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At least 37 records · Page 2

Isolation and Whole-Genome Sequencing of Environmental Campylobacter

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter has a significant impact on human health. In the developed world, most campylobacteriosis cases are attributed to the consumption of undercooked, contaminated poultry; however, it has been shown that Campylobacter can be transmitted to humans through contaminated water and other types of food, including beef and milk. As such, high-resolution microbial source-tracking is essential for health department officials to determine the source(s) of Campylobacter outbreaks. For these reasons, this paper provides the techniques needed for isolation of Campylobacter from agricultural and environmental sources, as well as human clinical specimens. Additionally, we describe a simple method for preparing high-quality genomic DNA that can be used for whole-genome sequencing and downstream bioinformatics analyses of Campylobacter genotypes.

59 BASIC BIOLOGICAL SCIENCES↗

Photometer for tracking a moving light source

A photometer that tracks a path of a moving light source with little or no motion of the photometer components. The system includes a non-moving, truncated paraboloid of revolution, having a paraboloid axis, a paraboloid axis, a small entrance aperture, a larger exit aperture and a light-reflecting inner surface, that receives and reflects light in a direction substantially parallel to the paraboloid axis. The system also includes a light processing filter to receive and process the redirected light, and to issue the processed, redirected light as processed light, and an array of light receiving elements, at least one of which receives and measures an associated intensity of a portion of the processed light. The system tracks a light source moving along a path and produces a corresponding curvilinear image of the light source path on the array of light receiving elements. Undesired light wavelengths from the light source may be removed by coating a selected portion of the reflecting inner surface or another light receiving surface with a coating that absorbs incident light in the undesired wavelength range.

Strawa, Anthony W.↗

Water balance model (WBM) v.1.0.0: a scalable gridded global hydrologic model with water-tracking functionality

Abstract. This paper describes the University of New Hampshire Water Balance Model, WBM, a process-based gridded global hydrologic model that simulates the land surface components of the global water cycle and includes water extraction for use in agriculture and domestic sectors. The WBM was first published in 1989; here, we describe the first fully open-source WBM version (v.1.0.0). Earlier descriptions of WBM methods provide the foundation for the most recent model version that is detailed here. We present an overview of the model functionality, utility, and evaluation of simulated global river discharge and irrigation water use. This new version adds a novel suite of water source tracking modules that enable the analysis of flow-path histories on water supply. A key feature of WBM v.1.0.0 is the ability to identify the partitioning of sources for each stock or flux within the model. Three different categories of tracking are available: (1) primary inputs of water to the surface of the terrestrial hydrologic cycle (liquid precipitation, snowmelt, glacier melt, and unsustainable groundwater); (2) water that has been extracted for human use and returned to the terrestrial hydrologic system; and (3) runoff originating from user-defined spatial land units. Such component tracking provides a more fully transparent model in that users can identify the underlying mechanisms generating the simulated behavior. We find that WBM v.1.0.0 simulates global river discharge and irrigation water withdrawals well, even with default parameter settings, and for the first time, we are able to show how the simulation arrives at these fluxes by using the novel tracking functions.

54 ENVIRONMENTAL SCIENCES↗

A demonstration of nanoradian VLBI tracking for deep space navigation

Differential VLBI measurements of the shift in angular position of P 0201+113 due to the effect of Jupiter's gravitational field demonstrate a nanoradian-level, natural-source tracking capability. The high accuracy was achieved by measuring the VLBI delay and delay rate of the target as well as the delays and rates of 5 or more natural radio sources, forming a local reference frame. This accuracy should also be attainable with spacecraft targets. A set of angular positions were inferred for each of two epochs in March and April of 1988. These positions were then differenced to measure the effect of the Jovian gravitational deflection. The differential measurement is largely insensitive to radio source position and structure errors. An additional analysis of the same data, using another source, P 0202+14, as the target, verified that a null planetary gravitational deflection result could also be obtained for a raypath far from any planet. For both targets, the RMS angular scatter of the differential deflections about their expected behavior was about 1.3 nanoradians.

Treuhaft, R. N.↗

Microbial diversity in an intensively managed landscape is structured by landscape connectivity

Intensively managed land increases the rate of nutrient and particle transport within a basin, but the impact of these changes on microbial community assembly patterns at the basin scale is not yet understood. The objective of this study was to investigate how landscape connectivity and dispersal impacts microbial diversity in an agricultural-dominated watershed. We characterized soil, sediment and water microbial communities along the Upper Sangamon River basin in Illinois-a 3600 km 2 watershed strongly influenced by human activity, especially landscape modification and extensive fertilization for agriculture. We employed statistical and network analyses to reveal the microbial community structure and interactions in the critical zone (water, soil and sediment media). Using a Bayesian source tracking approach, we predicted microbial community connectivity within and between the environments. We identified strong connectivity within environments (up to 85.4 ± 13.3% of sequences in downstream water samples sourced from upstream samples, and 44.7 ± 26.6% in soil and sediment samples), but negligible connectivity across environments, which indicates that microbial dispersal was successful within but not between environments. Species sorting based on sample media type and environmental parameters was the dominant driver of community dissimilarity. Lastly, we constructed operational taxonomic unit association networks for each environment and identified a number of co-occurrence relationships that were shared between habitats, suggesting that these are likely to be ecologically significant.

59 BASIC BIOLOGICAL SCIENCES↗

A Space Based Internet Protocol System for Sub-Orbital Tracking and Control

Personnel from the Goddard Space Flight Center Wallops Flight Facility (GSFC/WFF) in Virginia are responsible for the overall management of the NASA Sounding Rocket Program. Payloads are generally in support of NASA's Space Science Enterprise's missions and return a variety of scientific data as well as providing a reasonably economical means of conducting engineering tests for instruments and devices used on satellites and other spacecraft. The fifteen types of sounding rockets used by NASA can carry payloads of various weights to altitudes from 50 km to more than 1,300 km. Launch activities are conducted not only from established missile ranges, but also from remote locations worldwide requiring mobile tracking and command equipment to be transported and set up at considerable expense. The advent of low earth orbit (LEO) commercial communications satellites provides an opportunity to dramatically reduce tracking and control costs of launch vehicles and Unpiloted Aerial Vehicles (UAVs) by reducing or eliminating this ground infrastructure. Additionally, since data transmission is by packetized Internet Protocol (IP), data can be received and commands initiated from practically any location. A low cost Commercial Off The Shelf (COTS) system is currently under development for sounding rockets which also has application to UAVs and scientific balloons. Due to relatively low data rate (9600 baud) currently available, the system will first be used to provide GPS data for tracking and vehicle recovery. Range safety requirements for launch vehicles usually stipulate at least two independent tracking sources. Most sounding rockets flown by NASA now carry GPS receivers that output position data via the payload telemetry system to the ground station. The Flight Modem can be configured as a completely separate link thereby eliminating requirement for tracking radar. The system architecture which integrates antennas, GPS receiver, commercial satellite packet data modem, and a single board computer with custom software is described along with the technical challenges and the plan for their resolution. These include antenna development, high Doppler rates, reliability, environmental ruggedness, hand over between satellites and data security. An aggressive test plan is included which in addition to environmental testing measures bit error rate, latency and antenna patterns. Actual flight tests are planned for the near future on aircraft, long duration balloons and sounding rockets and these results as well as the current status of the project are reported.

Bull, Barton↗

A Space Based Internet Protocol System for Launch Vehicle Tracking and Control

Personnel from the Goddard Space Flight Center Wallops Flight Facility (GSFC/WFF) in Virginia are responsible for the overall management of the NASA Sounding Rocket and Scientific Balloon Programs. Payloads are generally in support of NASA's Space Science Enterprise's missions and return a variety of scientific data as well as providing a reasonably economical means of conducting engineering tests for instruments and devices used on satellites and other spacecraft. Sounding rockets used by NASA can carry payloads of various weights to altitudes from 50 km to more than 1,300 km. Scientific balloons can carry a payload weighing as much as 3,630 Kg to an altitude of 42 km. Launch activities for both are conducted not only from established ranges, but also from remote locations worldwide requiring mobile tracking and command equipment to be transported and set up at considerable expense. The advent of low earth orbit (LEO) commercial communications satellites provides an opportunity to dramatically reduce tracking and control costs of these launch vehicles and Unpiloted Aerial Vehicles (UAVs) by reducing or eliminating this ground infrastructure. Additionally, since data transmission is by packetized Internet Protocol (IP), data can be received and commands initiated from practically any location. A low cost Commercial Off The Shelf (COTS) system is currently under development for sounding rockets that also has application to UAVs and scientific balloons. Due to relatively low data rate (9600 baud) currently available, the system will first be used to provide GPS data for tracking and vehicle recovery. Range safety requirements for launch vehicles usually stipulate at least two independent tracking sources. Most sounding rockets flown by NASA now carry GP~ receivers that output position data via the payload telemetry system to the ground station. The Flight Modem can be configured as a completely separate link thereby eliminating the requirement for tracking radar. The system architecture that integrates antennas, GPS receiver, commercial satellite packet data modem, and a single board computer with custom software is described along with the technical challenges and the plan for their resolution. These include antenna development, high Doppler rates, reliability, environmental ruggedness, hand over between satellites, and data security. An aggressive test plan is included which, in addition to environmental testing, measures bit error rate, latency and antenna patterns. Actual launches on a sounding rocket and various aircraft flights have taken place. Flight tests are planned for the near future on aircraft, long duration balloons and sounding rockets. These results, as well as the current status of the project, are reported.

Bull, Barton↗

BrachyView, a novel in-body imaging system for HDR prostate brachytherapy: Experimental evaluation

Purpose: This paper presents initial experimental results from a prototype of high dose rate (HDR) BrachyView, a novel in-body source tracking system for HDR brachytherapy based on a multipinhole tungsten collimator and a high resolution pixellated silicon detector array. The probe and its associated position estimation algorithms are validated and a comprehensive evaluation of the accuracy of its position estimation capabilities is presented. Methods: The HDR brachytherapy source is moved through a sequence of positions in a prostate phantom, for various displacements in x, y, and z. For each position, multiple image acquisitions are performed, and source positions are reconstructed. Error estimates in each dimension are calculated at each source position and combined to calculate overall positioning errors. Gafchromic film is used to validate the accuracy of source placement within the phantom. Results: More than 90% of evaluated source positions were estimated with an error of less than one millimeter, with the worst-case error being 1.3 mm. Experimental results were in close agreement with previously published Monte Carlo simulation results. Conclusions: The prototype of HDR BrachyView demonstrates a satisfactory level of accuracy in its source position estimation, and additional improvements are achievable with further refinement of HDR BrachyView’s image processing algorithms.

60 APPLIED LIFE SCIENCES↗

Vulnerabilities in Artificial Intelligence and Machine Learning Applications and Data

Artificial intelligence (AI) applications driven by machine learning (ML) are transformational technologies within the international nuclear security regime. Advancements realized by AI—faster and improved data insights, more efficient and automated processes, reductions in human error—enable nuclear security applications such as behavior analysis for insider threat mitigation, source tracking of stolen nuclear material, and facial recognition software for physical protection. In addition to the advantages, however, there are also inherent vulnerabilities and threats associated with its use and risk mitigations must be built into any AI/ML-enabled systems. This work provides a background on AI and ML and different data types used in the field, including open-source intelligence information (OSINT) that is discoverable by AI tools and application data that are used by AI tools for decision-making and automation. Current and potential AI applications and vulnerabilities related to their use within the nuclear security regime are also discussed.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Comparison of ozone formation attribution techniques in the northeastern United States

The Integrated Source Apportionment Method (ISAM) has been revised in the Community Multiscale Air Quality (CMAQ) model. This work updates ISAM to maximize its flexibility, particularly for ozone (O 3 ) modeling, by providing multiple attribution options, including products inheriting attribution fully from nitrogen oxide reactants, fully from volatile organic compound (VOC) reactants, equally from all reactants, or dynamically from NO x or VOC reactants based on the indicator gross production ratio of hydrogen peroxide (H 2 O 2 ) to nitric acid (HNO 3 ). The updated ISAM has been incorporated into the most recent publicly accessible versions of CMAQ (v5.3.2 and beyond). This study's primary objective is to document these ISAM updates and demonstrate their impacts on source apportionment results for O 3 and its precursors. Additionally, the ISAM results are compared with the Ozone Source Apportionment Technology (OSAT) in the Comprehensive Air-quality Model with Extensions (CAMx) and the brute-force method (BF). All comparisons are performed for a 4 km horizontal grid resolution application over the northeastern US for a selected 2 d summer case study (9 and 10 August 2018). General similarities among ISAM, OSAT, and BF results add credibility to the new ISAM algorithms. However, some discrepancies in magnitude or relative proportions among tracked sources illustrate the distinct features of each approach, while others may be related to differences in model formulation of chemical and physical processes. Despite these differences, OSAT and ISAM still provide useful apportionment data by identifying the geographical and temporal contributions of O 3 and its precursors. Both OSAT and ISAM attribute the majority of O 3 and NO x contributions to boundary, mobile, and biogenic sources, whereas the top three contributors to VOCs are found to be biogenic, boundary, and area sources.

54 ENVIRONMENTAL SCIENCES↗

Characterizing scintillator detector response for correlated fission experiments with MCNP and associated packages

When multiple neutrons are emitted in a fission event they are correlated in both energy and their relative angle, which may impact the design of safeguards equipment and other instrumentation for non-proliferation applications. The most recent release of MCNP 6 . 2 contains the capability to simulate correlated fission neutrons using the event generators CGMF and FREYA . These radiation transport simulations will be post-processed by the detector response code, DRiFT , and compared directly to correlated fission measurements. DRiFT has been previously compared to single detector measurements, its capabilities have been recently expanded with correlated fission simulations in mind. Finally, this paper details updates to DRiFT specific to correlated fission measurements, including tracking source particle energy of all detector events (and non-events), expanded output formats, and digitizer waveform generation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Contribution of Vegetation to the Microbial Composition of Nearby Outdoor Air

Given that epiphytic microbes are often found in large population sizes on plants, we tested the hypothesis that plants are quantitatively important local sources of airborne microorganisms. The abundance of microbial communities, determined by quantifying bacterial 16S RNA genes and the fungal internal transcribed spacer (ITS) region, in air collected directly above vegetation was 2- to 10-fold higher than that in air collected simultaneously in an adjacent nonvegetated area 50 m upwind. Nonmetric multidimensional scaling revealed that the composition of airborne bacteria in upwind air samples grouped separately from that of downwind air samples, while communities on plants and downwind air could not be distinguished. In contrast, fungal taxa in air samples were more similar to each other than to the fungal epiphytes. A source-tracking algorithm revealed that up to 50% of airborne bacteria in downwind air samples were presumably of local plant origin. The difference in the proportional abundances of a given operational taxonomic unit (OTU) between downwind and upwind air when regressed against the proportional representation of this OTU on the plant yielded a positive slope for both bacteria and fungi, indicating that those taxa that were most abundant on plants proportionally contributed more to downwind air. Epiphytic fungi were less of a determinant of the microbiological distinctiveness of downwind air and upwind air than epiphytic bacteria. Emigration of epiphytic bacteria and, to a lesser extent, fungi, from plants can thus influence the microbial composition of nearby air, a finding that has important implications for surrounding ecosystems, including the built environment into which outdoor air can penetrate.

54 ENVIRONMENTAL SCIENCES↗

Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Microorganisms frequently colonize surfaces within food production facilities. Detection of Listeria monocytogenes in this setting relies on culture-dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remain largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from five seafood and seven dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between 355 samples taken from these 12 production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assemble L. monocytogenes metagenome-assembled genomes (MAGs) from 28 of the 32 culture-positive samples. We compared these MAGs to their corresponding whole-genome sequencing assemblies, which resulted in two polyphyletic clades consisting of L. monocytogenes lineages I and II with 13,195 and 25,556 single-nucleotide polymorphism sites, respectively. The remaining four MAGs did not produce sufficient genome coverage. To understand and establish limits for pathogen detection and subtyping using shotgun quasimetagenomics, these same data sets were downsampled in slilico to produce a titration series of abundances of L. monocytogenes and analyzed. Pathogen detection was achieved for all downsampled data sets, even those with only 3× genome coverage. This study contributes to the understanding of microbial diversity within food production environments and presents insights into the level of genome coverage needed in a metagenome sequencing data set to detect, subtype, and source track a foodborne pathogen.

59 BASIC BIOLOGICAL SCIENCES↗

DRiFT - Release 1.0.0 Organic Scintillators

DRiFT (a Detector Response Function Toolkit) is LANL-developed software that postprocesses output from the extensively validated radiation transport code, MCNP [1], and generates realistic nuclear instrumentation response. DRiFT is designed to be flexible, enabling users to specify detector type and many experimental settings, as well as accommodating the addition of their own desired features. Although DRiFT development has included scintillator [2], gas [3], and semiconductor features [4], the focus of this release is on organic scintillator and associated capabilities. Organic scintillators are widely used in the areas of nuclear safeguards and nuclear non-proliferation efforts [5, 6]. DRiFT has several diagnostic and detector physics features relevant to detailed scintillator simulations including: tracking source particle information, scintillation light production, the effects of PMT quantum efficiency and gain, and digitizer settings. Users can select responses from many scintillator and PMT types supported natively by DRiFT, or add their own by following the instructions in this document. We acknowledge that DRiFT is under active development, bug reports and general questions and comments should be directed to Madison Andrews, madison@lanl.gov. This manual is divided into four parts: I) An overview of DRiFT, including how to obtain and install the executable, II) A description of the detector physics related to scintillators available, III) a description of more general DRiFT features the user may find useful, and IV) a description of the test suite and examples made available with the code release.

61 RADIATION PROTECTION AND DOSIMETRY↗

DRiFT - Release 1.1.1: Organic Scintillators

DRiFT (a Detector Response Function Toolkit) is LANL-developed software that postprocesses output from the extensively validated radiation transport code, MCNP, and generates realistic nuclear instrumentation response. DRiFT is designed to be flexible, enabling users to specify detector type and many experimental settings, as well as accommodating the addition of their own desired features. Although DRiFT development has included scintillator, gas, and semiconductor features, the focus of this release is on organic scintillator and associated capabilities. Organic scintillators are widely used in the areas of nuclear safeguards and nuclear non-proliferation efforts. DRiFT has several diagnostic and detector physics features relevant to detailed scintillator simulations including: tracking source particle information, scintillation light production, the effects of PMT quantum efficiency and gain, and digitizer settings. Users can select responses from many scintillator and PMT types supported natively by DRiFT, or add their own by following the instructions in this document. We acknowledge that DRiFT is under active development, bug reports and general questions and comments should be directed to Madison Andrews, madison@lanl.gov. This manual is divided into four parts: I) An overview of DRiFT, including how to obtain and install the executable, II) A description of the detector physics related to scintillators available, III) a description of more general DRiFT features the user may find useful, and IV) a description of the test suite and examples made available with the code release.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DRiFT - Release 2.1.0: Organic Scintillators and Gas Detectors

DRiFT (a Detector Response Function Toolkit) is LANL-developed software that post-processes output from the extensively validated radiation transport code, MCNP, and generates realistic nuclear instrumentation response. DRiFT is designed to be flexible, enabling users to specify detector type and many experimental settings, as well as accommodating the addition of their own desired features. The focus of this release is on organic scintillator, gas detector, and associated capabilities, while semiconductor features are still under development. Organic scintillators are widely used in the areas of nuclear safeguards and nuclear non-proliferation efforts. DRiFT has several diagnostic and detector physics features relevant to detailed scintillator simulations including: tracking source particle information, scintillation light production, the effects of PMT quantum efficiency and gain, and digitizer settings. Users can select responses from many scintillator and PMT types supported natively by DRiFT, or add their own by following the instructions in this document. DRiFT also has several diagnostic and detector physics features relevant to neutron gas detector simulations including: gas detector wall effects, inactive areas at the end of detector tubes, and effects of a preamplifier. We acknowledge that DRiFT is under active development, bug reports and general questions and comments should be directed to Madison Andrews, madison@lanl.gov. This manual is divided into four parts: I) An overview of DRiFT, including how to obtain and install the executable, II) A description of the detector physics related to scintillators available, III) a description of more general DRiFT features the user may find useful, and IV) a description of the test suite and examples made available with the code release.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

High-revolution gamma-ray imaging from the moon

An observatory is suggested for exploiting unique lunar features to perform sensitive, subarcsecond cosmic X-ray and gamma-ray imaging. The observatory would be built in an evolutionary manner and would eventually include several different position-sensitive detector systems which together would cover a broad energy range and address a wide variety of astrophysical problems. High angular resolution would be obtained by using a mobile crane on the flat lunar mare regions to move a coded aperture mask for source tracking with detector/mask separations of up to 5 kilometers.

Mahoney, William A.↗