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At least 613 records · Page 34

Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS

Despite intense investigation for over 25 years, the in vivo structure of plant mitochondrial genomes remains uncertain. Mapping studies and genome sequencing generally produce large circular chromosomes, whereas electrophoretic and microscopic studies typically reveal linear and multibranched molecules. To more fully assess the structure of plant mitochondrial genomes, the complete sequence of the monkeyflower (Mimulus guttatus DC. line IM62) mitochondrial DNA was constructed from a large (35 kb) paired-end shotgun sequencing library to a high depth of coverage ( ~30x ). The complete genome maps as a 525,671 bp circular molecule and exhibits a fairly conventional set of features including 62 genes (encoding 35 proteins, 24 transfer RNAs, and 3 ribosomal RNAs), 22 introns, 3 large repeats (2.7, 9.6, and 29 kb), and 96 small repeats (40–293 bp). Most paired-end reads (71%) mapped to the consensus sequence at the expected distance and orientation across the entire genome, validating the accuracy of assembly. Another 10% of reads provided clear evidence of alternative genomic conformations due to apparent rearrangements across large repeats. Quantitative assessment of these repeat-spanning read pairs revealed that all large repeat arrangements are present at appreciable frequencies in vivo, although not always in equimolar amounts. The observed stoichiometric differences for some arrangements are inconsistent with a predominant master circular structure for the mitochondrial genome of M. guttatus IM62. Finally, because IM62 contains a cryptic cytoplasmic male sterility (CMS) system, an in silico search for potential CMS genes was undertaken. The three chimeric open reading frames (ORFs) identified in this study, in addition to the previously identified ORFs upstream of the nad6 gene, are the most likely CMS candidate genes in this line.

59 BASIC BIOLOGICAL SCIENCES↗

Verification and Validation of the FLAG Hydrocode for Impact Cratering Simulations

Verification and validation (V&V) are necessary processes to ensure accuracy of the computational methods used to solve problems key to vast numbers of applications and industries. Simulations are essential for addressing impact cratering problems, because these problems often exceed experimental capabilities. We show that the free Lagrange (FLAG) hydrocode, developed at Los Alamos National Laboratory (Los Alamos, NM), can be used for impact cratering simulations by verifying FLAG against two analytical models of aluminum-on-aluminum impacts at different impact velocities and validating FLAG against a glass-into-water laboratory impact experiment. Our verification results show good agreement with the theoretical maximum pressures, with relative errors as low in magnitude as 1.00%. Our validation results demonstrate FLAG's ability to model various stages of impact cratering, with crater radius relative errors as low as 3.48% and crater depth relative errors as low as 0.79%. Our mesh resolution study shows that FLAG converges at resolutions low enough to reduce the required computation time from about 28 h to about 25 min. We anticipate that FLAG can be used to model larger impact cratering problems with increased accuracy and decreased computational cost on current systems relative to other hydrocodes tested by Pierazzo et al. (2008, “Validation of Numerical Codes for Impact and Explosion Cratering: Impacts on Strengthless and Metal Targets,” MAPS, 43(12), pp. 1917–1938).

97 MATHEMATICS AND COMPUTING↗

Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation

Purpose: Visualization of anatomical structures using radiological imaging methods is an important tool in medicine to differentiate normal from pathological tissue and can generate large amounts of data for a radiologist to read. Integrating these large data sets is difficult and time-consuming. A new approach uses both supervised and unsupervised advanced machine learning techniques to visualize and segment radiological data. This study describes the application of a novel hybrid scheme, based on combining wavelet transform and nonlinear dimensionality reduction (NLDR) methods, to breast magnetic resonance imaging (MRI) data using three well-established NLDR techniques, namely, ISOMAP, local linear embedding (LLE), and diffusion maps (DfM), to perform a comparative performance analysis. Methods: Twenty-five breast lesion subjects were scanned using a 3T scanner. MRI sequences used were T1-weighted, T2-weighted, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE) imaging. The hybrid scheme consisted of two steps: preprocessing and postprocessing of the data. The preprocessing step was applied for B{sub 1} inhomogeneity correction, image registration, and wavelet-based image compression to match and denoise the data. In the postprocessing step, MRI parameters were considered data dimensions and the NLDR-based hybrid approach was applied to integrate the MRI parameters into a single image, termed the embedded image. This was achieved by mapping all pixel intensities from the higher dimension to a lower dimensional (embedded) space. For validation, the authors compared the hybrid NLDR with linear methods of principal component analysis (PCA) and multidimensional scaling (MDS) using synthetic data. For the clinical application, the authors used breast MRI data, comparison was performed using the postcontrast DCE MRI image and evaluating the congruence of the segmented lesions. Results: The NLDR-based hybrid approach was able to define and segment both synthetic and clinical data. In the synthetic data, the authors demonstrated the performance of the NLDR method compared with conventional linear DR methods. The NLDR approach enabled successful segmentation of the structures, whereas, in most cases, PCA and MDS failed. The NLDR approach was able to segment different breast tissue types with a high accuracy and the embedded image of the breast MRI data demonstrated fuzzy boundaries between the different types of breast tissue, i.e., fatty, glandular, and tissue with lesions (>86%). Conclusions: The proposed hybrid NLDR methods were able to segment clinical breast data with a high accuracy and construct an embedded image that visualized the contribution of different radiological parameters.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here, we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as the target to enable the discovery of protein materials with superior mechanical properties.

59 BASIC BIOLOGICAL SCIENCES↗

Multiplexed Optical Fiber Sensors for Coal Fired Advanced Fossil Energy Systems

This report summarizes technical progress on the program Multiplexed Optical Fiber Sensors for Coal Fired Advanced Fossil Energy Systems funded by the National Energy Technology Laboratory of the U.S. Department of Energy, and performed jointly by the Center for Photonics Technology of the Bradley Department of Electrical and Computer Engineering and the Department of Materials Science and Engineering at Virginia Tech. This three-year project started on October 1, 2008. In the project, a fiber optical sensing system based on intrinsic Fabry-Perot Interferometer (IFPI) was developed for strain and temperature measurements for Ultra Supercritical boiler condition assessment. Investigations were focused on sensor design, fabrication, attachment techniques and novel materials for high temperature and strain measurements. At the start of the project, the technical requirements for the sensing technology were determined together with our industrial partner Alstom Power. As is demonstrated in Chapter 4, all the technical requirements are successfully met. The success of the technology extended beyond laboratory test; its capability was further validated through the field test at DOE NETL, in which the sensors yielded distributed temperature mapping of a testing coupon installed in the turbine test rig. The measurement results agreed well with prior results generated with thermocouples. In this project, significant improvements were made to the IFPI sensor technology by splicing condition optimization, transmission loss reduction, sensor signal demodulation and sensor system design.

01 COAL, LIGNITE, AND PEAT↗

Measurement of Triple-Differential Inclusive Muon Neutrino Charged-Current Cross Sections on Argon with the MicroBooNE Detector

We report the first measurement of the differential cross section $d^2σ(E_ν)/dcos(θ_µ)dP_µ$for inclusive muon neutrino charged-current scattering on argon. This measurement utilizes data from6.5×10 20 protons on target of exposure collected using the MicroBooNE liquid argon time projection chamber located on-axis in the Fermilab Booster Neutrino Beam with a mean neutrino energy of approximately 0.8 GeV. In this note, the mapping from reconstructed kinematics to truth quantities, particularly from reconstructed to true neutrino energy, is validated by comparing the distribution of reconstructed hadronic energy in data to that of the model prediction in different muon scattering angle bins after conditional constraint from the muon momentum distribution in data. The success of this validation gives confidence that the missing energy in the MicroBooNE detector is well-modeled within its uncertainties in simulation, enabling the unfolding to an energy-dependent triple-differential measurement over muon momentum, muon scattering angle, and neutrino energy. The unfolded measurement covers an extensive phase space, providing a wealth of information useful for future LArTPC experiments measuring neutrino oscillations. Comparisons with model predictions show the best agreement with Neut 5.4.0.1 at low energy, and with NuWro 19.02.01 at higher energies, particularly at forward muon scattering angles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Experimental and Numerical Characterization of High Temperature Deformation Behavior of 347H Stainless Steel

This study investigates how temperature affects the plasticity and thermal creep behavior of 347H stainless steel under uniaxial tension. The research combined experimental testing with advanced computational modeling. Two types of experiments were conducted: uniaxial tensile tests at temperatures from 100°C to 750°C using strain rates of ~10⁻⁴ s⁻¹, and creep tests at temperatures between 600°C and 750°C under various stress levels. These experimental results were used to develop and validate a new integrated mechanistic model that can predict material behavior under any loading condition while accounting for both stress and temperature effects. The model was implemented using a polycrystalline microstructure simulation framework based on elasto-viscoplastic Fast Fourier Transform (EVPFFT). It incorporates three key deformation mechanisms: thermally activated dislocation glide, dislocation climb, and vacancy diffusional creep. The model accounts for internal stress distribution within single crystals and considers how precipitates and solute atoms (both interstitial and substitutional) affect dislocation movement. After validation against experimental data, the model was used to generate Ashby-Weertman deformation mechanism maps for 347H steel, providing new insights into how microstructure influences the activation of different creep mechanisms.

Joy, Jobin K.↗

A TOMS-Based View of Tropical Tropospheric Ozone (OTTO) From Large Fires Associated with the 1997-1998 El Nino

Since the launch of Earth-Probe TOMS in July 1 996, we have been producing tropical tropospheric ozone (TTO) maps (10S - 10N), in gridded format, l x 2 degrees, in near-real time. These images, along with images from the full ADEOS-TOMS record of TTO (Sept. 1996 - May 1997) can be viewed on a homepage: http://metosrv2.umd,edu/-tropo). The TTO maps, based on the modified-residual method of Hudson and Thompson [1998], have been validated using ozonesondes from Ascension (8S, 15W), Nairobi (2S, 36E) and American Samoa (14S, 171W). The fires associated with El Nino-induced dryness are exhibited regionally as high tropospheric ozone column (> 60 Dobson Units) with high absorbing aerosol (smoke) signal in TOMS [J. R. Herman, personal communication, 1998]. Episodes of high TTO in 1997-98 will be shown. Regional TTO over Indonesia during the 1997-98 period will be highlighted and comparisons will be made with TTO in that region taken from the 1979-92 Nimbus/TOMS TTO record.

Thompson, Anne M.↗

Predicting and Managing Lighting and Visibility for Human Operations in Space

Lighting is critical to human visual performance. On earth this problem is well understood and solutions are well defined and executed. Because the sun rises and sets on average every 45 minutes during Earth orbit, humans working in space must cope with ~ extremely dynamic lighting conditions varying from very low light conditions to severe glare and contrast conditions. For critical operations, it is essential that lighting conditions be predictable and manageable. Mission planners need to detelmine whether low-light video cameras are required or whether additional luminaires, or lamps, need to be flown . Crew and flight directors need to have up to date daylight orbit time lines showing the best and worst viewing conditions for sunlight and shadowing. Where applicable and possible, lighting conditions need to be part of crew training. In addition, it is desirable to optimize the quantity and quality of light because of the potential impacts on crew safety, delivery costs, electrical power and equipment maintainability for both exterior and interior conditions. Addressing these issues, an illumination modeling system has been developed in the Space Human Factors Laboratory at ASA Johnson Space Center. The system is the integration of a physically based ray-tracing package ("Radiance"), developed at the Lawrence Berkeley Laboratories, a human factors oriented geometric modeling system developed by NASA and an extensive database of humans and their work environments. Measured and published data has been collected for exterior and interior surface reflectivity; luminaire beam spread distribution, color and intensity and video camera light sensitivity and has been associated with their corresponding geometric models. Selecting an eye-point and one or more light sources, including sun and earthshine, a ~ snapshot of the light energy reaching the surfaces or reaching the eye point is computed. This energy map is then used to extract the required information needed for useful predictions. Using a validated, comprehensive illumination model integrated with empirically derived data, predictions of lighting and viewing conditions have been successfully used for Shuttle and Space Station planning and assembly operations. It has successfully balanced the needs for adequate human performance with the utili zation of resources. Keywords: Modeling, ray tracing, luminaires, refl ectivity, luminance, illuminance.

Maida, James C.↗

Modeling Weather Impact on Ground Delay Programs

Scheduled arriving aircraft demand may exceed airport arrival capacity when there is abnormal weather at an airport. In such situations, Federal Aviation Administration (FAA) institutes ground-delay programs (GDP) to delay flights before they depart from their originating airports. Efficient GDP planning depends on the accuracy of prediction of airport capacity and demand in the presence of uncertainties in weather forecast. This paper presents a study of the impact of dynamic airport surface weather on GDPs. Using the National Traffic Management Log, effect of weather conditions on the characteristics of GDP events at selected busy airports is investigated. Two machine learning methods are used to generate models that map the airport operational conditions and weather information to issued GDP parameters and results of validation tests are described.

Wang, Yao↗

Examples of Level Products Possible from Existing Assets

How do patterns of human environmental and infectious diseases respond to leading environmental changes, particularly to urban growth and change and the associated impacts of urbanization? We use HyspIRI high spatial resolution, multispectral, and multitemporal TIR data to track energy balance and energy flux characteristics for changing land covers/land uses through time to provide synoptic views of impacts on surface energy fluxes, emissivity and temperature and HyspIRI data in conjunction with spatial growth models to project land cover/land use changes in the future to assess impacts on natural and human ecosystems. We use multispectral thermal IR land cover maps at a high spatial resolution (60m) on a weekly basis for long-term validation of surface energy responses and changes in emissivity and integration of HyspIRI TIR data with spatial modeling to assess changes in land cover/land use through time and subsequent changes in thermal energy responses

Quattrochi, Dale A.↗

Assessment and Applications of NASA Ozone Data Products Derived from Aura OMI-MLS Satellite Measurements in Context of the GMI Chemical Transport Model

Measurements from the Ozone Monitoring Instrument (OMI) and Microwave Limb Sounder (MLS), both onboard the Aura spacecraft, have been used to produce daily global maps of column and profile ozone since August 2004. Here we compare and evaluate three strategies to obtain daily maps of tropospheric and stratospheric ozone from OMI and MLS measurements: trajectory mapping, direct profile retrieval, and data assimilation. Evaluation is based upon an assessment that includes validation using ozonesondes and comparisons with the Global Modeling Initiative (GMI) chemical transport model (CTM). We investigate applications of the three ozone data products from near-decadal and inter-annual timescales to day-to-day case studies. Zonally averaged inter-annual changes in tropospheric ozone from all of the products in any latitude range are of the order 1-2 Dobson Units while changes (increases) over the 8-year Aura record investigated http://eospso.gsfc.nasa.gov/atbd-category/49 vary approximately 2-4 Dobson Units. It is demonstrated that all of the ozone products can measure and monitor exceptional tropospheric ozone events including major forest fire and pollution transport events. Stratospheric ozone during the Aura record has several anomalous inter-annual events including stratospheric warming split events in the Northern Hemisphere extra-tropics that are well captured using the data assimilation ozone profile product. Data assimilation with continuous daily global coverage and vertical ozone profile information is the best of the three strategies at generating a global tropospheric and stratospheric ozone product for science applications.

GMI↗

Dynamic Modeling and Soil Mechanics for Path Planning of the Mars Exploration Rovers

To help minimize risk of high sinkage and slippage during drives and to better understand soil properties and rover terramechanics from drive data, a multidisciplinary team was formed under the Mars Exploration Rover project to develop and utilize dynamic computer-based models for rover drives over realistic terrains. The resulting system, named ARTEMIS (Adams-based Rover Terramechanics and Mobility Interaction System), consists of the dynamic model, a library of terramechanics subroutines, and the high-resolution digital elevation maps of the Mars surface. A 200-element model of the rovers was developed and validated for drop tests before launch, using Adams dynamic modeling software. The external library was built in Fortran and called by Adams to model the wheel-soil interactions include the rut-formation effect of deformable soils, lateral and longitudinal forces, bull-dozing effects, and applied wheel torque. The paper presents the details and implementation of the system. To validate the developed system, one study case is presented from a realistic drive on Mars of the Opportunity rover. The simulation results match well from the measurement of on-board telemetry data. In its final form, ARTEMIS will be used in a predictive manner to assess terrain navigability and will become part of the overall effort in path planning and navigation for both Martian and lunar rovers.

rover↗

Dynamic Modeling and Soil Mechanics for Path Planning of the Mars Exploration Rovers

To help minimize risk of high sinkage and slippage during drives and to better understand soil properties and rover terramechanics from drive data, a multidisciplinary team was formed under the Mars Exploration Rover (MER) project to develop and utilize dynamic computer-based models for rover drives over realistic terrains. The resulting tool, named ARTEMIS (Adams-based Rover Terramechanics and Mobility Interaction Simulator), consists of the dynamic model, a library of terramechanics subroutines, and the high-resolution digital elevation maps of the Mars surface. A 200-element model of the rovers was developed and validated for drop tests before launch, using MSC-Adams dynamic modeling software. Newly modeled terrain-rover interactions include the rut-formation effect of deformable soils, using the classical Bekker-Wong implementation of compaction resistances and bull-dozing effects. The paper presents the details and implementation of the model with two case studies based on actual MER telemetry data. In its final form, ARTEMIS will be used in a predictive manner to assess terrain navigability and will become part of the overall effort in path planning and navigation for both Martian and lunar rovers.

terramechanics↗

WGISS-45 International Directory Network (IDN) Report

The objective of this presentation is to provide IDN (International Directory Network) updates on features and activities to the Committee on Earth Observation Satellites (CEOS) Working Group on Information Systems and Services (WGISS) and provider community. The following topics will be will be discussed during the presentation: Transition of Providers DIF-9 (Directory Interchange Format-9) to DIF-10 Metadata Records in the Common Metadata Repository (CMR); GCMD (Global Change Master Directory) Keyword Update; DIF-10 and UMM-C (Unified Metadata Model-Collections) Schema Changes; Metadata Validation of Provider Metadata; docBUILDER for Submitting IDN Metadata to the CMR (i.e. Registration); and Mapping WGClimate Essential Climate Variable (ECV) Inventory to IDN Records.

WGISS↗

Prediction and Verification of Parker Solar Probe Solar Wind Sources at 13.3 Rs

Drawing connections between heliospheric spacecraft and solar wind sources is a vital step in understanding the evolution of the solar corona into the solar wind and contextualizing in situ timeseries. Furthermore, making advanced predictions of this linkage for ongoing heliospheric missions, such as Parker Solar Probe (Parker), is necessary for achieving useful coordinated remote observations and maximizing scientific return. The general procedure for estimating such connectivity is straightforward (i.e., magnetic field line tracing in a coronal model) but validating the resulting estimates is difficult due to the lack of an independent ground truth and limited model constraints. In its most recent orbits, Parker has reached perihelia of 13.3R⊙ and moreover travels extremely fast prograde relative to the solar surface, covering over 120° longitude in 3 days. Here we present footpoint predictions and subsequent validation efforts for Parker Encounter 10, the first of the 13.3R⊙ orbits, which occurred in November 2021. We show that the longitudinal dependence of in situ plasma data from these novel orbits provides a powerful method of footpoint validation. With reference to other encounters, we also illustrate that the conditions under which source mapping is most accurate for near-ecliptic spacecraft (such as Parker) occur when solar activity is low, but also require that the heliospheric current sheet is strongly warped by mid-latitude or equatorial coronal holes. Lastly, we comment on the large-scale coronal structure implied by the Encounter 10 mapping, highlighting an empirical equatorial cut of the Alfvèn surface consisting of localized protrusions above unipolar magnetic separatrices.

S. T. Badman↗

How do tradeoffs in satellite spatial and temporal resolution impact snow water equivalent reconstruction?

Given the tradeoffs between spatial and temporal resolution, questions about resolution optimality are fundamental to the study of global snow. Answers to these questions will inform future scientific priorities and mission specifications. Heterogeneity of mountain snowpacks drives a need for daily snow cover mapping at the slope scale (≤30 m) that is unmet for a variety of scientific users, ranging from hydrologists to the military to wildlife biologists. But finer spatial resolution usually requires coarser temporal or spectral resolution. Thus, no single sensor can meet all these needs. Recently, constellations of satellites and fusion techniques have made noteworthy progress. The efficacy of two such recent advances is examined: (1) a fused MODIS–Landsat product with daily 30 m spatial resolution and (2) a harmonized Landsat 8 and Sentinel 2A and B (HLS) product with 3–4 d temporal and 30 m spatial resolution. State-of-the-art spectral unmixing techniques are applied to surface reflectance products from 1 and 2 to create snow cover and albedo maps. Then an energy balance model was run to reconstruct snow water equivalent (SWE). For validation, lidar-based Airborne Snow Observatory SWE estimates were used. Results show that reconstructed SWE forced with 30 m resolution snow cover has lower bias, a measure of basin-wide accuracy, than the baseline case using MODIS (463 m cell size) but greater mean absolute error, a measure of per-pixel accuracy. However, the differences in errors may be within uncertainties from scaling artifacts, e.g., basin boundary delineation. Other explanations are (1) the importance of daily acquisitions and (2) the limitations of downscaled forcings for reconstruction. Conclusions are as follows: (1) spectrally unmixed snow cover and snow albedo from MODIS continue to provide accurate forcings for snow models and (2) finer spatial and temporal resolution through sensor design, fusion techniques, and satellite constellations are the future for Earth observations, but existing moderate-resolution sensors still offer value.

Edward H. Bair↗

A direct gravitational lensing test for 10 exp 6 solar masses black holes in halos of galaxies

We propose a method that will be able to detect or exclude the existence of 10 exp 6 solar masses black holes in the halos of galaxies. VLBA radio maps of two milliarcsecond jets of a gravitationally lensed quasar will show the signature of these black holes - if they exist. If there are no compact objects in this mass range along the line of sight, the two jets should be linear mappings of each other. If they are not, there must be compact objects of about 10 exp 6 solar masses in the halo of the galaxy that deform the images by gravitational deflection. We present numerical simulations for the two jets A and B of the double quasar 0957 + 561, but the method is valid for any gravitationally lensed quasar with structure on milliarcsecond scales. As a by-product from high-quality VLBA maps of jets A and B, one will be able to tell which features in the maps are intrinsic in the original jet and which are only an optical illusion, i.e., gravitational distortions by black holes along the line of sight.

Wambsganss, Joachim↗