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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy

Tuberculosis (TB) is the world’s deadliest infectious disease, with over 1.5 million deaths and 10 million new cases reported anually. The causative organism Mycobacterium tuberculosis (Mtb) can take nearly 40 d to culture, a required step to determine the pathogen’s antibiotic susceptibility. Both rapid identification and rapid antibiotic susceptibility testing of Mtb are essential for effective patient treatment and combating antimicrobial resistance. Here, we demonstrate a rapid, culture-free, and antibiotic incubation-free drug susceptibility test for TB using Raman spectroscopy and machine learning. We collect few-to-single-cell Raman spectra from over 25,000 cells of the Mtb complex strain Bacillus Calmette-Guérin (BCG) resistant to one of the four mainstay anti-TB drugs, isoniazid, rifampicin, moxifloxacin, and amikacin, as well as a pan-susceptible wildtype strain. By training a neural network on this data, we classify the antibiotic resistance profile of each strain, both on dried samples and on patient sputum samples. On dried samples, we achieve >98% resistant versus susceptible classification accuracy across all five BCG strains. In patient sputum samples, we achieve ~79% average classification accuracy. We develop a feature recognition algorithm in order to verify that our machine learning model is using biologically relevant spectral features to assess the resistance profiles of our mycobacterial strains. Finally, we demonstrate how this approach can be deployed in resource-limited settings by developing a low-cost, portable Raman microscope that costs <$5,000. We show how this instrument and our machine learning model enable combined microscopy and spectroscopy for accurate few-to-single-cell drug susceptibility testing of BCG.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Probing Systematic Bias in Low-redshift Type Ia Supernova Measurements by Cross Analyzing Surface Brightness and Hubble Residuals

For low-redshift (z < 0.1) SN Ia samples used in several cosmological analyses over the past decade, we probe for systematic bias by looking for correlations between surface brightness (SB) measurements and Hubble residuals (HR). For 292 SNe Ia, we measure SB at the location of the SN Ia from publicly available Pan-STARRS (PS1) images. The Hubble residuals are from two recent measurements with low-z SNe Ia that overlap the PS1 footprint: (1) the DES 3 yr cosmology analysis, with 120 overlapping low-z SNe Ia from the Harvard-Smithsonian Center for Astrophysics surveys and Carnegie Supernova Project, and (2) the PS1 single-telescope analysis, with 172 overlapping low-z SNe Ia from the Foundation Supernova Survey. This study is motivated by previous reports of anomalous inefficiencies and flux scatter for transients on bright galaxies. Here, we compare HR distributions of the bright and faint halves of the SB distribution: the mean HR values differ by ${\rm{\Delta }}\overline{\mathrm{HR}}$ = 0.031 ± 0.018, consistent with no difference at the 2σ level. We also perform a Kolmogorov–Smirnov (KS) test for the bright and faint half HR distributions, and conclude that the two distributions are statistically consistent with a KS p-value of 0.07. However, if future studies with larger data sets find ${\rm{\Delta }}\overline{\mathrm{HR}}\sim 0.03$ with high significance, this difference would be a leading systematic uncertainty in measurements of the dark energy equation of state, w.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Thoughts on the Kibble–Robinson theory

We revisit the Kibble–Robinson theory, first proposed in 2014 by Kibble and Robinson. This theory significantly simplifies the construction and operation of Kibble balances. We conducted a theoretical investigation of the theory’s assumptions, using a corner cube as the optical target in the interferometer for velocity measurement. We find that it is advantageous to build a mechanism whose output has minimal rotation and horizontal motion. For balances with relative uncertainty targets below $1\times10^{-6}$, the mass pan and the optical target should be suspended from a common gimbal so they have the same vertical velocity and no rotation. In this case, the measurement bias due to Abbe offset is minimized, and the bias due to corner loading is repeatable.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Pronounced and unavoidable impacts of low-end global warming on northern high-latitude land ecosystems

Arctic ecosystems are particularly vulnerable to climate change because of Arctic amplification. Here, we assessed the climatic impacts of low-end, 1.5 °C, and 2.0 °C global temperature increases above pre-industrial levels, on the warming of terrestrial ecosystems in northern high latitudes (NHL, above 60 °N including pan-Arctic tundra and boreal forests) under the framework of the Inter-Sectoral Impact Model Intercomparison Project phase 2b protocol. We analyzed the simulated changes of net primary productivity, vegetation biomass, and soil carbon stocks of eight ecosystem models that were forced by the projections of four global climate models and two atmospheric greenhouse gas pathways (RCP2.6 and RCP6.0). Our results showed that considerable impacts on ecosystem carbon budgets, particularly primary productivity and vegetation biomass, are very likely to occur in the NHL areas. The models agreed on increases in primary productivity and biomass accumulation, despite considerable inter-model and inter-scenario differences in the magnitudes of the responses. The inter-model variability highlighted the inadequacies of the present models, which fail to consider important components such as permafrost and wildfire. The simulated impacts were attributable primarily to the rapid temperature increases in the NHL and the greater sensitivity of northern vegetation to warming, which contrasted with the less pronounced responses of soil carbon stocks. The simulated increases of vegetation biomass by 30–60 Pg C in this century have implications for climate policy such as the Paris Agreement. Comparison between the results at two warming levels showed the effectiveness of emission reductions in ameliorating the impacts and revealed unavoidable impacts for which adaptation options are urgently needed in the NHL ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Shallow soils are warmer under trees and tall shrubs across Arctic and Boreal ecosystems

Soils are warming as air temperatures rise across the Arctic and Boreal region concurrent with the expansion of tall-statured shrubs and trees in the tundra. Changes in vegetation structure and function are expected to alter soil thermal regimes, thereby modifying climate feedbacks related to permafrost thaw and carbon cycling. However, current understanding of vegetation impacts on soil temperature is limited to local or regional scales and lacks the generality necessary to predict soil warming and permafrost stability on a pan-Arctic scale. Here we synthesize shallow soil and air temperature observations with broad spatial and temporal coverage collected across 106 sites representing nine different vegetation types in the permafrost region. We showed ecosystems with tall-statured shrubs and trees (> 40 cm) have warmer shallow soils than those with short-statured tundra vegetation when normalized to a constant air temperature. In tree and tall shrub vegetation types, cooler temperatures in the warm season do not lead to cooler mean annual soil temperature indicating that ground thermal regimes in the cold-season rather than the warm-season are most critical for predicting soil warming in ecosystems underlain by permafrost. Our results suggest that the expansion of tall shrubs and trees into tundra regions can amplify shallow soil warming, and could increase the potential for increased seasonal thaw depth and increase soil carbon cycling rates and lead to increased carbon dioxide loss and further permafrost thaw.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Variability in terrestrial characteristics and erosion rates on the Alaskan Beaufort Sea coast

Abstract Arctic coastal environments are eroding and rapidly changing. A lack of pan-Arctic observations limits our ability to understand controls on coastal erosion rates across the entire Arctic region. Here, we capitalize on an abundance of geospatial and remotely sensed data, in addition to model output, from the North Slope of Alaska to identify relationships between historical erosion rates and landscape characteristics to guide future modeling and observational efforts across the Arctic. Using existing datasets from the Alaska Beaufort Sea coast and a hierarchical clustering algorithm, we developed a set of 16 coastal typologies that captures the defining characteristics of environments susceptible to coastal erosion. Relationships between landscape characteristics and historical erosion rates show that no single variable alone is a good predictor of erosion rates. Variability in erosion rate decreases with increasing coastal elevation, but erosion rate magnitudes are highest for intermediate elevations. Areas along the Alaskan Beaufort Sea coast (ABSC) protected by barrier islands showed a three times lower erosion rate on average, suggesting that barrier islands are critical to maintaining mainland shore position. Finally, typologies with the highest erosion rates are not broadly representative of the ABSC and are generally associated with low elevation, north- to northeast-facing shorelines, a peaty pebbly silty lithology, and glaciomarine deposits with high ice content. All else being equal, warmer permafrost is also associated with higher erosion rates, suggesting that warming permafrost temperatures may contribute to higher future erosion rates on permafrost coasts. The suite of typologies can be used to guide future modeling and observational efforts by quantifying the distribution of coastlines with specific landscape characteristics and erosion rates.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A variant selection framework for genome graphs

Abstract Motivation Variation graph representations are projected to either replace or supplement conventional single genome references due to their ability to capture population genetic diversity and reduce reference bias. Vast catalogues of genetic variants for many species now exist, and it is natural to ask which among these are crucial to circumvent reference bias during read mapping. Results In this work, we propose a novel mathematical framework for variant selection, by casting it in terms of minimizing variation graph size subject to preserving paths of length α with at most δ differences. This framework leads to a rich set of problems based on the types of variants [e.g. single nucleotide polymorphisms (SNPs), indels or structural variants (SVs)], and whether the goal is to minimize the number of positions at which variants are listed or to minimize the total number of variants listed. We classify the computational complexity of these problems and provide efficient algorithms along with their software implementation when feasible. We empirically evaluate the magnitude of graph reduction achieved in human chromosome variation graphs using multiple α and δ parameter values corresponding to short and long-read resequencing characteristics. When our algorithm is run with parameter settings amenable to long-read mapping (α = 10 kbp, δ = 1000), 99.99% SNPs and 73% SVs can be safely excluded from human chromosome 1 variation graph. The graph size reduction can benefit downstream pan-genome analysis. Availability and implementation https://github.com/AT-CG/VF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Biosurfactant production by halophilic yeasts isolated from extreme environments in Botswana

ABSTRACT Nine morphologically distinct halophilic yeasts were isolated from Makgadikgadi and Sua pans, as pristine and extreme environments in Botswana. Screening for biosurfactant production showed that Rhodotorula mucilaginosa SP6 and Debaryomyces hansenii MK9 exhibited the highest biosurfactant activity using Xanthocercis zambesiaca seed powder as a novel and alternative inexpensive carbon substrate. Chemical characterization of the purified biosurfactants by Fourier Transform Infra-Red spectroscopy suggested that the biosurfactant from R. mucilaginosa SP6 was a rhamnolipid-type whereas the biosurfactant from D. hansenii MK9 was a sophorolipid-type. The two biosurfactants exhibited antimicrobial activities against eight pathogenic bacteria and fungal strains (Proteus vulgaris, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Micrococcus luteus, Cryptococcus neoformans, Candida albicans and Aspergilus niger). The sophorolopid-type biosurfactant was found to be the most potent among the antimicrobial drug resistant strains tested. The findings open up prospects for the development of environmentally friendly antimicrobial drugs that use an inexpensive source of carbon to reduce the costs associated with the production of biosurfactants.

Loeto, Daniel↗
DOE OSTI2023

Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates

Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. Here, we isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic “Toomer's Oak,” this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

Quercus virginiana↗
DOE OSTI2020

From the inner to outer Milky Way: a photometric sample of 2.6 million red clump stars

ABSTRACT Large pristine samples of red clump stars are highly sought after given that they are standard candles and give precise distances even at large distances. However, it is difficult to cleanly select red clumps stars because they can have the same Teff and log g as red giant branch stars. Recently, it was shown that the asteroseismic parameters, $\rm {\Delta }$P and $\rm {\Delta \nu }$, which are used to accurately select red clump stars, can be derived from spectra using the change in the surface carbon to nitrogen ratio ([C/N]) caused by mixing during the red giant branch. This change in [C/N] can also impact the spectral energy distribution. In this study, we predict the $\rm {\Delta }$P, $\rm {\Delta \nu }$, Teff, and log g using 2MASS, AllWISE, Gaia, and Pan-STARRS data in order to select a clean sample of red clump stars. We achieve a contamination rate of ∼20 per cent, equivalent to what is achieved when selecting from Teff and log g derived from low-resolution spectra. Finally, we present two red clump samples. One sample has a contamination rate of ∼20 per cent and ∼405 000 red clump stars. The other has a contamination of ∼33 per cent and ∼2.6 million red clump stars that includes ∼75 000 stars at distances >10 kpc. For |b| > 30 deg, we find ∼15 000 stars with contamination rate of ∼9 per cent. The scientific potential of this catalogue for studying the structure and formation history of the Galaxy is vast, given that it includes millions of precise distances to stars in the inner bulge and distant halo where astrometric distances are imprecise.

Lucey, Madeline↗
DOE OSTI2020

First discovery of an ultra-cool white dwarf benchmark in common proper motion with an M dwarf

Ultra-cool white dwarfs are among the oldest stellar remnants in the Universe. Their efficient gravitational settling and low effective temperatures are responsible for the smooth spectra they exhibit. For that reason, it is not possible to derive their radial velocities or to find the chemistry of the progenitors. The best that can be done is to infer such properties from associated sources, which are coeval. The simplest form of such a system is a common proper motion pair where one star is an evolved degenerate and the other a main-sequence star. Herein, we present the discovery of the first of such a system, the M dwarf LHS 6328 and the ultra-cool white dwarf PSO J1801+625, from the Pan-STARRS 1 3π survey and the Gaia Data Release 2. Follow-up spectra were collected covering a usable wavelength range of 3750–24 500 Å. Their spectra show that the white dwarf has an effective temperature of 3550 K and surface gravity of log $g$ = 7.45 ± 0.13 or log $g$ = 7.49 ± 0.13 for a CO or He core, respectively, when compared against synthetic spectra of ultra-cool white dwarf atmosphere models. The system has slightly subsolar metallicity with -0.25 < [Fe/H] < 0.0, and a spatial velocity of (U, V, W) = (-114.26 ± 0.24, 222.94 ± 0.60, 10.25 ± 0.34) km s -1 , the first radial velocity and metallicity measurements of an ultra-cool white dwarf. This makes it the first and only benchmark of its kind to date.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Subaru Hyper Suprime-Cam Survey of Cygnus OB2 Complex – I. Introduction, photometry, and source catalogue

ABSTRACT Low-mass star formation inside massive clusters is crucial to understand the effect of cluster environment on processes like circumstellar disc evolution, planet, and brown dwarf formation. The young massive association of Cygnus OB2, with a strong feedback from massive stars, is an ideal target to study the effect of extreme environmental conditions on its extensive low-mass population. We aim to perform deep multiwavelength studies to understand the role of stellar feedback on the IMF, brown dwarf fraction and circumstellar disc properties in the region. We introduce here, the deepest and widest optical photometry of 1.5○ diameter region centred at Cygnus OB2 in r2, i2, z, and Y-filters, using Subaru Hyper Suprime-Cam (HSC). This work presents the data reduction, source catalogue generation, data quality checks, and preliminary results about the pre-main sequence sources. We obtain 713 529 sources in total, with detection down to ∼28, 27, 25.5, and 24.5 mag in r2, i2, z, and Y-band, respectively, which is ∼3 – 5 mag deeper than the existing Pan-STARRS and GTC/OSIRIS photometry. We confirm the presence of a distinct pre-main sequence branch by statistical field subtraction of the central 18 arcmin region. We find the median age of the region as ∼5 ± 2 Myr with an average disc fraction of ∼9 per cent. At this age, combined with A $_V\, \sim$ 6 – 8 mag, we detect sources down to a mass range of ∼0.01–0.17 M⊙. The deep HSC catalogue will serve as the groundwork for further studies on this prominent active young cluster.

Gupta, Saumya (ORCID:0000000161843958)↗
DOE OSTI2021

Discovery of two bright high-redshift gravitationally lensed quasars revealed by Gaia

We present the discovery and preliminary characterisation of two high-redshift gravitationally lensed quasar systems in Gaia Data Release 2 (DR2). Candidates with multiple close-separation Gaia detections and quasar-like colours in WISE, Pan-STARRS, and DES are selected for follow-up spectroscopy with the New Technology Telescope. We confirm DES J215028.71-465251.3 as a $z$ = 4.130 ± 0.006 asymmetric, doubly imaged lensed quasar system and model the lensing mass distribution as a singular isothermal sphere. The system has an Einstein radius of 1.202 ± 0.005 arcsec and a predicted time delay of ~122.0 d between the quasar images, assuming a lensing galaxy redshift of $z$ = 0.5, making this a priority system for future optical monitoring. We confirm PS J042913.17+142840.9 as a $z$ = 3.866 ± 0.003 four-image quasar system in a cusp configuration, lensed by two foreground galaxies. The system is well modelled using a singular isothermal ellipsoid for the primary lens and a singular isothermal sphere for the secondary lens with Einstein radii 0.704 ± 0.006 and 0.241 ± 0.030 arcsec, respectively. A maximum predicted time delay of 9.6 d is calculated, assuming lensing galaxy redshifts of $z$ = 1.0. Furthermore, PS J042913.17+142840.9 exhibits a large flux ratio anomaly, up to a factor of 2.66 ± 0.37 in i band, that varies across optical and near-infrared wavelengths. We discuss LSST and its implications for future high-redshift lens searches and outline an extension to the search using supervised machine learning techniques.

Astronomy & Astrophysics↗
DOE OSTI2022

Four new deeply eclipsing white dwarfs in Zwicky Transient Facility

ABSTRACT We present the results of a search for deeply eclipsing white dwarfs in the Zwicky Transient Facility (ZTF) Data Release 4 (DR4). We identify nine deeply eclipsing white dwarf candidates, four of which we followed up with high-cadence photometry and spectroscopy. Three of these systems show total eclipses in the ZTF data and our follow-up Apache Point Observatory 3.5 m telescope observations. Even though the eclipse duration is consistent with sub-stellar companions, our analysis shows that all four systems contain a white dwarf with low-mass stellar companions of ∼0.1 M⊙. We provide mass and radius constraints for both stars in each system based on our photometric and spectroscopic fitting. Finally, we present a list of 41 additional eclipsing WD+M candidates identified in a preliminary search of ZTF DR7, including 12 previously studied systems. We identify two new candidate short-period, eclipsing, white dwarf–brown dwarf binaries within our sample of 41 WD+M candidates based on Pan-STARRS colours.

Kosakowski, A. (ORCID:0000000298781647)↗
DOE OSTI2022

Uniform modelling of the stellar density of thirteen tidal streams within the Galactic halo

ABSTRACT We present the results of fitting a flexible stellar stream density model to a collection of thirteen streams around the Milky Way, using photometric data from DES, DECaLS, and Pan-STARRS. We construct density maps for each stream and characterize their tracks on the sky, width, and distance modulus curves along the length of each stream. We use these measurements to compute lengths and total luminosities of streams and identify substructures. Several streams show prominent substructures, such as stream broadening, gaps, large deviations of stream tracks, and sharp changes in stream densities. Examining the group of streams as a population, as expected we find that streams with globular cluster progenitors are typically narrower than those with dwarf galaxy progenitors, with streams around 100 pc wide showing overlap between the two populations. We also note the average luminosity of globular cluster streams is significantly lower than the typical luminosity of intact globular clusters. The likely explanation is that observed globular cluster streams preferentially come from lower luminosity and lower density clusters. The stream measurements done in a uniform manner presented here will be helpful for more detailed stream studies such as identifying candidate stream members for spectroscopic follow up and stellar stream dynamical modelling.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Discovering vanishing objects in POSS I red images using the Virtual Observatory

ABSTRACT In this paper, we report a search for vanishing sources in POSS I red images using virtual observatory (VO) archives, tools, and services. The search, conducted in the framework of the VASCO project, aims at finding POSS I (red) sources not present in recent catalogues like Pan-STARRS DR2 (limiting magnitude r = 21.4) or Gaia EDR3 (limiting magnitude G = 21). We found 298 165 sources visible only in POSS I plates, out of which 288 770 had a cross-match within 5 arcsec in other archives (mainly in the infrared), 189 were classified as asteroids, 35 as variable objects, 3592 as artefacts from the comparison to a second digitization (Supercosmos), and 180 as high proper motion objects without information on proper motion in Gaia EDR3. The remaining unidentified transients (5399) as well as the 172 163 sources not detected in the optical but identified in the infrared regime are available from a VO compliant archive and can be of interest in searches for strong M-dwarf flares, high-redshift supernovae, asteroids, or other categories of unidentified red transients. No point sources were detected by both POSS-I and POSS-II before vanishing, setting the rate of failed supernovae in the Milky Way during 70 yr to less than one in one billion.

Solano, Enrique↗