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At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Multi-Energy Differential Evolution Reconstruction (MEnDER 1D) for Proton Deflectometry

This code is designed to reconstruct magnetic field deflections, and thus the path-integrated magnetic field, from sets of proton images at two distinct proton probe energies. A differential evolution (DE) algorithm is used to iteratively update a population of solution candidates of the magnetic deflections of the protons for reconstructing the input images, selecting improved candidates as they are discovered. This algorithm was written using MATLAB (R2019a) and makes use of the Image Processing and Parallel Processing Toolboxes.

Levesque, Joseph↗
DOE OSTI2023

CEDS Differential Privacy (CEDSDP) v0.1

A Python package that provides differentially private queries optimized for energy systems' data. It may be used to publish queries such as clustering, averaging, metadata inference, etc. that are useful for a variety of grid-related analytics, including cyberattack detection.

Peisert, Sean↗
DOE OSTI2021

Parameterized Pseudo-Differential Operators for Applying CNNs to Unstructured Mesh Data

SAND2021-15058 O This code accompanies the International Conference on Learning Representations (ICLR) paper entitled "Parameterized Pseudo-Differential Operators for Applying CNNs to Unstructured Mesh Data." Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Tencer, John↗
DOE OSTI2025

Differentially Private Map Matching (DPMM) v1.0

Human mobility trajectories provide valuable information for developing mobility applications, as they contain diverse and rich information about the users. User mobility data is valuable for various applications such as intelligent transportation systems (ITS), commercial business models, and disease-spread models. However, such spatio-temporal traces may pose a threat to user privacy. GPS trajectories in their raw form are not suitable for transportation studies, as they require matching locations with nearest road links — a process called map-matching. This software implements a differential privacy (DP)-based map-matching algorithm, called DPMM, that generates link-level location trajectories in a privacy-preserving manner to protect users' origin destinations (OD) and travel paths. OD privacy is achieved by injecting Planar Laplace noise to the user OD GPS points. Travel-path privacy is provided with randomized travel path construction using exponential DP mechanism. The injected noise level is selected adaptively, by considering the link density of the location and the functional category of the localized links. For path privacy, our mechanism samples waypoints and selects candidate paths between waypoints. DPMM provides privacy effectively with respect to link density instead of other trajectory samples in the database compared to other privacy mechanisms. Compared to the different baseline models our DP-based privacy model offers closer query responses to the raw data in terms of individual and aggregate trajectory-level statistics with an average at absolute deviation from the baseline for individual statistics on ϵ = 1.0. Beyond individual trajectory statistics, the DPMM outperforms the other benchmark DP-based mechanisms on different aggregate statistics with up to 8x improvement in utility.

Peisert, Sean [Lawrence Berkeley National Laborato↗
DOE OSTI2024

Learning Only on Boundaries: A Physics-Informed Neural Operator for Solving Parametric Partial Differential Equations in Complex Geometries

Recently, deep learning surrogates and neural operators have shown promise in solving partial differential equations (PDEs). However, they often require a large amount of training data and are limited to bounded domains. In this work, we present a novel physics-informed neural operator method to solve parameterized boundary value problems without labeled data. By reformulating the PDEs into boundary integral equations (BIEs), we can train the operator network solely on the boundary of the domain. This approach reduces the number of required sample points from $O(N^d)$ to $O(N^{d-1}$), where $d$ is the domain’s dimension, leading to a significant acceleration of the training process. Additionally, our method can handle unbounded problems, which are unattainable for existing physics-informed neural networks (PINNs) and neural operators. Finally, our numerical experiments show the effectiveness of parameterized complex geometries and unbounded problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Differential Credibility of Climate Modes in CMIP6

This work quantitatively evaluates the fidelity with which the northern annular mode (NAM), southern annular mode (SAM), Pacific–North American pattern (PNA), El Niño–Southern Oscillation (ENSO), Pacific decadal oscillation (PDO), Atlantic multidecadal oscillation (AMO), and the first-order mode interactions are represented in Earth system model (ESM) output from the CMIP6 archive. Several skill metrics are used as part of a differential credibility assessment (DCA) of both spatial and temporal characteristics of the modes across ESMs, ESM families, and specific ESM realizations relative to ERA5. The spatial patterns and probability distributions are generally well represented but skill scores that measure the degree to which the frequencies of maximum variance are captured are consistently lower for most ESMs and climate modes. Substantial variability in skill scores manifests across realizations from individual ESMs for the PNA and oceanic modes. Further, the ESMs consistently overestimate the strength of the NAM–PNA first-order interaction and underestimate the NAM–AMO connection. Furthermore, these results suggest that the choice of ESM and ESM realizations will continue to play a critical role in determining climate projections at the global and regional scale at least in the near term.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Partial differential equations preconditioner resilient to soft and hard faults

We present a domain-decomposition-based preconditioner for the solution of partial differential equations (PDEs) that is resilient to both soft and hard faults. The algorithm reformulates the PDE as a sampling problem, followed by a solution update through data manipulation that is resilient to both soft and hard faults. This reformulation allows us to recast the problem as a set of independent tasks, and exploit data locality to reduce global communication. We discuss two different parallel implementations: (a) a single program multiple data (SPMD) version based on a one-to-one mapping between subdomain and MPI processes responsible for both state and computation; and (b) an asynchronous server–client implementation where all state information is held by the servers and clients are designed solely as computational units. We present a scalability comparison of both implementations under nominal conditions, showing efficiency within ~80% for up to 12,000 cores. We present a resilience analysis under different fault scenarios based on the server–client implementation. This framework provides resiliency to hard faults such that if a client crashes, it stops asking for work, and the servers simply distribute the work among all of the other clients alive. Erroneous subdomain solves (e.g. due to soft faults) appear as corrupted data, which is either rejected if that causes a task to fail, or is seamlessly filtered out during the regression stage through a suitable noise model. Three different types of faults are modeled: hard faults modeling nodes (or clients) crashing; soft faults occurring during the communication of the tasks between server and clients; and soft faults occurring during task execution. We demonstrate the resiliency of the approach for a 2D elliptic PDE, and explore the effect of the faults at various failure rates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Differential patterns of reproductive and lifestyle risk factors for breast cancer according to birth cohorts among women in China, Japan and Korea

Background: The birth cohort effect has been suggested to influence the rate of breast cancer incidence and the trends of associated reproductive and lifestyle factors. We conducted a cohort study to determine whether a differential pattern of associations exists between certain factors and breast cancer risk based on birth cohorts. Methods: This was a cohort study using pooled data from 12 cohort studies. We analysed associations between reproductive (menarche age, menopause age, parity and age at first delivery) and lifestyle (smoking and alcohol consumption) factors and breast cancer risk. We obtained hazard ratios (HRs) with 95% confidence intervals (CIs) using the Cox proportional hazard regression analysis on the 1920s, 1930s, 1940s and 1950s birth cohorts. Results: Parity was found to lower the risk of breast cancer in the older but not in the younger birth cohort, whereas lifestyle factors showed associations with breast cancer risk only among the participants born in the 1950s. In the younger birth cohort group, the effect size was lower for parous women compared to the other cohort groups (HR [95% CI] 0.86 [0.66–1.13] compared to 0.60 [0.49–0.73], 0.46 [0.38–0.56] and 0.62 [0.51–0.77]). Meanwhile, a higher effect size was found for smoking (1.45 [1.14–1.84] compared to 1.25 [0.99–1.58], 1.06 [0.85–1.32] and 0.86 [0.69–1.08]) and alcohol consumption (1.22 [1.01–1.48] compared to 1.10 [0.90–1.33], 1.15 [0.96–1.38], and 1.07 [0.91–1.26]). Conclusion: We observed different associations of parity, smoking and alcohol consumption with breast cancer risk across various birth cohorts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

A cognitive electrophysiological signature differentiates amnestic mild cognitive impairment from normal aging

Background: Noninvasive and effective biomarkers for early detection of amnestic mild cognitive impairment (aMCI) before measurable changes in behavioral performance remain scarce. Cognitive event-related potentials (ERPs) measure synchronized synaptic neural activity associated with a cognitive event. Loss of synapses is a hallmark of the neuropathology of early Alzheimer’s disease (AD). In the present study, we tested the hypothesis that ERP responses during working memory retrieval discriminate aMCI from cognitively normal controls (NC) matched in age and education. Methods: Eighteen NC, 17 subjects with aMCI, and 13 subjects with AD performed a delayed match-to-sample task specially designed not only to be easy enough for impaired participants to complete but also to generate comparable performance between subjects with NC and those with aMCI. Scalp electroencephalography, memory accuracy, and reaction times were measured. Results: Whereas memory performance separated the AD group from the others, the performance of NC and subjects with aMCI was similar. In contrast, left frontal cognitive ERP patterns differentiated subjects with aMCI from NC. Enhanced P3 responses at left frontal sites were associated with nonmatching relative to matching stimuli during working memory tasks in patients with aMCI and AD, but not in NC. The accuracy of discriminating aMCI from NC was 85% by using left frontal match/nonmatch effect combined with nonmatch reaction time. Conclusions: The left frontal cognitive ERP indicator holds promise as a sensitive, simple, affordable, and noninvasive biomarker for detection of early cognitive impairment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability

Accurate predictions of the pathogenicity of mutations associated with genetic diseases are key to the success of precision medicine. Inherited missense mutations in the myocilin (MYOC) gene, within its olfactomedin (OLF) domain, constitute the strongest genetic link to primary open-angle glaucoma via a toxic gain of function, and thus MYOC is an attractive precision-medicine target. However, not all mutations in MYOC cause glaucoma, and common variants are expected to be neutral polymorphisms. The Genome Aggregation Database (gnomAD) lists ~100 missense variants documented within OLF, all of which are relatively rare (allele frequency <0.001%) and nearly all are of unknown pathogenicity. To distinguish disease-causing OLF variants from benign OLF variants, we first characterized the most prevalent population-based variants using a suite of cellular and biophysical assays, and identified two variants with features of aggregation-prone familial disease variants. Next, we considered all available biochemical and clinical data to demonstrate that pathogenic and benign variants can be differentiated statistically based on a single metric: the thermal stability of OLF. Our results motivate genotyping MYOC in patients for clinical monitoring of this widespread, painless and irreversible ocular disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

H 2 O absorption spectroscopy via focused laser differential interferometry

A modification of focused laser differential interferometry (FLDI) is demonstrated with an infrared tunable diode laser (TDL) to achieve simultaneous absorption spectroscopy (AS) measurements. Measurements from this absorbing-FLDI (A-FLDI) are shown for a Hencken burner plume. Initial comparison measurements are recorded using TDLAS and an electrical hygrometer. Raw voltage and estimated absorbance measurements illustrate that the technique detects five distinct absorbance peaks of the methane–air flame while retaining the expected behavior of typical FLDI. This modification furthers efforts to enable FLDI to conduct analysis of the pressures, temperatures, and molecular densities of flows. It also explores the potential for reducing path-integration (PI) effects in absorption spectroscopy and potentially enabling spatially and temporally resolved local flow measurements. Reductions in PI length as high as 82%–84% are observed.

Holladay, Seth (ORCID:0009000650875421)↗
DOE OSTI2018

Direct binary search for improved coherent beam shaping and optical differentiation wavefront sensing

Spatially dithered distributions of binary amplitude pixels are optimized using a full direct binary search taking into account the experimental configuration for amplitude modulation of coherent waves. This design process is shown to yield a significant reduction of the noise induced by binarization and pixelation over the region of interest. In this study, we demonstrate this approach for beam shaping and optical differentiation wavefront sensing, where the region of interest is in an image plane of the pixel distribution and in the far field of the pixel distribution, respectively. Lastly, the observed reduction in error compared to a standard error diffusion algorithm is significant for both applications because it improves performance without the tighter fabrication tolerance and cost associated with smaller pixels.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Adorym: a multi-platform generic X-ray image reconstruction framework based on automatic differentiation

We describe and demonstrate an optimization-based X-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dose-efficient automatic differentiation for ptychographic reconstruction

Ptychography, as a powerful lensless imaging method, has become a popular member of the coherent diffractive imaging family over decades of development. The ability to utilize low-dose X-rays and/or fast scans offers a big advantage in a ptychographic measurement (for example, when measuring radiation-sensitive samples), but results in low-photon statistics, making the subsequent phase retrieval challenging. Here, we demonstrate a dose-efficient automatic differentiation framework for ptychographic reconstruction (DAP) at low-photon statistics and low overlap ratio. As no reciprocal space constraint is required in this DAP framework, the framework, based on various forward models, shows superior performance under these conditions. It effectively suppresses potential artifacts in the reconstructed images, especially for the inherent periodic artifact in a raster scan. We validate the effectiveness and robustness of this method using both simulated and measured datasets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota , none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification of mosquito proteins that differentially interact with alphavirus nonstructural protein 3, a determinant of vector specificity

Chikungunya virus (CHIKV) and the closely related onyong-nyong virus (ONNV) are arthritogenic arboviruses that have caused significant, often debilitating, disease in millions of people. However, despite their kinship, they are vectored by different mosquito subfamilies that diverged 180 million years ago (anopheline versus culicine subfamilies). Previous work indicated that the nonstructural protein 3 (nsP3) of these alphaviruses was partially responsible for this vector specificity. To better understand the cellular components controlling alphavirus vector specificity, a cell culture model system of the anopheline restriction of CHIKV was developed along with a protein expression strategy. Mosquito proteins that differentially interacted with CHIKV nsP3 or ONNV nsP3 were identified. Six proteins were identified that specifically bound ONNV nsP3, ten that bound CHIKV nsP3 and eight that interacted with both. In addition to identifying novel factors that may play a role in virus/vector processing, these lists included host proteins that have been previously implicated as contributing to alphavirus replication.

Byers, Nathaniel M. (ORCID:0000000157725940)↗
DOE OSTI2018

A group of Populus trichocarpa DUF231 proteins exhibit differential O-acetyltransferase activities toward xylan

Wood represents the most abundant biomass produced by plants and one of its major components is acetyl xylan. Acetylation in xylan can occur at O-2 or O-3 of a xylosyl residue, at both O-2 and O-3 of a xylosyl residue, and at O-3 of a xylosyl residue substituted at O-2 with glucuronic acid. Acetyltransferases responsible for the regiospecific acetylation of xylan in tree species have not yet been characterized. Here we report the biochemical characterization of twelve Populus trichocarpa DUF231-containing proteins, named PtrXOATs, for their roles in the regiospecific acetylation of xylan. The PtrXOAT genes were found to be differentially expressed in Populus organs and among them, PtrXOAT1, PtrXOAT2, PtrXOAT9 and PtrXOAT10 exhibited the highest level of expression in stems undergoing wood formation. Activity assays of recombinant proteins demonstrated that all twelve PtrXOAT proteins were able to transfer acetyl groups from acetyl CoA onto a xylohexaose acceptor with PtrXOAT1, PtrXOAT2, PtrXOAT3, PtrXOAT11 and PtrXOAT12 having the highest activity. Structural analysis of the PtrXOAT-catalyzed reaction products using 1 H NMR spectroscopy revealed that PtrXOAT1, PtrXAOT2 and PtrXOAT3 mediated 2-O- and 3-O-monoacetylation and 2,3-di-O-acetylation of xylosyl residues and PtrXOAT11 and PtrXOAT12 only catalyzed 2-O- and 3-O-monoacetylation of xylosyl residues. Of the twelve PtrXOATs, only PtrXOAT9 and PtrXOAT10 were capable of transferring acetyl groups onto the O-3 position of 2-O-glucuronic acid-substituted xylosyl residues. Furthermore, when expressed in the Arabidopsis eskimo1 mutant, PtrXOAT1, PtrXAOT2 and PtrXOAT3 were able to rescue the defects in xylan acetylation. Together, these results demonstrate that the twelve PtrXOATs are acetyltransferases with different roles in xylan acetylation in P. trichocarpa.

09 BIOMASS FUELS↗