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At least 127 records · Page 7

Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species. However, as with any trait, comparing gene expression across species can be confounded by the non-independence of species due to shared ancestry, making standard hypothesis testing inappropriate. We compared RNA-Seq data across 18 fungal species using a multivariate Brownian Motion phylogenetic comparative method (PCM), which allowed us to quantify coevolution between protein pairs while directly accounting for the shared ancestry of the species. Our work indicates proteins which physically-interact show stronger signals of coevolution than randomly-generated pairs. Interactions with stronger empirical and computational evidence also showing stronger signals of coevolution. We examined the effects of number of protein interactions and gene expression levels on coevolution, finding both factors are overall poor predictors of the strength of coevolution between a protein pair. Simulations further demonstrate the potential issues of analyzing gene expression coevolution without accounting for shared ancestry in a standard hypothesis testing framework. Furthermore, our simulations indicate the use of a randomly-generated null distribution as a means of determining statistical significance for detecting coevolving genes with phylogenetically-uncorrected correlations, as has previously been done, is less accurate than PCMs, although is a significant improvement over standard hypothesis testing. These methods are further improved by using a phylogenetically-corrected correlation metric. Our work highlights potential benefits of using PCMs to detect gene expression coevolution from high-throughput omics scale data. This framework can be built upon to investigate other evolutionary hypotheses, such as changes in transcription regulatory mechanisms across species.

59 BASIC BIOLOGICAL SCIENCES↗

Discovering Active Subspaces for High-Dimensional Computer Models

Dimension reduction techniques have long been an important topic in statistics, and active subspaces (AS) have received much attention this past decade in the computer experiments literature. The most common approach towards estimating the AS is to use Monte Carlo with numerical gradient evaluation. While sensible in some settings, this approach has obvious drawbacks. Recent research has demonstrated that active subspace calculations can be obtained in closed form, conditional on a Gaussian process (GP) surrogate, which can be limiting in high-dimensional settings for computational reasons. In this paper, we produce the relevant calculations for a more general case when the model of interest is a linear combination of tensor products. These general equations can be applied to the GP, recovering previous results as a special case, or applied to the models constructed by other regression techniques including multivariate adaptive regression splines (MARS). Furthermore, using a MARS surrogate has many advantages including improved scaling, better estimation of active subspaces in high dimensions and the ability to handle a large number of prior distributions in closed form. In one real-world example, we obtain the active subspace of a radiation-transport code with 240 inputs and 9,372 model runs in under half an hour.

97 MATHEMATICS AND COMPUTING↗

Non-Gaussianity in the weak lensing correlation function likelihood – implications for cosmological parameter biases

ABSTRACT We study the significance of non-Gaussianity in the likelihood of weak lensing shear two-point correlation functions, detecting significantly non-zero skewness and kurtosis in 1D marginal distributions of shear two-point correlation functions in simulated weak lensing data. We examine the implications in the context of future surveys, in particular LSST, with derivations of how the non-Gaussianity scales with survey area. We show that there is no significant bias in 1D posteriors of Ωm and σ8 due to the non-Gaussian likelihood distributions of shear correlations functions using the mock data (100 deg2). We also present a systematic approach to constructing approximate multivariate likelihoods with 1D parametric functions by assuming independence or more flexible non-parametric multivariate methods after decorrelating the data points using principal component analysis (PCA). While the use of PCA does not modify the non-Gaussianity of the multivariate likelihood, we find empirically that the 1D marginal sampling distributions of the PCA components exhibit less skewness and kurtosis than the original shear correlation functions. Modelling the likelihood with marginal parametric functions based on the assumption of independence between PCA components thus gives a lower limit for the biases. We further demonstrate that the difference in cosmological parameter constraints between the multivariate Gaussian likelihood model and more complex non-Gaussian likelihood models would be even smaller for an LSST-like survey. In addition, the PCA approach automatically serves as a data compression method, enabling the retention of the majority of the cosmological information while reducing the dimensionality of the data vector by a factor of ∼5.

79 ASTRONOMY AND ASTROPHYSICS↗

Assessment of the ParFlow–CLM CONUS 1.0 integrated hydrologic model: evaluation of hyper-resolution water balance components across the contiguous United States

Abstract. Recent advancements in computational efficiency and Earth system modeling have awarded hydrologists with increasingly high-resolution models of terrestrial hydrology, which are paramount to understanding and predicting complex fluxes of moisture and energy. Continental-scale hydrologic simulations are, in particular, of interest to the hydrologic community for numerous societal, scientific, and operational benefits. The coupled hydrology–land surface model ParFlow–CLM configured over the continental United States (PFCONUS) has been employed in previous literature to study scale-dependent connections between water table depth, topography, recharge, and evapotranspiration, as well as to explore impacts of anthropogenic aquifer depletion to the water and energy balance. These studies have allowed for an unprecedented process-based understanding of the continental water cycle at high resolution. Here, we provide the most comprehensive evaluation of PFCONUS version 1.0 (PFCONUSv1) performance to date by comparing numerous modeled water balance components with thousands of in situ observations and several remote sensing products and using a range of statistical performance metrics for evaluation. PFCONUSv1 comparisons with these datasets are a promising indicator of model fidelity and ability to reproduce the continental-scale water balance at high resolution. Areas for improvement are identified, such as a positive streamflow bias at gauges in the eastern Great Plains, a shallow water table bias over many areas of the model domain, and low bias in seasonal total water storage amplitude, especially for the Ohio, Missouri, and Arkansas River basins. We discuss several potential sources for model bias and suggest that minimizing error in topographic processing and meteorological forcing would considerably improve model performance. Results here provide a benchmark and guidance for further PFCONUS model development, and they highlight the importance of concurrently evaluating all hydrologic components and fluxes to provide a multivariate, holistic validation of the complete modeled water balance.

O'Neill, Mary M. F. (ORCID:0000000221455165)↗

Human influence on joint changes in temperature, rainfall and continental aridity

Despite the pervasive impact of drought on human and natural systems, the large-scale mechanisms conducive to regional drying remain poorly understood. Here we use a multivariate approach to identify two distinct externally forced fingerprints from multiple ensembles of Earth system model simulations. The leading fingerprint, F M1 (x), is characterized by global warming, intensified wet–dry patterns and progressive large-scale continental aridification, largely driven by multidecadal increases in greenhouse gas (GHG) emissions. The second fingerprint, F M2 (x), captures a pronounced interhemispheric temperature contrast, associated meridional shifts in the intertropical convergence zone and correlated anomalies in precipitation and aridity over California, the Sahel and India. F M2 (x) exhibits nonlinear temporal behaviour: the intertropical convergence zone moves southwards before 1975 in response to increases in hemispherically asymmetric sulfate aerosol emissions, and it shifts northwards after 1975 due to reduced sulfur dioxide emissions and the GHG-induced warming of Northern Hemisphere landmasses. Both fingerprints are statistically identifiable in observations of joint changes in temperature, rainfall and aridity during 1950–2014. Furthermore, we show that the reliable simulation of these changes requires combined forcing by GHGs, direct and indirect effects of aerosols, and large volcanic eruptions. Our results suggest that GHG-induced aridification may be modulated regionally by future reductions in sulfate aerosol emissions.

54 ENVIRONMENTAL SCIENCES↗

Intrinsic Kinetics of Polyethylene Terephthalate Pyrolysis via Micropyrolysis and Multivariate Chromatographic Analysis

This study provides an in-depth investigation of the primary decomposition of polyethylene terephthalate (PET) via pyrolysis, employing an experimental-analytic workflow that integrates design of experiments (DoE), micropyrolysis coupled with comprehensive two-dimensional gas chromatography (GC×GC), and multivariate data analysis to verify intrinsic kinetic conditions and elucidate evolving product distributions for mapping key reaction pathways. Peaks that could not be identified using commercial spectral libraries were assigned using Mass Frontier simulations, enabling the identification of divinyl terephthalate, ethyl vinyl terephthalate, and 2-(benzoyloxy)ethyl vinyl terephthalate. A polar×polar (non-orthogonal) column set tailored for the detection of carboxylic acids enhanced the quantification of benzoic acid, 4-vinylbenzoic acid, 4-ethylbenzoic acid, and methylbenzoic acid by up to 6-fold relative to an orthogonal column combination (non-polar×mid-polar). Moreover, pyrolysis variables were systematically evaluated using a Box- Behnken design (BBD), encompassing pyrolysis temperature (500−600 °C), sample weight (50−150 μg), and carrier gas flow rate (100−300 mL min −1 ). Among these, pyrolysis temperature was the only statistically significant factor influencing product yields, ranging from 58.78 to 84.26 wt %. In contrast, neither the sample weight nor the carrier gas flow rate had a significant effect on product yields within the evaluated experimental space. At 600 °C, the major pyrolysis products were benzoic acid (up to 20.20 ± 1.46 wt %) and CO 2 (up to 21.28 ± 1.46 wt %), which can be produced through decarboxylation reactions. These findings underscore the critical importance of selecting appropriate analytical columns for the accurate quantification of heteroatomcontaining products such as carboxylic acids, which may otherwise be underestimated or undetected due to their reactivity with the stationary phase of non-polar and mid-polar columns, as well as other GC components. They also highlight the importance of selecting pyrolysis conditions for investigating the primary decomposition of PET under an isothermal kinetically limited regime.

aromatic compounds↗

Riders’ perceptions towards transit bus electrification: Evidence from Salt Lake City, Utah

While battery electric buses (BEBs) can lead to energy savings and reduced emissions, BEB adoption is developing slowly. Although BEBs offer quieter operations, better acceleration, and no smell of diesel or gas fumes, little focus has been placed on the user’s perspective. Here, this study investigates bus riders’ preferences toward BEBs. To achieve these objectives, a survey was designed and administered to solicit riders’ typical travel behaviors and patterns as well as preferences and opinions about BEBs’ performance in terms of emissions and noise. Statistical analysis showed that several factors influence rider perceptions towards transit bus electrification that include trip purpose, attitudes towards environmental issues and environmental impacts of BEBs, and certain non-instrumental ride factors such as ride comfort and social image. A better understanding of the importance of electrification to transit riders can help transit service providers adjust their marketing decisions and their systemwide operations to accommodate preferences towards BEBs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Machine learning approaches for structural and thermodynamic properties of a Lennard-Jones fluid

Predicting the functional properties of many molecular systems relies on understanding how atomistic interactions give rise to macroscale observables. However, current attempts to develop predictive models for the structural and thermodynamic properties of condensed-phase systems often rely on extensive parameter fitting to empirically selected functional forms whose effectiveness is limited to a narrow range of physical conditions. Here, we illustrate how these traditional fitting paradigms can be superseded using machine learning. Specifically, we use the results of molecular dynamics simulations to train machine learning protocols that are able to produce the radial distribution function, pressure, and internal energy of a Lennard-Jones fluid with increased accuracy in comparison to previous theoretical methods. The radial distribution function is determined using a variant of the segmented linear regression with the multivariate function decomposition approach developed by Craven et al. [J. Phys. Chem. Lett. 11, 4372 (2020)]. The pressure and internal energy are determined using expressions containing the learned radial distribution function and also a kernel ridge regression process that is trained directly on thermodynamic properties measured in simulation. The presented results suggest that the structural and thermodynamic properties of fluids may be determined more accurately through machine learning than through human-guided functional forms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Partial Least Squares, Experimental Design, and Near-Infrared Spectrophotometry for the Remote Quantification of Nitric Acid Concentration and Temperature

Near-infrared spectrophotometry and partial least squares regression (PLSR) were evaluated to create a pleasantly simple yet effective approach for measuring HNO3 concentration with varying temperature levels. A training set, which covered HNO3 concentrations (0.1–8 M) and temperature (10–40 °C), was selected using a D-optimal design to minimize the number of samples required in the calibration set for PLSR analysis. The top D-optimal-selected PLSR models had root mean squared error of prediction values of 1.4% for HNO 3 and 4.0% for temperature. The PLSR models built from spectra collected on static samples were validated against flow tests including HNO 3 concentration and temperature gradients to test abnormal conditions (e.g., bubbles) and the model performance between sample points in the factor space. Based on cross-validation and prediction modeling statistics, the designed near-infrared absorption approach can provide remote, quantitative analysis of HNO 3 concentration and temperature for production-oriented applications in facilities where laser safety challenges would inhibit the implementation of other optical techniques (e.g., Raman spectroscopy) and in which space, time, and/or resources are constrained. The experimental design approach effectively minimized the number of samples in the training set and maintained or improved PLSR model performance, which makes the described chemometric approach more amenable to nuclear field applications.

07 ISOTOPE AND RADIATION SOURCES↗

Small angle scattering of diblock copolymers profiled by machine learning

We outline a machine learning strategy for quantitively determining the conformation of AB-type diblock copolymers with excluded volume effects using small angle scattering. Complemented by computer simulations, a correlation matrix connecting conformations of different copolymers according to their scattering features is established on the mathematical framework of a Gaussian process, a multivariate extension of the familiar univariate Gaussian distribution. We show that the relevant conformational characteristics of copolymers can be probabilistically inferred from their coherent scattering cross sections without any restriction imposed by model assumptions. This work not only facilitates the quantitative structural analysis of copolymer solutions but also provides the reliable benchmarking for the related theoretical development of scattering functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interpolating between small- and large-$\mathscr{g}$ expansions using Bayesian model mixing

Bayesian model mixing (BMM) is a statistical technique that can be used to combine models that are predictive in different input domains into a composite distribution that has improved predictive power over the entire input space. We explore the application of BMM to the mixing of two expansions of a function of a coupling constant $\mathscr{g}$ that are valid at small and large values of $\mathscr{g}$ respectively. This type of problem is quite common in nuclear physics, where physical properties are straightforwardly calculable in strong and weak interaction limits or at low and high densities or momentum transfers, but difficult to calculate in between. Interpolation between these limits is often accomplished by a suitable interpolating function, e.g., Padé approximants, but it is then unclear how to quantify the uncertainty of the interpolant. We address this problem in the simple context of the partition function of zero-dimensional Φ 4 theory, for which the (asymptotic) expansion at small $\mathscr{g}$ and the (convergent) expansion at large $\mathscr{g}$ are both known. We consider three mixing methods: linear mixture BMM, localized bivariate BMM, and localized multivariate BMM with Gaussian processes. Here, we find that employing a Gaussian process in the intermediate region between the two predictive models leads to the best results of the three methods. The methods and validation strategies we present here should be generalizable to other nuclear physics settings.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Predicting Postoperative Injury and Military Discharge Status After Knee Surgery in the US Army

Background: Researchers have assessed postoperative injury or disability predictors in the military setting but typically focused on 1 type of surgical procedure at a time, used relatively small sample sizes, or investigated mixed cohorts with civilian populations. Purpose: To identify the relationship between baseline variables and injury incidence or military discharge status in US Army soldiers after knee surgery. Study Design: Case-control study; Level of evidence, 3. Methods: Data were obtained from a repository containing personnel, performance, and medical records for all active-duty US Army soldiers. Multivariate logistic regressions were used to estimate the effects of numerous variables on postoperative injury or on medical discharge. Variable selection and model validation were conducted using the k-fold method. Results: A total of 7567 soldiers underwent knee surgery between 2017 and 2019. Meniscal procedures were the most common type of surgery (39%), and approximately 71% of the cohort had a postoperative injury. Significant predictors for sustaining a postoperative injury included having a previous nonknee injury (odds ratio [OR], 1.5), female sex (OR, 1.3), and Black race (OR, 1.2). Within 4 years after surgery, 17% of soldiers were discharged from the military because of knee-related disability. Significant predictors for discharge from duty included enlisted rank (OR, 2.3), recent fitness test failure (OR, 1.9), number of previous knee surgeries (OR, 1.7), and having a previous nonknee injury (OR, 1.6). Conclusion: After knee surgery, nearly three-fourths of the soldiers in this cohort sustained a postoperative injury and almost one-fifth of soldiers were medically discharged from the military within 4 years. This study identified variables that indicate statistically increased risk for these postoperative outcomes and highlighted potentially modifiable factors.

Orthopedics↗

Uncertainty bounds for multivariate machine learning predictions on high-strain brittle fracture

Simulation of the crack network evolution on high strain rate impact experiments performed in brittle materials is very compute-intensive. The cost increases even more if multiple simulations are needed to account for the randomness in crack length, location, and orientation, which is inherently found in real-world materials. Constructing a machine learning emulator can make the process faster by orders of magnitude. There has been little work, however, on assessing the error associated with their predictions. Estimating these errors is imperative for meaningful overall uncertainty quantification. In this work, we extend the heteroscedastic uncertainty estimates to bound a multiple output machine learning emulator. Overall, we find that the response prediction is accurate within its predicted errors, but with a somewhat conservative estimate of uncertainty.

36 MATERIALS SCIENCE↗

Evaluating proxies for the drivers of natural gas productivity using machine-learning models

We report the extensive development of unconventional reservoirs using horizontal drilling and multistage hydraulic fracturing has generated large volumes of reservoir characterization and production data. The analysis of this abundant data using statistical methods and advanced machine-learning (ML) techniques can provide data-driven insights into well performance. Most predictive modeling studies have focused on the impact that different well completion and stimulation strategies have on well production but have not fully exploited the available in situ rock property data to determine its role in reservoir productivity. We have used machine-learning techniques to rank rock mechanical properties, microseismic attributes, and stimulation parameters in the order of their significance for predicting natural gas production from an unconventional reservoir. The data for this study came from a hydraulically fractured well in the Marcellus Shale in Monongalia County, West Virginia. The data classes included measurements aggregated by well completion stage that included (1) gas production, (2) well-log-derived measurements including bulk density, elastic moduli, shear impedance, compressional impedance, brittleness, and gamma measurements, (3) microseismic attributes, (4) long-period long-duration (LPLD) event counts, (5) fracture counts, and (6) stimulation parameters that included the fluid injection volume and average pumping pressure. To identify observable proxies for the drivers of gas production, we evaluated five commonly used ML approaches including multivariate adaptive regression spline, Gaussian mixture model, random forest, gradient boosting, and neural network. We selected five variables including LPLD event count, seismogenic b-value, hydraulic diffusivity, cumulative moment, and fluid volume as the features most likely to impact gas productivity at the stage level in the study area. The data-driven selection of these parameters for their importance in determining gas production can help reservoir engineers design more effective hydraulic-fracture treatments in the Marcellus Shale and other similar unconventional reservoirs. Plain language summary: We use machine-learning methods and data-driven selection of reservoir parameters to rank and better understand their importance in determining gas production, which can help reservoir engineers design more effective hydraulic-fracture treatments in the Marcellus Shale and other similar unconventional reservoirs.

58 GEOSCIENCES↗

Supervised machine learning-based multivariate regression of parallel closures for a high-collisionality deuterium-carbon plasma

Many plasmas of interest in laboratory experiments and space consist of multiple ion species. In tokamak edge plasmas, for instance, ionized impurities expelled from the vessel wall influence plasma transport. When describing multi-species plasmas using fluid equations, we need accurate closure relations to close the set of fluid equations. In this study, we introduce the development of fitting formulas for parallel closures using supervised machine learning, in conjunction with the recent closure theory, considering multi-ion collisions and arbitrary ion temperatures. We apply this approach to a high-collisionality deuterium-carbon plasma and demonstrate its effectiveness. As a result, the machine learning-based method for developing practical and accurate closures can be extended to a wider range of plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Kernel-based global sensitivity analysis obtained from a single data set

Results from global sensitivity analysis (GSA) often guide the understanding of complicated input–output systems. Kernel-based GSA methods have recently been proposed for their capability of treating a broad scope of complex systems. In this paper, we develop a new set of kernel GSA tools when only a single set of input–output data is available. Three key advances are made: (1) A new numerical estimator is proposed that demonstrates an empirical improvement over previous procedures. (2) A computational method for generating inner statistical functions from a single data set is presented. (3) A theoretical extension is made to define conditional sensitivity indices, which reveal the degree that the inputs carry shared information about the output when inherent input–input correlations are present. Utilizing these conditional sensitivity indices, a decomposition is derived for the output uncertainty based on what is called the optimal learning sequence of the input variables, which remains consistent when correlations exist between the input variables. Further, while these advances cover a range of GSA subjects, a common single data set numerical solution is provided by a technique known as the conditional mean embedding of distributions. The new methodology is implemented on benchmark systems to demonstrate the provided insights.

42 ENGINEERING↗

Association of Serum Bile Acid and Unsaturated Fatty Acid Profiles with the Risk of Diabetic Retinopathy in Type 2 Diabetic Patients

Aim: We aimed to identify the ability of serum bile acids (BAs) and unsaturated fatty acids (UFAs) profiles to predict the development of diabetic retinopathy (DR) in type 2 diabetes mellitus (T2DM) patients. Methods: We first used univariate and multivariate analysis to compare 15 serum BA and 11 UFA levels in healthy control (HC) group (n = 82), T2DM patients with DR (n = 58) and T2DM patients without DR (n = 60). Forty T2DM patients were considered for validation. Then, the receiver operating characteristic curve (ROC) and decision curve analysis were used to assess the diagnostic value and clinical benefit of serum biomarkers alone, clinical variables alone or in combination, and the area under the curve (AUC), integrated discrimination improvement (IDI), and net reclassification improvement (NRI) were used to further assess whether the addition of biomarkers significantly improved the predictive ability of the model. Results: Orthogonal partial least squares-discriminant analysis (OPLS-DA) of serum BAs and UFAs separated the three cohorts including HC, T2DM patients with or without DR. The difference in serum BA and UFA profiles of T2DM patients with or without DR was mainly manifested in the three metabolites of taurolithocholic acid (TLCA), tauroursodeoxycholic acid (TUDCA) and arachidonic acid (AA). Together, they had an AUC of 0.785 (0.918 for validation cohort) for predicting DR in T2DM patients. After adjusting for numerous confounding factors, TLCA, TUDCA, and AA were independent predictors that differentiated T2DM with or without DR. The results of AUC, IDI, and NRI demonstrated that adding these three biomarkers to a model with clinical variables statistically increased their predictive value and were replicated in our independent validation cohort. Conclusion: These findings highlight the association of three metabolites, TLCA, TUDCA and AA, with DR and may indicate their potential value in the pathogenesis of DR.

60 APPLIED LIFE SCIENCES↗

Lowering post‐construction yield assessment uncertainty through better wind plant power curves

Abstract Many operational analyses of wind power plants require a statistical relationship, which can be called the wind plant power curve, to be developed between wind plant energy production and concurrent atmospheric variables. Currently, a univariate linear regression at monthly resolution is the industry standard for post‐construction yield assessments. Here, we evaluate the benefits in augmenting this conventional approach by testing alternative regressions performed with multiple inputs, at a finer time resolution, and using nonlinear machine‐learning algorithms. We utilize the National Renewable Energy Laboratory's open‐source software package OpenOA to assess wind plant power curves for 10 wind plants. When a univariate generalized additive model at daily or hourly resolution is used, regression uncertainty is reduced, in absolute terms, by up to 1.0 % and 1.2 % (corresponding to a −59 % and −80 % relative change), respectively, compared to a univariate linear regression at monthly resolution; also, a more accurate assessment of the mean long‐term wind plant production is achieved. Additional input variables also reduce the regression uncertainty: when temperature is added as an input to the conventional monthly linear regression, the operational analysis uncertainty connected to regression is reduced, in absolute terms, by up to 0.5 % (−43 % relative change) for wind power plants with strong seasonal variability. Adding input variables to the machine‐learning model at daily resolution can further reduce regression uncertainty, with up to a −10 % relative change. Based on these results, we conclude that a multivariate nonlinear regression at daily or hourly resolution should be recommended for assessing wind plant power curves.

17 WIND ENERGY↗