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Performance Validation of Pulsed Thermal Imaging System for In-Service Applications

Additive manufacturing (AM) is an emerging method for cost-efficient fabrication of complex topology nuclear reactor parts from high-strength corrosion resistance alloys, such as stainless steel and Inconel. AM of metallic structures for nuclear energy applications is currently based on laser powder bed fusion (LPBF) process, which has the capability of melting metallic powder and net shaping the structures with relatively high precision. Some of the challenges with using LPBF method for nuclear manufacturing include the possibility of introducing pores into metallic structures. Integrity of AM structures needs to be evaluated nondestructively because material flaws could lead to premature failures in high temperature nuclear reactor environment. Currently, there exist limited capabilities to evaluate actual AM structures non-destructively. Pulsed Thermography Imaging (PTI) provides a capability for non-destructive evaluation (NDE) of subsurface defects in arbitrary size structures. The PTI method is based on recording material surface temperature transients with infrared (IR) camera following thermal pulse delivered on material surface with flash light. The PTI method has advantages for NDE of actual AM structures because the method involves one-sided non-contact measurements and fast processing of large sample areas captured in one image. Following initial qualification of an AM component for deployment in a nuclear reactor, a PTI system can also be used for in-service nondestructive evaluation (NDE) applications. In this report, we describe recent progress in enhancing PTI capabilities in detecting microscopic defects in metallic specimens. SS316 and IN718 specimens were developed with a pattern of subsurface calibrated flat bottom hole (FBH) defects with diameters from 500µm to 200µm. FBH’s were created with EDM (electron discharge machining) drill. PTI imaging data was processed Spatial Temporal Denoised Thermal Source Separation (STDTSS) unsupervised machine learning (ML) algorithm. We show that defects as small as 200µm in SS316 and IN718 can be detected with STDTSS algorithm. To the best of our knowledge, these are the smallest detected defects which are reported in literature.

42 ENGINEERING↗

Reaching during virtual rotation: context specific compensations for expected coriolis forces

Subjects who are in an enclosed chamber rotating at constant velocity feel physically stationary but make errors when pointing to targets. Reaching paths and endpoints are deviated in the direction of the transient inertial Coriolis forces generated by their arm movements. By contrast, reaching movements made during natural, voluntary torso rotation seem to be accurate, and subjects are unaware of the Coriolis forces generated by their movements. This pattern suggests that the motor plan for reaching movements uses a representation of body motion to prepare compensations for impending self-generated accelerative loads on the arm. If so, stationary subjects who are experiencing illusory self-rotation should make reaching errors when pointing to a target. These errors should be in the direction opposite the Coriolis accelerations their arm movements would generate if they were actually rotating. To determine whether such compensations exist, we had subjects in four experiments make visually open-loop reaches to targets while they were experiencing compelling illusory self-rotation and displacement induced by rotation of a complex, natural visual scene. The paths and endpoints of their initial reaching movements were significantly displaced leftward during counterclockwise illusory rotary displacement and rightward during clockwise illusory self-displacement. Subjects reached in a curvilinear path to the wrong place. These reaching errors were opposite in direction to the Coriolis forces that would have been generated by their arm movements during actual torso rotation. The magnitude of path curvature and endpoint errors increased as the speed of illusory self-rotation increased. In successive reaches, movement paths became straighter and endpoints more accurate despite the absence of visual error feedback or tactile feedback about target location. When subjects were again presented a stationary scene, their initial reaches were indistinguishable from pre-exposure baseline, indicating a total absence of aftereffects. These experiments demonstrate that the nervous system automatically compensates in a context-specific fashion for the Coriolis forces associated with reaching movements.

Clinical Trial↗

In Situ Inference for Earth System Predictability

Focal Area: Focal Area 3: Insight gleaned from complex simulated data using AI, big data analytics, and other advanced methods, including explainable AI and physics- or knowledge-guided AI. Science Challenge: An understanding of future evolution in precipitation extremes is critical to numerous DOE mission questions. Extreme events are by nature short time-scale events that are difficult to diagnose in available model data. Accurate modeling of extreme events necessarily requires high spatial resolution at the storm scale locally. However, the environment in which storms grow is dependent on global, remote, processes. These complex spatiotemporal relationships are impossible to diagnose at resolutions required to accurately model storms responsible for extreme precipitation. At exascale, climate simulations will produce results at fine enough resolution to investigate these relationships. However, the resulting data from these simulations will be far too large to save for post-simulation analysis. We advocate for fitting statistical models inside the simulations as they run, a context known as in situ, which will facilitate scientific investigations using the full fine-scale data stream. Figure 1 shows an example of the type of model we could consider, a Bayesian hierarchical spatial regression model. Precipitation extremes at each grid cell are modeled using extreme value distributions. Since extremes are rare, fitting models to individual grid cells can result in high variance and poor estimates. Instead, the model can be made more robust by smoothing the parameters of the extreme value model across space. Additionally, the parameters themselves can be functionally linked to other variables elsewhere in the simulation. Thus, we can use the fine-scale data to build more robust models for extremes that link extreme behavior to other climate patterns.

54 ENVIRONMENTAL SCIENCES↗

NASA Tech Briefs, September 2006

Topics covered include: Improving Thermomechanical Properties of SiC/SiC Composites; Aerogel/Particle Composites for Thermoelectric Devices; Patches for Repairing Ceramics and Ceramic- Matrix Composites; Lower-Conductivity Ceramic Materials for Thermal-Barrier Coatings; An Alternative for Emergency Preemption of Traffic Lights; Vehicle Transponder for Preemption of Traffic Lights; Automated Announcements of Approaching Emergency Vehicles; Intersection Monitor for Traffic-Light-Preemption System; Full-Duplex Digital Communication on a Single Laser Beam; Stabilizing Microwave Frequency of a Photonic Oscillator; Microwave Oscillators Based on Nonlinear WGM Resonators; Pointing Reference Scheme for Free-Space Optical Communications Systems; High-Level Performance Modeling of SAR Systems; Spectral Analysis Tool 6.2 for Windows; Multi-Platform Avionics Simulator; Silicon-Based Optical Modulator with Ferroelectric Layer; Multiplexing Transducers Based on Tunnel-Diode Oscillators; Scheduling with Automated Resolution of Conflicts; Symbolic Constraint Maintenance Grid; Discerning Trends in Performance Across Multiple Events; Magnetic Field Solver; Computing for Aiming a Spaceborne Bistatic- Radar Transmitter; 4-Vinyl-1,3-Dioxolane-2-One as an Additive for Li-Ion Cells; Probabilistic Prediction of Lifetimes of Ceramic Parts; STRANAL-PMC Version 2.0; Micromechanics and Piezo Enhancements of HyperSizer; Single-Phase Rare-Earth Oxide/Aluminum Oxide Glasses; Tilt/Tip/Piston Manipulator with Base-Mounted Actuators; Measurement of Model Noise in a Hard-Wall Wind Tunnel; Loci-STREAM Version 0.9; The Synergistic Engineering Environment; Reconfigurable Software for Controlling Formation Flying; More About the Tetrahedral Unstructured Software System; Computing Flows Using Chimera and Unstructured Grids; Avoiding Obstructions in Aiming a High-Gain Antenna; Analyzing Aeroelastic Stability of a Tilt-Rotor Aircraft; Tracking Positions and Attitudes of Mars Rovers; Stochastic Evolutionary Algorithms for Planning Robot Paths; Compressible Flow Toolbox; Rapid Aeroelastic Analysis of Blade Flutter in Turbomachines; General Flow-Solver Code for Turbomachinery Applications; Code for Multiblock CFD and Heat-Transfer Computations; Rotating-Pump Design Code; Covering a Crucible with Metal Containing Channels; Repairing Fractured Bones by Use of Bioabsorbable Composites; Kalman Filter for Calibrating a Telescope Focal Plane; Electronic Absolute Cartesian Autocollimator; Fiber-Optic Gratings for Lidar Measurements of Water Vapor; Simulating Responses of Gravitational-Wave Instrumentation; SOFTC: A Software Correlator for VLBI; Progress in Computational Simulation of Earthquakes; Database of Properties of Meteors; Computing Spacecraft Solar-Cell Damage by Charged Particles; Thermal Model of a Current-Carrying Wire in a Vacuum; Program for Analyzing Flows in a Complex Network; Program Predicts Performance of Optical Parametric Oscillators; Processing TES Level-1B Data; Automated Camera Calibration; Tracking the Martian CO2 Polar Ice Caps in Infrared Images; Processing TES Level-2 Data; SmaggIce Version 1.8; Solving the Swath Segment Selection Problem; The Spatial Standard Observer; Less-Complex Method of Classifying MPSK; Improvement in Recursive Hierarchical Segmentation of Data; Using Heaps in Recursive Hierarchical Segmentation of Data; Tool for Statistical Analysis and Display of Landing Sites; Automated Assignment of Proposals to Reviewers; Array-Pattern-Match Compiler for Opportunistic Data Analysis; Pre-Processor for Compression of Multispectral Image Data; Compressing Image Data While Limiting the Effects of Data Losses; Flight Operations Analysis Tool; Improvement in Visual Target Tracking for a Mobile Robot; Software for Simulating Air Traffic; Automated Vectorization of Decision-Based Algorithms; Grayscale Optical Correlator Workbench; "One-Stop Shopping" for Ocean Remote-Sensing and Model Data; State Analysis Database Tool; Generating CAHV and CAHVOmages with Shadows in ROAMS; Improving UDP/IP Transmission Without Increasing Congestion; FORTRAN Versions of Reformulated HFGMC Codes; Program for Editing Spacecraft Command Sequences; Flight-Tested Prototype of BEAM Software; Mission Scenario Development Workbench; Marsviewer; Tool for Analysis and Reduction of Scientific Data; ASPEN Version 3.0; Secure Display of Space-Exploration Images; Digital Front End for Wide-Band VLBI Science Receiver; Multifunctional Tanks for Spacecraft; Lightweight, Segmented, Mostly Silicon Telescope Mirror; Assistant for Analyzing Tropical-Rain-Mapping Radar Data; and Anion-Intercalating Cathodes for High-Energy- Density Cells.

Source record↗

Abiotic proxies for predictive mapping of nearshore benthic assemblages: implications for marine spatial planning

Marine spatial planning (MSP) should assist managers in guiding human activities toward sustainable practices and in minimizing user conflicts in our oceans. A necessary first step is to quantify spatial patterns of marine assemblages in order to understand the ecosystem's structure, function, and services. However, the large spatial scale, high economic value, and density of human activities in nearshore habitats often makes quantifying this component of marine ecosystems especially daunting. To address this challenge, we developed an assessment method that employs abiotic proxies to rapidly characterize marine assemblages in nearshore benthic environments with relatively high resolution. We evaluated this assessment method along 300 km of the State of Maine's coastal shelf (<100 m depth), a zone where high densities of buoyed lobster traps typically preclude extensive surveys by towed sampling gear (i.e., otter trawls). During the summer months of 2010–2013, we implemented a stratified-random survey using a small remotely operated vehicle that allowed us to work around lobster buoys and to quantify all benthic megafauna to species. Stratifying by substrate, depth, and coastal water masses, we found that abiotic variables explained a significant portion of variance (37–59%) in benthic species composition, diversity, biomass, and economic value. Generally, the density, diversity, and biomass of assemblages significantly increased with the substrate complexity (i.e., from sand-mud to ledge). The diversity, biomass, and economic value of assemblages also decreased significantly with increasing depth. Last, demersal fish densities, sessile invertebrate densities, species diversity, and assemblage biomass increased from east to west, while the abundance of mobile invertebrates and economic value decreased, corresponding mainly to the contrasting water mass characteristics of the Maine Coastal Current system (i.e., summertime current direction, speed, and temperature). Integrating modeled predictions with existing GIS layers for abiotic conditions allowed us to scale up important assemblage attributes to define key foundational ecological principles of MSP and to find priority regions where some bottom-disturbing activities would have minimal impact to benthic assemblages. We conclude that abiotic proxies can be strong forcing functions for the assembly of marine communities and therefore useful tools for spatial extrapolations of marine assemblages in congested (heavily used) nearshore habitats.

54 ENVIRONMENTAL SCIENCES↗

Identification of Differential Gene Expression Patterns after Acute Exposure to High and Low Doses of Low-LET Ionizing Radiation in a Reconstituted Human Skin Tissue

Our goal here was to identify dose and temporal dependent radiation responses in a complex tissue, reconstituted human skin. Direct sequencing of RNA (RNA-seq) was used to quantify altered transcripts following exposure to 0.1, 2 and 10 Gy of ionizing radiation at 3 and 8 hours. These doses include a low dose in the range of some medical diagnostic procedures (0.1 Gy), a dose typically received during radiotherapy (2.0 Gy) and a lethal dose (10 Gy). These doses could be received after an intentional or accidental radiation exposure and biomarkers are needed to rapidly and accurately triage exposed individuals. A total of 1701 genes were deemed to be significantly affected by high dose radiation exposure with the majority of genes affected at 10 Gy. A group of 29 genes including GDF15, BBC3, PPM1D, FDXR, GADD45A, MDM2, CDKN1A, TP53INP1, CYCSP27, SESN1, SESN2, PCNA, and AEN were similarly altered at both 2 and 10 Gy, but not 0.1 Gy, at multiple time points. A much larger group of up regulated genes, including those involved in inflammatory responses, was significantly altered only after a 10 Gy exposure. At high doses, down regulated genes were associated with cell cycle regulation and exhibited an apparent linear response between 2 and 10 Gy. While only a handful of genes were significantly affected by 0.1 Gy exposure using stringent statistical filters, groups of related genes regulating cell cycle progression and inflammatory responses consistently exhibited opposite trends in their regulation compared to the high dose exposures. Differential regulation of PLK1 signaling at low and high doses was confirmed using qRT-PCR. These results indicate that some alterations in gene expression are qualitatively different at low and high doses of radiation in this model system.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Integration of in silico approaches to determination of endocrine-disrupting perfluorinated chemicals binding potency with steroidogenic acute regulatory protein

A myriad of perfluorinated compounds (PFCs) have the ability to interfere with steroidogenic acute regulatory (StAR) protein. Consequently, PFCs breaches cholesterol biotransformation in mitochondria and cause fatal consequences in steroidogenesis, however, these were poorly characterized. In the present study, we have evaluated toxic potencies, nuclear mediated probabilities and interaction profiles with StAR of PFCs using computational system biology tools. Toxicity endpoints revealed that PFCs contain high carcinogenicity, developmental toxicity, skin sensitization effects with low mutagenic activity. Consensus qualitative nuclear receptor agonist models show higher probability rates towards ER and PPAR-γ receptor than AR and AhR models were observed. To poise the subtle fluctuations of actual predictions, balanced accuracy and MCC were computed, and they signify perfect correlation ranges in all models. Screening studies resulting protein-ligand interaction profiles showed that residues Asn148, Asn150, Glu169, Ala171, Arg182, Phe184, Arg188, Trp241, Thr263 and Phe267 were identified as novel hotspots, participated in halogen bonds, H-bonds, atomic π-stacking, π-cation interactions and salt-bridges formation. Thus, the additional bonds contribute conformer stability that holds the protein structure at flexible state, so that PFCs acts as a barrier to cholesterol binding. From docking outcomes, representation space was created, that specifies high and medium StAR binders were occupied in toxic endpoints space with active concern. PFCs restrain molecular features and mitochondrial membrane disruption functions were revealed by efficient toxicogenomics studies. These data indicate toxicity and StAR protein binding levels of PFCs, sorted pinpoints could be useful in a promising way to know the other environmental pollutants and health risks. - Highlights: • In this study, QSAR models were revealed that PFCs have greater adverse toxicity along with nuclear receptors interaction potencies. • Binding potencies of PFCs against the StAR protein revealed only potential novel residue hotspots showed various bond patterns, and they sustain stability and complexity of StAR. • Through that, PFCs acts as a barrier in cholesterol binding and leads fatal consequences in steroidogenesis.

60 APPLIED LIFE SCIENCES↗

Magnetoresistance anomaly during the electrical triggering of a metal-insulator transition

Phase separation naturally occurs in a variety of magnetic materials and it often has a major impact on both electric and magnetotransport properties. In resistive switching systems, phase separation can be created on demand by inducing local switching, which provides an opportunity to tune the electronic and magnetic state of the device by applying voltage. Here we explore the magnetotransport properties in the ferromagnetic oxide La 0.7 ⁢Sr 0.3 ⁢MnO 3 (LSMO) during the electrical triggering of an intrinsic metal-insulator transition (MIT), which produces volatile resistive switching. This switching occurs in a characteristic spatial pattern, i.e., the formation of a high-resistance barrier perpendicular to the current flow, enabling an electrically actuated ferromagnetic-paramagnetic-ferromagnetic phase separation. At the threshold voltage of the MIT triggering, both anisotropic and colossal magnetoresistances exhibit anomalies including a large increase in magnitude and a sign flip. Computational analysis revealed that these anomalies originate from the coupling between the switching-induced phase separation state and the intrinsic magnetoresistance of LSMO. Furthermore, this work demonstrates that driving the MIT material into an out-of-equilibrium resistive switching state provides the means for electrical control of the magnetotransport phenomena.

Complex oxides↗

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

Tree growth and survival differ strongly between canopy trees (those directly exposed to overhead light), and understory trees. However, the structural complexity of many tropical forests makes it difficult to determine canopy positions. The integration of remote sensing and ground-based data enables this determination and measurements of how canopy and understory trees differ in structure and dynamics. Here we analyzed 2 cm resolution RGB imagery collected by a Remotely Piloted Aircraft System (RPAS), also known as drone, together with two decades of bi-annual tree censuses for 2 ha of old growth forest in the Central Amazon. We delineated all crowns visible in the imagery and linked each crown to a tagged stem through field work. Canopy trees constituted 40% of the 1244 inventoried trees with diameter at breast height (DBH) > 10 cm, and accounted for ~70% of aboveground carbon stocks and wood productivity. The probability of being in the canopy increased logistically with tree diameter, passing through 50% at 23.5 cm DBH. Diameter growth was on average twice as large in canopy trees as in understory trees. Growth rates were unrelated to diameter in canopy trees and positively related to diameter in understory trees, consistent with the idea that light availability increases with diameter in the understory but not the canopy. The whole stand size distribution was best fit by a Weibull distribution, whereas the separate size distributions of understory trees or canopy trees > 25 cm DBH were equally well fit by exponential and Weibull distributions, consistent with mechanistic forest models. The identification and field mapping of crowns seen in a high resolution orthomosaic revealed new patterns in the structure and dynamics of trees of canopy vs. understory at this site, demonstrating the value of traditional tree censuses with drone remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗

Sonic Boom Prediction and Minimization of the Douglas Reference OPT5 Configuration

Conventional CFD methods and grids do not yield adequate resolution of the complex shock flow pattern generated by a real aircraft geometry. As a result, a unique grid topology and supersonic flow solver was developed at Northrop Grumman based on the characteristic behavior of supersonic wave patterns emanating from the aircraft. Using this approach, it was possible to compute flow fields with adequate resolution several body lengths below the aircraft. In this region, three-dimensional effects are diminished and conventional two-dimensional modified linear theory (MLT) can be applied to estimate ground pressure signatures or sonic booms. To accommodate real aircraft geometries and alleviate the burdensome grid generation task, an implicit marching multi-block, multi-grid finite-volume Euler code was developed as the basis for the sonic boom prediction methodology. The Thomas two-dimensional extrapolation method is built into the Euler code so that ground signatures can be obtained quickly and efficiently with minimum computational effort suitable to the aircraft design environment. The loudness levels of these signatures can then be determined using a NASA generated noise code. Since the Euler code is a three-dimensional flow field solver, the complete circumferential region below the aircraft is computed. The extrapolation of all this field data from a cylinder of constant radius leads to the definition of the entire boom corridor occurring directly below and off to the side of the aircraft's flight path yielding an estimate for the entire noise "annoyance" corridor in miles as well as its magnitude. An automated multidisciplinary sonic boom design optimization software system was developed during the latter part of HSR Phase 1. Using this system, it was found that sonic boom signatures could be reduced through optimization of a variety of geometric aircraft parameters. This system uses a gradient based nonlinear optimizer as the driver in conjunction with a computationally efficient Euler CFD solver (NIIM3DSB) for computing the three-dimensional near-field characteristics of the aircraft. The intent of the design system is to identify and optimize geometric design variables that have a beneficial impact on the ground sonic boom. The system uses a simple wave drag data format to specify the aircraft geometry. The geometry is internally enhanced and analytic methods are used to generate marching grids suitable for the multi-block Euler solver. The Thomas extrapolation method is integrated into this system, and hence, the aircraft's centerline ground sonic boom signature is also automatically computed for a specified cruise altitude and yields the parameters necessary to evaluate the design function. The entire design system has been automated since the gradient based optimization software requires many flow analyses in order to obtain the required sensitivity derivatives for each design variable in order to converge on an optimal solution. Hence, once the problem is defined which includes defining the objective function and geometric and aerodynamic constraints, the system will automatically regenerate the perturbed geometry, the necessary grids, the Euler solution, and finally the ground sonic boom signature at the request of the optimizer.

Siclari, Michael J.↗

Investigation into the effect on structure of oxoanion doping in Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O

In this paper an investigation into the effect of transition metal ion and selenate/fluorophosphate doping on the structures of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O (M=transition metal) materials is reported. In agreement with previous reports, the monoclinic (Kröhnkite) structure is adopted for M=Mn, Fe, Co, Cu, while for the smallest first row divalent transition metal ion, M=Ni, the triclinic (Fairfieldite structure) is adopted. On selenate doping there is a changeover in structure from monoclinic to triclinic for M=Fe, Co, Cu, with the larger Fe{sup 2+} system requiring the highest level of selenate to complete the changeover. Thus the results suggest that the relative stability of the two structure types is influenced by the relative size of the transition metal: oxoanion group, with the triclinic structure favoured for small transition metals/large oxoanions. The successful synthesis of fluorophosphate doped samples, Na{sub 2}M(SO{sub 4}){sub 2−x}(PO{sub 3}F){sub x}·2H{sub 2}O was also obtained for M=Fe, Co, Cu, with the results showing a changeover in structure from monoclinic to triclinic for M=Co, Cu for very low levels (x=0.1) of fluorophosphate. In the case of M=Fe, the successful synthesis of fluorophosphates samples was achieved for x≤0.3, although no change in cell symmetry was observed. Rather in this particular case, the X-ray diffraction patterns showed evidence for selective peak broadening, attributed to local disorder as a result of the fluorophosphate group disrupting the H-bonding network. Overall the work highlights how isovalent doping can be exploited to alter the structures of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O systems. - Graphical abstract: Partial substitution of sulfate in Na{sub 2}M(SO{sub 4}){sub 2}0.2H{sub 2}O (M=Co, Cu) by selenate or fluorophosphate leads to a structural change from the monoclinic Kröhnkite to the triclinic Fairfieldite structure. - Highlights: • The successful synthesis of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O (M=transition metal) phases doped with selenate and fluorophosphate. • A change in structure is observed on selenate doping for M=Fe, Co, Cu. • This change in structure is also observed on fluorophosphate doping for M=Co, Cu. • The work highlights how isovalent doping can be exploited to alter the structures of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteins were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to begin to assess the degree to which diagnostic meatbolic proteins are long-lived or acively synthesized in complex, slow-growing microbial communities. Our work here demonstrates that sediment-hosted microbial assemblages in marine methane seeps are dynamic, heterogeneous systems with broad functional diversity.

59 BASIC BIOLOGICAL SCIENCES↗

3-D Reconstruction of Macular Type II Cell Innervation Patterns in Space-Flight and Control Rats

A semiautomated method for reconstructing objects from serial thin sections has been developed in the Biocomputation Center. The method is being used to completely, for the first time, type II hair cells and their innervations. The purposes are to learn more about the fundamental circuitry of the macula on Earth and to determine whether changes in connectivities occur under space flight conditions. Data captured directly from a transmission electron microscope via a video camera are sent to a graphics workstation. There, the digitized micrographs are mosaicked into sections and contours are traced, registered and displayed by semiautomated methods. Current reconstructions are of type II cells from the medial part of rat maculas collected in-flight on the Space Life Sciences-2 mission, 4.5 hrs post-flight, and from a ground control. Results show that typical type II cells receive processes from tip to six nearby calyces or afferents. Nearly all processes are elongated and have bouton-like enlargements; some have numerous vesicles. Multiple (2 to 4) processes from a single calyx to a type II cell are common, and approximately 1/3 of the processes innervale 2 or 3 type II cells or a neighboring cluster. From 2% to 6% of the cells resemble type I cells morphologically but have demi-calyces. Thus far, increments in synaptic number in type II cells of flight rats are prominent along processes that supply two hair cells. It is clear that reconstruction methods provide insights into details of macular circuitry not obtainable by other techniques. The results demonstrate a morphological basis for interactions between adjacent receptive fields through feed back-feed forward connections, and for dynamic alterations in receptive field range and activity during preprocessing of linear acceleratory information by the maculas. The reconstruction method we have developed will find further applications in the study of the details of neuronal architecture of more complex systems, to seek out shared organizational properties or neuronal networks and to understand better localization of synaptic changes in altered environments.

Ross, Muriel Dorothy↗

Baselining PMU Data to Find Patterns and Anomalies

This paper looks at the application of situational awareness methodologies with respect to power grid data. These methodologies establish baselines that look for typical patterns and atypical behavior in the data. The objectives of the baselining analyses are to provide: real-time analytics, the capability to look at historical trends and events, and reliable predictions of the near future state of the grid. Multivariate algorithms were created to establish normal baseline behavior and then score each moment in time according to its variance from the baseline. Detailed multivariate analytical techniques are described in this paper that produced ways to identify typical patterns and atypical behavior. In this case, atypical behavior is behavior that is unenvisioned. Visualizations were also produced to help explain the behavior that was identified mathematically. Examples are shown to help describe how to read and interpret the analyses and visualizations. Preliminary work has been performed on PMU data sets from BPA (Bonneville Power Administration) and EI (Eastern Interconnect). Actual results are not fully shown here because of confidentiality issues. Comparisons between atypical events found mathematically and actual events showed that many of the actual events are also atypical events; however there are many atypical events that do not correlate to any actual events. Additional work needs to be done to help classify the atypical events into actual events, so that the importance of the events can be better understood.

Baselining analyses↗

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Abstract Background Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and experimental results from parallel sequencing provide available information about the affinity and accessibility of genome and are commonly used features in binding sites prediction. The attention mechanism in deep learning has shown its capability to learn long-range dependencies from sequential data, such as sentences and voices. Until now, no study has applied this approach in binding site inference from massively parallel sequencing data. The successful applications of attention mechanism in similar input contexts motivate us to build and test new methods that can accurately determine the binding sites of transcription factors. Results In this study, we propose a novel tool (named DeepGRN) for transcription factors binding site prediction based on the combination of two components: single attention module and pairwise attention module. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets. The results show that DeepGRN achieves higher unified scores in 6 of 13 targets than any of the top four methods in the DREAM challenge. We also demonstrate that the attention weights learned by the model are correlated with potential informative inputs, such as DNase-Seq coverage and motifs, which provide possible explanations for the predictive improvements in DeepGRN. Conclusions DeepGRN can automatically and effectively predict transcription factor binding sites from DNA sequences and DNase-Seq coverage. Furthermore, the visualization techniques we developed for the attention modules help to interpret how critical patterns from different types of input features are recognized by our model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation of Magmatic Activities on Early Mars Using Igneous Mineral Chemistry in Gale Crater, Mars

One objective of rover missions is exploring the geological context of the surroundings. Over the years, igneous petrology and sedimentology have been disconnected, the first investigating magmatic processes and volcanic activities, and the second seeking environmental conditions in the past and assessing the habitability of the planet. Although different, one is related to the other: igneous rocks are altered and broken down, leading to the formation of sedimentary rocks, which can in turn be used to back out the nature of their magmatic source. The Curiosity rover that landed in the 3.7 Gyr old impact crater Gale is traveling through sedimentary rocks. About fifty float rocks have been observed, and several of them with ambiguous texture and composition have been classified as igneous or sedimentary depending on studies such as Jake_M. The composition of several unambiguous igneous rocks has been analyzed [4- 6] but their heterogeneity at a larger instrumental (measurement size < 2 cm) scale prevents the measurement of a bulk composition as performed on Earth. An original approach avoiding these two last issues is to consider igneous mineral chemistry analyzed within igneous and sedimentary rocks to assess magmatic processes that could have formed them. Most Curiosity data are used to explore ancient environmental conditions, and a significant number of compositional analyses are under-explored for constraining magmatic activities. We will present how we can make use of sedimentary data for investigating igneous processes in the vicinity of Gale crater. Geological Context: We focus on the first 750 martian days, corresponding to measurements in a coherent lacustrine sedimentary unit called Bradbury, because all sedimentary rocks were sourced from the same watershed and appear to have a consistent source with minimal alteration [2-3]. Igneous detrital minerals including feldspar and pyroxene, are observed in sedimentary rocks. Monte Carlo models showed that minimal cation loss is observed based on the composition of all Bradbury rocks, implying negligible weathering [3]. Although clay minerals are detected in few rocks [7], chemical compositions of rocks can be explained by a mixture of primary igneous minerals [3]. Variation of composition within Bradbury rocks can be explained by mineral sorting and one distinct source component. While a common magmatic source is suggested, Bradbury sediments likely come from several volcanic eruptions from a single magmatic chamber [9- 10]. The occurrence of alkali minerals like sanidine and K-rich rocks throughout Bradbury supports the presence of a potassic component, likely trachytic, while plagioclase and a mafic composition suggest a basaltic component [8-9]. Instruments: Mineral chemistry can be estimated by three instruments onboard Curiosity. The CheMin instrument enables detection of mineral assemblages using X-ray diffraction (XRD). Using Rietveld refinement, each mineral is identified according to their 1D XRD pattern [11]. Note that distinction between pyroxene minerals is challenging with the CheMin instrument due to overlapping peaks on XRD patterns and low angular resolution of the instrument [12]. Then, using least square regression and optimization algorithms based on unit-cell parameters, mineral chemistry has been estimated by [11]. Plagioclase composition has been estimated using the NaAlSi3O8- CaAl2Si2O8 system and alkali feldspar is based on the NaAlSi3O8-KAlSi3O8 system (stars in Fig.1). Two mudstone samples (John Klein and Cumberland) and one sandstone sample (Windjana) were analyzed by CheMin at Yellowknife Bay and Kimberley, respectively. Figure 1. Ternary diagrams of feldspars (top) and pyroxene (bottom) quadrilateral. Stars correspond to CheMin composition and the gray patches to ChemCam composition. The colored dots are the composition of feldspar and pyroxene that crystallized during fractional crystallization at FMQ+1 of a melt extracted at distinct melting degree during the adiabatic ascent of a primitive mantle composition, without any water (left panels) and with 0.5 wt.% of water (right panels) at distinct pressure. The ChemCam instrument enables the analysis of the chemical compositions of rocks at hundreds of micrometer scale (350-550 μm) using laser induced breakdown spectroscopy (LIBS), which may provide the composition of minerals when they are larger than the beam spot (>550 μm) [13]. Within >5000 LIBS points, we performed a typical stoichiometric filtering allowing us to distinguish 56 feldspar and 10 pyroxene mineral compositions (grey patches in Fig. 1). Finally, the Alpha Particle X-ray Spectrometer (APXS) analyzes the composition of rocks with a 1.6 cm diameter spot size. Monte Carlo mass balance modeling allowed [3] to decipher a feldspar range varying between An30 and An40 (Fig. 1). Discussion: Although there could be a more complex history and other ways to form the whole compositional range of igneous minerals analyzed within the Bradbury formation, we are presenting here simple magmatic pathways commonly occurring on Earth using the thermodynamical softwares pMELTS and rhyoliteMELTS [14]. The objective is to find reasonable igneous processes that produce minerals that parallel the compositions of feldspar and pyroxene analyzed by the Curiosity rover. As commonly observed for mid-ocean ridge basalts, the adiabatic ascent of a primitive mantle composition [15] partially melting at 2 GPa has been modeled, followed by the extraction of a liquid at distinct degrees of partial melting, which undergoes fractional crystallization at an oxygen fugacity +1 log unit above the fayalite-magnetite-quartz (FMQ) buffer within the crust (0.02-0.4 GPa) with H2O = 0- 0.5 wt. %. These latter conditions correspond to those recorded within igneous clasts from the Noachian martian breccia NWA 7034 and paired and within Gale igneous rocks (colored dots in Fig. 1) [16-17]. To check the reliability of these 2-step models, we also tested fractional crystallization at similar conditions (FMQ+1; P=0.02-0.4 GPa; H2O = 0-0.5 wt. %) of starting compositions corresponding to that of magmas with distinct melting degrees obtained from isobaric experiments at 2 GPa [18]. Mineral compositions obtained from both models are similar. As shown on Fig. 1, the whole range of observed feldspar compositions cannot be reproduced by fractionation of one magma only. Indeed, while alkali feldspar and Na-plagioclase likely crystallized from fractional crystallization of a low-degree melt (here <15%), plagioclase and pyroxene can only be formed by fractional crystallization of a higher degree melt (here >19%). The corresponding liquid descent lines are broadly in agreement with compositions estimated by ChemCam corresponding to float igneous rocks (Fig. 2) [4-6]. Figure 2. Silica versus alkali content. Lines show the liquid lines of descent from magmas with distinct degrees of melting. Gray patches represents the composition of Gale igneous rocks [4-6]. Trachytic to rhyolitic magmas crystallize alkali feldspar, and andesite to dacite magmas likely form plagioclase. Therefore, at least two starting magmas at distinct melting degrees, which could easily come from a single mantle source, are necessary to explain the whole compositional range of feldspar and pyroxene analyzed within Bradbury rocks. Conclusion: Because rocks from the Bradbury formation are likely originating from the same magmatic source with minimal weathering as supported by several studies using different approaches, igneous mineral chemistry analyzed by CheMin and ChemCam allows us to back out reasonable magmatic pathways that could have crystallized them. Fractional crystallization of at least two starting magmas originating from distinct melting degrees of a single mantle source can explain the whole range of feldspar and pyroxene composition. Both alkaline and sub-alkaline liquids can be produced, with compositions corresponding to those of the igneous rocks analyzed by ChemCam within the Bradbury formation, highlighting the complexity of Mars magmatism.

Payre, V.↗

Nanotube/Quantum Dot-Polymer Solar Cells

Single wall carbon nanotubes used or this study were synthesized using the pulse laser vaporization technique. The as-produced SWNTs were collected from the condensed region on the quartz tube outside the furnace and purified by modification of the previously reported procedure. Preparation of the SWNT-P3OT composite solutions was performed using a series of mixing and sonication steps as previously demonstrated for other SWNT-polymer systems. Device fabrication involved the use of commercially-obtained, high quality (i.e., less than 10 W/sq.) ITO-coated polyethylene terapthalate (PET) substrates. Initially, an intrinsic layer of pristine P3OT is spray deposited (approx. 1-2 mL of the 15 mg/mL solution) onto the masked, 1 sq in. active area of the substrate. This is followed with spray deposition of the SWNT-P3OT composite solutions at similar volumes. As seen completion of the solar cell occurs when aluminum contacts (typical thicknesses of l000A) are applied to the IT0 and SWNT-P3OT composite film layers. The homogeneous distribution of SWNTs in a polymer matrix is dependent upon the ability of the polymer chain to associate with the SWNT superstructure. Stable composite dispersions of 0.1 % and 1.0% w/w SWNTs in P3OT were produced and analyzed in this study. Optical spectroscopy was conducted to observe the SWNT doping level effects on the absorption properties and infer potential electronic interactions between dopant and polymer. Shown is an overlay of these spectra where the pristine P3OT shows strong optical absorption at energies less than 2 eV. As expected, variation in absorption properties for the SWNT-P3OT composites is observed as the doping level increases. Through modification of the SWNT doping level in the polymer, it is possible to alter the absorption pattern of these composite materials. In fact, at these relatively low doping levels, the P3OT shows a significant enhancement in absorption through the near-IR and visible regions. The gray curve for purified SWNTs is offset from the other three for clarity, but indicates the typical complex pattern observed for this spectral range.

Bailey, Sheila G.↗