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For E. coli, C. thermocellum, Z. mobilis: shotgun proteomics analyses of tryptic digests of cell lysates; direct infusion of cell lysates spiked with isotopically labelled peptides to perform absolute quantification of specific proteins of interest, primarily related to glycolysis
Increased aerosols can modify the shape of the cloud Particle Size Distribution (PSD), thereby influencing the radiative properties of clouds, known as the Dispersion Effect (DE). However, a global, observation-based quantification of its impact on Aerosol-Cloud Interactions (ACI) is lacking, leading to DE being typically ignored in satellite-based estimates of ACI forcing. Here we propose a physics-based method that combines polarimetric satellite data on cloud PSD to achieve global observational quantification of DE’s impact on ACI in liquid-phase stratiform clouds. Globally, DE offsets ACI changes induced by droplet number concentration variation and liquid water path adjustment by 7% and −1.4%, respectively. Furthermore, a parameterization based on the global dataset of PSD shape parameters is developed to improve DE estimation in large-scale models. Both the quantification and parameterization enhance our understanding of DE and facilitate the inclusion of this non-negligible impact of DE on ACI in estimating aerosol climate forcing.
Data here corresponds to the data presented in the academic publication titled "1H NMR quantification of aromatic monomers from reductive catalytic fractionation" set to be published in ACS Sustainable Chemistry and Engineering. Data was gathered at the National Renewable Energy Laboratory From 2022-2025.
We quantify the accuracy of the temperature profiling from ground-based spectral infrared radiance observations at the American WAKE ExperimeNt (AWAKEN). Results from pre-campaign tests and comparisons with in-situ ground-based and airborne sensors at AWAKEN indicate that temperature profiles agree satisfactorily with traditional instruments for wind energy applications. The bias is within a fraction of a degree and appears to be related to atmospheric stability. Root-mean-square differences from the reference instruments are always smaller than a degree and are often well described by the online uncertainty estimation product. Height-to-height and site-to-site temperature differences are in excellent agreement with in-situ observations, which justifies the use of temperature profilers to characterize static stability and spatial gradients of temperature.
RNA abundance quantification has become routine and affordable thanks to high-throughput “short-read” technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. “Long-read” sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.
Reductive catalytic fractionation (RCF) can produce high yields of aromatic monomers from lignin in native biomass. Quantification of these aromatic monomers is a well-known but demanding task, in part due to the lack of commercially available standards. Here, we demonstrate 1 H NMR spectroscopy as a complementary method to rapidly quantify aromatic monomer concentrations in RCF oils. The method exhibited good agreement with measurements from ultrahigh pressure liquid chromatography (UHPLC) for 96 RCF oils with varying monomer selectivity, with average absolute deviations of individual monomer yields between 0.5 and 1.1 wt % (relative 11–17%) and R 2 values above 0.9 compared to conventional UHPLC quantification. Quantification of S-type monomers, including for 4-ethylsyringol and 4-propenylsyringol, was generally reliable. The validity of G-type monomer quantifications depended on reaction selectivity due to overlap between peaks of 4-ethylguaiacol and 4-(3-hydroxypropyl)-guaiacol. The method could be applied on crude RCF oils without needing to perform the liquid–liquid extraction typically done for RCF reactions, thereby providing a convenient way to quantify lignin extraction and aromatic monomer yield. Overall, 1 H NMR spectroscopy can serve as a rapid primary quantification or secondary validation method for RCF monomer yield and selectivity measurements.
A phase present in small quantities within materials may not simply serve as a secondary component; it can play a crucial role in determining the integrity, properties, and performance of the material. These minor but important phases usually draw attention in material design and processing for fundamental understanding as well as material quality control. Accurately quantifying a minor phase amid a majority phase, especially at extremely low fractions, remains a challenging task. Time-of-flight neutron diffraction, coupled with advanced pattern analysis techniques like Rietveld refinement, is a powerful tool for crystal structure identification and phase quantification. The deep penetrating capability of neutrons enables the detection and quantification of trace phases within materials. In this study, the quantification limits of time-of-flight neutron diffraction were explored using the VULCAN diffractometer at the Spallation Neutron Source, using Fe–Ni powder mixtures as a sample system. By comparing the refinement results to the known weighed values, it was determined that the reliable quantification of a minor Ni phase is achievable down to about 0.1 wt% while a Ni fraction as low as 0.02 wt% is difficult to trace. Effective control of the refinement parameters, especially the profile function parameters, are found to significantly influence the convergence of fittings and the accuracy of phase quantification.
Monitoring of the atmosphere for fission products ( 131m Xe, 133m Xe, 133 Xe, and 135 Xe) is performed by various laboratories to detect nuclear explosions. Quantification of 127 Xe is not routinely performed by laboratories measuring atmospheric radioxenon because it is not a fission product. 127 Xe was recently detected by a ground-based beta-gamma air monitoring system. When measured using beta-gamma coincidence detector systems, such as those in use on the International Monitoring System (IMS) of the Comprehensive Nuclear-Test-Ban Treaty (CTBT), 127 Xe can interfere with the quantification of fission product radioxenon due to overlap of the 127 Xe beta-gamma coincidence signatures with those of fission product radioxenon. Here, this work demonstrates quantification of 127 Xe at different laboratories with different measurement techniques. Production and purification of 127 Xe was performed by neutron activation of enriched 126 Xe. The purified 127 Xe was then split between laboratories, and detection and quantification methods were developed. At Idaho National Laboratory, a quantification method involving high purity germanium detectors was devised that included self-attenuation correction. At AWE, a beta-gamma coincidence counting method, as used in support of the IMS, was modified to enable the measurement and analysis of the 127 Xe samples. Corrections were made for self-attenuation, which showed a strong xenon volume dependency, for some coincidence signatures. The gas sample activity concentration was used as the comparison metric and it showed excellent agreement between the methods.
Technetium (Tc) is a very important element that is encountered in many aspects, from its presence in radioactive waste and its potential environmental impact to its use as a medical radioisotope. Its detection and quantification in liquid samples is traditionally cumbersome, involving detailed sample preparation and analysis by mass spectrometry or scintillation. This article demonstrates the first comprehensive emission spectral analysis of Tc from a liquid sample by immobilization in a polymer and analysis by laser-induced breakdown spectroscopy (LIBS). A survey of LIBS spectra was completed to identify the strongest analytical lines for quantification of trace Tc in the presence of Mo. The quantification of Tc in a Mo-containing matrix was selected because Tc radioisotopes are the daughter products of Mo isotope decay. The first reported calibration curves by LIBS are provided with limits of detection and quantification down to 0.710 µg mL −1 and 1.39 µg mL −1 , respectively. Ultimately, this study demonstrated the feasibility of trace Tc quantification using LIBS and will serve as a reference for future research related to monitoring this radioactive species.
This data release provides all data and code used in the paper " "Machine Learning Ensembles Can Enhance Hydrologic Predictions and Uncertainty Quantifications" Willard et al. (2025)" to model stream temperature, evaluate, and assess results. The associated manuscript explores the effect of different ensemble construction techniques across different common machine learning (ML) architectures for predictions in unmonitored basins. Modeling was done using long short-term memory (LSTM), gated recurrent unit (GRU), temporal convolution network (TCN), and extreme gradient boosting (XGBoost) models, and stream site coverage spans 1362 locations across the conterminous United States. The ensemble construction techniques investigated include ensemble by random weight initialization, differing hyperparameters, different random subsets of training data, different subselections of input features, different architectures, and Monte Carlo Dropout. The data is organized into these items items:Code repository and data for the paper " "Machine Learning Ensembles Can Enhance Hydrologic Predictions and Uncertainty Quantifications" Willard et al. (2025).Code: stream_temp_ml_regionalization.zip contains the code repositoryData to run the code:- data_dir.zip -- contains all files that should be moved to the "DATA_DIR" variable defined in the "set_env_vars.sh" script in the code repository- metadata_dir.zip -- contains all files that should be moved to the "METADATA_DIR" variable defined in the "set_env_vars.sh" script in the code repositoryData produced by the code and used in the paper:- outputs_dir.zip - contains model output and results (outputs_dir/results), model weights (outputs_dir/models), and all other outputs used for the paper including feature importances.To cite this code, please use the following BibTeX or MLA entries:bibtex:@misc{willard2025streamensembles,author = {Jared Willard and Charuleka Varadharajan},title = {Dataset for "Machine Learning Ensembles Can Enhance Hydrologic Predictions and Uncertainty Quantification"},year = {2024},doi = {10.15485/2527393},publisher = {ESS-DIVE Repository},url = {https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2527393}}MLA: Willard, Jared, et al. Dataset for "Machine Learning Ensembles Can Enhance Hydrologic Predictions and Uncertainty Quantification". 2025. ESS-DIVE Repository, doi:10.15485/2448016.
Over the operational lifespan of a nuclear reactor, reactor pressure vessel (RPV) steels are subjected to significant neutron irradiation, resulting in complex microstructural changes and the consequent degradation of mechanical properties. Various physically motivated correlation models have been developed to predict neutron irradiation-induced embrittlement of RPVs under different irradiation conditions. However, the efficient and accurate characterizations and quantification of radiation-induced clusters in RPVs are still challenging, which will affect the precision of the predictive models for embrittlement of RPV components. In the DOE Visiting Faculty Program (VFP) research work at Oak Ridge National Lab (ORNL), I integrate machine learning to aid Scanning Transmission Electron Microscopy – Energy Dispersive X-ray Spectroscopy (STEM-EDS) analyses, which improve the characterization and quantification of radiation-induced clusters in RPV steels, thereby enabling more accurate predictions of material behavior under irradiation. The surveillance base- and welded- RPV steels were annealed at various temperatures of 340 °C, 450 °C and 500 °C for up to 168 hours, respectively. Afterwards, I have characterized radiation-induced clusters using advanced STEM-EDS techniques and subsequently applying machine learning algorithms to analyze and refine STEM-EDS datasets, enhancing the quantification of clusters compositions and distributions. In the end, an efficient workflow for integrating STEM-EDS data analysis with machine learning to address challenges including noise reduction has been developed. The completion of this VFP work will support bridge critical gaps in the accurate quantification of radiation-induced clusters in RPV steels using STEM-EDS and support the development of more precise models for predicting RPV embrittlement in the Light Water Reactor Sustainability program supported by Department of Energy and enhancing the collaboration between ORNL and Alred University. The outcome of the VFP project will leverage a few research papers submission to peer-reviewed journals in the relevant scientific field and a few oral presentations at national and international conferences.
The quantification of 133 Xe in the presence of its mother radionuclide 133 mXe requires the full quantification of both to perform the ingrowth correction for 133 Xe. Due to the nature of both of these radionuclides, the 133 mXe requires significantly more time to quantify by High Purity Germanium (HPGe) detectors due to lower production yields, lower gamma emission probabilities, and lower detection efficiencies. This work shows that 133 Xe and 133 mXe quantification can be accelerated by measuring the 133m:133 activity ratio for a large batch of material and applying this activity ratio to assays of lower activity subsamples of the same batch of material. Included in this report are derivations of the required decay correction equations, and experiments using actual samples to validate the performance of these equations. A detector calibration method is also shown that leverages this method as an alternative to existing calibration methods for 133 mXe quantification.
As global demand for rare earth elements (REEs) increases, maintaining the production and supply chain is critical. Technologies capable of being used in the field and in situ in the subsurface for rapid REE detection and quantification facilitates the efficient mining of known resources and exploration of new and unconventional resources. Laser-induced breakdown spectroscopy (LIBS) is a promising technique for rapid elemental analysis both in the laboratory and in the field. Multiple articles have been published evaluating LIBS for detection and quantification of REEs; however, REEs in their natural deposits have not been adequately studied. In this work, detection and quantification of two REEs, La and Nd, have been studied in both synthetic and natural mineral matrices at concentrations relevant to REE extraction. Measurements were performed on REE-containing rock and coal samples (natural and synthetic) utilizing different LIBS instruments and techniques, specifically a commercial benchtop instrument, a custom benchtop instrument (single- and double-pulse modes), and a custom LIBS probe currently being developed for in situ, subsurface, borehole wall detection and quantification of REEs. Plasma expansion, emission intensity, detection limits, and double-pulse signal enhancement were studied. The limits of detection (LOD) were found to be 10/14 ppm for La and 15/25 ppm for Nd in simulated coal/rock matrices in single-pulse mode. Signal enhancement of 3.5 to 6-fold was obtained with double-pulse mode as compared to single-pulse operation.
Computer imaging is rapidly becoming an indispensable tool for the quantification of variables in research and medicine. Whilst its use in medicine has largely been limited to qualitative observations, imaging in applied basic sciences, medical research and biotechnology demands objective quantification of the variables in question. In black and white densitometry (0-256 levels of intensity) the separation of subtle differences between closely related hues from stains is sometimes very difficult. True-colour and real-time video microscopy analysis offer choices not previously available with monochrome systems. In this paper we demonstrate the usefulness of colour thresholding, which has so far proven indispensable for proper objective quantification of the products of histochemical reactions and/or subtle differences in tissue and cells. In addition, we provide interested, but untrained readers with basic information that may assist decisions regarding the most suitable set-up for a project under consideration. Data from projects in progress at Tulane are shown to illustrate the advantage of colour thresholding over monochrome densitometry and for objective quantification of subtle colour differences between experimental and control samples.
Computational fluid dynamics is now considered to be an indispensable tool for the design and development of scramjet engine components. Unfortunately, the quantification of uncertainties is rarely addressed with anything other than sensitivity studies, so the degree of confidence associated with the numerical results remains exclusively with the subject matter expert that generated them. This practice must be replaced with a formal uncertainty quantification process for computational fluid dynamics to play an expanded role in the system design, development, and flight certification process. Given the limitations of current hypersonic ground test facilities, this expanded role is believed to be a requirement by some in the hypersonics community if scramjet engines are to be given serious consideration as a viable propulsion system. The present effort describes a simple, relatively low cost, nonintrusive approach to uncertainty quantification that includes the basic ingredients required to handle both aleatoric (random) and epistemic (lack of knowledge) sources of uncertainty. The nonintrusive nature of the approach allows the computational fluid dynamicist to perform the uncertainty quantification with the flow solver treated as a "black box". Moreover, a large fraction of the process can be automated, allowing the uncertainty assessment to be readily adapted into the engineering design and development workflow. In the present work, the approach is applied to a model scramjet isolator problem where the desire is to validate turbulence closure models in the presence of uncertainty. In this context, the relevant uncertainty sources are determined and accounted for to allow the analyst to delineate turbulence model-form errors from other sources of uncertainty associated with the simulation of the facility flow.
We introduce GenAI4UQ, a software package for forward and inverse uncertainty quantification in model calibration, parameter estimation, and ensemble forecasting. GenAI4UQ leverages a generative AI-based conditional modeling framework to address limitations of traditional inverse modeling techniques, such as Markov Chain Monte Carlo (MCMC) methods. By replacing computationally intensive iterative processes with a direct, learned mapping, GenAI4UQ enables efficient calibration of input parameters and generation of predictions directly from observations. The software supports rapid ensemble forecasting with robust uncertainty quantification while maintaining computational and storage efficiency. Built-in auto-tuning of hyperparameters simplifies model training, ensuring accessibility for users with varying expertise. Its versatile conditional generative framework is applicable across diverse scientific domains. While GenAI4UQ offers significant advantages in flexibility and efficiency, users should interpret its uncertainty estimates with caution in data-sparse scenarios, as the model may overestimate uncertainty—an effect common to all surrogate-based approaches including MCMC with surrogate models. Despite this, GenAI4UQ transforms inverse modeling by providing a fast, reliable, and user-friendly solution. It empowers researchers and practitioners to quickly estimate parameter distributions and generate model predictions for new observations, facilitating efficient decision-making and advancing the state of uncertainty quantification in computational modeling.
A computational framework to support the quantification of system uncertainties and sensitivities for rotorcraft applications is presented using the NASA Design and Analysis of Rotorcraft (NDARC) conceptual sizing tool. A 90 passenger conceptual tiltrotor configuration was used for case demonstration in the modeling of uncertainties in NDARCs emission module. A non-intrusive forward propagation uncertainty quantification approach was applied to ensemble simulations using a Monte Carlo methodology with stratified Latin hypercube sampling. An off-the-shelf software, DAKOTA, which supports trade studies and design space exploration, including optimization, surrogate modeling and uncertainty analysis was used to address the research goals. A toolsuite was further developed incorporating DAKOTA with automated design processes and methods using function wrappers to execute program routines including support for data post-processing. Uncertainties in rotorcraft emissions modeling using the Average Temperature Response metric for a set mission profile were studied. It was shown that for the current study, using the base-line best estimate modeling parameters for the Average Temperature Response metric, NDARC under-estimates the effects of emissions when compared with results from Monte Carlo simulations. A global sensitivity analysis was further undertaken to quantify the contribution of the various emission species on output sensitivity, hence uncertainty. The work demonstrates that the developed toolsuite is robust and will support the quantification of system uncertainties and sensitivities in future rotorcraft design efforts.
The increasing interest in low-altitude unmanned aerial vehicle (UAV) operations is bringing along safety concerns. Performance of small, low-cost UAVs drastically changes with type, size and controller of the vehicle. Their reliability is lower when compared to reliability of commercial aircrafts, and the availability of on-board sensors for health and state awareness is extremely limited due to their size and propulsion capabilities. Uncertainty plays a dominant role in such a scenario, where a variety of UAVs of different size, propulsion systems, dynamic performance and reliability enters the low-altitude airspace. Unexpected failures could have dangerous consequences for both equipment and humans within that same airspace. As a result, a number of research works and methodologies are being proposed in the area of UAV dynamic modeling, health and safety monitoring, but uncertainty quantification is rarely addressed. Thus, this paper pro- poses a perspective towards uncertainty quantification for autonomous systems, giving special emphasis to a UAV health monitoring application. A formal approach to classify uncertainty is presented; it is utilized to identify the uncertainty sources in UAVs health and operations, and then map uncertainty within a predictive process. To show the application of the methodology proposed here, the design of a model-based powertrain health monitoring algorithm for small-size UAVs is used as case study. The example illustrates how the uncertainty quantification approach can help the modeling strategy, as well as the assessment of diagnostic and prognostic performance.