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At least 91 records · Page 5

Use of inelastic strain as a basis for analyzing thermomechanical test data

It was shown that the proposed data analysis method, based on inelastic strain-time response, can be used effectively to represent cyclic response at elevated temperatures for Hastelloy-X. A high level of confidence in this method was built by making comparisons of the experimental and fitted data in two forms. Because of this level of confidence, the analysis was taken one step further and inelastic strain rates were calculated from the derivatives of the fit equations.

Bartolotta, P. A.↗

Predictive models of the genetic bases underlying budding yeast fitness in multiple environments

Abstract The ability of organisms to adapt and survive depends on the effects of genes and the environment on fitness. However, the multigenic nature of fitness and genotype-by-environment interactions hinder our understanding of the genetic basis of fitness. Here, we established fitness prediction models for 35 environments using machine learning and existing fitness data and different genetic variant types for a Saccharomyces cerevisiae population. Models revealed that the predictive ability of genetic variants varied across environments, with copy number variants explaining the majority of fitness variation in most cases. Model interpretation showed that different variant types identified distinct gene sets associated with predictive variants. These gene sets were significantly enriched in experimentally validated genes affecting fitness in only a subset of environments, indicating that many genes influencing fitness remain unexplored. Notably, non-experimentally validated genes were more important than validated ones for fitness predictions. Gene contributions to predictions were both isolate- and environment-dependent, pointing to gene-by-gene and gene-by-environment interactions. Furthermore, models uncovered experimentally validated and novel candidate genetic interactions for a well-characterized stress, the fungicide benomyl. These findings highlight the feasibility of identifying the genetic basis of fitness by using different genetic variant types and offer novel targets for future functional analysis.

DNA copy number variations↗

Analysis of the Pioneer Venus Large Probe Neutral Mass Spectrometer Data Yields New Insights into the Composition of Venus’ Atmosphere

We present a new analysis of mass spectral data obtained by the Pioneer Venus (PV) Large Probe Neutral Mass Spectrometer (LNMS). To analyze the LNMS data, we constructed an analytical model that accounts for spectrometer performance at each altitude, provides CO2 abundances in units of density (kg/m3), and retains the resolving power of the LNMS through use of a targeted data-fitting routine. Our results provide new insights into the composition of Venus’ atmosphere and show that densities for CO2 increase towards the surface, which is suggestive of surface outgassing. Additionally, the data reveal partial obstructions of the LNMS inlet at <17 km, which is an likely important consideration for future missions. Re-analysis of the LNMS data may assist in revealing the past, present and/or future habitability of Venus’ clouds.

mass spectral data↗

Efficiency and mechanisms of Sb(III/V) removal by Fe-modified biochars using X-ray absorption spectroscopy

Fe-modified biochars (FeBC) are effective antimony (Sb) removal materials; however, the removal mechanisms require further investigation. In this study, aqueous Sb(III) and Sb(V) removal by FeBC (300, 600, and 900 °C) was evaluated, with the adsorption mechanisms investigated using X-ray absorption spectroscopy (XAS). Screening results (based on removal efficiencies) using different types of FeBC indicated the 900 °C FeCl3- modified biochar (FeCl3BC900) achieved the best Sb(III/V) removal performance. The kinetics of the Sb(III/V) removal process were best fitted by a pseudo-second-order model. Additionally, the isothermal results were described by Langmuir and Redlich-Peterson models. Aqueous analysis and X-ray absorption near-edge structure data fitting indicated Sb(III) was oxidized to Sb(V) in the Sb(III)-spiked system, and the oxidation extent increased with increasing pyrolysis temperature. The oxidation process rapidly occurred in both the solution and biochar. No Sb(V) was reduced to Sb(III) in the Sb(V)-spiked system. The XAS results of the isothermal experiment indicated the oxidation capacity of FeCl3BC900 was limited for high initial Sb(III) concentrations. The SbFe1 and Sb-Fe2 bonding distances were 3.05–3.10 and 3.47–3.54 Å, respectively, indicating inner-sphere complexes were formed during the Sb(III/V) removal processes. The Sb(III/V) removal mechanisms included electrostatic adsorption, inner-sphere complexes, and coprecipitation. Oxidation was also involved in Sb(III) removal.

Antimony↗

Deriving Stable Peak Models to Fit Complex XPS Data From Cu Contaminated Pt Electrocatalysts

X-ray Photoelectron Spectroscopy spectra peak models, designed to partition photoemission signals emanating from different elements or chemical states within an atom, are fitted to data limited to an energy interval over which inelastically scattered photoemission signal can be estimated. While the choice of background approximation and line shapes of components to the peak model requires careful consideration, the energy interval used to define the data to which the peak model is optimized has a significant impact on the final peak model. The relationship between the background intensity and data intensity at the start and end of the energy interval dictates the line shapes used in the peak model. In this work, we devise a method to peak fit a complex overlapping Cu 3p and Pt 4f XPS peak structure to perform the elemental quantification. We first use an Al 2s peak to illustrate how background curves approach data at the limits of the energy interval over which the background is defined, influencing the analysis of XPS spectra. Next, we demonstrate the nature of interactions between specific line shapes (Voigt and pseudo-Voigt profiles) suitable for photoemission peaks and a specific background curve (Shirley) and a peak model is presented that includes components to the peak model that accommodates background intensity during fitting of the peak model to data. The peak model allowed for quantification of the contributions of Pt 4f peaks emanating from the substrate that exhibits strong asymmetry in the presence of the inhomogeneously distributed Cu species, mostly of Lorentzian character.

XPS↗

More Tools for Visualization and Analysis of Small-Angle Neutron Scattering Data: Descriptions and Examples

With the adoption of drtsans as the data reduction software for the GP-SANS, Bio-SANS and EQ-SANS instruments at ORNL, tools for data visualization and analysis that can be integrated into drtsans scripts are needed to further improve the user experience. New tools that do not need to be incorporated directly into data reduction scripts can also positively impact users during their experiments. In this report, a new set of tools is presented that complements the previous set released. The set includes tools for both fitting data and for visualizing data.

42 ENGINEERING↗

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including $\tiny{L}$-glutamine, $\tiny{D}$-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.

59 BASIC BIOLOGICAL SCIENCES↗

Microwave signatures of snow, ice and soil at several wavelengths

Analyses of data obtained from aircraft-borne radiometers have shown that the microwave signatures of various parts of the terrain depend on both the volume scattering cross-section and the dielectric loss in the medium. In soil, it has been found that experimental data fit a model in which the scattering cross section is negligible compared to the dielectric loss. On the other hand, the volume scattering cross-section in snow and continental ice was found, from analyzing data obtained with aircraft- and spacecraft-borne radiometers, to be more important than the dielectric loss or surface reflectivity in determining the observed microwave emissivity. A model which assumes Mie scattering of ice particles of various sizes was found to be the dominant volume scattering mechanism in these media. Both spectral variation in the microwave signatures of snow and ice fields, as well as the variation in the emissivity of continental ice sheets such as those covering Greenland and Antarctica appear to be consistent with this model.

Gloersen, P.↗

Models for Single–Site Heterogeneous Catalysts on Carbon: MoO 2 Epoxidation Catalyst Anchored to a Fullerene

Single-site molybdenum dioxo catalysts, fullerenol/MoO 2 , are prepared via grafting precursor (DME)MoO 2 Cl 2 onto a highly polyhydroxylated fullerene (ful) and an isomerically-pure and well-defined fullerene (ful*). These catalyst structures are characterized by ICP-OES, XPS, XANES, EXAFS, DRIFT, Raman, and NMR spectroscopy, and DFT. Mo 3d 5/2 XPS and Mo K-edge XANES assign the oxidation state as Mo(VI). Mo EXAFS data fitting reveals two Mo=O double and two Mo–O single bonds at distances of 1.7 and 1.9 Å, respectively, while an Mo=O stretchingl mode is observed at ~950 cm –1 by DRIFT and Raman spectroscopy. These data align well with DFT computational results, supporting the proposed catalyst structure as Fullerene(-μ-O-) 2 M(=O) 2 . Additionally, DFT provides insight into the energetically favorable grafting sites for an isomerically pure fullerenol. The scope of fullerenol/MoO 2 mediated alkene epoxidation includes abiotic alkenes, natural occurring terpenes, and conjugated olefins. For cyclooctene the rate law is first-order in [Mo], near first order in [olefin] and zero-order in [t-butyl hydroperoxide]. A plausible reaction mechanism involves peroxide addition first and then cyclooctene addition directly across the peroxo bond forming the epoxide product, consistent with DFT computation. Overall, fullerenol/MoO 2 shows promise as a sustainable and structurally well-defined system with versatile catalytic activity and good epoxidation recyclability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TDRSS OVLBI experiment - Data correlation and results

The use of an orbiting antenna in a VLBI experiment complicates the data correlation, due to the spacecraft motion and the presence of the satellite-to-ground link. For this experiment, using a TDRSS satellite, a multistep method was used to calculate delay and phase for correlation and fringe-fitting. Data from three sources: 1510-089, NRAO 530 (1730-130), and 174l-038 were successfully correlated. The maximum projected baseline achieved was 1.4 earth diameters, for NRAO 530, with baselines longer than one earth diameter obtained for all three sources. Fringe visibilities for the maximum projected baselines were: 0.15 (1510-089), 0.05 (NRAO 530), and 0.50 (1741-038). The coherence of baselines to the orbiting antenna was 84 percent for 700 seconds. For a dedicated orbiting VLBI observatory (e.g., QUASAT), excellent coherence can be expected for integration times of several hundred seconds and observing frequencies as high as 20-30 GHz.

Linfield, R. P.↗

Characteristics of hypervelocity impact craters on LDEF experiment S1003 and implications of small particle impacts on reflective surfaces

The Ion Beam textured and coated surfaces EXperiment (IBEX), designated S1003, was flown on LDEF at a location 98 deg in a north facing direction relative to the ram direction. Thirty-six diverse materials were exposed to the micrometeoroid (and some debris) environment for 5.8 years. Optical property measurements indicated no changes for almost all of the materials except S-13G, Kapton, and Kapton-coated surfaces, and these changes can be explained by other environmental effects. From the predicted micrometeoroid flux of NASA SP-8013, no significant changes in optical properties of the surfaces due to micrometeoroids were expected. There were hypervelocity impacts on the various diverse materials flown on IBEX, and the characteristics of these craters were documented using scanning electron microscopy (SEM). The S1003 alumigold-coated aluminum cover tray was sectioned into 2 cm x 2 cm pieces for crater documentation. The flux curve generated from this crater data fits well between the 1969 micrometeoroid model and the Kessler debris model for particles less than 10(exp -9) gm which were corrected for the S1003 positions (98 deg to ram). As the particle mass increases, the S1003 impact data is greater than that predicted by even the debris model. This, however, is consistent with data taken on intercostal F07 by the Micrometeoroid/Debris Special Investigating Group (M/D SIG). The mirrored surface micrometeoroid detector flown on IBEX showed no change in solar reflectance and corroborated the S1003 flux curve, as well as results of this surface flown on SERT 2 and OSO 3 for as long as 21 years.

Mirtich, Michael J.↗

Comparison of aerobic fitness and space motion sickness during the Shuttle program

Space motion sickness (SMS) is an important problem for short-duration space flight; 71 percent of STS crewmembers develop SMS symptoms. The search for effective countermeasures and factors that correlate with sensitivity has been extensive. Recently, several investigators have linked aerobic fitness with motion sickness sensitivity in the 1-G or high-G environment. This paper compares the aerobic fitness of 125 Shuttle crewmembers with their SMS symptom category. Aerobic fitness data were obtained from the exercise tolerance test conducted nearest the time of launch. SMS data were derived from the medical debrief summaries. Mean maximum oxygen consumption values for crewmembers in four SMS categories (none, mild, moderate, severe) were 44.55, 44.08, 46.5, and 44.24 ml/kg per min, respectively. Scattergrams with linear regression analysis, comparing aerobic fitness and SMS symptom classification are presented. Correlation coefficients comparing SMS categories vs. aerobic fitness for men and women reveal no definite relationship between the two factors.

Jennings, Richard T.↗

Slow Crack Growth of Brittle Materials With Exponential Crack-Velocity Formulation: Constant Stress and Cyclic Stress Experiments - Part 3

The previously determined life prediction analysis based on an exponential crack-velocity formulation was examined using a variety of experimental data on advanced structural ceramics tested under constant stress and cyclic stress loading at ambient and elevated temperatures. The data fit to the relation between the time to failure and applied stress (or maximum applied stress in cyclic loading) was very reasonable for most of the materials studied. It was also found that life prediction for cyclic stress loading from data of constant stress loading in the exponential formulation was in good agreement with the experimental data, resulting in a similar degree of accuracy as compared with the power-law formulation. The major limitation in the exponential crack-velocity formulation, however, was that the inert strength of a material must be known a priori to evaluate the important slow-crack-growth (SCG) parameter n, a significant drawback as compared with the conventional power-law crack-velocity formulation.

Choi, Sung R.↗

Debye Dielectric Model Function for Seawater Based on Expanded L-Band Measurement Data Set

New seawater dielectric measurements have recently been made over a broad range of salinities and temperatures at the George Washington University (GW). These measurements have been used to refine the existing dielectric model function of seawater for salinity retrieval. The mathematical structure of the new model function has been investigated to: (a) look for a physical basis for the mathematical form; and (b) to optimize the accuracy of data fitting. The Debye model has been chosen to represent the dielectric constant of seawater as a function of salinity (S), temperature (T) and frequency (f). The retrieved salinity using the Debye model has good agreement with the in-situ data collected by Argo floats. The global differences in retrieved salinity and in-situ data will be presented at the meeting.

ocean salinity↗

RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling

Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive data set of functional evidence for the genetic basis of dicarboxylic and fatty acid metabolism using randomly barcoded transposon sequencing (RB-TnSeq). We identified four β-proteobacteria that displayed robust growth with dicarboxylic acid sole carbon source and cultured their mutant libraries with dicarboxylic and fatty acids with carbon chain lengths from C3 to C12. The resulting fitness data suggested that dicarboxylic and fatty acid metabolisms are largely distinct, and different sets of β-oxidation genes are required for catabolizing dicarboxylic versus fatty acids of the same carbon chain lengths. In addition, we identified transcriptional regulators and transporters with strong fitness phenotypes related to dicarboxylic acid utilization. In Ralstonia sp. UNC404CL21Col (R. CL21), we deleted two transcriptional repressors to improve its utilization of short-chain dicarboxylic acids. We exploited the diacid-utilizing catabolism of R. CL21 to upcycle a mock mixture of the dicarboxylic acids produced when polyethylene is oxidized. After introducing a heterologous indigoidine production pathway, this engineered Ralstonia produced 0.56 ± 0.02 g/L indigoidine from a mixture of dicarboxylic acids as a carbon source, demonstrating the potential of R. CL21 to upcycle plastic wastes to products derived from tricarboxylic acid (TCA) cycle intermediates. IMPORTANCE: Upcycling the carbon in plastic wastes to value-added products is a promising approach to address the plastic waste and climate crises, and dicarboxylic acid metabolism is an important facet of several approaches. Improving our understanding of the genetic basis of this metabolism has the potential to uncover new enzymes and genetic parts for engineered pathways involving dicarboxylic acids. Our data set is the most comprehensive interrogation of dicarboxylic acid catabolism to date, and this work will be of utility to researchers interested in both plastics bioproduction and upcycling applications.

Pearson, Allison N↗

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind’s predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server ( http://papers.genomics.lbl.gov/carbon ) and takes just 30 seconds for the typical genome.

59 BASIC BIOLOGICAL SCIENCES↗

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗

Initial measurement of reactor antineutrino oscillation at SNO+

The SNO+ collaboration reports its first spectral analysis of long-baseline reactor antineutrino oscillation using 114 tonne-years of data. Fitting the neutrino oscillation probability to the observed energy spectrum yields constraints on the neutrino mass-squared difference Δ$m^2_{21}$. In the ranges allowed by previous measurements, the best-fit Δ$m^2_{21}$ is ($8.85^{+1.10}_{-1.33}$) × 10 -5 eV 2 . This measurement is continuing in the next phases of SNO+ and is expected to surpass the present global precision on Δ$m^2_{21}$ with about three years of data. In the following, we first describe the configuration of the SNO+ detector when it was partially filled with scintillator, and a characterization of the detector response using intrinsic radioactivity. Next, we detail the event selection and expectations for reactor IBDs and (α, n) reactions. Then, we present the results of an energy spectrum analysis using 114 tonne-years of data. We conclude with prospects of future results from the SNO+ detector, which has been operating fully-filled with 780 tonnes of scintillator

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗