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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 667 records · Page 37

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗

Putting Data to Work (Final Technical Report)

The Putting Data to Work project was designed to pilot and summarize the use of building energy performance data to improve energy efficiency program design and delivery in DC and NYC. By doing this, the project aimed to expand the market for energy efficiency in multifamily and commercial buildings by producing a toolkit of resources for other jurisdictions to replicate the successes found in the project cities.

30 DIRECT ENERGY CONVERSION↗

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

We present that the fast-growing Gram-negative bacterium Vibrio natriegens is an attractive microbial system for molecular biology and biotechnology due to its remarkably short generation time and metabolic prowess. However, efforts to uncover and utilize the mechanisms underlying its rapid growth are hampered by the scarcity of functional genomic data. Here, we develop a pooled genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) screen to identify a minimal set of genes required for rapid wild-type growth. Targeting 4,565 (99.7%) of predicted protein-coding genes, our screen uncovered core genes comprising putative essential and growth-supporting genes that are enriched for respiratory pathways. We found that 96% of core genes were located on the larger chromosome 1, with growth-neutral duplicates of core genes located primarily on chromosome 2. Lastly, our screen also refines metabolic pathway annotations by distinguishing functional biosynthetic enzymes from those predicted on the basis of comparative genomics. Taken together, this work provides a broadly applicable platform for high-throughput functional genomics to accelerate biological studies and engineering of V. natriegens.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗

Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Leveraging genome and plasma proteome data from the INTERVAL study, we established and validated models to predict protein levels using genetic variants. By examining 8,275 PDAC cases and 6,723 controls, we identified 40 associated proteins, of which 16 are novel. Functionally validating these candidates by focusing on 2 selected novel protein-encoding genes, GOLM1 and B4GALT1, we demonstrated their pivotal roles in driving PDAC cell proliferation, migration, and invasion. Furthermore, we also identified potential drug repurposing opportunities for treating PDAC.

60 APPLIED LIFE SCIENCES↗

Data for "RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides"

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ ( R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides , providing a streamlined method for addressing genetic engineering challenges in the yeast.

gene editing↗

Data from A Genetic Toolbox for Metabolic Engineering of Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis , which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis .

Conversion↗

OC6 Phase III Definition Document

The objective of Phase III of the Offshore Code Comparison Collaboration, Continued, with Correlation and unCertainty (OC6) project was to evaluate the accuracy of aerodynamic load predictions by offshore wind modeling tools for a floating offshore wind turbine as it experiences large surge-translational and pitch-rotational motion, as would occur during normal operation. A variety of models were examined in the project, with the goal of performing a three-way validation between engineering-level tools, higher-fidelity tools, and measurement data from two wind tunnel experimental campaigns. This document provides the necessary information to model and simulate the system studied in the OC6 Phase III project. This information is not only useful for project participants, but also future modelers who want to replicate this work for verification and validation purposes.

17 WIND ENERGY↗

Data from: Niche differentiation of bacterial versus archaeal soil nitrifiers induced by ammonium inhibition along a management gradient

Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.

59 BASIC BIOLOGICAL SCIENCES↗

A note on the Bayesian analysis of experiments with correlated multiple responses using a matrix-logarithmic covariance model

In the literature, analysis of multiple responses from experiments with replicates has modeled the covariance matrix directly as linear models of the transformed variances and correlations, i.e., covariance modeling. This article considers models based on the matrix- logarithm of the covariance matrix. This so-called log-covariance modeling is illustrated with data from actual experiments and compared with the traditional covariance modeling.

97 MATHEMATICS AND COMPUTING↗

ROOT RNTuple and EOS: The Next Generation of Event Data I/O

For several years, the ROOT team is developing the new RNTuple I/O subsystem in preparation of the next generation of collider experiments. Both HL-LHC and DUNE are expected to start data taking by the end of this decade. They pose unprecedented challenges to event data I/O in terms of data rates, event sizes, and event complexity. At the same time, the I/O landscape is becoming more diverse. HPC cluster file systems and object stores, NVMe disk cache layers in analysis facilities, and S3 storage on cloud resources are mixing with traditional XRootD-managed spinning disk pools.The ROOT team will finalize a first production version of the RNTuple binary format by the end of 2024. After this point, ROOT will provide backward compatibility for RNTuple data. This contribution provides an overview of the RNTuple feature set, the related R&D activities and the long-term vision for RNTuple. We report on performance, interface design, tooling, robustness, integration with experiment frameworks, and validation results, as well as recent R&D on parallel reading and writing and exploitation of modern hardware and storage systems. We will give an outlook on possible future features after a first production release.Collaboratively, the IT and EP departments at CERN have launched a formal project within the Research and Computing sector to evaluate the novel data format for physics analysis data utilized in LHC experiments and other fields. This part of the project focuses on validating the scalability of the EOS storage backend during the transition from the over 25 years old TTree production format to the newly developed RNTuple format, using both replicated and erasure-coded storage profiles.

Blomer, Jakob [CERN]↗

Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein–RNA complex

Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ~2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. In this paper, we have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11-Å resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closely represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the “rule of six” that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. Finally, this rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.

59 BASIC BIOLOGICAL SCIENCES↗

SU-E-J-263: Repeatability of SUV and Texture Parameters in Serial PET Studies

Purpose: Standardized uptake values (SUV) are standard quantitative PET measures of FDG tumor uptake used,and are used as a tool to monitor response to therapy. Textural analysis is emerging as a new tool for assessing intratumoral heterogeneity which may allow better tissue characterization and improved prediction of response and survival rate.Understanding what variations may be expected in these parameters is key in order to make decisions based on how the change throughout the course of treatment. The aim of this study was to assess repeatability in SUV measures and texture parameters,and establish criteria that differentiate changes associated with treatment rather than statistical variability. Methods: Eighty patients,167 random lesions total,were scanned in a GE Discovery STE PET/CT Scanner. One field-of-view was chosen centered on the largest lesion observed in a clinical whole-body FDG PET.Immediately following,a gated 9 min scan was acquired in list mode,without changing the patient’s position between any scans. Data was replayed into 3 time bins,3 min each,in order to insure equivalent noise characteristics in each replicate.Data was reconstructed into 128×128×47 square matrices.One VOI was drawn over each lesion for each patient and used to segment all 3 replicates. The mean.max and peak SUV were calculated for each VOI and replicate. First-order textural features were also calculated (skewness and kurtosis). Repeatability was calculated as the average standard deviation over the mean for the 3 repeated measurements for each lesion. Results: The average percent error in the SUV max,peak and mean were 3.4%(0– 12.9%),1.9% (0–7.5%),2.8% (0–12.2%),respectively.For skewness and kurtosis they were 10.9% and 17.8%. Conclusion: We have shown that there is a large variation in %error in SUV measures across patients. SUVpeak is the least variable and kurtosis and skewness parameters are less reliable thatn SUVs.Higher order textures are be.

60 APPLIED LIFE SCIENCES↗

ACT University Collaboration Proposal: Role of manufacturing defects on material failure under dynamic loading for developing enhanced failure models and theories (Final Report)

Research on the tensile behavior of additively manufactured 316L stainless steel coupon specimens at increasing strain rates was conducted over the past year at Penn State. Dynamic loading rates into the 1000 1/s loading rates were performed on specimens with nearly 1.32” gage lengths. Stress-strain plots show ductile and plastic behavior well beyond 12% strain with necked specimens, having smaller effective gage lengths showing up to 56% ultimate strain. Additional tests performed on compact tension specimens helped with simulation work to understand the deformation behavior. Using finite elements, it was possible to determine the feasibility of a comprehensive experimental validation study towards an improved model for AM material failure – specifically, the Bai-Wierzbicki approach which accounts for lode angle and triaxiality. A non-significant number of tests are projected for eight specific failure nodes, with additional replicates to provide strain-rate capabilities to the existing formulation. One such correction factor is explored for quasi-static, notched specimens. Finally, stress intensity factor was explored using a set of compact-tension specimens which would also provide useful validation data for any simulation work.

36 MATERIALS SCIENCE↗

Acute toxicity of copper to the larval stage of three species of ambystomatid salamanders

Copper (Cu) appears to be consistently more toxic to anuran species relative to other vertebrate taxa. There are limited Cu toxicity data for salamanders; of the few studies conducted on salamanders, most examined Cu effects on the embryonic, but not the larval, stage. We performed acute toxicity experiments, to quantify LC50s, on Harrison stage 46 larvae (free swimming hatchlings with egg yolk completely absorbed) of three ambystomatid salamander species. Each LC50 experiment used exposure concentrations of 10, 20, 30, 40, 50, and 60 µg/L with 10 replicates per concentration each containing one larva. We found very high toxicity for all species compared to previously published research on the embryo stage. Specifically, the 4-d LC50s for Ambystoma tigrinum and A. opacum were 35.3 and 18.73 µg/L, respectively. The same Cu concentrations caused similar toxicity to A. talpoideum (LC50 = 47.88 µg/L), but exposures required up to 48 d to elicit the same level of mortality. A time-to-event analysis indicated that time to mortality was significantly affected by Cu concentration. Additionally, for A. talpoideum, we observed that elevated levels of Cu decreased growth rate. Finally, comparisons with previously reported Cu toxicity for embryos suggest that, as with fish, Cu may be more toxic to larval salamander stages than for embryos. Further, our data suggest that Cu is an important environmental contaminant that deserves increased scrutiny on the potential for population-level effects where contamination has occurred in wetlands and streams inhabited by salamanders.

59 BASIC BIOLOGICAL SCIENCES↗

An adaptable technique for comparative image assessment: Application to crosswell electromagnetic survey design for fluid monitoring

Reservoir integrity stewardship accompanying carbon capture and sequestration considers fluid extraction and reinjection as a risk-mitigating method against overpressuring that could lead to caprock damage and ensuing [Formula: see text] leakage. Crosswell electromagnetics offers a technically viable monitoring method with the spatial volume coverage necessary for reservoir-encompassing pressure management. However, a certain logistic dilemma for deep gas sequestration into saline and thus electrically conductive aquifers is that crosswell magnetic-field measurements underperform in the imaging of more resistive plume bodies, further exacerbated when vertical arrays intersect, as opposed to surround, plumes. Furthermore, comparative synthetic-data plume imaging of such scenarios rates the information content of magnetic-field versus electric-field 3D crosswell layouts for reservoir and infrastructure conditions of a representative pilot site in a coastal area in Florida. The image quality of the resulting plume replications can be ranked numerically through a newly proposed semblance qualifier, appraising the model goodness of fit to a given reference. In contrast to common least-squares measures for goodness of fit, the semblance formulation uses classifying logistic function types, thus enabling a better distinction of predefined anomaly features.

58 GEOSCIENCES↗