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DOE OSTI2020

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↗

DOE OSTI2022

Dietary B group vitamin intake and the bladder cancer risk: a pooled analysis of prospective cohort studies

Abstract Purpose Diet may play an essential role in the aetiology of bladder cancer (BC). The B group complex vitamins involve diverse biological functions that could be influential in cancer prevention. The aim of the present study was to investigate the association between various components of the B group vitamin complex and BC risk. Methods Dietary data were pooled from four cohort studies. Food item intake was converted to daily intakes of B group vitamins and pooled multivariate hazard ratios (HRs), with corresponding 95% confidence intervals (CIs), were obtained using Cox-regression models. Dose–response relationships were examined using a nonparametric test for trend. Results In total, 2915 BC cases and 530,012 non-cases were included in the analyses. The present study showed an increased BC risk for moderate intake of vitamin B1 (HR B1 : 1.13, 95% CI: 1.00–1.20). In men, moderate intake of the vitamins B1, B2, energy-related vitamins and high intake of vitamin B1 were associated with an increased BC risk (HR (95% CI): 1.13 (1.02–1.26), 1.14 (1.02–1.26), 1.13 (1.02–1.26; 1.13 (1.02–1.26), respectively). In women, high intake of all vitamins and vitamin combinations, except for the entire complex, showed an inverse association (HR (95% CI): 0.80 (0.67–0.97), 0.83 (0.70–1.00); 0.77 (0.63–0.93), 0.73 (0.61–0.88), 0.82 (0.68–0.99), 0.79 (0.66–0.95), 0.80 (0.66–0.96), 0.74 (0.62–0.89), 0.76 (0.63–0.92), respectively). Dose–response analyses showed an increased BC risk for higher intake of vitamin B1 and B12. Conclusion Our findings highlight the importance of future research on the food sources of B group vitamins in the context of the overall and sex-stratified diet.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in Aspergillus nidulans

The fungal cell-wall integrity signaling (CWIS) pathway regulates cellular response to environmental stress to enable wall repair and resumption of normal growth. This complex, interconnected, pathway has been only partially characterized in filamentous fungi. To better understand the dynamic cellular response to wall perturbation, a β-glucan synthase inhibitor (micafungin) was added to a growing A. nidulans shake-flask culture. From this flask, transcriptomic and phosphoproteomic data were acquired over 10 and 120 min, respectively. To differentiate statistically-significant dynamic behavior from noise, a multivariate adaptive regression splines (MARS) model was applied to both data sets. Over 1800 genes were dynamically expressed and over 700 phosphorylation sites had changing phosphorylation levels upon micafungin exposure. Twelve kinases had altered phosphorylation and phenotypic profiling of all non-essential kinase deletion mutants revealed putative connections between PrkA, Hk-8–4, and Stk19 and the CWIS pathway. Our collective data implicate actin regulation, endocytosis, and septum formation as critical cellular processes responding to activation of the CWIS pathway, and connections between CWIS and calcium, HOG, and SIN signaling pathways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Data-Driven Computation of Probabilistic Marching Cubes for Efficient Visualization of Level-Set Uncertainty

Uncertainty visualization is an important emerging research area. Being able to visualize data uncertainty can help scientists improve trust in analysis and decision-making. However, visualizing uncertainty can add computational overhead, which can hinder the efficiency of analysis. In this paper, we propose novel data-driven techniques to reduce the computational requirements of the probabilistic marching cubes (PMC) algorithm. PMC is an uncertainty visualization technique that studies how uncertainty in data affects level-set positions. However, the algorithm relies on expensive Monte Carlo (MC) sampling for the multivariate Gaussian uncertainty model because no closed-form solution exists for the integration of multivariate Gaussian. In this work, we propose the eigenvalue decomposition and adaptive probability model techniques that reduce the amount of MC sampling in the original PMC algorithm and hence speed up the computations. Our proposed methods produce results that show negligible differences compared with the original PMC algorithm demonstrated through metrics, including root mean squared error, maximum error, and difference images. We demonstrate the performance and accuracy evaluations of our data-driven methods through experiments on synthetic and real datasets.

Athawale, Tushar↗

DOE OSTI2020

Active Learning-driven Quantitative Synthesis-Structure-Property Relations for Improving Performance and Revealing Active Sites of Nitrogen-Doped Carbon for the Hydrogen Evolution Reaction

While quantitative structure-properties relations (QSPRs) have been developed successfully in multiple fields, catalyst synthesis affects structure and in turn performance, making simple QSPRs inadequate. Furthermore, catalysts often have multiple active sites preventing one from obtaining insights into structure-property relations. Here, we develop a data-driven quantitative synthesis-structure-property relation (QS2PRs) methodology to elucidate correlations between catalyst synthesis conditions, structural properties as well as observed performance and to provide fundamental insights into active sites and a systematic way to optimize practical catalysts. Here, we demonstrate the approach to the synthesis of nitrogen-doped catalysts (NDC) made via pyrolysis for the performance of the electrochemical hydrogen evolution reaction (HER), quantified by the onset potential and the current density. We determine crystallinity, nitrogen species type and fraction, surface area, and pore structure of the NDC’s using XRD, XPS, and BET characterization. We demonstrated that an active learning-based optimization combined with various elementary machine learning tools (regression, principal component analysis, partial least squares) can efficiently identify optimum pyrolysis conditions to tune structural characteristics and performance with concomitant savings in materials and experimental time. Unlike previous reports on the importance of pyridinic or graphitic nitrogen, we discover that the electrochemical performance is not driven by a single catalyst property; rather, it arises from a multivariate influence of nitrogen dopants, pore structure and disorder in the NDC materials. Identification of active sites can help mechanistic understanding and further catalyst improvement.

42 ENGINEERING↗

DOE OSTI2023

Design and Stability Analysis of Control System in Multiport Autonomous Reconfigurable Solar Power Plants (MARS)

The Multiport Autonomous Reconfigurable Solar Power Plant (MARS) is an integrated photovoltaic (PV) power generation and energy storage system (ESS), that is designed to connect to both alternating current (AC) transmission grids and high-voltage direct current (HVDC) links. It is a three-phase plant consisting of numerous components with a complex hardware and hierarchical control architecture. This paper presents an approach to decouple the multivariable system of MARS using a recursive reduced-order and boundary layer system methodology. This approach enables efficient computation of the control parameters for the Ll, L2, and L3 controllers. To validate the effectiveness of the proposed control strategy, cyclic tests in accordance with pre-defined performance criteria using controller Hardware-in-the-Loop (cHIL) experiments are conducted. The results demonstrate that the MARS system operates consistently under steady-state conditions. Furthermore, the dynamic response of the MARS system to various grid events is analyzed, underlining the resilience of MARS in presence of faults or loss of generation within the connected WECC system.

Xia, Qian↗

DOE OSTI2023

Observation of four-top-quark production in the multilepton final state with the ATLAS detector

This paper presents the observation of four-top-quark ($t$$\overline{t}$$t$$\overline{t}$) production in proton-proton collisions at the LHC. The analysis is performed using an integrated luminosity of 140 fb -1 at a centre-of-mass energy of 13 TeV collected using the ATLAS detector. Events containing two leptons with the same electric charge or at least three leptons (electrons or muons) are selected. Event kinematics are used to separate signal from background through a multivariate discriminant, and dedicated control regions are used to constrain the dominant backgrounds. The observed (expected) significance of the measured $t$$\overline{t}$$t$$\overline{t}$ signal with respect to the standard model (SM) background-only hypothesis is 6.1 (4.3) standard deviations. The $t$$\overline{t}$$t$$\overline{t}$ production cross section is measured to be ${22.5}^{+6.6}_{-5.5}$, consistent with the SM prediction of 12.0 ± 2.4 fb within 1.8 standard deviations. Data are also used to set limits on the three-top-quark production cross section, being an irreducible background not measured previously, and to constrain the top-Higgs Yukawa coupling and effective field theory operator coefficients that affect $t$$\overline{t}$$t$$\overline{t}$ production.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Real-time elemental analysis of liquids for process monitoring using laser-induced breakdown spectroscopy with a liquid wheel sampling approach

This article presents an engineered sampling system that used a rotating wheel to form a thin liquid layer, permitting the use of laser-induced breakdown spectroscopy (LIBS) for in situ, real-time elemental impurity quantification during liquid processing. The sampling approach was demonstrated on eight elements from across the periodic table (Na, Al, K, Ca, Ti, Sr, Mo, and Yb). Univariate and multivariate calibrations were presented for each element. The average value for percent root mean square errors of cross-validation for the multivariate models was 3.64%, highlighting the method's strong prediction accuracy. Additionally, the limits of detection for each analyte were estimated from their univariate models: Na = 0.0532, Al = 18.5, K = 0.105, Ca = 0.273, Ti = 67.7, Sr = 0.640, Mo = 22.4, and Yb = 22.9 μg mL –1 . Finally, a test in which multivariate models were used to monitor a liquid system for 80 min was performed to investigate the real-time monitoring capabilities of this liquid LIBS sampling approach. Rigorous measurements were performed to effectively predict the absence and concentrations of multiple analytes as they were spiked and diluted. This demonstration showed the feasibility of using LIBS for real-time liquid quantification models with estimated precision ≤ 8.1%. Finally, the limitations of this approach and potential future improvements are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Search for Baryon Number Violation in Top Quark Production and Decay Using Proton-Proton Collisions at $\sqrt{𝑠}$ = 13 TeV

A search is presented for baryon number violating interactions in top quark production and decay. The analysis uses data from proton-proton collisions at a center-of-mass energy of 13 TeV, collected with the CMS detector at the LHC with an integrated luminosity of 138 fb −1 . Candidate events are selected by requiring two oppositely charged leptons (electrons or muons) and exactly one jet identified as originating from a bottom quark. Multivariate discriminants are used to separate the signal from the background. No significant deviation from the standard model prediction is observed. Upper limits are placed on the strength of baryon number violating couplings. For the first time the production of single top quarks via baryon number violating interactions is studied. This allows the search to set the most stringent constraints to date on the branching fraction of the top quark decay to a lepton, an up-type quark (𝑢 or 𝑐), and a down-type quark (𝑑, 𝑠, or 𝑏). The results improve the previous bounds by 3 to 6 orders of magnitude based on the fermion flavor combination of the baryon number violating interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Organic matter distribution in the icy environments of Taylor Valley, Antarctica

Glaciers can accumulate and release organic matter affecting the structure and function of associated terrestrial and aquatic ecosystems. Here we analyzed 18 ice cores collected from six locations in Taylor Valley (McMurdo Dry Valleys), Antarctica to determine the spatial abundance and quality of organic matter, and the spatial distribution of bacterial density and community structure from the terminus of the Taylor Glacier to the coast (McMurdo Sound). Our results showed that dissolved and particulate organic carbon (DOC and POC) concentrations in the ice core samples increased from the Taylor Glacier to McMurdo Sound, a pattern also shown by bacterial cell density. Fluorescence Excitation Emission Matrices Spectroscopy (EEMs) and multivariate parallel factor (PARAFAC) modeling identified one humic-like (C1) and one protein-like (C2) component in ice cores whose fluorescent intensities all increased from the Polar Plateau to the coast. The fluorescence index showed that the bioavailability of dissolved organic matter (DOM) also decreased from the Polar Plateau to the coast. Partial least squares path modeling analysis revealed that bacterial abundance was the main positive biotic factor influencing both the quantity and quality of organic matter. Marine aerosol influenced the spatial distribution of DOC more than katabatic winds in the ice cores. Certain bacterial taxa showed significant correlations with DOC and POC concentrations. Collectively, our results show the tight connectivity among organic matter spatial distribution, bacterial abundance and meteorology in the McMurdo Dry Valley ecosystem.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Anomaly Detection for Online Monitoring of Thermocouple Sensors in the Advanced Test Reactor

This study explores data-driven anomaly detection methods to analyze sensor fail- ures in the Advanced Gas Reactor (AGR) nuclear fuel irradiation experiments. Specifically, we examine failures of thermocouples (TCs), which are critical for mon- itoring and controlling in-reactor temperatures during operation. Failures were pri- marily observed during abrupt power transitions and manifested as sensor drop-outs, drifts, or unexplained behavior. We applied three time-series analysis techniques— rolling mean smoothing, matrix profile, and vector auto-regression (VAR)—to de- tect anomalies in TC data prior to failure events. The rolling mean method effec- tively highlighted deviations aligned with reported failures, while the matrix profile provided partial early warning but sometimes flagged normal fluctuations during power-down periods. VAR shows potential in capturing multivariate dependencies but requires further calibration. A rare case of TC drift was also documented, which did not result in failure, underscoring the challenge of building predictive models with sparse positive examples. Our findings demonstrate that traditional statistical tools can aid anomaly detection but have limited predictive power without richer training data. We propose future directions including synthetic data generation, real- time surrogate modeling, and multi-modal feature integration. This work provides a foundation for applying robust anomaly detection frameworks to mission-critical sensor systems in experimental settings.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Search for Higgsinos in final states with low-momentum lepton-track pairs at 13 TeV

We present a search for the pair production of Higgsinos in final states with large missing transverse momentum and either two reconstructed muons or a reconstructed lepton (muon or electron) and an isolated track. The analyzed data correspond to proton-proton collisions with an integrated luminosity of 137 fb −1 , collected by the CMS experiment at $\sqrt{𝑠}$ =13 TeV in 2016, 2017, and 2018. The signal scenario assumes four nearly mass degenerate Higgsino mass eigenstates: two neutralino states $\tilde{𝜒}^0_2$ and $\tilde{𝜒}^0_1$ with a small mass difference in the range 1–10 GeV and two chargino states $\tilde{𝜒}^±_1$ with an intermediate mass. The analysis focuses on the decay of the heavier neutralino into the lighter one and a virtual 𝑍 boson, which decays into two same-flavor leptons. The leptons have small transverse momentum and/or a small opening angle between the identified muons. An isolated track is used to recover events in which only one of the two leptons is identified. Multivariate discriminants are used to enhance the sensitivity by efficiently rejecting backgrounds from SM processes or misreconstructed tracks and/or leptons. The search explores a unique phase space and probes a previously unexplored region of the signal model parameter space. Mass differences between the two neutralinos are probed down to 1.5 GeV, assuming a Higgsino mass of 100 GeV. The maximum excluded Higgsino mass is 115 GeV.

Hayrapetyan, A. [Yerevan Physics Institute]↗

DOE OSTI2024

Long-Term Statistical Process Monitoring of an Ultrafiltration Water Treatment Process

As water treatment technology has improved, the amount of available process data has substantially increased, making real-time, data-driven fault detection a reality. One shortcoming of the fault detection literature is that methods are usually evaluated by comparing their performance on hand-picked, short-term case studies, which yields no insight into long-term performance. In this work, we first evaluate multiple statistical and machine learning approaches for detrending process data. Then, we evaluate the performance of a PCA-based fault detection approach, applied to the detrended data, to monitor influent water quality, filtrate quality, and membrane fouling of an ultrafiltration membrane system for indirect potable reuse. Based on two short case studies, the adaptive lasso detrending method is selected, and the performance of the multivariate approach is evaluated over more than a year. The method is tested for different sets of three critical tuning parameters, and we find that for long-term, autonomous monitoring to be successful, these parameters should be carefully evaluated. However, in comparison with industry standards of simpler, univariate monitoring or daily pressure decay tests, multivariate monitoring produces substantial benefits in long-term testing.

ammonia↗

DOE OSTI2023

Concordance

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. This software takes a new approach towards estimating the active subspace, in which Multivariate Adaptive Regression Splines (MARS) is used as a surrogate model, and relevant calculation are obtained analytically. 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. This software is also capable of conducting a so-called "concordance analysis", using a generalization of ASs which we refer to as "Co-Active" subspaces.

Rumsey, Kelin↗

DOE OSTI2024

Regularized Differentiation for Bioburden Density Estimation in Planetary Protection

In this paper, we propose and investigate the performance of two novel shrinkage estimators for bioburden density estimation in planetary protection. The estimators are based on the regularized differentiation of a cumulative count of colony forming units collected throughout the data collecting session or the life cycle of the entire mission. The regularized differentiation recasts the problem of bioburden density estimation as a linear least squares problem. The least squares problem is then solved through regularization techniques, such as truncated singular value decomposition and penalized least squares. The regularization is necessary to avoid noise amplification during the differentiation of noisy data. The two regularization estimators are compared with four other commonly used estimators to simultaneously evaluate the means of multivariable independent Poisson distributions: the maximum likelihood, noninformative Bayes estimator with Jeffreys prior, Empirical Bayes using conjugate gamma-Poisson model with gamma parameters selected by method of moments, and the Clevenson-Zidek estimator. It is shown through computer-simulated data that the regularized differentiation based on ridge regression has the smallest mean-squared error among all estimators. The analysis of shrinkage mechanism implemented by regularized differentiation is performed, and it is shown that the regularized differentiation amounts to performing a weighted averaging of all the samples. The weights are determined by the regularization parameter automatically selected by the L-curve technique. Since the method of least squares makes no distributional assumptions about the data, it presents an attractive technique for bioburden density estimation when there are concerns about the misspecification of the distributional model. The paper concludes with the analysis of the bioburden data collected during InSight mission and directions for future work.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Modeling interval trendlines: Symbolic singular spectrum analysis for interval time series

Abstract In this article we propose an extension of singular spectrum analysis for interval‐valued time series. The proposed methods can be used to decompose and forecast the dynamics governing a set‐valued stochastic process. The resulting components on which the interval time series is decomposed can be understood as interval trendlines, cycles, or noise. Forecasting can be conducted through a linear recurrent method, and we devised generalizations of the decomposition method for the multivariate setting. The performance of the proposed methods is showcased in a simulation study. We apply the proposed methods so to track the dynamics governing the Argentina Stock Market (MERVAL) in real time, in a case study over a period of turbulence that led to discussions of the government of Argentina with the International Monetary Fund.

de Carvalho, Miguel↗

DOE OSTI2026

Measurement of the top quark pair production cross section in PbPb collisions at $\sqrt{s_{\mathrm{NN}}}=5.36$ TeV

The inclusive cross section for top quark pair ($\mathrm{t}\overline{\mathrm{t}}$) production in lead-lead (PbPb) collisions is reported for the first time at a center-of-mass energy per nucleon pair of 5.36 TeV. The analysis uses data corresponding to an integrated luminosity of 1.58 nb −1 collected by the CMS experiment at the CERN LHC in 2023. The $\mathrm{t}\overline{\mathrm{t}}$ production cross section, ${\sigma}_{\mathrm{t}\overline{\mathrm{t}}}={3.42}_{-0.51}^{+0.54}{\left(\mathrm{stat}\right)}_{-0.43}^{+0.50}\left(\mathrm{syst}\right)$ μb, is measured in dilepton final states using a fit to a multivariate discriminator that combines the decay electron and muon kinematic properties with the multiplicity of bottom quark jets. The result is consistent with perturbative quantum chromodynamics calculations at next-to-next-to-leading order (NNLO) accuracy employing several nuclear parton distribution functions. In addition, the Drell–Yan production cross section (σ DY ) for dilepton masses above 10 GeV and the ratio of $\mathrm{t}\overline{\mathrm{t}}$ to DY cross sections $\left({R}_{\mathrm{t}\overline{\mathrm{t}}/\mathrm{DY}}\right)$ are found to be compatible with the NNLO predictions. The observables ${\sigma}_{\mathrm{t}\overline{\mathrm{t}}}$, σ DY , and ${R}_{\mathrm{t}\overline{\mathrm{t}}/\mathrm{DY}}$ are measured separately for central and semicentral PbPb collisions to investigate for the first time the dependence of top quark production on the collision impact parameter.

Heavy Ion Experiments↗

DOE OSTI2025

Search for the production of a Higgs boson in association with a single top quark in pp collisions at $\sqrt{s}=13$ TeV with the ATLAS detector

A search for the production of a Higgs boson in association with a single top quark, tH, is presented. The analysis uses proton-proton collision data corresponding to an integrated luminosity of 140 fb −1 at a centre-of-mass energy of 13 TeV, collected by the ATLAS detector at the LHC. The search targets Higgs-boson decays into $b\bar{b}$, WW * , ZZ * , and ττ, accompanied by an isolated lepton (electron or muon) from the top-quark decay. Multivariate techniques are employed to enhance the separation between signal and background processes. The observed signal strength, μ tH , defined as the ratio between the measured cross-section and the predicted Standard Model value, is μ tH = 8.1 ± 2.6 (stat.) ± 2.0 (syst.). The significance of the observed (expected) signal above the background-only expectation is 2.8 (0.4) standard deviations. The corresponding observed (expected) upper limit at the 95% confidence level on the tH cross-section is found to be 13.9 (6.1) times the value predicted by the Standard Model. An interpretation with an inverted sign of the top-quark Yukawa coupling is performed, and the signal strength and corresponding limit are reported.

Hadron-Hadron Scattering↗