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At least 55 records · Page 3

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES

Algorithms for Haptic Rendering of 3D Objects

Algorithms have been developed to provide haptic rendering of three-dimensional (3D) objects in virtual (that is, computationally simulated) environments. The goal of haptic rendering is to generate tactual displays of the shapes, hardnesses, surface textures, and frictional properties of 3D objects in real time. Haptic rendering is a major element of the emerging field of computer haptics, which invites comparison with computer graphics. We have already seen various applications of computer haptics in the areas of medicine (surgical simulation, telemedicine, haptic user interfaces for blind people, and rehabilitation of patients with neurological disorders), entertainment (3D painting, character animation, morphing, and sculpting), mechanical design (path planning and assembly sequencing), and scientific visualization (geophysical data analysis and molecular manipulation).

Basdogan, Cagatay

Visualization of Concurrent Program Executions

Various program analysis techniques are efficient at discovering failures and properties. However, it is often difficult to evaluate results, such as program traces. This calls for abstraction and visualization tools. We propose an approach based on UML sequence diagrams, addressing shortcomings of such diagrams for concurrency. The resulting visualization is expressive and provides all the necessary information at a glance.

concurrent programs

An information maximization model of eye movements

We propose a sequential information maximization model as a general strategy for programming eye movements. The model reconstructs high-resolution visual information from a sequence of fixations, taking into account the fall-off in resolution from the fovea to the periphery. From this framework we get a simple rule for predicting fixation sequences: after each fixation, fixate next at the location that minimizes uncertainty (maximizes information) about the stimulus. By comparing our model performance to human eye movement data and to predictions from a saliency and random model, we demonstrate that our model is best at predicting fixation locations. Modeling additional biological constraints will improve the prediction of fixation sequences. Our results suggest that information maximization is a useful principle for programming eye movements.

NASA Discipline Neuroscience

Visual evoked potentials and selective attention to points in space

Visual evoked potentials (VEPs) were recorded to sequences of flashes delivered to the right and left visual fields while subjects responded promptly to designated stimuli in one field at a time (focused attention), in both fields at once (divided attention), or to neither field (passive). Three stimulus schedules were used: the first was a replication of a previous study (Eason, Harter, and White, 1969) where left- and right-field flashes were delivered quasi-independently, while in the other two the flashes were delivered to the two fields in random order (Bernoulli sequence). VEPs to attended-field stimuli were enhanced at both occipital (O2) and central (Cz) recording sites under all stimulus sequences, but different components were affected at the two scalp sites. It was suggested that the VEP at O2 may reflect modality-specific processing events, while the response at Cz, like its auditory homologue, may index more general aspects of selective attention.

Van Voorhis, S.

Petrologic evolution of CM chondrites: The difficulty of discriminating between nebular and parent-body effects

We wish to draw attention to a major controversy that has arisen in the area of CM-chondrite petrology. The problem is important because its resolution will have profound implications for ideas concerning nebular dynamics, gas-solid interactions in the nebula, and accretionary processes in the nebula, among other issues. On the one hand, cogent arguments have been presented that 'accretionary dust mantles,' were formed in the solar nebula prior to accretion of the CM parent asteroid(s). On the other hand, no-less-powerful arguments have been advanced that a significant fraction of the CM lithology is secondary, produced by aqueous alteration in the near-surface regions of an asteroid-sized object. Because most, if not all, CM chondrites are breccias, these two views could coexist harmoniously, were it not for the fact that some of the coarse-grained lithologies surrounded by 'accretion dust mantles' are themselves of apparently secondary origin. Such an observation must clearly force a reassessment of one or both of the present schools of thought. Our objective here is to stimulate such a reassessment. Four possible resolutions of this conflict may be postulated. First, perhaps nature found a way of permitting such secondary alteration to take place in the nebula. Second, maybe dust mantles could form in a regolith, rather than a nebular, environment. Third, it is possible that dust mantles around secondary lithologies are different from those around primary lithologies. Finally, perhaps formation of CM chondrites involved a more complex sequence of events than visualized so far, so that some apparently 'primary' processes postdated certain 'secondary' processes.

Kerridge, J. F.

Bottom-Up Simulation, Reconstruction, and Quantification of Macromolecule Sequences from Experimental Polymerizations

Motivated by the canonical sequence–structure–function paradigm, tools to characterize chemical patterning in natural biomacromolecules, from proteins to nucleic acids, have grown exponentially in recent years. However, analogous strategies for synthetic macromolecules remain in nascent stages, complicated by sequence polydispersity and analytical limitations. To address this, we have developed a comprehensive and open-source Python package, PRISM (polymer rate insights and sequence modeling), an end-to-end workflow that provides a path from experimental kinetics measurements to quantitative and qualitative metrics for describing chemical patterning in stochastic polymers. First, a numerical integration strategy was constructed to simulate and fit experimental data from reversible addition–fragmentation chain transfer (RAFT) polymerization kinetics, enabling the facile estimation of relevant reactivity ratios. These ratios were then used in a mechanism-specific stochastic kinetic simulation strategy to simulate sequence ensembles corresponding to model systems spanning experimental copolymers, classes of statistical polymers (e.g., alternating, block, and gradient), and multiblock copolymers. Lastly, inspired by sequence homology metrics from bioinformatics, we introduce visualization strategies and quantitative metrics to facilitate comparisons of different sequence ensembles. As the sequence–structure–function paradigm becomes increasingly central in de novo design of synthetic macromolecules, this toolkit provides a first step toward accurate and representative sequence description and featurization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Seeing tones and hearing rectangles - Attending to simultaneous auditory and visual events

The allocation of attention in dual-task situations depends on both the overall and the momentary demands associated with both tasks. Subjects in an inclusive- or reaction-time task responded to changes in simultaneous sequences of discrete auditory and visual stimuli. Performance on individual trials was affected by (1) the ratio of stimuli in the two tasks, (2) response demands of the two tasks, and (3) patterns inherent in the demands of one task.

Casper, Patricia A.

Feature and Pose Constrained Visual Aided Inertial Navigation for Computationally Constrained Aerial Vehicles

A Feature and Pose Constrained Extended Kalman Filter (FPC-EKF) is developed for highly dynamic computationally constrained micro aerial vehicles. Vehicle localization is achieved using only a low performance inertial measurement unit and a single camera. The FPC-EKF framework augments the vehicle's state with both previous vehicle poses and critical environmental features, including vertical edges. This filter framework efficiently incorporates measurements from hundreds of opportunistic visual features to constrain the motion estimate, while allowing navigating and sustained tracking with respect to a few persistent features. In addition, vertical features in the environment are opportunistically used to provide global attitude references. Accurate pose estimation is demonstrated on a sequence including fast traversing, where visual features enter and exit the field-of-view quickly, as well as hover and ingress maneuvers where drift free navigation is achieved with respect to the environment.

autonomous operation

NASA Tech Briefs, December 2012

The topics include: Pattern Generator for Bench Test of Digital Boards; 670-GHz Down- and Up-Converting HEMT-Based Mixers; Lidar Electro-Optic Beam Switch with a Liquid Crystal Variable Retarder; Feedback Augmented Sub-Ranging (FASR) Quantizer; Real-Time Distributed Embedded Oscillator Operating Frequency Monitoring; Software Modules for the Proximity-1 Space Link Interleaved Time Synchronization (PITS) Protocol; Description and User Instructions for the Quaternion to Orbit v3 Software; AdapChem; Mars Relay Lander and Orbiter Overflight Profile Estimation; Extended Testability Analysis Tool; Interactive 3D Mars Visualization; Rapid Diagnostics of Onboard Sequences; MER Telemetry Processor; pyam: Python Implementation of YaM; Process for Patterning Indium for Bump Bonding; Archway for Radiation and Micrometeorite Occurrence Resistance; 4D Light Field Imaging System Using Programmable Aperture; Device and Container for Reheating and Sterilization; Radio Frequency Plasma Discharge Lamps for Use as Stable Calibration Light Sources; Membrane Shell Reflector Segment Antenna; High-Speed Transport of Fluid Drops and Solid Particles via Surface Acoustic Waves; Compact Autonomous Hemispheric Vision System; A Distributive, Non-Destructive, Real-Time Approach to Snowpack Monitoring; Wideband Single-Crystal Transducer for Bone Characterization; Numerical Simulation of Rocket Exhaust Interaction With Lunar Soil; Motion Imagery and Robotics Application (MIRA): Standards-Based Robotics; Particle Filtering for Model-Based Anomaly Detection in Sensor Networks; Ka-band Digitally Beamformed Airborne Radar Using SweepSAR Technique; Composite With In Situ Plenums; Multi-Beam Approach for Accelerating Alignment and Calibration of HyspIRI-Like Imaging Spectrometers; JWST Lifting System; Next-Generation Tumbleweed Rover; Pneumatic System for Concentration of Micrometer-Size Lunar Soil.

Source record

Measurement of Visual Reaction Times Using Hand-held Mobile Devices

Modern mobile devices provide a convenient platform for collecting research data in the field. But,because the working of these devices is often cloaked behind multiple layers of proprietary system software, it can bedifficult to assess the accuracy of the data they produce, particularly in the case of timing. We have been collecting datain a simple visual reaction time experiment, as part of a fatigue testing protocol known as the Psychomotor Vigilance Test (PVT). In this protocol, subjects run a 5-minute block consisting of a sequence of trials in which a visual stimulus appears after an unpredictable variable delay. The subject is required to tap the screen as soon as possible after the appearance of the stimulus. In order to validate the reaction times reported by our program, we had subjects perform the task while a high-speed video camera recorded both the display screen, and a side view of the finger (observed in a mirror). Simple image-processing methods were applied to determine the frames in which the stimulus appeared and disappeared, and in which the finger made and broke contact with the screen. The results demonstrate a systematic delay between the initial contact by the finger and the detection of the touch by the software, having a value of 80 +- 20 milliseconds.

reaction time

Software For Graphical Representation Of A Network

System Visualization Tool (SVT) computer program developed to provide systems engineers with means of graphically representing networks. Generates diagrams illustrating structures and states of networks defined by users. Provides systems engineers powerful tool simplifing analysis of requirements and testing and maintenance of complex software-controlled systems. Employs visual models supporting analysis of chronological sequences of requirements, simulation data, and related software functions. Applied to pneumatic, hydraulic, and propellant-distribution networks. Used to define and view arbitrary configurations of such major hardware components of system as propellant tanks, valves, propellant lines, and engines. Also graphically displays status of each component. Advantage of SVT: utilizes visual cues to represent configuration of each component within network. Written in Turbo Pascal(R), version 5.0.

Mcallister, R. William

Visual display aid for orbital maneuvering - Design considerations

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.

Grunwald, Arthur J.

Science opportunity analyzer - a multi-mission tool for planning

For many years the diverse scientific community that supports JPL's wide variety ofinterplanetary space missions has needed a tool in order to plan and develop their experiments. The tool needs to be easily adapted to various mission types and portable to the user community. The Science Opportunity Analyzer, SOA, now in its third year of development, is intended to meet this need. SOA is a java-based application that is designed to enable scientists to identify and analyze opportunities for science observations from spacecraft. It differs from other planning tools in that it does not require an in-depth knowledge of the spacecraft command system or operation modes to begin high level planning. Users can, however, develop increasingly detailed levels of design. SOA consists of six major functions: Opportunity Search, Visualization, Observation Design, Constraint Checking, Data Output and Communications. Opportunity Search is a GUI driven interface to existing search engines that can be used to identify times when a spacecraft is in a specific geometrical relationship with other bodies in the solar system. This function can be used for advanced mission planning as well as for making last minute adjustments to mission sequences in response to trajectory modifications. Visualization is a key aspect of SOA. The user can view observation opportunities in either a 3D representation or as a 2D map projection. The user is given extensive flexibility to customize what is displayed in the view. Observation Design allows the user to orient the spacecraft and visualize the projection of the instrument field of view for that orientation using the same views as Opportunity Search. Constraint Checking is provided to validate various geometrical and physical aspects of an observation design. The user has the ability to easily create custom rules or to use official project-generated flight rules. This capability may also allow scientists to easily impact the cost to science if flight rule changes occur. Data Output generates information based on the spacecraft's trajectory, opportunity search results or based on a created observation. The data can be viewed either in tabular format or as a graph. Finally, SOA is unique in that it is designed to be able to communicate with a variety of existing planning and sequencing tools. From the very beginning SOA was designed with the user in mind. Extensive surveys of the potential user community were conducted in order to develop the software requirements. Throughout the development period, close ties have been maintained with the science community to insure that the tool maintains its user focus. Although development is still in its early stages, SOA is already developing a user community on the Cassini project, which is depending on this tool for their science planning. There are other tools at JPL that do various pieces of what SOA can do; however, there is no other tool which combines all these functions and presents them to the user in such a convenient, cohesive, and easy to use fashion.

SOA science planning mission operations sequence s

Science Opportunity Analyzer (SOA) Version 8

SOA allows scientists to plan spacecraft observations. It facilitates the identification of geometrically interesting times in a spacecraft s orbit that a user can use to plan observations or instrument-driven spacecraft maneuvers. These observations can then be visualized multiple ways in both two- and three-dimensional views. When observations have been optimized within a spacecraft's flight rules, the resulting plans can be output for use by other JPL uplink tools. Now in its eighth major version, SOA improves on these capabilities in a modern and integrated fashion. SOA consists of five major functions: Opportunity Search, Visualization, Observation Design, Constraint Checking, and Data Output. Opportunity Search is a GUI-driven interface to existing search engines that can be used to identify times when a spacecraft is in a specific geometrical relationship with other bodies in the solar system. This function can be used for advanced mission planning as well as for making last-minute adjustments to mission sequences in response to trajectory modifications. Visualization is a key aspect of SOA. The user can view observation opportunities in either a 3D representation or as a 2D map projection. Observation Design allows the user to orient the spacecraft and visualize the projection of the instrument field of view for that orientation using the same views as Opportunity Search. Constraint Checking is provided to validate various geometrical and physical aspects of an observation design. The user has the ability to easily create custom rules or to use official project-generated flight rules. This capability may also allow scientists to easily assess the cost to science if flight rule changes occur. Data Output allows the user to compute ancillary data related to an observation or to a given position of the spacecraft along its trajectory. The data can be saved as a tab-delimited text file or viewed as a graph. SOA combines science planning functionality unique to both JPL and the sponsoring spacecraft. SOA is able to ingest JPL SPICE Kernels that are used to drive the tool and its computations. A Percy search engine is then included that identifies interesting time periods for the user to build observations. When observations are then built, flight-like orientation algorithms replicate spacecraft dynamics to closely simulate the flight spacecraft s dynamics. SOA v8 represents large steps forward from SOA v7 in terms of quality, reliability, maintainability, efficiency, and user experience. A tailored agile development environment has been built around SOA that provides automated unit testing, continuous build and integration, a consolidated Web-based code and documentation storage environment, modern Java enhancements, and a focus on usability

Witoff, Robert J.

Microscopic and Metallurgical Aspects of the Space Shuttle Columbia Accident Investigation and Reconstruction

The Space Shuttle Columbia was descending for a landing at the Kennedy Space Center (KSC) on February 1, 2003. Approximately 20 minutes prior to touchdown, the Columbia began disintegrating over the western United States; the majority of debris eventually impacted in eastern Texas and western Louisiana. A monumental effort eventually recovered approximately 84,000 pieces of debris, approximately 38% of the Orbiter's original dry weight. The debris was transported to KSC, where the items were catalogued and evaluated. Critical areas of interest, such as the left and right leading edge surfaces and the underside of the ship, were placed upon a grid to aid in the reconstruction. Items of interest included metallic structures, reinforced carbon-carbon composites, and ceramic heat insulation tiles. Many of the leading edge elements had re-solidified metallic deposits spattered on them. These deposits became known as slag and were one of the main focuses of the investigation. In order to help determine the sequence of events inside the left wing during the accident, the slag's composition, layering order, and directionality of deposition were studied. A myriad of analytical tests were performed in an attempt to ascertain the compositional and depositional characteristics of selected slag deposits, including the ordering of deposited layers within each individual slag deposit harvested. Initially, Scanning Electron Microscopy and Energy Dispersive X-Ray Spectroscopy (SEM/EDX) were performed to quickly characterize the overall composition of individual slag deposits: SEM utilizes a narrowlyfocused high-energy electron beam impinging upon a specimen. The incident beam excites and liberates lower energy secondary electrons, which are detected and analyzed, providing a visual representation of the sample's surface topography. EDX also relies on an incident electron beam, except an EDX unit measures X-ray energies generated by the impinging beam. Each element generates a unique X-ray signature; the EDX detector measures these discreet energies. EDX actually penetrates approximately 2 microns into the bulk of the sample. However, random examination of various portions of slag, coupled with the semiquantitative nature of the SEM/EDX analysis, did not yield convincingly pertinent data. Therefore, X-ray dot mapping was conducted, which provided more understandable data, both in terms of slag layering and composition. An X-ray dot map is generated by performing numerous EDX scans for individual elements, then compiling the scans in a visual representation. Eventually, specimens consisting of not only the slag, but of the adjacent RCC substrate as well were cross-sectioned. X-Ray dot mapping of the materialographicallymounted and -polished cross- sections provided a visual representation of both the layering sequence and compositional characteristics of the slag. Contemporaneously, Electron Spectroscopy for Chemical Analysis/X-Ray Photoelectron Spectroscopy (ESCA/XPS) and powdered X-Ray Diffraction (XRD) were performed to further characterize the deposits and to attempt to identify what, if any, compounds were present. The ESCA/XPS analysis allowed the analyst to "sputter" into the sample with an electron gun, aiding in the identification of the layering sequence. XPS uses photons, rather than electrons, which impinge upon the surface of the sample. XPS measures the electrons emitted from within the first 5 nm of the sample's surface. The XRD measures the scatter angles of incident X-rays; the angle and intensity of scatter depend upon the crystalline structure of the pulverized sample. XRD is considered a qualitative rather than quantitative technique. ESCA/XPS revealed that the final layer to deposit was predominantly carbonaceous. XRD was successful in identifying specific compounds, such as Al 2O3, Al and/or Al3 21SiO47, mullite (3(Al2)O3 -SiO2), and nickel-aluminides. Eventually, Electron MicroProbe Analysis (EMPA) was conducted on the marialographically-prepared cross- sections of selected slag deposits. Microprobe combines SEM and Wavelength Dispersive X-Ray Spectroscopy (WDS), and, like EDX, uses a narrowly-focused high-energy electron beam impinging upon a specimen to elicit, in the case of EPMA, characteristic X-rays with specific wavelengths. This quantitative, analytical tool proved the most useful in determining depositional layering and composition of the slag deposits. This information was utilized in verifying the location of the breach in the left leading edge of the wing of the Columbia.

McDaniels, Steven J.