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At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Driver Identification Dataset

The ORNL Driver Identification Dataset was created to collect and analyze driving behavior data from 50 different drivers. Each driver operated a 2014 Kenworth T270 Class 6 truck around Fort Collins, Colorado while various data sources recorded their driving behavior and vehicle performance. The dataset includes CANbus (Controller Area Network) data, GPS data, inertial measurement data, and biometric data from a heart rate monitor. A cyberattack was executed during each drive, which caused multiple dashboard warning lights to illuminate and set the tachometer and speedometer to zero, regardless of actual speed. The attack was stopped either after one minute or if the driver pulled over. By downloading the dataset, you agree to the following: 1) I will not use or disclose the data for any purpose other than Research as that term is defined in 10 CFR 745.102. 2) I will not, under any circumstances, request or accept private or linking identifiers for the data used. 3) I will not attempt to determine the identity of the individuals associated with the data. 4) I will use appropriate safeguards to prevent the use or disclose of the data for any purpose other than Research.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2013

Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer

Introduction: Current markers for prostate cancer, such as PSA lack specificity. Therefore, novel biomarkers are needed. Unfortunately, biomarker discovery from body fluids is often hampered by the high abundance of many proteins unrelated to disease. An attractive alternative biomarker discovery approach is the isolation of small vesicles (exosomes, ~100 nm). They contain proteins that are specific to the tissue from which they are derived and therefore can be considered as treasure chests for disease-specific marker discovery. Profiling prostate cancer-derived exosomes could reveal new markers for this malignancy. Materials and Methods: Exosomes were isolated from 2 immortalized primary prostate epithelial cells (PNT2C2 and RWPE-1) and 2 PCa cell lines (PC346C and VCaP) by ultracentrifugation. Proteomic analyses utilized a nanoLC coupled with an LTQ-Orbitrap operated in tandem MS (MS/MS) mode, followed by the Accurate Mass and Time (AMT) tag approach. Exosomal proteins were validated by Western blotting. A Tissue Micro Array, containing 481 different PCa samples (radical prostatectomy), was used to correlate candidate markers with several clinical-pathological parameters such as PSA, Gleason score, biochemical recurrence, and (PCa-related) death. Results: Proteomic characterization resulted in the identification of 263 proteins by at least 2 peptides. Specifically analysis of exosomes from PNT2C2, RWPE-1, PC346C, and VCaP identified 248, 233, 169, and 216 proteins, respectively. Statistical analyses revealed 52 proteins differently expressed between PCa and control cells, 9 of which were more abundant in PCa. Validation by Western blotting confirmed a higher abundance of FASN, XPO1 and PDCD6IP (ALIX) in PCa exosomes. The Tissue Micro 4 Array showed strong correlation of higher Gleason scores and local recurrence with increased cytoplasmic XPO1 (P<0.001). Conclusions: Differentially abundant proteins of cell line-derived exosomes make a clear subdivision between benign and malignant origin. Validation showed a preferential abundance of PDCD6IP, FASN and XPO1. Cytoplasmic XPO1 is the most promising candidate biomarker.

biomarkers↗
DOE OSTI2014

Identification of a Novel Drug Lead That Inhibits HCV Infection and Cell-to-Cell Transmission by Targeting the HCV E2 Glycoprotein

We report that Hepatitis C Virus (HCV) infects 200 million individuals worldwide. Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin. Recently, two crystal structures of the core of the HCV E2 protein (E2c) have been determined, providing structural information that can now be used to target the E2 protein and develop drugs that disrupt the early stages of HCV infection by blocking E2’s interaction with different host factors. Using the E2c structure as a template, we have created a structural model of the E2 protein core (residues 421–645) that contains the three amino acid segments that are not present in either structure. Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction. We used surface plasmon resonance detection to screen the ligand set for binding to recombinant E2 protein, and the best binders were subsequently tested to identify compounds that inhibit the infection of Huh-7 cells by HCV. One compound, 281816, blocked E2 binding to CD81 and inhibited HCV infection in a genotype-independent manner with IC50’s ranging from 2.2 µM to 4.6 µM. 281816 blocked the early and late steps of cell-free HCV entry and also abrogated the cell-to-cell transmission of HCV. Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Systems Level Analysis and Identification of Pathways and Networks Associated with Liver Fibrosis

Toxic liver injury causes necrosis and fibrosis, which may lead to cirrhosis and liver failure. Despite recent progress in understanding the mechanism of liver fibrosis, our knowledge of the molecular-level details of this disease is still incomplete. The elucidation of networks and pathways associated with liver fibrosis can provide insight into the underlying molecular mechanisms of the disease, as well as identify potential diagnostic or prognostic biomarkers. Towards this end, we analyzed rat gene expression data from a range of chemical exposures that produced observable periportal liver fibrosis as documented in DrugMatrix, a publicly available toxicogenomics database. We identified genes relevant to liver fibrosis using standard differential expression and co-expression analyses, and then used these genes in pathway enrichment and protein-protein interaction (PPI) network analyses. We identified a PPI network module associated with liver fibrosis that includes known liver fibrosis-relevant genes, such as tissue inhibitor of metalloproteinase-1, galectin-3, connective tissue growth factor, and lipocalin-2. We also identified several new genes, such as perilipin-3, legumain, and myocilin, which were associated with liver fibrosis. We further analyzed the expression pattern of the genes in the PPI network module across a wide range of 640 chemical exposure conditions in DrugMatrix and identified early indications of liver fibrosis for carbon tetrachloride and lipopolysaccharide exposures. Although it is well known that carbon tetrachloride and lipopolysaccharide can cause liver fibrosis, our network analysis was able to link these compounds to potential fibrotic damage before histopathological changes associated with liver fibrosis appeared. These results demonstrated that our approach is capable of identifying early-stage indicators of liver fibrosis and underscore its potential to aid in predictive toxicity, biomarker identification, and to generally identify disease-relevant pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we then selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. For genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Finally, structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses

Quantitative gene expression analysis is an important tool in the scientist’s belt. The identification of evenly expressed reference genes is necessary for accurate quantitative gene expression analysis, whether by traditional RT-PCR (reverse-transcription polymerase chain reaction) or by qRT-PCR (quantitative real-time PCR; qPCR). In the Stramenopiles (the major line of eukaryotes that includes brown algae) there is a noted lack of known reference genes for such studies, largely due to the absence of available molecular tools. Here we present a set of nine reference genes (Elongation Factor 1 alpha (EF1A), Elongation Factor 2 alpha (EF2A), Elongation Factor 1 beta (EF1B), 14-3-3 Protein, Ubiquitin Conjugating Enzyme (UBCE2), Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH), Actin Related Protein Complex (ARP2/3), Ribosomal Protein (40s; S23), and Actin) for the brown alga Fucus distichus . These reference genes were tested on adult sporophytes across six abiotic stress conditions (desiccation, light and temperature modification, hormone addition, pollutant exposure, nutrient addition, and wounding). Suitability of these genes as reference genes was quantitatively evaluated across conditions using standard methods and the majority of the tested genes were evaluated favorably. However, we show that normalization genes should be chosen on a condition-by-condition basis. We provide a recommendation that at least two reference genes be used per experiment, a list of recommended pairs for the conditions tested here, and a procedure for identifying a suitable set for an experimenter’s unique design. With the recent expansion of interest in brown algal biology and accompanied molecular tools development, the variety of experimental conditions tested here makes this study a valuable resource for future work in basic biology and understanding stress responses in the brown algal lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

First comprehensive identification of cardiac proteins with putative increased O-GlcNAc levels during pressure overload hypertrophy

Protein posttranslational modifications (PTMs) by O-GlcNAc globally rise during pressure-overload hypertrophy (POH). However, a major knowledge gap exists on the specific proteins undergoing changes in O-GlcNAc levels during POH primarily because this PTM is low abundance and easily lost during standard mass spectrometry (MS) conditions used for protein identification. Methodologies have emerged to enrich samples for O-GlcNAcylated proteins prior to MS analysis. Accordingly, our goal was to identify the specific proteins undergoing changes in O-GlcNAc levels during POH. We used C57/Bl6 mice subjected to Sham or transverse aortic constriction (TAC) to create POH. From the hearts, we labelled the O-GlcNAc moiety with tetramethylrhodamine azide (TAMRA) before sample enrichment by TAMRA immunoprecipitation (IP). We used LC-MS/MS to identify and quantify the captured putative O-GlcNAcylated proteins. We identified a total of 700 putative O-GlcNAcylated proteins in Sham and POH. Two hundred thirty-three of these proteins had significantly increased enrichment in POH over Sham suggesting higher O-GlcNAc levels whereas no proteins were significantly decreased by POH. We examined two MS identified metabolic enzymes, CPT1B and the PDH complex, to validate by immunoprecipitation. We corroborated increased O-GlcNAc levels during POH for CPT1B and the PDH complex. Enzyme activity assays suggests higher O-GlcNAcylation increases CPT1 activity and decreases PDH activity during POH. In summary, we generated the first comprehensive list of proteins with putative changes in O-GlcNAc levels during POH. Our results demonstrate the large number of potential proteins and cellular processes affected by O-GlcNAc and serve as a guide for testing specific O-GlcNAc-regulated mechanisms during POH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Forward variable selection enables fast and accurate dynamic system identification with Karhunen-Loève decomposed Gaussian processes

A promising approach for scalable Gaussian processes (GPs) is the Karhunen-Loève (KL) decomposition, in which the GP kernel is represented by a set of basis functions which are the eigenfunctions of the kernel operator. Such decomposed kernels have the potential to be very fast, and do not depend on the selection of a reduced set of inducing points. However KL decompositions lead to high dimensionality, and variable selection thus becomes paramount. This paper reports a new method of forward variable selection, enabled by the ordered nature of the basis functions in the KL expansion of the Bayesian Smoothing Spline ANOVA kernel (BSS-ANOVA), coupled with fast Gibbs sampling in a fully Bayesian approach. It quickly and effectively limits the number of terms, yielding a method with competitive accuracies, training and inference times for tabular datasets of low feature set dimensionality. Theoretical computational complexities are O ( N P 2 ) in training and O ( P ) per point in inference, where N is the number of instances and P the number of expansion terms. The inference speed and accuracy makes the method especially useful for dynamic systems identification, by modeling the dynamics in the tangent space as a static problem, then integrating the learned dynamics using a high-order scheme. The methods are demonstrated on two dynamic datasets: a ‘Susceptible, Infected, Recovered’ (SIR) toy problem, along with the experimental ‘Cascaded Tanks’ benchmark dataset. Comparisons on the static prediction of time derivatives are made with a random forest (RF), a residual neural network (ResNet), and the Orthogonal Additive Kernel (OAK) inducing points scalable GP, while for the timeseries prediction comparisons are made with LSTM and GRU recurrent neural networks (RNNs) along with the SINDy package.

Hayes, Kyle↗
DOE OSTI2024

Identification and time evolution of thionyl chloride (SOCl 2 ) radiolysis products

In this study, innovative solutions are needed to reduce the amount of high-level waste generated by used nuclear fuel recycling strategies to support the widespread adoption of sustainable nuclear fission energy technologies. To this end, a new sulfur chloride-based process has been developed to recycle zirconium alloy-based materials, which make up a significant fraction of high-level radioactive waste. To support the continued development of this process, we present new data on the potential reaction pathways over time of the products arising from the gamma and electron beam radiolysis of neat thionyl chloride (SOCl 2 ). Interrogation of the gamma irradiated liquid by Raman spectroscopy provided more conclusive identification of the SOCl 2 degradation products, specifically sulfur dichloride (SCl 2 ), molecular chlorine (Cl 2 ), sulfur dioxide (SO 2 ), and sulfuryl chloride (SO 2 Cl 2 ). In comparison, the high dose rate (~10 7 Gy s -1 ) electron beam irradiations formed significantly more degradation products. For both cobalt-60 gamma and electron beam irradiations, the observed degradation products were found to evolve as a function of time post-irradiation via the same reaction pathways, with indication of a solvent regeneration mechanism. These findings are fortuitous for process development, as such a mechanism would be beneficial for process longevity and cost effectiveness.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Wildfires identification: Semantic segmentation using support vector machine classifier

This paper deals with wildfire identification in the Alaska regions as a semantic segmentation task using support vector machine classifiers. Instead of colour information represented by means of BGR channels, we proceed with a normalized reflectance over 152 days so that such time series is assigned to each pixel. We compare models associated with $\mathcal{l}1$-loss and $\mathcal{l}2$-loss functions and stopping criteria based on a projected gradient and duality gap in the presented benchmarks.

Pecha, Marek↗
DOE OSTI2013

Identification and Characterization of Soluble Factors Involved in Delayed Effects of Low Dose Radiation (Final Report)

This is a 'glue grant' that was part of a DOE Low Dose project entitled 'Identification and Characterization of Soluble Factors Involved in Delayed Effects of Low Dose Radiation'. This collaborative program has involved Drs. David L. Springer from Pacific Northwest National Laboratory (PNNL), John H. Miller from Washington State University, Tri-cities (WSU) and William F. Morgan then from the University of Maryland, Baltimore (UMB). In July 2008, Dr. Morgan moved to PNNL and Dr. Janet E. Baulch became PI for this project at University of Maryland. In November of 2008, a one year extension with no new funds was requested to complete the proteomic analyses. The project stemmed from studies in the Morgan laboratory demonstrating that genomically unstable cells secret a soluble factor or factors into the culture medium, that cause cytogenetic aberrations and apoptosis in normal parental GM10115 cells. The purpose of this project was to identify the death inducing effect (DIE) factor or factors, estimate their relative abundance, identify the cell signaling pathways involved and finally recapitulate DIE in normal cells by exogenous manipulation of putative DIE factors in culture medium. As reported in detail in the previous progress report, analysis of culture medium from the parental cell line, and stable and unstable clones demonstrated inconsistent proteomic profiles as relate to candidate DIE factors. While the proposed proteomic analyses did not provide information that would allow DIE factors to be identified, the analyses provided another important set of observations. Proteomic analysis suggested that proteins associated with the cellular response to oxidative stress and mitochondrial function were elevated in the medium from unstable clones in a manner consistent with mitochondrial dysfunction. These findings correlate with previous studies of these clones that demonstrated functional differences between the mitochondria of stable and unstable clones. These mitochondrial abnormalities in the unstable clones contributes to oxidative stress.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2013

Source identification in acoustics and structural mechanics using Sierra/SD.

In this report we derive both time and frequency-domain methods for inverse identification of sources in elastodynamics and acoustics. The inverse/design problem is cast in a PDE-constrained optimization framework with efficient computation of gradients using the adjoint method. The implementation of source inversion in Sierra/SD is described, and results from both time and frequency domain source inversion are compared to actual experimental data for a weapon store used in captive carry on a military aircraft. The inverse methodology is advantageous in that it provides a method for creating ground based acoustic and vibration tests that can reduce the actual number of flight tests, and thus, saving costs and time for the program.

Walsh, Timothy Francis↗
DOE OSTI2014

Technology Assessment for Proof-of-Concept UF6 Cylinder Unique Identification Task 3.1.2 Report – Survey and Assessment of Technologies

The National Nuclear Security Administration (NNSA) Office of Nonproliferation and International Security’s (NA-24) Next Generation Safeguards Initiative (NGSI) and the nuclear industry have begun to develop approaches to identify and monitor uranium hexafluoride (UF6) cylinders. The NA-24 interest in a global monitoring system for UF6 cylinders relates to its interest in supporting the International Atomic Energy Agency (IAEA) in deterring and detecting diversion of UF6 (e.g., loss of cylinder in transit) and undeclared excess production at conversion and enrichment facilities. The industry interest in a global monitoring system for UF6 cylinders relates to the improvements in operational efficiencies that such a system would provide. This task is part of an effort to survey and assess technologies for a UF6 cylinder to identify candidate technologies for a proof-of-concept demonstration and evaluation for the Cylinder Identification System (CIS).

Cylinder↗
DOE OSTI2014

Identification of Process Suitable Diluent

The Sigma Team for Minor Actinide Separation (STMAS) was formed within the USDOE Fuel Cycle Research and Development (FCRD) program in order to develop more efficient methods for the separation of americium and other minor actinides (MA) from used nuclear fuel. The development of processes for MA separations is driven by the potential benefits; reduced long-term radiotoxicty of waste placed in a geologic repository, reduced timeframe of waste storage, reduced repository heat load, the possibility of increased repository capacity, and increased utilization of energy potential of used nuclear fuel. The research conducted within the STMAS framework is focused upon the realization of significant simplifications to aqueous recycle processes proposed for MA separations. This report describes the research efforts focused upon the identification of a process suitable diluent for a flowsheet concept for the separation of MA which is based upon the dithiophosphinic acid (DPAH) extractants previously developed at the Idaho National Laboratory (INL).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2014

Optimality conditions for the numerical solution of optimization problems with PDE constraints: Theoretical framework and applications to parameter identification and optimal control problems

A theoretical framework for the numerical solution of partial differential equation (PDE) constrained optimization problems is presented in this report. This theoretical framework embodies the fundamental infrastructure required to efficiently implement and solve this class of problems. Detail derivations of the optimality conditions required to accurately solve several parameter identification and optimal control problems are also provided in this report. This will allow the reader to further understand how the theoretical abstraction presented in this report translates to the application.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Identification of genes that regulate phosphate acquisition and plant performance during arbuscular my corrhizal symbiosis in medicago truncatula and brachypodium distachyon

Most vascular flowering plants have the ability to form symbiotic associations with arbuscular mycorrhizal (AM) fungi. The symbiosis develops in the roots and can have a profound effect on plant productivity, largely through improvements in plant mineral nutrition. Within the root cortical cells, the plant and fungus create novel interfaces specialized for nutrient transfer, while the fungus also develops a network of hyphae in the rhizosphere. Through this hyphal network, the fungus acquires and delivers phosphate and nitrogen to the root. In return, the plant provides the fungus with carbon. In addition, to enhancing plant mineral nutrition, the AM symbiosis has an important role in the carbon cycle, and positive effects on soil health. Here we identified and characterized plant genes involved in the regulation and functioning of the AM symbiosis in Medicago truncatula and Brachypodium distachyon. This included the identification and and characterization of a M. truncatula transcription factors that are required for symbiosis. Additionally, we investigated the molecular basis of functional diversity among AM symbioses in B. distachyon and analysed the transcriptome of Brachypodium distachyon during symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Threat Identification Parameters for a Stolen Category 1 Radioactive Source

Radioactive sources are used very widely for research and practical applications across medicine, industry, government, universities, and agriculture. The risks associated with these sources vary widely depending on the specific radionuclide used to make the source, source activity, and its chemical and physical form. Sources are categorized by a variety of classification schemes according to the specific risk they pose to the public. This report specifically addresses sources that are classified in the highest category for health risk (category 1). Exposure to an unshielded or lightly shielded category 1 source is extremely dangerous to life and health and can be fatal in relatively short exposure times measured in seconds to minutes. A Category 1 source packaged according to the guidelines dictated by the NRC and U.S. Department of Transportation will typically be surrounded by a large amount of dense shielding material, but will still exhibit a significant dose rate in close proximity. Detection ranges for Category 1 gamma ray sources can extend beyond 5000 ft, but will depend mostly on the source isotope and activity, and the level of shielding around the source. Category 1 sources are easy to detect, but difficult to localize. Dose rates in proximity to an unshielded Category 1 source are extraordinarily high. At distances of a few hundred feet, the functionality of many commonly used handheld instruments will be extremely limited for both the localization and identification of the source. Radiation emitted from a Category 1 source will scatter off of both solid material (ground and buildings) and the atmosphere, a phenomenon known as skyshine. This scattering affects the ability to easily localize and find the source.

07 ISOTOPE AND RADIATION SOURCES↗