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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Species-specific transpiration responses to intermediate disturbance in a northern hardwood forest: Transpiration response to disturbance

Intermediate disturbances shape forest structure and composition, which may in turn alter carbon, nitrogen, and water cycling. We used a large-scale experiment in a forest in northern lower Michigan where we prescribed an intermediate disturbance by stem girdling all canopy-dominant early successional trees to simulate an accelerated age-related senescence associated with natural succession.Using 3 years of eddy covariance and sap flux measurements in the disturbed area and an adjacent control plot, we analyzed disturbance-induced changes to plot level and species-specific transpiration and stomatal conductance. We found transpiration to be ~15% lower in disturbed plots than in unmanipulated control plots. However, species-specific responses to changes in microclimate varied. While red oak and white pine showed increases in stomatal conductance during post disturbance (62.5 and 132.2%, respectively), redmaple reduced stomatal conductance by 36.8%. We used the hysteresis between sap flux and vapor pressure deficit to quantify diurnal hydraulic stress incurred by each species in both plots. Red oak, a ring porousanisohydric species, demonstrated the largest mean relative hysteresis, while red maple, bigtooth aspen, andpaper birch, all diffuse porous species, had the lowest relative hysteresis. We employed the Penman-Monteithmodel for LE to demonstrate that these species-specific responses to disturbance are not well captured using current modeling strategies and that accounting for changes to leaf area index and plot microclimate are insufffcient to fully describe the effects of disturbance on transpiration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Development of an empirical model relating permeability and specific stiffness for rough fractures from numerical deformation experiments: Fracture Permeability and Stiffness

The coupling between hydraulic and mechanical properties of porous and fractured geologic media are critical for many geophysical processes and practical applications. Thus, the prediction of this linkage between these properties is broadly important. Here we present a potentially predictive model that links fracture permeability and specific stiffness with empirical coefficients dependent on fracture roughness, correlation length of aperture field, and rock mechanical properties. The equation was developed empirically from results of modeling the deformation and flow through synthetic fractures with aperture fields that follow a normal distribution. The fractures were subjected to increasing normal stress and deformed following an elastic model. Specific stiffness was directly quantified from these numerical deformation experiments. Permeability was estimated through calculation of the local flow field while considering effects of local fracture roughness and tortuosity. The empirical model roughly captures the transition from effective medium to percolation flow regimes with increasing specific stiffness.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes

Abstract Combining surface‐initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI‐TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush‐functionalized DNA nanostructures. We demonstrate that SI‐TcEP can site‐specifically pattern DONs with brushes containing both natural and non‐natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse‐grained simulations predict the conformation of the brush‐functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush‐functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site‐specific growth of polynucleotide brushes. The ability to site‐specifically decorate DONs with brushes of natural and non‐natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

Yang, Yunqi↗
DOE OSTI2021

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. Here we demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗
DOE OSTI2025

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology↗
DOE OSTI2022

COMET: A Domain-Specific Compilation of High-Performance Computational Chemistry

The computational power increases over the past decades have greatly enhanced the ability to simulate chemical reactions and understand ever more complex transformations. Tensor contractions are the fundamental computational building block of these simulations. These simulations have often been tied to one platform and restricted in generality by the interface provided to the user. The expanding prevalence of accelerators and researcher demands necessitate a more general approach which is not tied to specific hardware or requires contortion of algorithms to specific hardware platforms. In this paper we present COMET, a domain-specific programming language and compiler infrastructure for tensor contractions targeting heterogeneous accelerators. We present a system of progressive lowering through multiple layers of abstraction and optimization that achieves up to 1.98×speedup for 30 tensor contractions commonly used in computational chemistry and beyond.

Mutlu, Erdal↗
DOE OSTI2022

Domain-Specific Type-Safe APIs for Hierarchical Scientific Data with Modern C++

General-purpose library application programming interfaces (APIs) for self-describing hierarchical scientific data storage, such as the HDF5 and NetCDF libraries, are traditionally of runtime nature. Runtime errors for entry existence and data types are typically caught later in the development process of higher-level application-specific APIs. In this paper, we propose exploiting modern C++ metaprogramming features to add compile-time type-safety to improve the interaction with a well-defined metadata-rich scientific schema in domain-specific hierarchical datasets. We tackle two aspects of common use: (i) direct data access, (ii) flexible “in-memory” index models for efficient search and data processing. The proposed APIs use C++17’s template type auto deduction features, C++11’s enum class for type-safety and C-style preprocessor macros for generative templated code. We showcase the pros and cons of our initial work on the standard NeXus schema used for annotating and storing experimental neutron scattering data at several facilities around the world on top of HDF5. Extendable compile-time type-safe APIs are a desirable feature that could be indexed by any modern integrated development environment (IDE). Hence, such APIs can help ease the learning curve for domain scientists using a less error-prone software interaction to enhance the findability of their data without resorting to a domain-specific language (DSL).

Godoy, William↗
DOE OSTI2018

Quantifying Analysis of Uncertainty in Medical Reporting: Creation of User and Context-Specific Uncertainty Profiles

While uncertainty is ubiquitous in medical practice, minimal work to date has been performed to analyze the cause and effect relationship between uncertainty and patient outcomes. In medical imaging practice, uncertainty in the radiology report has been well documented to be a source of clinician dissatisfaction. Before one can effectively create intervention strategies aimed at reducing uncertainty, it must first be better understood through context- and user-specific analysis. One strategy for accomplishing this task is to characterize the source of uncertainty and create user-specific uncertainty profiles which take into account a number of provider-specific variables which may contribute to report uncertainty. The resulting data can in turn be used to create real-time report uncertainty metrics aimed at providing uncertainty analytics at the point of care, for the combined purposes of decision support, improved communication, and enhanced clinical/economic outcomes.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Specificity and Engagement: Increasing ELSI s Relevance to Nano Scientists

Scholars studying the ethical, legal, and social issues (ELSI) associated with emerging technologies maintain the importance of considering these issues throughout the research and development cycle, even during the earliest stages of basic research. Embedding these considerations within the scientific process requires communication between ELSI scholars and the community of physical scientists who are conducting that basic research. We posit that this communication can be effective on a broad scale only if it links societal issues directly to characteristics of the emerging technology that are relevant to the physical and natural scientists involved in research and development. In this article, we examine nano-ELSI literature from 2003 to 2010 to discern the degree to which it makes these types of explicit connections. We find that, while the literature identifies a wide range of issues of societal concern, it generally does so in a non-specific manner. It neither links societal issues to particular forms or characteristics of widely divergent nanotechnologies nor to any of the many potential uses to which those nanotechnologies may be put. We believe that these kinds of specificity are essential to those engaged in nano-scale research. We also compare the literature-based findings to observations from interviews we conducted with nanoscientists and conclude that ELSI scholars should add technical- and application-related forms of specificity to their work and their writings to enhance effectiveness and impact in communicating with one important target audience members of the nanoscale science community.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2018

Real-Time In Situ Neutron Diffraction Investigation of Phase-Specific Load Sharing in a Cold-Rolled TRIP Sheet Steel

Real-time in situ neutron diffraction was used to investigate the loading-direction dependence of phase-specific load sharing in a cold-rolled TRIP 780 sheet steel under tension at room temperature. A slightly lower yield stress and relatively faster initial strain hardening were observed for the tension along the rolling direction (RD), than those along the transverse direction (TD) and the diagonal direction (DD). In all three loading directions, the redistribution of inter-phase and inter-granular load sharing occurs upon the yields of the BCC matrix and the FCC phase. The FCC phase is found to yield earlier along the RD than those along the TD and DD. Based on the Hooke’s law and the rule of mixture, it is found that the lattice strains of BCC-(211)/FCC-(311) reflections via single peak fit are better representative of phase elastic strains than the strains calculated via the lattice parameters by Rietveld refinement. The quantitative evolution of phase-specific stress indicates a rapid strain hardening in the FCC phase after yielding during the RD tension. Possible mechanisms of the direction-dependent phase-specific load sharing are discussed in association with the different initial textures in the RD, DD and TD.

Yu, Dunji↗
DOE OSTI2021

Analysis-Specific Fast Simulation at the LHC with Deep Learning

Abstract We present a fast-simulation application based on a deep neural network, designed to create large analysis-specific datasets. Taking as an example the generation of W + jet events produced in $$\sqrt{s}=$$ s = 13 TeV proton–proton collisions, we train a neural network to model detector resolution effects as a transfer function acting on an analysis-specific set of relevant features, computed at generation level, i.e., in absence of detector effects. Based on this model, we propose a novel fast-simulation workflow that starts from a large amount of generator-level events to deliver large analysis-specific samples. The adoption of this approach would result in about an order-of-magnitude reduction in computing and storage requirements for the collision simulation workflow. This strategy could help the high energy physics community to face the computing challenges of the future High-Luminosity LHC.

Chen, C.↗
DOE OSTI2013

PTPRT regulates the interaction of Syntaxin-binding protein 1 with Syntaxin 1 through dephosphorylation of specific tyrosine residue

Highlights: •PTPRT is a brain-specific, expressed, protein tyrosine phosphatase. •PTPRT regulated the interaction of Syntaxin-binding protein 1 with Syntaxin 1. •PTPRT dephosphorylated the specific tyrosine residue of Syntaxin-binding protein 1. •Dephosphorylation of Syntaxin-binding protein 1 enhanced the interaction with Syntaxin 1. •PTPRT appears to regulate the fusion of synaptic vesicle through dephosphorylation. -- Abstract: PTPRT (protein tyrosine phosphatase receptor T), a brain-specific tyrosine phosphatase, has been found to regulate synaptic formation and development of hippocampal neurons, but its regulation mechanism is not yet fully understood. Here, Syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, was identified as a possible interaction partner and an endogenous substrate of PTPRT. PTPRT interacted with Syntaxin-binding protein 1 in rat synaptosome, and co-localized with Syntaxin-binding protein 1 in cultured hippocampal neurons. PTPRT dephosphorylated tyrosine 145 located around the linker between domain 1 and 2 of Syntaxin-binding protein 1. Syntaxin-binding protein 1 directly binds to Syntaxin 1, a t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein, and plays a role as catalysts of SNARE complex formation. Syntaxin-binding protein 1 mutant mimicking non-phosphorylation (Y145F) enhanced the interaction with Syntaxin 1 compared to wild type, and therefore, dephosphorylation of Syntaxin-binding protein 1 appeared to be important for SNARE-complex formation. In conclusion, PTPRT could regulate the interaction of Syntaxin-binding protein 1 with Syntaxin 1, and as a result, the synaptic vesicle fusion appeared to be controlled through dephosphorylation of Syntaxin-binding protein 1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Differential concentration-specific effects of caffeine on cell viability, oxidative stress, and cell cycle in pulmonary oxygen toxicity in vitro

Highlights: • Caffeine at 0.05 mM decreases oxidative stress in hyperoxia. • Caffeine at 1 mM decreases cell viability, increases oxidative stress in hyperoxia. • Caffeine at 1 but not 0.05 mM, abrogates hyperoxia-induced G2/M arrest. - Abstract: Caffeine is used to prevent bronchopulmonary dysplasia (BPD) in premature neonates. Hyperoxia contributes to the development of BPD, inhibits cell proliferation and decreases cell survival. The mechanisms responsible for the protective effect of caffeine in pulmonary oxygen toxicity remain largely unknown. A549 and MLE 12 pulmonary epithelial cells were exposed to hyperoxia or maintained in room air, in the presence of different concentrations (0, 0.05, 0.1 and 1 mM) of caffeine. Caffeine had a differential concentration-specific effect on cell cycle progression, oxidative stress and viability, with 1 mM concentration being deleterious and 0.05 mM being protective. Reactive oxygen species (ROS) generation during hyperoxia was modulated by caffeine in a similar concentration-specific manner. Caffeine at 1 mM, but not at the 0.05 mM concentration decreased the G2 arrest in these cells. Taken together this study shows the novel funding that caffeine has a concentration-specific effect on cell cycle regulation, ROS generation, and cell survival in hyperoxic conditions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Isoform-specific proteasomal degradation of Rbfox3 during chicken embryonic development

Highlights: • Protein stability of Rbfox3 splice isoforms is differentially regulated. • Rbfox3-d31, an Rbfox3 isoform lacking the RRM, is highly susceptible to degradation. • The protein stability of Rbfox3-d31 is regulated by the ubiquitin–proteasome pathway. • Rbfox3-d31 inhibits the nuclear localization of Rbfox2. • Rbfox3-d31 inhibits the splicing activity of Rbfox2. - Abstract: Rbfox3, a neuron-specific RNA-binding protein, plays an important role in neuronal differentiation during development. An isoform Rbfox3-d31, which excludes the 93-nucleotide cassette exon within the RNA recognition motif of chicken Rbfox3, has been previously identified. However, the cellular functions of Rbfox3-d31 remain largely unknown. Here we find that Rbfox3-d31 mRNA is highly expressed during the early developmental stages of the chicken embryo, while Rbfox3-d31 protein is barely detected during the same stage due to its rapid degradation mediated by the ubiquitin–proteasome pathway. Importantly, this degradation is specific to the Rbfox3-d31 isoform and it does not occur with full-length Rbfox3. Furthermore, suppression of Rbfox3-d31 protein degradation with the proteasome inhibitor MG132 attenuates the splicing activity of another Rbfox family member Rbfox2 by altering the subcellular localization of Rbfox2. These results suggest that Rbfox3-d31 functions as a repressor for the splicing activity of the Rbfox family and its protein level is regulated in an isoform-specific manner in vivo.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Cardiomyocyte specific expression of Acyl-coA thioesterase 1 attenuates sepsis induced cardiac dysfunction and mortality

Compromised cardiac fatty acid oxidation (FAO) induced energy deprivation is a critical cause of cardiac dysfunction in sepsis. Acyl-CoA thioesterase 1 (ACOT1) is involved in regulating cardiac energy production via altering substrate metabolism. This study aims to clarify whether ACOT1 has a potency to ameliorate septic myocardial dysfunction via enhancing cardiac FAO. Transgenic mice with cardiomyocyte specific expression of ACOT1 (αMHC-ACOT1) and their wild type (WT) littermates were challenged with Escherichia coli lipopolysaccharide (LPS; 5 mg/kg i.p.) and myocardial function was assessed 6 h later using echocardiography and hemodynamics. Deteriorated cardiac function evidenced by reduction of the percentage of left ventricular ejection fraction and fractional shortening after LPS administration was significantly attenuated by cardiomyocyte specific expression of ACOT1. αMHC-ACOT1 mice exhibited a markedly increase in glucose utilization and cardiac FAO compared with LPS-treated WT mice. Suppression of cardiac peroxisome proliferator activated receptor alpha (PPARa) and PPARγ-coactivator-1α (PGC1a) signaling observed in LPS-challenged WT mice was activated by the presence of ACOT1. These results suggest that ACOT1 has potential therapeutic values to protect heart from sepsis mediated dysfunction, possibly through activating PPARa/PGC1a signaling. - Highlights: • ACOT1 has potential therapeutic values to protect heart from sepsis mediated dysfunction. • ACOT1 can regulate PPARa/PGC1a signaling pathway. • We first generate the transgenic mice with cardiomyocyte specific expression of ACOT1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Triptolide inhibits transcription of hTERT through down-regulation of transcription factor specificity protein 1 in primary effusion lymphoma cells

Primary effusion lymphoma (PEL) is a rare and aggressive non-Hodgkin's lymphoma. Human telomerase reverse transcriptase (hTERT), a key component responsible for the regulation of telomerase activity, plays important roles in cellular immortalization and cancer development. Triptolide purified from Tripterygium extracts displays a broad-spectrum bioactivity profile, including immunosuppressive, anti-inflammatory, and anti-tumor. In this study, it is investigated whether triptolide reduces hTERT expression and suppresses its activity in PEL cells. The mRNA and protein levels of hTERT were examined by real time-PCR and Western blotting, respectively. The activity of hTERT promoter was determined by Dual luciferase reporter assay. Our results demonstrated that triptolide decreased expression of hTERT at both mRNA and protein levels. Further gene sequence analysis indicated that the activity of hTERT promoter was suppressed by triptolide. Triptolide also reduced the half-time of hTERT. Additionally, triptolide inhibited the expression of transcription factor specificity protein 1(Sp1) in PEL cells. Furthermore, knock-down of Sp1 by using specific shRNAs resulted in down-regulation of hTERT transcription and protein expression levels. Inhibition of Sp1 by specific shRNAs enhanced triptolide-induced cell growth inhibition and apoptosis. Collectively, our results demonstrate that the inhibitory effect of triptolide on hTERT transcription is possibly mediated by inhibition of transcription factor Sp1 in PEL cells. - Highlights: • Triptolide reduces expression of hTERT by decreasing its transcription level. • Triptolide reduces promoter activity and stability of hTERT. • Triptolide down-regulates expression of Sp1. • Special Sp1 shRNAs inhibit transcription and protein expression of hTERT. • Triptolide and Sp1 shRNA2 induce cell proliferation inhibition and apoptosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

In vivo and in vitro characterization of site-specific recombination of a novel serine integrase from the temperate phage EFC-1

EFC-1 integrase is a site-specific recombinase that belongs to the large family of serine recombinase. In previously study, we isolated the temperate phage EFC-1, and characterized its genomic sequence. Within its genome, Orf28 was predicted encode a 464 amino acid of a putative integrase gene. In this study, EFC-1 integrase was characterized in vitro and in vivo. In vitro assay was performed using purified His-tag fusion integrase. Also, to identify which serine is involved in the catalytic domain, we used site-directed mutagenesis and analyzed by a recombination assay in vitro. In vivo assay involved PCR and confocal microscopy in HEK293 cells, and determined the minimal lengths of attP and attB sites. According to our results, the EFC-1 integrase-mediated recombination was site-specific and unidirectional system in vitro and in vivo. Serine 21 of EFC-1 integrase plays a major role in the catalytic domain, and minimal sizes of attB and attP was defined 48 and 54 bp. Our finding may help develop a useful tool for gene therapy and gene delivery system. - Highlights: • EFC-1 integrase-mediated recombination was site-specific and unidirectional system. • Serine 21 of EFC-1 integrase plays a major role in the catalytic domain. • The functional minimal sizes of attB and attP was defined 48 and 54 bp.

60 APPLIED LIFE SCIENCES↗