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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1976

Coding isotropic images

Rate distortion functions for two-dimensional homogeneous isotropic images are compared with the performance of 5 source encoders designed for such images. Both unweighted and frequency weighted mean square error distortion measures are considered. The coders considered are differential PCM (DPCM) using six previous samples in the prediction, herein called 6 pel (picutre element) DPCM; simple DPCM using single sample prediction; 6 pel DPCM followed by entropy coding; 8 x 8 discrete cosine transform coder, and 4 x 4 Hadamard transform coder. Other transform coders were studied and found to have about the same performance as the two transform coders above. With the mean square error distortion measure DPCM with entropy coding performed best. The relative performance of the coders changes slightly when the distortion measure is frequency weighted mean square error. The performance of all the coders was separated by only about 4 dB.

Oneal, J. B., Jr.↗
NASA NTRS1990

Optimal helicopter trajectory planning for terrain following flight

Helicopters operating in high threat areas have to fly close to the earth surface to minimize the risk of being detected by the adversaries. Techniques are presented for low altitude helicopter trajectory planning. These methods are based on optimal control theory and appear to be implementable onboard in realtime. Second order necessary conditions are obtained to provide a criterion for finding the optimal trajectory when more than one extremal passes through a given point. A second trajectory planning method incorporating a quadratic performance index is also discussed. Trajectory planning problem is formulated as a differential game. The objective is to synthesize optimal trajectories in the presence of an actively maneuvering adversary. Numerical methods for obtaining solutions to these problems are outlined. As an alternative to numerical method, feedback linearizing transformations are combined with the linear quadratic game results to synthesize explicit nonlinear feedback strategies for helicopter pursuit-evasion. Some of the trajectories generated from this research are evaluated on a six-degree-of-freedom helicopter simulation incorporating an advanced autopilot. The optimal trajectory planning methods presented are also useful for autonomous land vehicle guidance.

Menon, P. K. A.↗
NASA NTRS2003

Fully Nonlinear Modeling and Analysis of Precision Membranes

High precision membranes are used in many current space applications. This paper presents a fully nonlinear membrane theory with forward and inverse analyses of high precision membrane structures. The fully nonlinear membrane theory is derived from Jaumann strains and stresses, exact coordinate transformations, the concept of local relative displacements, and orthogonal virtual rotations. In this theory, energy and Newtonian formulations are fully correlated, and every structural term can be interpreted in terms of vectors. Fully nonlinear ordinary differential equations (ODES) governing the large static deformations of known axisymmetric membranes under known axisymmetric loading (i.e., forward problems) are presented as first-order ODES, and a method for obtaining numerically exact solutions using the multiple shooting procedure is shown. A method for obtaining the undeformed geometry of any axisymmetric membrane with a known inflated geometry and a known internal pressure (i.e., inverse problems) is also derived. Numerical results from forward analysis are verified using results in the literature, and results from inverse analysis are verified using known exact solutions and solutions from the forward analysis. Results show that the membrane theory and the proposed numerical methods for solving nonlinear forward and inverse membrane problems are accurate.

Pai, P. Frank↗
DOE OSTI2022

Transformative Technology for FLASH Radiation Therapy: A Snowmass 2021 White Paper

Conventional cancer therapies include surgery, radiation therapy, chemotherapy, and, more recently, immunotherapy. These modalities are often combined to improve the therapeutic index. The general concept of radiation therapy is to increase the therapeutic index by creating a physical dose differential between tumors and normal tissues through precision dose targeting, image guidance, and high radiation beams that deliver radiation dose with high conformality, e.g., protons and ions. However, treatment and cure are still limited by normal tissue radiation toxicity, with many patients experiencing acute and long-term side effects. Recently, however, a fundamentally different paradigm for increasing the therapeutic index of radiation therapy has emerged, supported by preclinical research, and based on the FLASH radiation effect. FLASH radiation therapy (FLASH-RT) is an ultra-high dose-rate delivery of a therapeutic radiation dose within a fraction of a second. Experimental studies have shown that normal tissues seem to be universally spared at these high dose rates, whereas tumors are not. The dose delivery conditions are not yet fully characterized. Still, it is currently estimated that large doses of 10 Gy or more delivered in 200 ms or less produce normal tissue sparing effects yet effectively kill tumor cells. There is a great opportunity, but also many technical challenges, for the accelerator community to create the required dose rates with novel and compact accelerators to ensure the safe delivery of FLASH radiation beams.

43 PARTICLE ACCELERATORS↗
NASA NTRS2001

TGF-beta1 release from biodegradable polymer microparticles: its effects on marrow stromal osteoblast function

BACKGROUND: Controlled release of transforming growth factor-beta1 (TGF-beta1) to a bone defect may be beneficial for the induction of a bone regeneration cascade. The objectives of this work were to assess the feasibility of using biodegradable polymer microparticles as carriers for controlled TGF-beta1 delivery and the effects of released TGF-beta1 on the proliferation and differentiation of marrow stromal cells in vitro. METHODS: Recombinant human TGF-beta1 was incorporated into microparticles of blends of poly(DL-lactic-co-glycolic acid) (PLGA) and poly(ethylene glycol) (PEG). Fluorescein isothiocynate-labeled bovine serum albumin (FITC-BSA) was co-encapsulated as a porogen. The effects of PEG content (0, 1, or 5% by weight [wt%]) and buffer pH (3, 5, or 7.4) on the protein release kinetics and the degradation of PLGA were determined in vitro for as long as 28 days. Rat marrow stromal cells were seeded on a biodegradable poly(propylene fumarate) (PPF) substrate. The dose response and biological activity of released TGF-beta1 was determined after 3 days in culture. The effects of TGF-beta1 released from PLGA/PEG microparticles on marrow stromal cell proliferation and osteoblastic differentiation were assessed during a 21-day period. RESULTS: TGF-beta1 was encapsulated along with FITC-BSA into PLGA/PEG blend microparticles and released in a multiphasic fashion including an initial burst for as long as 28 days in vitro. Increasing the initial PEG content resulted in a decreased cumulative mass of released proteins. Aggregation of FITC-BSA occurred at lower buffer pH, which led to decreased release rates of both proteins. The degradation of PLGA was increased at higher PEG content and significantly accelerated at acidic pH conditions. Rat marrow stromal cells cultured on PPF substrates showed a dose response to TGF-beta1 released from the microparticles similar to that of added TGF-beta1, indicating that the activity of TGF-beta1 was retained during microparticle fabrication and after growth factor release. At an optimal TGF-beta1 dosage of 1.0 ng/ml after 3 days, the released TGF-beta1 enhanced the proliferation and osteoblastic differentiation of marrow stromal cells over 21 days of culture, with increased total cell number, alkaline phosphatase activity, and osteocalcin production. CONCLUSIONS: PLGA/PEG blend microparticles can serve as delivery vehicles for controlled release of TGF-beta1, and the released growth factor enhances marrow stromal cell proliferation and osteoblastic differentiation in vitro. CLINICAL RELEVANCE: Controlled release of TGF-beta1 from PLGA/PEG microparticles is representative of emerging tissue engineering technologies that may modulate cellular responses to encourage bone regeneration at a skeletal defect site.

Non-NASA Center↗
NASA NTRS2008

On Certain New Methodology for Reducing Sensor and Readout Electronics Circuitry Noise in Digital Domain

NASA Hubble Space Telescope (HST) and upcoming cosmology science missions carry instruments with multiple focal planes populated with many large sensor detector arrays. These sensors are passively cooled to low temperatures for low-level light (L3) and near-infrared (NIR) signal detection, and the sensor readout electronics circuitry must perform at extremely low noise levels to enable new required science measurements. Because we are at the technological edge of enhanced performance for sensors and readout electronics circuitry, as determined by thermal noise level at given temperature in analog domain, we must find new ways of further compensating for the noise in the signal digital domain. To facilitate this new approach, state-of-the-art sensors are augmented at their array hardware boundaries by non-illuminated reference pixels, which can be used to reduce noise attributed to sensors. There are a few proposed methodologies of processing in the digital domain the information carried by reference pixels, as employed by the Hubble Space Telescope and the James Webb Space Telescope Projects. These methods involve using spatial and temporal statistical parameters derived from boundary reference pixel information to enhance the active (non-reference) pixel signals. To make a step beyond this heritage methodology, we apply the NASA-developed technology known as the Hilbert- Huang Transform Data Processing System (HHT-DPS) for reference pixel information processing and its utilization in reconfigurable hardware on-board a spaceflight instrument or post-processing on the ground. The methodology examines signal processing for a 2-D domain, in which high-variance components of the thermal noise are carried by both active and reference pixels, similar to that in processing of low-voltage differential signals and subtraction of a single analog reference pixel from all active pixels on the sensor. Heritage methods using the aforementioned statistical parameters in the digital domain (such as statistical averaging of the reference pixels themselves) zeroes out the high-variance components, and the counterpart components in the active pixels remain uncorrected. This paper describes how the new methodology was demonstrated through analysis of fast-varying noise components using the Hilbert-Huang Transform Data Processing System tool (HHT-DPS) developed at NASA and the high-level programming language MATLAB (Trademark of MathWorks Inc.), as well as alternative methods for correcting for the high-variance noise component, using an HgCdTe sensor data. The NASA Hubble Space Telescope data post-processing, as well as future deep-space cosmology projects on-board instrument data processing from all the sensor channels, would benefit from this effort.

Kizhner, Semion↗
DOE OSTI2024

The structure and interaction of polymers affects secondary cell wall banding patterns in Arabidopsis

Abstract Xylem tracheary elements (TEs) synthesize patterned secondary cell walls (SCWs) to reinforce against the negative pressure of water transport. VASCULAR-RELATED NAC-DOMAIN 7 (VND7) induces differentiation, accompanied by cellulose, xylan, and lignin deposition into banded domains. To investigate the effect of polymer biosynthesis mutations on SCW patterning, we developed a method to induce tracheary element transdifferentiation of isolated protoplasts, by transient transformation with VND7. Our data showed that proper xylan elongation is necessary for distinct cellulose bands, cellulose–xylan interactions are essential for coincident polymer patterns, and cellulose deposition is needed to override the intracellular organization that yields unique xylan patterns. These data indicate that a properly assembled cell wall network acts as a scaffold to direct polymer deposition into distinctly banded domains. We describe the transdifferentiation of protoplasts into TEs, providing an avenue to study patterned SCW biosynthesis in a tissue-free environment and in various mutant backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Advanced Monitoring and Control in the ANL METL Facility Using an Engineering Digital Twin

The potential benefits of using an engineering digital twin to achieve greater autonomy for monitoring and control functions in advanced reactors was investigated for the Mechanisms Engineering Test Loop (METL) liquid sodium facility at Argonne National Laboratory. The METL sodium purification system served as a representative system as it requires significant human in-the-loop interaction to accomplish its design function. The objective was to demonstrate how real-time operation could be automated while preserving oversight of the operator for ensuring that the system design functions are met. A digital twin model of the purification system was developed for both the cold trap purification loop and plugging meter diagnostic loop using information from the METL piping and instrumentation diagram (P&ID). Automated monitoring and diagnosis of component degradation in the METL facility was demonstrated in tests using the PRO-AID health monitoring software with the digital twin model incorporated in the library of components. Component failures were introduced and were successfully diagnosed in real time. These tests serve to demonstrate an advanced monitoring capability able to differentiate sensor degradation from component degradation, to generate a rank ordering of probabilities of different failure mechanisms that serves to circumvent the false alarm problem with current anomaly detection methods, and how facility monitoring can be transformed from anomaly detection to identification of a specific fault. Automated control of the purification system was demonstrated through simulations that exercised a model predictive controller designed using the digital twin model. Results of these simulations compared favorably with experimental data showing very good reference tracking response with negligible overshoot. In conclusion, these pilot tests and simulations successfully demonstrated the use of a digital twin for improved automation of monitoring and control. It was shown how the digital twin enables switching between control modes from cold trap operation where impurities are removed to plugging meter operation where impurity concentrations are measured.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS1980

Symbolic-numeric interface: A review

A survey of the use of a combination of symbolic and numerical calculations is presented. Symbolic calculations primarily refer to the computer processing of procedures from classical algebra, analysis, and calculus. Numerical calculations refer to both numerical mathematics research and scientific computation. This survey is intended to point out a large number of problem areas where a cooperation of symbolic and numerical methods is likely to bear many fruits. These areas include such classical operations as differentiation and integration, such diverse activities as function approximations and qualitative analysis, and such contemporary topics as finite element calculations and computation complexity. It is contended that other less obvious topics such as the fast Fourier transform, linear algebra, nonlinear analysis and error analysis would also benefit from a synergistic approach.

Ng, E. W.↗
NASA NTRS1983

Numerical computation of transonic flow governed by the full-potential equation

Basic concepts associated with the numerical solution of elliptic partial differential equations are introduced, and procedures used to solve the full potential equation for transonic flow fields are discussed. Governing equations, classical relaxation schemes and concepts regarding transonic, full potential equation algorithms are covered. The equation transformation and grid generation procedures; full potential spatial differencing schemes; full potential iteration schemes, emphasizing convergence acceleration; and three dimensional applications are presented.

Holst, T. L.↗
NASA NTRS1952

Theoretical damping in roll and rolling moment due to differential wing incidence for slender cruciform wings and wing-body combinations

A method of analysis based on slender-wing theory is developed to investigate the characteristics in roll of slender cruciform wings and wing-body combinations. The method makes use of the conformal mapping processes of classical hydrodynamics which transform the region outside a circle and the region outside an arbitrary arrangement of line segments intersecting at the origin. The method of analysis may be utilized to solve other slender cruciform wing-body problems involving arbitrarily assigned boundary conditions. (author)

Adams, Gaynor J↗
NASA NTRS1992

FT-IR microscopic mappings of early mineralization in chick limb bud mesenchymal cell cultures

Chick limb bud mesenchymal cells differentiate into chondrocytes and form a cartilaginous matrix in culture. In this study, the mineral formed in different areas within cultures supplemented with 4 mM inorganic phosphate, or 2.5, 5.0, and 10 mM beta-glycerophosphate (beta GP), was characterized by Fourier-transform infrared (FT-IR) microscopy. The relative mineral-to-matrix ratios, and distribution of crystal sizes at specific locations throughout the matrix were measured from day 14 to day 30. The only mineral phase detected was a poorly crystalline apatite. Cultures receiving 4 mM inorganic phosphate had smaller crystals which were less randomly distributed around the cartilage nodules than those in the beta GP-treated cultures. beta GP-induced mineral consisted of larger, more perfect apatite crystals. In cultures receiving 5 or 10 mM beta GP, the relative mineral-to-matrix ratios (calculated from the integrated intensities of the phosphate and amide I bands, respectively) were higher than in the cultures with 4 mM inorganic phosphate or in the in vivo calcified chick cartilage.

NASA Discipline Musculoskeletal↗
NASA NTRS1978

Response of the rat erythrocyte to ozone exposure

Sprague-Dawley rats were exposed to high (6-8 ppm) and moderate (1.5 ppm) amounts of ozone (O3) for various time periods. Response of the rat erythrocyte to ozone was monitored with red blood cell potassium (rubidium) influx studies, with storage stress combined with ultrastructural studies and with levels of erythrocyte glutathione peroxidase and superoxide dismutase. Erythrocytes of rats exposed to O3 showed no significant changes either in their potassium influx or in their glutathione peroxidase and superoxide dismutase activities compared to controls. Erythrocyte differential counts on O3-exposed animals showed significant changes initially as well as following storage stress compared to controls. Rats exposed to 8 ppm O3 for 4 h showed a marked increase in echinocytes. These consistent transformations from discocytes to echinocytes following O3 exposure suggest latent erythrocyte damage has occurred.

Larkin, E. C.↗
NASA NTRS1986

Formationkeeping of Spacecraft via Differential Drag

This paper examines the use of differential drag in the formationkeeping of spacecraft. In many future space missions one satellite will be required to fly in a specific position with respect to another satellite; this action is referred to as formationkeeping. In this study, differential drag is the difference in drag between the two satellites. Reasons to use differential drag as an actuator for formationkeeping include the avoidance of jet plume impingement effects on closely spaced satellites and possible fuel savings. The equations of relative motion between the two satellites are derived and a mathematical transformation is made to reduce the formationkeeping problem to the simultaneous solution of a double integrator and a harmonic oscillator. A two-part control law is developed that simultaneously and dependently solves the double oscillator and harmonic integrator. Results are presented of eight test cases being driven to a target position; two different simulations are used. The validity of assumptions made in the derivation of the control law is examined in the comparison of similar test cases run through different simulations. The control law developed can drive a satellite from an initial position to a target position and maintain the satellite at that location.

Leonard, Carolina Lee↗
NASA NTRS1997

The Topology of Symmetric Tensor Fields

Combinatorial topology, also known as "rubber sheet geometry", has extensive applications in geometry and analysis, many of which result from connections with the theory of differential equations. A link between topology and differential equations is vector fields. Recent developments in scientific visualization have shown that vector fields also play an important role in the analysis of second-order tensor fields. A second-order tensor field can be transformed into its eigensystem, namely, eigenvalues and their associated eigenvectors without loss of information content. Eigenvectors behave in a similar fashion to ordinary vectors with even simpler topological structures due to their sign indeterminacy. Incorporating information about eigenvectors and eigenvalues in a display technique known as hyperstreamlines reveals the structure of a tensor field. The simplify and often complex tensor field and to capture its important features, the tensor is decomposed into an isotopic tensor and a deviator. A tensor field and its deviator share the same set of eigenvectors, and therefore they have a similar topological structure. A a deviator determines the properties of a tensor field, while the isotopic part provides a uniform bias. Degenerate points are basic constituents of tensor fields. In 2-D tensor fields, there are only two types of degenerate points; while in 3-D, the degenerate points can be characterized in a Q'-R' plane. Compressible and incompressible flows share similar topological feature due to the similarity of their deviators. In the case of the deformation tensor, the singularities of its deviator represent the area of vortex core in the field. In turbulent flows, the similarities and differences of the topology of the deformation and the Reynolds stress tensors reveal that the basic addie-viscosity assuptions have their validity in turbulence modeling under certain conditions.

Levin, Yingmei↗
DOE OSTI2021

Gaussian process regression constrained by boundary value problems

We develop a framework for Gaussian processes regression constrained by boundary value problems. The framework may be applied to infer the solution of a well-posed boundary value problem with a known second-order differential operator and boundary conditions, but for which only scattered observations of the source term are available. Scattered observations of the solution may also be used in the regression. The framework combines co-kriging with the linear transformation of a Gaussian process together with the use of kernels given by spectral expansions in eigenfunctions of the boundary value problem. Furthermore, it benefits from a reduced-rank property of covariance matrices. We demonstrate that the resulting framework yields more accurate and stable solution inference as compared to physics-informed Gaussian process regression without boundary condition constraints.

42 ENGINEERING↗
DOE OSTI2021

Juqbox.jl

The Juqbox.jl package implements functionality for solving the quantum optimal control problem for realizing logical gates in closed quantum systems. The dynamics of the quantum system is modeled by Schroedinger's equation, which takes to form of a linear system of ordinary differential equations (ODE). Juqbox.jl solves this ODE by numerical time stepping and applies a gradient-based optimization technique to determine control pulses for driving an initial state to a final state, according to the desired logical gate transformation. To evaluate the gradient, Juqbox.jl applies the ``first discretize, then optimize'' approach based on a discrete adjoint time stepping technique. The actual optimization is performed by the open source Ipopt libaray. Juqbox.jl is written in the Julia programming language which, among many other features, provides a convenient interface to the Ipopt library.

PETERSSON, NILSA.↗