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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Distinct notch signaling expression patterns between nucleoside and nucleotide analogues treatment for hepatitis B virus infection

Highlights: • Notch signaling inhibited by nucleoside analogues treatment under HBV infection. • Upregulation of Notch signaling after nucleotide analogues administration. • Reduction of Foxp3 expression by both nucleotide and nucleoside analogues treatment. • Activation of phosphorylated mTORC2–Akt cascade after nucleotide analogue treatment. Nucleos(t)ide analogues therapies are currently approved for the treatment of chronic hepatitis B virus (HBV) infection, which effectively suppress HBV replication and correlate with the anti-HBV-specific immune response. Notch signaling serves pleiotropic roles in the immune system that also contribute to virus-specific immunity. In this study, we assessed Notch signal-related gene expression after administrating nucleoside or nucleotide analogues to HBV-replicating cells and clinical liver tissues. We found distinct Notch signaling expression patterns under nucleos(t)ide analogues therapies, with high expression for nucleotide analogues (adefovir pivoxil or tenofovir disoproxil fumarate) and low expression for nucleoside analogues (lamivudine or entecavir) in the presence of HBV infection. Furthermore, activation of mammalian target of rapamycin (mTOR)-Akt (Ser473) phosphorylation was also observed after nucleotide analogue treatment. In conclusion, nucleoside and nucleotide analogues displayed different patterns of Notch signaling activity under HBV infection, and the induction of mTORC2-Akt (Ser473) phosphorylation may contribute to nucleotide analogues-mediated Notch signaling activation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

St6gal1 knockdown alters HBV life cycle in HepAD38 cells

Highlights: • Host glycosyltransferase machinery knockdown alters HBV rcDNA level. • Only St6gal1 knockdown reduced the HBV rcDNA level among treatments. • Viral protein expressions, except the X protein, were affected by St6gal1 knockdown. • HBV cccDNA and pgRNA levels among the treatments were unaffected. Complex glycans at the cell surface play important roles, and their alteration is known to modulate cellular activity. Previously, we found that HBV replication in HepAD38 altered cell-surface sialylated N-glycan through the upregulation of St6gal1, Mgat2, and Mgat4a expression. Here we studied the effects of knocking them down on HBV replication in HepAD38. Our results showed that St6gal1 knockdown (KD) reduced intracellular HBV rcDNA level by 90%, that Mgat2 KD did not change the intracellular HBV rcDNA level, and that Mgat4 KD increased the intracellular HBV rcDNA level by 19 times compared to Tet(−). The changes in intracellular rcDNA level were followed by the alteration of Pol and HBc expression. Our study suggests that St6gal1 KD contributes more to the HBV life cycle than Mgat2 or Mgat4a KD through the modification of intracellular L, Pol, and HBc expression.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Transcriptome of porcine alveolar macrophages activated by interferon-gamma and lipopolysaccharide

The molecular repertoire of porcine alveolar macrophages (PAMs) is greatly affected by the microenvironment they are exposed to, and specifically by inflammatory cytokines, such as interferon gamma (IFN-γ) released by activated lymphocytes, and microbial products, such as lipopolysaccharide (LPS). In our previous study, we found that IFN-γ- and LPS-activated PAMs (M1) could inhibit porcine reproductive and respiratory syndrome virus (PRRSV) replication. In this study, comprehensive analysis of the expression profiles of the genes associated with the polarization of M0-type PAMs (resting) toward M1 phenotypes (activated by IFN-γ and LPS) led to the following main results: 1) 1551 and 1823 genes were upregulated or downregulated in M1-type PAMs, respectively, compared with M0-type PAMs; 2) Among these, genes encoding ASS1 and CRTAM were the most upregulated and downregulated, respectively; 3) Genes involved in cytokine-cytokine receptor interaction and the JAK/STAT signaling pathway were significantly upregulated, suggesting their critical role in cellular activation; and 4) Genes involved in antigen proteolysis and presentation (immunoproteasome subunits), and inhibition of virus replication (host restriction factors) were significantly upregulated, emphasizing the critical role of these cytokines in immunity. Thus, our results provide important information for future studies on the role of PAM polarization in modulation of infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

A historical survey of algorithms and hardware architectures for neural-inspired and neuromorphic computing applications

In this study, biological neural networks continue to inspire new developments in algorithms and microelectronic hardware to solve challenging data processing and classification problems. Here in this research, we survey the history of neural-inspired and neuromorphic computing in order to examine the complex and intertwined trajectories of the mathematical theory and hardware developed in this field. Early research focused on adapting existing hardware to emulate the pattern recognition capabilities of living organisms. Contributions from psychologists, mathematicians, engineers, neuroscientists, and other professions were crucial to maturing the field from narrowly-tailored demonstrations to more generalizable systems capable of addressing difficult problem classes such as object detection and speech recognition. Algorithms that leverage fundamental principles found in neuroscience such as hierarchical structure, temporal integration, and robustness to error have been developed, and some of these approaches are achieving world-leading performance on particular data classification tasks. Additionally, novel microelectronic hardware is being developed to perform logic and to serve as memory in neuromorphic computing systems with optimized system integration and improved energy efficiency. Key to such advancements was the incorporation of new discoveries in neuroscience research, the transition away from strict structural replication and towards the functional replication of neural systems, and the use of mathematical theory frameworks to guide algorithm and hardware developments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A guideline to document occupant behavior models for advanced building controls

The availability of computational power, and a wealth of data from sensors have boosted the development of model-based predictive control for smart and effective control of advanced buildings in the last decade. More recently occupant-behavior models have been developed for including people in the building control loops. However, while important objectives of scientific research are reproducibility and replicability of results, not all information is available from published documents. Therefore, the aim of this paper is to propose a guideline for a thorough and standardized occupant-behavior model documentation. For that purpose, the literature screening for the existing occupant behavior models in building control was conducted, and the occupant behavior modeling processes were studied to extract practices and gaps for each of the following phases: problem statement, data collection, and preprocessing, model development, model evaluation, and model implementation. Here, the literature screening pointed out that the current state-of-the-art on model documentation shows little unification, which poses a particular burden for the model application and replication in field studies. In addition to the standardized model documentation, this work presented a model-evaluation schema that enabled benchmarking of different models in field settings as well as the recommendations on how OB models are integrated with the building system.

Building control↗
DOE OSTI2023

Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants

The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ~1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6–2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA. We show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. Early phage genes are expressed from the EPI vesicle, demonstrating its functionality as a prokaryotic, transcriptionally active, membrane-bound organelle. We also show that the phage nucleus is essential, with genome replication beginning after the injected DNA is transferred from the EPI vesicle to the phage nucleus. Our results show that Chimalliviridae require two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive stages of the viral life cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Comparative Evaluation of Preprocessing Freeware on Chromatography/Mass Spectrometry Data for Signature Discovery

Preprocessing software is crucial for the discovery of chemical signatures in metabolomics, chemical forensics, and other signature-focused disciplines that involve analyzing large data sets from chemical instruments. Here, four freely available and published preprocessing tools known as metAlign, MZmine, SpectConnect, and XCMS were evaluated for impurity profiling using nominal mass GC/MS data and accurate mass LC/MS data. Both data sets were previously collected from the analysis of replicate samples from multiple stocks of a nerve-agent precursor. Each of the four tools had their parameters set for the untargeted detection of chromatographic peaks from impurities present in the stocks. The peak table generated by each preprocessing tool was analyzed to determine the number of impurity components detected in all replicate samples per stock. A cumulative set of impurity components was then generated using all available peak tables and used as a reference to calculate the percent of component detections for each tool, in which 100% indicated the detection of every component. For the nominal mass GC/MS data, metAlign performed the best followed by MZmine, SpectConnect, and XCMS with detection percentages of 83, 60, 47, and 42%, respectively. For the accurate mass LC/MS data, the order was metAlign, XCMS, and MZmine with detection percentages of 80, 45, and 35%, respectively. SpectConnect did not function for the accurate mass LC/MS data. Larger detection percentages were obtained by combining the top performer with at least one of the other tools such as 96% by combining metAlign with MZmine for the GC/MS data and 93% by combining metAlign with XCMS for the LC/MS data. In terms of quantitative performance, the reported peak intensities had average absolute biases of 41, 4.4, 1.3 and 1.3% for SpectConnect, metAlign, XCMS, and MZmine, respectively, for the GC/MS data. For the LC/MS data, the average absolute biases were 22, 4.5, and 3.1% for metAlign, MZmine, and XCMS, respectively. In summary, metAlign performed the best in terms of peak discovery; however, more than one preprocessing tool should be considered to avoid missing potential chemical signatures.

chemical forensics, chemometrics↗
DOE OSTI2026

Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme

RNase H enzymes are sequence-nonspecific endonucleases that cleave RNA strands in RNA/DNA hybrid duplexes, an enzymatic process essential in DNA replication and repair in both prokaryotes and eukaryotes. Also, RNase H activity of the reverse transcriptase in human immunodeficiency viruses (HIV-1 and HIV-2) is indispensable for the viral replication cycle. RNase H enzymes play an central role in the development of gene therapies and are targets for novel antivirals. It is therefore of great importance to gain a detailed understanding of the RNase H catalytic mechanism to improve drug design. We utilized Bacillus halodurans RNase H1 (BhRNase H1) to shed light on its function and catalytic mechanism. Room-temperature neutron crystallography of the wild-type and inactive D132N mutant enzymes revealed that E109, belonging to the catalytic DEDD motif, can change its protonation state, allowing us to propose its role in the protonation of the leaving O3′ hydroxyl group of RNA. X-ray crystallography has demonstrated the ability of the RNA/DNA duplex to slide along the protein surface upon metal ion binding at site M A , transforming a product mimic into a Michaelis-like complex, which confirms an essential role of the M A metal ion in catalysis.

Enzyme mechanisms↗
DOE OSTI2017

Mapping environmental sensitivity: A systematic online approach to support environmental assessment and planning

Environmental sensitivity analysis provides a framework for systematically and objectively determining the potential for significant environmental impacts. The higher the natural or acquired sensitivity of the receiving environment, the less capable it is to cope with human-induced change. Given that sensitivity is context- and spatially-specific, Geographic Information Systems have been applied to develop an operational Webtool to analyse it. The Webtool enables a rapid and replicable spatial examination of environmental sensitivities and potential for land-use conflicts that supports Strategic Environmental Assessment and, ultimately, informed planning and decision-making. The novelty is on the provision of an online geoprocessing Widget that enables creation of context-specific maps. Pilot testing the Webtool in land-use and renewable energy planning through stakeholder engagement has validated its applicability. Stakeholders confirmed that it enables replicating and, in some cases, improving in-house SEA mapping processes while saving time and effort. However, its full reliance on publicly available spatial datasets renders completeness and resolution issues. The Webtool provides a critical starting-point for sectoral planning discussions and for developing plan/programme alternatives that avoid or minimise potentially incompatible or unsustainable zonings, while promoting consistency and transparency in impact assessment. - Highlights: •Sensitivity mapping can enhance baseline information for environmental assessments. •A novel online geoprocessing tool supports systematic sensitivity assessment. •It enables combining context-specific environmental criteria and value judgments. •Pilot testing it through stakeholder engagement has validated its applicability. •The tool promotes assessment consistency and transparency but data issues remain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Can developing countries leapfrog the centralized electrification paradigm?

Due to the rapidly decreasing costs of small renewable electricity generation 'systems, centralized power systems are no longer a necessary condition of universal access to modern energy services. Developing countries, where centralized electricity infrastructures are less developed, may be able to adopt these new technologies more quickly. We first review the costs of grid extension and distributed solar home systems (SHSs) as reported by a number of different studies. We then present a general analytic framework for analyzing the choice between extending the grid and implementing distributed solar home systems. Drawing upon reported grid expansion cost data for three specific regions, we demonstrate this framework by determining the electricity consumption levels at which the costs of provision through centralized and decentralized approaches are equivalent in these regions. We then calculate SHS capital costs that are necessary for these technologies provide each of five tiers of energy access, as defined by the United Nations Sustainable Energy for All initiative. Our results suggest that solar home systems can play an important role in achieving universal access to basic energy services. The extent of this role depends on three primary factors: SHS costs, grid expansion costs, and centralized generation costs. Given current technology costs, centralized systems will still be required to enable higher levels of consumption; however, cost reduction trends have the potential to disrupt this paradigm. By looking ahead rather than replicating older infrastructure styles, developing countries can leapfrog to a more distributed electricity service model. (C) 2016 International Energy Initiative. Published by Elsevier Inc. All rights reserved.

distributed electrification↗
DOE OSTI2022

Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ

Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.

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

Coupled physics simulation of fracture in nuclear fuel pellets induced by resistive heating

While it is well known that the UO 2 fuel used in light-water reactors cracks early in its life in the reactor, it is very difficult to collect in-reactor data regarding fuel cracking initiation and propagation to validate fracture models in fuel performance codes. Most fracture data comes from the post-irradiation examination of fuel that has been subjected to long and complex power histories. Replicating the thermal gradients experienced in this fuel to study crack initiation and propagation in a laboratory environment is challenging. This is primarily because the fuel is heated volumetrically by fission, which is difficult to replicate. One way to approximate this volumetric heating out of the reactor is to use electrical resistance (or Joule heating). An electrical conductivity model has been developed and coupled with the existing thermomechanical modeling capability in the BISON nuclear fuel performance code. This will permit simulation of experiments that use resistive heating for the purpose of validating fracture models in BISON. The modeling approach developed here is applied to simulate both historical and current resistive heating experiments on ceramic nuclear fuel.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Quantifying the Influence of Size, Shape, and Density of Microplastics on Their Transport Modes: A Modeling Approach

Microplastics (MPs) pose significant risks to marine ecosystems and human health, necessitating accurate predictions of their distributions in aquatic environments for effective risk mitigation. However, understanding MP transport dynamics is challenging because of the inadequate representation of MP characteristics such as size, shape, and density in numerical models. Further, the accuracy of the MP vertical profiles in existing models has not been thoroughly validated. Thus, we developed an MP transport model within the Finite Volume Community Ocean Model framework (FVCOM-MP) by integrating MP characteristics. We validated FVCOM-MP against experimental and analytical data, focusing on various MP transport modes and transitions. FVCOM-MP successfully replicates MP profiles in different transport modes, including the bedload, surface-load, suspended-load, and mixed-load modes. Additionally, we introduce phase diagrams for classifying MP transport modes based on particle characteristics, enhancing our understanding of MP dynamics in aquatic systems. The transport modes for a number of real-world MP particles, including fishing line, plastic bag/bottle fragments, synthetic fibers, tire wear particles, polyvinyl chloride and expanded polystyrene pellets, were analyzed with these phase diagrams.

Microplastic transport, Settling velocity, Rising ↗
DOE OSTI2014

Reduced repair capacity of a DNA clustered damage site comprised of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 2-deoxyribonolactone results in an increased mutagenic potential of these lesions

A signature of ionizing radiation is the induction of DNA clustered damaged sites. Non-double strand break (DSB) clustered damage has been shown to compromise the base excision repair pathway, extending the lifetimes of the lesions within the cluster, compared to isolated lesions. This increases the likelihood the lesions persist to replication and thus increasing the mutagenic potential of the lesions within the cluster. Lesions formed by ionizing radiation include 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 2-deoxyribonolactone (dL). dL poses an additional challenge to the cell as it is not repaired by the short-patch base excision repair pathway. Here we show recalcitrant dL repair is reflected in mutations observed when DNA containing it and a proximal 8-oxodGuo is replicated in Escherichia coli . 8-oxodGuo in close proximity to dL on the opposing DNA strand results in an enhanced frequency of mutation of the lesions within the cluster and a 20 base sequence flanking the clustered damage site in an E. coli based plasmid assay. In vitro repair of a dL lesion is reduced when compared to the repair of an abasic (AP) site and a tetrahydrofuran (THF), and this is due mainly to a reduction in the activity of polymerase β, leading to retarded FEN1 and ligase 1 activities. This study has given insights in to the biological effects of clusters containing dL.

Cunniffe, Siobhan↗
DOE OSTI2022

Semi-empirical simulation of in-motion radiation detection systems

The Replicative Assessment of Spectroscopic Equipment (RASE) is an open-source software that uses experimental data as the basis to simulate the response of commercial radiation detectors to sources in various situations, particularly in the context of nuclear security and safeguards applications. Dynamic RASE introduces the capability to simulate scenarios where sources and detector are in relative motion. Position-dependent experimentally acquired gamma spectra are ingested by Dynamic RASE to build maps that describe the detector response over all space. These response maps are used to replicate the time-dependent energy spectra collected as sources move on a path near the detector. Here, a Gaussian process is used to build each map, incorporating a novel kernel adapted to the special case of radiation detection. The approach has been validated against experimental data acquired using a NaI-based detector for 137 Cs and 54 Mn sources. The capability to create accurate simulations using either long-dwell static measurements or dynamic pass-by measurements as source data has been demonstrated. Quantitative relative performance, benefits, and shortcomings are discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Using Artificial Soiling to Rank Anti-Soiling Coatings for Arid Climates

A simple method to evaluate (e.g., screen and rank) the performance of coatings that are fully or partially anti-soiling (AS) is lacking within the PV industry. Artificial soiling may be used as a rapid and economical assessment approach, offering an efficient alternative to time-intensive, site-specific field testing. In this study, we present an artificial soiling method to replicate the anti-soiling performance rankings of two groups of coated glass samples supplied by two manufacturers (group C with CA, CP, and CS coatings; group A with AC coating). These are compared to field aging in two climates: semi-arid Lemoore, California over 4 months, and the hot desert in Mesa, Arizona over 7 months. Both field and indoor performance ranking utilize the transmittance ratio, defined as the optical transmittance between a coated sample and an uncoated reference in each group, as an evaluation metric to assess the effectiveness of the artificial soiling approach in replicating field soiling. It is critical to mimic the dominant field meteorological conditions associated with soiling-prone days and vulnerable times of day during the soiling season. Our results reveal that the use of artificial soiling for field performance ranking among coatings strongly depends on the soil type (composition and particle distribution), dust surface density, and prevalent environmental factors (wetting saturation by humidity, dew condensation extent, and prior weathering history of the coating). The similar rank order relative to the field suggests that the artificial soiling approach presented may be used for down-selecting anti-soiling coatings prior to prolonged field validation.

14 SOLAR ENERGY↗