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At least 811 records · Page 45

Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)

Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.

60 APPLIED LIFE SCIENCES↗

Validation and moisture content sensitivity analysis of cross-laminated timber wall assemblies in EnergyPlus

Cross-laminated timber buildings are becoming more common in North America, with many numerical studies showing potential energy savings. However, no studies have validated any EnergyPlus heat transfer algorithms or quantified their accuracy in simulating CLT in building envelopes. This study empirically validates the heat flux predictions for each of EnergyPlus's heat transfer algorithms (Conduction Transfer Functions (CTF), Effective Moisture Penetration Depth (EMPD), Conduction Finite Difference (CondFD), and Heat and Moisture Transfer (HAMT)) for two different CLT ply thicknesses with both summer and winter boundary conditions measured in controlled lab experiments. It also evaluates the model sensitivity of heat flux and heating and cooling loads to moisture content. The 1D validation shows that the HAMT model is the most accurate among all algorithms. All EnergyPlus's heat flux predictions are accurate independent of CLT plate thickness for summer conditions. However, the three constant property algorithms (CTF, EMPD, and CondFD) underpredict heat flux throughout the whole day during winter conditions. The 1D sensitivity analysis indicates that elevated moisture content can increase peak heat fluxes through the material by up to 20 %. Finally, the whole building model sensitivity analysis shows increased heating load and slight cooling load variation due to increased moisture content when using constant property models. The analysis shows significantly lower peak thermal demand (7 % lower heating and 6 % lower cooling) and monthly thermal load (8 % less cooling and 6 % less heating) predictions when using HAMT vs a constant property model.

42 ENGINEERING↗

Layer-Dependent Bit Error Variation in 3-D NAND Flash Under Ionizing Radiation

In this paper, we studied the total ionization dose (TID) effects on the multilevel-cell (MLC) 3-D NAND flash memory using Co-60 gamma radiation. We found a significant page-to-page bit error variation within a physical memory block of the irradiated memory chip. Our analysis showed that the origin of the bit error variation is the unique vertical layer-dependent TID response of the 3-D NAND. We found that the memory pages located at the upper and lower layers of the 3-D stack show higher fails compared to the middle-layer pages of a given memory block. We confirmed our findings by comparing radiation response of four different chips of the same specification. In addition, we compared the TID response of the MLC 3-D NAND with that of the 2-D NAND chip, which showed less page-to-page variation in bit error within a given memory block. We discuss the possible application of our findings for the radiation-tolerant smart memory controller design.

3-D NAND flash↗

Amplicon Sequencing Assessment to Measure Microbial Community Response from Heavy Metal Contaminated Soils in Savannah River site, Tims Branch watershed

Long-term presence of heavy metal contamination in soils is correlated with changes in microbial community structures and can lead to the reduction of indigenous species. Tolerance to soil heavy metal toxicity varies among different microbial communities. It remains unclear whether long term effects caused by metal perturbations are associated with soil microbial community dysregulation in Tims Branch watershed. Research Questions: Does heavy metal contamination in Tims Branch soils decrease microbial species diversity significantly compared to non-contaminated soils? Does the species richness decrease in contaminated samples? between samples? Is diversity in low, mid and high contamination soils significantly different compared to control samples? Hypothesis: The relative abundance and diversity of species are significantly altered in soils which are contaminated with heavy metals in the Tims Branch watershed. Objectives: Use amplicon sequencing technology along with bioinformatics to compare bacterial communities between four sites in Tims Branch watershed. Evaluate the percent relative abundance and diversity across the site. Conclusions: All bacterial communities exposed to different heavy metal concentrations were dominated by four major groups (Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia). The dominant phyla Proteobacteria, Acidobacteria and Chloroflexi accounted for 61 % of the relative abundance. Soil bacterial α-diversity, expressed as observed species richness metric and Shannon's diversity index, was the highest in sample location four (high contamination). The lowest observed was at the control location. Species richness increased when concentrations of heavy metals were localized, inferring that the metals can alter microbial community structure. PERMANOVA analysis between contaminated groups tested significant using the Adonis (F (4,29) =1.9712; p < 0.001). There is a 20 percent variation explained between groups (R2 = 0.214). This analysis proves to be beneficial in detecting microbial communities altered by contaminated soils. Moreover, certain concentrations of heavy metals can alter microbial community structures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Modeling and Analysis of Wind Turbine Wake Vortex Evolution Due to Time-Constant Spatial Variations in Atmospheric Flow

Modern utility-scale wind turbines are evolving toward larger, lighter, and more flexible designs to meet the growing demand for renewable energy while minimizing logistical costs. However, these advancements in lightweight design result in heightened aeroelastic sensitivity, leading to complex interactions which affect the rotor’s capacity to withstand aerodynamic loading and the cascading effects that manifest in the wake’s vortex-structure evolution under variable atmospheric conditions. In this paper, we analyze the influence of stream-wise fluctuating atmospheric flow conditions on wind turbines with large, flexible rotors through simulations of the National Rotor Testbed (NRT) turbine, located at Sandia National Labs’ Scaled Wind Farm Technology (SWiFT) facility in Lubbock, Texas. The Common Ordinary Differential Equation Framework (CODEF) modeling suite is used to simulate wind turbine aeroelastic oscillatory behavior and wind farm vortex–wake interactions for a range of conditions with spatially variant atmospheric flow. CODEF solutions for turbine operation in wind conditions featuring only one parameter fluctuation are compared to wind conditions with several wind parameter variations in combination. By isolating individual inflow variations and comparing them to multi-parameter scenarios, we determine the contributions of each atmospheric factor to rotor dynamics, wake evolution, and downstream wind farm interactions. The purpose of this paper is to analyze the effects of spatial variations in atmospheric flow on the topological evolution of wind turbine vortex wakes, which constitutes a gap in the current understanding of wind turbine wake dynamics. The insights gained from this study are particularly valuable for the development of wind farm control strategies aimed at mitigating the adverse effects of wake interactions, enhancing energy capture, and improving the overall stability of wind farm operations. With these insights, we aim to contribute to the development of modeling and simulation tools to optimize utility-scale wind power plants operating in diverse atmospheric environments.

Farrell, Alayna (ORCID:000000023555720X)↗

A Quantitative Study of Oxygen as a Metabolic Regulator

An acute reduction in oxygen (O2) delivery to a tissue is generally associated with a decrease in phosphocreatine, increases in ADP, NADH/NAD, and inorganic phosphate, increased rates of glycolysis and lactate production, and reduced rates of pyruvate and fatty acid oxidation. However, given the complexity of the human bioenergetic system and its components, it is difficult to determine quantitatively how cellular metabolic processes interact to maintain ATP homeostasis during stress (e.g., hypoxia, ischemia, and exercise). Of special interest is the determination of mechanisms relating tissue oxygenation to observed metabolic responses at the tissue, organ, and whole body levels and the quantification of how changes in tissue O2 availability affect the pathways of ATP synthesis and the metabolites that control these pathways. In this study, we extend a previously developed mathematical model of human bioenergetics to provide a physicochemical framework that permits quantitative understanding of O2 as a metabolic regulator. Specifically, the enhancement permits studying the effects of variations in tissue oxygenation and in parameters controlling the rate of cellular respiration on glycolysis, lactate production, and pyruvate oxidation. The whole body is described as a bioenergetic system consisting of metabolically distinct tissue/organ subsystems that exchange materials with the blood. In order to study the dynamic response of each subsystem to stimuli, we solve the ordinary differential equations describing the temporal evolution of metabolite levels, given the initial concentrations. The solver used in the present study is the packaged code LSODE, as implemented in the NASA Lewis kinetics and sensitivity analysis code, LSENS. A major advantage of LSENS is the efficient procedures supporting systematic sensitivity analysis, which provides the basic methods for studying parameter sensitivities (i.e., changes in model behavior due to parameter variation). Sensitivity analysis establishes relationships between model predictions and problem parameters (i.e., initial concentrations, rate coefficients, etc). It helps determine the effects of uncertainties or changes in these input parameters on the predictions, which ultimately are compared with experimental observations in order to validate the model. Sensitivity analysis can identify parameters that must be determined accurately because of their large effect on the model predictions and parameters that need not be known with great precision because they have little or no effect on the solution. This capability may prove to be important in optimizing the design of experiments, thereby reducing the use of animals. This approach can be applied to study the metabolic effects of reduced oxygen delivery to cardiac muscle due to local myocardial ischemia and the effects of acute hypoxia on brain metabolism. Other important applications of sensitivity analysis include identification of quantitatively relevant pathways and biochemical species within an overall mechanism, when examining the effects of a genetic anomaly or pathological state on energetic system components and whole system behavior.

Radhakrishnan, Krishnan↗

Variations in eddy diffusion and associated transport processes

Variation in the eddy diffusion coefficient constitutes a momentum source. This variation near the turbopause affects both the composition and the wind and temperature fields of the thermosphere. Two types of calculations are carried out, for horizontal winds considered self-consistently in a three-dimensional dynamic model and horizontal winds artificially suppressed to simulate a one-dimensional model. Momentum transfer associated with variations in eddy diffusion coefficients represents the source function in the analysis presented. It is shown that for long-term variations in the thermosphere, the compositional dependence on variations in eddy diffusion coefficients can be entirely different in one and three dimensional models with horizontal winds included. Horizontal winds can greatly reduce the effects of eddy diffusion in general and the ratio between He and O amplitudes in particular.

Mayr, H. G.↗

Exploring the stellar populations of backsplash galaxies

Backsplash galaxies are those that traverse and overshoot cluster cores as they fall into these structures. They are affected by environment, and should stand out in contrast to the infalling population. We target galaxies in the vicinity of clusters (R≳R 200 ) and select a sample in projected phase space (PPS), from the compilation of Sampaio et al. based on SDSS data. We present a statistical analysis, comparing two regions in PPS, with the same projected distance to the cluster but different velocity. The analysis relies on the presence of variations in the stellar population content of backsplash galaxies. We find a lower limit in the fractional contribution of ∼5 per cent with respect to the general sample of infalling galaxies at similar group-centric distance when using single line strength analysis, or ∼15-30 per cent when adopting bivariate distributions. The stellar populations show a subtle but significant difference towards older ages, and a higher fraction of quiescent galaxies. We also compare this set with a general field sample, where a substantially larger difference in galaxy properties is found, with the field sample being consistently younger, metal poorer and with a lower fraction of quiescent galaxies. Noting that our ‘cluster’ sample is located outside of the virial radius, we expect this difference to be caused by pre-processing of the infalling galaxies in the overall higher density regions.

79 ASTRONOMY AND ASTROPHYSICS↗

Lunar lava tube radiation safety analysis

For many years it has been suggested that lava tubes on the Moon could provide an ideal location for a manned lunar base, by providing shelter from various natural hazards, such as cosmic radiation, meteorites, micrometeoroids, and impact crater ejecta, and also providing a natural environmental control, with a nearly constant temperature, unlike that of the lunar surface showing extreme variation in its diurnal cycle. An analysis of radiation safety issues on lunar lava tubes has been performed by considering radiation from galactic cosmic rays (GCR) and Solar Particle Events (SPE) interacting with the lunar surface, modeled as a regolith layer and rock. The chemical composition has been chosen as typical of the lunar regions where the largest number of lava tube candidates are found. Particles have been transported all through the regolith and the rock, and received particles flux and doses have been calculated. The radiation safety of lunar lava tubes environments has been demonstrated.

Non-programmatic↗

Postural control model interpretation of stabilogram diffusion analysis

Collins and De Luca [Collins JJ. De Luca CJ (1993) Exp Brain Res 95: 308-318] introduced a new method known as stabilogram diffusion analysis that provides a quantitative statistical measure of the apparently random variations of center-of-pressure (COP) trajectories recorded during quiet upright stance in humans. This analysis generates a stabilogram diffusion function (SDF) that summarizes the mean square COP displacement as a function of the time interval between COP comparisons. SDFs have a characteristic two-part form that suggests the presence of two different control regimes: a short-term open-loop control behavior and a longer-term closed-loop behavior. This paper demonstrates that a very simple closed-loop control model of upright stance can generate realistic SDFs. The model consists of an inverted pendulum body with torque applied at the ankle joint. This torque includes a random disturbance torque and a control torque. The control torque is a function of the deviation (error signal) between the desired upright body position and the actual body position, and is generated in proportion to the error signal, the derivative of the error signal, and the integral of the error signal [i.e. a proportional, integral and derivative (PID) neural controller]. The control torque is applied with a time delay representing conduction, processing, and muscle activation delays. Variations in the PID parameters and the time delay generate variations in SDFs that mimic real experimental SDFs. This model analysis allows one to interpret experimentally observed changes in SDFs in terms of variations in neural controller and time delay parameters rather than in terms of open-loop versus closed-loop behavior.

NASA Program Biomedical Research and Countermeasur↗

Global ozone - Solar activity relationship from satellite measurements

Global ozone variations are evaluated by analyzing satellite measurements, using the technique of integrating out dynamical effects causing large variations in total ozone at individual locations. Analysis of Nimbus 4 reprocessed BUV data was extended to cover the period from April 1970 through December 1975. Temporal and latitudinal variation of biases and yearly change in global biases between the satellite and ground based ozone measurements are indicated. The bias-corrected 6-month-running filtered global means are shown, and the correlation coefficient between ozone and the solar activity index remains high at 0.94. It is concluded that the results give a strong indication of an ozone-solar activity relationship that is caused by solar UV variability.

Keating, G. M.↗

Observations of shadow bands at the total solar eclipse of 16 February 1980

Photoelectric observations of short term light variations (shadow bands) at the 16 Feb. 1980 total solar eclipse have been made using a set of spatially separated PIN diodes. Light variations in a bandpass of 1-500 Hz were detected during the half-minutes preceding and following the total phase. Fourier analysis of the noise spectrum of the variations reveals a sharp drop-off for frequencies above 50 Hz and an overall spectrum quite similar to previously reported power spectra of stellar scintillation. This is consistent with an atmospheric origin for the shadow bands. Cross-correlations between the detector outputs are low, suggesting a short persistence time for the turbulent elements causing the patterns.

Marschall, L. A.↗

Potential impact of aerosols on convective clouds revealed by Himawari-8 observations over different terrain types in eastern China

Convective clouds are common and play a major role in Earth's water cycle and energy balance; they may even develop into storms and cause severe rainfall events. To understand the convective cloud development process, this study investigates the impact of aerosols on convective clouds by considering the influence of both topography and diurnal variation in radiation. By combining texture analysis, clustering, and thresholding methods, we identify all convective clouds in two warm seasons (May–September, 2016/17) in eastern China based on Himawari-8 Level 1 data. Having large diurnally resolved cloud data together with surface meteorological and environmental measurements, we investigate convective cloud properties and their variation, stratified by elevation and diurnal change. We then analyze the potential impact of aerosol on convective clouds under different meteorological conditions and topographies. In general, convective clouds tend to occur preferentially under polluted conditions in the morning, which reverses in the afternoon. Convective cloud fraction first increases then decreases with aerosol loading, which may contribute to this phenomenon. Topography and diurnal meteorological variations may affect the strength of aerosol microphysical and radiative effects. Updraft is always stronger along the windward slopes of mountains and plateaus, especially in northern China. The prevailing southerly wind near the foothills of mountains and plateaus is likely to contribute to this windward strengthening of updraft and to bring more pollutant into the mountains, thereby strengthening the microphysical effect, invigorating convective clouds. By comparison, over plain, aerosols decrease surface heating and suppress convection by blocking solar radiation reaching the surface.

clouds↗

Nonlinear Thermomechanical Response of Composite Panels with Continuous and Terminated Stiffeners

A two-phase approach and a computational procedure are used for predicting the variability of the response of stiffened composite panels associated with variations in the geometric and material parameters of the structures. In the first phase, hierarchical sensitivity analysis is used to identify the major parameters that have the most effect on the response quantities of interest. In the second phase, the major parameters are taken to be fuzzy parameters, and a fuzzy set analysis is used to determine the range of variation of the response, associated with preselected variations in the major parameters. Numerical results are presented showing the variability of the response of panels with both continuous and terminated stiffeners associated with variations in the micro mechanical and geometric parameters. Both flat and curved panels are considered.

Noor, Ahmed K.↗

Airborne Measurements of Scale‐Dependent Latent Heat Flux Impacted by Water Vapor and Vertical Velocity Over Heterogeneous Land Surfaces During the CHEESEHEAD19 Campaign

Abstract The water vapor transport associated with latent heat flux (LE) in the planetary boundary layer (PBL) is critical for the atmospheric hydrological cycle, radiation balance, and cloud formation. The spatiotemporal variability of LE and water vapor mixing ratio ( r v ) are poorly understood due to the scale‐dependent and nonlinear atmospheric transport responses to land surface heterogeneity. Here, airborne in situ measurements with the wavelet technique are utilized to investigate scale‐dependent relationships among LE, vertical velocity ( w ) variance (), and r v variance () over a heterogeneous surface during the Chequamegon Heterogeneous Ecosystem Energy‐balance Study Enabled by a High‐density Extensive Array of Detectors 2019 (CHEESEHEAD19) field campaign. Our findings reveal distinct scale distributions of LE, , and at 100 m height, with a majority scale range of 120 m–4 km in LE, 32 m–2 km in , and 200 m–8 km in . The scales are classified into three scale ranges, the turbulent scale (8–200 m), large‐eddy scale (200 m–2 km), and mesoscale (2–8 km) to evaluate scale‐resolved LE contributed by and . The large‐eddy scale in PBL contributes over 70% of the monthly mean total LE with equal parts (50%) of contributions from and . The monthly temporal variations mainly come from the first two major contributing classified scales in LE, , and . These results confirm the dominant role of the large‐eddy scale in the PBL in the vertical moisture transport from the surface to the PBL, while the mesoscale is shown to contribute an additional ∼20%. This analysis complements published scale‐dependent LE variations, which lack detailed scale‐dependent vertical velocity and moisture information.

54 ENVIRONMENTAL SCIENCES↗

A method to account for variation of average compressor inlet pressure during instantaneous distortion analyses

Instantaneous distortion analyses compare a time-varying value of an index (or 'surge margin used up') with a critical level (or 'available surge margin' of the compressor) to determine inlet-engine compatibility. Unless freestream conditions or propulsion system controls are changing, it is generally assumed that the available surge margin of the compressor is accurately determined from the steady-state operating point. Results are presented which show that variations of average compressor inlet pressure may occur without changes in freestream conditions or propulsion system controls. The volume dynamics of the compressor will cause these pressure variations to be attenuated and delayed by the time they reach the exit. This will cause the compressor pressure ratio (and available surge margin) to vary with time. A method is presented to calculate the available surge margin as a function of time and incorporate it into an instantaneous distortion analysis. Results show that inlet pressure variations which cause only a small change at the compressor exit can cause a significant variation in the available surge margin.

Burstadt, P. L.↗