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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deep learning applications in visual data for benign and malignant hematologic conditions: a systematic review and visual glossary

Deep learning (DL) is a subdomain of artificial intelligence algorithms capable of automatically evaluating subtle graphical features to make highly accurate predictions, which was recently popularized in multiple imaging-related tasks. Because of its capabilities to analyze medical imaging such as radiology scans and digitized pathology specimens, DL has significant clinical potential as a diagnostic or prognostic tool. Coupled with rapidly increasing quantities of digital medical data, numerous novel research questions and clinical applications of DL within medicine have already been explored. Similarly, DL research and applications within hematology are rapidly emerging, although these are still largely in their infancy. Given the exponential rise of DL research for hematologic conditions, it is essential for the practising hematologist to be familiar with the broad concepts and pitfalls related to these new computational techniques. This narrative review provides a visual glossary for key deep learning principles, as well as a systematic review of published investigations within malignant and non-malignant hematologic conditions, organized by the different phases of clinical care. In order to assist the unfamiliar reader, this review highlights key portions of current literature and summarizes important considerations for the critical understanding of deep learning development and implementations in clinical practice.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis

Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determine cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA) that relies on the patterns of isotope labeling of metabolites in the network. For metabolic systems, typical for plants, where all potentially labeled atoms effectively have only one source atom pool, only isotopically nonstationary MFA can provide information about intracellular fluxes. There are several global approaches that implement MFA for an entire metabolic network and estimate, at once, a steady-state flux distribution for all reactions with identifiable fluxes in the network. In contrast, local approaches deal with estimation of fluxes for a subset of reactions, with smaller data demand for flux estimation. Here we present a systematic comparative review and benchmarking of the existing local approaches for isotopically nonstationary MFA. The comparison is conducted with respect to the required data and underlying computational problems solved on a synthetic network example. Furthermore, we benchmark the performance of these approaches in estimating fluxes for a subset of reactions using data obtained from the simulation of nitrogen fluxes in the Arabidopsis thaliana core metabolism. The findings pinpoint practical aspects that need to be considered when applying local approaches for flux estimation in large-scale plant metabolic networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Knowledge, attitudes, and practices associated with bioterrorism preparedness in healthcare workers: a systematic review

Introduction Bioterrorism is an important issue in the field of biosecurity, and effectively dealing with bioterrorism has become an urgent task worldwide. Healthcare workers are considered bioterrorism first responders, who shoulder essential responsibilities and must be equipped to deal with bioterrorism. This study aims to extract and summarize the main research components of the bioterrorism knowledge, attitude, and practice dimensions among healthcare workers. Method This study utilized a systematic review research design based on the PRISMA 2020 guidelines. A literature search was conducted in the PubMed, Web of Science, and Scopus databases for peer-reviewed literature, and the Mixed Methods Appraisal Tool (MMAT) version 2018 was used to assess the quality of the literature. Result A total of 16 studies were included in the final selection. Through the analysis and summary of the included studies, three main aspects and 14 subaspects of the knowledge dimension, three main aspects and 10 subaspects of the attitude dimension, and two main aspects and six subaspects of the practice dimension were extracted. Conclusion This study conducted a literature review on bioterrorism knowledge, attitudes, and practices for healthcare workers based on the PRISMA 2020 guidelines. The findings can guide improvements in health literacy and provide beneficial information to professional organizations that need to respond effectively to bioterrorism.

Li, Tiantian↗
DOE OSTI2025

Optimizing ensemble NV − spin properties of fluorescent diamond microparticles by systematic low pressure high temperature annealing

Low pressure high temperature annealing is a means for driving nitrogen and defect diffusion in diamond to reduce internal lattice damage without the need for technically complicated high-pressure cells. Herein, we perform a systematic time (5, 15, and 30 min) and temperature (1200 °C–1800 °C) study of effects of low-pressure high temperature annealing on photoluminescence, spin concentrations, and spin relaxation properties of NV centers in ca. 3 μm synthetic type 1b diamond particles. Annealing in the temperature range of ca. 1400 °C–1700 °C for even 5 min leads to a higher optically detected magnetic resonance contrast as compared to standard annealing at 900 °C for 2 h. Particles annealed at 1700 °C for 5 min exhibit a contrast close to about 13% as compared to about 9% for those annealed at 900 °C for 2 h. A reduction in the zero-field splitting strain parameter from E ≈ 4.5 MHz to ≈ 2.5 MHz and spectral linewidth from Δν ≈ 7 MHz to ≈ 4 MHz are observed even after 5 min annealing at 1700 °C. Improvements in these spectral parameters resulted in a roughly 2-fold reduction in the noise level of temperature monitoring experiment utilizing an ensemble of NV centers in the particles. Annealing in the temperature range of 1600 °C for 15 or 30 min or 1700 °C for 5 min resulted in NV T 1 relaxation times approaching ca. 5 ms typically observed for bulk diamond. Quantitative electron paramagnetic resonance (EPR) allowed for estimations of thermal activation energies of paramagnetic center annihilation. Monitoring the primary defect concentration (P1 and other defects with half integer spins) and utilizing second order kinetic modeling, an activation energy of 3.63 ± 0.28 eV was estimated. Alternatively, using the NV half field EPR signal and first order kinetic modeling, a similar activation energy 3.89 ± 0.29 eV was estimated.

NV centers↗
DOE OSTI2022

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Finally, our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phylogeny and character evolution in the Dacrymycetes , and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1,RPB2,TEF-1α, 12S, andATP6DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted with in the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. Macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An Analysis of the Statistics and Systematics of Limb Anomaly Detections in HST/STIS Transit Images of Europa

Several recent studies derived the existence of plumes on Jupiter’s moon Europa. The only technique that provided multiple detections is the far-ultraviolet imaging observations of Europa in transit of Jupiter taken by the Space Telescope Imaging Spectrograph (STIS) on the Hubble Space Telescope (HST). In this study, we reanalyze the three HST/STIS transit images in which Sparks et al. identified limb anomalies as evidence for Europa’s plume activity. After reproducing the results of Sparks et al., we find that positive outliers are similarly present in the images as the negative outliers that were attributed to plume absorption. A physical explanation for the positive outliers is missing. We then investigate the systematic uncertainties and statistics in the images and identify two factors that are crucial when searching for anomalies around the limb. One factor is the alignment between the actual and assumed locations of Europa on the detector. A misalignment introduces distorted statistics, most strongly affecting the limb above the darker trailing hemisphere where the plumes were detected. The second factor is a discrepancy between the observation and the model used for comparison, adding uncertainty in the statistics. When accounting for these two factors, the limb minima (and maxima) are consistent with random statistical occurrence in a sample size given by the number of pixels in the analyzed limb region. The plume candidate features in the three analyzed images can be explained by purely statistical fluctuations and do not provide evidence for absorption by plumes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

A Systematic Search for Outbursting AM CVn Systems with the Zwicky Transient Facility

AM CVn systems are a rare type of accreting binary that consists of a white dwarf and a helium-rich, degenerate donor star. Using the Zwicky Transient Facility (ZTF), we searched for new AM CVn systems by focusing on blue, outbursting stars. We first selected outbursting stars using the ZTF alerts. We cross matched the candidates with Gaia and Pan-STARRS catalogs. The initial selection of candidates based on the Gaia BP-RP contains 1751 unknown objects. We used the Pan-STARRS g-r and r-i color in combination with the Gaia color to identify 59 strong AM CVn candidates. We obtained identification spectra of 35 sources, of which 18 are high-priority candidates, and discovered nine new AM CVn systems and one magnetic CV that shows only He-ii lines. Using the outburst recurrence time, we estimate the orbital periods of the nine new AM CVn systems that are in the range of 29–50 minutes. We conclude that targeted follow up of blue, outbursting sources is an efficient method to find new AM CVn systems and we plan to follow up all candidates we identified to systematically study the population of outbursting AM CVn systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Systematic KMTNet Planetary Anomaly Search. I. OGLE-2019-BLG-1053Lb, a Buried Terrestrial Planet

In order to exhume the buried signatures of “missing planetary caustics” in Korea Microlensing Telescope Network (KMTNet) data, we conducted a systematic anomaly search of the residuals from point-source point-lens fits, based on a modified version of the KMTNet EventFinder algorithm. This search revealed the lowest-mass-ratio planetary caustic to date in the microlensing event OGLE-2019-BLG-1053, for which the planetary signal had not been noticed before. The planetary system has a planet–host mass ratio of q = (1.25 ± 0.13) × 10{sup -5}. A Bayesian analysis yielded estimates of the mass of the host star, M{sub host}=0.61{sub -0.24}{sup +0.29} M{sub ⊙}, the mass of its planet, M{sub planet}=2.48{sub -0.98}{sup +1.19} M{sub ⊕}, the projected planet–host separation, a{sub ⊥}=3.4{sub -0.5}{sup +0.5} au, and the lens distance, D{sub L}=6.8{sub -0.9}{sup +0.6} kpc. The discovery of this very-low-mass-ratio planet illustrates the utility of our method and opens a new window for a large and homogeneous sample to study the microlensing planet–host mass ratio function down to q ~ 10{sup -5}.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

A Systematic Analysis of Stellar Populations in the Host Galaxies of Changing-look AGNs

“Changing-look” active galactic nuclei (CL-AGNs) are a newly discovered class of AGNs that show the appearance (or disappearance) of broad emission lines within short timescales (months to years),and are often associated with dramatic changes in their continuum emissions. They provide us with an unprecedented chance to directly investigate the host galaxy properties with minimal contamination from the luminous central engine during the turn-off state, which is difficult for normal luminous AGNs. In this work, for the first time, we systematically characterize the stellar populations and star formation histories of host galaxies for 26 turn-off CL-AGNs using the stellar population synthesis code STARLIGHT. We find that the stellar populations of CL-AGNs are similar to those of normal AGNs, except that the intermediate stellar populations contribute more fractions. We estimate their stellar velocity dispersions (σ * ) and black hole masses (M BH , vir ), and find that CL-AGNs also follow the overall M BH –σ * relationship. We also confirm the previous claims that CL-AGNs tend to be biased toward lower Eddington ratios, and that their extreme variabilities are more likely due to the intrinsic changes of the accretion rates. In addition, CL-AGNs with recent star formations tend to have higher Eddington ratios. Compared with previous studies, our analysis suggests that there may be a correlation between CL-AGN host galaxy properties and their CL phenomena.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The Atacama Cosmology Telescope: Systematic Transient Search of 3 Day Maps

We conduct a systematic search for transients in 3 yr of data (2017–2019) from the Atacama Cosmology Telescope (ACT). ACT covers 40% of the sky at three bands spanning from 77–277 GHz. Analysis of 3 day mean-subtracted sky maps, which were match filtered for point sources, yielded 29 transient detections. Eight of these transients are due to known asteroids, and three others were previously published. Four of these events occur in areas with poor noise models and thus we cannot be confident they are real transients. We are left with 14 new transient events occurring at 11 unique locations. All of these events are associated with either rotationally variable stars or cool stars. Ten events have flat or falling spectra indicating radiation from synchrotron emission. One event has a rising spectrum indicating a different engine for the flare.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The Atacama Cosmology Telescope: Systematic Transient Search of Single Observation Maps

We conduct a systematic search for astrophysical transients using data from the Atacama Cosmology Telescope. The data were taken from 2017 to 2022 in three frequency bands spanning 77 to 277 GHz. In this paper, we present a pipeline for transient detection using single-observation maps where each pixel of a map contains one observation with an integration time of approximately 4 minutes. We detect 34 transient events at 27 unique locations. All but two of the transients are associated with Galactic stars and exhibit a wide range of properties. We also detect an event coincident with the classical nova YZ Ret and one event consistent with a flaring active galactic nucleus. We notably do not detect any reverse shock emission from gamma-ray bursts, a nondetection that may be in tension with current models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Type Ia Supernova Growth-rate Measurement with LSST Simulations: Intrinsic Scatter Systematics

Measurement of the growth rate of structures (fσ 8 ) with Type Ia supernovae (SNe Ia) will improve our understanding of the nature of dark energy and enable tests of general relativity. In this paper, we generate simulations of the 10 yr SN Ia data set of the Rubin-LSST survey, including a correlated velocity field from an N-body simulation and realistic models of SNe Ia properties and their correlations with host-galaxy properties. We find, similar to SN Ia analyses that constrain the dark energy equation-of-state parameters w 0 w a , that constraints on fσ 8 can be biased depending on the intrinsic scatter of SNe Ia. While for the majority of intrinsic scatter models we recover fσ 8 with a precision of ∼13%–14%, for the most realistic dust-based model, we find that the presence of non-Gaussianities in Hubble diagram residuals leads to a bias on fσ 8 of ∼ −20%. When trying to correct for the dust-based intrinsic scatter, we find that the propagation of the uncertainty on the model parameters does not significantly increase the error on fσ 8 . We also find that while the main component of the error budget of fσ 8 is the statistical uncertainty (>75% of the total error budget), the systematic error budget is dominated by the uncertainty on the damping parameter, σ u , that gives an empirical description of the effect of redshift space distortions on the velocity power spectrum. Our results motivate a search for new methods to correct for the non-Gaussian distribution of the Hubble diagram residuals, as well as an improved modeling of the damping parameter.

Carreres, Bastien [Duke Univ., Durham, NC (United ↗
DOE OSTI2024

From Feast to Famine: A Systematic Study of Accretion onto Oblique Pulsars with 3D GRMHD Simulations

Disk-fed accretion onto neutron stars can power a wide range of astrophysical sources ranging from X-ray binaries, to accretion-powered millisecond pulsars, ultraluminous X-ray sources, and gamma-ray bursts. A crucial parameter controlling the gas–magnetosphere interaction is the strength of the stellar dipole. In addition, coherent X-ray pulsations in many neutron star systems indicate that the star's dipole moment is oblique relative to its rotation axis. Therefore, it is critical to systematically explore the 2D parameter space of the star's magnetic field strength and obliquity, which is what this work does, for the first time, in the framework of 3D general-relativistic magnetohydrodynamics. If the accretion disk carries its own vertical magnetic field, this introduces an additional factor: the relative polarity of the disk and stellar magnetic fields. We find that depending on the strength of the stellar dipole and the star–disk relative polarity, the neutron star's jet power can either increase or decrease with increasing obliquity. For weak dipole strength (equivalently, high accretion rate), the parallel polarity results in a positive correlation between jet power and obliquity, whereas the antiparallel orientation displays the opposite trend. For stronger dipoles, the relative-polarity effect disappears, and jet power always decreases with increasing obliquity. The influence of the relative polarity gradually disappears as obliquity increases. Highly oblique pulsars tend to have an increased magnetospheric radius, a lower mass accretion rate, and enter the propeller regime at lower magnetic moments than aligned stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Systematic and objective evaluation of Earth system models: PCMDI Metrics Package (PMP) version 3

Systematic, routine, and comprehensive evaluation of Earth system models (ESMs) facilitates benchmarking improvement across model generations and identifying the strengths and weaknesses of different model configurations. By gauging the consistency between models and observations, this endeavor is becoming increasingly necessary to objectively synthesize the thousands of simulations contributed to the Coupled Model Intercomparison Project (CMIP) to date. The Program for Climate Model Diagnosis and Intercomparison (PCMDI) Metrics Package (PMP) is an open-source Python software package that provides quick-look objective comparisons of ESMs with one another and with observations. The comparisons include metrics of large- to global-scale climatologies, tropical inter-annual and intra-seasonal variability modes such as the El Niño–Southern Oscillation (ENSO) and Madden–Julian Oscillation (MJO), extratropical modes of variability, regional monsoons, cloud radiative feedbacks, and high-frequency characteristics of simulated precipitation, including its extremes. The PMP comparison results are produced using all model simulations contributed to CMIP6 and earlier CMIP phases. An important objective of the PMP is to document the performance of ESMs participating in the recent phases of CMIP, together with providing version-controlled information for all datasets, software packages, and analysis codes being used in the evaluation process. Among other purposes, this also enables modeling groups to assess performance changes during the ESM development cycle in the context of the error distribution of the multi-model ensemble. Quantitative model evaluation provided by the PMP can assist modelers in their development priorities. In this paper, we provide an overview of the PMP, including its latest capabilities, and discuss its future direction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

A Systematic Framework for Tuning Open-Source Multifunctional IBR Models To Emulate OEM Black-Box Fault Dynamics

This paper presents a systematic framework to tune a generic IBR EMT model to match with an OEM provided balckbox inverter model based on the fault current responses. The key learnings and findings are summarized as follows: The tunable key parameters include inner control loops and current limiters to align the fault current magnitude, sequence content, and phase trajectories with the OEM models across diverse fault type and locations. The tuned model's fidelity is validated through comparative analysis with an OEM blackbox model, assessing both the fault current response and the responses of multiple relay elements. The results demonstrate the tuned generic model can trigger relay decision logic that is identical or near identical to that of the OEM model, thus generating very good match model for fault studies.

24 POWER TRANSMISSION AND DISTRIBUTION↗