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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Fast optical transport of ultracold molecules over long distances

Abstract Optically trapped laser-cooled polar molecules hold promise for new science and technology in quantum information and quantum simulation. Large numerical aperture optical access and long trap lifetimes are needed for many studies, but these requirements are challenging to achieve in a magneto-optical trap (MOT) vacuum chamber that is connected to a cryogenic buffer gas beam source, as is the case for all molecule laser cooling experiments so far. Long distance transport of molecules greatly eases fulfilling these requirements as molecules are placed into a region separate from the MOT chamber. We realize a fast transport method for ultracold molecules based on an electronically focus-tunable lens combined with an optical lattice. The high transport speed is achieved by the 1D red-detuned optical lattice, which is generated by interference of a focus-tunable laser beam and a focus-fixed laser beam. Efficiency of 48(8)% is realized in the transport of ultracold calcium monofluoride (CaF) molecules over 46 cm distance in 50 ms, with a moderate heating from 32(2) μ K to 53(4) μ K. Positional stability of the molecular cloud allows for stable loading of an optical tweezer array with single molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Inference of experimental radial impurity transport on Alcator C-Mod: Bayesian parameter estimation and model selection

We present a fully Bayesian approach for the inference of radial profiles of impurity transport coefficients and compare its results to neoclassical, gyrofluid and gyrokinetic modeling. Using nested sampling, the Bayesian Impurity Transport InferencE (BITE) framework can handle complex parameter spaces with multiple possible solutions, offering great advantages in interpretative power and reliability with respect to previously demonstrated methods. BITE employs a forward model based on the pySTRAHL package, built on the success of the well-known STRAHL code [Dux, IPP Report, 2004], to simulate impurity transport in magnetically-confined plasmas. In this paper, we focus on calcium (Ca, Z=20) Laser Blow-Off injections into Alcator C-Mod plasmas. Multiple Ca atomic lines are diagnosed via high-resolution X-ray Imaging Crystal Spectroscopy and Vacuum Ultra-Violet measurements. We analyze a sawtoothing I-mode discharge for which neoclassical and turbulent (quasilinear and nonlinear) predictions are also obtained. Here, we find good agreement in diffusion across the entire radial extent, while turbulent convection and density profile peaking are estimated to be larger in experiment than suggested by theory. Efforts and challenges associated with the inference of experimental pedestal impurity transport are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Accuracy of Thermodynamic Databases for Hydroxyapatite Dissolution Constant

We report that discrepancies have been noted in the solubility constant values of calcium phosphate minerals between various databases employed in widely-used aqueous speciation calculation software programs. This can cause serious errors in the calculated speciation of waters using these software programs. The aim of the present communication was to bring to light these discrepancies. Experimental determinations of the hydroxyapatite solubility product vary by as much as ten orders of magnitude as a result of experimental challenges related to the presence of impurities in the hydroxyapatite used, incongruent dissolution and the contamination of solutions with dissolved carbon dioxide. Finally, it is suggested that the value used in the database Thermo.dat is consistent with experimental data devoid of common experimental problems, while other common databases use values that lead to a vastly overestimated solubility of hydroxyapatite.

58 GEOSCIENCES↗
DOE OSTI2022

Integrating multimodal data through interpretable heterogeneous ensembles

Motivation: Integrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems. Results: We propose Ensemble Integration (EI) as a novel systematic implementation of the late integration approach. EI infers local predictive models from the individual data modalities using appropriate algorithms and uses heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data and mortality due to coronavirus disease 2019 (COVID-19) from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of a representative EI model for COVID-19 mortality prediction identified several disease-relevant features, such as laboratory test (blood urea nitrogen and calcium) and vital sign measurements (minimum oxygen saturation) and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Lipoprotein(a) is associated with the onset but not the progression of aortic valve calcification

Abstract Aim Lipoprotein(a) [Lp(a)] is a potential causal factor in the pathogenesis of aortic valve disease. However, the relationship of Lp(a) with new onset and progression of aortic valve calcium (AVC) has not been studied. The purpose of the study was to assess whether high serum levels of Lp(a) are associated with AVC incidence and progression. Methods and results A total of 922 individuals from the population-based Rotterdam Study (mean age 66.0±4.2 years, 47.7% men), whose Lp(a) measurements were available, underwent non-enhanced cardiac computed tomography imaging at baseline and after a median follow-up of 14.0 [interquartile range (IQR) 13.9–14.2] years. New-onset AVC was defined as an AVC score >0 on the follow-up scan in the absence of AVC on the first scan. Progression was defined as the absolute difference in AVC score between the baseline and follow-up scan. Logistic and linear regression analyses were performed to evaluate the relationship of Lp(a) with baseline, new onset, and progression of AVC. All analyses were corrected for age, sex, body mass index, smoking, hypertension, dyslipidaemia, and creatinine. AVC progression was analysed conditional on baseline AVC score expressed as restricted cubic splines. Of the 702 individuals without AVC at baseline, 415 (59.1%) developed new-onset AVC on the follow-up scan. In those with baseline AVC, median annual progression was 13.5 (IQR = 5.2–37.8) Agatston units (AU). Lipoprotein(a) concentration was independently associated with baseline AVC [odds ratio (OR) 1.43 for each 50 mg/dL higher Lp(a); 95% confidence interval (CI) 1.15–1.79] and new-onset AVC (OR 1.30 for each 50 mg/dL higher Lp(a); 95% CI 1.02–1.65), but not with AVC progression (β: −71 AU for each 50 mg/dL higher Lp(a); 95% CI −117; 35). Only baseline AVC score was significantly associated with AVC progression (P < 0.001). Conclusion In the population-based Rotterdam Study, Lp(a) is robustly associated with baseline and new-onset AVC but not with AVC progression, suggesting that Lp(a)-lowering interventions may be most effective in pre-calcific stages of aortic valve disease.

Kaiser, Yannick (ORCID:0000000168690042)↗
DOE OSTI2023

A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges

Abstract Calcareous sponges are an often overlooked element of sponge communities. In contrast to most other sponges, calcareous sponges produce calcium carbonate spicules, as opposed to the siliceous spicules of most sponges. Here, we investigated the bacterial communities of 17 sponge species, including type and paratype specimens of recently described calcareous species, sampled off the remote island of Rodrigues, in the Indian Ocean. The main axis of variation in a PCO analysis of all samples separated noncalcareous sponge species, including Axinyssa aplysinoides, Cinachyrella aff. australiensis, Petrosia seychellensis, Ircinia aff. variabilis, Spongia ceylonensis, Plakinastrella aff. clipptertonensis, Agelas aff. ceylonica, Agelas aff. mauritiana, and Hyrtios erectus from calcareous sponges, the noncalcareous Biemna tubulata, sediment, and seawater. Overall, the bacterial communities of calcareous sponges revealed unique prokaryotic profiles with low abundances of several bacterial phyla, and relatively high abundances of other taxa, for example, the phyla Fibrobacterota, Proteobacteria, and the SAR324 clade, the class Alphaproteobacteria, and orders Cytophagales and Cyanobacteriales, although there was considerable variation among species. Calcareous sponges also had a high dominance of unknown bacterial operational taxonomic units (OTUs). Considering the unique nature of these communities, further studies are needed to better understand the environmental and ecological drivers of calcareous sponge-associated bacterial communities and their relevance as potential sources of novel microbes of biotechnological interest.

Cleary, D. F. R. (ORCID:0000000261433390)↗
DOE OSTI2023

Grf10 regulates the response to copper, iron, and phosphate in Candida albicans

Abstract The pathogenic yeast, Candida albicans, and other microbes must be able to handle drastic changes in nutrient availability within the human host. Copper, iron, and phosphate are essential micronutrients for microbes that are sequestered by the human host as nutritional immunity; yet high copper levels are employed by macrophages to induce toxic oxidative stress. Grf10 is a transcription factor important for regulating genes involved in morphogenesis (filamentation, chlamydospore formation) and metabolism (adenylate biosynthesis, 1-carbon metabolism). The grf10Δ mutant exhibited resistance to excess copper in a gene dosage-dependent manner but grew the same as the wild type in response to other metals (calcium, cobalt, iron, manganese, and zinc). Point mutations in the conserved residues D302 and E305, within a protein interaction region, conferred resistance to high copper and induced hyphal formation similar to strains with the null allele. The grf10Δ mutant misregulated genes involved with copper, iron, and phosphate uptake in YPD medium and mounted a normal transcriptional response to high copper. The mutant accumulated lower levels of magnesium and phosphorus, suggesting that copper resistance is linked to phosphate metabolism. Our results highlight new roles for Grf10 in copper and phosphate homeostasis in C. albicans and underscore the fundamental role of Grf10 in connecting these with cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Pectin methylesterase selectively softens the onion epidermal wall yet reduces acid-induced creep

De-esterification of homogalacturonan (HG) is thought to stiffen pectin gels and primary cell walls by increasing calcium cross-linking between HG chains. Contrary to this idea, recent studies found that HG de-esterification correlated with reduced stiffness of living tissues, measured by surface indentation. The physical basis of such apparent wall softening is unclear, but possibly involves complex biological responses to HG modification. To assess the direct physical consequences of HG de-esterification on wall mechanics without such complications, we treated isolated onion (Allium cepa) epidermal walls with pectin methylesterase (PME) and assessed wall biomechanics with indentation and tensile tests. In nanoindentation assays, PME action softened the wall (reduced the indentation modulus). In tensile force/extension assays, PME increased plasticity, but not elasticity. These softening effects are attributed, at least in part, to increased electrostatic repulsion and swelling of the wall after PME treatment. Despite softening and swelling upon HG de-esterification, PME treatment alone failed to induce cell wall creep. Instead, acid-induced creep, mediated by endogenous α-expansin, was reduced. We conclude that HG de-esterification physically softens the onion wall, yet reduces expansin-mediated wall extensibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A leaf-level spectral library to support high-throughput plant phenotyping: predictive accuracy and model transfer

Abstract Leaf-level hyperspectral reflectance has become an effective tool for high-throughput phenotyping of plant leaf traits due to its rapid, low-cost, multi-sensing, and non-destructive nature. However, collecting samples for model calibration can still be expensive, and models show poor transferability among different datasets. This study had three specific objectives: first, to assemble a large library of leaf hyperspectral data (n=2460) from maize and sorghum; second, to evaluate two machine-learning approaches to estimate nine leaf properties (chlorophyll, thickness, water content, nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur); and third, to investigate the usefulness of this spectral library for predicting external datasets (n=445) including soybean and camelina using extra-weighted spiking. Internal cross-validation showed satisfactory performance of the spectral library to estimate all nine traits (mean R2=0.688), with partial least-squares regression outperforming deep neural network models. Models calibrated solely using the spectral library showed degraded performance on external datasets (mean R2=0.159 for camelina, 0.337 for soybean). Models improved significantly when a small portion of external samples (n=20) was added to the library via extra-weighted spiking (mean R2=0.574 for camelina, 0.536 for soybean). The leaf-level spectral library greatly benefits plant physiological and biochemical phenotyping, whilst extra-weight spiking improves model transferability and extends its utility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Abstract Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

The Pristine dwarf galaxy survey – IV. Probing the outskirts of the dwarf galaxy Boötes I

ABSTRACT We present a new spectroscopic study of the dwarf galaxy Boötes I (Boo I) with data from the Anglo-Australian Telescope and its AAOmega spectrograph together with the Two Degree Field multi-object system. We observed 36 high-probability Boo I stars selected using Gaia Early Data Release 3 proper motions and photometric metallicities from the Pristine survey. Out of those, 27 are found to be Boo I stars, resulting in an excellent success rate of 75 per cent at finding new members. Our analysis uses a new pipeline developed to estimate radial velocities and equivalent widths of the calcium triplet lines from Gaussian and Voigt line profile fits. The metallicities of 16 members are derived, including 3 extremely metal-poor stars ([Fe/H] < −3.0), which translates into a success rate of 25 per cent at finding them with the combination of Pristine and Gaia. Using the large spatial extent of our new members that spans up to 4.1 half-light radii and spectroscopy from the literature, we find a systemic velocity gradient of 0.40 ± 0.10 km s−1 arcmin−1 and a small but resolved metallicity gradient of −0.008 ± 0.003 dex arcmin−1. Finally, we show that Boo I is more elongated than previously thought with an ellipticity of ϵ = 0.68 ± 0.15. Its velocity and metallicity gradients as well as its elongation suggest that Boo I may have been affected by tides, a result supported by direct dynamical modelling.

Longeard, Nicolas↗
DOE OSTI2022

Discovering Ca II absorption lines with a neural network

Quasar absorption line analysis is critical for studying gas and dust components and their physical and chemical properties as well as the evolution and formation of galaxies in the early universe. Calcium II (Ca II ) absorbers, which are one of the dustiest absorbers and are located at lower redshifts than most other absorbers, are especially valuable when studying physical processes and conditions in recent galaxies. However, the number of known quasar Ca II absorbers is relatively low due to the difficulty of detecting them with traditional methods. In this work, we developed an accurate and quick approach to search for Ca II absorption lines using deep learning. In our deep learning model, a convolutional neural network, tuned using simulated data, is used for the classification task. The simulated training data are generated by inserting artificial Ca II absorption lines into original quasar spectra from the Sloan Digital Sky Survey (SDSS), while an existing Ca II catalogue is adopted as the test set. The resulting model achieves an accuracy of 96 per cent on the real data in the test set. Our solution runs thousands of times faster than traditional methods, taking a fraction of a second to analyse thousands of quasars, while traditional methods may take days to weeks. The trained neural network is applied to quasar spectra from SDSS’s DR7 and DR12 and discovered 399 new quasar Ca II absorbers. In addition, we confirmed 409 known quasar Ca II absorbers identified previously by other research groups through traditional methods.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Spectral analysis of ultra-cool white dwarfs polluted by planetary debris

ABSTRACT We identify two ultra-cool (${T_\mathrm{eff}}\lt 4000$ K) metal-polluted (DZ) white dwarfs WD J2147−4035 and WD J1922+0233 as the coolest and second coolest DZ stars known to date with ${T_\mathrm{eff}}\approx 3050$ K and ${T_\mathrm{eff}}\approx 3340$ K, respectively. Strong atmospheric collision-induced absorption (CIA) causes the suppression of red optical and infrared flux in WD J1922+0233, resulting in an unusually blue colour given its low temperature. WD J2147−4035 has moderate infrared CIA yet has the reddest optical colours known for a DZ white dwarf. Microphysics improvements to the non-ideal effects and CIA opacities in our model atmosphere code yields reasonable solutions to observations of these ultra-cool stars. WD J2147−4035 has a cooling age of over 10 Gyr which is the largest known for a DZ white dwarf, whereas WD J1922+0233 is slightly younger with a cooling age of 9 Gyr. Galactic kinematics calculations from precise Gaia EDR3 astrometry reveal these ultra-cool DZ stars as likely members of the Galactic disc thus they could be pivotal objects in future studies constraining an upper age limit for the disc of the Milky Way. We present intermediate-resolution spectroscopy for both objects, which provides the first spectroscopic observations of WD J2147−4035. Detections of sodium and potassium are made in both white dwarfs, in addition to calcium in WD J1922+0233 and lithium in WD J2147−4035. We identify the magnetic nature of WD J2147−4035 from Zeeman splitting in the lithium line and also make a tentative detection of carbon, so we classify this star as DZQH. WD J1922+0233 likely accreted planetary crust debris, while the debris composition that polluted WD J2147−4035 remains unconstrained.

Elms, Abbigail K. (ORCID:0000000176667416)↗
DOE OSTI2024

Measuring M31 globular cluster ages and metallicities using both photometry and spectroscopy

ABSTRACT The ages and metallicities of globular clusters play an important role not just in testing models for their formation and evolution but also in understanding the assembly history of their host galaxies. Here, we use a combination of imaging and spectroscopy to measure the ages and metallicities of globular clusters in M31, the closest massive galaxy to our own. We use the strength of the near-infrared calcium triplet spectral feature to provide a relatively age-insensitive prior on the metallicity when fitting stellar population models to the observed photometry. While the age–extinction degeneracy is an issue for globular clusters projected on to the disc of M31, we find generally old ages for globular clusters in the halo of M31 and in its satellite galaxy NGC 205 in line with previous studies. We measure ages for a number of outer halo globular clusters for the first time, finding that globular clusters associated with halo substructure extend to younger ages and higher metallicities than those associated with the smooth halo. This is in line with the expectation that the smooth halo was accreted earlier than the substructured halo.

Usher, Christopher (ORCID:0000000273837106)↗
DOE OSTI2024

Fermentation Practices Select for Thermostable Endolysins in Phages

Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Screening the complex biological behavior of late lanthanides through genome-wide interactions

Abstract Despite their similar physicochemical properties, recent studies have demonstrated that lanthanides can display different biological behaviors. Hence, the lanthanide series can be divided into three parts, namely early, mid, and late lanthanides, based on their interactions with biological systems. In particular, the late lanthanides demonstrate distinct, but poorly understood biological activity. In the current study, we employed genome-wide functional screening to help understand biological effects of exposure to Yb(III) and Lu(III), which were selected as representatives of the late lanthanides. As a model organism, we used Saccharomyces cerevisiae, since it shares many biological functions with humans. Analysis of the functional screening results indicated toxicity of late lanthanides is consistent with disruption of vesicle-mediated transport, and further supported a role for calcium transport processes and mitophagy in mitigating toxicity. Unexpectedly, our analysis suggested that late lanthanides target proteins with SH3 domains, which may underlie the observed toxicity. This study provides fundamental insights into the unique biological chemistry of late lanthanides, which may help devise new avenues toward the development of decorporation strategies and bio-inspired separation processes.

Pallares, Roger M. (ORCID:0000000174238706)↗
DOE OSTI2023

Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine

Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. Here, we show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanistic connection between Cu and Zn homeostasis. Transcriptomics, proteomics and elemental profiling revealed that Zn-limited Chlamydomonas cells up-regulate a subset of genes encoding “first responder” proteins involved in sulfur (S) assimilation and consequently accumulate more intracellular S, which is incorporated into L-cysteine, γ-glutamylcysteine, and homocysteine. Most prominently, in the absence of Zn, free L-cysteine is increased ~80-fold, corresponding to ~2.8 × 10 9 molecules/cell. Interestingly, classic S-containing metal binding ligands like glutathione and phytochelatins do not increase. X-ray fluorescence microscopy showed foci of S accumulation in Zn-limited cells that co-localize with Cu, phosphorus and calcium, consistent with Cu-thiol complexes in the acidocalcisome, the site of Cu(I) accumulation. Notably, cells that have been previously starved for Cu do not accumulate S or Cys, causally connecting cysteine synthesis with Cu accumulation. We suggest that cysteine is an in vivo Cu(I) ligand, perhaps ancestral, that buffers cytosolic Cu.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

URINARY EXCRETION OF PLUTONIUM IN MAYAK WORKERS DURING AND AFTER CA-DTPA ADMINISTRATION

Chelation therapy is sometimes used after potential exposures to plutonium to increase urinary excretion of the radionuclide to improve the accuracy of bioassay measurements. The purpose of this report is to describe the enhancement of urinary excretion of plutonium during and after the administration of the trisodium salt of calcium diethylenetriaminepentaacetate (Ca-DTPA) daily for 3 d to a group of male and female plutonium workers from the Mayak Production Association in Ozyorsk, Russia. One-hundred and two cases (18 females and 84 males) were selected where urinary contents of plutonium, prior to chelation, exceeded the detection threshold. Daily urine collections were obtained during the 3 d of Ca-DTPA treatments. In addition, 58 of these cases had urine bioassays at 1–45 d after chelation. The daily enhancement over baseline values excretion of plutonium was found to be 50.4×/1.4 (geometric mean and geometric standard deviation); 58.9×/1.2; 72.9×/1.4 in the first, second and third days of Ca-DTPA administration. The mean enhancement for the 3-d period was 60.1×/1.7. The rate of plutonium excretion from 1 to 45 d after chelation decreased with a half-period of 3.9 d and the chelation enhancement factor (Кenh-i) is described by the function Кenh-i = (0.79 ± 0.24) + (42.9 ± 1.2) × e-(0.18 ± 0.01) × day.

Environmental Sciences & Ecology↗