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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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44 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Scalable multiscale modeling of platelets with 100 million particles

Here, we developed the core components of the AI-aided multiple time stepping algorithm for multiscale modeling of cell dynamics. This algorithm was implemented and analyzed on two supercomputer architectures with an application of simulating the aggregation of 250 platelets, or 102 million particles. To scale on these computers with complex memory and network architectures with GPUs, we devised a biomechanics-informed task mapping scheme to optimize load imbalance, communications, and memory utilization. Our simulations, scaling well up to 192 nodes on a Summit-like supercomputer with a peak speed of 11 petaflops, achieved a rate of 423 μs/day which is 500 times faster than the conventional algorithm using static time step and this has enabled studies of record size blood clots at record spatial–temporal resolutions. Additionally, we discovered the sensitive dependence of the scalability and execution time on the methods of decomposition, CPU–GPU coupling, and task mapping.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Circadian rhythmicity of amyloid‐beta‐related molecules is disrupted in the choroid plexus of a female Alzheimer's disease mouse model

Abstract The choroid plexus (CP) is part of the blood‐cerebrospinal fluid barrier (BCSFB) and was recently described as an important component of the circadian clock system. It is the principal source of cerebrospinal fluid (CSF) and responsible for the synthesis and secretion of various neuroprotective peptides including those involved in amyloid‐β (Aβ) transport/degradation, contributing to Aβ homeostasis. Inadequate Aβ metabolic clearance and transport across the BCSFB have been associated with circadian dysfunctions in Alzheimer's disease (AD) patients. To investigate whether AD pathology influences Aβ scavengers circadian expression, we collected CP at different time points from an AD mouse model (APP/PS1) (female and male animals, aged 6‐ and 12‐months‐old) and analyzed their mRNA expression by Real‐time RT‐PCR. Only angiotensin‐converting enzyme (Ace) expression in 6‐month‐old female wild‐type mice and transthyretin (Ttr) expression in 12‐month‐old female wild‐type mice presented significant rhythmicity. The circadian rhythmicity of Ace and Ttr, prompt us to analyze the involvement of circadian rhythm in Aβ uptake. A human CP papilloma (HIBCPP) cell line was incubated with Aβ‐488 and uptake was evaluated at different time points using flow cytometry. Aβ uptake displayed circadian rhythmicity. Our results suggest that AD might affect Aβ scavengers rhythmicity and that Aβ clearance is a rhythmic process possibly regulated by the rhythmic expression of Aβ scavengers.

Furtado, André↗
DOE OSTI2021

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Longitudinal Plasma Proteomic Profiling Reveals Divergent Immune Responses in Durably Cured and Relapsed Pulmonary Tuberculosis

Background: Predicting the risk of tuberculosis (TB) relapse is vital to improving treatment outcomes. Although clinical risk factors of relapse are well characterized, the biological mechanisms driving relapse, particularly host immune responses, remain poorly understood. Elucidating these mechanisms is necessary to better predict relapse risk. Methods: We conducted a longitudinal, global proteomic study on 60 participants with active pulmonary TB, half who were durably cured and half who relapsed. Plasma was collected at seven time-points: at treatment initiation (baseline), during therapy, and 52 weeks post-baseline. Samples were analyzed by high-resolution LC-MS/MS. Results: 2,418 proteins were identified across all samples, with 1,756 being differentially expressed relative to baseline (unadjusted p < 0.05). 956 proteins were differentially abundant between cured and relapsed participants. Relapsed participants showed heightened humoral immunity throughout treatment, as well as upregulated complement activation and HDL particles. Cured participants exhibited elevated recovery-related pathways by week 4, including downregulated epithelial invasion and upregulated oxygen transport. Conclusions: Heightened humoral and innate immune responses were associated with relapse, whereas recovery signatures were associated with durable cure. These findings advance our understanding of host responses to treatment and provide a basis for developing blood-based biomarkers to identify patients at increased risk of relapse.

LC-MS/MS↗
DOE OSTI2021

Electropolymerized-molecularly imprinted polymers (E-MIPS) as sensing elements for the detection of dengue infection

Here, a straightforward in situ detection method for dengue infection was demonstrated through the molecular imprinting of a dengue nonstructural protein 1 (NS1) epitope into an electropolymerized molecularly imprinted polyterthiophene (E-MIP) film sensor. The key enabling step in the sensor fabrication is based on an epitope imprinting strategy, in which short peptide sequences derived from the original target molecules were employed as the main template for detection and analysis. The formation of the E-MIP sensor films was facilitated using cyclic voltammetry (CV) and monitored in situ by electrochemical quartz crystal microbalance (EC-QCM). Surface properties were analyzed using different techniques including atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and polarization modulation-infrared reflection-adsorption (PM-IRRAS). The standard calibration curve (R = 0.9830) was generated for the detection of the epitope, Ac-VHTWTEQYKFQ-NH 2 , with a linear range of 0.2 to 30 μg/mL and detection limit of 0.073 μg/mL. A separate calibration curve (R = 0.9786) was obtained using spiked buffered solutions of dengue NS1 protein, which resulted in a linear range of 0.2 to 10 μg/mL and a detection limit of 0.056 μg/mL. The fabricated E-MIP sensor exhibited long-term stability, high sensitivity, and good selectivity towards the targeted molecules. These results indicated that the formation of the exact and stable cavity imprints in terms of size, shape, and functionalities was successful. In our future work, we aim to use our E-MIP sensors for NS1 detection in real-life samples such as serum and blood.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Analysis of a new multispecies tumor growth model coupling 3D phase-fields with a 1D vascular network

In this study, we present and analyze a mathematical model for tumor growth incorporating ECM erosion, interstitial flow, and the effect of vascular flow and nutrient transport. The model is of phase-field or diffused-interface type in which multiple phases of cell species and other constituents are separated by smooth evolving interfaces. The model involves a mesoscale version of Darcy’s law to capture the flow mechanism in the tissue matrix. Modeling flow and transport processes in the vasculature supplying the healthy and cancerous tissue, one-dimensional (1D) equations are considered. Since the models governing the transport and flow processes are defined together with cell species models on a three-dimensional (3D) domain, we obtain a 3D–1D coupled model.

3D–1D coupled blood flow models↗
DOE OSTI2020

Tracking elemental changes in an ischemic stroke model with X-ray fluorescence imaging

Stroke is a leading cause of long-term disability in adults and a leading cause of death in developed nations. The cascade of cellular events and signalling that occur after cerebral ischemia are complex, however, analyzing global element markers of metabolic state affords the means to monitor stroke severity, status of injury, and recovery. These markers provide a multi-parameter method for assessing changes through the post-stroke time course. We employ synchrotron-based elemental mapping to follow elemental changes in the brain at 1 h, 1-, 2-, and 3-days, and at 1-, 2-, 3-, and 4-weeks post-stroke in a photothrombotic stroke model in mice. Our analysis reveals a highly consistent metabolic penumbra that can be readily identified based on the level of dysregulated potassium and other key elements. Maps of elemental distributions are also useful to demarcate events in the cellular response to the inflammatory cascade, including ion dysregulation, recruitment of cells to the lesion, and glial scar formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Triple Emission of 5'-( para -R-Phenylene)vinylene-2-(2'-hydroxyphenyl)benzoxazole (PVHBO). Part I: Dual Emission from the Neutral Species

The effects of 5'-(para-R-phenylene)vinylene (PV) substituents on the emission properties of 2-(2'-hydroxyphenyl)benzoxazole (HBO) are analyzed using steady-state and time-resolved absorption and emission spectroscopies in addition to quantum chemical calculations. All members in the series of PVHBOs are capable of excited-state intramolecular proton transfer (ESIPT) with a solvent sensitivity that is typical of a HBO derivative to produce a normal (aka enol) emission and an excited-state tautomer (aka keto) emission. These two emission bands of the neutral dyes are discussed in the current paper. The intermolecular proton transfer, i.e., the deprotonation, of a PVHBO results in the third band of the triple emission, which is described in the succeeding paper. The placement of an electron-withdrawing substituent R on the PVHBO scaffold increases the intensity of the keto emission relative to the enol emission in hydrogen-bonding solvents. The R substituents do not significantly alter the wavelengths of the enol and keto emission bands, which are located in the blue and green regions, respectively, of the visible spectrum. The ultrafast time-resolved spectroscopies and quantum chemical calculations offer explanations on how the R group and the solvent affect the enol and keto emission properties (i.e., wavelength, lifetime, fluorescence quantum yield, and relative ratio of their emissions). Here, the key findings include the following: (1) the emission energies of both enol and keto forms are not sensitively dependent on the R substituent and (2) the solvent-engaged enol excited state is quenched more efficiently as the R substituent becomes more electron-withdrawing. A PVHBO acts as a fusion of HBO and stilbenoid that intersect at the hydroxyphenyl moiety. Depending on the solvent and other environmental conditions, PVHBOs may exhibit the ESIPT property of HBO or the substituent-dependent emission of stilbenoid. This paper and the succeeding article provide a photophysical model of PVHBOs to explain the wavelengths and relative abundances of the three emission bands (enol, keto, and anion) that these compounds are able to produce. Judicial selection of the environmental factors may drive the emission of a PVHBO into the spectral regions of blue, green, and, in a couple of cases, orange or red.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗