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At least 1,495 records · Page 83

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes

One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96).

59 BASIC BIOLOGICAL SCIENCES↗

Formation of Double Neutron Star Systems

Double neutron star (DNS) systems represent extreme physical objects and the endpoint of an exotic journey of stellar evolution and binary interactions. Large numbers of DNS systems and their mergers are anticipated to be discovered using the Square Kilometre Array searching for radio pulsars, and the high-frequency gravitational wave detectors (LIGO/VIRGO), respectively. Here we discuss all key properties of DNS systems, as well as selection effects, and combine the latest observational data with new theoretical progress on various physical processes with the aim of advancing our knowledge on their formation. We examine key interactions of their progenitor systems and evaluate their accretion history during the high-mass X-ray binary stage, the common envelope phase, and the subsequent Case BB mass transfer, and argue that the first-formed NSs have accreted at most ∼0.02 M{sub ⊙}. We investigate DNS masses, spins, and velocities, and in particular correlations between spin period, orbital period, and eccentricity. Numerous Monte Carlo simulations of the second supernova (SN) events are performed to extrapolate pre-SN stellar properties and probe the explosions. All known close-orbit DNS systems are consistent with ultra-stripped exploding stars. Although their resulting NS kicks are often small, we demonstrate a large spread in kick magnitudes that may, in general, depend on the past interaction history of the exploding star and thus correlate with the NS mass. We analyze and discuss NS kick directions based on our SN simulations. Finally, we discuss the terminal evolution of close-orbit DNS systems until they merge and possibly produce a short γ-ray burst.

79 ASTRONOMY AND ASTROPHYSICS↗

Cluster analysis based on dimensional information with applications to feature selection and classification

A new clustering algorithm is presented that is based on dimensional information. The algorithm includes an inherent feature selection criterion, which is discussed. Further, a heuristic method for choosing the proper number of intervals for a frequency distribution histogram, a feature necessary for the algorithm, is presented. The algorithm, although usable as a stand-alone clustering technique, is then utilized as a global approximator. Local clustering techniques and configuration of a global-local scheme are discussed, and finally the complete global-local and feature selector configuration is shown in application to a real-time adaptive classification scheme for the analysis of remote sensed multispectral scanner data.

Eigen, D. J.↗

CCIR papers on telecommunications for deep space research

Mission requirements, equipment factors, and link performance define the frequency bands that are preferred for deep space research using manned and unmanned spacecraft. The preferred bands and selection considerations are presented.

Degroot, N. F.↗

Deconvolution of gas chromatographic data

The use of deconvolution methods on gas chromatographic data to obtain an accurate determination of the relative amounts of each material present by mathematically separating the merged peaks is discussed. Data were obtained on a gas chromatograph with a flame ionization detector. Chromatograms of five xylenes with differing degrees of separation were generated by varying the column temperature at selected rates. The merged peaks were then successfully separated by deconvolution. The concept of function continuation in the frequency domain was introduced in striving to reach the theoretical limit of accuracy, but proved to be only partially successful.

Howard, S.↗

Modal vector estimation for closely spaced frequency modes

Techniques for obtaining improved modal vector estimates for systems with closely spaced frequency modes are discussed. In describing the dynamical behavior of a complex structure modal parameters are often analyzed: undamped natural frequency, mode shape, modal mass, modal stiffness and modal damping. From both an analytical standpoint and an experimental standpoint, identification of modal parameters is more difficult if the system has repeated frequencies or even closely spaced frequencies. The more complex the structure, the more likely it is to have closely spaced frequencies. This makes it difficult to determine valid mode shapes using single shaker test methods. By employing band selectable analysis (zoom) techniques and by employing Kennedy-Pancu circle fitting or some multiple degree of freedom (MDOF) curve fit procedure, the usefulness of the single shaker approach can be extended.

Craig, R. R., Jr.↗

Formulation of blade-flutter spectral analyses in stationary reference frame

Analytic representations are developed for the discrete blade deflection and the continuous tip static pressure fields in a stationary reference frame. Considered are the sampling rates equal to the rotational frequency, equal to blade passing frequency, and for the pressure, equal to a multiple of the blade passing frequency. For the last two rates the expressions for determining the nodal diameters from the spectra are included. A procedure is presented for transforming the complete unsteady pressure field into a rotating frame of reference. The determination of the true flutter frequency by using two sensors is described. To illustrate their use, the developed procedures are used to interpret selected experimental results.

Kurkov, A. P.↗

Review of the frequency stabilization of TEA CO2 laser oscillators

Most applications of TEA CO2 lasers in heterodyne radar systems require that the transmitter has a high degree of frequency stability. This ensures good Doppler resolution and maximizes receiver sensitivity. However, the environment within the device is far from benign with fast acoustic and electrical transients being present. Consequently the phenomena which govern the frequency stability of pulsed lasers are quite different from those operative in their CW counterparts. This review concentrates on the mechanisms of chirping within the output pulse; pulse to pulse frequency drift may be eliminated by frequency measurement and correction on successive pulses. It emerges that good stability hinges on correct cavity design. The energy-dependent laser-induced frequency sweep falls dramatically as mode diameter is increased. Thus, it is necessary to construct resonators with good selectivity for single mode operation while having a large spot size.

Willetts, David V.↗

Aerospace induction motor actuators driven from a 20-kHz power link

Aerospace electromechanical actuators utilizing induction motors are under development in sizes up to 40 kW. While these actuators have immediate application to the Advanced Launch System (ALS) program, several potential applications are currently under study including the Advanced Aircraft Program. Several recent advances developed for the Space Station Freedom have allowed induction motors to be selected as a first choice for such applications. Among these technologies are bi-directional electronics and high frequency power distribution techniques. Each of these technologies are discussed with emphasis on their impact upon induction motor operation.

Hansen, Irving G.↗

A propagation experiment for modelling high elevation angle land mobile satellite channels

This paper summarizes the results of a feasibility study for conducting high elevation angle propagation experiments in the European region for land mobile satellite communication. The study addresses various aspects of a proposed experiment. These include the selection of a suitable source for transmission, possibility of gathering narrow and wide band propagation data in various frequency bands, types of useful data, data acquisition technique, possible experimental configuration, and other experimental details.

Richharia, M.↗

Optoelectronic associative memory

An associative optical memory including an input spatial light modulator (SLM) in the form of an edge enhanced liquid crystal light valve (LCLV) and a pair of memory SLM's in the form of liquid crystal televisions (LCTV's) forms a matrix array of an input image which is cross correlated with a matrix array of stored images. The correlation product is detected and nonlinearly amplified to illuminate a replica of the stored image array to select the stored image correlating with the input image. The LCLV is edge enhanced by reducing the bias frequency and voltage and rotating its orientation. The edge enhancement and nonlinearity of the photodetection improves the orthogonality of the stored image. The illumination of the replicate stored image provides a clean stored image, uncontaminated by the image comparison process.

Chao, Tien-Hsin↗

BOREAS RSS-17 Dielectric Constant Profile Measurements

The BOREAS RSS-17 team acquired and analyzed imaging radar data from the ESA's ERS-1 over a complete annual cycle at the BOREAS sites in Canada in 1994 to detect shifts in radar backscatter related to varying environmental conditions. This data set consists of dielectric constant profile measurements from selected trees at various BOREAS flux tower sites. The relative dielectric constant was measured at C-band (frequency = 5 GHz) as a function of depth into the trunk of three trees at each site, Measurements were made during April 1994 with an Applied Microwave Corporation field PDP fitted with a 0.358-cm (0.141-inch) diameter coaxial probe tip. The data are available in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Hall, Forrest G.↗

Novel diode laser-based sensors for gas sensing applications

The development of compact spectroscopic gas sensors and their applications to environmental sensing will be described. These sensors employ mid-infrared difference-frequency generation (DFG) in periodically poled lithium niobate (PPLN) crystals pumped by two single-frequency solid state lasers such as diode lasers, diode-pumped solid state, and fiber lasers. Ultrasensitive, highly selective, and real-time measurements of several important atmospheric trace gases, including carbon monoxide, nitrous oxide, carbon dioxide, formaldehyde [correction of formaldehye], and methane, have been demonstrated.

NASA Discipline Life Sciences Technologies↗

Effective Utilization of Commercial Wireless Networking Technology in Planetary Environments

The purpose of this research is to investigate the use of commercial, off-the-shelf wireless networking technology in planetary exploration applications involving rovers and sensor webs. The three objectives of this research project are to: 1) simulate the radio frequency environment of proposed landing sites on Mars using actual topographic data, 2) analyze the performance of current wireless networking standards in the simulated radio frequency environment, and 3) propose modifications to the standards for more efficient utilization. In this annual report, we present our results for the second year of research. During this year, the effort has focussed on the second objective of analyzing the performance of the IEEE 802.11a and IEEE 802.1lb wireless networking standards in the simulated radio frequency environment of Mars. The approach builds upon our previous results which deterministically modelled the RF environment at selected sites on Mars using high-resolution topographical data. These results provide critical information regarding antenna coverage patterns, maximum link distances, effects of surface clutter, and multipath effects. Using these previous results, the physical layer of these wireless networking standards has now been simulated and analyzed in the Martian environment. We are looking to extending these results to the and medium access layer next. Our results give us critical information regarding the performance (data rates, packet error rates, link distances, etc.) of IEEE 802.1 la/b wireless networks. This information enables a critical examination of how these wireless networks may be utilized in future Mars missions and how they may be possibly modified for more optimal usage.

Caulev, Michael↗

Finite-Element Methods for Real-Time Simulation of Surgery

Two finite-element methods have been developed for mathematical modeling of the time-dependent behaviors of deformable objects and, more specifically, the mechanical responses of soft tissues and organs in contact with surgical tools. These methods may afford the computational efficiency needed to satisfy the requirement to obtain computational results in real time for simulating surgical procedures as described in Simulation System for Training in Laparoscopic Surgery (NPO-21192) on page 31 in this issue of NASA Tech Briefs. Simulation of the behavior of soft tissue in real time is a challenging problem because of the complexity of soft-tissue mechanics. The responses of soft tissues are characterized by nonlinearities and by spatial inhomogeneities and rate and time dependences of material properties. Finite-element methods seem promising for integrating these characteristics of tissues into computational models of organs, but they demand much central-processing-unit (CPU) time and memory, and the demand increases with the number of nodes and degrees of freedom in a given finite-element model. Hence, as finite-element models become more realistic, it becomes more difficult to compute solutions in real time. In both of the present methods, one uses approximate mathematical models trading some accuracy for computational efficiency and thereby increasing the feasibility of attaining real-time up36 NASA Tech Briefs, October 2003 date rates. The first of these methods is based on modal analysis. In this method, one reduces the number of differential equations by selecting only the most significant vibration modes of an object (typically, a suitable number of the lowest-frequency modes) for computing deformations of the object in response to applied forces.

Basdogan, Cagatay↗

Low Cost Nuclear Thermal Rocket Cermet Fuel Element Environment Testing

Deep space missions with large payloads require high specific impulse and relatively high thrust to achieve mission goals in reasonable time frames.1,2 Conventional storable propellants produce average specific impulse. Nuclear thermal rockets capable of producing high specific impulse are proposed. Nuclear thermal rockets employ heat produced by fission reaction to heat and therefore accelerate hydrogen, which is then forced through a rocket nozzle providing thrust. Fuel element temperatures are very high (up to 3000 K), and hydrogen is highly reactive with most materials at high temperatures. Data covering the effects of high-temperature hydrogen exposure on fuel elements are limited.3 The primary concern is the mechanical failure of fuel elements that employ high-melting-point metals, ceramics, or a combination (cermet) as a structural matrix into which the nuclear fuel is distributed. The purpose of the testing is to obtain data to assess the properties of the non-nuclear support materials, as-fabricated, and determine their ability to survive and maintain thermal performance in a prototypical NTR reactor environment of exposure to hydrogen at very high temperatures. The fission process of the planned fissile material and the resulting heating performance is well known and does not therefore require that active fissile material be integrated in this testing. A small-scale test bed designed to heat fuel element samples via non-contact radio frequency heating and expose samples to hydrogen is being developed to assist in optimal material and manufacturing process selection without employing fissile material. This paper details the test bed design and results of testing conducted to date.

Bradley, D. E.↗

Radar velocity determination using direction of arrival measurements

The various technologies presented herein relate to utilizing direction of arrival (DOA) data to determine various flight parameters for an aircraft A plurality of radar images (e.g., SAR images) can be analyzed to identify a plurality of pixels in the radar images relating to one or more ground targets. In an embodiment, the plurality of pixels can be selected based upon the pixels exceeding a SNR threshold. The DOA data in conjunction with a measurable Doppler frequency for each pixel can be obtained. Multi-aperture technology enables derivation of an independent measure of DOA to each pixel based on interferometric analysis. This independent measure of DOA enables decoupling of the aircraft velocity from the DOA in a range-Doppler map, thereby enabling determination of a radar velocity. The determined aircraft velocity can be utilized to update an onboard INS, and to keep it aligned, without the need for additional velocity-measuring instrumentation.

47 OTHER INSTRUMENTATION↗

Representativeness and repeatability of microenvironmental personal and head exposures to radio-frequency electromagnetic fields

Highlights: • First time assessment of head exposure to RF-EMF in uncontrolled environments, in 15 microenvironments in Melbourne, Australia. • We show that our measurement protocol is repeatable over time. • We show that the paths selected in our protocol are representative for the larger areas in which they are defined. • Exposure to RF-EMF is higher in more dense urban areas than in less populated suburban areas in the outskirts of the city. The aims of this study were to: i) investigate the repeatability and representativeness of personal radio frequency-electromagnetic fields (RF-EMFs) exposure measurements, across different microenvironments, ii) perform simultaneous evaluations of personal RF-EMF exposures for the whole body and the head, iii) validate the data obtained with a head-worn personal distributed exposimeter (PDE) against those obtained with an on-body worn personal exposimeter (PEM). Data on personal and head RF-EMF exposures were collected by performing measurements across 15 microenvironments in Melbourne, Australia. A body-worn PEM and a head-worn PDE were used for measuring body and head exposures, respectively. The summary statistics obtained for total RF-EMF exposure showed a high representativeness (r{sup 2} > 0.66 for two paths in the same area) and a high repeatability over time (r{sup 2} > 0.87 for repetitions of the same path). The median head exposure in the 900 MHz downlink band ranged between 0.06 V/m and 0.31 V/m. The results obtained during simultaneous measurements using the two devices showed high correlations (0.42 < r{sup 2} < 0.94). The highest mean total RF-EMF exposure was measured in Melbourne's central business district (0.89 V/m), whereas the lowest mean total exposure was measured in a suburban residential area (0.05 V/m). This study shows that personal RF-EMF microenvironmental measurements in multiple microenvironments have high representativeness and repeatability over time. The personal RF-EMF exposure levels (i.e. body and head exposures) demonstrated moderate to high correlations.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗