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DOE OSTI2014

The Activities of the European Consortium on Nuclear Data Development and Analysis for Fusion

This paper presents an overview of the activities of the European Consortium on Nuclear Data Development and Analysis for Fusion. The Consortium combines available European expertise to provide services for the generation, maintenance, and validation of nuclear data evaluations and data files relevant for ITER, IFMIF and DEMO, as well as codes and software tools required for related nuclear calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2013

A bayesian approach to estimate the size and structure of the broad-line region in active galactic nuclei using reverberation mapping data

This is the first paper in a series devoted to the systematic study of the size and structure of the broad-line region (BLR) in active galactic nuclei (AGNs) using reverberation mapping (RM) data. We employ a recently developed Bayesian approach that statistically describes the variability as a damped random walk process and delineates the BLR structure using a flexible disk geometry that can account for a variety of shapes, including disks, rings, shells, and spheres. We allow for the possibility that the line emission may respond non-linearly to the continuum, and we detrend the light curves when there is clear evidence for secular variation. We use a Markov Chain Monte Carlo implementation based on Bayesian statistics to recover the parameters and uncertainties for the BLR model. The corresponding transfer function is obtained self-consistently. We tentatively constrain the virial factor used to estimate black hole masses; more accurate determinations will have to await velocity-resolved RM data. Application of our method to RM data with Hβ monitoring for about 40 objects shows that the assumed BLR geometry can reproduce quite well the observed emission-line fluxes from the continuum light curves. We find that the Hβ BLR sizes obtained from our method are on average ∼20% larger than those derived from the traditional cross-correlation method. Nevertheless, we still find a tight BLR size-luminosity relation with a slope of α = 0.55 ± 0.03 and an intrinsic scatter of ∼0.18 dex. In particular, we demonstrate that our approach yields appropriate BLR sizes for some objects (such as Mrk 142 and PG 2130+099) where traditional methods previously encountered difficulties.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Feasibility Analysis of Taxi Fleet Electrification Using 4.9 Million Miles of Real-World Driving Data: Preprint

Ride hailing activity is rapidly increasing, largely due to the growth of transportation network companies such as Uber and Lyft. However, traditional taxi companies continue to represent an important mobility option for travelers. Columbus Yellow Cab, a taxi company in Columbus, Ohio, offers traditional line-of-sight hailing as well as digital hailing through a mobile app. Data from Columbus Yellow Cab was provided to the National Renewable Energy Laboratory to analyze the potential for taxi electrification. Columbus Yellow Cab data contained information describing both global positioning system trajectories and taxi meter information. The data spanned a period of 13 months, containing approximately 70 million global system positioning system points, 840 thousand trips, and 170 unique vehicles. A variety of scenarios were evaluated using Columbus Yellow Cab data and the Electric Vehicle Infrastructure Projection Tool (EVI-Pro) to understand challenges and opportunities associated with operating an electrified taxi fleet. Two main factors-access to home charging and vehicle specifications-are shown to be major variables affecting successful electric fleet operation. The analysis indicates that 95.7% of taxi travel days can be successfully completed by a 250-mile-range electric vehicle assuming access to overnight and public charging infrastructure. However, when no overnight access is available to fleet vehicles, only 39.9% of taxi travel days are possible with 250-mile range electric vehicles. An additional scenario, reducing the vehicle range from 250 miles to 100 miles (while controlling for infrastructure access and permitting overnight charging) resulted in only 34.4% of taxi travel days being completed.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2014

Globus platform-as-a-service for collaborative science applications

Globus, developed as Software-as-a-Service (SaaS) for research data management, also provides APIs that constitute a flexible and powerful Platform-as-a-Service (PaaS) to which developers can outsource data management activities such as transfer and sharing, as well as identity, profile and group management. By providing these frequently important but always challenging capabilities as a service, accessible over the network, Globus PaaS streamlines web application development and makes it easy for individuals, teams, and institutions to create collaborative applications such as science gateways for science communities. We introduce the capabilities of this platform and review representative applications.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2012

Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain: ECF41 Sigma Factors

Bacteria need signal transducing systems to respond to environmental changes. Next to one- and two-component systems, alternative σ factors of the extracytoplasmic function (ECF) protein family represent the third fundamental mechanism of bacterial signal transduction. A comprehensive classification of these proteins identified more than 40 phylogenetically distinct groups, most of which are not experimentally investigated. Here, we present the characterization of such a group with unique features, termed ECF41. Among analyzed bacterial genomes, ECF41 σ factors are widely distributed with about 400 proteins from 10 different phyla. They lack obvious anti-σ factors that typically control activity of other ECF σ factors, but their structural genes are often predicted to be cotranscribed with carboxymuconolactone decarboxylases, oxidoreductases, or epimerases based on genomic context conservation. We demonstrate for Bacillus licheniformis and Rhodobacter sphaeroides that the corresponding genes are preceded by a highly conserved promoter motif and are the only detectable targets of ECF41-dependent gene regulation. In contrast to other ECF σ factors, proteins of group ECF41 contain a large C-terminal extension, which is crucial for σ factor activity. Our data demonstrate that ECF41 σ factors are regulated by a novel mechanism based on the presence of a fused regulatory domain.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Nucleation rate controlled grain boundary and lattice creep

Nucleation versus diffusion rate-limited bicrystal and single crystal creep exhibit different scaling dependencies that enable the mechanisms to be isolated when measured as a function of sample size. It has recently been suggested that nucleation rate-limited kinetic models generally describe the non-Newtonian portion of the creep response well, but more direct evidence is required. This work analyzes the grain boundary creep response of UO 2 , a pyrochlore high entropy oxide, silver, and palladium, along with the lattice creep of silver using small-scale in situ loading in the transmission electron microscope. At small sizes, each system exhibits scale dependence associated with nucleation rate-limited kinetics. Fits of the data produce activation volumes on the order of a few Burgers vectors cubed with positive temperature coefficients as expected for nucleation kinetics. The activation enthalpies fall in the range of about 0.4 eV to 1.7 eV, being lower for the metals and higher for the oxides.

36 MATERIALS SCIENCE↗

DOE OSTI2012

Silibinin attenuates allergic airway inflammation in mice

Highlights: Black-Right-Pointing-Pointer Silibinin diminishes ovalbumin-induced inflammatory reactions in the mouse lung. Black-Right-Pointing-Pointer Silibinin reduces the levels of various cytokines into the lung of allergic mice. Black-Right-Pointing-Pointer Silibinin prevents the development of airway hyperresponsiveness in allergic mice. Black-Right-Pointing-Pointer Silibinin suppresses NF-{kappa}B transcriptional activity. -- Abstract: Allergic asthma is a chronic inflammatory disease regulated by coordination of T-helper2 (Th2) type cytokines and inflammatory signal molecules. Silibinin is one of the main flavonoids produced by milk thistle, which is reported to inhibit the inflammatory response by suppressing the nuclear factor-kappa B (NF-{kappa}B) pathway. Because NF-{kappa}B activation plays a pivotal role in the pathogenesis of allergic inflammation, we have investigated the effect of silibinin on a mouse ovalbumin (OVA)-induced asthma model. Airway hyperresponsiveness, cytokines levels, and eosinophilic infiltration were analyzed in bronchoalveolar lavage fluid and lung tissue. Pretreatment of silibinin significantly inhibited airway inflammatory cell recruitment and peribronchiolar inflammation and reduced the production of various cytokines in bronchoalveolar fluid. In addition, silibinin prevented the development of airway hyperresponsiveness and attenuated the OVA challenge-induced NF-{kappa}B activation. These findings indicate that silibinin protects against OVA-induced airway inflammation, at least in part via downregulation of NF-{kappa}B activity. Our data support the utility of silibinin as a potential medicine for the treatment of asthma.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

PPAR-gamma pathways attenuate pulmonary granuloma formation in a carbon nanotube induced murine model of sarcoidosis

Peroxisome proliferator activated receptor gamma (PPARγ), a ligand activated nuclear transcription factor, is constitutively expressed in alveolar macrophages of healthy individuals. PPARγ deficiencies have been noted in several lung diseases including the alveolar macrophages of pulmonary sarcoidosis patients. We have previously described a murine model of multiwall carbon nanotubes (MWCNT) induced pulmonary granulomatous inflammation which bears striking similarities to pulmonary sarcoidosis, including the deficiency of alveolar macrophage PPARγ. Further studies demonstrate alveolar macrophage PPARγ deficiency exacerbates MWCNT-induced pulmonary granulomas. Based on these observations we hypothesized that activation of PPARγ via administration of the PPARγ-specific ligand rosiglitazone would limit MWCNT-induced granuloma formation and promote PPARγ-dependent pathways. Results presented here show that rosiglitazone significantly limits the frequency and severity of MWCNT-induced pulmonary granulomas. Furthermore, rosiglitazone attenuates alveolar macrophage NF-κB activity and downregulates the expression of the pro-inflammatory mediators, CCL2 and osteopontin. PPARγ activation via rosiglitazone also prevents the MWCNT-induced deficiency of PPARγ-regulated ATP-binding cassette lipid transporter-G1 (ABCG1) expression. ABCG1 is crucial to pulmonary lipid homeostasis. ABCG1 deficiency results in lipid accumulation which promotes pro-inflammatory macrophage activation. Our results indicate that restoration of homeostatic ABCG1 levels by rosiglitazone correlates with both reduced pulmonary lipid accumulation, and decreased alveolar macrophage activation. These data confirm and further support our previous observations that PPARγ pathways are critical in regulating MWCNT-induced pulmonary granulomatous inflammation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Acid ceramidase inhibition sensitizes human colon cancer cells to oxaliplatin through downregulation of transglutaminase 2 and β1 integrin/FAK−mediated signalling

Highlights: • Acid ceramidase is constitutively expressed in colorectal adenocarcinoma tissues. • Acid ceramidase expression is inversely correlated with the p53 activity. • Oxaliplatin cytotoxicity in colon cancer is augmented by acid ceramidase inhibition. • Acid ceramidase inhibition supresses oxaliplatin resistance-related signalling. Acid ceramidase (ASAH1) has been implicated in the progression and chemoresistance in different cancers. Its role in colon cancer biology and response to standard chemotherapy has been poorly addressed so far. Here, we have investigated ASAH1 expression at the protein level in human colon cancer cell lines and tissues from colon cancer patients, and have examined in vitro the possible link between ASAH1 expression and functional activity of p53 protein whose inactivation is associated with the progression from adenoma to malignant tumour in colon cancer. Finally, we have explored the role of ASAH1 in response and resistance mechanisms to oxaliplatin (OXA) in HCT 116 colon cancer cells. We have demonstrated that human colon cancer cells and colorectal adenocarcinoma tissues constitutively express ASAH1, and that its expression is higher in tumour tissues than in normal colonic mucosa. Furthermore, we found an inverse correlation between ASAH1 expression and p53 functional activity. Obtained data revealed that ASAH1 was involved in HCT 116 cell response to OXA and that anti-proliferative, pro-apoptotic, anti-migratory and anti-clonogenic effects of OXA could be significantly increased by combination treatment with ASAH1 inhibitor carmofur. Increased OXA sensitivity was associated with downregulation of signalling involved in acquired resistance to OXA in colon cancer, in particular transglutaminase 2 and β1 integrin/FAK, which resulted in the suppression of NF-κB and Akt. Thus, combination of OXA with ASAH1 inhibitors could be a promising strategy to counter chemoresistance and improve treatment outcome in advanced colon cancer.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Activation of neuregulin-4 in adipocytes improves metabolic health by enhancing adipose tissue angiogenesis

Highlights: • Targeted activation of Nrg4 in adipocytes enhanced adipose tissue angiogenesis. • Activation of Nrg4 in adipocytes improved systemic metabolic health. • Angiogenesis inhibition abolished the beneficial effects of Nrg4 on metabolic health. • Inhibition of ErbB signaling in EC abrogated the Nrg4-mediated angiogenesis. • ErbB signal inhibition canceled the beneficial effects of Nrg4 on metabolic health. Obesity often causes systemic metabolic disorders in close association with adipose tissue dysfunction. Adipose tissue contains well-developed vasculatures, and obesity mediates vascular rarefaction that causes hypoxia and triggers inflammation in adipose tissue. Adipose tissue-derived neuregulin-4 (Nrg4) is an immerging factor that is critically involved in metabolic homeostasis. We recently identified that Nrg4 is an angiogenic adipokine that plays an important role in maintaining adipose tissue vasculature. Here, we further validated its beneficial role in metabolic health primarily by enhancing adipose tissue angiogenesis. Targeted activation of Nrg4 in adipocytes improved metabolic health in mice under both normal and high fat dietary condition without changes in body weight. Activation of Nrg4 increased blood vessels in white adipose tissue, and ameliorated adipose tissue hypoxia under obese condition. Of note, inhibition of angiogenesis by sugen-treatment abolished the beneficial effects of Nrg4 on systemic metabolic health. Furthermore, targeted inhibition of Nrg4-ErbB signaling in adipose tissue vasculature using prohibitin binding peptide-conjugated nanocarrier abrogated the enhanced adipose tissue angiogenesis, and canceled the improved metabolic health induced by Nrg4 activation. These data further support a crucial role of Nrg4 in maintaining systemic metabolic homeostasis at least partially through enhancing adipose tissue angiogenesis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Plant myo -inositol transport influences bacterial colonization phenotypes

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites are consistently identified as important mediators of microbial interactions. We combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in seedlings of the model plant Arabidopsis thaliana to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions. While microbial catabolism of this compound has been linked to increased host colonization, we identify bacterial phenotypes that occur in both catabolism-dependent and -independent manners, suggesting that myo-inositol may additionally serve as a eukaryotic-derived signaling molecule to modulate microbial activities. Our data suggest host control of this compound and resulting microbial behavior are important mechanisms at play surrounding the host metabolite myo-inositol.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Greenhouse gas emissions from production chain of a cigarette manufacturing industry in Pakistan

This study quantified greenhouse gas (GHG) emissions from the Pakistan Tobacco Company (PTC) production using a life cycle approach. The PTC production chain comprises of two phases: agricultural activities (Phase I) and industrial activities (Phase II). Data related to agricultural and industrial activities of PTC production chain were collected through questionnaire survey from tobacco growers and records from PTC manufacturing units. The results showed that total GHG emissions from PTC production chain were 44,965, 42,875, and 43,839 tCO{sub 2}e respectively in 2009, 2010, and 2011. Among the agricultural activities, firewood burning for tobacco curing accounted for about 3117, 3565, and 3264 tCO{sub 2}e, fertilizer application accounted for 754, 3251, and 4761 tCO{sub 2}e in 2009, 2010, and 2011, respectively. Among the industrial activities, fossil fuels consumption in stationary sources accounted for 15,582, 12,733, and 13,203 tCO{sub 2}e, fossil fuels used in mobile sources contributed to 2693, 3038, and 3260 tCO{sub 2}e, and purchased electricity consumed resulted in 15,177, 13,556, and 11,380 tCO{sub 2}e in 2009, 2010, and 2011, respectively. The GHG emissions related to the transportation of raw materials and processed tobacco amounted to 6800, 6301, and 7317 respectively in 2009, 2010, and 2011. GHG emissions from energy use in the industrial activities constituted the largest emissions (i.e., over 80%) of GHG emissions as PTC relies on fossil fuels and fossil fuel based electrical power in industrial processes. The total emissions of carbon footprint (CFP) from PTC production were 0.647 tCO{sub 2}e per million cigarettes produced in 2009, 0.675 tCO{sub 2}e per million cigarettes in 2010 and 0.59 tCO{sub 2}e per million cigarettes in 2011. Potential strategies for GHG emissions reductions for PTC production chain include energy efficiency, reducing reliance on fossil fuels in non-mobile sources, adoption of renewable fuels including solar energy, energy from crop residues, and promotion of organic fertilizers. - Highlights: • We quantified greenhouse gas (GHG) emissions from the Pakistan Tobacco Company (PTC). • PTC production chain comprises of two phases: agricultural and industrial activities. • GHG emissions accounts to 44,965, 42,875 and 43,839 tCO{sub 2}e in 2009, 2010, and 2011, respectively. • GHG emissions from energy use in the industrial activities constituted the largest emissions i.e. 80%. • Implications for GHG emissions mitigation strategies for PTC are also discussed in detail.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection

Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed “discontinuous transcription” that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Heterogeneous damage in Li-ion batteries: Experimental analysis and theoretical modeling

We assess the heterogeneous electrochemistry and mechanics in a composite electrode of commercial batteries using synchrotron X-ray tomography analysis and microstructure-resolved computational modeling. We visualize the morphological defects at multi-scales ranging from the macroscopic composite, particle ensembles, to individual single particles. Particle fracture and interfacial debonding are identified in a large set of tomographic data of active particles. Mechanical failure in the regime near the separator is more severe than toward the current collector. The active particles close to the separator experience deeper charge and discharge over cycles and thus are more mechanically loaded. The difference in the Li activity originates from the polarization of the electrolyte potential and the non-uniform distribution of the activation energy for the charge transfer reaction. We model the kinetics of intergranular fracture and interfacial degradation to confirm that the various Li activities are the major cause of the heterogeneous damage. The interfacial failure may reconstruct the conductive network and redistribute the electrochemical activities that render a dynamic nature of electrochemistry and mechanics evolving over time in the composite electrode. We further quantify the influence of the mechanical damage on the metrics of battery performance. We simulate the electrochemical impedance profile to build a relationship between the interfacial debonding and the impedance of electron transport and surface charge transfer. Lastly, the mechanical failure disrupts the conduction path of electrons and results in significant polarization and capacity loss in batteries.

25 ENERGY STORAGE↗

DOE OSTI2020

Improved plutonium and americium photon branching ratios from microcalorimeter gamma spectroscopy

Photon branching ratios are critical input data for activities such as nuclear materials protection and accounting because they allow material compositions to be extracted from measurements of gamma-ray intensities. Uncertainties in these branching ratios are often a limiting source of uncertainty in composition determination. Here, we use high statistics, high resolution - (60–70 eV full-width-at-half-maximum at 100 keV) gamma-ray spectra acquired using microcalorimeter sensors to substantially reduce the uncertainties for 11 plutonium ( 238 Pu, 239 Pu, 241 Pu) and 241 Am branching ratios important for material control and accountability and nuclear forensics in the energy range of 125 keV to 208 keV. Lastly, we show a reduction in uncertainty of over a factor of three for one branching ratio and a factor of 2–3 for four branching ratios.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

PSelInv – A distributed memory parallel algorithm for selected inversion: The non-symmetric case

This paper generalizes the parallel selected inversion algorithm called PSelInv to sparse non-symmetric matrices. We assume a general sparse matrix A has been decomposed as $PAQ$ = $LU$ on a distributed memory parallel machine, where L, U are lower and upper triangular matrices, and P, Q are permutation matrices, respectively. The PSelInvmethod computes selected elements of $A$ -1 . The selection is confined by the sparsity pattern of the matrix A T . Here our algorithm does not assume any symmetry properties of A, and our parallel implementation is memory efficient, in the sense that the computed elements of $A$ -T overwrites the sparse matrix $L + U$ in situ . PSelInv involves a large number of collective data communication activities within different processor groups of various sizes. In order to minimize idle time and improve load balancing, tree-based asynchronous communication is used to coordinate all such collective communication. Numerical results demonstrate that PSelInv can scale efficiently to 6,400 cores for a variety of matrices.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Structure of Ddn, the Deazaflavin-Dependent Nitroreductase from Mycobacterium tuberculosis Involved in Bioreductive Activation of PA-824

Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica .Mutagenesis studies based on these structures identified residues important for binding of F and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs

Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. - Highlights: • MOV10 can function as a co-factor of HIV-1 Rev. • MOV10 facilitates Rev/RRE-dependent transport of viral mRNAs. • MOV10 interacts with Rev in an RNA-independent manner. • The DEAG-box of MOV10 is required for the enhancement of Rev/RRE-dependent export.

60 APPLIED LIFE SCIENCES↗