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At least 1,099 records · Page 61

The spatially resolved transcriptome signatures of glomeruli in chronic kidney disease

Here, we used digital spatial profiling (DSP) to describe the glomerular transcriptomic signatures that may characterize the complex molecular mechanisms underlying progressive kidney disease in Alport syndrome, focal segmental glomerulosclerosis, and membranous nephropathy. Our results revealed significant transcriptional heterogeneity among diseased glomeruli, and this analysis showed that histologically similar glomeruli manifested different transcriptional profiles. Using glomerular pathology scores to establish an axis of progression, we identified molecular pathways with progressively decreased expression in response to increasing pathology scores, including signal recognition particle–dependent cotranslational protein targeting to membrane and selenocysteine synthesis pathways. We also identified a distinct signature of upregulated and downregulated genes common to all the diseases investigated when compared with nondiseased tissue from nephrectomies. These analyses using DSP at the single-glomerulus level could help to increase insight into the pathophysiology of kidney disease and possibly the identification of biomarkers of disease progression in glomerulopathies.

60 APPLIED LIFE SCIENCES↗

Decision-making based on Markov decision process in integrated artificial reasoning framework—Part I: Theory

This paper presents a decision-making framework based on an integrated artificial reasoning framework and Markov decision process (MDP). The integrated artificial reasoning framework provides a physics-based approach that converts system information into state transition models, and the analysis result will be represented by the transition probabilities that can be used with an MDP to find a traceable and explainable optimal pathway. A dynamic Bayesian network (DBN) is well suited for representing the structure of an MDP. The causality information among process variables (or among subsystems) is mathematically represented in a DBN by the conditional probabilities of the node’s states provided different probabilities of the parent node’s states. To define node states in a physically understandable manner, we used multilevel flow modeling (MFM). An MFM follows the fundamental energy and mass conservation laws and supports the selection of process variables that represent the system of interest so that causal relations among process variables are properly captured. An MFM-based DBN supports developing state transition models in an MDP to capture the effect of process variables of system having physical relations. The operators of the target system can capture stochastic system dynamics as multiple subsystem state transitions based on their physical relations and uncertainties coming from component degradation or random failures. We analyzed a simplified exemplary system to illustrate an optimal operational policy using the suggested approach.

Markov decision process↗

Rooftop Solar in Lawrence, MA: Community Perspectives, Deceptive Practices, and Financing Options

This report was prepared as part of the U.S. Department of Energy's Communities Local Energy Action Program (Communities LEAP) pilot competitive technical assistance for the Lawrence Massachusetts Stakeholder Coalition (LSC) composed of The City of Lawrence, All In Energy, MassDevelopment, Mill City Community Investments, BlocPower and Groundwork Lawrence, and led by Browning the Green Space. The LSC identified rooftop solar photovoltaics as a top priority for this technical assistance opportunity. Lawrence faces high energy burden and electricity prices, thus rooftop solar can be a tool to help lower those costs. However, the coalition received feedback that some solar companies were using deceptive and unfair practices when marketing, selling, or financing solar energy, costing residents more money than utility rates and increasing the energy burden. This project sought to address rooftop solar community priorities through two pathways: 1. facilitating community engagement to understand community perspectives and experiences with rooftop solar development; and 2. conducting a financial cash-flow analysis highlighting the varying fiscal outcomes for rooftop solar adopters based off rooftop solar leasing, ownership, or buying electricity from the utility (National Grid).

14 SOLAR ENERGY↗

Moisture Metaphenome Incubation Analysis Results

The Birch effect, a pulse of CO2 release that occurs when dry soil is rewet, is commonly observed, yet the underlying biogeochemistry remains elusive. Using multi-omics data, real-time mass spectrometry and modeling approaches, we investigated the molecular response to rewetting of a soil microbiome exposed to drought for one and two weeks. The microbiome response was evaluated through analysis of transcript, protein, metabolite, and respiration profiles and metabolic modeling using an enhanced version of the Metabolite Expression Metabolic Network Integration for Pathway Identification and Selection (MEMPIS) algorithm (Roy Chowdhury et al, mSystems, 2019).

Lipton, Mary S [Pacific Northwest National Laborat↗

Evaluation of CALIOP 532-nm Aerosol Optical Depth Over Opaque Water Clouds

With its height-resolved measurements and near global coverage, the CALIOP lidar onboard the CALIPSO satellite offers a new capability for aerosol retrievals in cloudy skies. Validation of these retrievals is difficult, however, as independent, collocated and co-temporal data sets are generally not available. In this paper, we evaluate CALIOP aerosol products above opaque water clouds by applying multiple retrieval techniques to CALIOP Level 1 profile data and comparing the results. This approach allows us to both characterize the accuracy of the CALIOP above-cloud aerosol optical depth (AOD) and develop an error budget that quantifies the relative contributions of different error sources. We focus on two spatial domains: the African dust transport pathway over the tropical North Atlantic and the African smoke transport pathway over the southeastern Atlantic. Six years of CALIOP observations (2007-2012) from the northern hemisphere summer and early fall are analyzed. The analysis is limited to cases where aerosol layers are located above opaque water clouds so that a constrained retrieval technique can be used to directly retrieve 532 nm aerosol optical depth and lidar ratio. For the moderately dense Sahara dust layers detected in the CALIOP data used in this study, the mean/median values of the lidar ratios derived from a constrained opaque water cloud (OWC) technique are 45.1/44.4 +/- 8.8 sr, which are somewhat larger than the value of 40 +/- 20 sr used in the CALIOP Level 2 (L2) data products. Comparisons of CALIOP L2 AOD with the OWC-retrieved AOD reveal that for nighttime conditions the L2 AOD in the dust region is underestimated on average by approx. 26% (0.183 vs. 0.247). Examination of the error sources indicates that errors in the L2 dust AOD are primarily due to using a lidar ratio that is somewhat too small. The mean/median lidar ratio retrieved for smoke is 70.8/70.4 +/- 16.2 sr, which is consistent with the modeled value of 70 +/- 28 sr used in the CALIOP L2 retrieval. Smoke AOD is found to be underestimated, on average, by approx. 39% (0.191 vs. 0.311). The primary cause of AOD differences in the smoke transport region is the tendency of the CALIOP layer detection scheme to prematurely assign layer base altitudes and thus underestimate the geometric thickness of smoke layers.

Liu, Z.↗

Gene Expression and Structural Skeletal Responses to Long-Duration Simulated Microgravity in Rats

Spaceflight has deleterious effects on skeletal structure and function, specifically causingprofound loss in bone mass, density, and strength, as well as changes in expression levels of genes related to oxidative stress [Hyeon et al., Smith et al.]. It is known that bone resorption remains elevated after spaceflight and that bone density and strength fail to recover completely even years following spaceflight [Smith et al., Carpenter et al.]. However, our current understanding of the signaling pathways and molecular mechanisms that control bone loss and that link oxidative stress, bone resorption, and mechanical unloading of skeletal tissue is incomplete. Here, we aim to examine skeletal responses to simulated long-duration spaceflight on bone loss using the ground-based hindlimb unloading (HU) model in adult (9 months old) male rats. We hypothesized that simulated microgravity leads to the temporal regulation of oxidative-defense genes and pro-osteoclastogenic factors, showing progression and eventual plateau during long-term unloading, and that transient changes at early timepoints in these pathways precede skeletal adaptations to long-duration unloading. We will identify oxidativestress and bone resorption-related changes using global gene expression analysis (Affymetrix arrays) for both acute (within 14 days) and long-term timepoints (90 days). We will also use quantitative PCR to examine changes in expression of genes related to oxidative metabolism (e.g. Nrf2, SOD-1), bone turnover (resorption and formation markers, e.g. TRAP, osteocalcin respectively, SOST), and osteoclastogenesis (e.g. RANKL, OPG) at both early and late timepoints. We will then use detailed microarchitectural and structural analysis through microcomputed tomography to relate gene expression changes with structural changes in bone, expecting that plateaus in gene expression correlate with long-term changes in bone microarchitecture.

Rael, Victoria E.↗

Oculometric Analysis of Saccadic Compensation for Visual Motion Processing Impairment due to Alcohol and Sleep Disruption

The Visuomotor Control Laboratory at Ames Research Center has developed a 5-minute ocular tracking test that computes 21 largely independent metrics of visuomotor performance, reflecting neural signal processing along a number of distinct pathways through cortex, brainstem, and cerebellum. Human sensorimotor performance is resilient to the challenges and stressors of many operational environments, in part, because overall performance is achieved through multiple parallel systems. Our multidimensional oculometrics allow us to examine impacts on these sub-components separately. To illustrate this, we contrasted the effects of two mild neural stressors, acute sleep-deprivation and low-dose alcohol. We have previously shown that, in both cases, oculometric analysis is a highly sensitive indicator of impairment. Here we quantified not only the observed impact on the performance of one sub-system, smooth pursuit, which uses high-level cortical processing of visual motion to track a moving object, but also the observed (partial) compensation by an evolutionarily older mid-brain and brainstem subsystem, saccades, which generates jumps in eye position to catch up with the target when smooth pursuit is inadequate. Specifically, we examined the dose-response (effect size vs. dose size) of the ground lost (pursuit deficit) and the ground recouped (saccadic compensation) across three separate studies – acute low-dose alcohol administration (16 subjects), acute sleep loss (12 subjects), and acute sleep loss with caffeine intervention (9 subjects). We computed the dose-response slopes using linear regression. The figure below shows that, in the case of acute sleep deprivation, the resulting slopes for ground lost and ground recouped (mean ± SE across subjects) were significantly different (paired t-test, t(11) = 5.17, p < 0.001), indicating poor saccadic compensation. However, when sleep loss was coupled with caffeine ingestion, ground lost was decreased and ground recouped increased such that the slopes were no longer different (t(8) = -0.05, p = 0.965). With alcohol, the two slopes were large albeit not significantly different (t(15) = 0.96, p = 0.351), indicating significant pursuit impairment but effective saccadic compensation. Our findings show that sleep deprivation and alcohol affect oculomotor performance differently. Low-dose alcohol effects appear predominantly cortical, with effective brainstem compensation. Sleep loss and circadian disruption however appears to affect both cortical and brainstem pathways with caffeine providing an effective countermeasure to both effects. Beyond the mere detection of impairment, our oculometric assessment allows us to characterize the nature of the deficit, to provide insight into the neural substrate, and to assess the effectiveness of countermeasures.

pursuit↗

Modeling MTS pyrolysis and SiC deposition kinetics using principal component analysis and neural networks

Accurate chemical kinetics modeling is crucial for improving the efficiency of chemical processing and synthesis of ceramic matrix composites. Detailed kinetic models are computationally expensive due to the large number of transported chemical species, while the simplified physics-based models, such as single-step global mechanisms, are efficient but often overlook key chemical intermediates and pathways. Recent deep learning approaches promise accurate and cost-effective models. Yet, they require additional closures for the transported nonlinear latent variables, complicating integration with existing solvers. In this work, we develop a hybrid linear—nonlinear reduced model for silicon carbide deposition from methyltrichlorosilane precursor by combining principal component analysis (PCA) and autoencoder (AE) neural network (NN) approaches. PCA is used to identify a smaller set of linear transport variables, enabling direct reuse of conventional transport solvers. NNs then reconstruct the full chemical state from these reduced variables. We demonstrate the method on a chemical vapor deposition reactor—comprising a gas-phase pyrolysis plug flow reactor and a heterogeneous surface reactor—over a wide range of temperatures, pressures, and residence times. Our PCA–AE model achieves high accuracy with only five transported scalars, achieving an eightfold cost reduction compared to detailed mechanisms, in both a priori (using data from the test set only) and a posteriori (coupled with a differential equation solver). In conclusion, notable errors arise primarily near training domain boundaries and for long residence times, indicating the need for domain shift indicators and better long-horizon predictions in future reduced chemistry model development.

autoencoder neural networks↗

Pathways to a Sustainable Aviation Ecosystem: Flight DNA: An Anonymized Aviation Data Tool and Repository

The National Renewable Energy Laboratory (NREL) has deep experience developing secure, national data repositories, which it augments with analysis, technology and market expertise, high-performance computing, and innovative data visualization. By adapting the architecture of existing mobility databases (i.e., Fleet DNA, the Transportation Secure Data Center, the National Fuel Cell Technology Evaluation Center), NREL can build a powerful aviation data clearinghouse - Flight DNA - that helps stakeholders navigate the web of pitfalls and possibilities generated by new aviation technologies.

aviation↗

Analysis of Return and Forward Links from STARS' Flight Demonstration 1

Space-based Telemetry And Range Safety (STARS) is a Kennedy Space Center (KSC) led proof-of-concept demonstration, which utilizes NASA's space network of Tracking and Data Relay Satellites (TDRS) as a pathway for launch and mission related information streams. Flight Demonstration 1 concluded on July 15,2003 with the seventh flight of a Low Power Transmitter (LPT) a Command and Data Handler (C&DH), a twelve channel GPS receiver and associated power supplies and amplifiers. The equipment flew on NASA's F-I5 aircraft at the Dryden Flight Research Center located at Edwards Air Force Base in California. During this NASA-ASEE Faculty Fellowship, the author participated in the collection and analysis of data from the seven flights comprising Flight Demonstration 1. Specifically, the author examined the forward and return links bit energy E(sub B) (in Watt-seconds) divided by the ambient radio frequency noise N(sub 0) (in Watts / Hertz). E(sub b)/N(sub 0) is commonly thought of as a signal-to-noise parameter, which characterizes a particular received radio frequency (RF) link. Outputs from the data analysis include the construction of time lines for all flights, production of graphs of range safety values for all seven flights, histograms of range safety E(sub b)/N(sub 0) values in five dB increments, calculation of associated averages and standard deviations, production of graphs of range user E(sub b)/N(sub 0) values for the all flights, production of graphs of AGC's and E(sub b)/N(sub 0) estimates for flight 1, recorded onboard, transmitted directly to the launch head and transmitted through TDRS. The data and graphs are being used to draw conclusions related to a lower than expected signal strength seen in the range safety return link.

Gering, James A.↗

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical↗

NX Fuels H2 Shot Incubator Phase I (CRADA Final Report)

NX Fuels will work with NREL to perform Life-Cycle Analysis (LCA) and Techno-Economic Analysis (TEA) for NX Fuels' solar H 2 system. TEA/LCA modeling developed early on will provide insight on the most critical parameters related to the green H 2 cost and environmental impacts and help us create the business case at scale. This project will advance the Nation’s decarbonization goals by demonstrating the economic feasibility of NX Fuels clean hydrogen production pathway and evaluate its impact on CO 2 emissions.

08 HYDROGEN↗

Modeled production, oxidation, and transport processes of wetland methane emissions in temperate, boreal, and Arctic regions

Abstract Wetlands are the largest natural source of methane (CH 4 ) to the atmosphere. The eddy covariance method provides robust measurements of net ecosystem exchange of CH 4 , but interpreting its spatiotemporal variations is challenging due to the co‐occurrence of CH 4 production, oxidation, and transport dynamics. Here, we estimate these three processes using a data‐model fusion approach across 25 wetlands in temperate, boreal, and Arctic regions. Our data‐constrained model—iPEACE—reasonably reproduced CH 4 emissions at 19 of the 25 sites with normalized root mean square error of 0.59, correlation coefficient of 0.82, and normalized standard deviation of 0.87. Among the three processes, CH 4 production appeared to be the most important process, followed by oxidation in explaining inter‐site variations in CH 4 emissions. Based on a sensitivity analysis, CH 4 emissions were generally more sensitive to decreased water table than to increased gross primary productivity or soil temperature. For periods with leaf area index (LAI) of ≥20% of its annual peak, plant‐mediated transport appeared to be the major pathway for CH 4 transport. Contributions from ebullition and diffusion were relatively high during low LAI (<20%) periods. The lag time between CH 4 production and CH 4 emissions tended to be short in fen sites (3 ± 2 days) and long in bog sites (13 ± 10 days). Based on a principal component analysis, we found that parameters for CH 4 production, plant‐mediated transport, and diffusion through water explained 77% of the variance in the parameters across the 19 sites, highlighting the importance of these parameters for predicting wetland CH 4 emissions across biomes. These processes and associated parameters for CH 4 emissions among and within the wetlands provide useful insights for interpreting observed net CH 4 fluxes, estimating sensitivities to biophysical variables, and modeling global CH 4 fluxes.

Ueyama, Masahito↗

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗

In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway

The low-density lipoprotein receptor (LDLR) is a major apolipoprotein receptor that regulates cholesterol homeostasis. LDLR deficiency is associated with cognitive impairment by the induction of synaptopathy in the hippocampus. Despite the close relationship between LDLR and neurodegenerative disorders, proteomics research for protein profiling in the LDLR knockout (KO) model remains insufficient. Therefore, understanding LDLR KO-mediated differential protein expression within the hippocampus is crucial for elucidating a role of LDLR in neurodegenerative disorders. In this study, we conducted first-time proteomic profiling of hippocampus tissue from LDLR KO mice using tandem mass tag (TMT)-based MS analysis. LDLR deficiency induces changes in proteins associated with the transport of diverse molecules, and activity of kinase and catalyst within the hippocampus. Additionally, significant alterations in the expression of components in the major synaptic pathways were found. Furthermore, these synaptic effects were verified using a data-independent acquisition (DIA)-based proteomic method. In conclusion, our data will serve as a valuable resource for further studies to discover the molecular function of LDLR in neurodegenerative disorders.

60 APPLIED LIFE SCIENCES↗

Fast-Charging Aging Considerations: Incorporation and Alignment of Cell Design and Material Degradation Pathways

Fast charging of batteries for electric vehicles is seen as one of the most direct ways to enhance adoption. Currently, fast charging is limited by increased cell aging, which is primarily driven by Li plating and degradation of cathode materials. Here, using combined sets of experimental and computational analysis and a suite of different charge protocols, we begin to examine the interplay between failure mode, cell designs, and ultimately aging mechanisms. Slight variation in cell design and the subsequent impacts that charge protocols have on aging can create distinct cell-to-cell variation. As little as 2% difference in porosity change at the cell negative electrode during cycling due to early Li metal plating has been found to alter the aging pathway and either accelerate or inhibit the loss due to Li plating.

25 ENERGY STORAGE↗

Hydrogen Life-Cycle Analysis in Support of Clean Hydrogen Production

Hydrogen is a basic molecule which is commonly used in the production of chemicals or as an energy carrier or a fuel. Its zero-carbon content means that it does not produce carbon dioxide upon its use. However, depending on the energy source and technology for hydrogen production and delivery, there can be greenhouse gas (GHG) emissions associated with the hydrogen for various end use applications. To provide the largest reduction in GHG emissions, hydrogen produced from clean energy sources should be used. As concerns regarding climate change grows, there is an increasing focus on economic production of clean hydrogen to displace less climate neutral sources of hydrogen. However, there are many different methods of hydrogen production with unique processes that result in different levels of life cycle GHG emissions of hydrogen production and its end use applications. Therefore, a comprehensive life cycle accounting methodology that takes all these factors into account is required. he GREET ® (Greenhouse gases, Regulated Emissions, and Energy use in Technologies) model was first developed in 1995 by Argonne National Laboratory with the support from the various offices of the U.S. Department of Energy (DOE). GREET provides in-depth Life Cycle Analysis (LCA) simulations for a variety of products and is available as an Excel spreadsheet (GREET Excel), or as an application (GREET .Net). Both versions are available for public download at no cost. This report accompanies GREET 2022 release to describe the major updates and expansions to the hydrogen technology pathways, and to provide data sources and sample carbon intensity results for each of the pathways.

08 HYDROGEN↗

X-Ray Diffraction and Reflectance Spectroscopy of Murchison Powders (CM2) After Thermal Analysis Under Reducing Conditions to Final Temperatures Between 300 and 1300°c

The asteroids Ryugu and Bennu have spectral characteristics in common with CI/CM type carbonaceous chondrites and are target bodies for JAXA’s Hayabusa2 and NASA’s OSIRIS-Rex missions, respectively. Analog studies, based primarily on the Murchison CM2 chondrite, provide a pathway to separate spectral properties resulting space weathering from those inherent to parent-body, mineralogy, chemistry, and processes. Ryugu shares spectral properties with thermally metamorphosed and partly dehydrated CI/CM chondrites. We have undertaken a multidisciplinary study of the thermal decomposition of Murchison powder samples as an analog to metamorphic process that may have occurred on Ryugu. Bulk analyses include thermal And evolved gas analysis, X-ray diffraction (XRD), and VIS-NIR and Mössbauer spectroscopy; micro- to nanoscale analyses included scanning and transmission electron microscopy and electron probe micro analysisWe report here XRD and VIS-NIR analyses of pre- and post-heated Murchison powders, and in a companion paper report results from multiple electron beam techniques.

Morris, R. V.↗