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At least 361 records · Page 20

Modeling of Horns for Sonic/Ultrasonic Applications

JPL has a requirement for telerobotic tools for planetary sample acquisition, which require low power and have the ability to work in harsh environments. We are currently investigating the possibility of using ultrasonic horns to develop a family of ultrasonic tools for these environments. In an effort to determine control parameters a one-dimensional Mason's model for a stepped ultrasonic horn assembly was developed which includes the effects of mechanical and electrical losses in the piezoelectric material and acoustic elements. The model is separated into three regions; the piezoelectric stack including stress bolt the backing layer and the horn. The model is found to predict the impedance data of the horn assembly very accurately up to the first coupled (radial) resonance. The model also allows for the calculation of the velocity and force and power delivered to each acoustic element. FEM modeling and accelerometer data from the horn tip were used to corroborate the model. The difficulties associated with modeling the load impedance of various devices will be discussed and current directions noted.

Sherrit, Stewart↗

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes ( i.e ., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Less than 100 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg .

Lui, Lauren↗

Site and endmember spectra of terrestrial vegetation and soils for the Colorado Headwaters Ecological Spectroscopy Study, June-July 2025

This dataset provides site and endmember spectra collected during the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS) campaign. The site spectra were collected to help validate airborne hyperspectral data acquired by the National Ecological Observatory Network's aerial observation platform (NEON AOP). Endmember spectra were collected to augment existing spectral libraries with additional samples of bare surfaces and non-photosynthetic vegetation. All measurements were acquired with an Analytical Spectral Devices (ASD) FieldSpec4 Hi-Res NG (Next Generation) spectroradiometer, which records radiance at 1nm (nanometer) intervals from the ultraviolet to the short-wave infrared (350-2500 nm). The dataset includes spectra measured at meadow sites where the CHESS team also collected vegetation samples for trait analyses. The site spectra were collected with the ASD FieldSpec4 palm grip attachment using an 8° field-of-view foreoptic. Site spectra are integrated measurements of the entire surface within the foreoptic’s field of view. For site-level spectra, the sun is the illumination source. A Spectralon panel mounted on a tripod was used for instrument optimization and white reference measurements for all site spectra. Site spectra were acquired within two hours of solar noon and within 48 hours of a NEON AOP overflight. Site spectra are labeled by date, sampling area, and site number according to the naming conventions of the CHESS campaign’s data management plan. The dataset also contains endmember spectra in the following categories: photosynthetic vegetation (PV), non-photosynthetic vegetation (NPV), bare (soil/rock), and flowers. Endmember measurements were acquired using either the contact probe or the leaf clip attachments of the ASD FieldSpec4. In these configurations, the bulb inside the spectrometer provides the light source for the measurements. The spectrometer was optimized and white reference measurements were recorded using the circular white pucks attached to the contact probe and leaf clip. Because they do not rely on solar illumination, contact probe and leaf clip measurements were collected during a broader time frame than the palm grip site spectra. Some endmembers were measured at CHESS meadow sites, while others were collected within the larger sampling area or in nearby locations (e.g. Gothic Townsite) with similar characteristics. Radiance, reflectance, and metadata files are split into three subfolders according to measurement type: proximal/palm grip (prx), contact probe (cp), and leaf clip (lc). Radiance spectra are provided in ASD file format (.asd file extension). All ASD files can be opened using the provided scripts. Metadata is provided in two formats: CSV file format (no geolocation) and GEOJSON file format (includes geolocation for each spectra). The dataset includes a set of pre-processed reflectance spectra as CSV files (yyyymmdd_rfl.csv). The python scripts and jupyter notebook used to calculate reflectance spectra from the ASD radiance data is included here and was previously published at: https://doi.org/10.3334/ORNLDAAC/2446. There is also a folder of JPEG photographs corresponding to selected spectra. We include a protocol document with detailed steps for ASD FieldSpec4 assembly and operations. This data additionally contains a file level metadata (flmd.csv) and data dictionary (dd.csv) file. Geospatial information: Geospatial data for mapping measurement site locations are in the files CHESS_polygons_lai_UTM.geojson, CHESS_polygons_shrub_UTM.geojson, and CHESS_polygons_meadow_UTM.geojson in the companion geospatial package for the 2025 CHESS campaign, ‘CHESS 2025: Location data for field observations and sampling’ (Henderson et al., 2026). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004) and was funded by EMIT Extended Mission Phase E Science.

2018 NEON and 2025 CHESS Campaigns↗

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

59 BASIC BIOLOGICAL SCIENCES↗

An inventory of state natural resources information systems

Data bases and information systems developed and maintained by state agencies to support planning and management of environmental and nutural resources were inventoried for all 50 states, Puerto Rico, and U.S. Virgin Islands. The information obtained is assembled into a computerized data base catalog which is throughly cross-referecence. Retrieval is possible by code, state, data base name, data base acronym, agency, computer, GIS capability, language, specialized software, data category name, geograhic reference, data sources, and level of reliability. The 324 automated data bases identified are described.

Martinko, E. A.↗

The Lick Observatory CCD data acquisition system

An evolving system for CCD data acquisition is described. The electronics are subdivided into those attached to the dewar, a 'smart' controller near the dewar, and a computer connected by serial link to the smart controller. Software for the smart controller is in assembler code, while the data acquisition and on-line analysis software is written in 'C' and uses the UNIX operating system.

Robinson, L. B.↗

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗

National Criticality Experiments Research Center (NCERC) - capabilities and recent measurements

The National Criticality Experiments Research Center (NCERC) located at the Device Assembly Facility (DAF) at the Nevada National Security Site (NNSS) and operated by Los Alamos National Laboratory (LANL) is home to four critical assemblies which are used to support of range of missions, including nuclear criticality safety and nuclear nonproliferation. Additionally, subcritical systems can also be assembled at NCERC. NCERC is providing critical and subcritical experiments valuable to the nuclear data community and experiments performed at NCERC are often published as benchmarks in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. This manuscript will give a broad overview of recent experiments performed at NCERC, upcoming experiments, and why integral measurements are important and useful to the nuclear data community. The four critical assemblies are GODIVA IV, FLATTOP, COMET, and PLANET. GODIVA IV is a cylindrical metal fast burst reactor, the fourth in the GODIVA series that dates back to the 1950’s. FLATTOP is an highly enriched uranium (HEU) or Pu core reflected by natural uranium. COMET and PLANET are vertical lift assemblies, where one half of the reactor can be lifted to the upper half of the reactor to create a critical system. Some recent experiments include various critical intermediate energy assemblies with lead, and subcritical measurements of plutonium reflected by copper, tungsten, and nickel. Work is also underway to make a better measurement of the critical mass of neptunium, using a neptunium sphere surrounded by nickel shells. Additionally, measurements will be performed next year with HEU shells from Rocky Flats. These HEU shells will be stacked together to make larger systems, allowing for a large range of criticality (from subcritical to delayed critical). Other upcoming measurements include an HEU critical assembly sensitive to intermediate energy neutrons.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Pacific area data collection stations

The installation of environmental data collection systems at several remotely located sites in islands in the Pacific Ocean is summarized. The effort was designed to enhance the ability to collect hydrological information. The data collection station consists of a data acquisition system for handling data, a transmitter for uplinking information to the GOES-W geostationary satellite, and a variety of environmental sensors for data accumulation. Each system was assembled, tested, and deployed on designated islands. The concept of using microprocessors for handling data at remote sites and relaying it via a satellite link is a cost effective approach. Such systems require high reliability and proven performance in the field.

Rector, R. C.↗

DIVA/DeviceEditor (DIVA) v6.0.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface (DeviceEditor), submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones were identified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

Plahar, Hector↗

Space Shuttle Partial Stack Rollout Test Analytical Correlation In Support Of Fatigue Load Development

A rollout test with only the Solid Rocket Boosters was conducted in November 2003 to gather structural dynamic response data of the transportation environment from the Vehicle Assembly Building to the Launch Pad. The data was acquired to develop and validate analytical methods used to predict rollout Orbiter fatigue load spectra. Earlier predictions computed by a base drive approach with only 5 input drive degrees-of-freedom raised questions that commissioned the partial stack test. Not only was there a concern because of the input degree-of-freedom omission due to measurement limitations, but there was also a concern with the implementation of the "large mass" itself. Three methods were evaluated with the partial stack test data. The analytical correlations to measured strain derived SRB base loads and acceleration5 showed the earlier 5 degree-of-freedom base drive approach to yield the most conservative results for all quantities monitored except the SRB base moment about the axis in which the input drive was missing. This non-conservative shortcoming led to a recommendation to use either the 6 degree-of-freedom base drive or the 12 degree-of-freedom Craig-Bampton boundary drive methods whose results did not substantially differ.

DelBasso, Steve↗

Formation and vesiculation of biomembranes during spaceflight

Shuttle flight, sounding rocket flight, and parabolic flight experiments demonstrate the formation of bilayer membrane vesicles (liposomes) in reduced gravity, following the dilution of detergent from detergent-phospholipid mixed micelles. The reduction in detergent concentration initiates assembly of bilayer membrane sheets, which are sensitive to solution disturbances. An increase in disturbances by forced dilution results in small diameter liposomes (less than 150 nm), in both ground and flight samples. In the absence of forced dilution, liposomes remain small at 1-g, but exhibit much larger diameters at 0-g (1000-2000 nm). Our spaceflight data reveal that membrane assembly and vesiculation are strongly influenced by gravity-induced solution disturbances (e.g., convection currents), which limit vesicle diameter.

Claassen, Dale E.↗

High Speed PC Based Data Acquisition and Instrumentation for Measurement of Simulated Low Earth Orbit Thermally Induced Disturbances

The Hubble Space Telescope (HST) Disturbance Verification Test (DVT) was conducted to characterize responses of the Observatory's new set of rigid solar array's (SA3) to thermally induced 'creak' or stiction releases. The data acquired in the DVT were used in verification of the HST Pointing Control System on-orbit performance, post-Servicing Mission 3B (SM3B). The test simulated the on-orbit environment on a deployed SA3 flight wing. Instrumentation for this test required pretest simulations in order to select the correct sensitivities. Vacuum compatible, highly accurate accelerometers and force gages were used for this test. The complexity of the test, as well as a short planning schedule, required a data acquisition system that was easy to configure, highly flexible, and extremely robust. A PC Windows oriented data acquisition system meets these requirements, allowing the test engineers to minimize the time required to plan and perform complex environmental test. The SA3 DVT provided a direct practical and complex demonstration of the versatility that PC based data acquisition systems provide. Two PC based data acquisition systems were assembled to acquire, process, distribute, and provide real time processing for several types of transducers used in the SA3 DVT. A high sample rate digital tape recorder was used to archive the sensor signals. The two systems provided multi-channel hardware and software architecture and were selected based on the test requirements. How these systems acquire and processes multiple data rates from different transducer types is discussed, along with the system hardware and software architecture.

Sills, Joel W., Jr.↗

Summary of solar cell data from the Long Duration Exposure Facility (LDEF)

The contractor has obtained and reviewed data relating solar cells assemblies (SCA's) flown as part of the following LDEF experiments: the Advanced Photovoltaic Experiment (S0014); the Solar Array Materials Passive LDEF Experiment (A0171); the Advanced Solar Cell and Coverglass Analysis Experiment (M0003-4); the LDEF Heat Pipe Experiment (S1001); the Evaluation of Thermal Control Coatings Y Solar Cells Experiment (S1002); and the Space Plasma-High Voltage Drainage Experiment (A0054). Where possible, electrical data have been tabulated and correlated with various environmental effects, including meteoroid and debris impacts, radiation exposure, atomic oxygen exposure, contamination, UV radiation exposure, and thermal cycling. The type, configuration, and location of all SCA's are documented here. By gathering all data and results together, a comparison of the survivability of the various types and configurations can be made.

Hill, David C.↗

Architecture of a catalytically active homotrimeric plant cellulose synthase complex

Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Here, our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.

59 BASIC BIOLOGICAL SCIENCES↗

CAPRI: Using a Geometric Foundation for Computational Analysis and Design

CAPRI (Computational Analysis Programming Interface) is a software development tool intended to make computerized design, simulation and analysis faster and more efficient. The computational steps traditionally taken for most engineering analysis (Computational Fluid Dynamics (CFD), structural analysis, etc.) are: Surface Generation, usually by employing a Computer Aided Design (CAD) system; Grid Generation, preparing the volume for the simulation; Flow Solver, producing the results at the specified operational point; Post-processing Visualization, interactively attempting to understand the results. It should be noted that the structures problem is more tractable than CFD; there are fewer mesh topologies used and the grids are not as fine (this problem space does not have the length scaling issues of fluids). For CFD, these steps have worked well in the past for simple steady-state simulations at the expense of much user interaction. The data was transmitted between phases via files. In most cases, the output from a CAD system could go IGES files. The output from Grid Generators and Solvers do not really have standards though there are a couple of file formats that can be used for a subset of the gridding (i.e. PLOT3D) data formats and the upcoming CGNS). The user would have to patch up the data or translate from one format to another to move to the next step. Sometimes this could take days. Instead of the serial approach to analysis, CAPRI takes a geometry centric approach. CAPRI is a software building tool-kit that refers to two ideas: (1) A simplified, object-oriented, hierarchical view of a solid part integrating both geometry and topology definitions, and (2) programming access to this part or assembly and any attached data. The connection to the geometry is made through an Application Programming Interface (API) and not a file system.

Haimes, Robert↗

Statistical Approach on Utilizing Ground-based Experiments to Model Break-up Events

Two laboratory-based impact tests have been conducted to develop and extend the capability of NASA satellite breakup models. The first experiment, the Satellite Orbital Debris Characterization Impact Test (SOCIT), was conducted by the U.S. Department of Defense and NASA in 1992. It employed a fully functional U.S. Navy Transit spacecraft, fabricated from materials commonly used in the 1960s. SOCIT fragmentation data formed the basis of the current NASA Standard Satellite Breakup Model (SSBM). A second experiment, DebriSat, was conducted in 2014 by the DebriSat consortium: the NASA Orbital Debris Program Office; the United States Space Force Space Systems Command, formerly the Air Force Space and Missile Systems Center, the Air Force Arnold Engineering Development Complex, and the University of Florida. This impact test was performed on a high-fidelity mock-up satellite assembled from modern components. Data from both experiments are expected to contribute to the next-generation models for on-orbit breakup analyses, long-term environment predictions, and debris risk assessment. This paper uses the direct statistical sampling of the SOCIT and DebriSat data ensembles to model an on-orbit breakup event, rather than the analytic expressions estimated from the samples as with as with the NASA SSBM and its predecessor. This direct method involves drawing fragments (i.e., sampling with replacement) from each fragmentation data-subset containing mass, shape category, material density, characteristic length, mass, and cross-sectional area. As part of the sampling process, the properties of sampled fragment data (e.g., area-to-mass ratios) are numerically checked to ensure they do not contain unrealistic quantities. The process to simulate a breakup cloud composed of fragments from SOCIT and DebriSat datasets is discussed. The methodology for ensuring that conservation of overall mass of the sampled fragment cloud under this sampling approach is highlighted. Finally, the results are compared with simulated clouds generated from SSBM for specific historical breakup events.

Andrew Vavrin↗

Statistical Approach on Utilizing Ground-Based Experiments to Model Break-Up Events

Two laboratory-based impact tests have been conducted to develop and extend the capability of NASA satellite breakup models. The first experiment, the Satellite Orbital Debris Characterization Impact Test (SOCIT), was conducted by the U.S. Department of Defense and NASA in 1992. It employed a fully functional U.S. Navy Transit spacecraft, fabricated from materials commonly used in the 1960s. SOCIT fragmentation data formed the basis of the current NASA Standard Satellite Breakup Model (SSBM). A second experiment, DebriSat, was conducted in 2014 by the DebriSat consortium: the NASA Orbital Debris Program Office, the United States Space Force Space Systems Command, formerly the Air Force Space and Missile Systems Center, the Air Force Arnold Engineering Development Complex, and the University of Florida. This impact test was performed on a high-fidelity mock-up satellite assembled from modern components. Data from both experiments are expected to contribute to the next-generation models for on-orbit breakup analyses, long-term environment predictions, and debris risk assessment. This paper uses the direct statistical sampling of the SOCIT and DebriSat data ensembles to model an on-orbit breakup event, rather than the analytic expressions estimated from the samples in the SSBM and its predecessor. This direct method involves drawing fragments (i.e., sampling with replacement) from each fragmentation data-subset containing mass, shape category, material density, characteristic length, mass, and cross-sectional area. As part of the sampling process, the properties of sampled fragment data (e.g., area-to-mass ratios) are numerically checked to ensure they do not contain unrealistic quantities. The process to simulate a breakup cloud composed of fragments from SOCIT and DebriSat datasets is discussed. The methodology for ensuring that conservation of overall mass of the sampled fragment cloud under this sampling approach is highlighted. Finally, the results are compared with simulated clouds generated from SSBM for specific historical breakup events.

Andrew Vavrin↗