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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 109 records · Page 6

Gains in operational flexibility, safety margins, and cost efficiencies via integrated Plant Reload Optimization platform

The U.S. Department of Energy Light Water Reactor Sustainability Program Risk-Informed Systems Analysis Pathway Plant Reload Optimization Project aims to develop an integrated, comprehensive framework offering an all-in-one solution for reload evaluations with a special focus on optimizing core design. Optimizing the fuel loading pattern is one of the most important considerations in reducing the amount of new fuel used in the core. Due to thousands of possible core configuration options, finding optimal solutions is an unachievable task for a human. The Plant ReLoad Optimization platform, which supports artificial-intelligence-based reactor core designing, is now fully capable of handling realistic problems. The Plant ReLoad Optimization platform development project aims to build a reactor core design tool that includes reactor safety and fuel performance analyses and uses artificial intelligence to support the optimization of core design solutions. The NSGA-II (Non-dominated Sorting Genetic Algorithm II) optimizer was developed and tested within RAVEN (Risk Analysis and Virtual ENvironment) to handle many constraints by using an augmented objectives methodology. The demonstration was performed with constrained multiobjective optimization of a 17 × 17 pressurized-water reactor core loading patterns to minimize fuel cost and maximize fuel cycle length.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Local-scale panmixia in the lichenized fungus Xanthoria parietina contrasts with substantial genetic structure in its Trebouxia photobionts

Microsatellite markers can provide valuable information about gene flow and population history. We developed and tested new microsatellites for the nitrophilic lichenized fungus Xanthoria parietina and studied its genetic diversity and structure within the urban area of Munich, Bavaria. We compared its local genetic pattern with that of its photobiont partner Trebouxia decolorans, for which existing microsatellites were applied. For comparison, a reference site with clean air was included in the sampling. We found support for three genetic clusters in the fungus X. parietina, which occurred intermingled in collecting sites. There was a high degree of admixture within fungal populations and individuals, and analysis of molecular variance revealed a lack of population structure in the mycobiont. The Trebouxia photobiont, in contrast, exhibited structured populations which grouped into two to five genetic clusters, and individuals showed less admixture than in the mycobiont. This indicates that the two lichen partners differ in their ability to move around in the landscape. The microsatellite markers we report are polymorphic and are suitable for population genetic studies.

59 BASIC BIOLOGICAL SCIENCES↗

Testing for the Genomic Footprint of Conflict Between Life Stages in an Angiosperm and Moss Species

Abstract The maintenance of genetic variation by balancing selection is of considerable interest to evolutionary biologists. An important but understudied potential driver of balancing selection is antagonistic pleiotropy between diploid and haploid stages of the plant life cycle. Despite sharing a common genome, sporophytes (2n) and gametophytes (n) may undergo differential or even opposing selection. Theoretical work suggests antagonistic pleiotropy between life stages can generate balancing selection and maintain genetic variation. Despite the potential for far-reaching consequences of gametophytic selection, empirical tests of its pleiotropic effects (neutral, synergistic, or antagonistic) on sporophytes are generally lacking. Here, we examined the population genomic signals of selection across life stages in the angiosperm Rumex hastatulus and the moss Ceratodon purpureus. We compared gene expression between life stages and sexes, combined with neutral diversity statistics and the analysis of the distribution of fitness effects. In contrast to what would be predicted under balancing selection due to antagonistic pleiotropy, we found that unbiased genes between life stages were under stronger purifying selection, likely explained by a predominance of synergistic pleiotropy between life stages and strong purifying selection on broadly expressed genes. In addition, we found that 30% of candidate genes under balancing selection in R. hastatulus were located within inversion polymorphisms. Our findings provide novel insights into the genome-wide characteristics and consequences of plant gametophytic selection.

Evolutionary Biology↗

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9↗

Enhancing Thomson scattering polychromator performance with multi-pass spectral filters

In photon-deficient, noncollective Thomson scattering diagnostics, filter polychromators are typically employed in the spectral analysis of Thomson-scattered signals to achieve acceptable signal-to-noise performance. Currently, the most common polychromator filter configuration employs a set of single-passband optical filters that define individual spectral channels. Here, we introduce a new spectral analysis method for Thomson scattering based on spectral filters with multiple passbands, referred to as Thomson scattering spectral multiplexing. Implementing multi-bandpass spectral filters on polychromators increases the achievable range of electron temperature measurement for a given number of filters employed. In addition, Thomson scattering spectral multiplexing reduces systematic measurement uncertainty, with fewer required spectral channels, thereby decreasing light loss from reduced optical element interactions. A multi-bandpass filter set, optimized by a genetic algorithm, has been successfully installed and tested on the Helically Symmetric eXperiment (HSX), demonstrating the benefits of the Thomson scattering spectral multiplexing method.

Instruments & Instrumentation↗

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing↗

Demonstration of the Plant Fuel Reload Process Optimization for an Operating PWR

The United States (U.S.) nuclear industry is facing a strong challenge to maintain regulatory-required levels of safety while ensuring economic competitiveness to stay in business. Safety remains a key parameter for all aspects related to the operation of light water reactor (LWR) nuclear power plants (NPPs) and can be achieved more economically by using a risk-informed ecosystem such as that being developed by the Risk-Informed Systems Analysis (RISA) Pathway under the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program. The LWRS Program is promoting a wide range of research and development (R&D) activities with the goal to maximize both the safety and economically efficient performance of NPPs through improved scientific understanding, especially given that many plants are considering second license renewal. The RISA Pathway has two main goals: (1) the deployment of methodologies and technologies that enable better representation of safety margins and the factors that contribute to cost and safety; and (2) the development of advanced applications that enable cost-effective plant operation. This report summarizes the research outcomes in FY-2021, which the project progressed from the planning and methodology development phase to the early demonstration phase. The highlights of these activities are: (1) the development of a multi-objective optimization process using Genetic Algorithms (GAs); (2) the development and test of an approach for optimization process acceleration using artificial intelligence (AI) that significantly reduces the computational burden; (3) the demonstration of the fuel reload optimization framework for a generic pressurized water reactor (PWR); and (4) the demonstration of limiting design basis accident (DBA) scenarios for evaluation of the transition from deterministic to risk-informed approach for fuel reload optimization.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

60 APPLIED LIFE SCIENCES↗

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k -mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k -mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ~5% for virome and ~75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. Furthermore, for viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ~95% (whole genomes) down to ~80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses ‘hidden’ in diverse sequence datasets.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history

‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the ‘Ca. Liberibacter solanacearum’ species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the ‘Ca. L. capsica’ species based on high values of dN.

59 BASIC BIOLOGICAL SCIENCES↗

A Fast and Scalable Genetic Algorithm-Based Approach for Planning of Microgrids in Distribution Networks

As a result of climate change, extreme weather events are occurring more frequently and with increasing impact. This trend poses a significant challenge for distribution utilities and system operators to ensure that there is uninterrupted power supply to critical loads in their networks; thus, the level of proactive preparation of the distribution system to be able to handle severe impacts of extreme weather events represents the system's resilience. One method that distribution system planners can use to prepare for future extreme events is to plan multiple microgrids which can use local generation as much as possible to supply critical loads. But partitioning an existing distribution system such that multiple feasible islands are planned and which are capable of supporting critical loads is still challenging for distribution systems - first, because of the size of the network graph partitioning problem and, second, because of the difficulty in properly formulating the desired attributes of such islands or microgrids. Therefore, this paper presents a genetic algorithm based approach that facilitates incorporating multiple objectives for grid partitioning by formulating two types of problems - node allocation and edge elimination - and it considers multiple topological and resilience-enhancing objectives. The performance of the proposed genetic algorithm-based approach is numerically evaluated on multiple test systems as well as on a real distribution feeder in Colorado, United States.

genetic algorithm↗

Pressurized-Water Reactor Core Design using Multi-Objective Plant Fuel Reload Optimization Platform

The United States (U.S.) Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program Risk-Informed Systems Analysis (RISA) Pathway Plant Reload Optimization Project aims to develop an integrated, comprehensive framework offering an all-in-one solution for reload evaluations with a special focus on optimization of core design. The optimization of the fuel loading pattern is one of the most important considerations in reducing the amount of new fuel used in the core. Due to thousands of possible options of core configuration, finding optimal solutions is an unachievable task for a human. The Plant ReLoad Optimization (PRLO) platform which supports artificial-intelligence-based reactor core designing is now fully capable of handling realistic problems. The PRLO Platform development project aims to build a reactor core design tool that includes reactor safety and fuel performance analyses and uses artificial intelligence to support the optimization of core design solutions. The NSGA-II (Non-dominated Sorting Genetic Algorithm-II) optimizer was developed and tested within RAVEN (Risk Analysis and Virtual Environment) to handle many constraints by using an augmented objectives methodology. The demonstration was performed with constrained multi-objective optimization of a 17 × 17 pressurized-water reactor core loading patterns to minimize fuel cost and maximize fuel cycle length.

42 ENGINEERING↗

The genetic architecture of leaf stable carbon isotope composition in Zea mays and the effect of transpiration efficiency on leaf elemental accumulation

With increased demand on freshwater resources for agriculture, it is imperative that more water-use efficient crops are developed. Leaf stable carbon isotope composition, δ 13 C, is a proxy for transpiration efficiency and a possible tool for breeders, but the underlying mechanisms effecting δ 13 C in C 4 plants are not known. It has been suggested that differences in specific leaf area (SLA), which potentially reflects variation in internal CO 2 diffusion, can impact leaf δ 13 C. Furthermore, although it is known that water movement is important for elemental uptake, it is not clear how manipulation of transpiration for increased water-use efficiency may impact nutrient accumulation. Here, we characterize the genetic architecture of leaf δ 13 C and test its relationship to SLA and the ionome in five populations of maize. Five significant QTL for leaf δ 13 C were identified, including novel QTL as well as some that were identified previously in maize kernels. One of the QTL regions contains an Erecta-like gene, the ortholog of which has been shown to regulate transpiration efficiency and leaf δ 13 C in Arabidopsis. QTL for δ 13 C were located in the same general chromosome region, but slightly shifted, when comparing data from two different years. Our data does not support a relationship between δ 13 C and SLA, and of the 19 elements analyzed, only a weak correlation between molybdenum and δ 13 C was detected. Together these data add to the genetic understanding of leaf δ 13 C in maize and suggest that improvements to plant water use may be possible without significantly influencing elemental homeostasis.

59 BASIC BIOLOGICAL SCIENCES↗

Yeast Strain Development and Hardware Testing in Preparation of a Lunar BioSensor

With Artemis missions underway, it is clear we are going back to the Moon to stay. Before sending Astronauts for long-duration missions, it is crucial to understand the technological and biomedical countermeasures needed to protect them before they get there. We can use knowledge gained from biological CubeSats to guide the next generation of experiments to support human habitation on the Moon. Lunar Explorer Instrument for space biology Applications (LEIA) is NASA’s latest BioSensor, adapted BioSentinel, the only CubeSat to travel Beyond Low Earth Orbit. BioSentinel launched on Artemis I and is currently >50 million kilometers from Earth (as of July 2024). LEIA aims to identify biological responses to the Lunar environment, which unprotected against would pose a threat to astronauts (cancer, cardiovascular disease, neurological impairment). The suite of instruments within LEIA detects Lunar radiation using two on-board radiation sensors (ARES charged particle detector, Mini-Fast Neutron Detector), then monitors real-time biological responses to the Lunar environment via an autonomous microfluidic system, fit with 3-LED emitter and detector boards and the alamarBlue metabolic indicator dye. LEIA will use a genetic approach in addition to synthetic biology to test counter-measure production in space, with the goal to inform and protect astronauts for future Moon missions. We have conducted preliminary tests in preparation for launch to the anticipated South Pole of the Moon, optimizing the biology (strain down-selection, desiccation tolerance, radiation sensitivity) and improving the hardware (including a blue LED to detect the beta-carotene countermeasure product). Our team will discuss these findings in several parts – an overview of the LEIA mission (Mark Settles), adapting flexible CubeSat platforms for deep-space applications (Sergio Santa Maria, Kira Rienecker), developing new technologies to support LEIA ground studies (Chinmayee Govinda Raj), and yeast strain development and hardware testing in preparation for LEIA (presented here).

synthetic biology↗

A Fast and Scalable Genetic Algorithm-Based Approach for Planning of Microgrids in Distribution Networks: Preprint

As a result of climate change, extreme weather events are occurring more frequently and with increasing impact. This trend poses a significant challenge for distribution utilities and system operators to ensure that there is uninterrupted power supply to critical loads in their networks; thus, the level of proactive preparation of the distribution system to be able to handle severe impacts of extreme weather events represents the system's resilience. One method that distribution systems use to prepare for extreme events is to form multiple microgrids and thereby isolate themselves from the grid supply by using local generation as much as possible to supply critical loads. But partitioning an existing system into multiple feasible islands capable of supporting critical loads is still challenging for distribution systems - first, because of the size of the graph partitioning problem and, second, because of the difficulty in properly formulating the desired attributes of such islands or microgrids. Therefore, this paper presents a genetic algorithmbased approach that facilitates incorporating multiple objectives for grid partitioning by formulating two types of problems - node allocation and edge elimination - and it considers multiple topological and resilience-enhancing objectives. The performance of the proposed genetic algorithm-based approach is numerically evaluated on multiple test systems as well as on a real distribution feeder in Colorado, USA.

edge elimination↗

Improving tolerance of yeast to lignocellulosic-derived feedstocks and products

Combined substrate-product toxicity remains one of the main obstacles hampering the scale-up and cost-effectiveness of bioprocesses harnessing lignocellulosic feedstocks, the most abundant, renewable terrestrial resource. Hydrolytic pretreatments release numerous inhibitors impinging on cell viability: the three most acute to yeast S. cerevisiae (the industry dominant biocatalyst) — and universal to all plant sources — are furfural, hydroxymethylfurfural (HMF), and acetic acid. Likewise, desired fermentation products, such as fuel ethanol or commodity organic acids, are toxic to microbes, typically via unknown biological mechanisms. Here, we have engineered both hydrolysate and end-product tolerance in yeast by combining previously-shown alcohol protective modifications with evolved genetic activities targeting the major pretreatment inhibitors. When tested on a wide sampling of genuine lignocellulosic feedstocks, ethanol production increased by >30% on average to titers >100 g/L, achieving parity with clean-sugar equivalents where conditions permit. Furthermore, we designed the tolerance capability to be fully transferable to pre-existing metabolic chassis strains. As such, we “drop-in” hydrolysate competence into one producing lactic acid, demonstrating the first-ever production of a cellulosic plastic at industrial titers. Our advances thus renew the potential of cellulosic biomass utilization for sustainable fuel and non-fuel products at scale.

09 BIOMASS FUELS↗

Estimating the Adequacy of a Multi-Objective Optimization

Multi-objective optimization methods can be criticized for lacking a statistically valid measure of the quality and representativeness of a solution. This stance is especially relevant to metaheuristic optimization approaches but can also apply to other methods that typically might only report a small representative subset of a Pareto frontier. Here we present a method to address this deficiency based on random sampling of a solution space to determine, with a specified level of confidence, the fraction of the solution space that is surpassed by an optimization. The Superiority of Multi-Objective Optimization to Random Sampling, or SMORS method, can evaluate quality and representativeness using dominance or other measures, e.g., a spacing measure for high-dimensional spaces. SMORS has been tested in a combinatorial optimization context using a genetic algorithm but could be useful for other optimization methods.

42 ENGINEERING↗

Exploring Endothelial Function Risk Factors and Optic Disc Edema Changes During Strict 6º Head-Down Tilt Bed Rest

Approximately 20% of astronauts on International Space Station missions experience ophthalmic pathologies including optic disc edema, part of what is characterized as Spaceflight Associated Neuro-ocular Syndrome (SANS). While the cause of SANS is unknown, there are likely multiple contributing factors, including genetics, that may affect the response to spaceflight in affected individuals. B-vitamin status and the presence of specific one-carbon pathway single nucleotide polymorphism (SNP) alleles predicted the incidence of SANS pathologies in astronauts and in bed rest subjects. There are several hypotheses for how genetic variants could lead to SANS, specifically related to endothelial function. The biochemical pathway to which these genes are associated is intimately involved in maintaining endothelial function via nitric oxide synthase (eNOS) coupling and nitric oxide (NO) production. Furthermore, eNOS uncoupling can impair the functional status of the endothelial glycocalyx, which lines the entirety of the vascular lumen and affects endothelial function. Vascular distension, stasis and altered shear forces, which are associated with headward fluid shifts, may also contribute to glycocalyx dysfunction and shedding, resulting in endothelial dysfunction and increased vascular permeability and tissue edema, potentially contributing to optic nerve and optic disc edema in affected individuals. Given the findings relating genetics and the risk of optic disc edema in astronauts during flight and subjects during bed rest, further investigation is warranted. In this study, we will assess the same genetic variants in another bed rest study: AGBRESA. Some of the AGBRESA subjects developed optic disc edema, but their genetics have not been studied. Furthermore, we will test available urine samples from prior bed rest studies (VaPER and AGBRESA) for markers of glycocalyx degradation to expand our understanding of factors contributing to SANS.

S R Zwart↗