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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS2001

Relationship between radiation-induced aberrations in individual chromosomes and their DNA content: effects of interaction distance

PURPOSE: To study the effect of the interaction distance on the frequency of inter- and intrachromosome exchanges in individual chromosomes with respect to their DNA content. Assumptions: Chromosome exchanges are formed by misrejoining of two DNA double-strand breaks (DSB) induced within an interaction distance, d. It is assumed that chromosomes in G(0)/G(1) phase of the cell cycle occupy a spherical domain in a cell nucleus, with no spatial overlap between individual chromosome domains. RESULTS: Formulae are derived for the probability of formation of inter-, as well as intra-, chromosome exchanges relating to the DNA content of the chromosome for a given interaction distance. For interaction distances <1 microm, the relative frequency of interchromosome exchanges predicted by the present model is similar to that by Cigarran et al. (1998) based on the assumption that the probability of interchromosome exchanges is proportional to the "surface area" of the chromosome territory. The "surface area" assumption is shown to be a limiting case of d-->0 in the present model. The present model also predicts that the probability of intrachromosome exchanges occurring in individual chromosomes is proportional to their DNA content with correction terms. CONCLUSION: When the interaction distance is small, the "surface area" distribution for chromosome participation in interchromosome exchanges has been expected. However, the present model shows that for the interaction distance as large as 1 microm, the predicted probability of interchromosome exchange formation is still close to the surface area distribution. Therefore, this distribution does not necessarily rule out the formation of complex chromosomal aberrations by long-range misrejoining of DSB.

Non-programmatic↗
NASA NTRS1999

Effect of viewing distance on the generation of vertical eye movements during locomotion

Vertical head and eye coordination was studied as a function of viewing distance during locomotion. Vertical head translation and pitch movements were measured using a video motion analysis system (Optotrak 3020). Vertical eye movements were recorded using a video-based pupil tracker (Iscan). Subjects (five) walked on a linear treadmill at a speed of 1.67 m/s (6 km/h) while viewing a target screen placed at distances ranging from 0.25 to 2.0 m at 0. 25-m intervals. The predominant frequency of vertical head movement was 2 Hz. In accordance with previous studies, there was a small head pitch rotation, which was compensatory for vertical head translation. The magnitude of the vertical head movements and the phase relationship between head translation and pitch were little affected by viewing distance, and tended to orient the naso-occipital axis of the head at a point approximately 1 m in front of the subject (the head fixation distance or HFD). In contrast, eye velocity was significantly affected by viewing distance. When viewing a far (2-m) target, vertical eye velocity was 180 degrees out of phase with head pitch velocity, with a gain of 0. 8. This indicated that the angular vestibulo-ocular reflex (aVOR) was generating the eye movement response. The major finding was that, at a close viewing distance (0.25 m), eye velocity was in phase with head pitch and compensatory for vertical head translation, suggesting that activation of the linear vestibulo-ocular reflex (lVOR) was contributing to the eye movement response. There was also a threefold increase in the magnitude of eye velocity when viewing near targets, which was consistent with the goal of maintaining gaze on target. The required vertical lVOR sensitivity to cancel an unmodified aVOR response and generate the observed eye velocity magnitude for near targets was almost 3 times that previously measured. Supplementary experiments were performed utilizing body-fixed active head pitch rotations at 1 and 2 Hz while viewing a head-fixed target. Results indicated that the interaction of smooth pursuit and the aVOR during visual suppression could modify both the gain and phase characteristics of the aVOR at frequencies encountered during locomotion. When walking, targets located closer than the HFD (1.0 m) would appear to move in the same direction as the head pitch, resulting in suppression of the aVOR. The results of the head-fixed target experiment suggest that phase modification of the aVOR during visual suppression could play a role in generating eye movements consistent with the goal of maintaining gaze on targets closer than the HFD, which would augment the lVOR response.

NASA Discipline Neuroscience↗
NASA NTRS2009

LDPC Codes with Minimum Distance Proportional to Block Size

Low-density parity-check (LDPC) codes characterized by minimum Hamming distances proportional to block sizes have been demonstrated. Like the codes mentioned in the immediately preceding article, the present codes are error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels. The previously mentioned codes have low decoding thresholds and reasonably low error floors. However, the minimum Hamming distances of those codes do not grow linearly with code-block sizes. Codes that have this minimum-distance property exhibit very low error floors. Examples of such codes include regular LDPC codes with variable degrees of at least 3. Unfortunately, the decoding thresholds of regular LDPC codes are high. Hence, there is a need for LDPC codes characterized by both low decoding thresholds and, in order to obtain acceptably low error floors, minimum Hamming distances that are proportional to code-block sizes. The present codes were developed to satisfy this need. The minimum Hamming distances of the present codes have been shown, through consideration of ensemble-average weight enumerators, to be proportional to code block sizes. As in the cases of irregular ensembles, the properties of these codes are sensitive to the proportion of degree-2 variable nodes. A code having too few such nodes tends to have an iterative decoding threshold that is far from the capacity threshold. A code having too many such nodes tends not to exhibit a minimum distance that is proportional to block size. Results of computational simulations have shown that the decoding thresholds of codes of the present type are lower than those of regular LDPC codes. Included in the simulations were a few examples from a family of codes characterized by rates ranging from low to high and by thresholds that adhere closely to their respective channel capacity thresholds; the simulation results from these examples showed that the codes in question have low error floors as well as low decoding thresholds. As an example, the illustration shows the protograph (which represents the blueprint for overall construction) of one proposed code family for code rates greater than or equal to 1.2. Any size LDPC code can be obtained by copying the protograph structure N times, then permuting the edges. The illustration also provides Field Programmable Gate Array (FPGA) hardware performance simulations for this code family. In addition, the illustration provides minimum signal-to-noise ratios (Eb/No) in decibels (decoding thresholds) to achieve zero error rates as the code block size goes to infinity for various code rates. In comparison with the codes mentioned in the preceding article, these codes have slightly higher decoding thresholds.

Divsalar, Dariush↗
NASA NTRS2007

Optoelectronic System Measures Distances to Multiple Targets

An optoelectronic metrology apparatus now at the laboratory-prototype stage of development is intended to repeatedly determine distances of as much as several hundred meters, at submillimeter accuracy, to multiple targets in rapid succession. The underlying concept of optoelectronic apparatuses that can measure distances to targets is not new; such apparatuses are commonly used in general surveying and machining. However, until now such apparatuses have been, variously, constrained to (1) a single target or (2) multiple targets with a low update rate and a requirement for some a priori knowledge of target geometry. When fully developed, the present apparatus would enable measurement of distances to more than 50 targets at an update rate greater than 10 Hz, without a requirement for a priori knowledge of target geometry. The apparatus (see figure) includes a laser ranging unit (LRU) that includes an electronic camera (photo receiver), the field of view of which contains all relevant targets. Each target, mounted at a fiducial position on an object of interest, consists of a small lens at the output end of an optical fiber that extends from the object of interest back to the LRU. For each target and its optical fiber, there is a dedicated laser that is used to illuminate the target via the optical fiber. The targets are illuminated, one at a time, with laser light that is modulated at a frequency of 10.01 MHz. The modulated laser light is emitted by the target, from where it returns to the camera (photodetector), where it is detected. Both the outgoing and incoming 10.01-MHz laser signals are mixed with a 10-MHz local-oscillator to obtain beat notes at 10 kHz, and the difference between the phases of the beat notes is measured by a phase meter. This phase difference serves as a measure of the total length of the path traveled by light going out through the optical fiber and returning to the camera (photodetector) through free space. Because the portion of the path length inside the optical fiber is not ordinarily known and can change with temperature, it is also necessary to measure the phase difference associated with this portion and subtract it from the aforementioned overall phase difference to obtain the phase difference proportional to only the free-space path length, which is the distance that one seeks to measure. Therefore, the apparatus includes a photodiode and a circulator that enable measurement of the phase difference associated with propagation from the LRU inside the fiber to the target, reflection from the fiber end, and propagation back inside the fiber to the LRU. Because this phase difference represents twice the optical path length of the fiber, this phase difference is divided in two before subtraction from the aforementioned total-path-length phase difference. Radiation-induced changes in the photodetectors in this apparatus can affect the measurements. To enable calibration for the purpose of compensation for these changes, the apparatus includes an additional target at a known short distance, located inside the camera. If the measured distance to this target changes, then the change is applied to the other targets.

Liebe, Carl Christian↗
DOE OSTI2021

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

Abstract Background Estimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure features to predict the quality of protein models. Inter-residue distances are key information for predicting protein’s tertiary structures and therefore have good potentials to predict the quality of protein structural models. However, few methods have been developed to fully take advantage of predicted inter-residue distance maps to estimate the accuracy of a single protein structural model. Result We developed an attentive 2D convolutional neural network (CNN) with channel-wise attention to take only a raw difference map between the inter-residue distance map calculated from a single protein model and the distance map predicted from the protein sequence as input to predict the quality of the model. The network comprises multiple convolutional layers, batch normalization layers, dense layers, and Squeeze-and-Excitation blocks with attention to automatically extract features relevant to protein model quality from the raw input without using any expert-curated features. We evaluated DISTEMA’s capability of selecting the best models for CASP13 targets in terms of ranking loss of GDT-TS score. The ranking loss of DISTEMA is 0.079, lower than several state-of-the-art single-model quality assessment methods. Conclusion This work demonstrates that using raw inter-residue distance information with deep learning can predict the quality of protein structural models reasonably well. DISTEMA is freely at https://github.com/jianlin-cheng/DISTEMA

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Motor scaling by viewing distance of early visual motion signals during smooth pursuit

The geometry of gaze stabilization during head translation requires eye movements to scale proportionally to the inverse of target distance. Such a scaling has indeed been demonstrated to exist for the translational vestibuloocular reflex (TVOR), as well as optic flow-selective translational visuomotor reflexes (e.g., ocular following, OFR). The similarities in this scaling by a neural estimate of target distance for both the TVOR and the OFR have been interpreted to suggest that the two reflexes share common premotor processing. Because the neural substrates of OFR are partly shared by those for the generation of pursuit eye movements, we wanted to know if the site of gain modulation for TVOR and OFR is also part of a major pathway for pursuit. Thus, in the present studies, we investigated in rhesus monkeys whether initial eye velocity and acceleration during the open-loop portion of step ramp pursuit scales with target distance. Specifically, with visual motion identical on the retina during tracking at different distances (12, 24, and 60 cm), we compared the first 80 ms of horizontal pursuit. We report that initial eye velocity and acceleration exhibits either no or a very small dependence on vergence angle that is at least an order of magnitude less than the corresponding dependence of the TVOR and OFR. The results suggest that the neural substrates for motor scaling by target distance remain largely distinct from the main pathway for pursuit.

Non-NASA Center↗
NASA NTRS1996

Gravitational acceleration as a cue for absolute size and distance?

When an object's motion is influenced by gravity, as in the rise and fall of a thrown ball, the vertical component of acceleration is roughly constant at 9.8 m/sec2. In principle, an observer could use this information to estimate the absolute size and distance of the object (Saxberg, 1987a; Watson, Banks, von Hofsten, & Royden, 1992). In five experiments, we examined people's ability to utilize the size and distance information provided by gravitational acceleration. Observers viewed computer simulations of an object rising and falling on a trajectory aligned with the gravitational vector. The simulated objects were balls of different diameters presented across a wide range of simulated distances. Observers were asked to identify the ball that was presented and to estimate its distance. The results showed that observers were much more sensitive to average velocity than to the gravitational acceleration pattern. Likewise, verticality of the motion and visibility of the trajectory's apex had negligible effects on the accuracy of size and distance judgments.

NASA Discipline Space Human Factors↗
NASA NTRS2021

Tully-Fisher Distances and Dynamical Mass Constraints for 24 Host Galaxies of Reverberation-Mapped AGNs

We present Tully–Fisher distances for 24 active galactic nucleus (AGN) host galaxies with black hole mass (M(sub BH)) measurements from reverberation mapping, as well as the first calibration of the V-band Tully–Fisher relation. Combining our measurements of H I 21 cm emission with Hubble Space Telescope and ground-based optical and near-infrared images allows multiple distance measurements for 19 galaxies and single measurements for the remaining 5. Separation of the nucleus from its host galaxy via surface brightness decomposition yields galaxy-only luminosities, thus allowing measurements of the distance moduli free of contamination from the AGNs. For 14 AGN hosts, these are the first reported distances independent of redshift, and hence independent of peculiar velocities. For the remaining galaxies, we show good agreement between our distances and those previously reported from surface brightness fluctuations and Cepheids. We also determine the total galaxy mass enclosed within the estimated H I radius, which when compared to the baryonic content allows for constraints on the dark matter masses. We find a typical mass fraction of M(sub DM)/M(sub DYN) = 62%, and find significant correlations between M(sub BH)–M(sub DYN) and M(sub BH)–M(sub DM). Finally, we scale our galaxy radii based on estimated relationships between visible and halo radii and assume a flat rotation curve out to the halo radius to approximate M(sub HALO). Over the range of M(sub BH) and M(sub HALO) in this sample, we find good agreement with observationally constrained relationships between M(sub BH) and M(sub HALO) and with hydrodynamical simulations.

AGN host galaxies↗
DOE OSTI2021

$\mathrm{A}$ $\mathrm{CFT}$ distance conjecture

We formulate a series of conjectures relating the geometry of conformal manifolds to the spectrum of local operators in conformal field theories in d > 2 spacetime dimensions. We focus on conformal manifolds with limiting points at infinite distance with respect to the Zamolodchikov metric. Our central conjecture is that all theories at infinite distance possess an emergent higher-spin symmetry, generated by an infinite tower of currents whose anomalous dimensions vanish exponentially in the distance. Stated geometrically, the diameter of a non-compact conformal manifold must diverge logarithmically in the higher-spin gap. In the holographic context our conjectures are related to the Distance Conjecture in the swampland program. Interpreted gravitationally, they imply that approaching infinite distance in moduli space at fixed AdS radius, a tower of higher-spin fields becomes massless at an exponential rate that is bounded from below in Planck units. We discuss further implications for conformal manifolds of superconformal field theories in three and four dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Comparing Delay-, Distance-, and Cordon-Based Congestion Pricing Strategies Via Large-Scale Simulation

This study compares the impacts of delay-, distance-, and cordon-based congestion pricing strategies for Austin, Texas, using the POLARIS agent-based activity-based travel demand simulation model. This approach enables agent-level heterogeneity and realistic choice options (including destination, mode, and activity scheduling) for dynamic traffic assignment and congestion feedbacks across a major metro region, which are features lacking in past work. To ensure comparability, distance-based tolls were set to generate the same revenue as delay-based tolling of $3.5 M/day, averaging $1.17/resident/day or $0.42/vehicle-trip. Delay-based pricing delivers 44% lower network delay and 13% lower VHT compared to the no-toll baseline, levels unmatched by other pricing strategies. At the height of the AM peak, drivers pay up to $0.13/mile on average, though most links in the network remain untolled. Distance-based pricing is the most effective at reducing VMT (by 4%), but VHT reductions (of 6%) primarily stem from drivers selecting closer destinations, achieving only one-fourth the delay reduction of delay-based pricing. Across various implementations of delay- and distance-based pricing, the results suggest that spatial variations of tolls are far more important than temporal variations. Cordon tolls produce minimal impacts at the network-wide level, but offer substantial delay reductions inside the cordon. Other major findings include: 1) delay-based pricing increases trip-making during the PM peak period due to backward shifts in discretionary-activity start times by higher-income residents; and 2) tolls’ spatial impacts, including changes in network flows and tolls paid by residents, vary substantially between delay- and distance-based pricing strategies.

Agent-based modeling↗
DOE OSTI2021

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Abstract The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To further leverage the improved inter-residue distance predictions to enhance EMA, during the 2020 CASP14 experiment, we integrated several new inter-residue distance features with the existing model quality assessment features in several deep learning methods to predict the quality of protein structural models. According to the evaluation of performance in selecting the best model from the models of CASP14 targets, our three multi-model predictors of estimating model accuracy (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) achieve the averaged loss of 0.073, 0.079, and 0.081, respectively, in terms of the global distance test score (GDT-TS). The three methods are ranked first, second, and third out of all 68 CASP14 predictors. MULTICOM-DEEP, the single-model predictor of estimating model accuracy (EMA), is ranked within top 10 among all the single-model EMA methods according to GDT-TS score loss. The results demonstrate that inter-residue distance features are valuable inputs for deep learning to predict the quality of protein structural models. However, larger training datasets and better ways of leveraging inter-residue distance information are needed to fully explore its potentials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Constraining the distance to the North Polar Spur with Gaia DR2

ABSTRACT The North Polar Spur (NPS) is one of the largest structures observed in the Milky Way in both the radio and soft X-rays. While several predictions have been made regarding the origin of the NPS, modelling the structure is difficult without precise distance constraints. In this paper, we determine accurate distances to the southern terminus of the NPS and towards latitudes ranging up to 55°. First, we fit for the distance and extinction to stars towards the NPS using optical and near-infrared photometry and Gaia Data Release 2 astrometry. We model these per-star distance–extinction estimates as being caused by dust screens at unknown distances, which we fit for using a nested sampling algorithm. We then compare the extinction to the Spur derived from our 3D dust modelling with integrated independent measures from XMM–Newton X-ray absorption and H i column density measures. We find that we can account for nearly 100 per cent of the total column density of the NPS as lying within 140 pc for latitudes >26° and within 700 pc for latitudes <11°. Based on the results, we conclude that the NPS is not associated with the Galactic Centre or the Fermi bubbles. Instead, it is likely associated, especially at higher latitudes, with the Scorpius–Centaurus association.

Das, Kaustav K.↗
DOE OSTI2026

Extracting the Breakout Distance from the ECOT Trajectories: Gaussian Process Regression Approach

Enhanced Corner Turning (ECOT) experiments provide an important metric of performance of high explosive (HE) formulations. The breakout distance is a single scalar value that characterizes the corner turning efficiency of an HE. Extracting the breakout distance from the raw ECOT results, whether experimental or simulated, is a conceptually straightforward procedure which, however, is non-unique, especially in the presence of noise. More specifically, this procedure involves numerical smoothing and selecting particular values for parameters of this smoothing introduces human bias. In this work, we propose to use the Gaussian process regression to analyze ECOT results. This analysis involves the effective smoothing of the data, thus allowing for accurate extraction of the breakout distance. Most importantly, the parameters of this smoothing can be inferred from the ECOT data itself, rendering the approach effectively parameter-free and thus diminishing the human bias. An additional benefit of the Gaussian process regression, being a statistical inference method, is that not just the value of the breakout distance, but also its confidence interval can be extracted from the data. This report introduces the Gaussian process regression, as applied to ECOT, and demonstrates its usefulness by extracting the breakout distances for a selection of experimental and simulated data.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2024

Effect of Extinction on Quasar Luminosity Distances Determined from UV and X-Ray Flux Measurements

Abstract In Khadka et al., a sample of X-ray-detected reverberation-mapped quasars was presented and applied for the comparison of cosmological constraints inferred using two well-established relations in active galactic nuclei—the X-ray/UV luminosity ( L X – L UV ) relation and the broad-line region radius–luminosity ( R – L ) relation. L X – L UV and R – L luminosity distances to the same quasars exhibit a distribution of their differences that is generally asymmetric and positively shifted for the six cosmological models we consider. We demonstrate that this behavior can be interpreted qualitatively as arising as a result of the dust extinction of UV/X-ray quasar emission. We show that the extinction always contributes to the nonzero difference between L X – L UV -based and R – L -based luminosity distances and we derive a linear relationship between the X-ray/UV color index E X −UV and the luminosity-distance difference, which also depends on the value of the L X – L UV relation slope. Taking into account the median and the peak values of the luminosity-distance difference distributions, the average X-ray/UV color index falls in the range of E ¯ X − UV = 0.03 – 0.28 mag for the current sample of 58 sources. This amount of extinction is typical for the majority of quasars and can be attributed to the circumnuclear and interstellar media of host galaxies. After applying the standard hard X-ray and far-UV extinction cuts, heavily extincted sources are removed but overall the shift toward positive values persists. The effect of extinction on luminosity distances is more pronounced for the L X – L UV relation since the extinction of UV and X-ray emissions both contribute.

Astronomy & Astrophysics↗
NASA NTRS1971

The minimum distance approach to classification

The work to advance the state-of-the-art of miminum distance classification is reportd. This is accomplished through a combination of theoretical and comprehensive experimental investigations based on multispectral scanner data. A survey of the literature for suitable distance measures was conducted and the results of this survey are presented. It is shown that minimum distance classification, using density estimators and Kullback-Leibler numbers as the distance measure, is equivalent to a form of maximum likelihood sample classification. It is also shown that for the parametric case, minimum distance classification is equivalent to nearest neighbor classification in the parameter space.

Wacker, A. G.↗
NASA NTRS1974

Free distance bounds for convolutional codes

The best asymptotic bounds presently known on free distance for convolutional codes are presented from a unified point of view. Upper and lower bounds for both time-varying and fixed codes are obtained. A comparison is made between bounds for nonsystematic and systematic codes which shows that more free distance is available with nonsystematic codes. This result is important when selecting codes for use with sequential or maximum-likelihood (Viterbi) decoding since the probability of decoding error is closely related to the free distance of the code. An ancillary result, used in proving the lower bound on free distance for time-varying nonsystematic codes, furnishes a generalization of two earlier bounds on the definite decoding minimum distance of convolutional codes.

Costello, D. J., Jr.↗
NASA NTRS1977

Some rate 1/3 and 1/4 binary convolutional codes with an optimum distance profile

A tabulation of binary systematic convolutional codes with an optimum distance profile for rates 1/3 and 1/4 is given. A number of short rate 1/3 binary nonsystematic convolutional codes are listed. These latter codes are simultaneously optimal for the following distance measures: distance profile, minimum distance, and free distance; they appear attractive for use with Viterbi decoders. Comparisons with previously known codes are made.

Johannesson, R.↗