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At least 937 records · Page 52

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DOE OSTI2016

‘Candidatus Liberibacter asiaticus’, causal agent of citrus Huanglongbing, is reduced by treatment with Brassinosteroids

Huanglongbing (HLB) constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, ‘Candidatus Liberibacter asiaticus’. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with next generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. Lastly, the results demonstrate that epibrassinolide may provide a useful tool for the management of HLB.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis

With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations.

Science & Technology - Other Topics↗

DOE OSTI2021

Transmission of the atypical/Nor98 scrapie agent to Suffolk sheep with VRQ/ARQ, ARQ/ARQ, and ARQ/ARR genotypes

Scrapie is a transmissible spongiform encephalopathy that occurs in sheep. Atypical/Nor98 scrapie occurs in sheep that tend to be resistant to classical scrapie and it is thought to occur spontaneously. The purpose of this study was to test the transmission of the Atypical/Nor98 scrapie agent in three genotypes of Suffolk sheep and characterize the distribution of misfolded prion protein (PrP Sc ). Ten sheep were intracranially inoculated with brain homogenate from a sheep with Atypical/Nor98 scrapie. All sheep with the ARQ/ARQ and ARQ/ARR genotypes developed Atypical/Nor98 scrapie confirmed by immunohistochemistry, and one sheep with the VRQ/ARQ genotype had detectable PrP Sc consistent with Atypical/Nor98 scrapie at the experimental endpoint of 8 years. Sheep with mild early accumulations of PrP Sc in the cerebellum had concomitant retinal PrP Sc . Accordingly, large amounts of retinal PrP Sc were identified in clinically affected sheep and sheep with dense accumulations of PrP Sc in the cerebellum.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Environmental associations of Ophidiomyces ophidiicola , the causative agent of ophidiomycosis in snakes

Emerging pathogenic fungi have become a topic of conservation concern due to declines observed in several host taxa. One emerging fungal pathogen, Ophidiomyces ophidiicola, is well documented as the causative agent of ophidiomycosis, otherwise known as snake fungal disease (SFD). O. ophidiicola has been found to cause disease in a variety of snake species across the United States, including the eastern massasauga (Sistrurus catenatus), a federally threatened rattlesnake species. Most work to date has involved detecting O. ophidiicola for diagnosis of infection through direct sampling of snakes, and attempts to detect O. ophidiicola in the abiotic environment to better understand its distribution, seasonality, and habitat associations are lacking. We collected topsoil and groundwater samples from four macrohabitat types across multiple seasons in northern Michigan at a site where Ophidiomyces infection has been confirmed in eastern massasauga. Using a quantitative PCR (qPCR) assay developed for O. ophidiicola, we detected Ophidiomyces DNA in topsoil but observed minimal to no detection in groundwater samples. Detection frequency did not differ between habitats, but samples grouped seasonally showed higher detection during mid-summer. We found no relationships of detection with hypothesized environmental correlates such as soil pH, temperature, or moisture content. Furthermore, the distribution of Ophidiomyces positive samples across the site was not linked to estimated space use of massasaugas. Our data suggests that season has some effect on the presence of Ophidiomyces. Differences in presence between habitats may exist but are likely more dependent on the time of sampling and currently uninvestigated soil or biotic parameters. These findings build on our understanding of Ophidiomyces ecology and epidemiology to help inform where and when snakes may be exposed to the fungus in the environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Calibration verification for stochastic agent-based disease spread models

Accurate disease spread modeling is crucial for identifying the severity of outbreaks and planning effective mitigation efforts. To be reliable when applied to new outbreaks, model calibration techniques must be robust. However, current methods frequently forgo calibration verification (a stand-alone process evaluating the calibration procedure) and instead use overall model validation (a process comparing calibrated model results to data) to check calibration processes, which may conceal errors in calibration. In this work, we develop a stochastic agent-based disease spread model to act as a testing environment as we test two calibration methods using simulation-based calibration, which is a synthetic data calibration verification method. The first calibration method is a Bayesian inference approach using an empirically-constructed likelihood and Markov chain Monte Carlo (MCMC) sampling, while the second method is a likelihood-free approach using approximate Bayesian computation (ABC). Simulation-based calibration suggests that there are challenges with the empirical likelihood calculation used in the first calibration method in this context. These issues are alleviated in the ABC approach. Despite these challenges, we note that the first calibration method performs well in a synthetic data model validation test similar to those common in disease spread modeling literature. We conclude that stand-alone calibration verification using synthetic data may benefit epidemiological researchers in identifying model calibration challenges that may be difficult to identify with other commonly used model validation techniques.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

An Implementation for Transforming a Home Energy Management System to a Multi-agent System

In the United States, 41% of produced energy is consumed by the building sector, i.e. residential and commercial buildings (Building Energy Data Book, Buildings Sector, US Department of Energy, Office of Energy Efficiency and Renewable Energy, Building Technologies Office, 2012. n.d.). The anticipation is that Home Energy Management Systems (HEMS) will support energy efficiency gains through control of the devices in an optimal fashion. New opportunities are offering the ability to integrate grid type controls and the most suitable way to perform these controls is through a multi-agent system (MAS). In this paper, approaches on supporting a HEMS and MAS integration are discussed.

Zandi, Helia↗

DOE OSTI2019

Thermodynamic Studies on a Hydrogen Bonded Acidic (HBA) 3,5-bis(trifluoromethyl)phenol-Functionalized Polymer as a Gas Chromatography Stationary Phase for Selectively Speciating Chemical Warfare Agents

We used for the first time hydrogen bonded acidic (HBA) polymer, poly{methyl[3-(2-hydroxyl, 4,6-bistrifluoromethyl)phenyl]propylsiloxane } , (DKAP), as stationary phase for gas chromatography (GC) of chemical warfare agent (CWA) organophosphate (OP), surrogates, dimethylmethylphosphonate (DMMP), diisopropylmethylphosphonate (DIMP), diethylmethylphosphonate (DEMP), and trimethylphosphate (TMP), with high sensitivity and selectivity. Adsorption of OPs to DKAP was one-to-several orders of magnitude higher relative to commercial polar, mid-polar, and nonpolar stationary phases. We also performed for the first-time thermodynamic studies on the adsorption of OP vapors and obtained quantitative binding energy data for interactions with various stationary phases. These data help to identify the correct pair of hetero-polar columns for a two-dimensional system, employing nonpolar stationary phase as GC1, rejecting interfering molecules, and DKAP as GC2 stationary phase, for selective, sensitive, and rapid field detection of CWAs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2011

Report for Development of a Census Array and Evaluation of the Array to Detect Biothreat Agents and Environmental Samples for DHS

The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Census Array. We designed a Census/Detection Array to detect all sequenced viruses (including phage), bacteria (eubacteria), and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to be unique relative to the human genome. A combination of 'detection' probes with high levels of conservation within a family plus 'census' probes targeting strain/isolate specific regions enabled detection and taxonomic classification from the level of family down to the strain. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. We tested the array with purified bacterial and viral DNA/RNA samples, artificial mixes of known bacterial/viral samples, spiked DNA against complex background including BW aerosol samples and soil samples, and environmental samples to evaluate the array's sensitivity and forensic capability. The data were analyzed using our novel maximum likelihood software. For most of the organisms tested, we have achieved at least species level discrimination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Diffusion among cognitively complex agents (Final Report)

This is the final report for the Early Career LDRD ”Diffusion Among Cognitively Complex Agents” (DACCA). This report consists of three main parts. In the first part we overview the motivation and summarize our accomplishments. The second part provides a detailed description of the model and simulation results. The third part describes an Amazon Me chanical Turk based experiment design to gather data for calibrating and validating this model.

Lakkaraju, Kiran↗

DOE OSTI2012

Stability Study for Ultra-Dilute Chemical Warfare Agent Standards

Ultra-dilute (10 ppm) chemical warfare agent (CWA) standards are being supplied to the Environmental Response Laboratory Network (ERLN) laboratories to allow the use of authentic standards to assist in analyses required in the aftermath of a terrorist attack with CWAs. It is critical for the ERLN laboratories to be able to work with authentic CWA standards to allow the unambiguous identification and quantification of CWAs. The ultra dilute standards are synthesized in-house for use in analytical method development by the ERLN laboratories. However, data regarding the long-term stability of the ultra-dilute standards are lacking. For this reason, a study was undertaken to monitor the concentrations of CWAs in ultra-dilute standards as a function of time, under normal conditions of storage and use. The data collected in such a study could then be used to estimate reliable holding times for the ultra-dilute standards.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2013

EpiSimS: Large-Scale Agent-based Modeling of the Spread of Disease [Slides]

EpiSimS is a stochastic agent-based computer model that simulates the spread of disease in metropolitan areas.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2011

EconoSim: Discrete Event Simulations of an Agent-based Model of the U.S. Economy

EconoSim uses the SimCore library to implement discrete event simulations of an agent-based model of the U.S. economy. Events in a simulation are represented by Infos, which are sent to Services that reside on Entitys for processing. Entitys are the primary objects in a simulation, whose behaviors are implemented by the responses of the Services they provide to Infos.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2011

Report for Detection of Biothreat Agents and Environmental Samples using the LLNL Virulence Array for DHS

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Report for Evaluation of Canonical SNP Taqman Assays to Detect Biothreat Agents and Environmental Samples for DHS

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Superhydrophobic Powder Additives to Enhance Chemical Agent Resistant Coating Systems for Military Equipment for the US Marine Corps (USMC) Corrosion Prevention and Control (CPAC) Program

The primary goal of the CPAC program at ORNL was to explore the feasibility of introducing various silica-based superhydrophobic (SH) powder additives as a way to improve the corrosion resistance of US Department of Defense (DOD) military-grade chemical agent resistant coating (CARC) systems. ORNL had previously developed and patented several SH technologies of interest to the USMC, and one of the objectives of this program was to identify methods to incorporate these technologies into the USMC’s corrosion-resistance strategy. This report discusses findings of the CPAC and their application.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2015

Investigating the Hydrolysis Reactions of a Chemical Warfare Agent Surrogate: A Systematic Study using 1 H, 13 C, 17 O, 19 F, 31 P, and 35 Cl NMR Spectroscopy

During the summer of 2015, I participated in the DHS HS-STEM fellowship at Sandia National Laboratories (SNL, NM) under the supervision of Dr. Todd M. Alam in his Nuclear Magnetic Resonance (NMR) Spectroscopy research group. While with the group, my main project involved pursing various hydrolysis reactions with Diethyl Chlorophosphate (DECP), a surrogate for the agent Sarin (GB). Specifically, I performed different hydrolysis reactions, monitored and tracked the different phosphorous containing species using phosphorous ( 31 P) NMR spectroscopy. With the data collected, I performed kinetics studies mapping the rates of DECP hydrolysis. I also used the NMR of different nuclei such as 1 H, 13 C, 17 O, and 35 Cl to help understand the complexity of the reactions that take place. Finally, my last task at SNL was to work with Insensitive Nuclei Enhanced by Polarization Transfer (INEPT) NMR Spectroscopy optimizing conditions for 19 F- 31 P filtering NMR experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Highly Multiplexed Assays for Detection of Biothreat and Food Safety Agents, CRADA No. TC02156.0

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and BioSearch Technologies Inc. (BTI) of Novato, California, to develop Multiplexed Molecular Assays for the Rapid and Sensitive Detection of Microbial Agents of Concern for Bioterrorism and Food Safety for the Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition (CFSAN). There are no outstanding leans for this project.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2018

Highly Multiplexed Assays for Detection of Biothreat and Food Safety Agents Final Report CRADA No. TC02156.0

59 BASIC BIOLOGICAL SCIENCES↗