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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Parallelizing Single Source Shortest Path with OpenSHMEM

Single Source Shortest Path (SSSP) is one of the widely occurring graph problems where the paths are discovered from an origin vertex to all other vertices in the graph. In this paper, we discuss our experience parallelizing SSSP using OpenSHMEM. We start with the serial Dijkstra and Bellman-Ford algorithms, parallelize these algorithms, and adapt them to the Partitioned Global Address Space (PGAS) programming model. We implement the parallel algorithms using OpenSHMEM and introduce a series of optimizations to achieve higher scaling and performance characteristics. The implementation is evaluated on Titan with various graphs including synthetic Recursive Matrix (R-MAT) and small-world network graphs as well as real-world graphs from Facebook, Twitter, LiveJournal, and the road maps of California and Texas.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Delaunay walk for fast nearest neighbor: accelerating correspondence matching for ICP

Point set registration algorithms such as Iterative Closest Point (ICP) are commonly utilized in time-constrained environments like robotics. Finding the nearest neighbor of a point in a reference 3D point set is a common operation in ICP and frequently consumes at least 90% of the computation time. We introduce a novel approach to performing the distance-based nearest neighbor step based on Delaunay triangulation. This greedy algorithm finds the nearest neighbor of a query point by traversing the edges of the Delaunay triangulation created from a reference 3D point set. Our work integrates the Delaunay traversal into the correspondences search of ICP and exploits the iterative aspect of ICP by caching previous correspondences to expedite each iteration. An algorithmic analysis and comparison is conducted showing an order of magnitude speedup for both serial and vector processor implementation.

3d point cloud processing↗
DOE OSTI2015

Three-Dimensional Imaging of Lipids and Metabolites in Tissues by Nanospray Desorption Electrospray Ionization Mass Spectrometry

Abstract Three-dimensional (3D) imaging of tissue sections is a new frontier in mass spectrometry imaging (MSI). Here we report on fast 3D imaging of lipids and metabolites associated with mouse uterine decidual cells and embryo at the implantation site on day 6 of pregnancy. 2D imaging of 16-20 serial tissue sections deposited on the same glass slide was performed using nanospray desorption electrospray ionization (nano-DESI) – an ambient ionization technique that enables sensitive localized analysis of analytes on surfaces without special sample pre-treatment. In this proof-of-principle study, nano-DESI was coupled to a high-resolution Q-Exactive instrument operated at high repetition rate of >5 Hz with moderate mass resolution of 35,000 (m/Δm at m/z 200), which enabled acquisition of the entire 3D image with a spatial resolution of ~150 μm in less than 4.5 hours. The results demonstrate localization of acetylcholine in the primary decidual zone (PDZ) of the implantation site throughout the depth of the tissue examined, indicating an important role of this signaling molecule in decidualization. Choline and phosphocholine – metabolites associated with cell growth – are enhanced in the PDZ and abundant in other cellular regions of the implantation site. Very different 3D distributions were obtained for fatty acids (FA), oleic acid and linoleic acid (FA 18:1 and FA 18:2), differing only by one double bond. Localization of FA 18:2 in the PDZ indicates its important role in decidualization while FA 18:1 is distributed more evenly throughout the tissue. In contrast, several lysophosphatidylcholines (LPC) observed in this study show donut-like distributions with localization around the PDZ. Complementary distributions with minimal overlap were observed for LPC 18:0 and FA 18:2 while the 3D image of the potential precursor phosphatidylcholine (PC 36:2) showed a significant overlap with both LPC 18:0 and FA 18:2.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC–ESI-MS–MS

Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections using a fully automated droplet-based liquid microjunction surface sampling-HPLC-ESI-MS/MS system for spatially resolved sampling, HPLC separation, and mass spectral detection. Excellent correlation was found between the protein distribution data obtained with this droplet-based liquid microjunction surface sampling-HPLC-ESI-MS/MS system and those data obtained with matrix assisted laser desorption ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland. AVP was most abundant in the posterior pituitary gland region (neurohypophysis) and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH secreting adenomas and in normal anterior adenohypophysis compared to non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis as anticipated. This work demonstrates that a fully automated droplet-based liquid microjunction surface sampling system coupled to HPLC-ESI-MS/MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, such as AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity and specificity of the current methodology support the potential of this basic technology with further advancement for assisting surgical decision-making.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Transnasal stent-assisted targeting technique for percutaneous jejunostomy placement in patients with hiatal hernias

Purpose: To report the transnasal stent-assisted targeting technique for percutaneous jejunostomy placement in patients with hiatal hernias. Materials and methods: Four patients, including three (75%) females and one (25%) male, with mean age of 77.5 years (range 73–78 years), and with a hiatal hernia and intrathoracic stomach precluding gastrostomy placement and loop snare placement into the mid-jejunum underwent the transnasal stent-assisted targeting technique for percutaneous jejunostomy placement. In all patients, a duodenal stent was inserted into the jejunum in a transnasal fashion. The stent was partially unsheathed in an anterior loop of jejunum and percutaneously targeted using an 18-gauge needle through which a guidewire was advanced, trapped within the stent, and removed through the nose. The tract was serially dilated and a jejunostomy was placed. Technical success, procedure time, fluoroscopy time, radiation exposure, complications, time to enteral feeding, and follow-up were recorded. Results: Technical success was 100% (4/4) with all four patients requiring only one needle pass before successful jejunal cannulation. Mean procedure time was 108 min. Mean fluoroscopy time was 44 min. Mean dose area product was 3969.3 μGym{sup 2}. No minor or major complications occurred. All four patients received enteral feeding one day after the procedure. Mean follow-up was 366 days. Conclusion: The transnasal stent-assisted targeting technique is a novel method for primary jejunostomy placement in patients with hiatal hernias.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Identification of the feeding arteries of hepatocellular carcinomas by performing dual arterial phase CT during pre-transarterial chemoembolization angiography

Purpose: This study evaluated the usefulness of performing dual arterial phase computed tomography (CT) during pre-transarterial chemoembolization (TACE) angiography for identifying the feeding arteries of hepatocellular carcinomas (HCC). Materials and methods: Dual arterial phase CT was performed during pre-TACE angiography in 73 patients with 139 HCC. Ten HCC underwent this procedure twice, so the total number of examined HCC was 149. Early and late arterial phase images were obtained 6 seconds after injection of an iodinated contrast material serially during a single breath-hold. The feeding artery was defined as the branch of the hepatic artery that was connected to the enhanced areas of the tumor. For HCC that could not be visualized on the early arterial phase images, fusion images superimposing the early and late arterial phase images were constructed. Furthermore, technical success defined as successful catheterization of the subsegmental or more distal feeding artery was evaluated. Results: The feeding artery was correctly identified on dual arterial phase CT in 146 of the 149 tumors (98.0%). In two HCC, the feeding arteries could not be identified due to severe motion artifacts, and in one, due to the presence of anastomosis between the right and left hepatic arteries. Catheterization of the subsegmental feeding artery was successful in all TACE procedures (technical success rate: 100%). Conclusion: Performing dual arterial phase CT during angiography appears to be useful for identifying the feeding arteries of HCC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

ViennaX: a parallel plugin execution framework for scientific computing

We present the free open source plugin execution framework ViennaX for modularizing and parallelizing scientific simulations. In general, functionality is abstracted by the notion of a task, which is implemented as a plugin. The plugin system facilitates the utilization of both, already available functionality as well as new implementations. Each task can define arbitrary data dependencies which are used by ViennaX to build a task graph. The framework supports the execution of this dependence graph based on the message passing interface in either a serial or a parallel fashion. The applied modular approach allows for defining highly flexible simulations, as plugins can be easily exchanged. The framework's general design as well as implementation details are discussed. Applications based on the Mandelbrot set and the solution of a partial differential equation are investigated, and performance results are shown.

Weinbub, Josef↗
DOE OSTI2017

Climate controls over ecosystem metabolism: insights from a fifteen-year inductive artificial neural network synthesis for a subalpine forest

Eddy covariance (EC) datasets have provided insight into climate determinants of net ecosystem productivity (NEP) and evapotranspiration (ET) in natural ecosystems for decades, but most EC studies were published in serial fashion such that one study’s result became the following study’s hypothesis. Our approach reflects the hypothetico-deductive process by focusing on previously derived hypotheses. A synthesis of this type of sequential inference reiterates subjective biases and may amplify past assumptions about the role, and relative importance, of cont rols over ecosystem metabolism. Long-term EC datasets facilitate an alternative approach to synthesis: the use of inductive data-based analyses to re-examine past deductive studies of the same ecosystem. Here we examined the seasonal climate determinants of NEP and ET by analyzing a 15-year EC time-series from a subalpine forest using an ensemble of Artificial Neural Networks (ANNs) at the half-day (daytime/nighttime) time-step. We also extracted relative rankings of climate drivers and driver–response relationships directly from the dataset with minimal a priori assumptions. The ANN analysis revealed temperature variables as primary climate drivers of NEP and daytime ET, when all seasons are considered, consistent with the assembly of past studies. New relations uncovered by the ANN approach include the role of soil moisture in driving daytime NEP during the snowmelt period, the nonlinear response of NEP to temperature across seasons, and the low relevance of summer rainfall for NEP or ET at the same daytime/nighttime time step. These new results offer a more complete perspective of climate–ecosystem interactions at this site than traditional deductive analyses alone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Analysis and modeling of Nannochloropsis growth in lab, greenhouse, and raceway experiments

Efficient production of algal biofuels could reduce dependence on foreign oil by providing a domestic renewable energy source. Moreover, algae-based biofuels are attractive for their large oil yield potential despite decreased land use and natural resource (e.g., water and nutrients) requirements compared to terrestrial energy crops. Important factors controlling algal lipid productivity include temperature, nutrient availability, salinity, pH, and the light-to-biomass conversion rate. Here, computational approaches allow for inexpensive predictions of algae growth kinetics for various bioreactor sizes and geometries without the need for multiple, expensive measurement systems. Parametric studies of algal species include serial experiments that use off-line monitoring of growth and lipid levels. Such approaches are time consuming and usually incomplete, and studies on the effect of the interaction between various parameters on algal growth are currently lacking. However, these are the necessary precursors for computational models, which currently lack the data necessary to accurately simulate and predict algae growth. In this work, we conduct a lab-scale parametric study of the marine alga Nannochloropsis salina and apply the findings to our physics-based computational algae growth model. We then compare results from the model with experiments conducted in a greenhouse tank and an outdoor, open-channel raceway pond. Results show that the computational model effectively predicts algae growth in systems across varying scale and identifies the causes for reductions in algal productivities. Applying the model facilitates optimization of pond designs and improvements in strain selection.

09 BIOMASS FUELS↗
DOE OSTI2017

Effect of Varying Filler Concentration on Zinc Oxide Nanoparticle Embedded Chitosan Films as Potential Food Packaging Material

Prevailing scenario of non-biodegradable food packaging materials worldwide was the motivation for this research. More than half of the packaging materials used today are non-biodegradable and lack one or the other feature that keeps it from being an ideal food packaging material. Based on the current need of food grade packaging materials, the present study illustrates the amelioration of the properties of biodegradable chitosan films with the incorporation of zinc oxide (ZnO) nanoparticles in varying concentration. The ZnO nanoparticles (ZnONPs) used as fillers in the chitosan films were synthesized by supersaturation method. They were characterized using UV–visible spectrophotometry, X-ray diffraction and field emission scanning electron microscopy (FE-SEM). The particles were observed to be around 100–200 nm in size. The chitosan films with varying concentration of ZnONPs were synthesized and characterized using Fourier transform infrared spectroscopy and FE-SEM. The films were studied for their thermal stability, water vapor transmission rate (WVTR) and mechanical properties. The thermal stability, as determined by Thermo Gravimetric Analysis and Differential Scanning Calorimetry increased slightly with increasing percentage of embedded ZnONPs while a substantial decrease in WVTR was observed. Mechanical properties also showed improvements with 77% increment in tensile modulus and 67% increment in tensile strength. The antimicrobial activity of the films was also studied on gram positive bacterium Bacillus subtilis (B. subtilis) and gram negative bacterium Escherichia coli (E. coli) by serial dilution method. A twofold and 1.5-fold increment in the antimicrobial activity was observed for B. subtilis and E. coli, respectively, with increased ZnONPs concentration in the films from 0(w/w) to 2%(w/w). Films thus prepared can prove to be of immense potential in the near future for antimicrobial food packaging applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Abstract Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn’s oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S 1 state. However, significant discrepancies are observed for the excited XFEL states (S 2 , S 3, and S 0 ) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Plant Sciences↗
DOE OSTI2025

Probing substrate water access through the O1 channel of Photosystem II by single site mutations and membrane inlet mass spectrometry

Abstract Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO 2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn 4 CaO 5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated fromThermosynechococcus vestitus(T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn 4 CaO 5 cluster during its S 2 →S 3 and S 3 →S 4 →S 0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacteriumSynechocystis sp.PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitusnumbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn 4 CaO 5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn 4 CaO 5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

Plant Sciences↗
DOE OSTI2017

Spatial distribution of metals within the liver acinus and their perturbation by PCB126

Animal studies show that exposure to the environmental pollutant 3,3',4,4',5-pentachlorobiphenyl (PCB126) causes alterations in hepatic metals as measured in acid-digested volume-adjusted tissue. These studies lack the detail of the spatial distribution within the liver. Here we use X-ray fluorescence microscopy (XFM) to assess the spatial distribution of trace elements within liver tissue. Liver samples from male Sprague Dawley rats, treated either with vehicle or PCB126, were formalin fixed and paraffin embedded. Serial sections were prepared for traditional H&E staining or placed on silicon nitride windows for XFM. With XFM, metal gradients between the portal triad and the central vein were seen, especially with copper and iron. These gradients change with exposure to PCB126, even reverse. This is the first report of how micronutrients vary spatially within the liver and how they change in response to toxicant exposure. In addition, high concentrations of zinc clusters were discovered in the extracellular space. PCB126 treatment did not affect their presence, but did alter their elemental makeup suggesting a more general biological function. Further work is needed to properly evaluate the gradients and their alterations as well as classify the zinc clusters to determine their role in liver function and zinc homeostasis.

copper↗
DOE OSTI2020

Triaxial Constraint and Tensile Strength Enhancement in Brazed Joints

A brazed joint consists of a low-melting point and thin interlayer sandwiched between the high-melting-point base materials, in which the interlayer strength is typically lower than that of the base material. When this butt-joined composite is loaded uniaxially in the direction perpendicular to the plane of the brazing layer, the tensile strength is found to be much higher than that of the braze. This seems to violate the iso-stress condition in such a butt-joint serial configuration. Furthermore, the stress triaxiality has been usually ascribed, but without a quantitative rationalization, as being responsible for this tensile strength enhancement. Here a complete finite element simulation has been conducted to study the dependence of triaxiality and strength enhancement on geometric and material parameters. Two asymptotic limit solutions (based on Bridgman and Xia–Shih solutions, respectively) have been identified to understand the simulation results. The critical role of void evolution has been revealed when making a quantitative comparison to available experiments. In addition, ductility of the brazed joint, which has not been fully addressed in literature, is investigated by the Gurson–Tvergaard–Needleman model.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Defect Characterization Using Positron Annihilation Spectroscopy on Laser-Ablated Surfaces

In recent years, short, pulsed laser ablation has been gaining popularity for machining small-scale test geometries from bulk samples and for efficient serial sectioning. These laser-based techniques are being added to the toolbox in material science, which makes it necessary to understand the changes in the material that occur from the laser–material interaction. Positron annihilation spectroscopy is a unique, nondestructive technique to investigate small defects in materials difficult to investigate by other tools. In this work, Doppler broadening and positron lifetime annihilation spectroscopy are utilized to help quantify the damage in materials treated with short, pulsed lasers. Using a femtosecond laser on single crystal silicon, this manuscript shows that clusters of vacancy-like defects and small voids increase systematically with laser power. Lastly, the damage induced by the laser can also reach to micrometer depths.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Emerging Role of Coronary Computed Tomography Angiography in Lipid-Lowering Therapy: a Bridge to Image-Guided Personalized Medicine

Purpose of Review: To summarize the current status of coronary computed tomography angiography (CTA) in the assessment of coronary plaques and discuss the ability of serial coronary CTA to quantitatively measure changes in the plaque burden in response to lipid-lowering therapy. Recent Findings: Recent advances in coronary CTA have allowed identification of high-risk coronary features in acute coronary syndrome and measurement of changes in the coronary plaque burden with good reproducibility. Statin therapy may delay plaque progression and change some plaque features. However, the clinical relevance of quantitative changes in coronary plaques and the optimal methods to reduce the plaque burden remain unclear. Summary: Despite guideline-directed lipid-lowering therapy, adverse events still occur in substantial numbers of patients receiving statins. Coronary CTA is noninvasive and has high diagnostic performance in patients with coronary artery disease, making change in the plaque burden an applicable biomarker for individualized assessment of future risk.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Process model for multilayer slide coating of polymer electrolyte membrane fuel cells

Slide coating is a precision method suitable for depositing multiple liquid-film layers simultaneously. Originally developed in the photographic film industry, it has been deployed for manufacturing of other products that benefit from multilayer coatings. One emerging application is the manufacture of polymer electrolyte membrane fuel cells (PEMFCs), which are used to produce electricity through electrochemical reactions of hydrogen and oxygen gas. The membrane-electrode assembly (MEA), in which key electrochemical reactions occur, consists of three layers that are typically deposited separately in serial fashion and then laminated together to form the three-layer MEA, i.e., three sequential steps of coat and dry. Adapting the process to simultaneous, multilayer slide coating of all three layers will save equipment cost and space while minimizing possible exposure to contaminants during transition between the steps. We are developing a three-layer slide coating model to aid the manufacturing process design of PEMFC. The model accounts for rheology of each layer, which typically exhibit shear thinning behavior. Model predictions are used to investigate simultaneous coatability of catalyst inks and to determine the best layer-by-layer ink selection.

25 ENERGY STORAGE↗
DOE OSTI2019

Imaging the event-prone coronary artery plaque

Acute coronary events, the dreaded manifestation of coronary atherosclerosis, remain one of the main contributors to mortality and disability in the developed world. The majority of those events are associated with atherosclerotic plaques-related thrombus formation following an acute disruption, that being rupture or erosion, of an event-prone lesion. These historically termed vulnerable plaques have been the target of numerous benchtop and clinical research endeavors, yet to date without solid results that would allow for early identification and potential treatment. Technological leaps in cardiovascular imaging have provided novel insights into the formation and role of the event-prone plaques. From intracoronary optical coherence tomography that has enhanced our understanding of the pathophysiological mechanisms of plaque disruption, over coronary computed tomography angiography that enables non-invasive serial plaque imaging, and positron emission tomography poised to be rapidly implemented into clinical practice to the budding field of plaque imaging with cardiac magnetic resonance, we summarize the invasive and non-invasive imaging modalities currently available in our armamentarium. Finally, the current status and potential future imaging directions are critically appraised.

62 RADIOLOGY AND NUCLEAR MEDICINE↗