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At least 217 records · Page 12

All sources NASA NTRS DOE OSTI

DOE OSTI2015

Structural integration in hypoxia-inducible factors

The hypoxia-inducible factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating transcriptional programs in erythropoiesis, angiogenesis and metabolism. These programs promote the growth and progression of many tumours, making HIFs attractive anticancer targets. Transcriptionally active HIFs consist of HIF-alpha and ARNT (also called HIF-1 beta) subunits. Here we describe crystal structures for each of mouse HIF-2 alpha-ARNT and HIF-1 alpha-ARNT heterodimers in states that include bound small molecules and their hypoxia response element. A highly integrated quaternary architecture is shared by HIF-2 alpha-ARNT and HIF-1 alpha-ARNT, wherein ARNT spirals around the outside of each HIF-alpha subunit. Five distinct pockets are observed that permit small-molecule binding, including PAS domain encapsulated sites and an interfacial cavity formed through subunit heterodimerization. The DNA-reading head rotates, extends and cooperates with a distal PAS domain to bind hypoxia response elements. HIF-alpha mutations linked to human cancers map to sensitive sites that establish DNA binding and the stability of PAS domains and pockets.

Wu, Dalei↗

NASA NTRS1972

Coordination and establishment of centralized facilities and services for the University of Alaska ERTS survey of the Alaskan environment

The author has identified the following significant results. Specifications have been prepared for the engineering design and construction of a digital color display unit which will be used for automatic processing of ERTS data. The color display unit is a disk refresh memory with computer interfaced input and a color cathode ray tube output display. The system features both analog and digital post disk data manipulation and a versatile color coding device suitable for displaying not only images, but also computer generated graphics such as diagrams, maps, and overlays. Input is from IBM compatible 9 track, 800 BPI tapes, as generated by an IBM 360 computer. ERTS digital tapes are read into the 360, where various analyses such as maximum likelihood classification are performed and the results are written on a magnetic tape which is the input to the color display unit. The greatest versatility in the data manipulation area is provided by the minicomputer built into the color display unit, which is off-line from the main 360 computer. The minicomputer is able to read any line from the refresh disk and place it in its 4K-16 bit memory. Considerable flexibility is available for post-processing enhancement of images by the investigator.

Belon, A. E.↗

NASA NTRS1974

Scientific and economic potential of the SEASAT Program

The SEASAT satellite system is planned as a user-oriented system for timely monitoring of global ocean dynamics and mapping the global ocean geoid. The satellite instrumentation and modular concept are discussed. Operational data capabilities will include oceanographic data services, direct satellite read-out to users, and conversational retrieval and analysis of stored data. A case-study technique, generalized through physical and econometric modeling, indicates potential economic benefit from SEASAT to users in the following areas: ship routing, iceberg reconnaissance, arctic operations, Alaska pipeline ship link, and off-shore oil production.

Mccandless, S. W.↗

DOE OSTI2024

Interpreting the spatial distribution of soil properties with a physically-based distributed hydrological model

Digital soil maps are commonly data-driven as the development of physically-based models for soil mapping is difficult due to the complexity of soils. However, physically-based hydrologic models have been successful in simulating water dynamics. Since water movement is a major driver of pedogenesis, the physical rules that govern water movement might help explain and predict the spatial variation of soil properties. Here, we demonstrate the novel use of a physically-based, distributed hydrologic model to inform the spatial distribution of soil properties. The Distributed Hydrology Soil Vegetation Model (DHSVM) was utilized to simulate soil moisture content (SM) and water table depth (WTD) in two hillslope catchments under pasture and forest management wherein hydrologic model outputs were then compared with soil properties measured in situ. SM sensors and wells were installed in both catchments to validate simulations of soil water movement via Nash-Sutcliffe Efficiency (E). In-situ observations were made at 87 sites within both catchments to study the connection between simulated water movement (SM and WTD) and observed soil properties, namely the depth and thickness of the argillic (Bt), fragic (Btx), and C horizons, and the depth of redoximorphic features. The simulated time series of SM and WTD were also clustered per season using Dynamic Time Warping (DTW), which identified similarity among time series at varying timescales. Model validation suggested that simulations of surficial SM (0–20 cm) were reasonable (E = 0.45), however, simulated subsurface SM (45–60 cm) and WTD were not sufficiently accurate. The thickness of Btx horizons were spatially grouped into different populations by SM clusters from every season except spring. For the other properties, only SM dynamics of specific seasons grouped into significantly different populations, suggesting that the explanatory power of simulated water movement varies seasonally and was greater during winter. Here, we show clusters of simulated SM separated soil properties into statistically different populations, showing that hydrologic models could inform areas that followed different water dynamics related to pedogenic trajectories and related biogeochemical processes not necessarily simulated by the model. As such, physically-based modeling of water dynamics can, therefore, inform and advance digital soil mapping by linking water movement patterns stemming from hydrologic model outputs to spatial patterns of soil properties and pedogenesis.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2003

Three-Dimensional Venturi Sensor for Measuring Extreme Winds

A three-dimensional (3D) Venturi sensor is being developed as a compact, rugged means of measuring wind vectors having magnitudes of as much as 300 mph (134 m/s). This sensor also incorporates auxiliary sensors for measuring temperature from -40 to +120 F (-40 to +49 C), relative humidity from 0 to 100 percent, and atmospheric pressure from 846 to 1,084 millibar (85 to 108 kPa). Conventional cup-and-vane anemometers are highly susceptible to damage by both high wind forces and debris, due to their moving parts and large profiles. In addition, they exhibit slow recovery times contributing to an inaccurately high average-speed reading. Ultrasonic and hot-wire anemometers overcome some of the disadvantages of the cup and-vane anemometers, but they have other disadvantageous features, including limited dynamic range and susceptibility to errors caused by external acoustic noise and rain. In contrast, the novel 3D Venturi sensor is less vulnerable to wind damage because of its smaller profile and ruggedness. Since the sensor has no moving parts, it provides increased reliability and lower maintenance costs. It has faster response and recovery times to changing wind conditions than traditional systems. In addition, it offers wide dynamic range and is expected to be relatively insensitive to rain and acoustic energy. The Venturi effect in this sensor is achieved by the mirrored double-inflection curve, which is then rotated 360 to create the desired detection surfaces. The curve is optimized to provide a good balance of pressure difference between sensor ports and overall maximum fluid velocity while in the shape. Four posts are used to separate the two shapes, and their size and location were chosen to minimize effects on the pressure measurements. The 3D Venturi sensor has smart software algorithms to map the wind pressure exerted on the surfaces of the design. Using Bernoulli's equation, the speed of the wind is calculated from the differences among the pressure readings at the various ports. The direction of the wind is calculated from the spatial distribution and magnitude of the pressure readings. All of the pressure port sizes and locations have been optimized to minimize measurement errors and to reside in areas demonstrating a stable pressure reading proportional to the velocity range.

Zysko, Jan A.↗

NASA NTRS1985

Early evaluation of Thematic Mapper data for coastal process studies

Two sets of TM data taken over the ocean off the coast of the Southeastern U.S. Bight were studied for the applicability of TM data to marine environments. First, the results of applying TM and TMS data to determine chlorophyll concentration in the ocean are presented. Chlorophyll quantification in the range of 0.5 to 2.0 mg/cu m was achieved by taking the ratio of TM band-1/band-2. Second, the results of applying TM band-6 data to monitor sea surface temperature are described. A comparison of TM data with AVHRR data shows TM readings coincide with AVHRR data within a scatter of 0.5 deg C in most of the areas studied. Lastly, the results of a technique to map the water depths of coral reefs in the Great Bahama Bank are demonstrated. Depths from 0 to 20 meters were delineated using TM band-1. The classification accuracy and origins of anomalous depth points are discussed.

Kim, H. H.↗

DOE OSTI2022

Accelerating shared file checkpoint with local burst buffers

A data management system and method for accelerating shared file checkpointing. Written application data is aggregated in an application data file created in a local burst buffer memory at a compute node, and an associated data mapping built index to maintain information related to the offsets into a shared file at which segments of the application data is to be stored in a parallel file system, and where in the buffer those segments are located. The node asynchronously transfers a data file containing the application data and the associated data mapping index to a file server for shared file storage. The data management system and method further accelerates shared file checkpointing in which a shared file, together with a map file that specifies how the shared file is to be distributed, is asynchronously transferred to local burst buffer memories at the nodes to accelerate reading of the shared file.

Gooding, Thomas↗

NASA NTRS2013

Mapping Electrical Crosstalk in Pixelated Sensor Arrays

The effects of inter pixel capacitance in a pixilated array may be measured by first resetting all pixels in the array to a first voltage, where a first image is read out, followed by resetting only a subset of pixels in the array to a second voltage, where a second image is read out, where the difference in the first and second images provide information about the inter pixel capacitance. Other embodiments are described and claimed.

Seshadri, Suresh↗

NASA NTRS2017

Mapping Electrical Crosstalk in Pixelated Sensor Arrays

Seshadri, Suresh↗

DOE OSTI2021

PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R

Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of MS data is hindered by proprietary proteomics visualization software designed for particular workflows and academic software that lack visualization tools. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search tools, labelling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing) is available for easy local installation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2019

File transfers between machines without target CPU intervention

Techniques for transferring files between machines include creating a zero-length target file on non-volatile storage, truncating the file to a desired size, and allocating storage on the non-volatile storage for each block of the target file. The technique also includes determining a logical block address (LBA) for each location in the target file. The technique further includes sending a request to an input/output (I/O) node to transfer a source file to the non-volatile storage, where the request includes a mapping between the LBAs and file offsets. The technique includes opening the source file and a block device at the I/O node. The technique further includes reading each block from the source file and writing each block to the target file on the non-volatile storage utilizing the block device, and then closing the source file and the block device.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Assessment of attenuation correction for myocardial PET imaging using combined PET/MRI

Objective: To evaluate the frequency of artifacts in MR-based attenuation correction (AC) maps and their impact on the quantitative accuracy of PET-based flow and metabolism measurements in a cohort of consecutive heart failure patients undergoing combined PET/MR imaging. Methods: Myocardial viability studies were performed in 20 patients following a dual-tracer protocol involving the assessment of myocardial perfusion ({sup 13}N-NH{sub 3}: 813 ± 86 MBq) and metabolism ({sup 18}F-FDG: 335 ± 38 MBq). All acquisitions were performed using a fully-integrated PET/MR system, with standard DIXON-attenuation correction (DIXON-AC) mapping for each PET scan. All AC maps were examined for spatial misalignment with the emission data, total lung volume, susceptibility artifacts, and tissue inversion (TI). Misalignment and susceptibility artifacts were corrected using rigid co-registration and retrospective filling of the susceptibility-induced gaps, respectively. The effects of the AC artifacts were evaluated by relative difference measures and perceived changes in clinical interpretations. Results: Average respiratory misalignment of (7 ± 4) mm of the PET-emission data and the AC maps was observed in 18 (90%) patients. Substantial changes in the lung volumes of the AC maps were observed in the test–retest analysis (ratio: 1.0 ± 0.2, range: 0.8-1.4). Susceptibility artifacts were observed in 10 (50%) patients, while six (30%) patients had TI artifacts. Average differences of 14 ± 10% were observed for PET images reconstructed with the artifactual AC maps. The combined artifact effects caused false-positive findings in three (15%) patients. Conclusion: Standard DIXON-AC maps must be examined carefully for artifacts and misalignment effects prior to AC correction of cardiac PET/MRI studies in order to avoid misinterpretation of biased perfusion and metabolism readings from the PET data.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2021

Annealing of focused ion beam damage in gold microcrystals: an in situ Bragg coherent X-ray diffraction imaging study

Focused ion beam (FIB) techniques are commonly used to machine, analyse and image materials at the micro- and nanoscale. However, FIB modifies the integrity of the sample by creating defects that cause lattice distortions. Methods have been developed to reduce FIB-induced strain; however, these protocols need to be evaluated for their effectiveness. Here, non-destructive Bragg coherent X-ray diffraction imaging is used to study the in situ annealing of FIB-milled gold microcrystals. Two non-collinear reflections are simultaneously measured for two different crystals during a single annealing cycle, demonstrating the ability to reliably track the location of multiple Bragg peaks during thermal annealing. The thermal lattice expansion of each crystal is used to calculate the local temperature. This is compared with thermocouple readings, which are shown to be substantially affected by thermal resistance. To evaluate the annealing process, each reflection is analysed by considering facet area evolution, cross-correlation maps of the displacement field and binarized morphology, and average strain plots. The crystal's strain and morphology evolve with increasing temperature, which is likely to be caused by the diffusion of gallium in gold below ~280°C and the self-diffusion of gold above ~280°C. The majority of FIB-induced strains are removed by 380–410°C, depending on which reflection is being considered. These observations highlight the importance of measuring multiple reflections to unambiguously interpret material behaviour.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Securing 3D NAND Without Density Loss via In-Situ Encryption Using a Single Transistor XOR Cell

In this article, we push lightweight XOR-based in-situ encryption to extreme density by proposing a singletransistor XOR memory cell and applying it to 3D NAND, enabling secure data storage without density loss. Using a ferroelectric field-effect transistor (FeFET) as an example technology, we demonstrate that: i) a single-transistor memory can realize the XOR function by exploiting the ability to charge the source and drain separately and control current flow direction, eliminating the need for conventional encrypted cells that rely on complementary devices; ii) with a XOR-based cipher, encryption and decryption can be mapped to in-situ array operations, where ciphertext is stored as the threshold voltage (VTH) states of FeFETs in a NAND string, and decryption is achieved through read operations using key-dependent complementary source/drain bias; iii) the proposed technique is scalable to multi-level cell (MLC) storage by encrypting and decrypting data bit by bit; iv) using an integrated NAND FeFET array, we experimentally demonstrate encryption and decryption operations for both single-level cell (SLC) and MLC storage; v) systemlevel benchmarking shows that the proposed technique achieves 48× and 278× improvements in encryption and decryption throughput, respectively, compared to AES.

36 MATERIALS SCIENCE↗

NASA NTRS2019

Space Communications and Navigation Validation: Extracting Data for the Strategic Center for Networking, Integration, and Communications Scheduling Algorithms

Efficiency in communication system architecture performance between Space Communications and Navigation (SCaN) assets and missions is crucial, as space communication is varied, complex, and often not utilized to its full potential. The SCaN Strategic Center for Networking, Integration, and Communications (SCENIC) new scheduling algorithms, which are designed to simulate the allocation of resources between SCaN assets and missions, have the potential to simulate an increase of this efficiency; however, they require real-world data to be validated against. The purpose of this project was to extract said validation data, which details the frequency and duration of utilized contact windows between missions and assets in the Near Earth Network (NEN), Space Network (SN), and Deep Space Network (DSN). Stored as images in daily operations summaries (DOSs), the tabular data existed in a variety of file formats such as.pdf, .docx, and .doc. Since the tables were stored as images, ABBYY® FineReader® (ABBYY Software Ltd.) optical character recognition (OCR) was implemented, which is a proprietary software that reads images from text. The comma separated value (CSV) output was utilized as input to a series of MATLAB® (The MathWorks, Inc.) methods for reformatting, at which point it was ready to be machine-read. Finally, the results were converted to a Microsoft Excel format for human readability. Along with being used for validation purposes, the data will also be used to map equipment degradation as a function of time to analyze the reliability of network assets.

Kontur, Noah P.↗

DOE OSTI2014

Reader set encoding for directory of shared cache memory in multiprocessor system

In a parallel processing system with speculative execution, conflict checking occurs in a directory lookup of a cache memory that is shared by all processors. In each case, the same physical memory address will map to the same set of that cache, no matter which processor originated that access. The directory includes a dynamic reader set encoding, indicating what speculative threads have read a particular line. This reader set encoding is used in conflict checking. A bitset encoding is used to specify particular threads that have read the line.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Using the Model Perennial Grass Brachypodium sylvaticum to Engineer Resistance to Multiple Abiotic Stresses

We are using the perennial model grass Brachypodium sylvaticum to identify combinations of transgenes that enhance tolerance to multiple, simultaneous abiotic stresses. The most successful transgene combinations will ultimately be used to create improved switchgrass (Panicum virgatum L.) cultivars. To further develop B. sylvaticum as a perennial model grass, and facilitate our planned transcriptional profiling, we are sequencing and annotating the genome. We have generated ~40x genome coverage using PacBio sequencing of the largest possible size selected libraries (18, 22, 25 kb). Our initial assembly using only long-read sequence contained 320 Mb of sequence with an N50 contig length of 315 kb and an N95 contig length of 40 kb. This assembly consists of 2,430 contigs, the largest of which was 1.6 Mb. The estimated genome size based on c-values is 340 Mb indicating that about 20 Mb of presumably repetitive DNA remains yet unassembled. Significantly, this assembly is far superior to an assembly created from paired-end short-read sequence, ~100x genome coverage. The short-read-only assembly contained only 226 Mb of sequence in 19k contigs. To aid the assembly of the scaffolds into chromosome-scale assemblies we produced an F2 mapping population and have genotyped 480 individuals using a genotype by sequence approach. One of the reasons for using B. sylvaticum as a model system is to determine if the transgenes adversely affect perenniality and winter hardiness. Toward this goal, we examined the freezing tolerance of wild type B. sylvaticum lines to determine the optimal conditions for testing the freezing tolerance of the transgenics. A survey of seven accessions noted significant natural variation in freezing tolerance. Seedling or adult Ain-1 plants, the line used for transformation, survived an 8 hour challenge down to -6 oC and 50% survived a challenge down to -9 oC. Thus, we will be able to easily determine if the transgenes compromise freezing tolerance. In the effort to develop biotechnological tools for perennial grass improvement, we have completed the transformation of B. sylvaticum with constructs containing 20 genes shown to be associated with enhanced abiotic stress tolerance in monocots. In addition, we have transformed plants with constructs containing a combination of genes (i.e. SARK::IPT- Ubi::HSR1::Ubi::NHX1) in order to simultaneously overexpress genes associated with drought + heat tolerance + salt tolerance. We generated single copy insert T1 lines for all constructs and the generation and bulking of homozygous T2 lines is well underway. In addition to our B. sylvaticum transgenics, we transformed B. distachyon with many of the same genes. Some of the transgenic B. distachyon plants subjected to a combined stress of both drought and salinity were able to produced higher yields than wild type plants. Our results indicate a great potential for the development of grasses with improved performance and yield in water-limited areas.

Gordon, Sean↗