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At least 1,711 records · Page 95

Saccharomycotina yeasts defy long-standing macroecological patterns

The Saccharomycotina yeasts (“yeasts” hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild. Here, we trained machine learning models on 12,816 terrestrial occurrence records and 96 environmental variables to infer global distribution maps at ~1 km2 resolution for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversity. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high-diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many long-standing macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and a positive relationship between latitude and range size (Rapoport’s rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.

59 BASIC BIOLOGICAL SCIENCES↗

Collaborative investigation of the internal flow and near-nozzle flow of an eight-hole gasoline injector (Engine Combustion Network Spray G)

The internal details of fuel injectors have a profound impact on the emissions from gasoline direct injection engines. However, the impact of injector design features is not currently understood, due to the difficulty in observing and modeling internal injector flows. Gasoline direct injection flows involve moving geometry, flash boiling, and high levels of turbulent two-phase mixing. In order to better simulate these injectors, five different modeling approaches have been employed to study the engine combustion network Spray G injector. Here these simulation results have been compared to experimental measurements obtained, among other techniques, with X-ray diagnostics, allowing the predictions to be evaluated and critiqued. The ability of the models to predict mass flow rate through the injector is confirmed, but other features of the predictions vary in their accuracy. The prediction of plume width and fuel mass distribution varies widely, with volume-of-fluid tending to overly concentrate the fuel. All the simulations, however, seem to struggle with predicting fuel dispersion and by inference, jet velocity. This shortcoming of the predictions suggests a need to improve Eulerian modeling of dense fuel jets.

ECN↗

Prediction and Inference of Multi-scale Electrical Properties of Geomaterials

Motivated by the need for improved forward modeling and inversion capabilities of geophysical response in geologic settings whose fine--scale features demand accountability, this project describes two novel approaches which advance the current state of the art. First is a hierarchical material properties representation for finite element analysis whereby material properties can be prescribed on volumetric elements, in addition to their facets and edges. Hence, thin or fine--scaled features can be economically represented by small numbers of connected edges or facets, rather than 10's of millions of very small volumetric elements. Examples of this approach are drawn from oilfield and near--surface geophysics where, for example, electrostatic response of metallic infastructure or fracture swarms is easily calculable on a laptop computer with an estimated reduction in resource allocation by 4 orders of magnitude over traditional methods. Second is a first-ever solution method for the space--fractional Helmholtz equation in geophysical electromagnetics, accompanied by newly--found magnetotelluric evidence supporting a fractional calculus representation of multi-scale geomaterials. Whereas these two achievements are significant in themselves, a clear understanding the intermediate length scale where these two endmember viewpoints must converge remains unresolved and is a natural direction for future research. Additionally, an explicit mapping from a known multi-scale geomaterial model to its equivalent fractional calculus representation proved beyond the scope of the present research and, similarly, remains fertile ground for future exploration.

42 ENGINEERING↗

Characterization of low-mass, wide-separation substellar companions to stars in upper SCORPIUS: Near-infrared photometry and spectroscopy

We present new 0.9–2.45 μm spectroscopy (R∼1000 ), and Y, J, H, K{sub s}, L{sup ′} photometry, obtained at Gemini North, of three low-mass brown dwarf companions on wide orbits around young stars of the Upper Scorpius OB association: HIP 78530 B, [PGZ 2001] J161031.9-191305 B, and GSC 06214-00210 B. We use these data to assess the companions’ spectral type, temperature, surface gravity, and mass, as well as the ability of the BT-SETTL and Drift-Phoenix atmosphere models to reproduce the spectral features of young substellar objects. For completeness, we also analyze the archival spectroscopy and photometry of the Upper Scorpius planetary mass companion 1RXS J160929.1-210524 b. Based on a comparison with model spectra we find that the companions, in the above order, have effective temperatures of 2700 ± 100, 2500 ± 200, 2300 ± 100, and 1700 ± 100 K. These temperatures are consistent with our inferred spectral types, respectively M7 β, M9 γ, M9 γ, and L4 γ, obtained from spectral indices and comparisons with templates. From bolometric luminosities estimated from atmosphere model spectra adjusted to our photometry, and using evolution models at 5–10 Myr, we estimate masses of 21–25, 28–70, 14–17, and 7–12 M{sub Jup}, respectively. [PGZ 2001] J161031.9-191305 B appears significantly overluminous for its inferred temperature, which explains its higher mass estimate. Synthetic spectra based on the BT-Settl and Drift-Phoenix atmosphere models generally offer a good fit to our observed spectra, although our analysis has highlighted a few problems. For example, the best fits in the individual near-infrared bands occur at different model temperatures. Also, temperature estimates based on a comparison of the broadband magnitudes and colors of the companions to synthetic magnitudes from the models are systematically lower than the temperature estimates based on a comparison with synthetic spectra.

79 ASTRONOMY AND ASTROPHYSICS↗

Analytic Neural Network Gaussian Process Enabled Chance-Constrained Voltage Regulation for Active Distribution Systems with PVs, Batteries and EVs

This paper proposes an analytic neural network Gaussian process (NNGP)-based chance-constrained real-time voltage regulation method for active distribution systems with photovoltaics (PVs), batteries, and electric vehicles (EVs). NNGP can utilize historical measurement data to achieve real-time probabilistic node voltage estimation through Bayesian inference. Then, NNGP is fully analytically embedded into the optimal power flow model to perform voltage regulation and adapt to various topological changes. The uncertainties of voltage estimations are easily considered via the chance constraint, and it has been shown that the adoption of this chance constraint can significantly improve the reliability of voltage regulation under various scenarios. The comparison results with other methods, carried out on a real 759-node distribution system located in western Colorado, U.S., show that the proposed method can achieve accurate voltage estimation across different topologies and reliably perform voltage regulation considering PVs, batteries, and EVs.

active distribution systems↗

Nonparametric extensions of nuclear equations of state: Probing the breakdown scale of relativistic mean-field theory

Phenomenological calculations of the properties of dense matter, such as relativistic mean-field theories, represent a pathway to predicting the microscopic and macroscopic properties of neutron stars. However, such theories do not generically have well-controlled uncertainties and may break down within neutron stars. To faithfully represent the uncertainty in this breakdown scale, we develop a hybrid representation of the dense-matter equation of state, which assumes the form of a relativistic mean-field theory at low densities, while remaining agnostic to any nuclear theory at high densities. To achieve this, we use a nonparametric equation of state model to incorporate the correlations of the underlying relativistic mean-field theory equation of state at low pressures and transition to more flexible correlations above some chosen pressure scale. We perform astrophysical inference under various choices of the transition pressure between the theory-informed and theory-agnostic models. Here, we further study whether the chosen relativistic mean-field theory breaks down above some particular pressure and find no such evidence. Using simulated data for future astrophysical observations at about two-to-three times the precision of current constraints, we show that our method can identify the breakdown pressure associated with a potential strong phase transition.

Equations of state of nuclear matter↗

Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification

Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences.

59 BASIC BIOLOGICAL SCIENCES↗

STELLAR POPULATIONS IN THE OUTER HALO OF THE MASSIVE ELLIPTICAL M49

We use deep surface photometry of the giant elliptical M49 (NGC 4472), obtained as part of our survey for diffuse light in the Virgo Cluster, to study the stellar populations in its outer halo. Our data trace M49's stellar halo out to {approx}100 kpc (7r{sub e}), where we find that the shallow color gradient seen in the inner regions becomes dramatically steeper. The outer regions of the galaxy are quite blue (B - V {approx} 0.7); if this is purely a metallicity effect, it argues for extremely metal-poor stellar populations with [Fe/H] < -1. We also find that the extended accretion shells around M49 are distinctly redder than the galaxy's surrounding halo, suggesting that we are likely witnessing the buildup of both the stellar mass and metallicity in M49's outer halo due to late time accretion. While such growth of galaxy halos is predicted by models of hierarchical accretion, this growth is thought to be driven by more massive accretion events which have correspondingly higher mean metallicity than inferred for M49's halo. Thus the extremely metal-poor nature of M49's extended halo provides some tension against current models for elliptical galaxy formation.

79 ASTRONOMY AND ASTROPHYSICS↗

A physics-constrained neural ordinary differential equations approach for robust learning of stiff chemical kinetics

The high computational cost associated with solving for detailed chemistry poses a significant challenge for predictive computational fluid dynamics (CFD) simulations of turbulent reacting flows. While deep learning techniques have been explored to develop faster surrogate models, they often fail to integrate reliably with CFD solvers. This instability arises because traditional deep learning approaches optimize for training error without ensuring compatibility with ordinary differential equation (ODE) solvers, resulting in accumulation of errors over time. Recently, neuralODE (NODE) based approaches have been shown to be a promising technique to emulate and accelerate detailed chemistry computations. Here, in the present work, we extend this NODE framework for stiff chemical kinetics by incorporating mass conservation constraints directly into the loss function during training. This ensures that the total mass as well as the individual elemental species masses are conserved in an a-posteriori manner. Proof-of-concept studies are performed with the novel physics-constrained NODE (PC-NODE) approach for homogeneous autoignition of hydrogen-air mixture over a range of composition and thermodynamic conditions. It is demonstrated that the PC-NODE framework not only improves the physical consistency of the resulting data-driven model with respect to mass conservation criteria, but also improves training efficiency. PC-NODE is shown to achieve 2–100× speedup relative to the hydrogen-air detailed chemical mechanism depending on the type of the ODE solver (implicit or explicit) used during autoregressive inference tests. Lastly, a-posteriori studies are performed wherein the trained PC-NODE model is coupled with a CFD solver. It is shown that higher accuracy is achieved with PC-NODE relative to the purely data-driven NODE approach. Moreover, PC-NODE also exhibits robustness and generalizability to unseen initial conditions from within (interpolative capability) as well as outside (extrapolative capability) the training regime.

computational combustion↗

Quantifying and Reducing Curve-Fitting Uncertainty in Isc: Preprint

Current-voltage (I-V) curve measurements of photovoltaic (PV) devices are used to determine performance parameters and to establish traceable calibration chains. Measurement standards specify localized curve fitting methods, e.g., straight-line interpolation/extrapolation of the I-V curve points near short-circuit current, Isc. By considering such fits as statistical linear regressions, uncertainties in the performance parameters are readily quantified. However, the legitimacy of such a computed uncertainty requires that the model be a valid (local) representation of the I-V curve and that the noise be sufficiently well characterized. Using more data points often has the advantage of lowering the uncertainty. However, more data points can make the uncertainty in the fit arbitrarily small, and this fit uncertainty misses the dominant residual uncertainty due to so-called model discrepancy. Using objective Bayesian linear regression for straight-line fits for Isc, we investigate an evidence-based method to automatically choose data windows of I-V points with reduced model discrepancy. We also investigate noise effects. Uncertainties, aligned with the Guide to the Expression of Uncertainty in Measurement (GUM), are quantified throughout.

14 SOLAR ENERGY↗

Topographical Controls on Hillslope-Scale Hydrology Drive Shrub Distributions on the Seward Peninsula, Alaska

Observations indicate shrubs are expanding across the Arctic tundra, mainly on hillslopes and primarily in response to climate warming. However, the impact topography exerts on hydrology, nutrient dynamics, and plant growth can make untangling the mechanisms behind shrub expansion difficult. We examined the role topography plays in determining shrub expansion by applying a coupled transect version of a mechanistic ecosystem model (ecosys) in a tundra hillslope site in the Seward Peninsula, Alaska. Modeled biomass of the dominant plant functional types agreed well with field measurements (R 2 = 0.89) and accurately represented shrub expansion over the past 30 years inferred from satellite observations. In the well-drained crest position, canopy water potential and plant nitrogen (N) uptake was modeled to be low from plant and microbial water stress. Intermediate soil water content in the mid-slope position enhanced mineralization and plant N uptake, increasing shrub biomass. The deciduous shrub growth in the mid-slope position was further enhanced by symbiotic N 2 fixation primed by increased root carbon allocation. The gentle slope in the poorly drained lower-slope position resulted in saturated soil conditions that reduced soil O 2 concentrations, leading to lower root O 2 uptake and lower nutrient uptake and plant biomass. Additionally, a simulation that removed topographical interconnectivity between grid cells resulted in (1) a 28% underestimate of mean shrub biomass and (2) over or underestimated shrub productivity at the various hillslope positions. Our results indicate that land models need to account for hillslope-scale coupled surface and subsurface hydrology to accurately predict current plant distributions and future trajectories in Arctic ecosystems.

54 ENVIRONMENTAL SCIENCES↗

A NICER View of PSR J0030+0451: Millisecond Pulsar Parameter Estimation

Here, we report on Bayesian parameter estimation of the mass and equatorial radius of the millisecond pulsar PSR J0030+0451, conditional on pulse-profile modeling of Neutron Star Interior Composition Explorer X-ray spectral-timing event data. We perform relativistic ray-tracing of thermal emission from hot regions of the pulsar's surface. We assume two distinct hot regions based on two clear pulsed components in the phase-folded pulse-profile data; we explore a number of forms (morphologies and topologies) for each hot region, inferring their parameters in addition to the stellar mass and radius. For the family of models considered, the evidence (prior predictive probability of the data) strongly favors a model that permits both hot regions to be located in the same rotational hemisphere. Models wherein both hot regions are assumed to be simply connected circular single-temperature spots, in particular those where the spots are assumed to be reflection-symmetric with respect to the stellar origin, are strongly disfavored. For the inferred configuration, one hot region subtends an angular extent of only a few degrees (in spherical coordinates with origin at the stellar center) and we are insensitive to other structural details; the second hot region is far more azimuthally extended in the form of a narrow arc, thus requiring a larger number of parameters to describe. The inferred mass M and equatorial radius R eq are, respectively, ${1.34}_{-0.16}^{+0.15}\,{M}_{\odot }$ and ${12.71}_{-1.19}^{+1.14}\,\mathrm{km}$, while the compactness ${GM}/{R}_{\mathrm{eq}}{c}^{2}={0.156}_{-0.010}^{+0.008}$ is more tightly constrained; the credible interval bounds reported here are approximately the 16% and 84% quantiles in marginal posterior mass.

79 ASTRONOMY AND ASTROPHYSICS↗

Pulse profile modelling of thermonuclear burst oscillations – II. Handling variability

ABSTRACT Pulse profile modelling is a relativistic ray-tracing technique that can be used to infer masses, radii, and geometric parameters of neutron stars. In a previous study, we looked at the performance of this technique when applied to thermonuclear burst oscillations from accreting neutron stars. That study showed that ignoring the variability associated with burst oscillation sources resulted in significant biases in the inferred mass and radius, particularly for the high count rates that are nominally required to obtain meaningful constraints. In this follow-on study, we show that the bias can be mitigated by slicing the bursts into shorter segments where variability can be neglected, and jointly fitting the segments. Using this approach, the systematic uncertainties on the mass and radius are brought within the range of the statistical uncertainty. With about 106 source counts, this yields uncertainties of approximately 10 per cent for both the mass and radius. However, this modelling strategy requires substantial computational resources. We also confirm that the posterior distributions of the mass and radius obtained from multiple bursts of the same source can be merged to produce outcomes comparable to that of a single burst with an equivalent total number of counts.

Astronomy & Astrophysics↗

A Review of Bayesian Networks for Spatial Data

We report Bayesian networks are a popular class of multivariate probabilistic models as they allow for the translation of prior beliefs about conditional dependencies between variables to be easily encoded into their model structure. Due to their widespread usage, they are often applied to spatial data for inferring properties of the systems under study and also generating predictions for how these systems may behave in the future. We review published research on methodologies for representing spatial data with Bayesian networks and also summarize the application areas for which Bayesian networks are employed in the modeling of spatial data. We find that a wide variety of perspectives are taken, including a GIS-centric focus on efficiently generating geospatial predictions, a statistical focus on rigorously constructing graphical models controlling for spatial correlation, as well as a range of problem-specific heuristics for mitigating the effects of spatial correlation and dependency arising in spatial data analysis. Special attention is also paid to potential future directions for integration of Bayesian networks with spatial processes.

97 MATHEMATICS AND COMPUTING↗

TCAD-Machine Learning Enabled TID Compact Model Development for Commercial SiC MOSFET

We propose a TCAD (Technology Computer Aided Design)-machine learning coupled approach that combines a TCAD tool (Charon), optimization/uncertainty quantification tool (Dakota), surrogate models, and Bayesian learning capabilities. The coupling approach is used for accurate modeling and calibration of total ionizing dose (TID) induced threshold voltage (V th ) shifts in Commercial-Off-The-Shelf (COTS) semiconductor devices and to develop physics-informed TID compact models. This versatile approach is applied to model the TID effect in an exemplar COTS 3.3 kV SiC power MOSFET (Metal-Oxide-Semiconductor Field-Effect Transistor). With the Charon-Dakota coupling, we can determine key device geometry and doping values based on device physics, which are difficult to obtain or not available for COTS devices but important for TCAD simulation; additionally, we can efficiently generate thousands of simulation results in a large parameter space, which makes it possible to develop data-driven surrogate models and perform Bayesian calibration. Utilizing the full tool-coupling approach, we achieve calibrated TCAD simulation models that accurately capture the average TID-induced V th shifts behavior with total doses and V th shifts saturation at high doses as observed in experimental data. More importantly, the calibrated TCAD simulations are obtained with determined TID model parameters (e.g., hole trap density and capture cross section) values that contain well quantified uncertainties. Furthermore, we can isolate and quantify the noises that are not captured by the TCAD models but exist in the measured data due to measurements and devices variabilities. Lastly, the calibrated surrogate models are used to develop physics-informed TID compact models. The method is generalizable to other devices and/or radiation conditions with few modifications and can provide well-determined uncertainties.

COTS↗

Adaptive Neuro Fuzzy Inference System for Cyber-Intrusion Detection in a Smart Grid

The evolution of the power grid has brought increasing deployment of advance metering infrastructure, penetration of intelligent electronic devices, and integration of physical power system components with information and communications technologies. With the fast-expanding connectivity, cyber vulnerabilities arise due to the use of internet-based communication systems. These systems are targets of cyber-intrusions which attempt to disturb the normal power system functions. Traditional intrusion detection algorithms have been developed without an explicit model of the cyber components. In this paper, an algorithm to detect false data injections in the power system is proposed considering both cyber and physical models of the power system. The algorithm is based on an Adaptive Neuro Fuzzy Inference System (ANFIS) which collects information from state variables of the cyber-physical system to meet the performance requirements of the grid. Simulations of the proposed approach using the IEEE 13-bus test system validate the effectiveness of this artificial intelligence-based algorithm.

Adaptive Neuro Fuzzy Inference System (ANFIS), cyb↗

Soil Water Characteristics of Cores from Low- and High-Centered Polygons, Utqiagvik (Barrow), Alaska, 2012

This dataset includes soil water characteristic curves for soil and permafrost in two representative frozen cores collected from a high-center polygon (HCP) and a low-center polygon (LCP) from the Barrow Environmental Observatory. Data include soil water content and soil water potential measured using the simple evaporation method for hydrological and biogeochemical simulations and experimental data analysis. Data can be used to generate a soil moisture characteristic curve, which can be fit to a variety of hydrological functions to infer critical parameters for soil physics. Considering the measured the soil water properties, the van Genuchten model predicted well the HCP, in contrast, the Kosugi model well fitted LCP which had more saturated condition. This dataset includes 8 zipped files, one txt files, and one pdf file.Data were collected to estimate soil water potential and water availability at various temperatures and conditions for hydrological and biogeochemical simulations and experimental data analysis. Data can be used to generate a soil moisture characteristic curve, which can be fit to a variety of hydrological functions to infer critical parameters for soil physics.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

Protein Quantitation, proteomics↗