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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Amplification and adaptation of centromeric repeats in polyploid switchgrass species

Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Toward adaptive radiotherapy for head and neck patients: Uncertainties in dose warping due to the choice of deformable registration algorithm

Purpose: The aims of this work were to evaluate the performance of several deformable image registration (DIR) algorithms implemented in our in-house software (NiftyReg) and the uncertainties inherent to using different algorithms for dose warping. Methods: The authors describe a DIR based adaptive radiotherapy workflow, using CT and cone-beam CT (CBCT) imaging. The transformations that mapped the anatomy between the two time points were obtained using four different DIR approaches available in NiftyReg. These included a standard unidirectional algorithm and more sophisticated bidirectional ones that encourage or ensure inverse consistency. The forward (CT-to-CBCT) deformation vector fields (DVFs) were used to propagate the CT Hounsfield units and structures to the daily geometry for “dose of the day” calculations, while the backward (CBCT-to-CT) DVFs were used to remap the dose of the day onto the planning CT (pCT). Data from five head and neck patients were used to evaluate the performance of each implementation based on geometrical matching, physical properties of the DVFs, and similarity between warped dose distributions. Geometrical matching was verified in terms of dice similarity coefficient (DSC), distance transform, false positives, and false negatives. The physical properties of the DVFs were assessed calculating the harmonic energy, determinant of the Jacobian, and inverse consistency error of the transformations. Dose distributions were displayed on the pCT dose space and compared using dose difference (DD), distance to dose difference, and dose volume histograms. Results: All the DIR algorithms gave similar results in terms of geometrical matching, with an average DSC of 0.85 ± 0.08, but the underlying properties of the DVFs varied in terms of smoothness and inverse consistency. When comparing the doses warped by different algorithms, we found a root mean square DD of 1.9% ± 0.8% of the prescribed dose (pD) and that an average of 9% ± 4% of voxels within the treated volume failed a 2%pD DD-test (DD{sub 2%-pp}). Larger DD{sub 2%-pp} was found within the high dose gradient (21% ± 6%) and regions where the CBCT quality was poorer (28% ± 9%). The differences when estimating the mean and maximum dose delivered to organs-at-risk were up to 2.0%pD and 2.8%pD, respectively. Conclusions: The authors evaluated several DIR algorithms for CT-to-CBCT registrations. In spite of all methods resulting in comparable geometrical matching, the choice of DIR implementation leads to uncertainties in dose warped, particularly in regions of high gradient and/or poor imaging quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-CD-202-11: Implications for Online Adaptive and Non-Adaptive Radiotherapy of Gastic and Gastroesophageal Junction Cancers Using MRI-Guided Radiotherapy

Purpose: Radiotherapy for gastric and gastroesophageal junction (GEJ) tumors commonly requires large margins due to deformation, motion and variable changes of the stomach anatomy, at the risk of increased normal tissue toxicities. This work quantifies the interfraction variation of stomach deformation from daily MRI-guided radiotherapy to allow for a more targeted determination of margin expansion in the treatment of gastric and GEJ tumors. Methods: Five patients treated for gastric (n=3) and gastroesophageal junction (n=2) cancers with conventionally fractionated radiotherapy underwent daily MR imaging on a clinical MR-IGRT system. Treatment planning and contours were performed based on the MR simulation. The stomach was re-contoured on each daily volumetric setup MR. Dice similarity coefficients (DSC) of the daily stomach were computed to evaluate the stomach interfraction deformation. To evaluate the stomach margin, the maximum Hausdorff distance (HD) between the initial and fractional stomach surface was measured for each fraction. The margin expansion, needed to encompass all fractions, was evaluated from the union of all fractional stomachs. Results: In total, 94 fractions with daily stomach contours were evaluated. For the interfraction stomach differences, the average DSC was 0.67±0.1 for gastric and 0.62±0.1 for GEJ cases. The maximum HD of each fraction was 3.5±2.0cm (n=94) with mean HD of 0.8±0.4cm (across all surface voxels for all fractions). The margin expansion required to encompass all individual fractions (averaged across 5 patients) was 1.4 cm(superior), 2.3 cm(inferior), 2.5 cm(right), 3.2 cm(left), 3.7 cm(anterior), 3.4 cm(posterior). Maximum observed difference for margin expansion was 8.7cm(posterior) among one patient. Conclusion: We observed a notable interfractional change in daily stomach shape (i.e., mean DSC of 0.67, p<0.0001) in both gastric and GEJ patients, for which adaptive radiotherapy is indicated. A minimum PTV margin of 3 cm is indicated to account for interfraction stomach changes when adaptive radiotherapy is not available. M. Bassetti: Travel funding from ViewRay, Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Adapt: A Weather Radar Data Analysis and Nowcasting Platform for Informed Adaptive Scanning

SF-26-021 Adapt is a data processing platform for real-time data analysis, short term prediction of targets convective cells and tracking for archived data. It provides tools for downloading, processing, segmenting, projecting, analyzing, and visualizing storm cell data from weather radar. The pipeline includes cell detection, motion estimation using optical flow, cell property extraction, and persistence to NetCDF and SQLite/Parquet for guiding adaptive scanning.

Raut, Bhupendra Ashokrao [Argonne National Laborat↗
DOE OSTI2023

Adaptive methods of generating complex light arrays

Structured light arrays of various shapes have been a cornerstone in optical science, driven by the complexities of precise and adaptable generation. This study introduces an approach using a spatial light modulator (SLM) as a generator for these arrays. By projecting a holographic mask onto the SLM, it functions simultaneously as an optical convolution device, focusing mechanism, and structured light beam mask. Our approach offers unmatched versatility, allowing for the experimental fabrication of traditional beam arrays like azimuthal Laguerre–Gaussian (LG), Bessel–Gaussian (BG), and Hermite–Gauss (HG) in the far-field. Notably, it has enabled a method of generating Ince–Gauss (IG) and LG radial mode beam arrays using a convolution solution. Our system provides exceptional control over array periodicity and intensity distribution, bypassing the Talbot self-imaging phenomenon seen in traditional setups. We provide an in-depth theoretical discussion, supported by empirical evidence, of our far-field results. This method has vast potential for applications in optical communication, data processing, and multi-particle manipulation. It paves the way for rapid generation of structured light with high spatial frequencies and complex shapes, promising transformative advances in these domains.

Optics↗
DOE OSTI2016

WHITE DWARF MERGERS ON ADAPTIVE MESHES. I. METHODOLOGY AND CODE VERIFICATION

The Type Ia supernova (SN Ia) progenitor problem is one of the most perplexing and exciting problems in astrophysics, requiring detailed numerical modeling to complement observations of these explosions. One possible progenitor that has merited recent theoretical attention is the white dwarf (WD) merger scenario, which has the potential to naturally explain many of the observed characteristics of SNe Ia. To date there have been relatively few self-consistent simulations of merging WD systems using mesh-based hydrodynamics. This is the first paper in a series describing simulations of these systems using a hydrodynamics code with adaptive mesh refinement. In this paper we describe our numerical methodology and discuss our implementation in the compressible hydrodynamics code CASTRO, which solves the Euler equations, and the Poisson equation for self-gravity, and couples the gravitational and rotation forces to the hydrodynamics. Standard techniques for coupling gravitation and rotation forces to the hydrodynamics do not adequately conserve the total energy of the system for our problem, but recent advances in the literature allow progress and we discuss our implementation here. We present a set of test problems demonstrating the extent to which our software sufficiently models a system where large amounts of mass are advected on the computational domain over long timescales. Future papers in this series will describe our treatment of the initial conditions of these systems and will examine the early phases of the merger to determine its viability for triggering a thermonuclear detonation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

H-AMR: A New GPU-accelerated GRMHD Code for Exascale Computing with 3D Adaptive Mesh Refinement and Local Adaptive Time Stepping

General relativistic magnetohydrodynamic (GRMHD) simulations have revolutionized our understanding of black hole accretion. Here, we present a GPU-accelerated GRMHD code H-AMR with multifaceted optimizations that, collectively, accelerate computation by 2–5 orders of magnitude for a wide range of applications. First, it introduces a spherical grid with 3D adaptive mesh refinement that operates in each of the three dimensions independently. This allows us to circumvent the Courant condition near the polar singularity, which otherwise cripples high-resolution computational performance. Second, we demonstrate that local adaptive time stepping on a logarithmic spherical-polar grid accelerates computation by a factor of ≲10 compared to traditional hierarchical time-stepping approaches. Jointly, these unique features lead to an effective speed of ~10 9 zone cycles per second per node on 5400 NVIDIA V100 GPUs (i.e., 900 nodes of the OLCF Summit supercomputer). We illustrate H-AMR's computational performance by presenting the first GRMHD simulation of a tilted thin accretion disk threaded by a toroidal magnetic field around a rapidly spinning black hole. With an effective resolution of 13,440 × 4608 × 8092 cells and a total of ≲22 billion cells and ~0.65 × 10 8 time steps, it is among the largest astrophysical simulations ever performed. We find that frame dragging by the black hole tears up the disk into two independently precessing subdisks. The innermost subdisk rotation axis intermittently aligns with the black hole spin, demonstrating for the first time that such long-sought alignment is possible in the absence of large-scale poloidal magnetic fields.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1972

Vestibular adaptation in man - Effects of increased acceleration during different phases of adaptation.

The purpose of this study was to investigate the course of vestibular adaptation following a temporary increase in angular acceleration (A). Eight normal subjects, who were rotated in a precision rotation device, gave periodic magnitude estimates of their perceived velocity throughout a prolonged 1 deg per sec per sec acceleration, which was briefly increased to either 2 or 3 deg per sec per sec at four points in the adaptation cycle. The data, tested with analysis of variance, showed that the size of the magnitude estimates was influenced by the magnitude and position of the altered A. The duration of subjective response was affected only by the position of the altered A.

Luster, T.↗
NASA NTRS1982

Rapid perceptual adaptation to high gravitoinertial force levels Evidence for context-specific adaptation

Subjects exposed to periodic variations in gravitoinertial force (2-G peak) in parabolic flight maneuvers quickly come to perceive the peak force level as having decreased in intensity. By the end of a 40-parabola flight, the decrease in apparent force is approximately 40%. On successive flight days, the apparent intensity of the force loads seems to decrease as well, indicating a cumulative adaptive effect. None of the subjects reported feeling abnormally 'light' for more than a minute or two after return to 1-G background force levels. The pattern of findings suggests a context-specific adaptation to high-force levels.

Lackner, J. R.↗
NASA NTRS1986

Initial adaptation testing of the bidimensionally self-adapting wall of the French T2 wind tunnel, around a three-dimensional object

The test series was carried out at ONERA/CERT at the T2 wind tunnel in September 1984. The objective of this series was to minimize wall interference through a bidimensional adaptation around the models, inducing tridimensional flows. For this, three different models were used, measuring either the pressures or the forces and moment of pitch (balance). The adaptation was derived from a correction computation in the compressible axisymmetric tridimensional.

Archambaud, J. P.↗
NASA NTRS1993

Transfer of perceptual adaptation to space sickness: What enhances an individual's ability to adapt?

The objectives of this project were to explore systematically the determiners of transfer of perceptual adaptation as these principles might apply to the space adaptation syndrome. The perceptual experience of an astronaut exposed to the altered gravitational forces involved in spaceflight shares much with that of the subject exposed in laboratory experiments to optically induced visual rearrangement with tilt and dynamic motion illusions such as vection; and experiences and symptoms reported by the trainee who is exposed to the compellingly realistic visual imagery of flight simulators and virtual reality systems. In both of these cases the observer is confronted with a variety of inter- and intrasensory conflicts that initially disrupt perception, as well as behavior, and also produce symptoms of motion sickness.

Source record↗
DOE OSTI2021

Structured Adaptive Mesh Refinement Adaptations to Retain Performance Portability With Increasing Heterogeneity

Adaptive mesh refinement (AMR) is an important method that enables many mesh-based applications to run at effectively higher resolution within limited computing resources by allowing high resolution only where really needed. This advantage comes at a cost, however: greater complexity in the mesh management machinery and challenges with load distribution. With the current trend of increasing heterogeneity in hardware architecture, AMR presents an orthogonal axis of complexity. Additionally, the usual techniques, such as asynchronous communication and hierarchy management for parallelism and memory that are necessary to obtain reasonable performance are very challenging to reason about with AMR. Different groups working with AMR are bringing different approaches to this challenge. Here, we examine the design choices of several AMR codes and also the degree to which demands placed on them by their users influence these choices.

42 ENGINEERING↗
DOE OSTI2017

Estuary ecosystem restoration: implementing and institutionalizing adaptive management: Institutionalizing adaptive management

We successfully implemented and institutionalized an adaptive management (AM) process for the Columbia Estuary Ecosystem Restoration Program, which is a large-scale restoration program focused on improving ecosystem conditions in the 234-km lower Columbia River and estuary. For our purpose, “institutionalized” means the AM process and restoration program are embedded in the work flow of the implementing agencies and affected parties. While plans outlining frameworks, processes, or approaches to AM of ecosystem restoration programs are commonplace, establishment for the long term is not. This paper presents the basic AM framework and explains how AM was implemented and institutionalized. Starting with a common goal, we pursued included a well-understood governance and decision-making structure, routine coordination and communication activities, data and information sharing, commitment from partners and upper agency management to the AM process, and meaningful cooperation among program managers and partners. The overall approach and steps to implement and institutionalize AM for ecosystem restoration explained here are applicable to situations where it has been less than successful or, as in our case, the restoration program is just getting started.

adaptive management↗
DOE OSTI2022

Multiscale analysis in solids with unseparated scales: fine-scale recovery, error estimation, and coarse-scale adaptivity

There are several engineering applications in which the assumptions of homogenization and scale separation may be violated, in particular, for metallic structures constructed through additive manufacturing. Instead of resorting to direct numerical simulation of the macroscale system with an embedded fine scale, an alternative approach is to use an approximate macroscale constitutive model, but then estimate the model-form error using a posteriori error estimation techniques and subsequently adapt the macroscale model to reduce the error for a given boundary value problem and quantity of interest. Here, we investigate this approach to multiscale analysis in solids with unseparated scales using the example of an additively manufactured metallic structure consisting of a polycrystalline microstructure that is neither periodic nor statistically homogeneous. As a first step to the general nonlinear case, we focus here on linear elasticity in which each grain within the polycrystal is linear elastic but anisotropic.

42 ENGINEERING↗
DOE OSTI2016

An adaptive Gaussian process-based method for efficient Bayesian experimental design in groundwater contaminant source identification problems: ADAPTIVE GAUSSIAN PROCESS-BASED INVERSION

Surrogate models are commonly used in Bayesian approaches such as Markov Chain Monte Carlo (MCMC) to avoid repetitive CPU-demanding model evaluations. However, the approximation error of a surrogate may lead to biased estimations of the posterior distribution. This bias can be corrected by constructing a very accurate surrogate or implementing MCMC in a two-stage manner. Since the two-stage MCMC requires extra original model evaluations, the computational cost is still high. If the information of measurement is incorporated, a locally accurate approximation of the original model can be adaptively constructed with low computational cost. Based on this idea, we propose a Gaussian process (GP) surrogate-based Bayesian experimental design and parameter estimation approach for groundwater contaminant source identification problems. A major advantage of the GP surrogate is that it provides a convenient estimation of the approximation error, which can be incorporated in the Bayesian formula to avoid over-confident estimation of the posterior distribution. The proposed approach is tested with a numerical case study. Without sacrificing the estimation accuracy, the new approach achieves about 200 times of speed-up compared to our previous work using two-stage MCMC.

Zhang, Jiangjiang↗