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NASA NTRS2003

The VISAR Process

The Video Image Stabilization And Registration (VISAR) process is an award winning video image processing software developed at NASA's Marshall Space Flight Center. VISAR has a wide variety of application areas where the refinement of digital video is needed. It is used to correct jitter, rotation, and zoom effects by registering and processing on individual image captures that are a part of normal video capturing. Its most prominent uses were the 1996 Olympic Bombing case and in identifying Saddam Hussein during the Iraq war. Based on first-hand knowledge, this paper describes the VISAR process, which consists of several steps designed to refine digital video using VISAR software. The process determines the differences between two video images so that one, or both, of the images can be changed in ways that make them match as well as possible. Corrections include changes in position (horizontal and vertical image shifts), changes in orientation (image rotation), and changes in magnification (image zoom). While much of the VISAR process is automated, in its current embodiment it requires the user to initially identify the area of interest and to reset a threshold parameter if the default gives unacceptable results. The basic process that is used is an old tried and true method that determines how well the two images match. This process is called cross-correlation. It gives a single number, the correlation coefficient, that is equal to 1.0 if the images are perfectly matched, is equal to 0.0 if the images have nothing in common, and is equal to -1.0 if one image is the negative of the other. This basic process is used by many image stabilization methods. With VISAR we use it in a manner that provides statistical information needed to best determine orientation and magnification.

Hathaway, David↗
NASA NTRS1992

Effect of antiorthostatic BedRest (BR) on GastroIntestinal Motility (GIM) of normal subjects

The combined effects of postural changes, fluid shifts and diuresis associated with the absence of the gravity vector may decrease gastrointestinal motility (GIM) during space flight. GIM can be estimated from the mouth to cecum transit time (MCTT) of orally administered lactulose (LAC); this test is used to assess changes in GIM in normal subjects and in patients with GI pathology and related disease conditions. Since bedrest (BR) mimics some of the physiological changes that occur during space flight, the effect of ten days of BR on GIM was evaluated from the MCTT of LAC. Methods: Subjects were 12 nonsmoking males between the ages of 35 and 50. After an 8-10 hour fast, subjects ingested Cephulac (registered) (20 g solution) with a low-fiber breakfast on four different days (45, 30, 25, and 20) before BR and on three separate days (4, 7, and 10) during BR. Breath-H2 concentrations were measured before and at 10 minute intervals for 4 hours after breakfast using a Quintron breathalyzer and MCTT was determined from these data. Results: MCTT ranged between 10 and 122 minutes during ambulation and 80 to 120 minutes during BR with means of 79 minutes and 122 minutes respectively. Conclusion: Mean MCTT during BR was 54 percent longer than during ambulation, suggesting that absorption and availability of orally administered medications and nutrients may be delayed or impaired as a result of decreased GIM during bedrest.

Putcha, L.↗
NASA NTRS1991

Perceiving the coherent movements of spatially-separated features

When a partially-occluded object is represented in an image, it is defined by a set of spatially-separated features that may be registered at different spatial scales. To understand the image, human vision must organize these fragmented optical features into common and distinct object surfaces. Although the common fate of moving features often is considered a primary source of reliable information for image segmentation, little is known of the visual system's capacity to discriminate the coherent relative movements of spatially-separated features. In a series of experiments, observers viewed elements whose movements were correlated (direction and magnitude) or were uncorrelated. Our results indicate that observers can discriminate the two types of movement about as well as they can detect any movement at all. Moreover, the ability to perceive coherent movements is maintained under a variety of conditions including differences in the elements' spatial frequency content, spatial position and contrast, and temporal phase shifts between the spatially-correlated displacements. These results suggest that coherent relative motion may be a fundamental source of information exploited by vision, despite considerable variability in the spatial and temporal characteristics of the individual features.

Mowafy, Lyn↗
NASA NTRS2014

Focal Gray Matter Plasticity as a Function of Long Duration Bedrest: Preliminary Results

Long duration spaceflight (i.e., 22 days or longer) has been associated with changes in sensorimotor systems, resulting in difficulties that astronauts experience with posture control, locomotion, and manual control. It is unknown whether and how spaceflight impacts sensorimotor brain structure and function, and whether such changes may potentially underlie behavioral effects. Long duration head down tilt bed rest has been used repeatedly as an exclusionary analog to study microgravity effects on the sensorimotor system [1]. Bed rest mimics microgravity in body unloading and bodily fluid shifts. We are currently testing sensorimotor function, brain structure, and brain function pre and post a 70‐day bed rest period. We will acquire the same measures on NASA crewmembers starting in 2014. Here we present the results of the first eight bed rest subjects. Subjects were assessed at 12 and 7 days before‐, at 7, 30, and ~70 days in‐, and at 8 and 12 days post 70 days of bed rest at the NASA bed rest facility, UTMB, Galveston, TX, USA. At each time point structural MRI scans (i.e., high resolution T1‐weighted imaging and Diffusion Tensor Imaging (DTI)) were obtained using a 3T Siemens scanner. Focal changes over time in gray matter density were assessed using the voxel based morphometry 8 (VBM8) toolbox under SPM. Focal changes in white matter microstructural integrity were assessed using tract based spatial statistics (TBSS) as part of the FMRIB software library (FSL). TBSS registers all DTI scans to standard space. It subsequently creates a study specific white matter skeleton of the major white matter tracts. Non‐parametric permutation based t‐tests and ANOVA's were used for voxel‐wise comparison of the skeletons. For both VBM and TBSS, comparison of the two pre bed rest measurements did not show significant differences. VBM analysis revealed decreased gray matter density in bilateral areas including the frontal medial cortex, the insular cortex and the caudate nucleus from pre to in bed rest. Over the same time period, there was an increase in gray matter density in the cerebellum, occipital, and parietal cortices. The majority of these changes did not recover from during to post bed rest. TBSS analyses will also be presented. Extended bed rest, which is an analog for microgravity, can result in gray matter changes and potentially in microstructural white matter changes in areas that are important for neuromotor behavior and cognition. These changes did not recover at two weeks post bed rest. These results have significant public health implications, and will also aid in interpretation of our future data obtained pre and post spaceflight. Whether the effects of bed rest wear off at longer times post bed rest, and if they are associated with behavior are important questions that warrant further research.

Koppelmans, V.↗
NASA NTRS1997

Efficacy of Code Optimization on Cache-based Processors

The current common wisdom in the U.S. is that the powerful, cost-effective supercomputers of tomorrow will be based on commodity (RISC) micro-processors with cache memories. Already, most distributed systems in the world use such hardware as building blocks. This shift away from vector supercomputers and towards cache-based systems has brought about a change in programming paradigm, even when ignoring issues of parallelism. Vector machines require inner-loop independence and regular, non-pathological memory strides (usually this means: non-power-of-two strides) to allow efficient vectorization of array operations. Cache-based systems require spatial and temporal locality of data, so that data once read from main memory and stored in high-speed cache memory is used optimally before being written back to main memory. This means that the most cache-friendly array operations are those that feature zero or unit stride, so that each unit of data read from main memory (a cache line) contains information for the next iteration in the loop. Moreover, loops ought to be 'fat', meaning that as many operations as possible are performed on cache data-provided instruction caches do not overflow and enough registers are available. If unit stride is not possible, for example because of some data dependency, then care must be taken to avoid pathological strides, just ads on vector computers. For cache-based systems the issues are more complex, due to the effects of associativity and of non-unit block (cache line) size. But there is more to the story. Most modern micro-processors are superscalar, which means that they can issue several (arithmetic) instructions per clock cycle, provided that there are enough independent instructions in the loop body. This is another argument for providing fat loop bodies. With these restrictions, it appears fairly straightforward to produce code that will run efficiently on any cache-based system. It can be argued that although some of the important computational algorithms employed at NASA Ames require different programming styles on vector machines and cache-based machines, respectively, neither architecture class appeared to be favored by particular algorithms in principle. Practice tells us that the situation is more complicated. This report presents observations and some analysis of performance tuning for cache-based systems. We point out several counterintuitive results that serve as a cautionary reminder that memory accesses are not the only factors that determine performance, and that within the class of cache-based systems, significant differences exist.

VanderWijngaart, Rob F.↗
NASA NTRS1976

Long-latency evoked potentials to irrelevant, deviant stimuli

Occasional shifts of loudness in a repetitive train of clicks elicited a late-positive wave (P3a) in nonattending subjects which peaked at a mean latency of 258 msec and had a frontocentral scalp distribution; P3a was typically preceded by an 'N2' component at 196 msec. The P3a wave was distinguishable from the longer-latency (378 msec) parietocentrally distributed 'P3b' wave that was evoked by the same stimulus in an actively attending subject, thus confirming the findings of Squires et al. (1975). Infrequently presented single sounds did not produce large or consistent N2-P3a components; the critical condition for the generation of an N2-P3a wave seemed to be that the infrequent sounds represent a deviation (intensity increment or decrement) from a repetitive background. Furthermore, increasing the repetition rate of the background clicks drastically reduced N1-P2 amplitude but had little effect on the amplitude of N2-P3a. This suggests that N2-P3a is not simply a delayed N1-P2 'vertex potential', but rather reflects the operation of a 'mismatch' detector, which registers deviations from an ongoing auditory background.

Snyder, E.↗
NASA NTRS2014

Focal Gray Matter Plasticity as a Function of Long Duration Head Down Tilted Bed Rest: Preliminary Results

Long duration spaceflight (i.e., 22 days or longer) has been associated with changes in sensorimotor systems, resulting in difficulties that astronauts experience with posture control, locomotion, and manual control. The microgravity environment is an important causal factor for spaceflight induced sensorimotor changes. Whether these sensorimotor changes are solely related to peripheral changes from reduced vestibular stimulation, body unloading, body fluid shifts or that they may be related to structural and functional brain changes is yet unknown. However, a recent study reported associations between microgravity and flattening of the posterior eye globe and protrusion of the optic nerve [1] possibly as the result of increased intracranial pressure due to microgravity induced bodily fluid shifts [3]. Moreover, elevated intracranial pressure has been related to white matter microstructural damage [2]. Thus, it is possible that spaceflight may affect brain structure and thereby cognitive functioning. Long duration head down tilt bed rest has been suggested as an exclusionary analog to study microgravity effects on the sensorimotor system [4]. Bed rest mimics microgravity in body unloading and bodily fluid shifts. In consideration of the health and performance of crewmembers both in- and post-flight, we are conducting a prospective longitudinal 70-day bed rest study as an analog to investigate the effects of microgravity on brain structure [5]. Here we present results of the first six subjects. Six subjects were assessed at 12 and 7 days before-, at 7, 30, and ~70 days in-, and at 8 and 12 days post 70 days of bed rest at the NASA bed rest facility in UTMB, Galveston, TX, USA. At each time point structural MRI scans (i.e., high resolution T1-weighted imaging and Diffusion Tensor Imaging (DTI)) were obtained using a 3T Siemens scanner. Focal changes over time in gray matter density were assessed using the voxel based morphometry 8 (VBM8) toolbox under SPM. Longitudinal processing in VBM8 includes linear registration of each scan to the mean of the subject and subsequently transforming all scans in to MNI space by applying the warp from the mean subject to MNI to the individual gray matter segmentations. Modulation was applied so that all images represented the volume of the original structure in native space. Voxel wise analysis was carried out on the gray matter images after smoothing, using a flexible factorial design with family wise error correction. Focal changes in white matter microstructural integrity were assessed using tract based spatial statistics (TBSS) as part of FMRIB software library (FSL). TBSS registers all DTI scans to standard space. It subsequently creates a study specific white matter skeleton of the major white matter tracts. For each subject, for each DTI metric (i.e. fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD)), the maximum value in a line perpendicular to the skeleton tract is projected to the skeleton. Non-parametric permutation based t-tests and ANOVA's were used for voxel-wise comparison of the skeletons. For both VBM and TBSS, comparison of pre bed rest measurements did not show significant differences. VBM analysis revealed decreased gray matter density in bilateral areas including the frontal medial cortex, the insular cortex and the caudate (see Figure) from 'pre to in bed rest'. Over the same time period, there was an increase in gray matter density in the cerebellum, occipital-, and parietal cortex, including the precuneus (see Figure). The majority of these changes did not recover from 'during to post bed rest'. TBSS analysis did not reveal significant changes in white matter microstructural integrity after correction for multiple comparisons. Uncorrected analyses (p<.015) revealed an increase in RD in the cerebellum and brainstem from pre bed rest to the first week in bed rest that did not recover post bed rest. Extended bed rest, which is an analog for microgravity, can result in gray matter changes and potentially in microstructural white matter changes in areas that are important for neuro motor behavior and cognition. These changes did not recover at two weeks post bed rest. Whether the effects of bed rest wear off at longer times post bed rest, and if they are associated with behavior are important questions that warrant further research.

Koppelmans, V.↗
DOE OSTI2025

Montane Conifer, Aspen, Meadow, and Sagebrush Metagenome Resolved Genomes and Traits in East River Watershed, Colorado, USA

Climate change is driving vegetation shifts in mountain watersheds, with unknown impacts on biogeochemical cycles. We hypothesize that these shifts will reshape soil microbiomes and associated biogeochemical processes. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed microbiome and microbial functional trait differences between soils under conifer, aspen, forby meadows, and sagebrush across the East River Watershed, CO, controlling for elevation and aspect.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from soils 0-20cm in depth across three locations in the watershed—Headwaters, Upper Reaches, and Lower Reaches from August 3-11th 2016. Each location was further subdivided into two blocks, with one block on a west facing aspect, and two on the east aspect of the valley. Within blocks, two samples per vegetation type were taken (one at each depth). This resulted in 66 samples, which were sequenced at JGI and can be found under the Joint Genome Institute (JGI) Genomes Online Database (GOLD) sequencing project Gs0118068. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>75%) and contamination (<25%), and dereplicated at 95% ANI using drep. The dataset includes a zip file of 687 genomes (Vegtype_MAGS.zip), the accession numbers for the underlying metagenomes, a csv file with MAG quality metrics and taxonomy from Genome Taxonomy Database (GTDB) and National Center for Biotechnology Information (NCBI) taxonomic representative genome proteins (EastRiver_Vegtype_drep_genome_info.csv), and a file containing MAG quality metrics and taxonomy (gtdb_drep_bin_taxonomy.csv). The dataset additionally includes a sample metadata file (EastRiver_Vegtype_sample_metadata.csv), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a Google KML file for the sampled locations (sample_collection_sites.kml), a location metadata file (locations.csv), a file-level metadata file (flmd.csv), and a data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗