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149 records · Page 9

Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, and some studies have performed system-level analysis, few have been able to provide a network-based model of the TRN that also provides the relative shifts in transcriptional regulator activity triggered by changing environments. Here, we compiled a compendium of nearly 650 publicly available, high quality M. tuberculosis RNA-sequencing data sets and applied an unsupervised machine learning method to obtain a quantitative, top-down TRN. It consists of 80 independently modulated gene sets known as “iModulons,” 41 of which correspond to known regulons. These iModulons explain 61% of the variance in the organism’s transcriptional response. We show that iModulons (i) reveal the function of poorly characterized regulons, (ii) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and infection events, and (iii) identify intrinsic clusters of regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.

59 BASIC BIOLOGICAL SCIENCES↗

Improved Infrared Optical Constants from Pressed Pellets: II. Ellipsometric n and k Values for Ammonium Sulfate with Variability Analysis

Infrared spectral imaging is facilitated via the comparison of spectra recorded in situ to a databank of actual or synthetic infrared reflectance spectra. It has recently been shown that reference spectra corresponding to the many different morphological forms of the same chemical can be generated synthetically using the imaginary, k, and real, n, components of the complex refractive index, n~ = n + ik. One method to obtain the n and k vectors is infrared ellipsometry, which measures the changes in amplitude, tan ?, and phase, ?, of polarized light reflected from the sample both as a function of wavenumber and angle of incidence. The method requires specularly reflected light so best results are usually obtained with polished planar samples of large surface area. Due to the difficulties of obtaining such samples, however, we investigate the possibility of pressing powders of neat materials and obtaining the corresponding optical constants from the pellets. In this paper, variability in the sample pellet and preparation method is investigated, as is variability in the fitting procedure for the derived optical constants. The n/k vectors are derived from the measured ellipsometric parameters, tan ? and ?, as they are fit by an oscillator model which yield n(?) and k(?) vectors as a function of wavenumber, ?. Construction of the oscillator model is not automatic and depends on significant input from the analyst as well as the sample’s physical characteristics. For the pellet pressing, the experimental variability was found to be minimized for size-selected powdered samples as gauged by the minimal variance in ? and ? for three different pellets; similarly, the analytical precision for multiple measurements of the same pellet was also quite good, suggesting that a pressed pellet is a viable sample preparation method. The greatest variability came in the analytic fitting procedure with differences up to 20% arising from four different fits to the same data set. The final ellipsometric n/k data are compared to literature values obtained from crystalline (NH4)2SO4 samples as well as single-angle reflectance measurements that also used pressed pellets. Comparison with the previous literature values shows generally good agreement although higher k-values are observed for the independent sets of data derived from pressed pellets. These data are suggested as an improved set of optical constants for (NH4)2SO4.

optical constants, ellipsometry, ammonium sulfate,↗

Advancing Development of Emissions Detection (Final Report)

This document is the final report to the U.S. Department of Energy (DOE for contract DE-FE0031873) awarded to Colorado State University (CSU). CSU and partners at Harrisburg University of Science and Technology, University of Texas Arlington, and University of Texas at Austin organized several testing rounds to provide knowledge focused on advancing the detection capabilities of emissions monitoring devices. With this funding opportunity the research group began by establishing the Advancing the Development of Emission Detection (ADED) program, with the goal focused on enhancing the accuracy, reliability, and field applicability of methane detection technologies. This effort aimed to address the critical challenges of identifying and quantifying methane emissions while enabling industry stakeholders to meet regulatory compliance and environmental sustainability goals. The program engaged with industry, government, and technology stakeholders to promote adoption and consensus on testing techniques for methane detection solutions. Methane, a potent greenhouse gas, contributes significantly to global warming, and the oil and natural gas (O&G) sector is a primary source of methane emissions. Regulatory measures such as leak detection and repair (LDAR) programs have been implemented to address emissions. However, traditional LDAR approaches, reliant on handheld and component-level measurements, are resource-intensive. To address these limitations and move with evolving regulations, advanced methane technologies are emerging. These solutions include ground-based sensors, mobile systems (e.g., drones, vehicles, and aircraft), and satellite-based platforms. They offer innovative capabilities for autonomous monitoring, larger spatial coverage, and emission quantification using methods such as tracer gas techniques and inverse modeling with Gaussian plume analysis. The ADED program began with creating protocols for methane controlled release (CR) testing these continuous monitoring (CM) and survey technologies that detect and monitor methane emissions at O&G facilities. The protocols were then implemented throughout testing of CM and survey devices at CSU’s Methane Emissions Technology Evaluation Center (METEC) facility from 2021 through 2024. As apart of the protocol, solutions that tested under the ADED program installed their solutions at METEC, documented their system under test, and provided detection reports to the METEC team for analysis. The METEC team would provide the solutions with analyzed reports of their emissions and ground truth data of the releases conducted during their testing session. Under the ADED program, CMs were also tested at O&G facilities for a six week test run of challenge release (ChR) releases. The findings from the ADED program underscore the critical role of collaborative research and innovation in tackling methane emissions, offering a pathway for the oil and gas sector to achieve significant environmental and economic benefits. Results from METEC testing saw improvement of performance and accuracy across all solutions over the extent of the ADED experiments. The results also showed a variance in CM solution performance between CRs and ChRs. That variance pushed the team to further analyze the differences between CR testing environments and field conditions. With the drive from regulations and that variance in field conditions, the ADED team began designing a new CR testing protocol and additions to the METEC testing facility. The METEC team is furthering the progress made through the ADED program with awarded funding from DE-FE0032276. This funding pushes the development of METEC’s addition with new equipment, allowing for an updated facility layout. METEC still facilitates for traditional facilities, with a legacy pad, while expanding an new design based on how O&G infrastructure has Final Report - Contract Number: DE-FE0031873 been changed over the last decade. Throughout the ADED program the team has also been working with international partners to ensure staying in the trend globally. International partners have been essential in moving the new protocol forward to implement into CR testing at the METEC facility in Spring 2025.

42 ENGINEERING↗

Uncovering hidden bias in neutron diffraction residual strain measurements

When calculating residual strain via neutron or X-ray diffraction, uncertainties propagated from the peak fit are often inadequate to describe the true scatter of measurements about a singular strain state, such as one that should describe a macroscopic continuum. Because diffraction is inherently a selective process, orientation-dependent scatter arises from the sub-sampling of strong microstructure and strain gradients. This paper investigates the appropriateness of propagated uncertainties with reference to their original intention, i.e. noise about a mean value. Thirty-six unique orientations of strain measurements are taken at multiple locations within an additive friction-stir deposition component with fine-scale gradients (∼200 µm) of plastic strain, texture and residual elastic strain. Multiple strain and stress calculation pathways are compared: direct substitution of three measurements into Hooke's law, direct inversion of any six unique orientations into the strain state tensor and thirty-six measurement least-squares estimation. For the last two cases, the appropriateness of the uncertainty interval is statistically evaluated on the basis of a physical constraint: common agreement under the strain transformation law. For this sample, the direct inversion of six measurements retains a conservative estimate of the uncertainty. However, propagated uncertainties in the least-squares solution greatly underestimate the true experimental scatter. A simple pathway to estimate appropriate uncertainty intervals is suggested. These results demonstrate that the interpretation of uncertainty in residual strain is strongly dependent on intrinsic sample-dependent effects, and that oversampling orientations and statistical analysis can give more accurate results with realistic uncertainties.

36 MATERIALS SCIENCE↗

STITCHES: creating new scenarios of climate model output by stitching together pieces of existing simulations

Abstract. Climate model output emulation has long been attempted to support impact research, mainly to fill in gaps in the scenario space. Given the computational cost of running coupled earth system models (ESMs), which are usually the domain of supercomputers and require on the order of days to weeks to complete a century-long simulation, only a handful of different scenarios are usually chosen to externally force ESM simulations. An effective emulator, able to run on standard computers in times of the order of minutes rather than days could therefore be used to derive climate information under scenarios that were not run by ESMs. Lately, the necessity of accounting for internal variability has also made the availability of initial-condition ensembles, under a specific scenario, important, further increasing the computational demand. At least so far, emulators have been limited to simplified ESM-like output, either seasonal, annual, or decadal averages of basic quantities, like temperature and precipitation, often emulated independently of one another. With this work, we propose a more comprehensive solution to ESM output emulation. Our emulator, STITCHES, uses existing archives of earth system models' (ESMs) scenario experiments to construct ESM-like output under new scenarios or enrich existing initial-condition ensembles, which is what other emulators also aim to do. Importantly, however, STITCHES' output has the same characteristics of the ESM output it sets out to emulate: multivariate, spatially resolved, and high frequency, representing both the forced component and the internal variability around it. STITCHES extends the idea of time sampling – according to which climate outcomes are stratified by the global warming level at which they manifest themselves, irrespective of the scenario and time at which they occur – to the construction of a continuous history of ESM-like output over the whole 21st century, consistent with a 21st-century trajectory of global surface air temperature (GSAT) derived from the scenario that has been chosen as the target of the emulation. STITCHES does so by first splitting the target GSAT trajectory into decade-long windows, then matching each window in turn to a decade-long window within an existing model simulation from the available scenario runs according to its proximity to the target in absolute size of the temperature anomaly and its rate of change. A look-up table is therefore created of a sequence of existing experiment–time-window combinations that, when stitched together, create a GSAT trajectory “similar” to the target. Importantly, we can then stitch together much more than GSAT from these windows, i.e., any output that the ESM has saved for these existing experiment–time-window combinations, at any frequency and spatial scale available in its archive. We show that the stitching does not introduce artifacts in the great majority of cases (we look at temperature and precipitation at monthly frequency and on the native grid of the ESM and at an index of ENSO activity, the Southern Oscillation Index). This is true even if the criteria for the identification of the decades to be stitched together are chosen to work for a smoothed time series of annual GSAT, a result we expect given the larger amount of noise affecting most other variables at finer spatial scales and higher frequencies, which therefore are more “forgiving” of the stitching. We successfully test the method's performance over many ESMs and scenarios. Only a few exceptions surface, but these less-than-optimal outcomes are always associated with a scarcity of the archived simulations from which we can gather the decade-long windows that form the building blocks of the emulated time series. In the great majority of cases, STITCHES' performance is satisfactory according to metrics that reward consistency in trends, interannual and inter-ensemble variance, and autocorrelation structure of the time series stitched together. The method therefore can be used to create ESM-like output according to new scenarios, on the basis of a trajectory of GSAT produced according to that scenario, which could be easily obtained by a simple climate model. It can also be used to increase the size of existing initial-condition ensembles. There are aspects of our emulator that will immediately disqualify it for specific applications, like when climate information is needed whose characteristics result from accumulated quantities over windows of times longer than those used as pieces by STITCHES, droughts longer than a decade for example. But for many applications, we argue that a stitched product can satisfy the climate information needs of impact researchers. STITCHES cannot emulate ESM output from scenarios that result in GSAT trajectories outside of the envelope available in the archive, nor can it emulate trajectories with shapes different from existing ones (overshoots with negative derivative, for example). Therefore, the size and characteristics of the available archives of ESM output are the principal limitations for STITCHES' deployment. Thus, we argue for the possibility of designing scenario experiments within, for example, the next phase of the Coupled Model Intercomparison Project according to new principles, relieved of the need to produce a number of similar trajectories that vary only in radiative forcing strength but more strategically covering the space of temperature anomalies and rates of change.

54 ENVIRONMENTAL SCIENCES↗