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Identification of host response signatures of infection

Sinha, Anupama; Bent, Zachary

Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to the pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for large-scale, highly-efficient efforts to identify and verify infection-specific host NA signatures in human populations.

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TYPE SAND Report YEAR 2013
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Development of a statistically based access delay timeline methodology

Rivera, W.G.; Robinson, David G.; Wyss, Gregory D.; Hendrickson, Stacey M.

The charter for adversarial delay is to hinder access to critical resources through the use of physical systems increasing an adversarys task time. The traditional method for characterizing access delay has been a simple model focused on accumulating times required to complete each task with little regard to uncertainty, complexity, or decreased efficiency associated with multiple sequential tasks or stress. The delay associated with any given barrier or path is further discounted to worst-case, and often unrealistic, times based on a high-level adversary, resulting in a highly conservative calculation of total delay. This leads to delay systems that require significant funding and personnel resources in order to defend against the assumed threat, which for many sites and applications becomes cost prohibitive. A new methodology has been developed that considers the uncertainties inherent in the problem to develop a realistic timeline distribution for a given adversary path. This new methodology incorporates advanced Bayesian statistical theory and methodologies, taking into account small sample size, expert judgment, human factors and threat uncertainty. The result is an algorithm that can calculate a probability distribution function of delay times directly related to system risk. Through further analysis, the access delay analyst or end user can use the results in making informed decisions while weighing benefits against risks, ultimately resulting in greater system effectiveness with lower cost.

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TYPE SAND Report YEAR 2013
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Task mapping for non-contiguous allocations

Leung, Vitus J.

This paper examines task mapping algorithms for non-contiguously allocated parallel jobs. Several studies have shown that task placement affects job running time for both contiguously and non-contiguously allocated jobs. Traditionally, work on task mapping either uses a very general model where the job has an arbitrary communication pattern or assumes that jobs are allocated contiguously, making them completely isolated from each other. A middle ground between these two cases is the mapping problem for non-contiguous jobs having a specific communication pattern. We propose several task mapping algorithms for jobs with a stencil communication pattern and evaluate them using experiments and simulations. Our strategies improve the running time of a MiniApp by as much as 30% over a baseline strategy. Furthermore, this improvement increases markedly with the job size, demonstrating the importance of task mapping as systems grow toward exascale.

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TYPE SAND Report YEAR 2013
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Nowcasting influenza outbreaks using open-source media report

Ray, Jaideep

We construct and verify a statistical method to nowcast influenza activity from a time-series of the frequency of reports concerning influenza related topics. Such reports are published electronically by both public health organizations as well as newspapers/media sources, and thus can be harvested easily via web crawlers. Since media reports are timely, whereas reports from public health organization are delayed by at least two weeks, using timely, open-source data to compensate for the lag in %E2%80%9Cofficial%E2%80%9D reports can be useful. We use morbidity data from networks of sentinel physicians (both the Center of Disease Control's ILINet and France's Sentinelles network) as the gold standard of influenza-like illness (ILI) activity. The time-series of media reports is obtained from HealthMap (http://healthmap.org). We find that the time-series of media reports shows some correlation ( 0.5) with ILI activity; further, this can be leveraged into an autoregressive moving average model with exogenous inputs (ARMAX model) to nowcast ILI activity. We find that the ARMAX models have more predictive skill compared to autoregressive (AR) models fitted to ILI data i.e., it is possible to exploit the information content in the open-source data. We also find that when the open-source data are non-informative, the ARMAX models reproduce the performance of AR models. The statistical models are tested on data from the 2009 swine-flu outbreak as well as the mild 2011-2012 influenza season in the U.S.A.

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TYPE SAND Report YEAR 2013
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Radar range measurements in the atmosphere

Doerry, Armin W.

The earth's atmosphere affects the velocity of propagation of microwave signals. This imparts a range error to radar range measurements that assume the typical simplistic model for propagation velocity. This range error is a function of atmospheric constituents, such as water vapor, as well as the geometry of the radar data collection, notably altitude and range. Models are presented for calculating atmospheric effects on radar range measurements, and compared against more elaborate atmospheric models.

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Burnup Concept for a Long-Life Fast Reactor Core using MCNPX

Parma, Edward J.; Lewis, Tom G.

This report describes a reactor design with a burnup concept for a long-life fast reactor core that was evaluated using Monte Carlo N-Particle eXtended (MCNPX). The current trend in advanced reactor design is the concept of a small modular reactor (SMR). However, very few of the SMR designs attempt to substantially increase the lifetime of a reactor core, especially without zone loading, fuel reshuffling, or other artificial mechanisms in the core that “flatten” the power profile, including non-uniform cooling, non-uniform moderation, or strategic poison placement. Historically, the limitations of computing capabilities have prevented acceptable margins in the temporal component of the spatial excess reactivity in a reactor design, due primarily to the error in burnup calculations. This research was performed as an initial scoping analysis into the concept of a long-life fast reactor. It can be shown that a long-life fast reactor concept can be modeled using MCNPX to predict burnup and neutronics behavior. The inherent characteristic of this conceptual design is to minimize the change in reactivity over the lifetime of the reactor. This allows the reactor to operate substantially longer at full power than traditional Light Water Reactors (LWRs) or other SMR designs. For the purpose of this study, a single core design was investigated: a relatively small reactor core, yielding a medium amount of power (~200 to 400 MWth). The results of this scoping analysis were successful in providing a preliminary reactor design involving metal U-235/U-238 fuel with HT-9 fuel cladding and sodium coolant at a 20% volume fraction.

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The SNL100-01 blade :

Griffith, Daniel

A series of design studies to investigate the effect of carbon on blade weight and performance for large blades was performed using the Sandia 100-meter All-glass Baseline Blade design as a starting point. This document provides a description of the final carbon blade design, which is termed as SNL100-01. This report includes a summary of the design modifications applied to the baseline all-glass 100-meter design and a description of the NuMAD model files that are made publicly available. This document is intended primarily to be a companion document to the distribution of the NuMAD blade model files for SNL100-01.

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Preliminary photovoltaic arc-fault prognostic tests using sacrificial fiber optic cabling

Johnson, Jay D.; Blemel, Kenneth D.; Peter, Francis

Through the New Mexico Small Business Assistance Program, Sandia National Laboratories worked with Sentient Business Systems, Inc. to develop and test a novel photovoltaic (PV) arc-fault detection system. The system operates by pairing translucent polymeric fiber optic sensors with electrical circuitry so that any external abrasion to the system or internal heating causes the fiber optic connection to fail or detectably degrade. A periodic pulse of light is sent through the optical path using a transmitter-receiver pair. If the receiver does not detect the pulse, an alarm is sounded and the PV system can be de-energized. This technology has the unique ability to prognostically determine impending failures to the electrical system in two ways: (a) the optical connection is severed prior to physical abrasion or cutting of PV DC electrical conductors, and (b) the polymeric fiber optic cable melts via Joule heating before an arc-fault is established through corrosion. Three arc-faults were created in different configurations found in PV systems with the integrated fiber optic system to determine the feasibility of the technology. In each case, the fiber optic cable was broken and the system annunciated the fault.

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Sandia National Laboratories land use permit for operations at Oliktok Alaska Long Range Radar Station

Catechis, Christopher S.

The property subject to this Environmental Baseline Survey (EBS) is located at the Oliktok Long Range Radar Station (LRRS). The Oliktok LRRS is located at 70À 30 W latitude, 149À 53 W longitude. It is situated at Oliktok Point on the shore of the Beaufort Sea, east of the Colville River. The purpose of this EBS is to document the nature, magnitude, and extent of any environmental contamination of the property; identify potential environmental contamination liabilities associated with the property; develop sufficient information to assess the health and safety risks; and ensure adequate protection for human health and the environment related to a specific property.

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Dynamic defense workshop :

Haas, Jason J.; Doak, Justin E.; Crosby, Sean M.; Helinski, Ryan; Lamb, Chris

On September 5th and 6th, 2012, the Dynamic Defense Workshop: From Research to Practice brought together researchers from academia, industry, and Sandia with the goals of increasing collaboration between Sandia National Laboratories and external organizations, de ning and un- derstanding dynamic, or moving target, defense concepts and directions, and gaining a greater understanding of the state of the art for dynamic defense. Through the workshop, we broadened and re ned our de nition and understanding, identi ed new approaches to inherent challenges, and de ned principles of dynamic defense. Half of the workshop was devoted to presentations of current state-of-the-art work. Presentation topics included areas such as the failure of current defenses, threats, techniques, goals of dynamic defense, theory, foundations of dynamic defense, future directions and open research questions related to dynamic defense. The remainder of the workshop was discussion, which was broken down into sessions on de ning challenges, applications to host or mobile environments, applications to enterprise network environments, exploring research and operational taxonomies, and determining how to apply scienti c rigor to and investigating the eld of dynamic defense.

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TYPE SAND Report YEAR 2013
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Precomparator and postcomparator errors in monopulse

Bickel, Douglas L.

Monopulse radar is a well-established technique for extracting accurate target location information in the presence of target scintillation. It relies on the comparison of at least two patterns being received simultaneously by the antenna. These two patterns are designed to differ in the direction in which we wish to obtain the target angle information. The two patterns are compared to each other through a standard method, typically by forming the ratio of the difference of the patterns to the sum of the patterns. The key to accurate angle information using monopulse is that the mapping function from the target angle to this ratio is well-behaved and well-known. Errors in the amplitude and phase of the signals prior and subsequent to the comparison operation affect the mapping function. The purpose of this report is to provide some intuition into these error effects upon the mapping function.

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Design and evaluation of the ReKon : an integrated detection and assessment perimeter system

Dabling, J.; Andersen, Jason J.

Kontek Industries (Kannapolis, NC) and their subsidiary, Stonewater Control Systems (Kannapolis, NC), have entered into a cooperative research and development agreement with Sandia to jointly develop and evaluate an integrated perimeter security system solution, one that couples access delay with detection and assessment. This novel perimeter solution was designed to be configurable for use at facilities ranging from high-security military sites to commercial power plants, to petro/chemical facilities of various kinds. A prototype section of the perimeter has been produced and installed at the Sandia Test and Evaluation Center in Albuquerque, NM. This prototype system integrated fiber optic break sensors, active infrared sensors, fence disturbance sensors, video motion detection, and ground sensors. This report documents the design, testing, and performance evaluation of the developed ReKon system. The ability of the system to properly detect pedestrian or vehicle attempts to bypass, breach, or otherwise defeat the system is characterized, as well as the Nuisance Alarm Rate.

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TYPE SAND Report YEAR 2013
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Scandium separation from tungsten crucibles

Boyle, Timothy J.; Hess, Ryan; Neville, Michael L.; Howard, Panit C.

The first step in an attempt to isolate Sc° from a W° crucible was explored by soaking the samples in a series of organic (HOAc) and inorganic (HCl, H2SO4, H3PO4, HNO3) acids. All samples, except the HOAc, yielded a powder. The weight loss suggests that HNO3 is the most efficient solvent; however, the powders were tentatively identified by PXRD and found to contain both W and Sc by-products. The higher weight loss may also indicate dissolution of the Wo crucible, which was further evidenced upon visual inspection of the crucible. The H3PO4 acid soak yielded the cleanest removal of Sc from the crucible. More work to understand the separation of the Sc° from the W° crucible is necessary but the acid routes appear to hold promise under not as of yet established criteria.

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Temperature-package power correlations for open-mode geologic disposal concepts

Hardin, Ernest

Logistical simulation of spent nuclear fuel (SNF) management in the U.S. combines storage, transportation and disposal elements to evaluate schedule, cost and other resources needed for all major operations leading to final geologic disposal. Geologic repository reference options are associated with limits on waste package thermal power output at emplacement, in order to meet limits on peak temperature for certain key engineered and natural barriers. These package power limits are used in logistical simulation software such as CALVIN, as threshold requirements that must be met by means of decay storage or SNF blending in waste packages, before emplacement in a repository. Geologic repository reference options include enclosed modes developed for crystalline rock, clay or shale, and salt. In addition, a further need has been addressed for open modes in which SNF can be emplaced in a repository, then ventilated for decades or longer to remove heat, prior to permanent repository closure. For each open mode disposal concept there are specified durations for surface decay storage (prior to emplacement), repository ventilation, and repository closure operations. This study simulates those steps for several timing cases, and for SNF with three fuel-burnup characteristics, to develop package power limits at which waste packages can be emplaced without exceeding specified temperature limits many years later after permanent closure. The results are presented in the form of correlations that span a range of package power and peak postclosure temperature, for each open-mode disposal concept, and for each timing case. Given a particular temperature limit value, the corresponding package power limit for each case can be selected for use in CALVIN and similar tools.

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Identification of volatile butyl rubber thermal-oxidative degradation products by cryofocusing gas chromatography/mass spectrometry (cryo-GC/MS)

Samberson, Jonell N.; White, Michael I.; Bernstein, Robert; Hochrein, James M.

Chemical structure and physical properties of materials, such as polymers, can be altered as aging progresses, which may result in a material that is ineffective for its envisioned intent. Butyl rubber formulations, starting material, and additives were aged under thermal-oxidative conditions for up to 413 total days at up to 124 ÀC. Samples included: two formulations developed at Kansas City Plant (KCP) (#6 and #10), one commercially available formulation (#21), Laxness bromobutyl 2030 starting material, and two additives (polyethylene AC-617 and Vanax MBM). The low-molecular weight volatile thermal-oxidative degradation products that collected in the headspace over the samples were preconcentrated, separated, and detected using cryofocusing gas chromatography mass spectrometry (cryo-GC/MS). The majority of identified degradation species were alkanes, alkenes, alcohols, ketones, and aldehydes. Observations for Butyl #10 aged in an oxygen-18 enriched atmosphere (18O2) were used to verify when the source of oxygen in the applicable degradation products was from the gaseous environment rather than the polymeric mixture. For comparison purposes, Butyl #10 was also aged under non-oxidative thermal conditions using an argon atmosphere.

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Initial Assessment of an Airborne Ku-band Polarimetric SAR

Raynal, Ann M.; Doerry, Armin W.

Polarimetric synthetic aperture radar (SAR) has been used for a variety of dual-use research applications since the 1940's. By measuring the direction of the electric field vector from radar echoes, polarimetry may enhance an analyst's understanding of scattering effects for both earth monitoring and tactical surveillance missions. Polarimetry may provide insight into surface types, materials, or orientations for natural and man-made targets. Polarimetric measurements may also be used to enhance the contrast between scattering surfaces such as man-made objects and their surroundings. This report represents an initial assessment of the utility of, and applications for, polarimetric SAR at Ku-band for airborne or unmanned aerial systems.

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Simulating higher-dimensional geometries in GADRAS using approximate one-dimensional solutions

Thoreson, Gregory; Mitchell, Dean J.; Harding, Lee

The Gamma Detector Response and Analysis Software (GADRAS) software package is capable of simulating the radiation transport physics for one-dimensional models. Spherical shells are naturally one-dimensional, and have been the focus of development and benchmarking. However, some objects are not spherical in shape, such as cylinders and boxes. These are not one-dimensional. Simulating the radiation transport in two or three dimensions is unattractive because of the extra computation time required. To maintain computational efficiency, higher-dimensional geometries require approximations to simulate them in one-dimension. This report summarizes the theory behind these approximations, tests the theory against other simulations, and compares the results to experimental data. Based on the results, it is recommended that GADRAS users always attempt to approximate reality using spherical shells. However, if fissile material is present, it is imperative that the shape of the one-dimensional model matches the fissile material, including the use of slab and cylinder geometry.

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Environmental Management System (EMS) Objectives & Targets (Annual Results Summary – FY2012)

Vetter, Douglas W.

Sandia National Laboratories/New Mexico's (SNL/NM) Environmental Management System is the integrated approach for members of the workforce to identify and manage environmental risks. Each Fiscal Year (FY) SNL/NM performs an analysis to identify environmental aspects, and the environmental programs associated with them are charged with the task of routinely monitoring and measuring the objectives and targets that are established to mitigate potential impacts of SNL/NM's operations on the environment. An annual summary of the results achieved towards meeting established objectives and targets provides a connection to, and rational for, annually revised environmental aspects. The purpose of this document is to summarize the results achieved and documented in FY2012.

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Builtin vs. auxiliary detection of extrapolation risk

Munson, Miles A.

A key assumption in supervised machine learning is that future data will be similar to historical data. This assumption is often false in real world applications, and as a result, prediction models often return predictions that are extrapolations. We compare four approaches to estimating extrapolation risk for machine learning predictions. Two builtin methods use information available from the classification model to decide if the model would be extrapolating for an input data point. The other two build auxiliary models to supplement the classification model and explicitly model extrapolation risk. Experiments with synthetic and real data sets show that the auxiliary models are more reliable risk detectors. To best safeguard against extrapolating predictions, however, we recommend combining builtin and auxiliary diagnostics.

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Results 61401–61600 of 101,000
Results 61401–61600 of 101,000
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