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At least 1,585 records · Page 88

Demonstration of a Submillimeter-Wave HEMT Oscillator Module at 330 GHz

In this work, radial transitions have been successfully mated with a HEMT-based MMIC (high-electron-mobility-transistor-based monolithic microwave integrated circuit) oscillator circuit. The chip has been assembled into a WR2.2 waveguide module for the basic implementation with radial E-plane probe transitions to convert the waveguide mode to the MMIC coplanar waveguide mode. The E-plane transitions have been directly integrated onto the InP substrate to couple the submillimeter-wave energy directly to the waveguides, thus avoiding wire-bonds in the RF path. The oscillator demonstrates a measured 1.7 percent DC-RF efficiency at the module level. The oscillator chip uses 35-nm-gate-length HEMT devices, which enable the high frequency of oscillation, creating the first demonstration of a packaged waveguide oscillator that operates over 300 GHz and is based on InP HEMT technology. The oscillator chip is extremely compact, with dimensions of only 1.085 x 320 sq mm for a total die size of 0.35 sq mm. This fully integrated, waveguide oscillator module, with an output power of 0.27 mW at 330 GHz, can provide low-mass, low DC-power-consumption alternatives to existing local oscillator schemes, which require high DC power consumption and large mass. This oscillator module can be easily integrated with mixers, multipliers, and amplifiers for building high-frequency transmit and receive systems at submillimeter wave frequencies. Because it requires only a DC bias to enable submillimeter wave output power, it is a simple and reliable technique for generating power at these frequencies. Future work will be directed to further improving the applicability of HEMT transistors to submillimeter wave and terahertz applications. Commercial applications include submillimeter-wave imaging systems for hidden weapons detection, airport security, homeland security, and portable low-mass, low-power imaging systems

Radisic, Vesna↗

Unsupervised atomic data mining via multi-kernel graph autoencoders for machine learning force fields

Constructing a chemically diverse dataset while avoiding sampling bias is critical to training efficient and generalizable force fields. However, in computational chemistry and materials science, many common dataset generation techniques are prone to oversampling regions of the potential energy surface. Furthermore, these regions can be difficult to identify and isolate from each other or may not align well with human intuition, making it challenging to systematically remove bias in the dataset. While traditional clustering and pruning (down-sampling) approaches can be useful for this, they can often lead to information loss or a failure to properly identify distinct regions of the potential energy surface due to difficulties associated with the high dimensionality of atomic descriptors. In this work, we introduce the Multi-kernel Edge Attention-based Graph Autoencoder (MEAGraph) model, an unsupervised approach for analyzing atomic datasets. MEAGraph combines multiple linear kernel transformations with attention-based message passing to capture geometric sensitivity and enable effective dataset pruning without relying on labels or extensive training. Demonstrated applications on niobium, tantalum, and iron datasets show that MEAGraph efficiently groups similar atomic environments, allowing for the use of basic pruning techniques for removing sampling bias. This approach provides an effective method for representation learning and clustering that can be used for data analysis, outlier detection, and dataset optimization.

Materials science↗

Streamlining and Transparently Automating Complex Waste Determinations at Los Alamos National Laboratory - 17286

Environmental programs at Los Alamos National Laboratory (LANL) generate a large amount of sampling activities that can result in waste that needs to be characterized and properly disposed. Since 2011, sampling results are managed in the cloud-based Environmental Information Management (EIM) database, which contains over 16 million current and historical data records. In many cases, the database's analytical records are used to characterize and dispose waste from environmental operations. Three factors contribute to streamlining of the waste disposition operations: (1) if possible, use of the existing analytical data for waste characterization to avoid additional laboratory analysis; (2) reduction in time spent on data evaluation for various waste acceptance criteria; and (3) choice of the proper and least expensive disposal alternative. Use of the existing analytical data, when allowed by law, creates some paradoxical problems: when chemical analysis is requested with the purpose of characterizing waste, it creates only 100 to 400 analytical records. However, use of exiting analytical data at LANL may lead to evaluation of tens of thousands of analytical records, with many records for each single analyte. This occurs because data were collected for environmental characterization and not waste characterization. To streamline data analysis for waste disposition using existing data, LANL has created a Waste Data Summary (WDS) module in the site's EIM database. Recognizing that waste determination is performed by groups outside the environmental program at LANL, the WDS allows for logically guided data selection for a specific waste determination (solids, liquids, radiological, etc.) and reduces potentially thousands of rows of data into simple formatted data reports that are easy to comprehend and process. This allows the waste evaluators to review data using multiple approaches to make their own determination on the most appropriate disposal method. There are four basic principles of WDS operation: (1) The highest detected analytical result is evaluated for the selected samples (or the lowest undetected result if there are no detected results); (2) All approved disposal pathways are evaluated; (3) Any failures of the Waste Acceptance Criteria are visibly highlighted to focus the attention of the evaluator; and (4) The decision of the disposal path is left to the trained waste evaluator (WDS does not choose or suggest any disposal paths). The summary results are presented as the set of short data reports. These reports can be divided into two groups: general comparison reports and disposal pathway specific forms. The general comparison forms show all Resource Conservation and Recovery Act (RCRA) analytes with pass/fail evaluation and with preference for toxicity characteristic leaching procedure (TCLP) results (or 20x rule) for solid samples, the potential RCRA hazard codes assignment for detected analytes, and all rad results. The detected chemical and radioactivity results are compared to the background values and to Soil Screening and Soil Action limits (SSL/SAL limits). Disposal pathway specific forms follow Waste Acceptance Criteria requirements for all disposal pathways available at LANL. The programming of the WDS tries to maximize existing data by analyte substitutions (like using gross alpha for necessary alpha emitting isotopes) or by making calculations when analytical results do not agree with legal requirements (like total chlordane in the RCRA regulations, which is most often analyzed and reported as individual isomers). All forms may be annotated by the waste evaluator to provide additional information to support decision making. Upon final decision of a disposal path, the complete dataset used in the evaluation and the WDS forms with annotations is 'frozen' as an un-editable PDF export to document the data used in the waste disposal determination. The streamlined process results in less work for waste evaluators and reduces overall labor and analytical costs. By comparison, a full review of a 10,000 record parent dataset may take a waste evaluator over a week to review, whereas with the WDS module, the task can be accomplished in less than one hour with clear, reproducible results. These results can be reviewed and checked at any time by quality assurance personnel, thus ensuring transparency in the decision making process. LANL believes this approach has broad applicability to other sites where waste determination is based on review of existing data collected for more generalized environmental purposes. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Do LIGO/Virgo Black Hole Mergers Produce AGN Flares? The Case of GW190521 and Prospects for Reaching a Confident Association

The recent report of an association of the gravitational-wave (GW) binary black hole (BBH) merger GW190521 with a flare in the active galactic nuclei (AGNs) J124942.3 + 344929 has generated tremendous excitement. However, GW190521 has one of the largest localization volumes among all of the GW events detected so far. The 90% localization volume likely contains 7400 unobscured AGNs brighter than g ≤ 20.5 AB mag, and it results in a ≳70% probability of chance coincidence for an AGN flare consistent with the GW event. We present a Bayesian formalism to estimate the confidence of an AGN association by analyzing a population of BBH events with dedicated follow-up observations. Depending on the fraction of BBHs arising from AGNs, counterpart searches of $\mathcal{O}(1) - \mathcal{O}(100)$ GW events are needed to establish a confident association, and more than an order of magnitude more for searches without follow-up (i.e., using only the locations of AGN and GW events). Follow-up campaigns of the top ~5% (based on volume localization and binary mass) of BBH events with total rest-frame mass ≥50 M ⊙ are expected to establish a confident association during the next LIGO/Virgo/KAGRA observing run (O4), as long as the true value of the fraction of BBHs giving rise to AGN flares is >0.1. Our formalism allows us to jointly infer cosmological parameters from a sample of BBH events that include chance coincidence flares. Until the confidence of AGN associations is established, the probability of chance coincidence must be taken into account to avoid biasing astrophysical and cosmological constraints.

79 ASTRONOMY AND ASTROPHYSICS↗

Use of a Prototype Airborne Separation Assurance System for Resolving Near-Term Conflicts During Autonomous Aircraft Operations

NASA is currently investigating a new concept of operations for the National Airspace System, designed to improve capacity while maintaining or improving current levels of safety. This concept, known as Distributed Air/Ground Traffic Management (DAGTM), allows appropriately equipped autonomous aircraft to maneuver freely for flight optimization while resolving conflicts with other traffic and staying out of special use airspace and hazardous weather. In order to perform these tasks, pilots use prototype conflict detection, prevention, and resolution tools, collectively known as an Airborne Separation Assurance System (ASAS). While ASAS would normally allow pilots to resolve conflicts before they become hazardous, evaluation of system performance in sudden, near-term conflicts is needed in order to determine concept feasibility. An experiment was conducted in NASA Langley's Air Traffic Operations Lab to evaluate the prototype ASAS for enabling pilots to resolve near-term conflicts and examine possible operational effects associated with the use of lower separation minimums. Sixteen commercial airline pilots flew a total of 32 traffic scenarios that required them to use prototype ASAS tools to resolve close range pop-up conflicts. Required separation standards were set at either 3 or 5 NM lateral spacing, with 1000 ft vertical separation being used for both cases. Reducing the lateral separation from 5 to 3 NM did not appear to increase operational risk, as indicated by the proximity to the intruder aircraft. Pilots performed better when they followed tactical guidance cues provided by ASAS than when they didn't follow the guidance. In an effort to improve compliance rate, ASAS design changes are currently under consideration. Further studies will of evaluate these design changes and consider integration issues between ASAS and existing Airborne Collision Avoidance Systems (ACAS).

Barhydt, Richard↗

Fleetwide data-enabled reliability improvement of wind turbines

Wind farms are an indispensable driver toward renewable and nonpolluting energy resources. However, as ideal sites are limited, placement in remote and challenging locations results in higher logistics costs and lower average wind speeds. Therefore, it is critical to increase the reliability of the turbines to reduce maintenance costs. Robust implementation requires a thorough understanding of the loads subject to the turbine's control. Yet, such dynamically changing multidimensional loads are uncommon with other machinery, and generally underresearched. Therefore, a multitiered approach is proposed to investigate the load spectrum occurring in wind farms. Our approach relies on both fundamental research using controllable test rigs, as well as analyses of real-world loading conditions in high-frequency supervisory control and data acquisition data. A method is introduced to detect operational zones in wind farm data and link them with load distributions. Additionally, while focused research further investigates the load spectrum, a method is proposed that continuously optimizes the farm's control protocols without the need to fully understand the loads that occur. A case of gearbox failure is investigated based on a vast body of past experiments and suspect loads are identified. Starting from this evidence on the cause and effects of dynamic loads, the potential of our methods is shown by analyzing real-world farm loading conditions on a steady-state case of wake and developing a preventive row-based control protocol for a case of cascading emergency brakes induced by a storm.

17 WIND ENERGY↗

A universal setup for active control of a single-photon detector

The influence of bright light on a single-photon detector has been described in a number of recent publications. The impact on quantum key distribution (QKD) is important, and several hacking experiments have been tailored to fully control single-photon detectors. Special attention has been given to avoid introducing further errors into a QKD system. We describe the design and technical details of an apparatus which allows to attack a quantum-cryptographic connection. This device is capable of controlling free-space and fiber-based systems and of minimizing unwanted clicks in the system. With different control diagrams, we are able to achieve a different level of control. The control was initially targeted to the systems using BB84 protocol, with polarization encoding and basis switching using beamsplitters, but could be extended to other types of systems. We further outline how to characterize the quality of active control of single-photon detectors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Implementation of an Open-Scenario, Long-Term Space Debris Simulation Approach

This paper provides a status update on the implementation of a flexible, long-term space debris simulation approach. The motivation is to build a tool that can assess the long-term impact of various options for debris-remediation, including the LightForce space debris collision avoidance concept that diverts objects using photon pressure [9]. State-of-the-art simulation approaches that assess the long-term development of the debris environment use either completely statistical approaches, or they rely on large time steps on the order of several days if they simulate the positions of single objects over time. They cannot be easily adapted to investigate the impact of specific collision avoidance schemes or de-orbit schemes, because the efficiency of a collision avoidance maneuver can depend on various input parameters, including ground station positions and orbital and physical parameters of the objects involved in close encounters (conjunctions). Furthermore, maneuvers take place on timescales much smaller than days. For example, LightForce only changes the orbit of a certain object (aiming to reduce the probability of collision), but it does not remove entire objects or groups of objects. In the same sense, it is also not straightforward to compare specific de-orbit methods in regard to potential collision risks during a de-orbit maneuver. To gain flexibility in assessing interactions with objects, we implement a simulation that includes every tracked space object in Low Earth Orbit (LEO) and propagates all objects with high precision and variable time-steps as small as one second. It allows the assessment of the (potential) impact of physical or orbital changes to any object. The final goal is to employ a Monte Carlo approach to assess the debris evolution during the simulation time-frame of 100 years and to compare a baseline scenario to debris remediation scenarios or other scenarios of interest. To populate the initial simulation, we use the entire space-track object catalog in LEO. We then use a high precision propagator to propagate all objects over the entire simulation duration. If collisions are detected, the appropriate number of debris objects are created and inserted into the simulation framework. Depending on the scenario, further objects, e.g. due to new launches, can be added. At the end of the simulation, the total number of objects above a cut-off size and the number of detected collisions provide benchmark parameters for the comparison between scenarios. The simulation approach is computationally intensive as it involves tens of thousands of objects; hence we use a highly parallel approach employing up to a thousand cores on the NASA Pleiades supercomputer for a single run. This paper describes our simulation approach, the status of its implementation, the approach to developing scenarios and examples of first test runs.

laser↗

The Evolution of Planetary Protection Implementation on Mars Landed Missions

NASA has developed requirements dedicated to the prevention of forward and backward contamination during space exploration. Historically, international agreements provided guidelines to prevent contamination of the Moon and other celestial bodies, as well as the Earth (e.g., sample return missions). The UN Outer Space Treaty was established in 1967 and the Committee on Space Research (COSPAR) maintains a planetary protection policy complying with Article IX of this treaty. By avoiding forward contamination, the integrity of scientific exploration is preserved. Planetary Protection mission requirements are levied on missions to control contamination. These requirements are dependent on the science of the mission and on the celestial bodies encountered or targeted along the way. Consequently, categories are assigned to missions, and specific implementation plans are developed to meet the planetary protection requirements. NASA missions have evolved over time with increasingly more demanding scientific objectives and more complex flight systems to achieve those objectives and, thus, planetary protection methods and processes used for implementation have become much more intricate, complicated, and challenging. Here, we will portray the evolution of planetary protection implementation at JPL in several important areas throughout the course of NASA sponsored robotic Mars lander or rover missions, starting from Mars Pathfinder through the beginning of Mars 2020. Highlighted in the discussion will be process changes in planetary protection requirements development and flow down. Development and implementation of new and improved methods used in the reduction of spacecraft bioburden will be discussed as well as approaches and challenges that come along with setting up remote laboratories to perform bioassays. The consequences and forward planning of delays on missions will be highlighted as well as lessons learned on the impact of communication and training in achieving planetary protection requirements. The evolution of methods used for the detection of microbial bioburden on spacecraft hardware will be considered. These methods use standard microbiology as well as the adaptation of advances in biotechnology, molecular biology, and bioinformatics. Technical approaches developed for the prevention of contamination and recontamination of hardware during Assembly, Test, and Launch Operations will be discussed.

Kazarians, Gayane A.↗

Grassland Bird Distribution and Raptor Flight Patterns in the Competitive Renewable Energy Zones of the Texas Panhandle [Thesis]

The consistent wind resource in the Great Plains of North America has encouraged the development of wind energy facilities across this region. In the Texas Panhandle, a high quality wind resource is only one factor that has led to the expansion of wind energy development. Other factors include federal tax incentives and the availability of subsidies. Moreover, the State Renewable Portfolio Standards (RPS), mandating production of 10,000 mega-watts of renewable energy in the state by 2025, has contributed to an amicable regulatory and permitting environment (State Energy Conservation Office 2010). Considering the current rate of development, the RPS will be met in coming years (American Wind Energy Association 2011) and the rate of development is likely to continue. To meet increased energy demands in the face of a chronically constrained transmission grid, Texas has developed a comprehensive plan that organizes and prioritizes new transmission systems in high quality wind resource areas called Competitive Renewable Energy Zones (CREZ). The CREZ plan provides developers a solution to transmission constraints and unlocks large areas of undeveloped wind resource areas. In the northern Texas panhandle, there are two CREZs that are classified Class 3 wind (Class 5 is the highest) and range from 862,725 to 1,772,328 ha in size (Public Utility Commission of Texas 2008). Grassland bird populations have declined more than any other bird group in North America (Peterjohn and Sauer 1999, Sauer et al. 2004). Loss of grassland habitat from agricultural development has been the greatest contributor to the decline of grassland bird populations, but development of non-renewable (i.e., oil, coal, and gas) and renewable energy (i.e., wind, solar, biomass, and geothermal) sources have contributed to the decline as well (Pimentel et al. 2002, Maybe and Paul 2007). The effects of wind energy development on declining grassland bird populations has become an area of extensive research, as we attempt to understand and minimize potential impacts of a growing energy sector on declining bird populations. Based on data from post-construction fatality surveys, two grassland bird groups have been the specific focus of research, passerines (songbird guild) and raptors (birds of prey). The effects of wind energy development on these two groups of birds, both of conservation concern, have been examined over the last decade. The primary focus of this research has been on mortality resulting from collision with wind turbines (Kuvlesky et al. 2007). Most studies just quantify post-construction fatality levels (e.g., Erickson et al. 2002) while very few studies provide a comparison of bird populations prior to development through a Before-After-Control-Impact (BACI) study design. Before-After-Control-Impact studies provide powerful evidence of avian/wind energy relationships (Anderson et al. 1999). Despite repeated urgency on conducting these types of studies (Anderson et al. 1999, Madders and Whitfield 2006, Kuvelsky et al. 2007), few have been conducted in North America. Although several European researchers (Larsson 1994, de Lucas et al. 2007) have used BACI designs to examine whether wind facilities modified raptor behavior, there is a scarcity of BACI data relating to North America grassland ecosystems that examine avian-wind energy relationships. There are less than a handful of studies in the entire United States, let alone the southern short grass prairie ecosystem, that incorporate preconstruction data to form the baseline for post-construction impact estimates (Johnson et al. 2000, Erickson et al. 2002). Although declines in grassland bird populations are well-documented (Peterjohn and Sauer 1999, Sauer et al. 2004), the causal mechanisms affecting the decline of grassland birds with increasing wind energy development in the southern short grass prairie are not well-understood (Kuvlesky et al. 2007, Maybe and Paul 2007). Several factors may potentially affect the bird population when wind turbines are constructed in areas with high bird densities (de Lucas et al. 2007). Habitat fragmentation, noise from turbines, physical movement of turbine blades, and increased vehicle traffic have been suggested as causes of decreased density of nesting grassland birds in Minnesota (Leddy et al. 1999), Oklahoma (O’Connell and Piorkowski 2006), and South Dakota (Shaffer and Johnson 2008). Similarly, constructing turbines in areas where bird flight patterns place them at similar heights of turbine blades increases the potential for bird collisions (Johnson et al. 2000, Hoover 2002). Raptor fatalities have been associated with topographic features such as ridges, saddles and rims where birds use updrafts from prevailing winds (Erickson et al. 2000, Johnson et al. 2000, Barrios and Rodriquez 2004, Hoover and Morrison 2005). Thus, wind energy development can result in indirect (e.g., habitat avoidance, decreased nest success) and direct (e.g., collision fatalities) impacts to bird populations (Anderson et al. 1999). Directly quantifying the level of potential impacts (e.g., estimated fatalities/mega-watthour) from wind energy development is beyond the scope of this study. Instead, I aim to quantify density, occupancy and flight behavior for the two bird groups mentioned earlier: obligate grassland songbirds and raptors, respectively, predict where impacts may occur, and provide management recommendations to minimize potential impacts. The United States Department of Energy (DOE), through the Office of Energy Efficiency and Renewable Energy Allocation, contracted Texas Tech University to investigate grassland bird patterns of occurrence in the anticipated CREZ in support of DOE’s 20% Wind Energy by 2030 initiative. In cooperation with Iberdrola Renewables, Inc., studies initiated by Wulff (2010) at Texas Tech University were continued at an area proposed for wind energy development and a separate reference site unassociated with wind energy development. I focused on four primary objectives and this thesis is accordingly organized in four separate chapters that address grassland bird density, grassland bird occupancy, raptor flight patterns, and finally I summarize species diversity and composition. The following chapters use formatting from the Journal of Wildlife Management guidelines (Block et al. 2011) with modifications as required by the Texas Tech University Graduate School. 1) I estimate pre-construction bird density patterns using methods that adjust for imperfect detection. I used a distance sampling protocol that effectively accounts for incomplete detection in the field where birds are present but not detected (Buckland et al. 2001). I improved density estimates with hierarchical distance sampling models, a modeling technique that effectively incorporates the detection process with environmental covariates that further influence bird density (Royle et al. 2004, Royle and Dorazio 2008). Covariates included road density and current oil and gas infrastructure to determine the relationship between existing energy development and bird density patterns. Further, I used remote sensing techniques and vegetation field data to investigate how landcover characteristics influenced bird density patterns. I focused species-specific analyses on obligate grassland birds with >70 detections per season namely grasshopper sparrow (Ammodramus savannarum) and horned lark (Eremophila alpestris). Chapter II focuses on hierarchical models that model and describe relationships between grassland bird density and anthropogenic and landscape features. 2) A large number of bird detections (>70) are needed to estimate density using distance sampling and collection of such quantity are often not feasible, particularly for cryptic species or species that naturally occur at low densities (Buckland et al. 2001). Occupancy models operate with far fewer data and are often used as a surrogate for bird abundance when there are fewer detections (MacKenzie and Nichols 2004). I used occupancy models that allow for the possibility of imperfect detection and species abundance to improve estimates of occurrence probability (Royal 2004). I focused species-specific analyses on grassland birds with few detections: Cassin’s sparrow (Peucaea cassinii), eastern meadowlark (Sturnella magna), and upland sandpiper (Bartramia longicauda). Chapter III uses a multi-season dynamic site occupancy model that incorporates bird abundance to better estimate occurrence probability. 3) When I considered the topographic relief of the study sites, the proposed design of the wind facility and its location within the central U.S. migratory corridor, I expanded the study to investigate raptor abundance and flight behavior (Hoover 2002, Miller 2008). I developed a new survey technique that improved the accuracy of raptor flight height estimates and compared seasonal counts and flight heights at the plateau rim and areas further inland. I used counts and flight behaviors to calculate species-specific collision risk indices for raptors based on topographic features. I focused species-specific analyses on raptors with the highest counts: American kestrel (Falco sparverius), northern harrier (Circus cyaneus), red-tailed hawk (Buteo jamaicensis), Swainson’s hawk (Buteo swainsoni), and turkey vulture (Cathartes aura). Chapter IV describes patterns of seasonal raptor abundance and flight behavior and how topography modulates collision risk with proposed wind energy turbines. 4) Finally, for completeness, in Chapter V I summarize morning point count data for all species and provide estimates of relative composition and species diversity with the Shannon-Wiener Diversity Index (Shannon and Weaver 1949).

17 WIND ENERGY↗

Development of electrical-erosion instrument for direct write micro-patterning on large area conductive thin films

We have developed a complete instrument to perform direct, dry, and cost-effective lithography on conductive materials, based on localized electrical discharges, which avoids using masks or chemicals typical of conventional photolithography. The technique is considered fully compatible with substrate transport based systems, like roll-to-roll technology. The prototype is based on two piezo nano-steppers coupled to three linear micro-stages to cover a large scale operation from micrometers to centimeters. The operation mode consists of a spring probe biased at low DC voltage with respect to a grounded conductive layer. The tip slides on the target layer keeping contact with the material in room conditions, allowing continuous electric monitoring of the process, and also real-time tilt correction via software. The sliding tip leaves an insulating path (limited by the tip diameter) along the material, enabling to draw electrically insulated tracks and pads. The physical principle of operation is based in the natural self-limitation of the discharge due to material removal or insulation. The so produced electrical discharges are very fast, in the range of μs, so features may be performed at speeds of few cm/s, enabling scalability to large areas. The instrument has been tested on different conducting materials as gold, indium tin oxide, and aluminum, allowing the fabrication of alphanumeric displays based on passive matrix of organic light emitting diodes without the use of masks or photoresists. We have verified that the highest potential is achieved on graphene, where no waste material is detected, producing excellent well defined edges. This allows manufacturing graphene micro-ribbons with a high aspect ratio up to 1200:1.

36 MATERIALS SCIENCE↗

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut

Microbes alter their transcriptomic profiles in response to the environment. The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. In this study we describe an approach to address these difficulties. Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the “diametric ratio” method. We used this approach to probe the environmental conditions experienced by Escherichia spp. in the gut of 4 premature infants, 2 of whom developed necrotizing enterocolitis (NEC), a severe inflammatory intestinal disease. We analyzed twenty fecal samples taken from four premature infants (4–6 time points from each infant), and found significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC. We also show this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure. These study results should be treated with caution, due to the presence of confounding factors that might also distinguish between NEC and control infants. Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. Results from similar studies can be further applied for designing diagnostic methods to detect NEC in its early developmental stages.

59 BASIC BIOLOGICAL SCIENCES↗

X-Ray Fluorescence Solvent Detection at the Substrate-Adhesive Interface

With environmental regulations limiting the use of volatile organic compounds, low-vapor pressure solvents have replaced traditional degreasing solvents for bond substrate preparation. When used to clean and prepare porous bond substrates such as phenolic composites, low vapor pressure solvents can penetrate deep into substrate pore networks and remain there for extended periods. Trapped solvents can interact with applied adhesives either prior to or during cure, potentially compromising bond properties. Currently, methods for characterizing solvent time-depth profiles in bond substrates are limited to bulk gravimetric or sectioning techniques. While sectioning techniques such as microtome allow construction of solvent depth profiles, their depth resolution and reliability are limited by substrate type. Sectioning techniques are particularly limited near the adhesive-substrate interface where depth resolution is further limited by adhesive-substrate hardness and, in the case of a partially cured adhesive, mechanical properties differences. Additionally, sectioning techniques cannot provide information about lateral solvent diffusion. Cross-section component mapping is an alternative method for measuring solvent migration in porous substrates that eliminates the issues associated with sectioning techniques. With cross-section mapping, the solvent-wiped substrate is sectioned perpendicular rather than parallel to the wiped surface, and the sectioned surface is analyzed for the solvent or solvent components of interest using a two-dimensional mapping or imaging technique. Solvent mapping can be performed using either direct or indirect methods. With a direct method, one or more solvent components are mapped using red or Raman spectroscopy together with a moveable sample stage and/or focal plane array detector. With an indirect method, an elemental "tag" not present in the substrate is added to the solvent before the substrate is wiped. Following cross sectioning, the tag element can then be mapped by its characteristic x-ray emission using either x-ray fluorescence, or electron-beam energy-and wavelength-dispersive x-ray spectrometry. The direct mapping techniques avoid issues of different diffusion or migration rates of solvents and elemental tags, while the indirect techniques avoid spectral resolution issues in cases where solvents and substrates have adjacent or overlapping peaks. In this study, cross-section component indirect mapping is being evaluated as a method for measuring migration of d-limonene based solvents in glass-cloth phenolic composite (GCP) prior to and during subsequent bonding and epoxy adhesive cure.

Wurth, Laura↗

Evaluation of SWIR Crop Residue Bands for the Landsat Next Mission

This research reports the findings of a Landsat Next expert review panel that evaluated the use of narrow shortwave infrared (SWIR) reflectance bands to measure ligno-cellulose absorption features centered near 2100 and 2300 nm, with the objective of measuring and mapping non-photosynthetic vegetation (NPV), crop residue cover, and the adoption of conservation tillage practices within agricultural landscapes. Results could also apply to detection of NPV in pasture, grazing lands, and non-agricultural settings. Currently, there are no satellite data sources that provide narrowband or hyperspectral SWIR imagery at sufficient volume to map NPV at a regional scale. The Landsat Next mission, currently under design and expected to launch in the late 2020’s, provides the opportunity for achieving increased SWIR sampling and spectral resolution with the adoption of new sensor technology. This study employed hyperspectral data collected from 916 agricultural field locations with varying fractional NPV, fractional green vegetation, and surface moisture contents. These spectra were processed to generate narrow bands with centers at 2040, 2100, 2210, 2260, and 2230 nm, at various bandwidths, that were subsequently used to derive 13 NPV spectral indices from each spectrum. For crop residues with minimal green vegetation cover, two-band indices derived from 2210 and 2260 nm bands were top performers for measuring NPV (R^(2) = 0.81, RMSE = 0.13) using bandwidths of 30 to 50 nm, and the addition of a third band at 2100 nm increased resistance to atmospheric correction residuals and improved mission continuity with Landsat 8 Operational Land Imager Band 7. For prediction of NPV over a full range of green vegetation cover, the Cellulose Absorption Index, derived from 2040, 2100, and 2210 nm bands, was top performer (R^(2) = 0.77, RMSE = 0.17), but required a narrow (≤20 nm) bandwidth at 2040 nm to avoid interference from atmospheric carbon dioxide absorption. In comparison, broadband NPV indices utilizing Landsat 8 bands centered at 1610 and 2200 nm performed poorly in measuring fractional NPV (R^(2) = 0.44), with significantly increased interference from green vegetation

Wells Dean Hively↗

Deriving Deformable Mirror Performance Requirements in Simulation with Experimental Verification

Coronagraph instruments rely on predictable and stable deformable mirror (DM) surface displacement to achieve the contrast required to detect Earth-sized exoplanets orbiting nearby Solar-type stars. Anomalous DM behavior, such as unstable or pinned actuators, can limit contrast in coronagraphs. Simulating how these undesired behaviors affect the performance of a high contrast imaging architecture is important for developing requirements on their associated hardware. Simulating a vortex coronagraph (VC) with two deformable mirrors, this study quantifies how the number of pinned actuators affect the performance of Focal Plane Wavefront Sensing and Control algorithms using both Grid Search Electric Field Conjugation (EFC) and Planned EFC, which uses Beta-Bumping. The simulation also quantifies how various types of voltage noise such as zero-mean Gaussian noise, zero-mean periodic noise, and drift can affect the contrast of a VC during an observation run. A tolerance of a change in the Mean Normalized Intensity of ${1\times10^{-11}}$ is allocated to both types of error. If Planned EFC is used, only 1 pinned actuator on both DMs can be tolerated. If only pure Grid Search EFC is used the DMs cannot have any pinned actuators. For the case of zero-mean Gaussian noise and zero-mean periodic noise, one can tolerate a noise standard deviation of no more than ${\sigma = 0.45 \text{ mV}}$. For drift, we can only tolerate ${\sigma = 0.30 \text{ mV}}$ or less. These results show that the DM electronics and the DM themselves need to be nearly defect free to avoid having more than 1 pinned actuator. The electronics need to be tested for different types of noise statistics and that both the average and standard deviation of the noise should be measured.

Dean L. Palmer↗

Recursive Partitioning Analysis Index Is Predictive for Overall Survival in Patients Undergoing Spine Stereotactic Body Radiation Therapy for Spinal Metastases

Purpose: To generate a prognostic index using recursive partitioning analysis (RPA) for patients undergoing spine stereotactic body radiation therapy (sSBRT) for spinal metastases (sMet). Methods and Materials: From an institutional review board-approved database, 174 patients were treated for sMet with sSBRT between February 2006 and August 2009. Median dose was 14 Gy (range, 8-24 Gy), typically in a single fraction (range, 1-5). Kaplan-Meier analysis was performed to detect any correlation between survival and histology. Histologies were divided into favorable (breast and prostate), radioresistant (renal cell, melanoma and sarcoma), and other (all other histologies). RPA was performed to identify any association of the following variables with overall survival (OS) following sSBRT: histology, gender, age, Karnofsky performance status (KPS), control of primary, extraosseous metastases, time from primary diagnosis (TPD), dose of sSBRT ({<=}14 Gy vs. >14 Gy), extent of spine disease (epidural only, bone and epidural, bone only), upfront or salvage treatment, presence of paraspinal extension, and previous surgery. Results: Median follow-up was 8.9 months. Median OS time from sSBRT was 10.7 months. Median OS intervals for favorable histologies were 14 months, 11.2 months for radioresistant histologies, and 7.3 months for other histologies (p = 0.02). RPA analysis resulted in three classes (p < 0.0001). Class 1 was defined as TPD of >30 months and KPS of >70; Class 2 was TPD of >30 months and KPS of {<=}70 or a TPD of {<=}30 months and age <70 years old; Class 3 was TPD of {<=}30 months and age {>=}70 years old. Median OS was 21.1 months for Class 1 (n = 59), 8.7 months for Class 2 (n = 104), and 2.4 months for Class 3 (n = 11). Conclusion: sSBRT patients treated for sMet have a wide variability in OS. We developed an RPA classification system that is predictive of OS. While many patients are treated for palliation of pain or to avoid symptomatic progression, this index may be used to predict which patients may benefit most from sSBRT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Cyber Friendly Fire

Cyber friendly fire (FF) is a new concept that has been brought to the attention of Department of Defense (DoD) stakeholders through two workshops that were planned and conducted by the Air Force Research Laboratory (AFRL) and research conducted for AFRL by the Pacific Northwest National Laboratory. With this previous work in mind, we offer a definition of cyber FF as intentional offensive or defensive cyber/electronic actions intended to protect cyber systems against enemy forces or to attack enemy cyber systems, which unintentionally harms the mission effectiveness of friendly or neutral forces. Just as with combat friendly fire, a fundamental need in avoiding cyber FF is to maintain situation awareness (SA). We suggest that cyber SA concerns knowledge of a system's topology (connectedness and relationships of the nodes in a system), and critical knowledge elements such as the characteristics and vulnerabilities of the components that comprise the system (and that populate the nodes), the nature of the activities or work performed, and the available defensive (and offensive) countermeasures that may be applied to thwart network attacks. A training implication is to raise awareness and understanding of these critical knowledge units; an approach to decision aids and/or visualizations is to focus on supporting these critical knowledge units. To study cyber FF, we developed an unclassified security test range comprising a combination of virtual and physical devices that present a closed network for testing, simulation, and evaluation. This network offers services found on a production network without the associated costs of a real production network. Containing enough detail to appear realistic, this virtual and physical environment can be customized to represent different configurations. For our purposes, the test range was configured to appear as an Internet-connected Managed Service Provider (MSP) offering specialized web applications to the general public. The network is essentially divided into a production component that hosts the web and network services, and a user component that hosts thirty employee workstations and other end devices. The organization's network is separated from the Internet by a Cisco ASA network security device that both firewalls and detects intrusions. Business sensitive information is stored in various servers. This includes data comprising thousands of internal documents, such as finance and technical designs, email messages for the organization's employees including the CEO, CFO, and CIO, the organization's source code, and Personally Identifiable client data. Release of any of this information to unauthorized parties would have a significant, detrimental impact on the organization's reputation, which would harm earnings. The valuable information stored in these servers pose obvious points of interest for an adversary. We constructed several scenarios around this environment to support studies in cyber SA and cyber FF that may be run in the test range. We describe mitigation strategies to combat cyber FF including both training concepts and suggestions for decision aids and visualization approaches. Finally, we discuss possible future research directions.

99 GENERAL AND MISCELLANEOUS↗

Optical CT imaging of solid radiochromic dosimeters in mismatched refractive index solutions using a scanning laser and large area detector

Purpose: The practical use of the PRESAGE® solid plastic dosimeter is limited by the inconvenience of immersing it in high-viscosity oils to achieve refractive index matching for optical computed tomography (CT) scanning. The oils are slow to mix and difficult to clean from surfaces, and the dosimeter rotation can generate dynamic Schlieren inhomogeneity patterns in the reference liquid, limiting the rotational and overall scan speed. Therefore, it would be beneficial if lower-viscosity, water-based solutions with slightly unmatched refractive index could be used instead. The purpose of this work is to demonstrate the feasibility of allowing mismatched conditions when using a scanning laser system with a large acceptance angle detector. A fiducial-based ray path measurement technique is combined with an iterative CT reconstruction algorithm to reconstruct images. Methods: A water based surrounding liquid with a low viscosity was selected for imaging PRESAGE® solid dosimeters. Liquid selection was optimized to achieve as high a refractive index as possible while avoiding rotation-induced Schlieren effects. This led to a refractive index mismatch of 6% between liquid and dosimeters. Optical CT scans were performed with a fan-beam scanning-laser optical CT system with a large area detector to capture most of the refracted rays. A fiducial marker placed on the wall of a cylindrical sample occludes a given light ray twice. With knowledge of the rotation angle and the radius of the cylindrical object, the actual internal path of each ray through the dosimeter can be calculated. Scans were performed with 1024 projections of 512 data samples each, and rays were rebinned to form 512 parallel-beam projections. Reconstructions were performed on a 512 × 512 grid using 100 iterations of the SIRT iterative CT algorithm. Proof of concept was demonstrated with a uniformly attenuating solution phantom. PRESAGE® dosimeters (11 cm diameter) were irradiated with Cobalt-60 irradiator to achieve either a uniform dose or a 2-level “step-dose” pattern. Results: With 6% refractive index mismatching, a circular field of view of 85% of the diameter of a cylindrical sample can be reconstructed accurately. Reconstructed images of the test solution phantom were uniform (within 3%) inside this radius. However, the dose responses of the PRESAGE® samples were not spatially uniform, with variations of at least 5% in sensitivity. The variation appears as a “cupping” artifact with less sensitivity in the middle than at the periphery of the PRESAGE® cylinder. Polarization effects were also detected for these samples. Conclusions: The fiducial-based ray path measurement scheme, coupled with an iterative reconstruction algorithm, enabled optical CT scanning of PRESAGE® dosimeters immersed in mismatched refractive index solutions. However, improvements to PRESAGE® dose response uniformity are required.

60 APPLIED LIFE SCIENCES↗