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At least 685 records · Page 38

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale

Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.

3D cell mapping↗

Exploiting Colorimetry for Fidelity in Data Visualization

Advances in multimodal characterization methods fuel the generation of increasing immense hyper-dimensional data sets. Color mapping is employed for conveying higher dimensional data in two-dimensional (2D) representations for human consumption without relying on multiple projections. How one constructs these color maps, however, critically affects how accurately one perceives data. For simple scalar fields, perceptually uniform color maps and color selection have been shown to improve data readability and interpretation across research fields. In this work, we review core concepts underlying the design of perceptually uniform color maps and extend the concepts from scalar fields to two-dimensional vector fields and three-component composition fields frequently found in materials-chemistry research to enable high-fidelity visualization. Additionally, we develop the software tools PAPUC and CMPUC to enable researchers to utilize these colorimetry principles and employ perceptually uniform color spaces for rigorously meaningful color mapping of higher dimensional data representations. Last, we demonstrate how these approaches deliver immediate improvements in data readability and interpretation in microscopies and spectroscopies routinely used in discerning materials structure, chemistry, and properties.

36 MATERIALS SCIENCE↗

"Land-Cover Conversion in Amazonia, The Role of ENV" Ironment and Substrate composition in Modifying SOI

LBA research from the first phase of LBA focused on three broad categories: 1) mapping land cover and quantifying rates of change, persistence of pasture, and area of recovering forest; 2) evaluating the role of environmental factors and land-use history on soil biogeochemistry; and 3) quantifying the natural and human controls on stream nutrient concentrations. The focus of the research was regional, concentrating primarily in the state of RondBnia, but also included land-cover mapping in the vicinity of Maraba, Para, and Manaus, Amazonas. Remote sensing analysis utilized Landsat Thematic Mapper (TM) and Multispectral Scanner (MS S) data to map historical patterns of land-cover change. Specific questions addressed by the remote sensing component of the research included: 1) what is the areal extent of dominant land-cover classes? 2) what are the rates of change of dominant land cover through processes of deforestation, disturbance and regeneration? and 3) what are the dynamic properties of each class that characterize temporal variability, duration, and frequency of repeat disturbance? Biogeochemical analysis focused on natural variability and impacts of land-use/land-cover changes on soil and stream biogeochemical properties at the regional scale. An emphasis was given to specific soil properties considered to be primary limiting factors regionally, including phosphorus, nitrogen, base cations and cation-exchange properties. Stream sampling emphasized the relative effects of the rates and timing of land-cover change on stream nutrients, demonstrating that vegetation conversion alone does not impact nutrients as much as subsequent land use and urbanization.

Roberts, Dar A.↗

Mineralogical Composition of the Different Types of Bright Deposits on Vesta

VIR-MS, Dawn's Visible and Infrared Mapping Spectrometer, obtained hyperspectral images of a wide part of Vesta's surface at a variety of spatial resolutions [1]. Vesta spectra are similar to those of the howardite-eucrite-diogenite (HED) meteorites. Moreover, they are characterized by the two iron-bearing pyroxene bands at 0.9 (band I) and 1.9 microns (band II). Vesta surface's is dominated by eucrite/howardite with some diogenitic regions situated in the southern hemisphere near the Rheasilvia basin [2]. The surface is heavily craterized and impacts can expose fresh material, thus generating the Bright Material Deposits (BMD) observed within and surrounding certain craters. BMD can be classified into six different types based on their morphological characteristics: Crater Wall/Scarp Material (CWM), Radial Material (RM), Slope Material (SM), Patchy Material (PM), Spot Material (SpM) and Diffuse Plains Material (DPM) [3]. The most widespread BMD are CWM, SM and RM. CWM, SM, RM originate from impacts. CWM is situated on the edge of the craters. Mass wasting from the crater walls and generates the SM, while RM is associated with the ejecta of the craters [4]. BMD are characterized by albedo greater than that of the vestan average, 0.38 [5]. Therefore the different types of deposits present distinct levels of reflectance respect to the Surrounding Regions (SR), in particular: the CWM and SM is approx.40% brighter, the RM is approx.30- 40% brighter; the SpM is about 20-25% brighter and the PM is about 20% brighter. Near the edge of the Rheasilvia basin it is possible to find some extremely bright areas ~80% brighter than the vestan average [6].

Zambon, F.↗

Chemical Evidence for Smectites and Zeolites on Mars: Criteria and Limitations

Aqueous alteration on Mars can produce a range of tell-tale secondary minerals [1]. Surface missions typically obtain detailed and highly localized element compositional information, but not always mineralogical information, whereas orbital missions deduce mineralogy from relatively high spatial resolution IR spectral mapping (decameters scale, for CRISM), but obtain element data only over much larger areas of martian terrain (~200 km). Surface missions have also discovered several occurrences of major geochemical alteration of igneous precursors, for many of which elemental compositional is the only diagnostic information available. Many types of clays and zeolites have quasi-unique element profiles which may be used to implicate their presence. In some cases, one or more candidate minerals are sufficiently close in their component elements and their stoichiometry that ambiguity must remain, unless other constraints can be brought to bear. Geochemical characteristics of alteration products most likely on Mars can be compared to results from MER and MSL rover missions (e.g. Independence [4] and Esperance samples). These considerations are needed for MER Opportunity rover now that Mini-TES is no longer operational. It also has importance for exploration by the MSL Curiosity rover because inferences and deductions available from ChemCam (CCAM) remote LIBS and/or in situ x-ray fluorescence (APXS) can be used as indicators for triage to select materials to sample for limited-resource instruments, SAM and Chemin.

Clark, B. C.↗

Observations of the plant growth and annual flooding in the inland delta of the Niger River, west Africa

The author has identified the following significant results. A large potential irrigation area with water delivery system in place was identified from ERTS-1 imagery. The site is in the Sahara Desert. Color additive change detection imagery was used to assess ground water potentials in the Savannah in conjunction with a major US AID-Mali livestock sector initiative. The potential capacity to map laterite deposits in the Inland Delta from space was established with the help of aerial and ground surveys. A color composite of the Inland Delta could have saved French biogeographers 3 5/6 man-years of professional field work had it been available, according to the man who prepared a plant community map of part of the southern Inland Delta.

Macleod, N. H.↗

Next generation Arctic vegetation maps: Aboveground plant biomass and woody dominance mapped at 30 m resolution across the tundra biome

The Arctic is warming faster than anywhere else on Earth, placing tundra ecosystems at the forefront of global climate change. Plant biomass is a fundamental ecosystem attribute that is sensitive to changes in climate, closely tied to ecological function, and crucial for constraining ecosystem carbon dynamics. However, the amount, functional composition, and distribution of plant biomass are only coarsely quantified across the Arctic. Therefore, we developed the first moderate resolution (30 m) maps of live aboveground plant biomass (g m −2 ) and woody plant dominance (%) for the Arctic tundra biome, including the mountainous Oro Arctic. We modeled biomass for the year 2020 using a new synthesis dataset of field biomass harvest measurements, Landsat satellite seasonal synthetic composites, ancillary geospatial data, and machine learning models. Additionally, we quantified pixel-wise uncertainty in biomass predictions using Monte Carlo simulations and validated the models using a robust, spatially blocked and nested cross-validation procedure. Observed plant and woody plant biomass values ranged from 0 to ∼6000 g m −2 (mean ≈ 350 g m −2 ), while predicted values ranged from 0 to ∼4000 g m −2 (mean ≈ 275 g m −2 ), resulting in model validation root-mean-squared-error (RMSE) ≈ 400 g m −2 and R 2 ≈ 0.6. Our maps not only capture large-scale patterns of plant biomass and woody plant dominance across the Arctic that are linked to climatic variation (e.g., thawing degree days), but also illustrate how fine-scale patterns are shaped by local surface hydrology, topography, and past disturbance. By providing data on plant biomass across Arctic tundra ecosystems at the highest resolution to date, our maps can significantly advance research and inform decision-making on topics ranging from Arctic vegetation monitoring and wildlife conservation to carbon accounting and land surface modeling.

Climate change↗

Mid-Latitude Composition of Mars from Thermal and Epithermal Neutrons

Epithermal neutron data acquired by Mars Odyssey have been analyzed to determine global maps of water-equivalent hydrogen abundance. By assuming that hydrogen was distributed uniformly with depth within the surface, a map of minimum water abundance was obtained. The addition of thermal neutrons to this analysis could provide information needed to determine water stratigraphy. For example, thermal and epithermal neutrons have been used together to determine the depth and abundance of water-equivalent hydrogen of a buried layer in the south polar region. Because the emission of thermal neutrons from the Martian surface is sensitive to absorption by elements other than hydrogen, analysis of stratigraphy requires that the abundance of these elements be known. For example, recently published studies of the south polar region assumed that the Mars Pathfinder mean soil composition is representative of the regional soil composition. This assumption is partially motivated by the fact that Mars appears to have a well-mixed global dust cover and that the Pathfinder soil composition is representative of the mean composition of the Martian surface. In this study, we have analyzed thermal and epithermal neutron data measured by the neutron spectrometer subsystem of the gamma ray spectrometer to determine the spatial distribution of the composition of elements other than hydrogen. We have restricted our analysis to mid-latitude regions for which we have corrected the neutron counting data for variations in atmospheric thickness.

T H Prettyman↗

Structure-aware methods for expensive derivative-free nonsmooth composite optimization

We present new methods for solving a broad class of bound-constrained nonsmooth composite minimization problems. These methods are specially designed for objectives that are some known mapping of outputs from a computationally expensive function. We provide accompanying implementations of these methods: in particular, a novel manifold sampling algorithm (MS-P) with subproblems that are in a sense primal versions of the dual problems solved by previous manifold sampling methods and a method (GOOMBAH) that employs more difficult optimization subproblems. For these two methods, we provide rigorous convergence analysis and guarantees. We demonstrate extensive testing of these methods. Open-source implementations of the methods developed in this manuscript can be found at https://github.com/POptUS/ IBCDFO/.

97 MATHEMATICS AND COMPUTING↗

MBE growth and donor doping of coherent ultrawide bandgap AlGaN alloy layers on single-crystal AlN substrates

Single-crystal Aluminum Nitride (AlN) crystals enable the epitaxial growth of ultrawide bandgap Al(Ga)N alloys with drastically lower extended defect densities. Here, we report the plasma-MBE growth conditions for high Al-composition AlGaN alloys on single-crystal AlN substrates. An AlGaN growth guideline map is developed, leading to pseudomorphic Al x Ga 1–x N epitaxial layers with x ~0.6–1.0 Al contents at a growth rate of ~0.3 μm/h. These epitaxial layers exhibit atomic steps, indicating step flow epitaxial growth, and room-temperature band edge emission from ~4.5 to 5.9 eV. Growth conditions are identified in which the background impurity concentrations of O, C, Si, and H in the MBE layers are found to be very near or below detection limits. An interesting Si segregation and gettering behavior is observed at the epitaxial AlGaN/AlN heterojunction with significant implications for the formation and transport of 2D electron or hole gases. Well-controlled intentional Si doping ranging from ~2 × 10 17 to 3 × 10 19 atoms/cm 3 is obtained, with sharp dopant density transition profiles. In Si-doped Al 0.6 Ga 0.4 N epilayers, a room-temperature free electron concentration of ~3 × 10 19 /cm 3 , an electron mobility of ~27 cm 2 /V s, and an n-type resistivity of ~7.5 m Ω cm are obtained. Here, the implications of these findings on electronic and photonic devices on single-crystal AlN substrates are discussed.

36 MATERIALS SCIENCE↗

Multivariate analysis: An essential for studying complex glasses

Understanding the impact of individual compositional components on the devitrification of complex multicomponent glasses, for example, 10–50+ oxides, typically requires numerous studies to examine each component's impact. Here we apply exploratory data analysis (EDA) to a heterogeneous data set of silicate glasses to determine the cations’ individual and interacting effects on the crystallization of nepheline (nominally NaAlSiO 4 ). Our data consisted of 795 simulated high-level nuclear waste glasses composed of, on average, 50 oxide components. We determine the interactions in the heterogeneous data that cause deviations from the behavior found in simplified composition studies. Using both univariate and bivariate EDA techniques, we demonstrate the importance of including calculated structural glass parameters on nepheline's devitrification, including field strength, cation-to-anion radius ratio, and single-bond strength. Here, we also show that studies with simplified glass compositions may fall short in generating knowledge directly transferrable to complex glass compositions. The method used in this study has the potential to inform experimental design for simplified compositions (~6+ oxides) that can generate knowledge directly transferrable to complex, multivariable compositions. The observations reported here have broad implications for any study attempting to map the physical properties of a complex glass containing numerous cations.

36 MATERIALS SCIENCE↗

Improved Biofuel Production through Discovery and Engineering of Terpene Metabolism in Switchgrass

Project Objectives - Of the myriad specialized metabolites that plants deploy to adapt to environmental challenges, terpenes form the largest group. In many major crops, unique terpene blends serve as key stress defenses that directly impact plant fitness and yield. In addition, terpenes, such as bisabolene and pinene, are used for producing renewable biofuels. Essential to advancing a broader use of terpenes for biofuel feedstock engineering is a system-wide knowledge of the diverse biosynthetic machinery and defensive potential of often species-specific terpene blends. The proposed project would merge genome-wide enzyme discovery with comparative –omics, protein structural and plant microbiome studies to define the biosynthesis and stress-defensive functions of the switchgrass (Panicum virgatum) terpene network. These insights would be combined with developing and applying non-transgenic genome editing tools to design plants with desirable terpene blends for higher productivity and biofuel production on marginal lands. As a dedicated lignocellulosic feedstock for U.S. biofuel production with high net energy yield, stress tolerance, and available genome resources, switchgrass is well-suited for devising new avenues for biofuel production. Project Description – The diversity of plant terpene defenses is governed by species-specific families of terpene synthase (TPS) and cytochrome P450 monooxygenase (P450) enzymes. Mining of the switchgrass genome (genotype Alamo) identified ~100 TPS and P450 candidate genes, and combinatorial biochemical analysis of synthesized TPSs and P450s revealed more than a dozen enzymes with common and novel activities. In addition, several identified terpene metabolites and the corresponding transcripts were up-regulated in response to abiotic stressors. These findings demonstrate a unique switchgrass terpene network with probable importance to abiotic stress tolerance, thus providing a large chemical portfolio for optimizing crop resistance, yield, and biofuel composition. Leveraging these preliminary data, we propose to generate a genome-wide map of the switchgrass terpene metabolic network through multi-gene co-expression analyses that allow the efficient cross-validation of TPS and P450 functions. Key enzymes would further be applied to structure-function studies via X-ray protein crystallography, homology modeling and site-directed mutagenesis to gain mechanistic insight into the catalytic specificity of switchgrass terpene metabolism and provide gene and amino acid targets for genome editing. In tandem with terpene pathway discovery, system-wide metabolomics, transcriptomics and proteomics studies in switchgrass accessions of contrasting drought tolerance would define the role of switchgrass terpene metabolism in conferring abiotic stress resilience. Metabolic changes would be assessed in a combined approach of targeted (terpenes) and untargeted metabolite profiling using a high-resolution LC-MS/MS approach, differential gene expression analyses through multiplexed Illumina RNA sequencing, and quantitative analysis of high-priority pathway enzymes using multiple reaction monitoring (MRM). Drawing on these insights, knock-down/out mutants of stress-associated pathway nodes would be generated by optimizing transient virus-induced gene silencing (VIGS) and CRISPR/Cas9 systems under control of the Tobacco Rattle Virus (TRV). The resulting mutant lines would then be analyzed for stress susceptibility and the impact on the root microbiome to define gene functions in planta. Knowledge of terpene pathways, enzyme mechanisms and bioactivities would be applied to enhance switchgrass stress resilience and to tailor-make terpene blends for biofuel production. Here, TRV-enabled CRISPR/Cas9 genome editing, including allele-specific knock-out of redundant genes, engineering of enzyme specificity via structure-guided point mutations, and overexpression of terpene genes relevant to stress-protection or biofuel production, would be used to increase metabolic flux toward desired pathways. Broader Impacts - Integrating the system-wide discovery, mechanistic analysis and non-transgenic genome engineering of the switchgrass terpene network aligns the required steps to unlock the chemical potential of this important metabolite class to generate crops that are more resistant to stress and provide advanced biofuel production in light of rising climate pressures as foreseeable challenges for bioenergy crop cultivation. The proposed project would further offer interdisciplinary student training through active involvement in the project and integration of research concepts and outcomes into newly-developed graduate and undergraduate courses on Plant Biotechnology.

09 BIOMASS FUELS↗

Fuel Effects on Advanced Compression Ignition Load Limits

In order to increase the efficiency of light-duty gasoline engines, the Co-Optimization of Fuels and Engines (Co-Optima) initiative from the U.S. Department of Energy is investigating multi-mode combustion strategies. Multi-mode combustion can be describe as using conventional spark-ignited combustion at high loads, and at the part-load operating conditions, various advanced compression ignition (ACI) strategies are being investigated to increase efficiency. Of particular interest to the Co-Optima initiative is the extent to which optimal fuel properties and compositions can enable higher efficiency ACI combustion over larger portions of the operating map. Extending the speed-load range of these ACI modes can enable greater part-load efficiency improvements for multi-mode combustion strategies. In this manuscript, we investigate fuel effects for six different fuels, including four with a research octane number (RON) of 98 and differing fuel chemistries, iso-octane, and a market representative E10 fuel, on the load limits for two different ACI strategies: spark-assisted compression ignition (SACI) and partial fuel stratification-gasoline compression ignition (PFS-GCI) operation. Experimental results show that limits to intake boosting limit high load operation for most fuels, but high smoke emissions for high particulate matter index (PMI) fuels under SACI conditions could also be a limitation. Contrastingly, low load is limited by combustion efficiency, but these effects have more pronounced variation with fuel chemistry for PFS-GCI than with SACI. Additional, distinct effects affecting autoignition timing and peak heat release at higher speeds were identified for fuels having different low temperature heat release (LTHR) propensities for both ACI modes.

33 ADVANCED PROPULSION SYSTEMS↗

Late diagenetic indicators of buried oil and gas. 2: Direct detection experiment at Cement and Garza fields, Oklahoma and Texas, using enhanced LANDSAT 1 and 2 images

The author has identified the following significant results. The Cement oil field, Oklahoma, was a test site for an experiment designed to evaluate LANDSAT's capability to detect an alteration zone in surface rocks caused by hydrocarbon microseepage. Loss of iron and impregnation of sandstone by carbonate cements and replacement of gypsum by calcite were the major alteration phenomena at Cement. The bedrock alterations were partially masked by unaltered overlying beds, thick soils, and dense natural and cultivated vegetation. Interpreters, biased by detailed ground truth, were able to map the alteration zone subjectively using a magnified, filtered, and sinusoidally stretched LANDSAT composite image; other interpreters, unbiased by ground truth data, could not duplicate that interpretation.

Donovan, T. J.↗

Finding the lost river gas field - Lineament density analysis in hydrocarbon exploration

A comparative trial analysis of lineament density in 1:500,000 Landsat and 1:48,000 aerial Landsat-simulator images of a gas-field region in West Virginia is presented. The high-contrast, band 4, 5, 7 color composite Landsat image was interpreted independently by two analysts. The slightly different lineament maps were evaluated in terms of lineament-density variation in 10 x 10-km areas, and the resulting areal-variation maps are found to be statistically equivalent. High lineament density is shown to be associated with productive gas wells. Comparison of ground-based substructural contour maps and lineament-density analyses of the Landsat-simulator images reveals good correlation between density maxima or isopleths and substructural features associated with hydrocarbon formations. A hydrocarbon-exploration strategy using both Landsat and aerial images is proposed.

Lang, H. R.↗

Growth and characterization of Hg(1-x)Zn(x)Se

Hg sub 1-xZn sub xSe alloys of composition x=0.10 were grown in a Bridgman-Stockbarger growth furnace at translation rates of 0.3 and 0.1 micron sec. The axial and radial composition profiles were determined using precision density measurements and IR transmission-edge-mapping, respectively. A more radially homogeneous alloy was produced at the slower growth rate, while the faster growth rate produced more axially homogeneous alloys. A determination of the electrical properties of the Hg sub 1-xZn sub xSe samples in the temperature range 300K-20K was also made. Typical carrier concentrations were on the order of magnitude of 10 to the 18th power cu/cm, and remained fairly constant as a function of temperature. A study was also made of the temperature dependence of the resistivity and Hall mobility. The effect of annealing in a selenium vapor on both the IR transmission and the electrical properties was determined. Annealing was effective in reducing the number of native donor defects and at the resulting lower carrier concentrations, charge carrier concentration was shown to be a function of temperature. Annealing caused the mobility to increase, primarily at the lower temperature, and the room temperature resistivity to increase. Annealing was also observed to greatly enhance the % IR transmittance of the samples. This was due primarily to the effect of annealing on decreasing the charge carrier concentration.

Andrews, R. N.↗

Roosevelt County 075: A petrologic chemical and isotopic study of the most unequilibrated known H chondrite

Roosevelt County (RC) 075 was recovered in 1990 as a single 258-gram stone. Classification of this meteorite is complicated by its highly unequilibrated nature and its severe terrestrial weathering, but we favor H classification. This is supported by O isotopes and estimates of the original Fe, Ni metal content. The O isotopic composition is similar to that of a number of reduced ordinary chondrites (e.g., Cerro los Calvos, Willaroy), although RC 075 exhibits no evidence of reduced mineral compositions. Chondrule diameters are consistent with classification as an L chondrite, but large uncertainties in chondrule diameters of RC 075 and poorly constrained means of H, L and LL chondrites prevent use of this parameter for reliable classification. Other parameters are compromised by severe weathering (e.g., siderophile element abundances) or unsuitable for discrimination between unequilibrated H, L and LL chondrites (e.g., Co in kamacite delta C-13). Petrologic subtype 3.2 +/- 0.1 is suggested by the degree of olivine heterogeneity, the compositions of chondrule olivines, the thermoluminescence sensitivity, the abundances and types of chondrules mapped on cathodoluminescence mosaics, and the amount of presolar SiC. The meteorite is very weakly shocked (S2), with some chondrules essentially unshocked and, thus, is classified as an H3.2(S2) chondrite. Weathering is evident by a LREE enrichment due to clay contamination, reduced levels of many siderophile elements, the almost total loss of Fe, Ni metal and troilite, and the reduced concentrations of noble gases. Some components of the meteorite (e.g., type IA chondrules, SiC) appear to preserve their nebular states, with little modification from thermal metamorphism. We conclude that RC 075 is the most equilibrated H chondrite yet recovered and may provide additional insights into the origin of primitive materials in the solar nebula.

Mccoy, T. J.↗