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At least 1,027 records · Page 57

All sources NASA NTRS DOE OSTI

DOE OSTI2015

Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission

Some previous studies have demonstrated that single HIV-1 genotypes are commonly transmitted from mother to child, but such analyses primarily used single samples from mother and child. It is possible that in a single sample, obtained early after infection, only the most replication competent virus is detected even when other forms may have been transmitted. Such forms may have advantages later in infection, and may thus be detected in follow-up samples. Furthermore, because HIV-1 frequently recombines, phylogenetic analyses that ignore recombination may miss transmission of multiple forms if they recombine after transmission. Moreover, recombination may facilitate adaptation, thus providing an advantage in establishing infection. The effect of recombination on viral evolution in HIV-1 infected children has not been well defined.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Specific wavelength colorimeter

A self contained, specific wavelength, single beam colorimeter is described for direct spectrophotometric measurement of the concentration of a given solute in a test sample. An electrical circuit employing a photoconductive cell converts the optical output into a linear, directly readable meter output. The colorimeter is simple to operate and is adapted for use in zero gravity conditions. In a specific application, the colorimeter is designed to analyze the concentration of iodine in potable water carried aboard a space vehicle such as the 4B stage of Skylab.

Brawner, C. C.↗

NASA NTRS1992

Unsupervised segmentation of polarimetric SAR data using the covariance matrix

A method for unsupervised segmentation of polarimetric synthetic aperture radar (SAR) data into classes of homogeneous microwave polarimetric backscatter characteristics is presented. Classes of polarimetric backscatter are selected on the basis of a multidimensional fuzzy clustering of the logarithm of the parameters composing the polarimetric covariance matrix. The clustering procedure uses both polarimetric amplitude and phase information, is adapted to the presence of image speckle, and does not require an arbitrary weighting of the different polarimetric channels; it also provides a partitioning of each data sample used for clustering into multiple clusters. Given the classes of polarimetric backscatter, the entire image is classified using a maximum a posteriori polarimetric classifier. Four-look polarimetric SAR complex data of lava flows and of sea ice acquired by the NASA/JPL airborne polarimetric radar (AIRSAR) are segmented using this technique. The results are discussed and compared with those obtained using supervised techniques.

Rignot, Eric J. M.↗

NASA NTRS1993

Design and testing of a unique randomized gravity, continuous flow bioreactor

A rotating, null gravity simulator, or Couette bioreactor was successfully used for the culture of mammalian cells in a simulated microgravity environment. Two limited studies using Lipomyces starkeyi and Streptomyces clavuligerus were also conducted under conditions of simulated weightlessness. Although these studies with microorganisms showed promising preliminary results, oxygen limitations presented significant limitations in studying the biochemical and cultural characteristics of these cell types. Microbial cell systems such as bacteria and yeast promise significant potential as investigative models to study the effects of microgravity on membrane transport, as well as substrate induction of inactive enzyme systems. Additionally, the smaller size of the microorganisms should further reduce the gravity induced oscillatory particle motion and thereby improve the microgravity simulation on earth. Focus is on the unique conceptual design, and subsequent development of a rotating bioreactor that is compatible with the culture and investigation of microgravity effects on microbial systems. The new reactor design will allow testing of highly aerobic cell types under simulated microgravity conditions. The described reactor affords a mechanism for investigating the long term effects of reduced gravity on cellular respiration, membrane transfer, ion exchange, and substrate conversions. It offers the capability of dynamically altering nutrients, oxygenation, pH, carbon dioxide, and substrate concentration without disturbing the microgravity simulation, or Couette flow, of the reactor. All progeny of the original cell inoculum may be acclimated to the simulated microgravity in the absence of a substrate or nutrient. The reactor has the promise of allowing scientists to probe the long term effects of weightlessness on cell interactions in plants, bacteria, yeast, and fungi. The reactor is designed to have a flow field growth chamber with uniform shear stress, yet transfer high concentrations of oxygen into the culture medium. The system described allows for continuous, on line sampling for production of product without disturbing fluid and particle dynamics in the reaction chamber. It provides for the introduction of substrate, or control substances after cell adaptation to simulated microgravity has been accomplished. The reactor system provides for the nondisruptive, continuous flow replacement of nutrient and removal of product. On line monitoring and control of growth conditions such as pH and nutrient status are provided. A rotating distribution valve allows cessation of growth chamber rotation, thereby preserving the simulated microgravity conditions over longer periods of time.

Lassiter, Carroll B.↗

NASA NTRS1997

Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

Non-NASA Center↗

DOE OSTI2017

Full information acquisition in scanning probe microscopy and spectroscopy

Apparatus and methods are described for scanning probe microscopy and spectroscopy based on acquisition of full probe response. The full probe response contains valuable information about the probe-sample interaction that is lost in traditional scanning probe microscopy and spectroscopy methods. The full probe response is analyzed post data acquisition using fast Fourier transform and adaptive filtering, as well as multivariate analysis. The full response data is further compressed to retain only statistically significant components before being permanently stored.

36 MATERIALS SCIENCE↗

DOE OSTI2024

A Framework to Demonstrate a DNP3 Interface With a CIM-Based Data Integration Platform: Preprint

The contemporary electrical grid is characterized by its complexity and abundance of data. A control-rich environment supported by information and communication technologies within an Advanced Distribution Management System (ADMS) presents a viable and cost-effective option for utility companies aiming to implement advanced real-time analytical schemes for monitoring and remotely controlling distribution feeders. Modular platform-based approaches to distribution operations require a structured framework for acquiring field device measurements, performing analytics, converting the setpoint to the correct protocol, and sending it on the appropriate communications network to the field devices. We present the development and deployment of an application service to integrate an open-source standardsbased platform with an ADMS test bed with field devices using the Distributed Network Protocol (DNP3) for data exchange. The step-by-step procedure for establishing the DNP3-Master service on an open-source distribution platform is outlined, comprehensively explaining the Master setup process. Moreover, sample use case results highlight the capabilities of the DNP3- Master service setup. Results demonstrate the scalability and configurability of the DNP3-Master service, making it adaptable for integration with other relevant applications, thus providing potential opportunities for real-world field trials and real-time assessments.

ADMS↗

DOE OSTI2016

Marine Corps Base Camp Lejeune MARDIS Database

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of encroachment pressures in surrounding areas, impairments due to other anthropogenic disturbances, and changes in climate and sea level. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and also optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the second 5 years of the program (DCERP2) are presented in the DCERP2 Final Report.There were four overarching objectives of DCERP2. The first objective was to understand the effects of climate change impacts, including warming temperatures, variability in the hydrological cycle, storm events, and sea level rise on the coastal ecosystems at MCBCL from observations and measurements made over the 10-year program. The second objective was to understand the carbon cycle of the coastal and terrestrial ecosystems at MCBCL through a highly integrated sampling program. The third objective was to develop models, tools, and indicators to evaluate current and projected future ecosystem state changes and translate scientific findings into actionable information for installation managers. The last objective was to recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.The Defense Coastal/Estuarine Research Program (DCERP) Monitoring and Research Data Information System (MARDIS) database is the long-term repository for all DCERP monitoring and research data. Metadata provide supporting information about monitoring and research data that include, but are not limited to, a description of the location where the data were collected, the field and laboratory methods used to collect and analyze the data, and the spatial extent and temporal frequency of the data collected. In MARDIS, metadata fields have been combined with the actual sampling data fields; therefore, DCERP metadata are not a separate element, table, or document, but instead they are an integral component of each data record.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Longitudinal proteomics analysis in the immediate microenvironment of islet allografts during progression of rejection

The applicability and benefits of pancreatic islet transplantation are limited due to various issues including the need to avoid immune-mediated rejection. In the present study, we used our experimental platform of allogeneic islet transplant in the anterior chamber of the eye (ACE-platform) to longitudinally monitor the progress of rejection in mice and obtain aqueous humor samples representative of the microenvironment of the graft for accurately-timed proteomic analyses. LC-MS/MS-based proteomics performed on such mass-limited samples (~5 μL) identified a total of 1296 proteins. Various analyses revealed distinct protein patterns associated with the mounting of the inflammatory and immune responses and their evolution with the progression of the rejection. Pathway analyses indicated predominant changes in cytotoxic functions, cell movement, and innate and adaptive immune responses. Furthermore, network prediction analyses revealed transition from humoral to cellular immune response and exacerbation of pro-inflammatory signaling. One of the proteins identified by this localized proteomics as a candidate biomarker of islet rejection, Cystatin 3, was further validated by ELISA in the aqueous humor. This study provides (1) experimental evidence demonstrating the feasibility of longitudinal localized proteomics using small aqueous humor samples and (2) proof-of-concept for the discovery of biomarkers of impending immune attack from the immediate local microenvironment of ACE-transplanted islets.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1988

Issues in development, evaluation, and use of the NASA Preflight Adaptation Trainer (PAT)

The Preflight Adaptation Trainer (PAT) is intended to reduce or alleviate space adaptation syndrome by providing opportunities for portions of that adaptation to occur under normal gravity conditions prior to space flight. Since the adaptation aspects of the PAT objectives involve modification not only of the behavior of the trainee, but also of sensiomotor skills which underly the behavioral generation, the defining of training objectives of the PAT utilizes four mechanisms: familiarization, demonstration, training and adaptation. These mechanisms serve as structural reference points for evaluation, drive the content and organization of the training procedures, and help to define the roles of the PAT instructors and operators. It was determined that three psychomotor properties are most critical for PAT evaluation: reliability; sensitivity; and relevance. It is cause for concern that the number of measures available to examine PAT effects exceed those that can be properly studied with the available sample sizes; special attention will be required in selection of the candidate measure set. The issues in PAT use and application within a training system context are addressed through linking the three training related mechanisms of familiarization, demonstration and training to the fourth mechanism, adaptation.

Lane, Norman E.↗

DOE OSTI2024

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated ß-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-?B signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

proteomics, PTM, automation, SP3, cysteine thiol o↗

DOE OSTI2018

Sensitivity Analysis and Emulation for Functional Data using Bayesian Adaptive Splines

When a computer code is used to simulate a complex system, one of the fundamental tasks is to assess the sensitivity of the simulator to the different input parameters. In the case of computationally expensive simulators, this is often accomplished via a surrogate statistical model, a statistical output emulator. An effective emulator is one that provides good approximations to the computer code output for wide ranges of input values. In addition, an emulator should be able to handle large dimensional simulation output for a relevant number of inputs; it should flexibly capture heterogeneities in the variability of the response surface; it should be fast to evaluate for arbitrary combinations of input parameters, and it should provide an accurate quantification of the emulation uncertainty. In this paper we discuss the Bayesian approach to multivariate adaptive regression splines (BMARS) as an emulator for a computer model that outputs curves. We introduce modifications to traditional BMARS approaches that allow for fitting large amounts of data and allow for more efficient MCMC sampling. We emphasize the ease with which sensitivity analysis can be performed in this situation. We present a sensitivity analysis of a computer model of the deformation of a protective plate used in pressure-driven experiments. Our example serves as an illustration of the ability of BMARS emulators to fulfill all the necessities of computability, flexibility and reliable calculation on relevant measures of sensitivity.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2004

Simple broadband implementation of a phase contrast wavefront sensor for adaptive optics

The most critical element of an adaptive optics system is its wavefront sensor, which must measure the closed-loop difference between the corrected wavefront and an ideal template at high speed, in real time, over a dense sampling of the pupil. Most high-order systems have used Shack-Hartmann wavefront sensors, but a novel approach based on Zernike's phase contrast principle appears promising. In this paper we discuss a simple way to achromatize such a phase contrast wavefront sensor, using the pi/2 phase difference between reflected and transmitted rays in a thin, symmetric beam splitter. We further model the response at a range of wavelengths to show that the required transverse dimension of the focal-plane phase-shifting spot, nominally lambda/D, may not be very sensitive to wavelength, and so in practice additional optics to introduce wavelength-dependent transverse magnification achromatizing this spot diameter may not be required. A very simple broadband implementation of the phase contrast wavefront sensor results.

wavefront sensors↗

DOE OSTI2015

Image Reconstruction from Under sampled Fourier Data Using the Polynomial Annihilation Transform

Fourier samples are collected in a variety of applications including magnetic resonance imaging and synthetic aperture radar. The data are typically under-sampled and noisy. In recent years, l 1 regularization has received considerable attention in designing image reconstruction algorithms from under-sampled and noisy Fourier data. The underlying image is assumed to have some sparsity features, that is, some measurable features of the image have sparse representation. The reconstruction algorithm is typically designed to solve a convex optimization problem, which consists of a fidelity term penalized by one or more l 1 regularization terms. The Split Bregman Algorithm provides a fast explicit solution for the case when TV is used for the l1l1 regularization terms. Due to its numerical efficiency, it has been widely adopted for a variety of applications. A well known drawback in using TV as an l 1 regularization term is that the reconstructed image will tend to default to a piecewise constant image. This issue has been addressed in several ways. Recently, the polynomial annihilation edge detection method was used to generate a higher order sparsifying transform, and was coined the “polynomial annihilation (PA) transform.” This paper adapts the Split Bregman Algorithm for the case when the PA transform is used as the l 1 regularization term. In so doing, we achieve a more accurate image reconstruction method from under-sampled and noisy Fourier data. Our new method compares favorably to the TV Split Bregman Algorithm, as well as to the popular TGV combined with shearlet approach.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Constant-Depth Preparation of Matrix Product States with Adaptive Quantum Circuits

Adaptive quantum circuits, which combine local unitary gates, midcircuit measurements, and feedforward operations, have recently emerged as a promising avenue for efficient state preparation, particularly on near-term quantum devices limited to shallow-depth circuits. Matrix product states (MPS) comprise a significant class of many-body entangled states, efficiently describing the ground states of one-dimensional gapped local Hamiltonians and finding applications in a number of recent quantum algorithms. Recently, it has been shown that the Affleck-Kennedy-Lieb-Tasaki state—a paradigmatic example of an MPS—can be exactly prepared with an adaptive quantum circuit of constant depth, an impossible feat with local unitary gates alone due to its nonzero correlation length [Smith , PRX Quantum 4, 020315 (2023)]. In this work, we broaden the scope of this approach and demonstrate that a diverse class of MPS can be exactly prepared using constant-depth adaptive quantum circuits, outperforming theoretically optimal preparation with unitary circuits. We show that this class includes short- and long-ranged entangled MPS, symmetry-protected topological (SPT) and symmetry-broken states, MPS with finite Abelian, non-Abelian, and continuous symmetries, resource states for MBQC, and families of states with tunable correlation length. Moreover, we illustrate the utility of our framework for designing constant-depth sampling protocols, such as for random MPS or for generating MPS in a particular SPT phase. We present sufficient conditions for particular MPS to be preparable in constant time, with global on-site symmetry playing a pivotal role. Altogether, this work demonstrates the immense promise of adaptive quantum circuits for efficiently preparing many-body entangled states and provides explicit algorithms that outperform known protocols to prepare an essential class of states. Published by the American Physical Society 2024

Smith, Kevin C. (ORCID:0000000223971518)↗

DOE OSTI2015

Transcriptome sequencing and differential gene expression analysis in Viola yedoensis Makino (Fam. Violaceae) responsive to cadmium (Cd) pollution

Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V. yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V. yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de novo assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V. yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae. - Highlights: • A de novo assembly generated 109,800 unigenes and 5,4479 of them were annotated. • 31,285 could be classified into 26 COG categories. • 263 biosynthesis pathways were predicted and classified into five categories. • 892 DEGs were detected and 15 of them were validated by qRT-PCR.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Visualization of hydraulic fracture using physics-informed clustering to process ultrasonic shear waves

Ultrasonic transmission is sensitive to the spatial variation in mechanical properties of materials due to the presence of cracks/fractures. Wave propagation through fractured media introduces changes in the frequency content, travel time and transmission coefficient of the wave. A workflow based on physics-informed unsupervised learning is developed to process the transmitted ultrasonic-shear waveforms to non-invasively visualize the geomechanical alterations due to hydraulic fracturing. Novelty of the work involves the assignment of both statistically consistent and physically consistent clusters to the measurements of shear waveforms acquired across the one axial and two frontal planes. Physically consistent/relevant information is incorporated by considering the travel time of the peak of spectral energy and transmission coefficient of the transmitted waveform. The proposed workflow generates maps of geomechanical alterations across the frontal and axial planes of the sample. The outputs of the workflow are in good agreement with independent techniques viz. acoustic emission and X-ray computed tomography. Finally, the proposed workflow can be adapted for improved fracture characterization in the subsurface when processing sonic-logging, cross-wellbore seismic or surface seismic waveform data.

42 ENGINEERING↗

DOE OSTI2025

Point cloud-based diffusion models for the Electron-Ion Collider

At high-energy collider experiments, generative models can be used for a wide range of tasks, including fast detector simulations, unfolding, searches of physics beyond the Standard Model, and inference tasks. In particular, it has been demonstrated that score-based diffusion models can generate high-fidelity and accurate samples of jets or collider events. This work expands on previous generative models in three distinct ways. First, our model is trained to generate entire collider events, including all particle species with complete kinematic information. We quantify how well the model learns event-wide constraints such as the conservation of momentum and discrete quantum numbers. We focus on the events at the future Electron-Ion Collider, but we expect that our results can be extended to proton-proton and heavy-ion collisions. Second, previous generative models often relied on image-based techniques. The sparsity of the data can negatively affect the fidelity and sampling time of the model. We address these issues using point clouds and a novel architecture combining edge creation with transformer modules called Point Edge Transformers. Third, we adapt the foundation model OmniLearn, to generate full collider events. This approach may indicate a transition toward adapting and fine-tuning foundation models for downstream tasks instead of training new models from scratch.

Araz, Jack Y. [Stony Brook Univ., NY (United State↗