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At least 1,045 records · Page 58

Fast and efficient identification of anomalous galaxy spectra with neural density estimation

ABSTRACT Current large-scale astrophysical experiments produce unprecedented amounts of rich and diverse data. This creates a growing need for fast and flexible automated data inspection methods. Deep learning algorithms can capture and pick up subtle variations in rich data sets and are fast to apply once trained. Here, we study the applicability of an unsupervised and probabilistic deep learning framework, the probabilistic auto-encoder, to the detection of peculiar objects in galaxy spectra from the SDSS survey. Different to supervised algorithms, this algorithm is not trained to detect a specific feature or type of anomaly, instead it learns the complex and diverse distribution of galaxy spectra from training data and identifies outliers with respect to the learned distribution. We find that the algorithm assigns consistently lower probabilities (higher anomaly score) to spectra that exhibit unusual features. For example, the majority of outliers among quiescent galaxies are E+A galaxies, whose spectra combine features from old and young stellar population. Other identified outliers include LINERs, supernovae, and overlapping objects. Conditional modelling further allows us to incorporate additional information. Namely, we evaluate the probability of an object being anomalous given a certain spectral class, but other information such as metrics of data quality or estimated redshift could be incorporated as well. We make our code publicly available.

Böhm, Vanessa↗

Neutrino signatures of 100 2D Axisymmetric Core-Collapse Supernova Simulations

ABSTRACT We present in this paper a public data release of an unprecedentedly large set of core-collapse supernova (CCSN) neutrino emission models, comprising 100 detailed 2D axisymmetric radiation-hydrodynamic simulations evolved out to as late as ∼5 s post-bounce and spanning an extensive range of massive-star progenitors. The motivation for this paper is to provide a physically and numerically uniform benchmark data set to the broader neutrino detection community to help it characterize and optimize subsurface facilities for what is likely to be a once-in-a-lifetime galactic supernova burst event. With this release, we hope to (1) help the international experiment and modelling communities more efficiently optimize the retrieval of physical information about the next galactic CCSN, (2) facilitate the better understanding of core-collapse theory and modelling among interested experimentalists, and (3) help further integrate the broader supernova neutrino community.

Astronomy & Astrophysics↗

The Dark Energy Spectroscopic Instrument: one-dimensional power spectrum from first Ly α forest samples with Fast Fourier Transform

ABSTRACT We present the one-dimensional Ly α forest power spectrum measurement using the first data provided by the Dark Energy Spectroscopic Instrument (DESI). The data sample comprises 26 330 quasar spectra, at redshift z > 2.1, contained in the DESI Early Data Release and the first 2 months of the main survey. We employ a Fast Fourier Transform (FFT) estimator and compare the resulting power spectrum to an alternative likelihood-based method in a companion paper. We investigate methodological and instrumental contaminants associated with the new DESI instrument, applying techniques similar to previous Sloan Digital Sky Survey (SDSS) measurements. We use synthetic data based on lognormal approximation to validate and correct our measurement. We compare our resulting power spectrum with previous SDSS and high-resolution measurements. With relatively small number statistics, we successfully perform the FFT measurement, which is already competitive in terms of the scale range. At the end of the DESI survey, we expect a five times larger Ly α forest sample than SDSS, providing an unprecedented precise one-dimensional power spectrum measurement.

79 ASTRONOMY AND ASTROPHYSICS↗

Unveiling the purely young star formation history of the SMC’s northeastern shell from colour–magnitude diagram fitting

ABSTRACT We obtain a quantitative star formation history (SFH) of a shell-like structure (‘shell’) located in the northeastern part of the Small Magellanic Cloud (SMC). We use the Survey of the MAgellanic Stellar History to derive colour–magnitude diagrams (CMDs), reaching below the oldest main-sequence turnoff, from which we compute the SFHs with CMD-fitting techniques. We present, for the first time, a novel technique that uses red clump (RC) stars from the CMDs to assess and account for the SMC’s line-of-sight depth effect present during the SFH derivation. We find that accounting for this effect recovers a more accurate SFH. We quantify an $\sim$7 kpc line-of-sight depth present in the CMDs, in good agreement with depth estimates from RC stars in the northeastern SMC. By isolating the stellar content of the northeastern shell and incorporating the line-of-sight depth into our calculations, we obtain an unprecedentedly detailed SFH. We find that the northeastern shell is primarily composed of stars younger than $\sim$500 Myr, with significant star formation enhancements around $\sim$250 and $\sim$450 Myr. These young stars are the main contributors to the shell’s structure. We show synchronicity between the northeastern shell’s SFH with the Large Magellanic Cloud’s (LMC) northern arm, which we attribute to the interaction history of the SMC with the LMC and the Milky Way (MW) over the past $\sim$500 Myr. Our results highlight the complex interplay of ram pressure stripping and the influence of the MW’s circumgalactic medium in shaping the SMC’s northeastern shell.

Sakowska, Joanna D. (ORCID:0000000215941466)↗

Redshift evolution and covariances for joint lensing and clustering studies with DESI Y1

ABSTRACT Galaxy–galaxy lensing (GGL) and clustering measurements from the Dark Energy Spectroscopic Instrument Year 1 (DESI Y1) data set promise to yield unprecedented combined-probe tests of cosmology and the galaxy–halo connection. In such analyses, it is essential to identify and characterize all relevant statistical and systematic errors. We forecast the covariances of DESI Y1 GGL + clustering measurements and the systematic bias due to redshift evolution in the lens samples. Focusing on the projected clustering and GGL correlations, we compute a Gaussian analytical covariance, using a suite of N-body and lognormal simulations to characterize the effect of the survey footprint. Using the DESI one percent survey data, we measure the evolution of galaxy bias parameters for the DESI luminous red galaxy (LRG) and bright galaxy survey (BGS) samples. We find mild evolution in the LRGs in $0.4 < z < 0.8$, subdominant to the expected statistical errors. For BGS, we find less evolution for brighter absolute magnitude cuts, at the cost of reduced sample size. We find that for a redshift bin width $\Delta z = 0.1$, evolution effects on DESI Y1 GGL is negligible across all scales, all fiducial selection cuts, all fiducial redshift bins. Galaxy clustering is more sensitive to evolution due to the bias squared scaling. Nevertheless the redshift evolution effect is insignificant for clustering above the 1-halo scale of $0.1h^{-1}$ Mpc. For studies that wish to reliably access smaller scales, additional treatment of redshift evolution is likely needed. This study serves as a reference for GGL and clustering studies using the DESI Y1 sample.

79 ASTRONOMY AND ASTROPHYSICS↗

BOSS quasar outflows traced by C iv

ABSTRACT We investigate possible factors that drive fast quasar outflows using a sample of 39 249 quasars at median redshift 〈z〉 ≈ 2.17. Unique to this study, the quasar redshifts are re-measured based on the Mg ii emission line, and explore unprecedented outflow velocities (>6000 km s−1), while maintaining statistical significance. We measure reliable C iv blueshifts for 1178 quasars with velocities >2500 km s−1. From those, 255(13) quasars have blueshifts above 4000(6000) km s−1, with the highest C iv velocity ≈7000 km s−1. Several correlations are observed, where higher C iv blueshifts in general are in quasars with broader, weaker C iv emission profiles, weak He ii emission, larger Eddington ratios, and bluer ultraviolet (UV) continuum slope across the rest-frame UV to near-infrared. Analysis reveals two primary factors contributing to faster outflows: higher Eddington ratios, and softer far-UV continuum (hν >24.6 eV). We find supporting evidence that radiative line driving may generate extreme outflow velocities, influenced by multiple factors as suggested by the aforementioned correlations. This evidence highlights the importance of considering a multidimensional parameter space in future studies when analyzing large C iv blueshifts to determine the fundamental causes of outflows.

Gillette, Jarred (ORCID:0000000185284839)↗

Astronomaly at scale: searching for anomalies amongst 4 million galaxies

ABSTRACT Modern astronomical surveys are producing data sets of unprecedented size and richness, increasing the potential for high-impact scientific discovery. This possibility, coupled with the challenge of exploring a large number of sources, has led to the development of novel machine-learning-based anomaly detection approaches, such as astronomaly. For the first time, we test the scalability of astronomaly by applying it to almost 4 million images of galaxies from the Dark Energy Camera Legacy Survey. We use a trained deep learning algorithm to learn useful representations of the images and pass these to the anomaly detection algorithm isolation forest, coupled with astronomaly’s active learning method, to discover interesting sources. We find that data selection criteria have a significant impact on the trade-off between finding rare sources such as strong lenses and introducing artefacts into the data set. We demonstrate that active learning is required to identify the most interesting sources and reduce artefacts, while anomaly detection methods alone are insufficient. Using astronomaly, we find 1635 anomalies among the top 2000 sources in the data set after applying active learning, including eight strong gravitational lens candidates, 1609 galaxy merger candidates, and 18 previously unidentified sources exhibiting highly unusual morphology. Our results show that by leveraging the human–machine interface, astronomaly is able to rapidly identify sources of scientific interest even in large data sets.

Astronomy & Astrophysics↗

Reducing model error using optimized galaxy selection: weak lensing cluster mass estimation

Galaxy clusters are one of the most powerful probes to study extensions of General Relativity and the Standard Cosmological Model. Upcoming surveys like the Vera Rubin Observatory’s Legacy Survey of Space and Time are expected to revolutionise the field, by enabling the analysis of cluster samples of unprecedented size and quality. To reach this era of high-precision cluster cosmology, the mitigation of sources of systematic error is crucial. A particularly important challenge is bias in cluster mass measurements induced by the mismodelling of photometric redshift estimates of source galaxies. This work proposes a method to optimise the source sample selection in cluster weak lensing analyses drawn from wide-field survey lensing catalogs to reduce the bias on reconstructed cluster masses. We use a combinatorial optimisation scheme and methods from variational inference to select galaxies in latent space to produce a probabilistic galaxy source sample catalog for highly accurate cluster mass estimation. We show that our method reduces the critical surface mass density Σ crit relative modelling bias on the 60-70% level, while maintaining up to 90% of galaxies. We highlight that our methodology has applications beyond cluster mass estimation as an approach to jointly combine galaxy selection and model inference under sources of systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

Mapping the cosmic gamma-ray horizon: the 1CGH catalogue of Fermi -LAT detections above 10 GeV

ABSTRACT We present the First Cosmic Gamma-ray Horizon (1CGH) catalogue, featuring $\gamma$-ray detections above 10 GeV based on 16 yr of observations with the Fermi Large Area Telescope (Fermi-LAT) satellite. After carefully selecting a sample of blazars and blazar candidates from catalogues in the literature, we performed a binned likelihood analysis and identified 2791 $\gamma$-ray emitters above 10 GeV, at >3$\sigma$ level, including 62 that are new $\gamma$-ray detections. For each source, we estimated the mean energy of the highest energy bin and analysed them in the context of the cosmic gamma-ray horizon. By adopting a reference model for the extragalactic background light (EBL), we identified a subsample of 525 sources where moderate to severe $\gamma$-ray absorption could be detected across the redshift range of 0–3. This work provides the most up-to-date compilation of detections above 10 GeV, along with their redshift information. We condense extensive results from the literature, including reports on observational campaigns dedicated to blazars and $\gamma$-ray sources, thereby delivering an unprecedented review of the redshift information for sources detected above 10 GeV. Additionally, we highlight key 1CGH sources where redshift information remains incomplete, offering guidance for future optical observation campaigns. The 1CGH catalogue aims to track the most significant sources for studying the $\gamma$-ray transparency of the Universe. Furthermore, it provides a targeted subsample where the EBL optical depth, $\tau _{(E,z)}$, can be robustly measured using Fermi-LAT data.

Arsioli, Bruno (ORCID:0000000181666602)↗

Deep-field analytical calibration

The next generation of imaging surveys, including the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST), Euclid, and the Nancy Grace Roman Space Telescope, will provide unprecedented constraints on cosmology using weak gravitational lensing. To fully exploit this statistical power, shear measurement methods must achieve sub- per cent accuracy while mitigating systematic biases from noise, the point-spread function (PSF), blending, and shear-dependent detection. The analytical calibration framework (AnaCal) has demonstrated such accuracy but requires adding noise to images, reducing effective depth. We introduce Deep-Field Analytical Calibration (DEEP-FIELD AnaCal), an extension of AnaCal that uses deep-field images to compute shear responses while preserving the statistical power of wide-field data. We validate DEEP-FIELD AnaCal on isolated and blended galaxy image simulations with LSST-like conditions, finding it meets the stringent requirement of multiplicative bias $|m| < 3\times 10^{-3}$ at 99.7 per cent confidence. Compared to standard AnaCal applied to wide-field images, DEEP-FIELD AnaCal increases the effective galaxy number density from 17 to 30 arcmin$^{-2}$ for simulated 10-yr LSST data. With deep fields $10\times$ longer than the wide field, we find pixel noise variance in shear estimation is reduced by 30 per cent and overall uncertainty by $\sim 25~{{\ \rm per\ cent}}$. Finally, using the LSST Deep Drilling Fields strategy, we assess sample variance and find an equivalent calibration uncertainty of $\lesssim 0.3~{{\ \rm per\ cent}}$. These results demonstrate that DEEP-FIELD AnaCal offers a promising path to achieve the required shear calibration for upcoming weak lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

Abstract Integrative genetic elements (IGEs) are mobile multigene DNA units that integrate into and excise from host bacterial genomes. Each IGE usually targets a specific site within a conserved host gene, integrating in a manner that preserves target gene function. However, a small number of bacterial genes are known to be inactivated upon IGE integration and reactivated upon excision, regulating phenotypes of virulence, mutation rate, and terminal differentiation in multicellular bacteria. The list of regulated gene integrity (RGI) cases has been slow-growing because IGEs have been challenging to precisely and comprehensively locate in genomes. We present software (TIGER) that maps IGEs with unprecedented precision and without attB site bias. TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE integration module (i.e. its int-attP region) is cohesive. The resultant IGEs from 2168 genomes, along with integrase phylogenetic analysis and gene inactivation tests, revealed 19 new cases of genes whose integrity is regulated by IGEs (including dut, eccCa1, gntT, hrpB, merA, ompN, prkA, tqsA, traG, yifB, yfaT and ynfE), as well as recovering previously known cases (in sigK, spsM, comK, mlrA and hlb genes). It also recovered known clades of site-promiscuous integrases and identified possible new ones.

59 BASIC BIOLOGICAL SCIENCES↗

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Abstract Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.

59 BASIC BIOLOGICAL SCIENCES↗

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

59 BASIC BIOLOGICAL SCIENCES↗

Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar K D

Fluorogenic RNA aptamer tags with high affinity enable RNA purification and imaging. The G-quadruplex (G4) based Mango (M) series of aptamers were selected to bind a thiazole orange based (TO1-Biotin) ligand. Using a chemical biology and reselection approach, we have produced a MII.2 aptamer–ligand complex with a remarkable set of properties: Its unprecedented K D of 45 pM, formaldehyde resistance (8% v/v), temperature stability and ligand photo-recycling properties are all unusual to find simultaneously within a small RNA tag. Crystal structures demonstrate how MII.2, which differs from MII by a single A23U mutation, and modification of the TO1-Biotin ligand to TO1-6A-Biotin achieves these results. MII binds TO1-Biotin heterogeneously via a G4 surface that is surrounded by a stadium of five adenosines. Breaking this pseudo-rotational symmetry results in a highly cooperative and homogeneous ligand binding pocket: A22 of the G4 stadium stacks on the G4 binding surface while the TO1-6A-Biotin ligand completely fills the remaining three quadrants of the G4 ligand binding face. Similar optimization attempts with MIII.1, which already binds TO1-Biotin in a homogeneous manner, did not produce such marked improvements. We use the novel features of the MII.2 complex to demonstrate a powerful optically-based RNA purification system.

59 BASIC BIOLOGICAL SCIENCES↗

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks

Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.

Shen, Runze [Univ. of Texas, Houston, TX (United S↗

Recent progress in MnBi2 n Te3 n +1 intrinsic magnetic topological insulators: crystal growth, magnetism and chemical disorder

ABSTRACT The search for magnetic topological materials has been at the forefront of condensed matter research for their potential to host exotic states such as axion insulators, magnetic Weyl semimetals, Chern insulators, etc. To date, the MnBi2nTe3n+1 family is the only group of materials showcasing van der Waals-layered structures, intrinsic magnetism and non-trivial band topology without trivial bands at the Fermi level. The interplay between magnetism and band topology in this family has led to the proposal of various topological phenomena, including the quantum anomalous Hall effect, quantum spin Hall effect and quantum magnetoelectric effect. Among these, the quantum anomalous Hall effect has been experimentally observed at record-high temperatures, highlighting the unprecedented potential of this family of materials in fundamental science and technological innovation. In this paper, we provide a comprehensive review of the research progress in this intrinsic magnetic topological insulator family, with a focus on single-crystal growth, characterization of chemical disorder, manipulation of magnetism through chemical substitution and external pressure, and important questions that remain to be conclusively answered.

36 MATERIALS SCIENCE↗