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DOE OSTI2024

Investigating genomic prediction strategies for grain carotenoid traits in a tropical/subtropical maize panel

Abstract Vitamin A deficiency remains prevalent on a global scale, including in regions where maize constitutes a high percentage of human diets. One solution for alleviating this deficiency has been to increase grain concentrations of provitamin A carotenoids in maize (Zea mays ssp. mays L.)—an example of biofortification. The International Maize and Wheat Improvement Center (CIMMYT) developed a Carotenoid Association Mapping panel of 380 inbred lines adapted to tropical and subtropical environments that have varying grain concentrations of provitamin A and other health-beneficial carotenoids. Several major genes have been identified for these traits, 2 of which have particularly been leveraged in marker-assisted selection. This project assesses the predictive ability of several genomic prediction strategies for maize grain carotenoid traits within and between 4 environments in Mexico. Ridge Regression-Best Linear Unbiased Prediction, Elastic Net, and Reproducing Kernel Hilbert Spaces had high predictive abilities for all tested traits (β-carotene, β-cryptoxanthin, provitamin A, lutein, and zeaxanthin) and outperformed Least Absolute Shrinkage and Selection Operator. Furthermore, predictive abilities were higher when using genome-wide markers rather than only the markers proximal to 2 or 13 genes. These findings suggest that genomic prediction models using genome-wide markers (and assuming equal variance of marker effects) are worthwhile for these traits even though key genes have already been identified, especially if breeding for additional grain carotenoid traits alongside β-carotene. Predictive ability was maintained for all traits except lutein in between-environment prediction. The TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) Genomic Selection plugin performed as well as other more computationally intensive methods for within-environment prediction. The findings observed herein indicate the utility of genomic prediction methods for these traits and could inform their resource-efficient implementation in biofortification breeding programs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa

Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Mineralogy, fabric and deformation domains in D" across the southwestern border of the African LLSVP

Recent advances in seismic anisotropy studies that jointly use reflections and shear wave splitting have proven to place tight constraints on the plausible anisotropic and deformation scenarios in the D" region. We apply this novel methodology to a large area of the D" region beneath the South Atlantic, in proximity to and within the African large low seismic velocity province (LLSVP). This area of the mantle is characterized by a transition from fast to slow seismic velocity anomalies and it is thought to be the location of deep-seated plumes responsible for hotspot volcanism. Attempting to probe mantle composition and deformation along the LLSVP borders may provide key information on mantle dynamics. By analysing seismic phases sampling this region, we detect a D" discontinuity over a large area beneath the South Atlantic, with inferred depth ranges ~170 to ~240 km above the core–mantle boundary. We find evidence for a D" reflector within the area of the LLSVP. Shear wave splitting observations suggest that anisotropy is present in this region of the mantle, in agreement with previous studies that partially sampled this region. We model the observations considering lattice- and shape-preferred orientation of materials expected in the D" region. A regional variation of mineralogy, phase transition boundaries, and deformation direction is required to explain the data. We infer two distinct domains of mineralogy and deformation: aligned post-perovskite outside the LLSVP and aligned bridgmanite within the LLSVP. Finally, the scenario depicted by this study agrees well with the current hypotheses for the composition of the LLSVP and with the prevalence of vertical deformation directions expected to occur along the LLSVPs borders.

58 GEOSCIENCES↗

DOE OSTI2020

The effect of school intervention programs on the body mass index of adolescents: a systematic review with meta-analysis

Abstract Effective obesity interventions in adolescent populations have been identified as an immediate priority action to stem the increasing prevalence of adult obesity. The purpose of this meta-analysis was to make a quantitative analysis of the impact of school-based interventions on body mass index during adolescence. Studies were retrieved from PubMed, Scopus, Science Direct and Web of Science databases. Results were pooled using a random-effects model with 95% confidence interval considered statistically significant. Of the 18 798 possible relevant articles identified, 12 articles were included in this meta-analysis. The global result showed a low magnitude effect, though it was statistically significant (N = 14 428), global e.s. = −0.055, P = 0.004 (95% CI = −0.092, −0.017). Heterogeneity was low among the studies (I2 = 9.017%). The funnel plot showed no evidence of publication bias. The rank-correlation test of Begg (P = 0.45641) and Egger’s regression (P = 0.19459) confirmed the absence of bias. This meta-analysis reported a significant effect favoring the interventions; however, future research are needed since the reported the evidence was of low magnitude, with the studies following a substantial range of approaches and mostly had a modest methodological quality.

Saavedra Dias, R.↗

DOE OSTI2024

Gut microbiota carbon and sulfur metabolisms support Salmonella infections

Abstract Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes

Drylands cover one-third of the Earth’s surface and are one of the largest terrestrial sinks for methane. Understanding the structure–function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors—water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m 2 h −1 , peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum , two Methylobacter , and uncultivated Methylococcaceae ). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum . Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

Abstract Poorly understood microorganisms “short-circuit” the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.

Environmental Sciences & Ecology↗

DOE OSTI2025

Pseudomonas aeruginosa : One Health approach to deciphering hidden relationships in Northern Portugal

Abstract Aims Antimicrobial resistance in Pseudomonas aeruginosa represents a major global challenge in public and veterinary health, particularly from a One Health perspective. This study aimed to investigate antimicrobial resistance, the presence of virulence genes, and the genetic diversity of P. aeruginosa isolates from diverse sources. Methods and results The study utilized antimicrobial susceptibility testing, genomic analysis for resistance and virulence genes, and multilocus sequence typing to characterize a total of 737 P. aeruginosa isolates that were collected from humans, domestic animals, and aquatic environments in Northern Portugal. Antimicrobial resistance profiles were analyzed, and genomic approaches were employed to detect resistance and virulence genes. The study found a high prevalence of multidrug-resistant isolates, including high-risk clones such as ST244 and ST446, particularly in hospital sources and wastewater treatment plants. Key genes associated with resistance and virulence, including efflux pumps (e.g. MexA and MexB) and secretion systems (T3SS and T6SS), were identified. Conclusions This work highlights the intricate dynamics of multidrug-resistant P. aeruginosa across interconnected ecosystems in Northern Portugal. It underscores the importance of genomic studies in revealing the mechanisms of resistance and virulence, contributing to the broader understanding of resistance dynamics and informing future mitigation strategies.

de Sousa, Telma↗

DOE OSTI2022

Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports

One of the goals of the Surveillance, Epidemiology, and End Results (SEER) program is to estimate incidence, prevalence, and mortality of all cancers. To that end, cancer registries across the country maintain a massive database of cancer pathology reports which contain rich information to understand cancer trends. However, these reports are stored in the form of unstructured text, and human annotators are required to read and extract relevant information. In this article, we show that existing deep learning models for automating information extraction from cancer pathology reports can be significantly improved by using ensemble model distillation. We found that by training multiple predictive models and transferring their knowledge to a single, low-resource model, we can reduce the number of highly confident wrong predictions. Our results show that our implemented methods could save 1000s of manual annotation hours.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Effect of nitrogen management in cultivation on the stability and microbial community of post-harvest Monoraphidium sp. algae biomass

Seasonal variation in algae biomass productivity is a significant obstacle to the economical production of fuels and chemicals from algae biomass. Long-term storage is necessary to guarantee a constant supply to a conversion facility and harvested microalgae biomass (20% solids) is subject to degradation immediately upon harvesting as a result of aerobic instability. Ensiling has been successfully used to preserve microalgal biomass, but biomass attributes that contribute to successful storage are poorly understood. Storage studies of Monoraphidium sp. biomass indicate a strong correlation between nitrogen management in algae cultivation and stability of post-harvest algae biomass in 30 days of anaerobic storage. Algae cultivated with periodic nitrogen addition stored poorly (> 20% loss, dry basis), while algae biomass from cultures that were allowed to continue growing after nitrogen depletion was more stable in storage (8% loss, dry basis). A follow-up study aimed at exploring the relationship between nitrogen management in cultivation and stability of post-harvest algae biomass stored Monoraphidium biomass cultivated in nitrogen deplete and nitrogen replete conditions, as well as with blends of each in varying ratios. Monoraphidium biomass from nitrogen replete cultivations experienced the largest degradation (24%, dry basis), while nitrogen deplete biomass experienced the least (10%, dry basis). Dry matter loss experienced during storage of blends was positively correlated with the amount of nitrogen replete biomass that a blend contained. Further, the composition of the post-storage algae microbial community was also strongly affected by cultivation conditions, with Clostridia species being more prevalent in stored biomass obtained from nitrogen replete cultivations. Nitrogen management has long been known to influence algae biomass productivity and biochemical composition; here, we demonstrate that it also strongly influences the stability of post-harvest algae biomass in anaerobic storage.

09 BIOMASS FUELS↗

DOE OSTI2023

The increasing threat of Rift Valley fever virus globalization: strategic guidance for protection and preparation

Rift Valley fever virus (RVFV) (Bunyavirales: Phlebovirus) is a prominent vector-borne zoonotic disease threat to global agriculture and public health. Risks of introduction into nonendemic regions are tied to changing climate regimes and other dynamic environmental factors that are becoming more prevalent, as well as virus evolutionary factors and human/animal movement. Endemic to the African continent, RVFV has caused large epizootics at the decadal scale since the early 20th century but has spread to the Arabian Peninsula and shows increasing patterns of interepizootic transmission on the annual scale. This virus can be transmitted by mosquitoes as well as through direct contact with infected tissues and can cause sporadic to widespread morbidity and mortality in domestic ungulate livestock as well as humans. High viremias in infected livestock moved for legal and illegal trade as well as in infected mosquitoes or human travelers can spread this virus worldwide. With increasing global commerce, it is likely RVFV will be introduced to new areas with suitable hosts, mosquito vector species, and environments. However, the strong mosquito component of RVFV epidemiology combined with advancements in vaccines, diagnostics, and virus evolutionary factors create opportunities for strategies to leverage models of connectivity among potential source and emerging regions to target surveillance and mitigation activities to reduce the risk of RVFV introduction, or contain the virus should it be introduced, into new regions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. Furthermore, this provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

Arabidopsis↗

DOE OSTI2023

Polymerase chain reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain

Abstract A globally circulating strain of Salmonella enterica serotype Infantis containing the pESI plasmid has increased in prevalence in poultry meat samples and cases of human infections. In this study, a polymerase chain reaction (PCR) protocol was designed to detect the pESI plasmid and confirm the Infantis serotype of Salmonella isolates. Primers were tested bioinformatically to predict specificity, sensitivity, and precision. A total of 54 isolates of Salmonella serotypes Infantis, Senftenberg, and Alachua were tested, with and without the pESI plasmid carriage. Isolates of 31 additional serotypes were also screened to confirm specificity to Infantis. Specificity, sensitivity, and precision of each primer were >0.95. All isolates tested produced the expected band sizes. This PCR protocol provides a rapid and clear result for the detection of the pESI plasmid and serotype Infantis and will allow for the in vitro detection for epidemiological studies where whole-genome sequencing is not available.

McMillan, Elizabeth A. (ORCID:000000027503514X)↗

DOE OSTI2022

Deprojection of X-ray data in galaxy clusters: confronting simulations with observations

ABSTRACT Numerical simulations with varying realism indicate an emergent principle−multiphase condensation and large cavity power occur when the ratio of the cooling time to the free-fall time (tcool/tff) falls below a threshold value close to 10. Observations indeed show cool-core signatures when this ratio falls below 20–30, but the prevalence of cores with tcool/tff ratio below 10 is rare as compared to simulations. In X-ray observations, we obtain projected spectra from which we have to infer radial gas density and temperature profiles. Using idealized models of X-ray cavities and multiphase gas in the core and 3D hydro jet-ICM simulations, we quantify the biases introduced by deprojection based on the assumption of spherical symmetry in determining tcool/tff. We show that while the used methods are able to recover the tcool/tff ratio for relaxed clusters, they have an uncertainty of a factor of 2−3 in systems containing large cavities (≳ 20 kpc). We also show that the mass estimates from these methods, in the absence of X-ray spectra close to the virial radius, suffer from a degeneracy between the virial mass (M200) and the concentration parameter (c) in the form of M200c2 ≈ constant. Additionally, the lack of soft-X-ray (≲ 0.5 keV) coverage and poor spatial resolution makes us overestimate min(tcool/tff) by a factor of few in clusters with min(tcool/tff) ≲ 5. This bias can largely explain the lack of cool-core clusters with min(tcool/tff) ≲ 5.

Sarkar, Kartick C. (ORCID:0000000277678472)↗

DOE OSTI2022

Fundamental differences in the properties of red and blue quasars: measuring the reddening and accretion properties with X-shooter

ABSTRACT We have recently found fundamental differences in the radio properties of red quasars when compared to typical blue quasars. In this paper, we use data from the X-shooter spectrograph on the Very Large Telescope, providing spectral coverage from ∼3000–$25\,000\,$ Å, of a sample of 40 red and blue luminous quasars at 1.45 < z < 1.65 to explore the connections between the radio, emission-line, and accretion-disc properties. We fit various dust-extinction curves to the data and find that dust reddening can fully explain the observed colours for the majority of the red quasars in our sample, with moderate extinctions ranging from AV ∼ 0.06–0.7 mag. We confront our spectra with a simple thin accretion-disc model and find this can describe the continua of both the blue and red quasars, once corrected for dust extinction; we also find no significant differences in the accretion properties. We detect ionized outflows in a number of red and blue quasars, but do not find any significant evidence that they are more prevalent in the red quasar population. Overall our findings imply that the radio emission is more closely connected to circumnuclear/ISM opacity rather than accretion disc or outflow differences.

Fawcett, V. A. (ORCID:000000031251532X)↗

DOE OSTI2023

SDSS-IV MaNGA: The incidence of major mergers in type I and II AGN host galaxies in the DR15 sample

We present a study on the incidence of major mergers and their impact on the triggering of nuclear activity in 47 type I and 236 type II optically selected AGN from the MaNGA DR15 sample. From an estimate of non-parametric image predictors (Gini, M_20, concentration (C), asymmetry (A), clumpiness (S), Sérsic index (n), and shape asymmetry ()) using the SDSS images, in combination with a Linear Discriminant Analysis Method, we identified major mergers and merger stages. We reinforced our results by looking for bright tidal features in our post-processed SDSS and DESI legacy images. We find a statistically significant higher incidence of major mergers of 29 per cent ± 3 per cent in our type I+II AGN sample compared to 22 per cent ± 0.8 per cent for a non-AGN sample matched in redshift, stellar mass, colour, and morphological type, finding also a prevalence of post-coalescence (51 per cent ± 5 per cent) over pre-coalescence (23 per cent ± 6 per cent) merger stages. The levels of AGN activity among our massive major mergers are similar to those reported in other works using [O iii] tracers. However, similar levels are produced by our AGN-galaxies hosting stellar bars, suggesting that major mergers are important promoters of nuclear activity but are not the main nor the only mechanism behind the AGN triggering. The tidal strength parameter Q was considered at various scales looking for environmental differences that could affect our results on the merger incidence, finding non-significant differences. Finally, the H-H β diagram could be used as an empirical predictor for the flux coming from an AGN source, useful to correct photometric quantities in large AGN samples emerging from surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Discovery of double Hall pattern associated with collisionless magnetic reconnection in dusty plasmas

ABSTRACT Magnetic reconnection is prevalent in magnetized plasmas in space and laboratories. Despite significant investigations on reconnection in electron–ion plasmas, studies of reconnection in magnetized plasmas with negatively charged dust grains are quite sparse. Here, we report the first fully kinetic simulations of collisionless reconnection in a three-species (i.e. electron, proton, and negatively charged dust grain) dusty plasma, through which the discovery of double Hall pattern is made. The double Hall pattern consists of a traditional Hall quadruple current in between the ion and electron diffusion region and a reversed Hall current in between the boundary of the ion and dust diffusion region. The analysis of the reconnection rate is also given. This study may be applicable to explain observations of planetary magnetospheres and the astrophysical objects, and may be realized in the laboratory studies of dusty plasmas.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Understanding the origin of early-type dwarfs: the spectrophotometric study of CGCG014−074

ABSTRACT Early-type dwarf galaxies constitute a prevalent population in the central regions of rich groups and clusters in the local Universe. These low-luminosity and low-mass stellar systems play a fundamental role in the assembly of the luminous galaxies observed today, according to the Lambda cold dark matter hierarchical theory. The origin of early-type dwarfs has been linked to the transformation of disc galaxies interacting with the intracluster medium, especially in dense environments. However, the existence of low-luminosity early-type galaxies in low-density environments presents a challenge to this scenario. This study presents a comprehensive photometric and spectroscopic analysis of the early-type dwarf galaxy CGCG014−074 using deep Gemini GMOS (Gemini Multi-Object Spectrograph) data, focusing on its peculiarities and evolutionary implications. CGCG014−074 exhibits distinct features, including a rotating inner disc, an extended stellar formation with a quiescent phase since about 2 Gyr ago, and the presence of boxy isophotes. From the kinematic analysis, we confirm CGCG014−074 as a nucleated early-type dwarf galaxy with embedded disc. The study of its stellar population parameters using different methods provides significant insights into the galaxy’s evolutionary history. These results show an old and metal-poor nucleus (${\sim}9.3$ Gyr and $\mathrm{[Z/H]}\sim -0.84$ dex), while the stellar disc is younger (${\sim}4.4$ Gyr) with a higher metallicity ($\mathrm{[Z/H]}\sim -0.40$ dex). These distinctive features collectively position CGCG014−074 as a likely building block galaxy that has evolved passively throughout its history.

Astronomy & Astrophysics↗