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DOE OSTI2014

Uncertainty in least-squares fits to the thermal noise spectra of nanomechanical resonators with applications to the atomic force microscope

Thermal noise spectra of nanomechanical resonators are used widely to characterize their physical properties. These spectra typically exhibit a Lorentzian response, with additional white noise due to extraneous processes. Least-squares fits of these measurements enable extraction of key parameters of the resonator, including its resonant frequency, quality factor, and stiffness. Here, we present general formulas for the uncertainties in these fit parameters due to sampling noise inherent in all thermal noise spectra. Good agreement with Monte Carlo simulation of synthetic data and measurements of an Atomic Force Microscope (AFM) cantilever is demonstrated. These formulas enable robust interpretation of thermal noise spectra measurements commonly performed in the AFM and adaptive control of fitting procedures with specified tolerances.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2013

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Background: Preterm infants represent a unique patient population that is born functionally immature and must accomplish development under the influence of a hospital environment. Neonatal necrotizing enterocolitis (NEC) is an inflammatory intestinal disorder affecting preterm infants. The purpose of this study was to evaluate the progression of intestinal microbiota community development between preterm infants who remained healthy compared to preterm infants who developed NEC. Results: Weekly fecal samples from ten preterm infants, five with NEC and five matched healthy controls were obtained. Bacterial DNA from individual fecal samples was subjected to sequencing of 16S rRNA-based inventories using the 454 GS-FLX platform. Fecal samples from control infants demonstrated a temporal pattern in their microbiota, which converged toward that of a healthy full term breast-fed infant. Microbiota development in NEC patients diverged from controls beginning three weeks prior to diagnosis. Shotgun metagenomic sequencing was performed to identify functional differences in the respective microbiota of fecal samples from a set of twins in which one twin developed NEC and one did not. The majority of the differentially abundant genes in the NEC patient were associated with carbohydrate metabolism and mapped to members of the family Enterobacteriaceae. This may indicate an adaptation of the community to an altered profile of substrate availability for specific members as a first step towards the development of NEC. We propose that the microbial communities as a whole may metabolize milk differently, resulting in differential substrate availability for specific microbial groups. Additional differentially represented gene sets of interest were related to antibiotic resistance and vitamin biosynthesis. Conclusions: Our results suggest that there is a temporal component to microbiome development in healthy preterm infants. Thus, bacteriotherapy for the treatment or prevention of NEC must consider this temporal component of the microbial community in addition to its taxonomic composition and functional content.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Evaluation of the Lawrence Livermore Microbal Detection Array at the Statens Serum Institut CRADA No. TC02189

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Statens Serum Institut to evaluate and transition the Lawrence Livermore Microarray Detection Array (LLMDA) analysis software package, the Composite Likelihood Maximization method (CLiMax) to the SSI. The SSI is a public enterprise under the Danish Ministry of Health that operates a microbiology reference laboratory for the Danish population and analyzes tens to thousands of human clinical samples annually. SSI has been collaborating with the LLNL team for several years to use the LLMDA to analyze viral and bacterial infections from human clinical samples. The collaboration has resulted in two joint publications thus far, describing improvements to LLMDA sample preparation, and the utility of the LLMDA for detecting emerging viruses in clinical samples. Under our previous collaboration, SSI has performed LLMDA experiments at their facility and then transferred the raw LLMDA data to LLNL for analysis. SSI had purchased LLMDA microarrays directly from the manufacturer, Roche NimbleGen. The main purpose of the current collaboration was to adapt the CLiMax analysis software so that it could run on a computer located at SSI. Additional effort was budgeted for LLNL staff to assist SSI with the transition and the operation of the software. The primary deliverable is the CLiMax software, installed on a computer at SSI.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1982

Precipitation measurements from space - Workshop summary 28 April-1 May 1981, Greenbelt, MD

The goals and methods for global precipitation measurements from space are examined. Records currently exist only for visible and IR scans of cloud properties, and are applied from GEO for detecting diurnal variations in precipitation. Microwave radiometry is noted to be a suitable method for supplementing the visible and IR data for measuring stratiform oceanic precipitation, and when used at up to 3 microns can detect areas, if not amounts, of precipitation from GEO. Applications of radar altimeters are proposed in terms of modifications to the Seasat-type 2.2 cm radar, the use of surface target attentuation radar, of frequency agile rain radar, or of adaptive pointing radar. Soil moisture sensing is available with passive microwave radiometry in the 20-50 cm bands, or active sensing in the 5-8 cm bands. The utilization of GARP ground truth data is explored, along with statistical methods for treating the data samples.

Atlas, D.↗

NASA NTRS1989

Data compression experiments with LANDSAT thematic mapper and Nimbus-7 coastal zone color scanner data

A case study is presented where an image segmentation based compression technique is applied to LANDSAT Thematic Mapper (TM) and Nimbus-7 Coastal Zone Color Scanner (CZCS) data. The compression technique, called Spatially Constrained Clustering (SCC), can be regarded as an adaptive vector quantization approach. The SCC can be applied to either single or multiple spectral bands of image data. The segmented image resulting from SCC is encoded in small rectangular blocks, with the codebook varying from block to block. Lossless compression potential (LDP) of sample TM and CZCS images are evaluated. For the TM test image, the LCP is 2.79. For the CZCS test image the LCP is 1.89, even though when only a cloud-free section of the image is considered the LCP increases to 3.48. Examples of compressed images are shown at several compression ratios ranging from 4 to 15. In the case of TM data, the compressed data are classified using the Bayes' classifier. The results show an improvement in the similarity between the classification results and ground truth when compressed data are used, thus showing that compression is, in fact, a useful first step in the analysis.

Tilton, James C.↗

NASA NTRS1994

Sampling Particles In Hot Gas Plumes

Sampling darts and launching apparatus built to collect particles in vertical plume of hot gas. In original application, hot gas plume is rocket-engine exhaust during test firing. Dart passes made at various heights, depending on launch angle and launch-gas pressure. Adaptable to variety of terrestrial uses like research on particulate emissions of volcanoes or determining origin of building fire while still burning.

Taylor, James F.↗

NASA NTRS1999

Collection and Analysis of Aircraft Emitted Particles

The University of Denver Aerosol Group proposed to adapt an impactor system for the collection of particles emitted by aircraft. The collection substrates were electron microscope grids which were analyzed by Dr. Pat Sheridan using a transmission electron microscope. The impactor was flown in the SNIFF behind aircraft and engine emissions were sampled. This report details the results of that work.

Wilson, James Charles↗

NASA NTRS1996

On the search for extant life on Mars

Proposals for continuing the search for extant life on Mars are primarily predicated on the assumption that specialized environmental niches that could support a biota may exist on the planet. Before attempting any critical tests for extant organisms, either in situ or on returned samples, it is imperative to determine whether any such sites actually exist. If, through remote sensing and landed instrumentation, sites of potential biological interest are discovered and characterized, biological tests can then more effectively be planned to elicit the presence of organisms that are adapted to living in these particular environments.

NASA Discipline Exobiology↗

NASA NTRS2016

Enabling the Direct Detection of Earth-Sized Exoplanets with the LBTI HOSTS Project: A Progress Report

NASA has funded a project called the Hunt for Observable Signatures of Terrestrial Systems (HOSTS) to survey nearby solar type stars to determine the amount of warm zodiacal dust in their habitable zones. The goal is not only to determine the luminosity distribution function but also to know which individual stars have the least amount of zodiacal dust. It is important to have this information for future missions that directly image exoplanets as this dust is the main source of astrophysical noise for them. The HOSTS project utilizes the Large Binocular Telescope Interferometer (LBTI), which consists of two 8.4-m apertures separated by a 14.4-m baseline on Mt. Graham, Arizona. The LBTI operates in a nulling mode in the mid-infrared spectral window (8-13 micrometers), in which light from the two telescopes is coherently combined with a 180 degree phase shift between them, producing a dark fringe at the location of the target star. In doing so the starlight is greatly reduced, increasing the contrast, analogous to a coronagraph operating at shorter wavelengths. The LBTI is a unique instrument, having only three warm reflections before the starlight reaches cold mirrors, giving it the best photometric sensitivity of any interferometer operating in the mid-infrared. It also has a superb Adaptive Optics (AO) system giving it Strehl ratios greater than 98% at 10 micrometers. In 2014 into early 2015 LBTI was undergoing commissioning. The HOSTS. project team passed its Operational Readiness Review (ORR) in April 2015. The team recently published papers on the target sample, modeling of the nulled disk images, and initial results such as the detection of warm dust around eta Corvi. Recently a paper was published on the data pipeline and on-sky performance. An additional paper is in preparation on Beta Leo. We will discuss the scientific and programmatic context for the LBTI project, and we will report recent progress, new results, and plans for the science verification phase that started in February 2016, and for the survey.

Hunt for Observable Signatures of Terrestrial Syst↗

DOE OSTI2014

Solution Hybrid Selection Capture for the Recovery of Functional Full-Length Eukaryotic cDNAs From Complex Environmental Samples

Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae . Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1993

Adaptive wavelet collocation methods for initial value boundary problems of nonlinear PDE's

We have designed a cubic spline wavelet decomposition for the Sobolev space H(sup 2)(sub 0)(I) where I is a bounded interval. Based on a special 'point-wise orthogonality' of the wavelet basis functions, a fast Discrete Wavelet Transform (DWT) is constructed. This DWT transform will map discrete samples of a function to its wavelet expansion coefficients in O(N log N) operations. Using this transform, we propose a collocation method for the initial value boundary problem of nonlinear PDE's. Then, we test the efficiency of the DWT transform and apply the collocation method to solve linear and nonlinear PDE's.

Cai, Wei↗

DOE OSTI2016

TU-H-CAMPUS-JeP3-02: Automated Dose Accumulation and Dose Accuracy Assessment for Online Or Offline Adaptive Replanning

Purpose: With introduction of high-quality treatment imaging during radiation therapy (RT) delivery, e.g., MR-Linac, adaptive replanning of either online or offline becomes appealing. Dose accumulation of delivered fractions, a prerequisite for the adaptive replanning, can be cumbersome and inaccurate. The purpose of this work is to develop an automated process to accumulate daily doses and to assess the dose accumulation accuracy voxel-by-voxel for adaptive replanning. Methods: The process includes the following main steps: 1) reconstructing daily dose for each delivered fraction with a treatment planning system (Monaco, Elekta) based on the daily images using machine delivery log file and considering patient repositioning if applicable, 2) overlaying the daily dose to the planning image based on deformable image registering (DIR) (ADMIRE, Elekta), 3) assessing voxel dose deformation accuracy based on deformation field using predetermined criteria, and 4) outputting accumulated dose and dose-accuracy volume histograms and parameters. Daily CTs acquired using a CT-on-rails during routine CT-guided RT for sample patients with head and neck and prostate cancers were used to test the process. Results: Daily and accumulated doses (dose-volume histograms, etc) along with their accuracies (dose-accuracy volume histogram) can be robustly generated using the proposed process. The test data for a head and neck cancer case shows that the gross tumor volume decreased by 20% towards the end of treatment course, and the parotid gland mean dose increased by 10%. Such information would trigger adaptive replanning for the subsequent fractions. The voxel-based accuracy in the accumulated dose showed that errors in accumulated dose near rigid structures were small. Conclusion: A procedure as well as necessary tools to automatically accumulate daily dose and assess dose accumulation accuracy is developed and is useful for adaptive replanning. Partially supported by Elekta, Inc.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2018

Auto-Gopher-2 – An Autonomous Wireline Rotary Piezo-Percussive Deep Drilling Mechanism

Drilling deep into the subsurface of planetary bodies in the Solar System for samples acquisition enables critical capabilities for future NASA exploration missions in its quest to understand the origins of the Solar System and potentially the search for life. Such planetary bodies as Mars and Europa are key targets for potential missions that would require reaching great depths. Performing drilling while using minimal mass/volume systems and with low energy consumption are the main requirements that are imposed on such technologies. A wireline deep drill, called Auto-Gopher-2, is currently being developed as a joint effort between JPL and Honeybee Robotics Ltd. The Auto-Gopher II is a wireline rotary piezo-percussive deep drilling mechanism that combines formation breaking by rotating and piezoelectric actuator hammering and cuttings removal by rotating a fluted bit. The hammering mechanism is based on the Ultrasonic/Sonic Drill/Corer (USDC) mechanism that has been developed as an adaptable tool for many drilling and coring applications. The USDC uses an intermediate ball-shape free-mass to transform high frequency vibrations of a piezoelectric transducer horn tip into sonic hammering of the drill bit. The lessons learned from the previous studies are being implemented into the development of the Auto-Gopher-II, an autonomous deep wireline drill with integrated cuttings and sample management and drive electronics. Subsystems of the wireline drill are being developed in parallel at JPL and Honeybee Robotics, Ltd. Issues related to the bit and its ability to retain the cuttings for caching and removal are currently being addressed. This paper presents the development efforts of the piezoelectric actuator, cuttings removal and retention flutes and drive electronics.

Bar-Cohen, Yoseph↗

NASA NTRS2017

Passive Earth Entry Vehicle Landing Test

Two full-scale passive Earth Entry Vehicles (EEV) with realistic structure, surrogate sample container, and surrogate Thermal Protection System (TPS) were built at NASA Langley Research Center (LaRC) and tested at the Utah Test and Training Range (UTTR). The main test objective was to demonstrate structural integrity and investigate possible impact response deviations of the realistic vehicle as compared to rigid penetrometer responses. With the exception of the surrogate TPS and minor structural differences in the back shell construction, the two test vehicles were identical in geometry and both utilized the Integrated Composite Stiffener Structure (ICoSS) structural concept in the forward shell. The ICoSS concept is a lightweight and highly adaptable composite concept developed at NASA LaRC specifically for entry vehicle TPS carrier structures. The instrumented test vehicles were released from a helicopter approximately 400 m above ground. The drop height was selected such that at least 98% of the vehicles terminal velocity would be achieved. While drop tests of spherical penetrometers and a low fidelity aerodynamic EEV model were conducted at UTTR in 1998 and 2000, this was the first time a passive EEV with flight-like structure, surrogate TPS, and sample container was tested at UTTR for the purpose of complete structural system validation. Test results showed that at a landing vertical speed of approximately 30 m/s, the test vehicle maintained structural integrity and enough rigidity to penetrate the sandy clay surface thus attenuating the landing load, as measured at the vehicle CG, to less than 600 g. This measured deceleration was found to be in family with rigid penetrometer test data from the 1998 and 2000 test campaigns. Design implications of vehicle structure/soil interaction with respect to sample container and sample survivability are briefly discussed.

Kellas, Sotiris↗

DOE OSTI2013

The Gemini NICI planet-finding campaign: The companion detection pipeline

We present high-contrast image processing techniques used by the Gemini NICI Planet-Finding Campaign to detect faint companions to bright stars. The Near-Infrared Coronographic Imager (NICI) is an adaptive optics instrument installed on the 8 m Gemini South telescope, capable of angular and spectral difference imaging and specifically designed to image exoplanets. The Campaign data pipeline achieves median contrasts of 12.6 mag at 0.''5 and 14.4 mag at 1'' separation, for a sample of 45 stars (V = 4.3-13.9 mag) from the early phase of the campaign. We also present a novel approach to calculating contrast curves for companion detection based on 95% completeness in the recovery of artificial companions injected into the raw data, while accounting for the false-positive rate. We use this technique to select the image processing algorithms that are more successful at recovering faint simulated point sources. We compare our pipeline to the performance of the Locally Optimized Combination of Images (LOCI) algorithm for NICI data and do not find significant improvement with LOCI.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Magnetized interstellar molecular clouds – I. Comparison between simulations and Zeeman observations

The most accurate measurements of magnetic fields in star-forming gas are based on the Zeeman observations analysed by Crutcher et al. Here, we show that their finding that the 3D magnetic field scales approximately as density 0.65 can also be obtained from analysis of the observed line-of-sight fields. We present two large-scale adaptive-mesh-refinement magnetohydrodynamic simulations of several thousand M ⊙ of turbulent, isothermal, self-gravitating gas, one with a strong initial magnetic field (Alfven Mach number $\mathcal{M}_{A,0}=1$) and one with a weak initial field ($\mathcal{M}_{A,0}=10$). We construct samples of the 100 most massive clumps in each simulation and show that they exhibit a power-law relation between field strength and density ($\bar{n}_H$) in excellent agreement with the observed one. Our results imply that the average field in molecular clumps in the interstellar medium (ISM) is $\langle B_{tot}(\bar{n}_H)\rangle ≈ 43\bar{n}^{0.65}_{H,4}μG$. Furthermore, the median value of the ratio of the line-of-sight field to density 0.65 in the simulations is within a factor of about (1.3, 1.7) of the observed value for the strong- and weak-field cases, respectively. The median value of the mass-to-flux ratio, normalized to the critical value, is 70 per cent of the line-of-sight value. This is larger than the 50 per cent usually cited for spherical clouds because the actual mass-to-flux ratio depends on the volume-weighted field, whereas the observed one depends on the mass-weighted field. Our results indicate that the typical molecular clump in the ISM is significantly supercritical (! factor of 3). The results of our strong-field model are in very good quantitative agreement with the observations of Li et al., which show a strong correlation in field orientation between small and large scales. Because there is a negligible correlation in the weak-field model, we conclude that molecular clouds form from strongly magnetized (although magnetically supercritical) gas, in agreement with the conclusion of Li et al.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

Abstract Background Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. Results Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. Conclusion Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Designing an Optimal Sensor Network via Minimizing Information Loss

Optimal experimental design is a classic topic in statistics, with many well-studied problems, applications, and solutions. The design problem we study is the placement of sensors to monitor spatiotemporal processes, explicitly accounting for the temporal dimension in our modeling and optimization. We observe that recent advancements in computational sciences often yield large datasets based on physics-based simulations, which are rarely leveraged in experimental design. We introduce a novel model-based sensor placement criterion, along with a highly-efficient optimization algorithm, which integrates physics-based simulations and Bayesian experimental design principles to identify sensor networks that “minimize information loss” from simulated data. Our technique relies on sparse variational inference and (separable) Gauss-Markov priors, and thus may adapt many techniques from Bayesian experimental design. We validate our method through a case study monitoring air temperature in Phoenix, Arizona, using state-of-the-art physics-based simulations. Our results show our framework to be superior to random or quasi-random sampling, particularly with a limited number of sensors. We conclude by discussing practical considerations and implications of our framework, including more complex modeling tools and real-world deployments.

54 ENVIRONMENTAL SCIENCES↗