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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Spatial and temporal overlap between hatchery- and natural-origin steelhead and Chinook Salmon during spawning in the Klickitat River, Washington, USA

Abstract Objective A goal of many segregated salmonid hatchery programs is to minimize potential interbreeding between hatchery- and natural-origin fish. Our objective was to assess this on the Klickitat River, Washington, USA. Methods We used radiotelemetry to evaluate spatiotemporal spawning overlap between hatchery- and natural-origin steelhead Oncorhynchus mykiss and spring Chinook Salmon O. tshawytscha. We estimated percentages of tagged fish that spawned naturally in the Klickitat River subbasin, emigrated from the Klickitat River, or died before spawning. A kernel density analysis was used to estimate probability of spatiotemporal overlap between hatchery- and natural-origin spawners. Result For steelhead, 12% of hatchery-origin and 50% of natural-origin fish spawned naturally. For spring Chinook Salmon, 18% of hatchery-origin and 44% of natural-origin fish spawned naturally. Tag loss may result in underestimates in these percentages. Most hatchery-origin steelhead (90%) spawned downstream of river kilometer (rkm) 32, and 75% spawned from November to mid-March. The majority of natural-origin steelhead (64%) spawned upstream of rkm 32, and 75% spawned from mid-March to late May. Spawn timing of hatchery-origin Chinook Salmon (early August to mid-September) overlapped with that of natural-origin Chinook Salmon (late July to late September), and fish of both origins spawned in the same 30-km reach of the river. We estimated the percentage of hatchery-origin spawners (pHOS) on the natural spawning grounds to be 12% for steelhead and 40% for spring Chinook Salmon across all study years. For steelhead, we estimated the overlap probability to be 25% (95% CI = 22.5–28%). For spring Chinook Salmon, tight spatial clustering of hatchery-origin fish resulted in a lower overlap estimate of 21% (13–31%). Conclusion We suggest adjusting pHOS estimates using these overlap estimates or similar spatiotemporal data on actual spawner proximity and possible interactions, and that these types of analyses be used in conjunction with gene flow analysis to accurately evaluate effects of individual hatchery programs.

Zendt, Joseph S.↗
DOE OSTI2023

Optimized attenuated interaction: Enabling stochastic Bethe–Salpeter spectra for large systems

We develop an improved stochastic formalism for the Bethe–Salpeter equation (BSE), based on an exact separation of the effective-interaction W into two parts, W = (W – vW) + vW, where the latter is formally any translationally invariant interaction, vW(r – r'). When optimizing the fit of the exchange kernel vW to W, using a stochastic sampling W, the difference W – vW becomes quite small. Then, in the main BSE routine, this small difference is stochastically sampled. Furthermore, the number of stochastic samples needed for an accurate spectrum is then largely independent of system size. While the method is formally cubic in scaling, the scaling prefactor is small due to the constant number of stochastic orbitals needed for sampling W.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Three-nucleon force in relativistic three-nucleon Faddeev calculations

We extend our formulation of relativistic three-nucleon Faddeev equations to include both pairwise interactions and a three-nucleon force. Exact Poincare invariance is realized by adding interactions to the mass Casimir operator (rest Hamiltonian) of the noninteracting system without changing the spin Casimir operator. This is achieved by using interactions defined by rotationally invariant kernels that are functions of internal momentum variables and single-particle spins that undergo identical Wigner rotations. To solve the resulting equations one needs matrix elements of the three-nucleon force with these properties in a momentum-space partial-wave basis. We present two methods to calculate matrix elements of three-nucleon forces with these properties. For a number of examples we show that at higher energies, where effects of relativity and of three-nucleon forces are non-negligible, a consistent treatment of both is required to properly analyze the data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2011

Consistent description of hindrance in sub-barrier fusion of {sup 48}Ca with {sup 36}S, {sup 48}Ca, and {sup 96}Zr

Recent fusion reaction data for the systems {sup 36}S+{sup 48}Ca, {sup 48}Ca+{sup 48}Ca, and {sup 96}Zr+{sup 48}Ca are analyzed within the coupled-channel formalism. The heavy-ion entrance channel potential is calculated employing an improved double-folding prescription. The nonlocal kernel arising from the knock-on exchange component of the effective N-N interaction is localized within the lowest order of the Perey-Saxon approach, including full recoil. The single-particle densities entering the folding integrals are prescribed according to the density matrix expansion method. The investigation is more elaborated because each case is tested with four different types of N-N effective forces: The two standard parametrizations of the density-independent M3Y force (Reid and Paris) and two parametrizations of the density-dependent Gogny force (D1S and D1N). A consistent description of all three reactions is achieved by keeping fixed the nuclear structure input for {sup 48}Ca. The inclusion of 2{sup +} and 3{sup -} phonon states in the coupled-channel calculation, within an energy excitation window identical for all three reactions explains better the hindrance in extreme sub-barrier fusion cross sections. The interactions providing the best fit to the data are not pointing to a possible maximum in the astrophysical S factor, thereby confirming the conclusion reached by the Legnaro group for these cases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

WE-AB-204-02: Molecular-Imaging Based Assessment of Liver Complications for Yttrium-90 Microsphere Treatments: Can Existing NTCP Models Explain Clinical Outcomes?

Purpose: To evaluate weather the current radiobiological models can predict the normal liver complications of radioactive Yttrium-90 ({sup 90}Y) selective-internal-radiation-treatment (SIRT) for metastatic liver lesions based on the post-infusion {sup 90}Y PET images. Methods: A total of 20 patients with metastatic liver tumors treated with SIRT that received a post-infusion {sup 90}Y-PET/CT scan were analyzed in this work. The 3D activity distribution of the PET images was converted into a 3D dose distribution via a kernel convolution process. The physical dose distribution was converted into the equivalent dose (EQ2) delivered at 2 Gy based on the linear-quadratic (LQ) model considering the dose rate effect. The biological endpoint of this work was radiation-induce liver disease (RILD). The NTCPs were calculated with four different repair-times (T1/2-Liver-Repair= 0,0.5,1.0,2.0 hr) and three published NTCP models (Lyman-external-RT, Lyman 90Y-HCC-SIRT, parallel model) were compared to the incidence of RILD of the recruited patients to evaluate their ability of outcome prediction. Results: The mean normal liver physical dose (avg. 51.9 Gy, range 31.9–69.8 Gy) is higher than the suggested liver dose constraint for external beam treatment (∼30 Gy). However, none of the patients in our study developed RILD after the SIRT. The estimated probability of ‘no patient developing RILD’ obtained from the two Lyman models are 46.3% to 48.3% (T1/2-Liver-Repair= 0hr) and <1% for all other repair times. For the parallel model, the estimated probability is 97.3% (0hr), 51.7% (0.5hr), 2.0% (1.0hr) and <1% (2.0hr). Conclusion: Molecular-images providing the distribution of {sup 90}Y enable the dose-volume based dose/outcome analysis for SIRT. Current NTCP models fail to predict RILD complications in our patient population, unless a very short repair-time for the liver is assumed. The discrepancy between the Lyman {sup 90}Y-HCC-SIRT model predicted and the clinically observed outcomes further demonstrates the need of an NTCP model specific to the metastatic liver SIRT.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Online MCMC Thinning with Kernelized Stein Discrepancy

A fundamental challenge in Bayesian inference is efficient representation of a target distribution. Many nonparametric approaches do so by sampling a large number of points using variants of Markov chain Monte Carlo (MCMC). Here, we propose an MCMC variant that retains only those posterior samples which exceed a kernelized Stein discrepancy (KSD) threshold, which we call KSD thinning. We establish the convergence and complexity trade-offs for several settings of KSD thinning as a function of the KSD threshold parameter, sample size, and other problem parameters. We provide experimental comparisons against other online nonparametric Bayesian methods that generate low-complexity posterior representations. We observe superior consistency/complexity trade-offs across a range of settings including MCMC sampling on two Bayesian inference problems from the biological sciences, and 10 × inference speedup and storage reduction for Bayesian neural networks with no loss of accuracy and no increase in training time. Our code is available at https://github.com/colehawkins/KSD-Thinning.

Bayesian inference↗
DOE OSTI2023

Codebase release 0.1 for infstat

We propose an intuitive, machine-learning approach to multiparameter inference, dubbed the InferoStatic Networks (ISN) method, to model the score and likelihood ratio estimators in cases when the probability density can be sampled but not computed directly. The ISN uses a backend neural network that models a scalar function called the inferostatic potential \varphi φ . In addition, we introduce new strategies, respectively called Kernel Score Estimation (KSE) and Kernel Likelihood Ratio Estimation (KLRE), to learn the score and the likelihood ratio functions from simulated data. We illustrate the new techniques with some toy examples and compare to existing approaches in the literature. We mention en passant some new loss functions that optimally incorporate latent information from simulations into the training procedure.

Kong, Kyoungchul↗
DOE OSTI2012

Petascale Data Storage Institute (Final Report)

pNFS is an extension to NFSv4 that helps clients overcome NFS scalability and performance barriers. Like NFS, pNFS is a client/server protocol implemented with secure and reliable remote procedure calls. pNFS departs from conventional NFS by allowing clients to access storage directly and in parallel. This helps overcome server bottlenecks inherent to NAS access methods. Making pNFS available to petascale researchers required coordinated progress in several dimensions, a confluence of multiple processes that took nearly ten years. The protocol had to be specified and published by the IETF. Nascent implementations had to track changes in the draft specification, changes in the Linux kernel, and interoperate with one another. The process by which modifications are accepted into the Linux kernel by maintainers and developers (and ultimately by Linus Torvalds himself) itself required consensus and compromise. Finally, pNFS support needed to be provided by the major Linux distributors (Red Hat, SUSE, etc.) and storage vendors (Netapp, EMC, IBM, Microsoft, etc.) on both the engineering and product sides. The specification requirement was met in December 2008, when the IETF approved the NFSv4.1 specification, which incorporates pNFS and pNFS file layouts, as a Proposed Standard as well as the (separate) specifications of pNFS object and block layouts. Throughout the PDSI project, CITI was the key contributor to the Linux-based, open source implementation of NFSv4.1 and pNFS. Considerable effort was devoted to the process of refining the IETF specification, which underwent dozens of preliminary drafts, rebasing implementations to the latest Linux kernel, which itself changed quarterly, and to testing interoperability with other developers. At last, the Linux pNFS implementation was incorporated into the Linux mainline kernel, although this was achieved after the PDSI project ended.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Quantitative Performance Assessment of Proxy Apps and Parents (ECP Proxy App Project Milestone ADCD-504-9)

This report presents highlights of these efforts. Section 2 describes work that has been done to compare the performance of proxy applications on AMD MI60 vs. Nvidia V100 GPUs. So far only a small set of ECP proxies are running on AMD GPUs, but we will continue to expand this analysis as additional proxies become available. We find that although the MI60 and V100 have nearly the same measured memory bandwidth, memory bound proxy app kernels perform 20-30% worse on the MI60. Further work is needed to refine these comparisons to determine whether the root cause is due to differences in the hardware, software stack, platform specific optimization, or some combination of the three. Section 3 describes our continuing effort to find methods to accurately assess the similarity of proxies and parents. We have recently seen very encouraging results using a cosine similarity metric. This technique uses the angle between two vectors of hardware performance counters to characterize the similarity (or difference) between two applications or proxies. We show not only that several widely used proxies are highly similar to their parents, but also that they differ from non-related codes. We also show that cosine similarity can be used to identify gaps and redundancies in suites and even to gain insight into the effects of architectural differences between platforms. Our work on assessing the Exascale toolchain is ongoing. Our successes with performance measurement tools are evident from the data provided in this report. However, our assessments across the broader tool chain are still too incomplete to provide a meaningful report at this time. We will continue to assess tools and work with vendors and third party developers as issues are identified.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1974

Nonparametric maximum likelihood estimation of probability densities by penalty function methods

When it is known a priori exactly to which finite dimensional manifold the probability density function gives rise to a set of samples, the parametric maximum likelihood estimation procedure leads to poor estimates and is unstable; while the nonparametric maximum likelihood procedure is undefined. A very general theory of maximum penalized likelihood estimation which should avoid many of these difficulties is presented. It is demonstrated that each reproducing kernel Hilbert space leads, in a very natural way, to a maximum penalized likelihood estimator and that a well-known class of reproducing kernel Hilbert spaces gives polynomial splines as the nonparametric maximum penalized likelihood estimates.

Demontricher, G. F.↗
DOE OSTI2018

Fundamental Operator-Valued Functions of Singular Integrodifferential Operators in Banach Spaces

In this paper, using methods of the theory of generalized functions in Banach spaces, we examine the Cauchy problem for an abstract integrodifferential equation of a specific type. Under the assumption that there exist the complete Jordan structure of the differential part of the equation and the order of the zero of the kernel of the integral part, the fundamental operator-valued function (the fundamental solution) is constructed for the corresponding integrodifferential operator, which is used for further investigation of the problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Aspects of effective action for super Chern-Simons-Matter models

We develop the superfield background field method and study the effective action in the N = 2, d3 supersymmetric Chern-Simons-matter systems. The one-loop low-energy effective action for non-Abelian supersymmetric Chern-Simons theory is computed to order F{sup 4} by use of N = 2 superfield heat kernel techniques.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Tiling Framework for Heterogeneous Computing of Matrix based Tiled Algorithms

Tiling matrix operations can improve the load balancing and performance of applications on heterogeneous computing resources. Writing a tile-based algorithm for each operation with a traditional, hand-tuned tiling approach that uses for loops in C/C++ is cumbersome and error prone. Moreover, it must enable and support the heterogeneous memory management of data objects and also explore architecture-supported, native, tiled-data transfer APIs instead of copying the tiled data to continuous memory before the data transfer. The tiling framework provides a tiled data structure for heterogeneous memory mapping and parameterization to a heterogeneous task specification API. We have integrated our tiled framework into MatRIS (Math kernels library using IRIS). IRIS is a heterogeneous run-time framework with a heterogeneous programming model, memory model, and task execution model. Experiments reveal that the tiled framework for BLAS operations has improved the programmability of tiled BLAS and improved performance by ~20% when compared against the traditional method that copies the data to continuous memory locations for heterogeneous computing.

Miniskar, Narasinga Rao↗
NASA NTRS1976

A computer program to find the kernel of a polynomial operator

This paper presents a FORTRAN program written to solve for the kernel of a matrix of polynomials with real coefficients. It is an implementation of Sain's free modular algorithm for solving the minimal design problem of linear multivariable systems. The structure of the program is discussed, together with some features as they relate to questions of implementing the above method. An example of the use of the program to solve a design problem is included.

Gejji, R. R.↗
NASA NTRS1978

Numerical solution of a class of integral equations arising in two-dimensional aerodynamics

We consider the numerical solution of a class of integral equations arising in the determination of the compressible flow about a thin airfoil in a ventilated wind tunnel. The integral equations are of the first kind with kernels having a Cauchy singularity. Using appropriately chosen Hilbert spaces, it is shown that the kernel gives rise to a mapping which is the sum of a unitary operator and a compact operator. This allows the problem to be studied in terms of an equivalent integral equation of the second kind. A convergent numerical algorithm for its solution is derived by using Galerkin's method. It is shown that this algorithm is numerically equivalent to Bland's collocation method, which is then used as the method of computation. Extensive numerical calculations are presented establishing the validity of the theory.

Fromme, J.↗
NASA NTRS1989

The Raid distributed database system

Raid, a robust and adaptable distributed database system for transaction processing (TP), is described. Raid is a message-passing system, with server processes on each site to manage concurrent processing, consistent replicated copies during site failures, and atomic distributed commitment. A high-level layered communications package provides a clean location-independent interface between servers. The latest design of the package delivers messages via shared memory in a configuration with several servers linked into a single process. Raid provides the infrastructure to investigate various methods for supporting reliable distributed TP. Measurements on TP and server CPU time are presented, along with data from experiments on communications software, consistent replicated copy control during site failures, and concurrent distributed checkpointing. A software tool for evaluating the implementation of TP algorithms in an operating-system kernel is proposed.

Bhargava, Bharat↗
DOE OSTI2022

Multiscale, mechanistic calculation of the effective silver diffusion coefficient in polycrystalline silicon carbide: application to silver release in AGR-1 TRISO particles

The silicon carbide (SiC) layer in tristructural isotropic (TRISO) fuel particles serves as a barrier to prevent the escape of fission from the fuel kernel. The release of silver (Ag) is a concern due to the long half-life of the 110mAg isotope. In this study, the effective diffusion coefficient of the fission product Ag through the grain boundary (GB) network is calculated using a combination of atomistic and phase-field methods. Atomistic calculations of Ag diffusivity in SiC bulk and GBs are leveraged to develop a mesoscale effective Ag diffusion coefficient (Deff) in SiC. Since GBs serve as pathways for Ag diffusion, Deff is defined as a function of temperature, microstructure variables, and fluence. Deff is implemented in the fuel performance code Bison to predict Ag release from AGR-1 TRISO fuel particles. We hereby quantify the impact of SiC grain size and irradiation on Ag release and improve Bison's predictions.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2013

Experimentally studied dynamic dose interplay does not meaningfully affect target dose in VMAT SBRT lung treatments

Purpose: The effects of respiratory motion on the tumor dose can be divided into the gradient and interplay effects. While the interplay effect is likely to average out over a large number of fractions, it may play a role in hypofractionated [stereotactic body radiation therapy (SBRT)] treatments. This subject has been extensively studied for intensity modulated radiation therapy but less so for volumetric modulated arc therapy (VMAT), particularly in application to hypofractionated regimens. Also, no experimental study has provided full four-dimensional (4D) dose reconstruction in this scenario. The authors demonstrate how a recently described motion perturbation method, with full 4D dose reconstruction, is applied to describe the gradient and interplay effects during VMAT lung SBRT treatments.Methods: VMAT dose delivered to a moving target in a patient can be reconstructed by applying perturbations to the treatment planning system-calculated static 3D dose. Ten SBRT patients treated with 6 MV VMAT beams in five fractions were selected. The target motion (motion kernel) was approximated by 3D rigid body translation, with the tumor centroids defined on the ten phases of the 4DCT. The motion was assumed to be periodic, with the period T being an average from the empirical 4DCT respiratory trace. The real observed tumor motion (total displacement ≤8 mm) was evaluated first. Then, the motion range was artificially increased to 2 or 3 cm. Finally, T was increased to 60 s. While not realistic, making T comparable to the delivery time elucidates if the interplay effect can be observed. For a single fraction, the authors quantified the interplay effect as the maximum difference in the target dosimetric indices, most importantly the near-minimum dose (D{sub 99%}), between all possible starting phases. For the three- and five-fractions, statistical simulations were performed when substantial interplay was found.Results: For the motion amplitudes and periods obtained from the 4DCT, the interplay effect is negligible (<0.2%). It is also small (0.9% average, 2.2% maximum) when the target excursion increased to 2–3 cm. Only with large motion and increased period (60 s) was a significant interplay effect observed, with D{sub 99%} ranging from 16% low to 17% high. The interplay effect was statistically significantly lower for the three- and five-fraction statistical simulations. Overall, the gradient effect dominates the clinical situation.Conclusions: A novel method was used to reconstruct the volumetric dose to a moving tumor during lung SBRT VMAT deliveries. With the studied planning and treatment technique for realistic motion periods, regardless of the amplitude, the interplay has nearly no impact on the near-minimum dose. The interplay effect was observed, for study purposes only, with the period comparable to the VMAT delivery time.

62 RADIOLOGY AND NUCLEAR MEDICINE↗