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At least 235 records · Page 13

Quantitative Proteomic Analysis of the Senescence-Associated Secretory Phenotype by Data-Independent Acquisition

Cellular senescence is a complex stress response that induces an essentially permanent cell cycle arrest and a complex secretory phenotype termed the senescence-associated secretory phenotype (SASP), which drives numerous aging pathologies. Characterization of the SASP can provide insights into aging and disease mechanisms, aging biomarker candidates, and targets for counteracting the deleterious effects of senescent cells. Here we describe a mass spectrometry (MS)-compatible protocol to (1) generate senescent cells using different stimuli, (2) collect conditioned medium containing proteins secreted by senescent cells (i.e., SASP), and (3) prepare the SASP for quantitative proteomic analysis using data-independent acquisition (DIA) MS. Basic Protocol 1: Generating ionizing radiation-induced senescent and control cells Alternate Protocol 1: Generating doxorubicin-induced senescent and control cells Alternate Protocol 2: Generating oncogenic RAS-induced senescent and control cells Alternate Protocol 3: Generating mitochondrial dysfunction-induced senescent and control cells Alternate Protocol 4: Generating atazanavir/ritonavir-induced senescent and control cells Support Protocol: A multiple-assay approach to confirm the phenotype of senescent cells Basic Protocol 2: Generating conditioned medium from senescent cells cultured in low serum and quiescent control cells Alternate Protocol 5: Generating conditioned medium from senescent cells cultured in complete medium and quiescent control cells Basic Protocol 3: Quantitative proteomic analysis of the SASP.

60 APPLIED LIFE SCIENCES↗

Experiment K-7-18: Effects of Spaceflight in the Muscle Adductor Longus of Rats Flown in the Soviet Biosatellite Cosmos 2044: Quantitative Autoradiographic Analysis of Gaba (Benzodiazepine) and Muscarinic (Cholinergic) Receptors in the Forebrain of Rats Flown on Cosmos 2044 - Part 2

Quantitative autoradiographic analysis of receptors for GABA and acetylcholine in the forebrain of rats flown on COSMOS 2044 was undertaken as part of a joint US-Soviet study to determine the effects of microgravity on the central nervous system, and in particular on the sensory and motor portions of the forebrain. Changes in binding of these receptors in tissue from animals exposed to microgravity would provide evidence for possible changes in neural processing as a result of exposure to microgravity. Tritium-labelled diazepam and Quinuclidinyl-benzilate (QNB) were used to visualize GABA (benzodiazepine) and muscarinic (cholinergic) receptors, respectively. The density of tritium-labelled radioligands bound to various regions in the forebrain of both flight and control animals were measured from autoradiograms. Data from rats flown in space and from ground-based control animals that were not exposed to microgravity were compared.

Wu, L.↗

Solar cities: A case study analysis of city-level enablers of expanded solar energy access

Rooftop solar photovoltaic (PV) adoption can benefit households by reducing electricity bills and enhancing energy resiliency. Low and moderate-income (LMI) households have been less likely to adopt PV and experience these benefits in the United States than higher-income households. Adopter income trends are often explored through quantitative analysis with limited explanatory power. Our quantitative analysis only explains around one-third of city-level variation in LMI adoption trends through socioeconomic factors such as median home values and income inequality and PV market factors such as cumulative adoption and incentives. We implement semi-structured interviews in three case studies of cities with relatively high rates of LMI PV adoption to better understand the factors that explain PV adopter income trends. The case studies partly reiterate findings from quantitative analysis, such as the role of PV incentives. The case studies reveal a broader set of LMI adoption drivers that are missed in quantitative analyses. The case studies show how city contexts can affect LMI adoption, such as the role of supportive city governments. The case studies also reveal the importance of partnerships, such as partnerships between city governments and state LMI PV program implementers. Finally, interviewees emphasized the importance of building trust among prospective LMI PV adopters. Interviewees suggested that partnerships, outreach, and consumer protection measures were crucial to building trust in PV installers among LMI households.

Adoption↗

Neurological applications of man-machine systems analysis

Quantitative descriptions of human control properties are formulated that take into account the dynamics of muscle actuation units, neuromuscular sensor units, and sensory feedback mechanics. Detailed dynamic measurements on neurologically disordered patients are correlated with clinical manifestations of various neurological syndromes to quantify operator behavior.

Mcruer, D. T.↗

Quantitative Phenotypic Analysis of Arabidopsis Thaliana Grown in Microgravity Using Soap, an Applied Artificial Intelligence

Phenotypic analysis is an essential step in studying the gravitropic responses and gravitational stress experienced by plants grown in microgravity. Many of the phenotypic traits analyzed in gravitropism studies, such as root length, leaf area, secondary root count, and number of root hairs, currently rely upon manual measurement methods for quantification. However, new advances in data analysis technology using artificial intelligence offer an opportunity for more efficient phenotypic analysis and a reduction of time spent in the data collection phase. In this project, the ability of a new artificially intelligent data collection software, SOAP (Simple Object Access Protocol), to collect and quantify phenotypic traits of Arabidopsis thaliana will be assessed. This project will test the measurements taken by an initial draft of the software. SOAP will take measurements of shoot length, a key phenotype used to assess A. thaliana stress response when grown in microgravity conditions. Shoot length measurements made by SOAP will be compared against a series of manual shoot length measurements. The comparison between the two methods of data measurement will provide valuable insight into the relative accuracy of SOAP and the margin of human error when conducting lab measurements.

Arabidopsis↗

Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially Resolved Tissue Profiling

Traditionally, proteomic studies have been carried out on whole tissues or organs enabling the profiling of thousands of proteins within a single LC-MS analysis. A disadvantage of this approach is that proteomes generated from whole tissues are an “average” that represents a blend of cell types and distinct anatomical regions which can obscure important biological phenomena. Laser capture microdissection (LCM) is an elegant method that allows tissue features of interest, as small as a single cell, to be identified and isolated for downstream analysis. Herein we describe an approach that utilizes an immobilized enzyme reactor (IMER) coupled directly to nanoLC-MS/MS for highly sensitive, automated, quantitative proteomic analysis of the microscopic tissue specimens generated by LCM.

Piehowski, Paul D.↗

Affine Transformations to Enable Machine Learning for Semi-Quantitative EDS Analysis

Energy Dispersive X-ray Spectroscopy (EDS) is an essential technique for determining elemental concentrations and distributions within microstructures, critical for materials discovery, optimization, and qualification. However, most published EDS data is qualitative because current quantitative EDS analysis methods require extensive calibration and post-processing, limiting their practicality and widespread adoption. This work seeks to establish a framework for accelerated EDS characterization and spectrum analysis that can leverage ML to analyze correlations between various elemental compositions and resulting EDS spectra. The complex physics and data result in a high-dimensional problem that grows exponentially with the number of elements in the system and the complexity of the spectrum analysis. ML provides a way to compute and optimize the results of this highly dimensional problem in a flexible way to tailor it to the user’s specific needs and material system. However, the framework emphasizes transparency through a strictly mathematical affine transformation, so the analysis remains understandable and reviewable to facilitate adoption by the scientific community. While currently implemented methods are simplistic and unvalidated, further development and demonstration of this framework could enable high-throughput, accurate, and accessible EDS characterization.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Spatially resolved absolute quantitation in thin tissue by mass spectrometry

Mass spectrometry (MS) has become the de facto tool for routine quantitative analysis of biomolecules. MS is increasingly being used to reveal the spatial distribution of proteins, metabolites, and pharmaceuticals in tissue and interest in this area has led to a number of novel spatially resolved MS technologies. Most spatially resolved MS measurements are qualitative in nature due to a myriad of potential biases, such as sample heterogeneity, sampling artifacts, and ionization effects. As applications of spatially resolved MS in the pharmacological and clinical fields increase, demand has become high for quantitative MS imaging and profiling data. As a result, several varied technologies now exist that provide differing levels of spatial and quantitative information. Furthermore, this review provides an overview of MS profiling and imaging technologies that have demonstrated quantitative analysis from tissue. Focus is given on the fundamental processes affecting quantitative analysis in an array of MS imaging and profiling technologies and methods to address these biases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitative Uncertainty Analysis for Diffraction

Current software uses a least squares statistical method. For each model parameter, current software yields a point estimate and estimated standard error for each point estimate. In contrast, we have employed a Bayesian approach with sampling algorithm to provide a full posterior probability density function on each model parameter. This yields a different type of solution (probabilistic) with better fidelity. The Quantitative Uncertainty Analysis for Diffraction (QUAD) package returns a matrix of affect model parameters as a function of iteration through the MCMC analysis. QUAD is a Python code that allows for analysis of X-ray and neutron diffraction data to infer the structure of materials with quantifiable certainty. The code uses Bayesian statistics and Markov chain sampling algorithms to create posterior probability distributions on all material structure parameters that are modeled by a researcher. The statistical packages use the open source GSASII project as a library to calculate model diffraction patterns.

Fancher, ChristopherM↗

Evidence of an oxidation induced phase transformation for a delta phase plutonium-gallium alloy

The oxidation of an ~1.5 at% Ga plutonium metal alloy in dry air as a function of time was studied using a combination of FIB-SEM, AES, and XRD. Analysis of SEM images of FIB cross-sections of the oxide allowed for direct measurement of the oxide thickness as well as determination of heterogeneity in the extent of the oxide. AES analysis performed on cross-sections of the oxide allowed for quantitative analysis of the atomic composition and semi-quantitative analysis of the chemical composition. Initial preparation of the sample was found to induce a martensitic transformation to α' - Pu with an average thickness of 233 nm. Electropolishing was found to be sufficient to fully remove the α' layer with creation of only a minimum oxide layer. Growth of the oxide in dry air was found to initially follow parabolic kinetics, with a parabolic rate constant orders of magnitude higher than expected for δ-Pu but in-line with values extrapolated to room temperature for α-Pu. Following complete oxidation of the initial α` layer, further regions of plutonium metal depleted in gallium were observed to form at the oxide / metal interface. However, gallium, as Ga 2 O 3 , was found to be enriched at the surface and present in the oxide in an amount comparable to the relative Ga:Pu ratio of the bulk metal alloy. Finally, the results presented here serve to bridge a diverse array of previous experimental and theoretical data and provide the first comprehensive view of the fate of the δ-stabilizer during formation of an oxide.

36 MATERIALS SCIENCE↗

Quantitative defect analysis in MOCVD GaN-on-GaN using cathodoluminescence

Cathodoluminescence (CL) is used as a quantitative characterization technique to probe impurities at the metal-organic chemical vapor deposition (MOCVD) grown GaN-on-GaN homoepitaxial interfaces. CL intensity contrast shows a strong correlation with the interfacial impurity concentrations. Based on the analysis of recombination mechanisms of electron beam induced non-equilibrium carriers, an analytical model is proposed to quantitatively determine the impurity concentrations from CL intensity. The extracted interfacial impurity concentrations from the analytical model show a good agreement with the compensation levels obtained from capacitance-voltage measurement, signifying the potential of CL for probing the quantitative impurity levels in GaN-on-GaN structures. This approach can also be extended to be applied in other material systems.

Chen, Zhaoying↗

Applying Graph Analytics to Understand Compute Core Usage and Publication Trends in a Petascale Supercomputing Facility

The Oak Ridge Leadership Computing Facility (OLCF) runs Titan, the No. 4 supercomputer in the world, to deliver over four billion compute core hours every year to several scientific domains, in their pursuit of leadership science. In this paper, we analyze four years worth of heterogeneous log data sources from the OLCF resource fabric, capturing metadata on entities such as users (2,546), scientific project allocations (674), jobs (1,352,402) and publications (1,146), to derive insights into the trends in core hour usage and publications, across 35 science domains. We have constructed a scalable graph to represent the OLCF entities and apply rich graph analytics for our analysis. Based on this, we have analyzed the metadata across five dimensions, namely (1) quantitative analysis of Titan system usage, (2) quantitative analysis of OLCF publications, (3) correlation analysis between system usage and publications, (4) text analysis to derive OLCF research trends, and (5) utilization of graph mining for association analysis. To the best of our knowledge, our work is the first of its kind to apply graph- based big data techniques to provide comprehensive insights on an HPC center's core hour usage and users' publication trends. Our results provide valuable details into an HPC center's core allocation program, measuring the productivity of scientific domains, the interplay between core usage and research output, accelerating collaboration, and in predicting new connections between resource entities.

Lee, Sangkeun (Matt)↗

An infrared analysis of Puppis A

A quantitative analysis of the infrared emission of the supernova remnant (SNR) Puppis A as seen by the Infrared Astronomical Satellite is presented. Physical parameters of the remnant (and the surrounding interstellar medium), including density, mass, temperature, and age are estimated. The infrared spectrum of Puppis A is fit by models of thermal emission from interstellar dust grains which have been swept up into the SNR where they are collisionally heated by the shocked gas. Evidence of an enhanced abundance of very small grains in the interstellar medium near Puppis A, and evidence of their destruction by the advancing blast wave, are found.

Arendt, Richard G.↗

Convergence Estimates for Multidisciplinary Analysis and Optimization

A quantitative analysis of coupling between systems of equations is introduced. This analysis is then applied to problems in multidisciplinary analysis, sensitivity, and optimization. For the sensitivity and optimization problems both multidisciplinary and single discipline feasibility schemes are considered. In all these cases a "convergence factor" is estimated in terms of the Jacobians and Hessians of the system, thus it can also be approximated by existing disciplinary analysis and optimization codes. The convergence factor is identified with the measure for the "coupling" between the disciplines in the system. Applications to algorithm development are discussed. Demonstration of the convergence estimates and numerical results are given for a system composed of two non-linear algebraic equations, and for a system composed of two PDEs modeling aeroelasticity.

Arian, Eyal↗

Database for LDV Signal Processor Performance Analysis

A comparative and quantitative analysis of various laser velocimeter signal processors is difficult because standards for characterizing signal bursts have not been established. This leaves the researcher to select a signal processor based only on manufacturers' claims without the benefit of direct comparison. The present paper proposes the use of a database of digitized signal bursts obtained from a laser velocimeter under various configurations as a method for directly comparing signal processors.

Baker, Glenn D.↗

Single Quadrupole Multiple Fragment Ion Monitoring Quantitative Mass Spectrometry

Single quadrupole mass spectrometry (MS) with enhanced in-source multiple fragment ion monitoring was designed to perform high sensitivity quantitative mass analyses. Enhanced in-source fragmentation amplifies fragmentation from traditional soft electrospray ionization producing fragment ions that have been found to be identical to those generated in tandem MS. We have combined enhanced in-source fragmentation data with criteria established by the European Union Commission Directive 2002/657/EC for electron ionization single quadrupole quantitative analysis to perform quantitative analyses. These experiments were performed on multiple types of complex samples that included a mixture of 50 standards, as well as cell and plasma extracts. The dynamic range for these quantitative analyses was comparable to triple quadrupole multiple reaction monitoring (MRM) analyses at up to 5 orders of magnitude with the cell and plasma extracts showing similar matrix effects across both platforms. Amino acid and fatty acid measurements performed from certified NIST 1950 plasma with isotopically labeled standards demonstrated accuracy in the range of 91–110% for the amino acids, 76–129% for the fatty acids, and good precision (coefficient of variation <10%). To enhance specificity, a newly developed correlated ion monitoring algorithm was designed to facilitate these analyses. This algorithm autonomously processes, aligns, filters, and compiles multiple ions within one chromatogram enabling both precursor and in-source fragment ions to be correlated within a single chromatogram, also enabling the detection of coeluting species based on precursor and fragment ion ratios. Single quadrupole instrumentation can provide MRM level quantitative performance by monitoring/correlating precursor and fragment ions facilitating high sensitivity analysis on existing single quadrupole instrumentation that are generally inexpensive, easy to operate, and technically less complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitative Particle Analysis of Neptunium-237 Oxides: Optimization of MAMA Analysis for Modified Direct Denitration Products

The production of plutonium-238 through irradiation of neptunium-237 ( 237 Np) target materials for the use in radioisotope thermoelectric generators is paramount for continued deep space exploration. This work employs scanning electron microscopy to analyze 237 Np materials coupled with a well-developed image analysis framework (Morphological Analysis for Material Attribution, or MAMA) to determine the degree of micron-scale homogeneity in the materials. This work demonstrated how the quantification of particle characteristics can validate production materials and affirm the qualitative similarities observed in micrographs. The 237 Np oxide particle analysis determined that the materials from five production runs were quantitatively homogenous (significant at α = 0.05) in particle area, circularity, equivalent circular diameter, and ellipse aspect ratio, with two of the sampling dates having statistically significant different means for one of the four characteristics. Furthermore, these metrics not only confirm general homogeneity of the material but also expand the application of MAMA workflows to 237 Np materials, demonstrating the utility of MAMA analysis for a wider breadth of nuclear materials than previously reported. In the open literature, this study is the first time that these microanalytical techniques were applied to 237 Np materials to this degree.

MAMA↗

A Quantitative Failure Analysis on Capacity Fade in Rechargeable Lithium Metal Cells

Rechargeable lithium battery (RLB) technology is transforming portable devices, vehicle electrification, and grid modernization. To make RLB durable, reliable and safe, conducting failure mode and effect analysis (FMEA) to identify failure mechanism under the operating conditions is very desirable. However, this ability is often overlooked or even lacking. The failure analysis (FA) is often conducted by laboratory testing and postmortem analysis, and the knowledge typically empirical. Here we present a quantitative approach for FMEA that can reveal how failure modes and effects reduce the capacity of a RLB. This approach is based on the state of the battery for FMEA, contrary to the conventional approach based on operating or testing conditions. The key aspect of this FMEA method is to convert the experimental results to a state-of-charge (SOC)-based analytic methodology. Such a conversion can separate the thermodynamic and kinetic attributes of capacity fade based on compositional correspondence in the electrode, so the loss and the decreased utilization of the active materials can be determined respectively.

25 ENERGY STORAGE↗