g., Diefendorf and Dodge, 1908). We developed a 15-minute behavioral tracking protocol consisting of randomized stepramp radial target motion to assess several aspects of the behavioral response to dynamic visual motion, including pursuit initiation, steadystate tracking, direction-tuning, and speed-tuning thresholds. This set of oculomotor metrics provide valid and reliable measures of dynamic visual performance (Stone and Krauzlis, 2003; Krukowski and Stone, 2005; Stone et al, 2009; Liston and Stone, 2014), and may prove to be a useful assessment tool for functional impairments of dynamic visual processing.

DVA as a Diagnostic Test for Vestibulo-Ocular Reflex Function

NASA Technical Reports Server (NTRS)

Wood, Scott J.; Appelbaum, Meghan

2010-01-01

The vestibulo-ocular reflex (VOR) stabilizes vision on earth-fixed targets by eliciting eyes movements in response to changes in head position. How well the eyes perform this task can be functionally measured by the dynamic visual acuity (DVA) test. We designed a passive, horizontal DVA test to specifically study the acuity and reaction time when looking in different target locations. Visual acuity was compared among 12 subjects using a standard Landolt C wall chart, a computerized static (no rotation) acuity test and dynamic acuity test while oscillating at 0.8 Hz (+/-60 deg/s). In addition, five trials with yaw oscillation randomly presented a visual target in one of nine different locations with the size and presentation duration of the visual target varying across trials. The results showed a significant difference between the static and dynamic threshold acuities as well as a significant difference between the visual targets presented in the horizontal plane versus those in the vertical plane when comparing accuracy of vision and reaction time of the response. Visual acuity increased proportional to the size of the visual target and increased between 150 and 300 msec duration. We conclude that dynamic visual acuity varies with target location, with acuity optimized for targets in the plane of rotation. This DVA test could be used as a functional diagnostic test for visual-vestibular and neuro-cognitive impairments by assessing both accuracy and reaction time to acquire visual targets.

SOCR "Motion Charts": An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data

ERIC Educational Resources Information Center

Al-Aziz, Jameel; Christou, Nicolas; Dinov, Ivo D.

2010-01-01

The amount, complexity and provenance of data have dramatically increased in the past five years. Visualization of observed and simulated data is a critical component of any social, environmental, biomedical or scientific quest. Dynamic, exploratory and interactive visualization of multivariate data, without preprocessing by dimensionality…

Cognitive Strategies for Learning from Static and Dynamic Visuals.

ERIC Educational Resources Information Center

Lewalter, D.

2003-01-01

Studied the effects of including static or dynamic visuals in an expository text on a learning outcome and the use of learning strategies when working with these visuals. Results for 60 undergraduates for both types of illustration indicate different frequencies in the use of learning strategies relevant for the learning outcome. (SLD)

How Spatial Abilities and Dynamic Visualizations Interplay When Learning Functional Anatomy with 3D Anatomical Models

ERIC Educational Resources Information Center

Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

2015-01-01

The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material…

Flow Visualization of Dynamic Stall on an Oscillating Airfoil

DTIC Science & Technology

1989-09-01

Dynamic Stall; Dynamic lift, ’Unsteady lift; Helicopter retreating blade stall; Oscillating airfoil ; Flow visualization,’Schlieren method ;k ez.S-,’ .0...the degree of MASTER OF SCIENCE IN AERONAUTICAL ENGINEERING from the NAVAL POSTGRADUATE SCHOOL September 1989 Author...and moment behavior is quite different from the static stall associated with fixed-wing airfoils . Helicopter retreating blade stall is a dynamic

Neural correlates of the perception of dynamic versus static facial expressions of emotion.

PubMed

Kessler, Henrik; Doyen-Waldecker, Cornelia; Hofer, Christian; Hoffmann, Holger; Traue, Harald C; Abler, Birgit

2011-04-20

This study investigated brain areas involved in the perception of dynamic facial expressions of emotion. A group of 30 healthy subjects was measured with fMRI when passively viewing prototypical facial expressions of fear, disgust, sadness and happiness. Using morphing techniques, all faces were displayed as still images and also dynamically as a film clip with the expressions evolving from neutral to emotional. Irrespective of a specific emotion, dynamic stimuli selectively activated bilateral superior temporal sulcus, visual area V5, fusiform gyrus, thalamus and other frontal and parietal areas. Interaction effects of emotion and mode of presentation (static/dynamic) were only found for the expression of happiness, where static faces evoked greater activity in the medial prefrontal cortex. Our results confirm previous findings on neural correlates of the perception of dynamic facial expressions and are in line with studies showing the importance of the superior temporal sulcus and V5 in the perception of biological motion. Differential activation in the fusiform gyrus for dynamic stimuli stands in contrast to classical models of face perception but is coherent with new findings arguing for a more general role of the fusiform gyrus in the processing of socially relevant stimuli.

The Evolution of Three Dimensional Visualization for Commanding the Mars Rovers

NASA Technical Reports Server (NTRS)

Hartman, Frank R.; Wright, John; Cooper, Brian

2014-01-01

NASA's Jet Propulsion Laboratory has built and operated four rovers on the surface of Mars. Two and three dimensional visualization has been extensively employed to command both the mobility and robotic arm operations of these rovers. Stereo visualization has been an important component in this set of visualization techniques. This paper discusses the progression of the implementation and use of visualization techniques for in-situ operations of these robotic missions. Illustrative examples will be drawn from the results of using these techniques over more than ten years of surface operations on Mars.

Recent Advances in Immersive Visualization of Ocean Data: Virtual Reality Through the Web on Your Laptop Computer

NASA Astrophysics Data System (ADS)

Hermann, A. J.; Moore, C.; Soreide, N. N.

2002-12-01

Ocean circulation is irrefutably three dimensional, and powerful new measurement technologies and numerical models promise to expand our three-dimensional knowledge of the dynamics further each year. Yet, most ocean data and model output is still viewed using two-dimensional maps. Immersive visualization techniques allow the investigator to view their data as a three dimensional world of surfaces and vectors which evolves through time. The experience is not unlike holding a part of the ocean basin in one's hand, turning and examining it from different angles. While immersive, three dimensional visualization has been possible for at least a decade, the technology was until recently inaccessible (both physically and financially) for most researchers. It is not yet fully appreciated by practicing oceanographers how new, inexpensive computing hardware and software (e.g. graphics cards and controllers designed for the huge PC gaming market) can be employed for immersive, three dimensional, color visualization of their increasingly huge datasets and model output. In fact, the latest developments allow immersive visualization through web servers, giving scientists the ability to "fly through" three-dimensional data stored half a world away. Here we explore what additional insight is gained through immersive visualization, describe how scientists of very modest means can easily avail themselves of the latest technology, and demonstrate its implementation on a web server for Pacific Ocean model output.

Visual Sensing for Urban Flood Monitoring

PubMed Central

Lo, Shi-Wei; Wu, Jyh-Horng; Lin, Fang-Pang; Hsu, Ching-Han

2015-01-01

With the increasing climatic extremes, the frequency and severity of urban flood events have intensified worldwide. In this study, image-based automated monitoring of flood formation and analyses of water level fluctuation were proposed as value-added intelligent sensing applications to turn a passive monitoring camera into a visual sensor. Combined with the proposed visual sensing method, traditional hydrological monitoring cameras have the ability to sense and analyze the local situation of flood events. This can solve the current problem that image-based flood monitoring heavily relies on continuous manned monitoring. Conventional sensing networks can only offer one-dimensional physical parameters measured by gauge sensors, whereas visual sensors can acquire dynamic image information of monitored sites and provide disaster prevention agencies with actual field information for decision-making to relieve flood hazards. The visual sensing method established in this study provides spatiotemporal information that can be used for automated remote analysis for monitoring urban floods. This paper focuses on the determination of flood formation based on image-processing techniques. The experimental results suggest that the visual sensing approach may be a reliable way for determining the water fluctuation and measuring its elevation and flood intrusion with respect to real-world coordinates. The performance of the proposed method has been confirmed; it has the capability to monitor and analyze the flood status, and therefore, it can serve as an active flood warning system. PMID:26287201

H.264/AVC digital fingerprinting based on spatio-temporal just noticeable distortion

NASA Astrophysics Data System (ADS)

Ait Saadi, Karima; Bouridane, Ahmed; Guessoum, Abderrezak

2014-01-01

This paper presents a robust adaptive embedding scheme using a modified Spatio-Temporal noticeable distortion (JND) model that is designed for tracing the distribution of the H.264/AVC video content and protecting them from unauthorized redistribution. The Embedding process is performed during coding process in selected macroblocks type Intra 4x4 within I-Frame. The method uses spread-spectrum technique in order to obtain robustness against collusion attacks and the JND model to dynamically adjust the embedding strength and control the energy of the embedded fingerprints so as to ensure their imperceptibility. Linear and non linear collusion attacks are performed to show the robustness of the proposed technique against collusion attacks while maintaining visual quality unchanged.

Image segmentation for enhancing symbol recognition in prosthetic vision.

PubMed

Horne, Lachlan; Barnes, Nick; McCarthy, Chris; He, Xuming

2012-01-01

Current and near-term implantable prosthetic vision systems offer the potential to restore some visual function, but suffer from poor resolution and dynamic range of induced phosphenes. This can make it difficult for users of prosthetic vision systems to identify symbolic information (such as signs) except in controlled conditions. Using image segmentation techniques from computer vision, we show it is possible to improve the clarity of such symbolic information for users of prosthetic vision implants in uncontrolled conditions. We use image segmentation to automatically divide a natural image into regions, and using a fixation point controlled by the user, select a region to phosphenize. This technique improves the apparent contrast and clarity of symbolic information over traditional phosphenization approaches.

A self-organizing model of perisaccadic visual receptive field dynamics in primate visual and oculomotor system.

PubMed

Mender, Bedeho M W; Stringer, Simon M

2015-01-01

We propose and examine a model for how perisaccadic visual receptive field dynamics, observed in a range of primate brain areas such as LIP, FEF, SC, V3, V3A, V2, and V1, may develop through a biologically plausible process of unsupervised visually guided learning. These dynamics are associated with remapping, which is the phenomenon where receptive fields anticipate the consequences of saccadic eye movements. We find that a neural network model using a local associative synaptic learning rule, when exposed to visual scenes in conjunction with saccades, can account for a range of associated phenomena. In particular, our model demonstrates predictive and pre-saccadic remapping, responsiveness shifts around the time of saccades, and remapping from multiple directions.

A self-organizing model of perisaccadic visual receptive field dynamics in primate visual and oculomotor system

PubMed Central

Mender, Bedeho M. W.; Stringer, Simon M.

2015-01-01

We propose and examine a model for how perisaccadic visual receptive field dynamics, observed in a range of primate brain areas such as LIP, FEF, SC, V3, V3A, V2, and V1, may develop through a biologically plausible process of unsupervised visually guided learning. These dynamics are associated with remapping, which is the phenomenon where receptive fields anticipate the consequences of saccadic eye movements. We find that a neural network model using a local associative synaptic learning rule, when exposed to visual scenes in conjunction with saccades, can account for a range of associated phenomena. In particular, our model demonstrates predictive and pre-saccadic remapping, responsiveness shifts around the time of saccades, and remapping from multiple directions. PMID:25717301

High resolution imaging of the dynamics of nanoparticles in/on liquids

NASA Astrophysics Data System (ADS)

Kim, Paul; Ribbe, Alexander; Russell, Thomas; Hoagland, David

Electron microscopy for the study of nanoscale structure and dynamics in solvated soft materials has only recently been proposed, and since this technique requires high vacuum, significant challenges must be confronted. Specimens can be encapsulated in vacuum-sealed devices for TEM but this approach is not without difficulties, including beam damage, cumbersome specimen handling, and propensity for wall artifacts. Here, we report an alternative SEM approach, obviating need for a liquid cell by exploiting the nonvolatility of ionic liquids, which is illustrated by visualizations of nanoscale dynamics for two solvated systems, dispersed nanospheres and nanorods in/on thin, free-standing IL films. The translational and rotational Brownian of these nanoparticles were quantitatively tracked. In ultra-thin films, a striking and unanticipated dynamical pairing of the nanospheres was observed, manifesting a balance of capillary and hydrodynamic interactions. Concentrated nanorods were seen to assemble into finite stacks that could be tracked over their entire lifetimes. Broadly applicable to solvated soft nanoscopic materials, the new imaging protocol offers a breakthrough in the study of their structure and dynamics.

[Basic research on vocal fold dynamics: three-dimensional vibration analysis of human and canine larynges].

PubMed

Döllinger, M; Rosanowski, F; Eysholdt, U; Lohscheller, J

2008-12-01

The understanding of normal and pathological vocal fold dynamics is the basis for a pathophysiological motivated voice therapy. Crucial vocal fold dynamics concerning voice production occur at the medial part of the vocal fold which is seen as the most critical region of mucosal wave propagation. Due to the limited size of the larynx the possibilities of laryngeal imaging by endoscopic techniques are limited. This work describes an experimental set-up that enables quantification of the entire medial and superior vocal fold surface using excised human and in vivo canine larynges. The data obtained enable analysis of vocal fold deflections, velocities, and mucosal wave propagation. The reciprocal dependencies can be examined and different areas of vocal fold dynamics located. The vertical components obscured in clinical endoscopy can be visualized. This is not negligible. In particular it is shown that the vertical deflection, which cannot be observed by clinical examination, plays an important part in the dynamics and therefore cannot be omitted for therapeutic procedures. The theoretically assumed entrainment and influence of the two main vibration modes enabling normal phonation is confirmed.

Spectral fingerprints of large-scale cortical dynamics during ambiguous motion perception.

PubMed

Helfrich, Randolph F; Knepper, Hannah; Nolte, Guido; Sengelmann, Malte; König, Peter; Schneider, Till R; Engel, Andreas K

2016-11-01

Ambiguous stimuli have been widely used to study the neuronal correlates of consciousness. Recently, it has been suggested that conscious perception might arise from the dynamic interplay of functionally specialized but widely distributed cortical areas. While previous research mainly focused on phase coupling as a correlate of cortical communication, more recent findings indicated that additional coupling modes might coexist and possibly subserve distinct cortical functions. Here, we studied two coupling modes, namely phase and envelope coupling, which might differ in their origins, putative functions and dynamics. Therefore, we recorded 128-channel EEG while participants performed a bistable motion task and utilized state-of-the-art source-space connectivity analysis techniques to study the functional relevance of different coupling modes for cortical communication. Our results indicate that gamma-band phase coupling in extrastriate visual cortex might mediate the integration of visual tokens into a moving stimulus during ambiguous visual stimulation. Furthermore, our results suggest that long-range fronto-occipital gamma-band envelope coupling sustains the horizontal percept during ambiguous motion perception. Additionally, our results support the idea that local parieto-occipital alpha-band phase coupling controls the inter-hemispheric information transfer. These findings provide correlative evidence for the notion that synchronized oscillatory brain activity reflects the processing of sensory input as well as the information integration across several spatiotemporal scales. The results indicate that distinct coupling modes are involved in different cortical computations and that the rich spatiotemporal correlation structure of the brain might constitute the functional architecture for cortical processing and specific multi-site communication. Hum Brain Mapp 37:4099-4111, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans

PubMed Central

Wu, Yicong; Ghitani, Alireza; Christensen, Ryan; Santella, Anthony; Du, Zhuo; Rondeau, Gary; Bao, Zhirong; Colón-Ramos, Daniel; Shroff, Hari

2011-01-01

The Caenorhabditis elegans embryo is a powerful model for studying neural development, but conventional imaging methods are either too slow or phototoxic to take full advantage of this system. To solve these problems, we developed an inverted selective plane illumination microscopy (iSPIM) module for noninvasive high-speed volumetric imaging of living samples. iSPIM is designed as a straightforward add-on to an inverted microscope, permitting conventional mounting of specimens and facilitating SPIM use by development and neurobiology laboratories. iSPIM offers a volumetric imaging rate 30× faster than currently used technologies, such as spinning-disk confocal microscopy, at comparable signal-to-noise ratio. This increased imaging speed allows us to continuously monitor the development of C, elegans embryos, scanning volumes every 2 s for the 14-h period of embryogenesis with no detectable phototoxicity. Collecting ∼25,000 volumes over the entirety of embryogenesis enabled in toto visualization of positions and identities of cell nuclei. By merging two-color iSPIM with automated lineaging techniques we realized two goals: (i) identification of neurons expressing the transcription factor CEH-10/Chx10 and (ii) visualization of their neurodevelopmental dynamics. We found that canal-associated neurons use somal translocation and amoeboid movement as they migrate to their final position in the embryo. We also visualized axon guidance and growth cone dynamics as neurons circumnavigate the nerve ring and reach their targets in the embryo. The high-speed volumetric imaging rate of iSPIM effectively eliminates motion blur from embryo movement inside the egg case, allowing characterization of dynamic neurodevelopmental events that were previously inaccessible. PMID:22006307

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

How Dynamic Visualization Technology can Support Molecular Reasoning

NASA Astrophysics Data System (ADS)

Levy, Dalit

2013-10-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and gas. They interact with the visualizations and carry out inquiry activities to make and refine connections between observable phenomena and atomic level processes related to phase change. The explanations proposed by 300 pairs of students in response to pre/post-assessment items have been analyzed using a scale for measuring the level of molecular reasoning. Results indicate that from pretest to posttest, students make progress in their level of molecular reasoning and are better able to connect intermolecular forces and phase change in their explanations. The paper presents the results through the lens of improvement patterns and the metaphor of the "ladder of molecular reasoning," and discusses how this adds to our understanding of the benefits of interacting with dynamic molecular visualizations.

Wind Energy Program Summary. Volume 2: Research summaries, fiscal year 1988

NASA Astrophysics Data System (ADS)

1989-04-01

Activities by the Federal Wind Energy program since the early 1980s have focused on developing a technology base necessary for industry to demonstrate the viability of wind energy as an alternative energy supply. The Federal Wind Energy Program's research has targeted the sciences of wind turbine dynamics and the development of advanced components and systems. These efforts have resulted in major advancements toward the development and commercialization of wind technology as an alternative energy source. The installation of more than 16,000 wind turbines in California by the end of 1987 provides evidence that commercial use of wind energy technology can be a viable source of electric power. Research in wind turbine sciences has focused on atmospheric fluid dynamics, aerodynamics, and structural dynamics. As outlines in the projects that are described in this document, advancements in atmospheric fluid dynamics have been made through the development and refinement of wind characterization models and wind/rotor interaction prediction codes. Recent gains in aerodynamics can be attributed to a better understanding of airfoil operations, using innovative research approaches such as flow-visualization techniques. Qualitative information and data from laboratory and field tests are being used to document fatigue damage processes. These data are being used to develop new theories and data bases for structural dynamics, and will help to achieve long-term unit life and lower capital and maintenance costs. Material characterization and modeling techniques have been improved to better analyze effects of stress and fatigue on system components.

Audio-Visual Speaker Diarization Based on Spatiotemporal Bayesian Fusion.

PubMed

Gebru, Israel D; Ba, Sileye; Li, Xiaofei; Horaud, Radu

2018-05-01

Speaker diarization consists of assigning speech signals to people engaged in a dialogue. An audio-visual spatiotemporal diarization model is proposed. The model is well suited for challenging scenarios that consist of several participants engaged in multi-party interaction while they move around and turn their heads towards the other participants rather than facing the cameras and the microphones. Multiple-person visual tracking is combined with multiple speech-source localization in order to tackle the speech-to-person association problem. The latter is solved within a novel audio-visual fusion method on the following grounds: binaural spectral features are first extracted from a microphone pair, then a supervised audio-visual alignment technique maps these features onto an image, and finally a semi-supervised clustering method assigns binaural spectral features to visible persons. The main advantage of this method over previous work is that it processes in a principled way speech signals uttered simultaneously by multiple persons. The diarization itself is cast into a latent-variable temporal graphical model that infers speaker identities and speech turns, based on the output of an audio-visual association process, executed at each time slice, and on the dynamics of the diarization variable itself. The proposed formulation yields an efficient exact inference procedure. A novel dataset, that contains audio-visual training data as well as a number of scenarios involving several participants engaged in formal and informal dialogue, is introduced. The proposed method is thoroughly tested and benchmarked with respect to several state-of-the art diarization algorithms.

Parsing Heterogeneity in Autism Spectrum Disorders: Visual Scanning of Dynamic Social Scenes in School-Aged Children

ERIC Educational Resources Information Center

Rice, Katherine; Moriuchi, Jennifer M.; Jones, Warren; Klin, Ami

2012-01-01

Objective: To examine patterns of variability in social visual engagement and their relationship to standardized measures of social disability in a heterogeneous sample of school-aged children with autism spectrum disorders (ASD). Method: Eye-tracking measures of visual fixation during free-viewing of dynamic social scenes were obtained for 109…

Radiation Mitigation and Power Optimization Design Tools for Reconfigurable Hardware in Orbit

NASA Technical Reports Server (NTRS)

French, Matthew; Graham, Paul; Wirthlin, Michael; Wang, Li; Larchev, Gregory

2005-01-01

The Reconfigurable Hardware in Orbit (RHinO)project is focused on creating a set of design tools that facilitate and automate design techniques for reconfigurable computing in space, using SRAM-based field-programmable-gate-array (FPGA) technology. In the second year of the project, design tools that leverage an established FPGA design environment have been created to visualize and analyze an FPGA circuit for radiation weaknesses and power inefficiencies. For radiation, a single event Upset (SEU) emulator, persistence analysis tool, and a half-latch removal tool for Xilinx/Virtex-II devices have been created. Research is underway on a persistence mitigation tool and multiple bit upsets (MBU) studies. For power, synthesis level dynamic power visualization and analysis tools have been completed. Power optimization tools are under development and preliminary test results are positive.

Microradiography with Semiconductor Pixel Detectors

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

Jakubek, Jan; Cejnarova, Andrea; Dammer, Jiri

High resolution radiography (with X-rays, neutrons, heavy charged particles, ...) often exploited also in tomographic mode to provide 3D images stands as a powerful imaging technique for instant and nondestructive visualization of fine internal structure of objects. Novel types of semiconductor single particle counting pixel detectors offer many advantages for radiation imaging: high detection efficiency, energy discrimination or direct energy measurement, noiseless digital integration (counting), high frame rate and virtually unlimited dynamic range. This article shows the application and potential of pixel detectors (such as Medipix2 or TimePix) in different fields of radiation imaging.

Computer aided drug design

NASA Astrophysics Data System (ADS)

Jain, A.

2017-08-01

Computer based method can help in discovery of leads and can potentially eliminate chemical synthesis and screening of many irrelevant compounds, and in this way, it save time as well as cost. Molecular modeling systems are powerful tools for building, visualizing, analyzing and storing models of complex molecular structure that can help to interpretate structure activity relationship. The use of various techniques of molecular mechanics and dynamics and software in Computer aided drug design along with statistics analysis is powerful tool for the medicinal chemistry to synthesis therapeutic and effective drugs with minimum side effect.

Generalizing the extensibility of a dynamic geometry software

NASA Astrophysics Data System (ADS)

Herceg, Đorđe; Radaković, Davorka; Herceg, Dejana

2012-09-01

Plug-and-play visual components in a Dynamic Geometry Software (DGS) enable development of visually attractive, rich and highly interactive dynamic drawings. We are developing SLGeometry, a DGS that contains a custom programming language, a computer algebra system (CAS engine) and a graphics subsystem. The basic extensibility framework on SLGeometry supports dynamic addition of new functions from attribute annotated classes that implement runtime metadata registration in code. We present a general plug-in framework for dynamic importing of arbitrary Silverlight user interface (UI) controls into SLGeometry at runtime. The CAS engine maintains a metadata storage that describes each imported visual component and enables two-way communication between the expressions stored in the engine and the UI controls on the screen.

The nature of the (visualization) game: Challenges and opportunities from computational geophysics

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

As the geosciences enters the era of big data, modeling and visualization become increasingly vital tools for discovery, understanding, education, and communication. Here, we focus on modeling and visualization of the structure and dynamics of the Earth's surface and interior. The past decade has seen accelerated data acquisition, including higher resolution imaging and modeling of Earth's deep interior, complex models of geodynamics, and high resolution topographic imaging of the changing surface, with an associated acceleration of computational modeling through better scientific software, increased computing capability, and the use of innovative methods of scientific visualization. The role of modeling is to describe a system, answer scientific questions, and test hypotheses; the term "model" encompasses mathematical models, computational models, physical models, conceptual models, statistical models, and visual models of a structure or process. These different uses of the term require thoughtful communication to avoid confusion. Scientific visualization is integral to every aspect of modeling. Not merely a means of communicating results, the best uses of visualization enable scientists to interact with their data, revealing the characteristics of the data and models to enable better interpretation and inform the direction of future investigation. Innovative immersive technologies like virtual reality, augmented reality, and remote collaboration techniques, are being adapted more widely and are a magnet for students. Time-varying or transient phenomena are especially challenging to model and to visualize; researchers and students may need to investigate the role of initial conditions in driving phenomena, while nonlinearities in the governing equations of many Earth systems make the computations and resulting visualization especially challenging. Training students how to use, design, build, and interpret scientific modeling and visualization tools prepares them to better understand the nature of complex, multiscale geoscience data.

Computer Science Techniques Applied to Parallel Atomistic Simulation

NASA Astrophysics Data System (ADS)

Nakano, Aiichiro

1998-03-01

Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

Visual search for facial expressions of emotions: a comparison of dynamic and static faces.

PubMed

Horstmann, Gernot; Ansorge, Ulrich

2009-02-01

A number of past studies have used the visual search paradigm to examine whether certain aspects of emotional faces are processed preattentively and can thus be used to guide attention. All these studies presented static depictions of facial prototypes. Emotional expressions conveyed by the movement patterns of the face have never been examined for their preattentive effect. The present study presented for the first time dynamic facial expressions in a visual search paradigm. Experiment 1 revealed efficient search for a dynamic angry face among dynamic friendly faces, but inefficient search in a control condition with static faces. Experiments 2 to 4 suggested that this pattern of results is due to a stronger movement signal in the angry than in the friendly face: No (strong) advantage of dynamic over static faces is revealed when the degree of movement is controlled. These results show that dynamic information can be efficiently utilized in visual search for facial expressions. However, these results do not generally support the hypothesis that emotion-specific movement patterns are always preattentively discriminated. (c) 2009 APA, all rights reserved

Authoring Tours of Geospatial Data With KML and Google Earth

NASA Astrophysics Data System (ADS)

Barcay, D. P.; Weiss-Malik, M.

2008-12-01

As virtual globes become widely adopted by the general public, the use of geospatial data has expanded greatly. With the popularization of Google Earth and other platforms, GIS systems have become virtual reality platforms. Using these platforms, a casual user can easily explore the world, browse massive data-sets, create powerful 3D visualizations, and share those visualizations with millions of people using the KML language. This technology has raised the bar for professionals and academics alike. It is now expected that studies and projects will be accompanied by compelling, high-quality visualizations. In this new landscape, a presentation of geospatial data can be the most effective form of advertisement for a project: engaging both the general public and the scientific community in a unified interactive experience. On the other hand, merely dumping a dataset into a virtual globe can be a disorienting, alienating experience for many users. To create an effective, far-reaching presentation, an author must take care to make their data approachable to a wide variety of users with varying knowledge of the subject matter, expertise in virtual globes, and attention spans. To that end, we present techniques for creating self-guided interactive tours of data represented in KML and visualized in Google Earth. Using these methods, we provide the ability to move the camera through the world while dynamically varying the content, style, and visibility of the displayed data. Such tours can automatically guide users through massive, complex datasets: engaging a broad user-base, and conveying subtle concepts that aren't immediately apparent when viewing the raw data. To the casual user these techniques result in an extremely compelling experience similar to watching video. Unlike video though, these techniques maintain the rich interactive environment provided by the virtual globe, allowing users to explore the data in detail and to add other data sources to the presentation.

Effect of Cognitive Demand on Functional Visual Field Performance in Senior Drivers with Glaucoma.

PubMed

Gangeddula, Viswa; Ranchet, Maud; Akinwuntan, Abiodun E; Bollinger, Kathryn; Devos, Hannes

2017-01-01

Purpose: To investigate the effect of cognitive demand on functional visual field performance in drivers with glaucoma. Method: This study included 20 drivers with open-angle glaucoma and 13 age- and sex-matched controls. Visual field performance was evaluated under different degrees of cognitive demand: a static visual field condition (C1), dynamic visual field condition (C2), and dynamic visual field condition with active driving (C3) using an interactive, desktop driving simulator. The number of correct responses (accuracy) and response times on the visual field task were compared between groups and between conditions using Kruskal-Wallis tests. General linear models were employed to compare cognitive workload, recorded in real-time through pupillometry, between groups and conditions. Results: Adding cognitive demand (C2 and C3) to the static visual field test (C1) adversely affected accuracy and response times, in both groups ( p < 0.05). However, drivers with glaucoma performed worse than did control drivers when the static condition changed to a dynamic condition [C2 vs. C1 accuracy; glaucoma: median difference (Q1-Q3) 3 (2-6.50) vs. 2 (0.50-2.50); p = 0.05] and to a dynamic condition with active driving [C3 vs. C1 accuracy; glaucoma: 2 (2-6) vs. 1 (0.50-2); p = 0.02]. Overall, drivers with glaucoma exhibited greater cognitive workload than controls ( p = 0.02). Conclusion: Cognitive demand disproportionately affects functional visual field performance in drivers with glaucoma. Our results may inform the development of a performance-based visual field test for drivers with glaucoma.

Correlation of two-photon in vivo imaging and FIB/SEM microscopy

PubMed Central

Blazquez-Llorca, L; Hummel, E; Zimmerman, H; Zou, C; Burgold, S; Rietdorf, J; Herms, J

2015-01-01

Advances in the understanding of brain functions are closely linked to the technical developments in microscopy. In this study, we describe a correlative microscopy technique that offers a possibility of combining two-photon in vivo imaging with focus ion beam/scanning electron microscope (FIB/SEM) techniques. Long-term two-photon in vivo imaging allows the visualization of functional interactions within the brain of a living organism over the time, and therefore, is emerging as a new tool for studying the dynamics of neurodegenerative diseases, such as Alzheimer’s disease. However, light microscopy has important limitations in revealing alterations occurring at the synaptic level and when this is required, electron microscopy is mandatory. FIB/SEM microscopy is a novel tool for three-dimensional high-resolution reconstructions, since it acquires automated serial images at ultrastructural level. Using FIB/SEM imaging, we observed, at 10 nm isotropic resolution, the same dendrites that were imaged in vivo over 9 days. Thus, we analyzed their ultrastructure and monitored the dynamics of the neuropil around them. We found that stable spines (present during the 9 days of imaging) formed typical asymmetric contacts with axons, whereas transient spines (present only during one day of imaging) did not form a synaptic contact. Our data suggest that the morphological classification that was assigned to a dendritic spine according to the in vivo images did not fit with its ultrastructural morphology. The correlative technique described herein is likely to open opportunities for unravelling the earlier unrecognized complexity of the nervous system. Lay Description Neuroscience and the understanding of brain functions are closely linked to the technical advances in microscopy. In this study we performed a correlative microscopy technique that offers the possibility to combine 2 photon in vivo imaging and FIB/SEM microscopy. Long term 2 photon in vivo imaging allows the visualization of functional interactions within the brain of a living organism over the time, and therefore, is emerging as a new tool to study the dynamics of neurodegenerative diseases, such as Alzheimer’s disease. However, light microscopy has important limitations in revealing synapses that are the connections between neurons, and for this purpose, the electron microscopy is necessary. FIB/SEM microscopy is a novel tool for three-dimensional (3D) high resolution reconstructions since it acquires automated serial images at ultrastructural level. This correlative technique will open up new horizons and opportunities for unravelling the complexity of the nervous system. PMID:25786682

PathFinder: reconstruction and dynamic visualization of metabolic pathways.

PubMed

Goesmann, Alexander; Haubrock, Martin; Meyer, Folker; Kalinowski, Jörn; Giegerich, Robert

2002-01-01

Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized metabolic pathways provides valuable information on gene expression and regulation. Detection of incomplete pathways helps to improve a constantly evolving genome annotation or discover alternative biochemical pathways. To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed. PathFinder is a tool for the dynamic visualization of metabolic pathways based on annotation data. Pathways are represented as directed acyclic graphs, graph layout algorithms accomplish the dynamic drawing and visualization of the metabolic maps. A more detailed analysis of the input data on the level of biochemical pathways helps to identify genes and detect improper parts of annotations. As an Relational Database Management System (RDBMS) based internet application PathFinder reads a list of EC-numbers or a given annotation in EMBL- or Genbank-format and dynamically generates pathway graphs.

A survey of visualization systems for network security.

PubMed

Shiravi, Hadi; Shiravi, Ali; Ghorbani, Ali A

2012-08-01

Security Visualization is a very young term. It expresses the idea that common visualization techniques have been designed for use cases that are not supportive of security-related data, demanding novel techniques fine tuned for the purpose of thorough analysis. Significant amount of work has been published in this area, but little work has been done to study this emerging visualization discipline. We offer a comprehensive review of network security visualization and provide a taxonomy in the form of five use-case classes encompassing nearly all recent works in this area. We outline the incorporated visualization techniques and data sources and provide an informative table to display our findings. From the analysis of these systems, we examine issues and concerns regarding network security visualization and provide guidelines and directions for future researchers and visual system developers.

The development of laser speckle or particle image displacement velocimetry. Part 1: The role of photographic parameters

NASA Technical Reports Server (NTRS)

Lourenco, L. M. M.; Krothapalli, A.

1987-01-01

One of the difficult problems in experimental fluid dynamics remains the determination of the vorticity field in fluid flows. Recently, a novel velocity measurement technique, commonly known as Laser Speckle or Particle Image Displacement Velocimetry became available. This technique permits the simultaneous visualization of the 2 dimensional streamline pattern in unsteady flows and the quantification of the velocity field. The main advantage of this new technique is that the whole 2 dimensional velocity field can be recorded with great accuracy and spatial resolution, from which the instantaneous vorticity field can be easily obtained. A apparatus used for taking particle displacement images is described. Local coherent illumination by the probe laser beam yielded Young's fringes of good quality at almost every location of the flow field. These fringes were analyzed and the velocity and vorticity fields were derived. Several conclusions drawn are discussed.

Persistence Mapping Using EUV Solar Imager Data

NASA Technical Reports Server (NTRS)

Thompson, B. J.; Young, C. A.

2016-01-01

We describe a simple image processing technique that is useful for the visualization and depiction of gradually evolving or intermittent structures in solar physics extreme-ultraviolet imagery. The technique is an application of image segmentation, which we call "Persistence Mapping," to isolate extreme values in a data set, and is particularly useful for the problem of capturing phenomena that are evolving in both space and time. While integration or "time-lapse" imaging uses the full sample (of size N ), Persistence Mapping rejects (N - 1)/N of the data set and identifies the most relevant 1/N values using the following rule: if a pixel reaches an extreme value, it retains that value until that value is exceeded. The simplest examples isolate minima and maxima, but any quantile or statistic can be used. This paper demonstrates how the technique has been used to extract the dynamics in long-term evolution of comet tails, erupting material, and EUV dimming regions.

FEM Techniques for High Stress Detection in Accelerated Fatigue Simulation

NASA Astrophysics Data System (ADS)

Veltri, M.

2016-09-01

This work presents the theory and a numerical validation study in support to a novel method for a priori identification of fatigue critical regions, with the aim to accelerate durability design in large FEM problems. The investigation is placed in the context of modern full-body structural durability analysis, where a computationally intensive dynamic solution could be required to identify areas with potential for fatigue damage initiation. The early detection of fatigue critical areas can drive a simplification of the problem size, leading to sensible improvement in solution time and model handling while allowing processing of the critical areas in higher detail. The proposed technique is applied to a real life industrial case in a comparative assessment with established practices. Synthetic damage prediction quantification and visualization techniques allow for a quick and efficient comparison between methods, outlining potential application benefits and boundaries.

The Generation of Novel MR Imaging Techniques to Visualize Inflammatory/Degenerative Mechanisms and the Correlation of MR Data with 3D Microscopic Changes

DTIC Science & Technology

2013-09-01

existing MR scanning systems providing the ability to visualize structures that are impossible with current methods . Using techniques to concurrently...and unique system for analysis of affected brain regions and coupled with other imaging techniques and molecular measurements holds significant...scanning systems providing the ability to visualize structures that are impossible with current methods . Using techniques to concurrently stain

Visualizing water

NASA Astrophysics Data System (ADS)

Baart, F.; van Gils, A.; Hagenaars, G.; Donchyts, G.; Eisemann, E.; van Velzen, J. W.

2016-12-01

A compelling visualization is captivating, beautiful and narrative. Here we show how melding the skills of computer graphics, art, statistics, and environmental modeling can be used to generate innovative, attractive and very informative visualizations. We focus on the topic of visualizing forecasts and measurements of water (water level, waves, currents, density, and salinity). For the field of computer graphics and arts, water is an important topic because it occurs in many natural scenes. For environmental modeling and statistics, water is an important topic because the water is essential for transport, a healthy environment, fruitful agriculture, and a safe environment.The different disciplines take different approaches to visualizing water. In computer graphics, one focusses on creating water as realistic looking as possible. The focus on realistic perception (versus the focus on the physical balance pursued by environmental scientists) resulted in fascinating renderings, as seen in recent games and movies. Visualization techniques for statistical results have benefited from the advancement in design and journalism, resulting in enthralling infographics. The field of environmental modeling has absorbed advances in contemporary cartography as seen in the latest interactive data-driven maps. We systematically review the design emerging types of water visualizations. The examples that we analyze range from dynamically animated forecasts, interactive paintings, infographics, modern cartography to web-based photorealistic rendering. By characterizing the intended audience, the design choices, the scales (e.g. time, space), and the explorability we provide a set of guidelines and genres. The unique contributions of the different fields show how the innovations in the current state of the art of water visualization have benefited from inter-disciplinary collaborations.

The NAS Computational Aerosciences Archive

NASA Technical Reports Server (NTRS)

Miceli, Kristina D.; Globus, Al; Lasinski, T. A. (Technical Monitor)

1995-01-01

In order to further the state-of-the-art in computational aerosciences (CAS) technology, researchers must be able to gather and understand existing work in the field. One aspect of this information gathering is studying published work available in scientific journals and conference proceedings. However, current scientific publications are very limited in the type and amount of information that they can disseminate. Information is typically restricted to text, a few images, and a bibliography list. Additional information that might be useful to the researcher, such as additional visual results, referenced papers, and datasets, are not available. New forms of electronic publication, such as the World Wide Web (WWW), limit publication size only by available disk space and data transmission bandwidth, both of which are improving rapidly. The Numerical Aerodynamic Simulation (NAS) Systems Division at NASA Ames Research Center is in the process of creating an archive of CAS information on the WWW. This archive will be based on the large amount of information produced by researchers associated with the NAS facility. The archive will contain technical summaries and reports of research performed on NAS supercomputers, visual results (images, animations, visualization system scripts), datasets, and any other supporting meta-information. This information will be available via the WWW through the NAS homepage, located at http://www.nas.nasa.gov/, fully indexed for searching. The main components of the archive are technical summaries and reports, visual results, and datasets. Technical summaries are gathered every year by researchers who have been allotted resources on NAS supercomputers. These summaries, together with supporting visual results and references, are browsable by interested researchers. Referenced papers made available by researchers can be accessed through hypertext links. Technical reports are in-depth accounts of tools and applications research projects performed by NAS staff members and collaborators. Visual results, which may be available in the form of images, animations, and/or visualization scripts, are generated by researchers with respect to a certain research project, depicting dataset features that were determined important by the investigating researcher. For example, script files for visualization systems (e.g. FAST, PLOT3D, AVS) are provided to create visualizations on the user's local workstation to elucidate the key points of the numerical study. Users can then interact with the data starting where the investigator left off. Datasets are intended to give researchers an opportunity to understand previous work, 'mine' solutions for new information (for example, have you ever read a paper thinking "I wonder what the helicity density looks like?"), compare new techniques with older results, collaborate with remote colleagues, and perform validation. Supporting meta-information associated with the research projects is also important to provide additional context for research projects. This may include information such as the software used in the simulation (e.g. grid generators, flow solvers, visualization). In addition to serving the CAS research community, the information archive will also be helpful to students, visualization system developers and researchers, and management. Students (of any age) can use the data to study fluid dynamics, compare results from different flow solvers, learn about meshing techniques, etc., leading to better informed individuals. For these users it is particularly important that visualization be integrated into dataset archives. Visualization researchers can use dataset archives to test algorithms and techniques, leading to better visualization systems, Management can use the data to figure what is really going on behind the viewgraphs. All users will benefit from fast, easy, and convenient access to CFD datasets. The CAS information archive hopes to serve as a useful resource to those interested in computational sciences. At present, only information that may be distributed internationally is made available via the archive. Studies are underway to determine security requirements and solutions to make additional information available. By providing access to the archive via the WWW, the process of information gathering can be more productive and fruitful due to ease of access and ability to manage many different types of information. As the archive grows, additional resources from outside NAS will be added, providing a dynamic source of research results.

A collection of flow visualization techniques used in the Aerodynamic Research Branch

NASA Technical Reports Server (NTRS)

1984-01-01

Theoretical and experimental research on unsteady aerodynamic flows is discussed. Complex flow fields that involve separations, vortex interactions, and transonic flow effects were investigated. Flow visualization techniques are used to obtain a global picture of the flow phenomena before detailed quantitative studies are undertaken. A wide variety of methods are used to visualize fluid flow and a sampling of these methods is presented. It is emphasized that the visualization technique is a thorough quantitative analysis and subsequent physical understanding of these flow fields.

Is the Oxygen Atom Static or Dynamic? The Effect of Generating Animations on Students' Mental Models of Atomic Structure

ERIC Educational Resources Information Center

Akaygun, Sevil

2016-01-01

Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…

A training tool in group dynamics. The camel-trading incident.

PubMed

Henke, B

1982-01-01

The objective of this training tool in group dynamics is to have the participants' experience and identify barriers to the accomplishment of group tasks and to give the trainer an opportunity to observe interaction within a particular group of participants. This exercise works best for groups which have been together long enough to establish mutual trust. There can be 10 to 20 participants and one should allow 1 1/2 to 2 hours. The materials required are pieces of paper to represent currency, paper for computation and notes, and writing implements. Details of the procedure are given. The material was prepared by INTRAH staff members. Other materials include how to use tracing techniques to create visual aids, how to evaluate teaching and how to create a family health case study.

Integration of scheduling and discrete event simulation systems to improve production flow planning

NASA Astrophysics Data System (ADS)

Krenczyk, D.; Paprocka, I.; Kempa, W. M.; Grabowik, C.; Kalinowski, K.

2016-08-01

The increased availability of data and computer-aided technologies such as MRPI/II, ERP and MES system, allowing producers to be more adaptive to market dynamics and to improve production scheduling. Integration of production scheduling and computer modelling, simulation and visualization systems can be useful in the analysis of production system constraints related to the efficiency of manufacturing systems. A integration methodology based on semi-automatic model generation method for eliminating problems associated with complexity of the model and labour-intensive and time-consuming process of simulation model creation is proposed. Data mapping and data transformation techniques for the proposed method have been applied. This approach has been illustrated through examples of practical implementation of the proposed method using KbRS scheduling system and Enterprise Dynamics simulation system.

Modeling and stochastic analysis of dynamic mechanisms of the perception

NASA Astrophysics Data System (ADS)

Pisarchik, A.; Bashkirtseva, I.; Ryashko, L.

2017-10-01

Modern studies in physiology and cognitive neuroscience consider a noise as an important constructive factor of the brain functionality. Under the adequate noise, the brain can rapidly access different ordered states, and provide decision-making by preventing deadlocks. Bistable dynamic models are often used for the study of the underlying mechanisms of the visual perception. In the present paper, we consider a bistable energy model subject to both additive and parametric noise. Using the catastrophe theory formalism and stochastic sensitivity functions technique, we analyze a response of the equilibria to noise, and study noise-induced transitions between equilibria. We demonstrate and analyse the effect of hysteresis squeezing when the intensity of noise is increased. Stochastic bifurcations connected with the suppression of oscillations by parametric noises are discussed.

Visualizing the dynamic structure of the plant photosynthetic membrane.

PubMed

Ruban, Alexander V; Johnson, Matthew P

2015-11-03

The chloroplast thylakoid membrane is the site for the initial steps of photosynthesis that convert solar energy into chemical energy, ultimately powering almost all life on earth. The heterogeneous distribution of protein complexes within the membrane gives rise to an intricate three-dimensional structure that is nonetheless extremely dynamic on a timescale of seconds to minutes. These dynamics form the basis for the regulation of photosynthesis, and therefore the adaptability of plants to different environments. High-resolution microscopy has in recent years begun to provide new insights into the structural dynamics underlying a number of regulatory processes such as membrane stacking, photosystem II repair, photoprotective energy dissipation, state transitions and alternative electron transfer. Here we provide an overview of the essentials of thylakoid membrane structure in plants, and consider how recent advances, using a range of microscopies, have substantially increased our knowledge of the thylakoid dynamic structure. We discuss both the successes and limitations of the currently available techniques and highlight newly emerging microscopic methods that promise to move the field beyond the current 'static' view of membrane organization based on frozen snapshots to a 'live' view of functional membranes imaged under native aqueous conditions at ambient temperature and responding dynamically to external stimuli.

Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering

NASA Astrophysics Data System (ADS)

Shrestha, Utsab R.; Bhowmik, Debsindhu; Mamontov, Eugene; Chu, Xiang-Qiang

Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the dark-state rhodopsin and opsin dynamics, which can be further applied to other GPCR systems to interpret various dynamic behaviors in ligand-bound and ligand-free protein.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

PubMed

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

PubMed Central

2013-01-01

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176

Effect of Selected Balance Exercises on the Dynamic Balance of Children with Visual Impairments

ERIC Educational Resources Information Center

Jazi, Shirin Davarpanah; Purrajabi, Fatemeh; Movahedi, Ahmadreza; Jalali, Shahin

2012-01-01

Introduction: Maintaining balance while walking is of utmost importance for individuals with visual impairments because deficits in dynamic balance have been associated with a high risk of falling. Thus, the primary aim of the study presented here was to determine whether balance training effects the dynamic balance of children with visual…

Enhanced visualization of MR angiogram with modified MIP and 3D image fusion

NASA Astrophysics Data System (ADS)

Kim, JongHyo; Yeon, Kyoung M.; Han, Man Chung; Lee, Dong Hyuk; Cho, Han I.

1997-05-01

We have developed a 3D image processing and display technique that include image resampling, modification of MIP, volume rendering, and fusion of MIP image with volumetric rendered image. This technique facilitates the visualization of the 3D spatial relationship between vasculature and surrounding organs by overlapping the MIP image on the volumetric rendered image of the organ. We applied this technique to a MR brain image data to produce an MRI angiogram that is overlapped with 3D volume rendered image of brain. MIP technique was used to visualize the vasculature of brain, and volume rendering was used to visualize the other structures of brain. The two images are fused after adjustment of contrast and brightness levels of each image in such a way that both the vasculature and brain structure are well visualized either by selecting the maximum value of each image or by assigning different color table to each image. The resultant image with this technique visualizes both the brain structure and vasculature simultaneously, allowing the physicians to inspect their relationship more easily. The presented technique will be useful for surgical planning for neurosurgery.

Visual acuity and quality of life in dry eye disease: Proceedings of the OCEAN group meeting.

PubMed

Benítez-Del-Castillo, José; Labetoulle, Marc; Baudouin, Christophe; Rolando, Maurizio; Akova, Yonca A; Aragona, Pasquale; Geerling, Gerd; Merayo-Lloves, Jesús; Messmer, Elisabeth M; Boboridis, Kostas

2017-04-01

Dry eye disease (DED) results in tear film instability and hyperosmolarity, inflammation of the ocular surface and, ultimately, visual disturbance that can significantly impact a patient's quality of life. The effects on visual acuity result in difficulties with driving, reading and computer use and negatively impact psychological health. These effects also extend to the workplace, with a loss of productivity and quality of work causing substantial economic losses. The effects of DED and the impact on vision experienced by patients may not be given sufficient importance by ophthalmologists. Functional visual acuity (FVA) is a measure of visual acuity after sustained eye opening without blinking for at least 10 s and mimics the sustained visual acuity of daily life. Measuring dynamic FVA allows the detection of impaired visual function in patients with DED who may display normal conventional visual acuity. There are currently several tests and methods that can be used to measure dynamic visual function: the SSC-350 FVA measurement system, assessment of best-corrected visual acuity decay using the interblink visual acuity decay test, serial measurements of ocular and corneal higher order aberrations, and measurement of dynamic vision quality using the Optical Quality Analysis System. Although the equipment for these methods may be too large or unaffordable for use in clinical practice, FVA testing is an important assessment for DED. Copyright © 2016 Elsevier Inc. All rights reserved.

Decoding the time-course of object recognition in the human brain: From visual features to categorical decisions.

PubMed

Contini, Erika W; Wardle, Susan G; Carlson, Thomas A

2017-10-01

Visual object recognition is a complex, dynamic process. Multivariate pattern analysis methods, such as decoding, have begun to reveal how the brain processes complex visual information. Recently, temporal decoding methods for EEG and MEG have offered the potential to evaluate the temporal dynamics of object recognition. Here we review the contribution of M/EEG time-series decoding methods to understanding visual object recognition in the human brain. Consistent with the current understanding of the visual processing hierarchy, low-level visual features dominate decodable object representations early in the time-course, with more abstract representations related to object category emerging later. A key finding is that the time-course of object processing is highly dynamic and rapidly evolving, with limited temporal generalisation of decodable information. Several studies have examined the emergence of object category structure, and we consider to what degree category decoding can be explained by sensitivity to low-level visual features. Finally, we evaluate recent work attempting to link human behaviour to the neural time-course of object processing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mapping and characterization of positive and negative BOLD responses to visual stimulation in multiple brain regions at 7T.

PubMed

Jorge, João; Figueiredo, Patrícia; Gruetter, Rolf; van der Zwaag, Wietske

2018-06-01

External stimuli and tasks often elicit negative BOLD responses in various brain regions, and growing experimental evidence supports that these phenomena are functionally meaningful. In this work, the high sensitivity available at 7T was explored to map and characterize both positive (PBRs) and negative BOLD responses (NBRs) to visual checkerboard stimulation, occurring in various brain regions within and beyond the visual cortex. Recently-proposed accelerated fMRI techniques were employed for data acquisition, and procedures for exclusion of large draining vein contributions, together with ICA-assisted denoising, were included in the analysis to improve response estimation. Besides the visual cortex, significant PBRs were found in the lateral geniculate nucleus and superior colliculus, as well as the pre-central sulcus; in these regions, response durations increased monotonically with stimulus duration, in tight covariation with the visual PBR duration. Significant NBRs were found in the visual cortex, auditory cortex, default-mode network (DMN) and superior parietal lobule; NBR durations also tended to increase with stimulus duration, but were significantly less sustained than the visual PBR, especially for the DMN and superior parietal lobule. Responses in visual and auditory cortex were further studied for checkerboard contrast dependence, and their amplitudes were found to increase monotonically with contrast, linearly correlated with the visual PBR amplitude. Overall, these findings suggest the presence of dynamic neuronal interactions across multiple brain regions, sensitive to stimulus intensity and duration, and demonstrate the richness of information obtainable when jointly mapping positive and negative BOLD responses at a whole-brain scale, with ultra-high field fMRI. © 2018 Wiley Periodicals, Inc.

Human Actions Analysis: Templates Generation, Matching and Visualization Applied to Motion Capture of Highly-Skilled Karate Athletes

PubMed Central

Piekarczyk, Marcin; Ogiela, Marek R.

2017-01-01

The aim of this paper is to propose and evaluate the novel method of template generation, matching, comparing and visualization applied to motion capture (kinematic) analysis. To evaluate our approach, we have used motion capture recordings (MoCap) of two highly-skilled black belt karate athletes consisting of 560 recordings of various karate techniques acquired with wearable sensors. We have evaluated the quality of generated templates; we have validated the matching algorithm that calculates similarities and differences between various MoCap data; and we have examined visualizations of important differences and similarities between MoCap data. We have concluded that our algorithms works the best when we are dealing with relatively short (2–4 s) actions that might be averaged and aligned with the dynamic time warping framework. In practice, the methodology is designed to optimize the performance of some full body techniques performed in various sport disciplines, for example combat sports and martial arts. We can also use this approach to generate templates or to compare the correct performance of techniques between various top sportsmen in order to generate a knowledge base of reference MoCap videos. The motion template generated by our method can be used for action recognition purposes. We have used the DTW classifier with angle-based features to classify various karate kicks. We have performed leave-one-out action recognition for the Shorin-ryu and Oyama karate master separately. In this case, 100% actions were correctly classified. In another experiment, we used templates generated from Oyama master recordings to classify Shorin-ryu master recordings and vice versa. In this experiment, the overall recognition rate was 94.2%, which is a very good result for this type of complex action. PMID:29125560

Feasibility of MDCT angiography for determination of tumor-feeding vessels in chemoembolization of hepatocellular carcinoma.

PubMed

Kim, Inwha; Kim, Dae Jung; Kim, Kyoung Ah; Yoon, Sang Wook; Lee, Jong Tae

2014-01-01

To investigate the feasibility and accuracy of multidetector computed tomography (MDCT) angiography for assessment of subsegmental tumor-feeding vessels in transarterial chemoembolization (TACE) of hepatocellular carcinoma (HCC). A total of 23 patients with 36 HCCs who underwent TACE during a 14-month period were enrolled. All patients underwent 3-phase dynamic MDCT within a month before TACE. Arterial phase MDCT images were retrospectively reformatted and analyzed for determination of single subsegmental tumor-feeding vessel using maximum intensity projection (MIP) and volume-rendering technique (VRT). Two radiologists independently assessed and scored the MIP and VRT images using 4-grade visual scores (grade 1, no depiction of tumor-feeding vessel; grade 2, indeterminate tumor-feeding vessel; grade 3, probable tumor-feeding vessel; and grade 4, good depiction of tumor-feeding vessel). The weighted kappa test was used to determine interobserver variability, and Wilcoxon signed rank test was used to differentiate visual scores of each technique. Results of digital subtraction angiography were defined as the criterion standard; therefore, assessment of subsegmental tumor-feeding vessel using MIP or VRT was compared with digital subtraction angiography, and the accuracy of each technique was calculated. Interobserver agreement (weighted kappa, 0.746 on VRT and 0.806 on MIP) was substantial to almost perfect. The visual scores for MIP (mean, 3.64 for reviewer 1 and 3.5 for reviewer 2) were higher than those for VRT (mean, 2.11 for reviewer 1 and 2.22 for reviewer 2; P = 0.000). The accuracy for assessing subsegmental tumor-feeding vessel was 22.2% for VRT and 77.8% for MIP. Multidetector CT angiography using MIP showed good imaging quality and high accuracy for determination of subsegmental tumor-feeding vessels.

Activity in early visual areas predicts interindividual differences in binocular rivalry dynamics

PubMed Central

Yamashiro, Hiroyuki; Mano, Hiroaki; Umeda, Masahiro; Higuchi, Toshihiro; Saiki, Jun

2013-01-01

When dissimilar images are presented to the two eyes, binocular rivalry (BR) occurs, and perception alternates spontaneously between the images. Although neural correlates of the oscillating perception during BR have been found in multiple sites along the visual pathway, the source of BR dynamics is unclear. Psychophysical and modeling studies suggest that both low- and high-level cortical processes underlie BR dynamics. Previous neuroimaging studies have demonstrated the involvement of high-level regions by showing that frontal and parietal cortices responded time locked to spontaneous perceptual alternation in BR. However, a potential contribution of early visual areas to BR dynamics has been overlooked, because these areas also responded to the physical stimulus alternation mimicking BR. In the present study, instead of focusing on activity during perceptual switches, we highlighted brain activity during suppression periods to investigate a potential link between activity in human early visual areas and BR dynamics. We used a strong interocular suppression paradigm called continuous flash suppression to suppress and fluctuate the visibility of a probe stimulus and measured retinotopic responses to the onset of the invisible probe using functional MRI. There were ∼130-fold differences in the median suppression durations across 12 subjects. The individual differences in suppression durations could be predicted by the amplitudes of the retinotopic activity in extrastriate visual areas (V3 and V4v) evoked by the invisible probe. Weaker responses were associated with longer suppression durations. These results demonstrate that retinotopic representations in early visual areas play a role in the dynamics of perceptual alternations during BR. PMID:24353304

Application of Sequence-Dependent Electrophoresis Fingerprinting in Exploring Biodiversity and Population Dynamics of Human Intestinal Microbiota: What Can Be Revealed?

PubMed Central

Huys, Geert; Vanhoutte, Tom; Vandamme, Peter

2008-01-01

Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of complex microbial ecosystems independent of their culturability and without prior knowledge on the complexity and diversity of the ecosystem. Mainly using the prokaryotic 16S rRNA gene as PCR amplification target, SDE-based community fingerprinting turned into one of the leading molecular tools to unravel the diversity and population dynamics of human intestinal microbiota. The first part of this review covers the methodological concept of SDE fingerprinting and the technical hurdles for analyzing intestinal samples. Subsequently, the current state-of-the-art of DGGE and related techniques to analyze human intestinal microbiota from healthy individuals and from patients with intestinal disorders is surveyed. In addition, the applicability of SDE analysis to monitor intestinal population changes upon nutritional or therapeutic interventions is critically evaluated. PMID:19277102

An effective parameter optimization technique for vibration flow field characterization of PP melts via LS-SVM combined with SALS in an electromagnetism dynamic extruder

NASA Astrophysics Data System (ADS)

Xian, Guangming

2018-03-01

A method for predicting the optimal vibration field parameters by least square support vector machine (LS-SVM) is presented in this paper. One convenient and commonly used technique for characterizing the the vibration flow field of polymer melts films is small angle light scattering (SALS) in a visualized slit die of the electromagnetism dynamic extruder. The optimal value of vibration vibration frequency, vibration amplitude, and the maximum light intensity projection area can be obtained by using LS-SVM for prediction. For illustrating this method and show its validity, the flowing material is used with polypropylene (PP) and fifteen samples are tested at the rotation speed of screw at 36rpm. This paper first describes the apparatus of SALS to perform the experiments, then gives the theoretical basis of this new method, and detail the experimental results for parameter prediction of vibration flow field. It is demonstrated that it is possible to use the method of SALS and obtain detailed information on optimal parameter of vibration flow field of PP melts by LS-SVM.

Effects of porous insert on flame dynamics in a lean premixed swirl-stabilized combustor

NASA Astrophysics Data System (ADS)

Brown, Marcus; Agrawal, Ajay; Allen, James; Kornegay, John

2016-11-01

In this study, we investigated different methods of determining the effect a porous insert has on flame dynamics during lean premixed combustion. A metallic porous insert is used to mitigate instabilities in a swirl-stabilized combustor. Thermoacoustic instabilities are seen as negative consequences of lean premixed combustion and eliminating them is the motivation for our research. Three different diagnostics techniques with high-speed Photron SA5 cameras were used to monitor flame characteristics. Particle image velocimetry (PIV) was used to observe vortical structures and recirculation zones within the combustor. Using planar laser induced fluorescence (PLIF), we were able to observe changes in the reaction zones during instabilities. Finally, utilizing a color high-speed camera, visual images depicting a flame's oscillations during the instability were captured. Using these monitoring techniques, we are able to support the claims made in previous studies stating that the porous insert in the combustor significantly reduces the thermoacoustic instability. Funding for this research was provided by the NSF REU site Grant EEC 1358991 and NASA Grant NNX13AN14A.

Single-molecule studies of multi-protein machines

NASA Astrophysics Data System (ADS)

van Oijen, Antoine

2010-03-01

Advances in optical imaging and molecular manipulation techniques have made it possible to observe individual enzymes and record molecular movies that provide new insight into their dynamics and reaction mechanisms. In a biological context, most of these enzymes function in concert with other enzymes in multi-protein complexes, so an important future direction will be the utilization of single-molecule techniques to unravel the orchestration of large macromolecular assemblies. Our group is developing the single-molecule tools that will make it possible to study biochemical pathways of arbitrary complexity at the single-molecule level. I will discuss results of single-molecule experiments on the replisome, the molecular machinery that is responsible for replication of DNA. We stretch individual DNA molecules and use their elastic properties to obtain dynamic information on the proteins that unwind the double helix and copy its genetic information. Furthermore, we visualize fluorescently labeled components of the replisome and thus obtain information on stochiometry and exchange kinetics. This simultaneous observation of catalytic activity and composition allows us to gain deeper insight into the structure-function relationship of the replisome.

Live-cell Imaging of Fungal Cells to Investigate Modes of Entry and Subcellular Localization of Antifungal Plant Defensins.

PubMed

Islam, Kazi T; Shah, Dilip M; El-Mounadi, Kaoutar

2017-12-24

Small cysteine-rich defensins are one of the largest groups of host defense peptides present in all plants. Many plant defensins exhibit potent in vitro antifungal activity against a broad-spectrum of fungal pathogens and therefore have the potential to be used as antifungal agents in transgenic crops. In order to harness the full potential of plant defensins for diseases control, it is crucial to elucidate their mechanisms of action (MOA). With the advent of advanced microscopy techniques, live-cell imaging has become a powerful tool for understanding the dynamics of the antifungal MOA of plant defensins. Here, a confocal microscopy based live-cell imaging method is described using two fluorescently labeled plant defensins (MtDef4 and MtDef5) in combination with vital fluorescent dyes. This technique enables real-time visualization and analysis of the dynamic events of MtDef4 and MtDef5 internalization into fungal cells. Importantly, this assay generates a wealth of information including internalization kinetics, mode of entry and subcellular localization of these peptides. Along with other cell biological tools, these methods have provided critical insights into the dynamics and complexity of the MOA of these peptides. These tools can also be used to compare the MOA of these peptides against different fungi.

Photon gating in four-dimensional ultrafast electron microscopy.

PubMed

Hassan, Mohammed T; Liu, Haihua; Baskin, John Spencer; Zewail, Ahmed H

2015-10-20

Ultrafast electron microscopy (UEM) is a pivotal tool for imaging of nanoscale structural dynamics with subparticle resolution on the time scale of atomic motion. Photon-induced near-field electron microscopy (PINEM), a key UEM technique, involves the detection of electrons that have gained energy from a femtosecond optical pulse via photon-electron coupling on nanostructures. PINEM has been applied in various fields of study, from materials science to biological imaging, exploiting the unique spatial, energy, and temporal characteristics of the PINEM electrons gained by interaction with a "single" light pulse. The further potential of photon-gated PINEM electrons in probing ultrafast dynamics of matter and the optical gating of electrons by invoking a "second" optical pulse has previously been proposed and examined theoretically in our group. Here, we experimentally demonstrate this photon-gating technique, and, through diffraction, visualize the phase transition dynamics in vanadium dioxide nanoparticles. With optical gating of PINEM electrons, imaging temporal resolution was improved by a factor of 3 or better, being limited only by the optical pulse widths. This work enables the combination of the high spatial resolution of electron microscopy and the ultrafast temporal response of the optical pulses, which provides a promising approach to attain the resolution of few femtoseconds and attoseconds in UEM.

Photon gating in four-dimensional ultrafast electron microscopy

PubMed Central

Hassan, Mohammed T.; Liu, Haihua; Baskin, John Spencer; Zewail, Ahmed H.

2015-01-01

Ultrafast electron microscopy (UEM) is a pivotal tool for imaging of nanoscale structural dynamics with subparticle resolution on the time scale of atomic motion. Photon-induced near-field electron microscopy (PINEM), a key UEM technique, involves the detection of electrons that have gained energy from a femtosecond optical pulse via photon–electron coupling on nanostructures. PINEM has been applied in various fields of study, from materials science to biological imaging, exploiting the unique spatial, energy, and temporal characteristics of the PINEM electrons gained by interaction with a “single” light pulse. The further potential of photon-gated PINEM electrons in probing ultrafast dynamics of matter and the optical gating of electrons by invoking a “second” optical pulse has previously been proposed and examined theoretically in our group. Here, we experimentally demonstrate this photon-gating technique, and, through diffraction, visualize the phase transition dynamics in vanadium dioxide nanoparticles. With optical gating of PINEM electrons, imaging temporal resolution was improved by a factor of 3 or better, being limited only by the optical pulse widths. This work enables the combination of the high spatial resolution of electron microscopy and the ultrafast temporal response of the optical pulses, which provides a promising approach to attain the resolution of few femtoseconds and attoseconds in UEM. PMID:26438835

Evaluation of normal swallowing functions by using dynamic high-density surface electromyography maps.

PubMed

Zhu, Mingxing; Yu, Bin; Yang, Wanzhang; Jiang, Yanbing; Lu, Lin; Huang, Zhen; Chen, Shixiong; Li, Guanglin

2017-11-21

Swallowing is a continuous process with substantive interdependencies among different muscles, and it plays a significant role in our daily life. The aim of this study was to propose a novel technique based on high-density surface electromyography (HD sEMG) for the evaluation of normal swallowing functions. A total of 96 electrodes were placed on the front neck to acquire myoelectric signals from 12 healthy subjects while they were performing different swallowing tasks. HD sEMG energy maps were constructed based on the root mean square values to visualize muscular activities during swallowing. The effects of different volumes, viscosities, and head postures on the normal swallowing process were systemically investigated by using the energy maps. The results showed that the HD sEMG energy maps could provide detailed spatial and temporal properties of the muscle electrical activity, and visualize the muscle contractions that closely related to the swallowing function. The energy maps also showed that the swallowing time and effort was also explicitly affected by the volume and viscosity of the bolus. The concentration of the muscular activities shifted to the opposite side when the subjects turned their head to either side. The proposed method could provide an alternative method to physiologically evaluate the dynamic characteristics of normal swallowing and had the advantage of providing a full picture of how different muscle activities cooperate in time and location. The findings from this study suggested that the HD sEMG technique might be a useful tool for fast screening and objective assessment of swallowing disorders or dysphagia.

Ex vivo Live Imaging of Lung Metastasis and Their Microenvironment

PubMed Central

Maynard, Carrie; Plaks, Vicki

2016-01-01

Metastasis is a major cause for cancer-related morbidity and mortality. Metastasis is a multistep process and due to its complexity, the exact cellular and molecular processes that govern metastatic dissemination and growth are still elusive. Live imaging allows visualization of the dynamic and spatial interactions of cells and their microenvironment. Solid tumors commonly metastasize to the lungs. However, the anatomical location of the lungs poses a challenge to intravital imaging. This protocol provides a relatively simple and quick method for ex vivo live imaging of the dynamic interactions between tumor cells and their surrounding stroma within lung metastasis. Using this method, the motility of cancer cells as well as interactions between cancer cells and stromal cells in their microenvironment can be visualized in real time for several hours. By using transgenic fluorescent reporter mice, a fluorescent cell line, injectable fluorescently labeled molecules and/or antibodies, multiple components of the lung microenvironment can be visualized, such as blood vessels and immune cells. To image the different cell types, a spinning disk confocal microscope that allows long-term continuous imaging with rapid, four-color image acquisition has been used. Time-lapse movies compiled from images collected over multiple positions and focal planes show interactions between live metastatic and immune cells for at least 4 hr. This technique can be further used to test chemotherapy or targeted therapy. Moreover, this method could be adapted for the study of other lung-related pathologies that may affect the lung microenvironment. PMID:26862704

Aging and the rate of visual information processing.

PubMed

Guest, Duncan; Howard, Christina J; Brown, Louise A; Gleeson, Harriet

2015-01-01

Multiple methods exist for measuring how age influences the rate of visual information processing. The most advanced methods model the processing dynamics in a task in order to estimate processing rates independently of other factors that might be influenced by age, such as overall performance level and the time at which processing onsets. However, such modeling techniques have produced mixed evidence for age effects. Using a time-accuracy function (TAF) analysis, Kliegl, Mayr, and Krampe (1994) showed clear evidence for age effects on processing rate. In contrast, using the diffusion model to examine the dynamics of decision processes, Ratcliff and colleagues (e.g., Ratcliff, Thapar, & McKoon, 2006) found no evidence for age effects on processing rate across a range of tasks. Examination of these studies suggests that the number of display stimuli might account for the different findings. In three experiments we measured the precision of younger and older adults' representations of target stimuli after different amounts of stimulus exposure. A TAF analysis found little evidence for age differences in processing rate when a single stimulus was presented (Experiment 1). However, adding three nontargets to the display resulted in age-related slowing of processing (Experiment 2). Similar slowing was observed when simply presenting two stimuli and using a post-cue to indicate the target (Experiment 3). Although there was some interference from distracting objects and from previous responses, these age-related effects on processing rate seem to reflect an age-related difficulty in processing multiple objects, particularly when encoding them into visual working memory.

Dynamic visual noise affects visual short-term memory for surface color, but not spatial location.

PubMed

Dent, Kevin

2010-01-01

In two experiments participants retained a single color or a set of four spatial locations in memory. During a 5 s retention interval participants viewed either flickering dynamic visual noise or a static matrix pattern. In Experiment 1 memory was assessed using a recognition procedure, in which participants indicated if a particular test stimulus matched the memorized stimulus or not. In Experiment 2 participants attempted to either reproduce the locations or they picked the color from a whole range of possibilities. Both experiments revealed effects of dynamic visual noise (DVN) on memory for colors but not for locations. The implications of the results for theories of working memory and the methodological prospects for DVN as an experimental tool are discussed.

Math Majors' Visual Proofs in a Dynamic Environment: The Case of Limit of a Function and the ?-d Approach

ERIC Educational Resources Information Center

Caglayan, Günhan

2015-01-01

Despite few limitations, GeoGebra as a dynamic geometry software stood as a powerful instrument in helping university math majors understand, explore, and gain experiences in visualizing the limits of functions and the ?-d formalism. During the process of visualizing a theorem, the order mattered in the sequence of constituents. Students made use…

Effects of Using Dynamic Mathematics Software on Preservice Mathematics Teachers' Spatial Visualization Skills: The Case of Spatial Analytic Geometry

ERIC Educational Resources Information Center

Kösa, Temel

2016-01-01

The purpose of this study was to investigate the effects of using dynamic geometry software on preservice mathematics teachers' spatial visualization skills and to determine whether spatial visualization skills can be a predictor of success in learning analytic geometry of space. The study used a quasi-experimental design with a control group.…

Effect of Cognitive Demand on Functional Visual Field Performance in Senior Drivers with Glaucoma

PubMed Central

Gangeddula, Viswa; Ranchet, Maud; Akinwuntan, Abiodun E.; Bollinger, Kathryn; Devos, Hannes

2017-01-01

Purpose: To investigate the effect of cognitive demand on functional visual field performance in drivers with glaucoma. Method: This study included 20 drivers with open-angle glaucoma and 13 age- and sex-matched controls. Visual field performance was evaluated under different degrees of cognitive demand: a static visual field condition (C1), dynamic visual field condition (C2), and dynamic visual field condition with active driving (C3) using an interactive, desktop driving simulator. The number of correct responses (accuracy) and response times on the visual field task were compared between groups and between conditions using Kruskal–Wallis tests. General linear models were employed to compare cognitive workload, recorded in real-time through pupillometry, between groups and conditions. Results: Adding cognitive demand (C2 and C3) to the static visual field test (C1) adversely affected accuracy and response times, in both groups (p < 0.05). However, drivers with glaucoma performed worse than did control drivers when the static condition changed to a dynamic condition [C2 vs. C1 accuracy; glaucoma: median difference (Q1–Q3) 3 (2–6.50) vs. controls: 2 (0.50–2.50); p = 0.05] and to a dynamic condition with active driving [C3 vs. C1 accuracy; glaucoma: 2 (2–6) vs. controls: 1 (0.50–2); p = 0.02]. Overall, drivers with glaucoma exhibited greater cognitive workload than controls (p = 0.02). Conclusion: Cognitive demand disproportionately affects functional visual field performance in drivers with glaucoma. Our results may inform the development of a performance-based visual field test for drivers with glaucoma. PMID:28912712

Flow Charts: Visualization of Vector Fields on Arbitrary Surfaces

PubMed Central

Li, Guo-Shi; Tricoche, Xavier; Weiskopf, Daniel; Hansen, Charles

2009-01-01

We introduce a novel flow visualization method called Flow Charts, which uses a texture atlas approach for the visualization of flows defined over curved surfaces. In this scheme, the surface and its associated flow are segmented into overlapping patches, which are then parameterized and packed in the texture domain. This scheme allows accurate particle advection across multiple charts in the texture domain, providing a flexible framework that supports various flow visualization techniques. The use of surface parameterization enables flow visualization techniques requiring the global view of the surface over long time spans, such as Unsteady Flow LIC (UFLIC), particle-based Unsteady Flow Advection Convolution (UFAC), or dye advection. It also prevents visual artifacts normally associated with view-dependent methods. Represented as textures, Flow Charts can be naturally integrated into hardware accelerated flow visualization techniques for interactive performance. PMID:18599918

Comparison of deep neural networks to spatio-temporal cortical dynamics of human visual object recognition reveals hierarchical correspondence

PubMed Central

Cichy, Radoslaw Martin; Khosla, Aditya; Pantazis, Dimitrios; Torralba, Antonio; Oliva, Aude

2016-01-01

The complex multi-stage architecture of cortical visual pathways provides the neural basis for efficient visual object recognition in humans. However, the stage-wise computations therein remain poorly understood. Here, we compared temporal (magnetoencephalography) and spatial (functional MRI) visual brain representations with representations in an artificial deep neural network (DNN) tuned to the statistics of real-world visual recognition. We showed that the DNN captured the stages of human visual processing in both time and space from early visual areas towards the dorsal and ventral streams. Further investigation of crucial DNN parameters revealed that while model architecture was important, training on real-world categorization was necessary to enforce spatio-temporal hierarchical relationships with the brain. Together our results provide an algorithmically informed view on the spatio-temporal dynamics of visual object recognition in the human visual brain. PMID:27282108

Comparison of deep neural networks to spatio-temporal cortical dynamics of human visual object recognition reveals hierarchical correspondence.

PubMed

Cichy, Radoslaw Martin; Khosla, Aditya; Pantazis, Dimitrios; Torralba, Antonio; Oliva, Aude

2016-06-10

The complex multi-stage architecture of cortical visual pathways provides the neural basis for efficient visual object recognition in humans. However, the stage-wise computations therein remain poorly understood. Here, we compared temporal (magnetoencephalography) and spatial (functional MRI) visual brain representations with representations in an artificial deep neural network (DNN) tuned to the statistics of real-world visual recognition. We showed that the DNN captured the stages of human visual processing in both time and space from early visual areas towards the dorsal and ventral streams. Further investigation of crucial DNN parameters revealed that while model architecture was important, training on real-world categorization was necessary to enforce spatio-temporal hierarchical relationships with the brain. Together our results provide an algorithmically informed view on the spatio-temporal dynamics of visual object recognition in the human visual brain.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

Atomic-scale dynamics of a model glass-forming metallic liquid: Dynamical crossover, dynamical decoupling, and dynamical clustering

DOE PAGES

Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang

2015-04-01

The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu 40Zr 51Al 9 using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at T x ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (T m ~ 900K),more » and the crossover temperature is roughly twice of the glass-transition temperature (T g). Below T x, we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a non-parametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below T x and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter and the four-point correlation function.« less

Profiling Oman education data using data visualization technique

NASA Astrophysics Data System (ADS)

Alalawi, Sultan Juma Sultan; Shaharanee, Izwan Nizal Mohd; Jamil, Jastini Mohd

2016-10-01

This research works presents an innovative data visualization technique to understand and visualize the information of Oman's education data generated from the Ministry of Education Oman "Educational Portal". The Ministry of Education in Sultanate of Oman have huge databases contains massive information. The volume of data in the database increase yearly as many students, teachers and employees enter into the database. The task for discovering and analyzing these vast volumes of data becomes increasingly difficult. Information visualization and data mining offer a better ways in dealing with large volume of information. In this paper, an innovative information visualization technique is developed to visualize the complex multidimensional educational data. Microsoft Excel Dashboard, Visual Basic Application (VBA) and Pivot Table are utilized to visualize the data. Findings from the summarization of the data are presented, and it is argued that information visualization can help related stakeholders to become aware of hidden and interesting information from large amount of data drowning in their educational portal.

Understanding the Role of Hemodynamics in the Initiation, Progression, Rupture, and Treatment Outcome of Cerebral Aneurysm from Medical Image-Based Computational Studies

PubMed Central

Castro, Marcelo A.

2013-01-01

About a decade ago, the first image-based computational hemodynamic studies of cerebral aneurysms were presented. Their potential for clinical applications was the result of a right combination of medical image processing, vascular reconstruction, and grid generation techniques used to reconstruct personalized domains for computational fluid and solid dynamics solvers and data analysis and visualization techniques. A considerable number of studies have captivated the attention of clinicians, neurosurgeons, and neuroradiologists, who realized the ability of those tools to help in understanding the role played by hemodynamics in the natural history and management of intracranial aneurysms. This paper intends to summarize the most relevant results in the field reported during the last years. PMID:24967285

An interactive driving simulation for driver control and decision-making research

NASA Technical Reports Server (NTRS)

Allen, R. W.; Hogge, J. R.; Schwartz, S. H.

1975-01-01

Display techniques and equations of motion for a relatively simple fixed base car simulation are described. The vehicle dynamics include simplified lateral (steering) and longitudinal (speed) degrees of freedom. Several simulator tasks are described which require a combination of operator control and decision making, including response to wind gust inputs, curved roads, traffic signal lights, and obstacles. Logic circuits are used to detect speeding, running red lights, and crashes. A variety of visual and auditory cues are used to give the driver appropriate performance feedback. The simulated equations of motion are reviewed and the technique for generating the line drawing CRT roadway display is discussed. On-line measurement capabilities and experimenter control features are presented, along with previous and current research results demonstrating simulation capabilities and applications.

Optical and force nanoscopy in microbiology.

PubMed

Xiao, Jie; Dufrêne, Yves F

2016-10-26

Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.

Preparing Colorful Astronomical Images and Illustrations

NASA Astrophysics Data System (ADS)

Levay, Z. G.; Frattare, L. M.

2001-12-01

We present techniques for using mainstream graphics software, specifically Adobe Photoshop and Illustrator, for producing composite color images and illustrations from astronomical data. These techniques have been used with numerous images from the Hubble Space Telescope to produce printed and web-based news, education and public presentation products as well as illustrations for technical publication. While Photoshop is not intended for quantitative analysis of full dynamic range data (as are IRAF or IDL, for example), we have had much success applying Photoshop's numerous, versatile tools to work with scaled images, masks, text and graphics in multiple semi-transparent layers and channels. These features, along with its user-oriented, visual interface, provide convenient tools to produce high-quality, full-color images and graphics for printed and on-line publication and presentation.

RGB-NDVI colour composites for visualizing forest change dynamics

NASA Technical Reports Server (NTRS)

Sader, S. A.; Winne, J. C.

1992-01-01

The study presents a simple and logical technique to display and quantify forest change using three dates of satellite imagery. The normalized difference vegetation index (NDVI) was computed for each date of imagery to define high and low vegetation biomass. Color composites were generated by combining each date of NDVI with either the red, green, or blue (RGB) image planes in an image display monitor. Harvest and regeneration areas were quantified by applying a modified parallelepiped classification creating an RGB-NDVI image with 27 classes that were grouped into nine major forest change categories. Aerial photographs and stand history maps are compared with the forest changes indicated by the RGB-NDVI image. The utility of the RGB-NDVI technique for supporting forest inventories and updating forest resource information systems are presented and discussed.

Visualization of 3D CT-based anatomical models

NASA Astrophysics Data System (ADS)

Alaytsev, Innokentiy K.; Danilova, Tatyana V.; Manturov, Alexey O.; Mareev, Gleb O.; Mareev, Oleg V.

2018-04-01

Biomedical volumetric data visualization techniques for the exploration purposes are well developed. Most of the known methods are inappropriate for surgery simulation systems due to lack of realism. A segmented data visualization is a well-known approach for the visualization of the structured volumetric data. The research is focused on improvement of the segmented data visualization technique by the aliasing problems resolution and the use of material transparency modeling for better semitransparent structures rendering.

Advanced Visualization and Interactive Display Rapid Innovation and Discovery Evaluation Research (VISRIDER) Program Task 6: Point Cloud Visualization Techniques for Desktop and Web Platforms

DTIC Science & Technology

2017-04-01

ADVANCED VISUALIZATION AND INTERACTIVE DISPLAY RAPID INNOVATION AND DISCOVERY EVALUATION RESEARCH (VISRIDER) PROGRAM TASK 6: POINT CLOUD...To) OCT 2013 – SEP 2014 4. TITLE AND SUBTITLE ADVANCED VISUALIZATION AND INTERACTIVE DISPLAY RAPID INNOVATION AND DISCOVERY EVALUATION RESEARCH...various point cloud visualization techniques for viewing large scale LiDAR datasets. Evaluate their potential use for thick client desktop platforms

Experimental investigations of the time and flow-direction responses of shear-stress-sensitive liquid crystal coatings

NASA Technical Reports Server (NTRS)

Reda, Daniel C.; Muratore, Joseph J., Jr.; Heineck, James T.

1993-01-01

Time and flow-direction responses of shearstress-sensitive liquid crystal coatings were explored experimentally. For the time-response experiments, coatings were exposed to transient, compressible flows created during the startup and off-design operation of an injector-driven supersonic wind tunnel. Flow transients were visualized with a focusing Schlieren system and recorded with a 1000 frame/sec color video camera. Liquid crystal responses to these changing-shear environments were then recorded with the same video system, documenting color-play response times equal to, or faster than, the time interval between sequential frames (i.e., 1 millisecond). For the flow-direction experiments, a planar test surface was exposed to equal-magnitude and known-direction surface shear stresses generated by both normal and tangential subsonic jet-impingement flows. Under shear, the sense of the angular displacement of the liquid crystal dispersed (reflected) spectrum was found to be a function of the instantaneous direction of the applied shear. This technique thus renders dynamic flow reversals or flow divergences visible over entire test surfaces at image recording rates up to 1 KHz. Extensions of the technique to visualize relatively small changes in surface shear stress direction appear feasible.

Plant Phenotyping using Probabilistic Topic Models: Uncovering the Hyperspectral Language of Plants

PubMed Central

Wahabzada, Mirwaes; Mahlein, Anne-Katrin; Bauckhage, Christian; Steiner, Ulrike; Oerke, Erich-Christian; Kersting, Kristian

2016-01-01

Modern phenotyping and plant disease detection methods, based on optical sensors and information technology, provide promising approaches to plant research and precision farming. In particular, hyperspectral imaging have been found to reveal physiological and structural characteristics in plants and to allow for tracking physiological dynamics due to environmental effects. In this work, we present an approach to plant phenotyping that integrates non-invasive sensors, computer vision, as well as data mining techniques and allows for monitoring how plants respond to stress. To uncover latent hyperspectral characteristics of diseased plants reliably and in an easy-to-understand way, we “wordify” the hyperspectral images, i.e., we turn the images into a corpus of text documents. Then, we apply probabilistic topic models, a well-established natural language processing technique that identifies content and topics of documents. Based on recent regularized topic models, we demonstrate that one can track automatically the development of three foliar diseases of barley. We also present a visualization of the topics that provides plant scientists an intuitive tool for hyperspectral imaging. In short, our analysis and visualization of characteristic topics found during symptom development and disease progress reveal the hyperspectral language of plant diseases. PMID:26957018

Radioluminescence Microscopy: Measuring the Heterogeneous Uptake of Radiotracers in Single Living Cells

PubMed Central

Pratx, Guillem; Chen, Kai; Sun, Conroy; Martin, Lynn; Carpenter, Colin M.; Olcott, Peter D.; Xing, Lei

2012-01-01

Radiotracers play an important role in interrogating molecular processes both in vitro and in vivo. However, current methods are limited to measuring average radiotracer uptake in large cell populations and, as a result, lack the ability to quantify cell-to-cell variations. Here we apply a new technique, termed radioluminescence microscopy, to visualize radiotracer uptake in single living cells, in a standard fluorescence microscopy environment. In this technique, live cells are cultured sparsely on a thin scintillator plate and incubated with a radiotracer. Light produced following beta decay is measured using a highly sensitive microscope. Radioluminescence microscopy revealed strong heterogeneity in the uptake of [18F]fluoro-deoxyglucose (FDG) in single cells, which was found consistent with fluorescence imaging of a glucose analog. We also verified that dynamic uptake of FDG in single cells followed the standard two-tissue compartmental model. Last, we transfected cells with a fusion PET/fluorescence reporter gene and found that uptake of FHBG (a PET radiotracer for transgene expression) coincided with expression of the fluorescent protein. Together, these results indicate that radioluminescence microscopy can visualize radiotracer uptake with single-cell resolution, which may find a use in the precise characterization of radiotracers. PMID:23056276

Exploring Verbal, Visual and Schematic Learners' Static and Dynamic Mental Images of Scientific Species and Processes in Relation to Their Spatial Ability

ERIC Educational Resources Information Center

Al-Balushi, Sulaiman M.; Coll, Richard Kevin

2013-01-01

The current study compared different learners' static and dynamic mental images of unseen scientific species and processes in relation to their spatial ability. Learners were classified into verbal, visual and schematic. Dynamic images were classified into: appearing/disappearing, linear-movement, and rotation. Two types of scientific entities and…

Enhanced truncated-correlation photothermal coherence tomography with application to deep subsurface defect imaging and 3-dimensional reconstructions

NASA Astrophysics Data System (ADS)

Tavakolian, Pantea; Sivagurunathan, Koneswaran; Mandelis, Andreas

2017-07-01

Photothermal diffusion-wave imaging is a promising technique for non-destructive evaluation and medical applications. Several diffusion-wave techniques have been developed to produce depth-resolved planar images of solids and to overcome imaging depth and image blurring limitations imposed by the physics of parabolic diffusion waves. Truncated-Correlation Photothermal Coherence Tomography (TC-PCT) is the most successful class of these methodologies to-date providing 3-D subsurface visualization with maximum depth penetration and high axial and lateral resolution. To extend the depth range and axial and lateral resolution, an in-depth analysis of TC-PCT, a novel imaging system with improved instrumentation, and an optimized reconstruction algorithm over the original TC-PCT technique is developed. Thermal waves produced by a laser chirped pulsed heat source in a finite thickness solid and the image reconstruction algorithm are investigated from the theoretical point of view. 3-D visualization of subsurface defects utilizing the new TC-PCT system is reported. The results demonstrate that this method is able to detect subsurface defects at the depth range of ˜4 mm in a steel sample, which exhibits dynamic range improvement by a factor of 2.6 compared to the original TC-PCT. This depth does not represent the upper limit of the enhanced TC-PCT. Lateral resolution in the steel sample was measured to be ˜31 μm.

Parameter Identification and Uncertainty Analysis for Visual MODFLOW based Groundwater Flow Model in a Small River Basin, Eastern India

NASA Astrophysics Data System (ADS)

Jena, S.

2015-12-01

The overexploitation of groundwater resulted in abandoning many shallow tube wells in the river Basin in Eastern India. For the sustainability of groundwater resources, basin-scale modelling of groundwater flow is essential for the efficient planning and management of the water resources. The main intent of this study is to develope a 3-D groundwater flow model of the study basin using the Visual MODFLOW package and successfully calibrate and validate it using 17 years of observed data. The sensitivity analysis was carried out to quantify the susceptibility of aquifer system to the river bank seepage, recharge from rainfall and agriculture practices, horizontal and vertical hydraulic conductivities, and specific yield. To quantify the impact of parameter uncertainties, Sequential Uncertainty Fitting Algorithm (SUFI-2) and Markov chain Monte Carlo (MCMC) techniques were implemented. Results from the two techniques were compared and the advantages and disadvantages were analysed. Nash-Sutcliffe coefficient (NSE) and coefficient of determination (R2) were adopted as two criteria during calibration and validation of the developed model. NSE and R2 values of groundwater flow model for calibration and validation periods were in acceptable range. Also, the MCMC technique was able to provide more reasonable results than SUFI-2. The calibrated and validated model will be useful to identify the aquifer properties, analyse the groundwater flow dynamics and the change in groundwater levels in future forecasts.

Analyzing simulation-based PRA data through traditional and topological clustering: A BWR station blackout case study

DOE PAGES

Maljovec, D.; Liu, S.; Wang, B.; ...

2015-07-14

Here, dynamic probabilistic risk assessment (DPRA) methodologies couple system simulator codes (e.g., RELAP and MELCOR) with simulation controller codes (e.g., RAVEN and ADAPT). Whereas system simulator codes model system dynamics deterministically, simulation controller codes introduce both deterministic (e.g., system control logic and operating procedures) and stochastic (e.g., component failures and parameter uncertainties) elements into the simulation. Typically, a DPRA is performed by sampling values of a set of parameters and simulating the system behavior for that specific set of parameter values. For complex systems, a major challenge in using DPRA methodologies is to analyze the large number of scenarios generated,more » where clustering techniques are typically employed to better organize and interpret the data. In this paper, we focus on the analysis of two nuclear simulation datasets that are part of the risk-informed safety margin characterization (RISMC) boiling water reactor (BWR) station blackout (SBO) case study. We provide the domain experts a software tool that encodes traditional and topological clustering techniques within an interactive analysis and visualization environment, for understanding the structures of such high-dimensional nuclear simulation datasets. We demonstrate through our case study that both types of clustering techniques complement each other for enhanced structural understanding of the data.« less

Evaluation of stiffness feedback for hard nodule identification on a phantom silicone model

PubMed Central

Konstantinova, Jelizaveta; Xu, Guanghua; He, Bo; Aminzadeh, Vahid; Xie, Jun; Wurdemann, Helge; Althoefer, Kaspar

2017-01-01

Haptic information in robotic surgery can significantly improve clinical outcomes and help detect hard soft-tissue inclusions that indicate potential abnormalities. Visual representation of tissue stiffness information is a cost-effective technique. Meanwhile, direct force feedback, although considerably more expensive than visual representation, is an intuitive method of conveying information regarding tissue stiffness to surgeons. In this study, real-time visual stiffness feedback by sliding indentation palpation is proposed, validated, and compared with force feedback involving human subjects. In an experimental tele-manipulation environment, a dynamically updated color map depicting the stiffness of probed soft tissue is presented via a graphical interface. The force feedback is provided, aided by a master haptic device. The haptic device uses data acquired from an F/T sensor attached to the end-effector of a tele-manipulated robot. Hard nodule detection performance is evaluated for 2 modes (force feedback and visual stiffness feedback) of stiffness feedback on an artificial organ containing buried stiff nodules. From this artificial organ, a virtual-environment tissue model is generated based on sliding indentation measurements. Employing this virtual-environment tissue model, we compare the performance of human participants in distinguishing differently sized hard nodules by force feedback and visual stiffness feedback. Results indicate that the proposed distributed visual representation of tissue stiffness can be used effectively for hard nodule identification. The representation can also be used as a sufficient substitute for force feedback in tissue palpation. PMID:28248996

Evaluation of stiffness feedback for hard nodule identification on a phantom silicone model.

PubMed

Li, Min; Konstantinova, Jelizaveta; Xu, Guanghua; He, Bo; Aminzadeh, Vahid; Xie, Jun; Wurdemann, Helge; Althoefer, Kaspar

2017-01-01

Haptic information in robotic surgery can significantly improve clinical outcomes and help detect hard soft-tissue inclusions that indicate potential abnormalities. Visual representation of tissue stiffness information is a cost-effective technique. Meanwhile, direct force feedback, although considerably more expensive than visual representation, is an intuitive method of conveying information regarding tissue stiffness to surgeons. In this study, real-time visual stiffness feedback by sliding indentation palpation is proposed, validated, and compared with force feedback involving human subjects. In an experimental tele-manipulation environment, a dynamically updated color map depicting the stiffness of probed soft tissue is presented via a graphical interface. The force feedback is provided, aided by a master haptic device. The haptic device uses data acquired from an F/T sensor attached to the end-effector of a tele-manipulated robot. Hard nodule detection performance is evaluated for 2 modes (force feedback and visual stiffness feedback) of stiffness feedback on an artificial organ containing buried stiff nodules. From this artificial organ, a virtual-environment tissue model is generated based on sliding indentation measurements. Employing this virtual-environment tissue model, we compare the performance of human participants in distinguishing differently sized hard nodules by force feedback and visual stiffness feedback. Results indicate that the proposed distributed visual representation of tissue stiffness can be used effectively for hard nodule identification. The representation can also be used as a sufficient substitute for force feedback in tissue palpation.

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

Carranza, Arturo; Gewin, Mariah; Pojman, John A., E-mail: japojman@lsu.edu

In this study, we present an inexpensive and practical method that allows the monitoring and visualization of front polymerization, propagation, and dynamics. Commercially available europium-doped aluminum oxide powders were combined with video imaging to visualize free-radical propagating polymer fronts. In order to demonstrate the applicability of this method, frontal copolymerization reactions of propoxylated glycerin triacrylate (EB53), pentaerythritol triacrylate (PETA), and pentaerythritol tetra-acrylate (PETEA) with 1,1-Bis(tert-butylperoxy)-3,3,5-trimethylcyclohexane (Luperox 231®) as an initiator were studied and compared to the results obtained by IR imaging. Systems exhibiting higher filler loading, higher EB53 content, and less acrylated monomers showed a marked decrease in front velocity,more » while those with more acrylated monomers and higher crosslinking density showed a marked increase in front velocity. Finally, in order to show the potential of the imaging technique, we studied fronts propagating in planar and spherical geometries.« less

Robust lane detection and tracking using multiple visual cues under stochastic lane shape conditions

NASA Astrophysics Data System (ADS)

Huang, Zhi; Fan, Baozheng; Song, Xiaolin

2018-03-01

As one of the essential components of environment perception techniques for an intelligent vehicle, lane detection is confronted with challenges including robustness against the complicated disturbance and illumination, also adaptability to stochastic lane shapes. To overcome these issues, we proposed a robust lane detection method named classification-generation-growth-based (CGG) operator to the detected lines, whereby the linear lane markings are identified by synergizing multiple visual cues with the a priori knowledge and spatial-temporal information. According to the quality of linear lane fitting, the linear and linear-parabolic models are dynamically switched to describe the actual lane. The Kalman filter with adaptive noise covariance and the region of interests (ROI) tracking are applied to improve the robustness and efficiency. Experiments were conducted with images covering various challenging scenarios. The experimental results evaluate the effectiveness of the presented method for complicated disturbances, illumination, and stochastic lane shapes.

Integration of Real-Time Intraoperative Contrast-Enhanced Ultrasound and Color Doppler Ultrasound in the Surgical Treatment of Spinal Cord Dural Arteriovenous Fistulas.

PubMed

Della Pepa, Giuseppe Maria; Sabatino, Giovanni; Sturiale, Carmelo Lucio; Marchese, Enrico; Puca, Alfredo; Olivi, Alessandro; Albanese, Alessio

2018-04-01

In the surgical treatment of spinal dural arteriovenous fistulas (DAVFs), intraoperative definition of anatomic characteristics of the DAVF and identification of the fistulous point is mandatory to effectively exclude the DAVF. Intraoperative ultrasound and contrast-enhanced ultrasound integrated with color Doppler ultrasound was applied in the surgical setting for a cervical DAVF to identify the fistulous point and evaluate correct occlusion of the fistula. Integration of intraoperative ultrasound and contrast-enhanced ultrasound is a simple, cost-effective technique that provides an opportunity for real-time dynamic visualization of DAVF vascular patterns, identification of the fistulous point, and assessment of correct exclusion. Compared with other intraoperative tools, such as indocyanine green videoangiography, it allows the surgeon to visualize hidden anatomic and vascular structures, minimizing surgical manipulation and guiding the surgeon during resection. Copyright © 2018 Elsevier Inc. All rights reserved.

Creative user-centered visualization design for energy analysts and modelers.

PubMed

Goodwin, Sarah; Dykes, Jason; Jones, Sara; Dillingham, Iain; Dove, Graham; Duffy, Alison; Kachkaev, Alexander; Slingsby, Aidan; Wood, Jo

2013-12-01

We enhance a user-centered design process with techniques that deliberately promote creativity to identify opportunities for the visualization of data generated by a major energy supplier. Visualization prototypes developed in this way prove effective in a situation whereby data sets are largely unknown and requirements open - enabling successful exploration of possibilities for visualization in Smart Home data analysis. The process gives rise to novel designs and design metaphors including data sculpting. It suggests: that the deliberate use of creativity techniques with data stakeholders is likely to contribute to successful, novel and effective solutions; that being explicit about creativity may contribute to designers developing creative solutions; that using creativity techniques early in the design process may result in a creative approach persisting throughout the process. The work constitutes the first systematic visualization design for a data rich source that will be increasingly important to energy suppliers and consumers as Smart Meter technology is widely deployed. It is novel in explicitly employing creativity techniques at the requirements stage of visualization design and development, paving the way for further use and study of creativity methods in visualization design.

Processing and statistical analysis of soil-root images

NASA Astrophysics Data System (ADS)

Razavi, Bahar S.; Hoang, Duyen; Kuzyakov, Yakov

2016-04-01

Importance of the hotspots such as rhizosphere, the small soil volume that surrounds and is influenced by plant roots, calls for spatially explicit methods to visualize distribution of microbial activities in this active site (Kuzyakov and Blagodatskaya, 2015). Zymography technique has previously been adapted to visualize the spatial dynamics of enzyme activities in rhizosphere (Spohn and Kuzyakov, 2014). Following further developing of soil zymography -to obtain a higher resolution of enzyme activities - we aimed to 1) quantify the images, 2) determine whether the pattern (e.g. distribution of hotspots in space) is clumped (aggregated) or regular (dispersed). To this end, we incubated soil-filled rhizoboxes with maize Zea mays L. and without maize (control box) for two weeks. In situ soil zymography was applied to visualize enzymatic activity of β-glucosidase and phosphatase at soil-root interface. Spatial resolution of fluorescent images was improved by direct application of a substrate saturated membrane to the soil-root system. Furthermore, we applied "spatial point pattern analysis" to determine whether the pattern (e.g. distribution of hotspots in space) is clumped (aggregated) or regular (dispersed). Our results demonstrated that distribution of hotspots at rhizosphere is clumped (aggregated) compare to control box without plant which showed regular (dispersed) pattern. These patterns were similar in all three replicates and for both enzymes. We conclude that improved zymography is promising in situ technique to identify, analyze, visualize and quantify spatial distribution of enzyme activities in the rhizosphere. Moreover, such different patterns should be considered in assessments and modeling of rhizosphere extension and the corresponding effects on soil properties and functions. Key words: rhizosphere, spatial point pattern, enzyme activity, zymography, maize.