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At least 55 records · Page 3

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗

SDSS-IV MaNGA: drivers of stellar metallicity in nearby galaxies

The distribution of stellar metallicities within and across galaxies is an excellent relic of the chemical evolution across cosmic time. Here we present a detailed analysis of spatially resolved stellar populations based on >2.6 million spatial bins from 7439 nearby galaxies in the Sloan Digital Sky Survey-IV (SDSS-IV) Mapping Nearby Galaxies at APO (MaNGA) survey. To account for accurate inclination corrections, we derive an equation for morphology-dependent determination of galaxy inclinations. Our study goes beyond the well-known global mass–metallicity relation and radial metallicity gradients by providing a statistically sound exploration of local relations between stellar metallicity [Z/H], stellar surface mass density Σ ⋆ , and galactocentric distance in the global mass–morphology plane. We find a significant resolved mass density–metallicity relation rΣ ⋆ ZR for galaxies of all types and masses above 10 9.8 M ⊙ ⁠. Different radial distances make an important contribution to the spread of the relation. Particularly, in low- and intermediate-mass galaxies, we find that at fixed Σ ⋆ metallicity increases with radius independently of morphology. For high masses, this radial dependence is only observed in high Σ ⋆ regions of spiral galaxies. This result calls for a driver of metallicity, in addition to Σ ⋆ that promotes chemical enrichment in the outer parts of galaxies more strongly than in the inner parts. We discuss gas accretion, outflows, recycling, and radial migration as possible scenarios.

79 ASTRONOMY AND ASTROPHYSICS↗

Biasing from galaxy trough and peak profiles with the DES Y3 redMaGiC galaxies and the weak lensing mass map

We measure the correspondence between the distribution of galaxies and matter around troughs and peaks in the projected galaxy density, by comparing redMaGiC galaxies (0.15 < z < 0.65) to weak lensing mass maps from the Dark Energy Survey (DES) Y3 data release. We obtain stacked profiles, as a function of angle θ, of the galaxy density contrast δ g and the weak lensing convergence κ, in the vicinity of these identified troughs and peaks, referred to as ‘void’ and ‘cluster’ superstructures. The ratio of the profiles depend mildly on θ, indicating good consistency between the profile shapes. We model the amplitude of this ratio using a function $F(\boldsymbol{\eta }, \theta )$ that depends on cosmological parameters $\boldsymbol{\eta }$, scaled by the galaxy bias. We construct templates of $F(\boldsymbol{\eta }, \theta )$ using a suite of N-body (‘Gower Street’) simulations forward-modelled with DES Y3-like noise and systematics. We discuss and quantify the caveats of using a linear bias model to create galaxy maps from the simulation dark matter shells. We measure the galaxy bias in three lens tomographic bins (near to far): $2.32^{+0.86}_{-0.27}, 2.18^{+0.86}_{-0.23}, 1.86^{+0.82}_{-0.23}$ for voids, and $2.46^{+0.73}_{-0.27}, 3.55^{+0.96}_{-0.55}, 4.27^{+0.36}_{-1.14}$ for clusters, assuming the best-fit Planck cosmology. Similar values with ∼0.1σ shifts are obtained assuming the mean DES Y3 cosmology. The biases from troughs and peaks are broadly consistent, although a larger bias is derived for peaks, which is also larger than those measured from the DES Y3 3 × 2-point analysis. This method shows an interesting avenue for measuring field-level bias that can be applied to future lensing surveys.

cosmology: observations↗

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗

Precision Kinematic Sunyaev--Zel'dovich Measurements Across Halo Mass and Redshift with DESI DR2 and ACT DR6: Part II. Bright Galaxy Survey and Emission-Line Galaxies

We present the first high-significance spectroscopic stacked kinetic Sunyaev-Zel'dovich (kSZ) measurements of circumgalactic gas profiles for both Bright Galaxy Survey (BGS) and Emission Line Galaxy (ELG) tracers, combining DESI Data Release 2 with ACT Data Release 6. Using reconstructed line-of-sight velocities from the DESI galaxies and high-resolution ACT temperature maps, we detect the kSZ signal at high significance, reaching signal-to-noise ratios of up to $\sim$9 for BGS and $\sim$7.5 for ELGs in optimal stellar-mass selections. Together with the LRG measurements presented in Paper I, these constitute the most significant kSZ detections from any spectroscopic survey to date. We perform the analysis in both real and harmonic space, obtaining consistent results. By splitting both tracers into stellar-mass bins, we study the scaling of the kSZ amplitude with galaxy properties. Combining the kSZ measurements with ACT Data Release 6 (DR6) CMB lensing maps enables a joint calibration of the galaxy-halo connection and the gas fractions of host halos. For the BGS galaxies, we observe low gas fractions around the virial radius relative to standard expectations, likely attributable to active galactic nuclei (AGN) activity. We find some evidence for higher-mass halos retaining a larger fraction of their baryons, consistent with more efficient feedback in lower-mass systems. For the ELG sample, dominated by blue, star-forming galaxies, we provide the first detection of the gas distribution in ELG host halos. The ELGs appear to exhibit relatively high gas fractions, which points to the possibility of weaker feedback (due to e.g. low AGN and supernova feedback activity) at their mass scale. Finally, we present generalized Navarro-Frenk-White (GNFW) fits to the harmonic-space measurements, providing a compact parametrization of gas profiles for forward modeling in large-scale structure analyses.

Hadzhiyska, B. [Cambridge U.; Cambridge U., Inst. ↗

Dark Energy Survey Year 3 results: redshift calibration of the weak lensing source galaxies

ABSTRACT Determining the distribution of redshifts of galaxies observed by wide-field photometric experiments like the Dark Energy Survey (DES) is an essential component to mapping the matter density field with gravitational lensing. In this work we describe the methods used to assign individual weak lensing source galaxies from the DES Year 3 Weak Lensing Source Catalogue to four tomographic bins and to estimate the redshift distributions in these bins. As the first application of these methods to data, we validate that the assumptions made apply to the DES Y3 weak lensing source galaxies and develop a full treatment of systematic uncertainties. Our method consists of combining information from three independent likelihood functions: self-organizing map p(z) (sompz), a method for constraining redshifts from galaxy photometry; clustering redshifts (WZ), constraints on redshifts from cross-correlations of galaxy density functions; and shear ratios (SRs), which provide constraints on redshifts from the ratios of the galaxy-shear correlation functions at small scales. Finally, we describe how these independent probes are combined to yield an ensemble of redshift distributions encapsulating our full uncertainty. We calibrate redshifts with combined effective uncertainties of σ〈z〉 ∼ 0.01 on the mean redshift in each tomographic bin.

79 ASTRONOMY AND ASTROPHYSICS↗

Planck 2018 results

We analyse the Planck full-mission cosmic microwave background (CMB) temperature and E -mode polarization maps to obtain constraints on primordial non-Gaussianity (NG). We compare estimates obtained from separable template-fitting, binned, and optimal modal bispectrum estimators, finding consistent values for the local, equilateral, and orthogonal bispectrum amplitudes. Our combined temperature and polarization analysis produces the following final results: f NL local = -0.9 ± 5.1; f NL equil = -26 ± 47; and f NL ortho = -38 ± 24 (68% CL, statistical). These results include low-multipole (4 ≤ ℓ < 40) polarization data that are not included in our previous analysis. The results also pass an extensive battery of tests (with additional tests regarding foreground residuals compared to 2015), and they are stable with respect to our 2015 measurements (with small fluctuations, at the level of a fraction of a standard deviation, which is consistent with changes in data processing). Polarization-only bispectra display a significant improvement in robustness; they can now be used independently to set primordial NG constraints with a sensitivity comparable to WMAP temperature-based results and they give excellent agreement. In addition to the analysis of the standard local, equilateral, and orthogonal bispectrum shapes, we consider a large number of additional cases, such as scale-dependent feature and resonance bispectra, isocurvature primordial NG, and parity-breaking models, where we also place tight constraints but do not detect any signal. The non-primordial lensing bispectrum is, however, detected with an improved significance compared to 2015, excluding the null hypothesis at 3.5 σ . Beyond estimates of individual shape amplitudes, we also present model-independent reconstructions and analyses of the Planck CMB bispectrum. Our final constraint on the local primordial trispectrum shape is g NL local = (-5.8 ± 6.5) × 10 4 (68% CL, statistical), while constraints for other trispectrum shapes are also determined. Exploiting the tight limits on various bispectrum and trispectrum shapes, we constrain the parameter space of different early-Universe scenarios that generate primordial NG, including general single-field models of inflation, multi-field models (e.g. curvaton models), models of inflation with axion fields producing parity-violation bispectra in the tensor sector, and inflationary models involving vector-like fields with directionally-dependent bispectra. Our results provide a high-precision test for structure-formation scenarios, showing complete agreement with the basic picture of the ΛCDM cosmology regarding the statistics of the initial conditions, with cosmic structures arising from adiabatic, passive, Gaussian, and primordial seed perturbations.

79 ASTRONOMY AND ASTROPHYSICS↗

Dataset for the Danczak et al., 2025 manuscript about bacterial-fungal interactions

We generated genome-resolved multiomics data from a series of metagenomic and metatranscriptomic sequencing. Specifically, we acquired, functionally annotated, and taxonomically classified both bacterial and eukaryotic metagenome assembled genomes (MAGs). For bacterial MAGs, we assembled eukaryotic float metagenomic sequencing data from JGI using MEGAHIT, binned and refined MAGs using MetaWRAP and dRep, functionally annotated MAGs using eggNOG mapper, and assigned taxonomy using GTDB-tk. For eukaryotic MAGs, we first identified potentially eukaryotic contigs from a coassembly of eukaryotic float metagenomic sequencing data from JGI using EukRep and Whokaryote, binned MAGs using MetaBAT2, functionally annotated MAGs using eggNOG mapper, and assigned taxonomy using Eukulele. Bulk metatranscriptomic reads were mapped to bacterial MAGs and polyA-metatranscriptomic read were mapped to eukaryotic MAGs using bbmap.

Danczak, Robert E. [Pacific Northwest National Lab↗

The DECADE cosmic shear project II: photometric redshift calibration of the source galaxy sample

We present the photometric redshift characterization and calibration for the Dark Energy Camera All Data Everywhere (DECADE) weak lensing dataset: a catalog of 107 million galaxies observed by the Dark Energy Camera (DECam) in the northern Galactic cap. The redshifts are estimated from a combination of wide-field photometry, deep-field photometry with associated redshift estimates, and a transfer function between the wide field and deep field that is estimated using a source injection catalog. We construct four tomographic bins for the galaxy catalog, and estimate the redshift distribution, $n(z)$, within each one using the Self-organizing Map Photo-Z (SOMPZ) methodology. Our estimates include the contributions from sample variance, zeropoint calibration uncertainties, and redshift biases, as quantified for the deep-field dataset. The total uncertainties on the mean redshifts are $σ_{\langle}$$_z$$_{\rangle} ≈ 0.01$. The SOMPZ estimates are then compared to those from the clustering redshift method, obtained by cross-correlating our source galaxies with galaxies in spectroscopic surveys, and are shown to be consistent with each other.

Anbajagane, D. [Univ. of Chicago, IL (United State↗

Neural posterior unfolding

Differential cross section measurements are the currency of scientific exchange in particle and nuclear physics. A key challenge for these analyses is the correction for detector distortions, known as deconvolution or unfolding. Binned unfolding of cross section measurements traditionally rely on the regularized inversion of the response matrix that represents the detector response, mapping pre-detector (`particle level') observables to post-detector (`detector level') observables. In this paper we introduce Neural Posterior Unfolding, a modern, Bayesian approach that leverages normalizing flows for unfolding. By using normalizing flows for neural posterior estimation, NPU offers several key advantages including implicit regularization through the neural network architecture, fast amortized inference that eliminates the need for repeated retraining, and direct access to the full uncertainty in the unfolded result. In addition to introducing NPU, we implement a classical Bayesian unfolding method called Fully Bayesian Unfolding (FBU) in modern Python so it can also be studied. These tools are validated on simple Gaussian examples and then tested on simulated jet substructure examples from the Large Hadron Collider (LHC). We find that the Bayesian methods are effective and worth additional development to be analysis ready for cross section measurements at the LHC and beyond.

Analysis and statistical methods↗

Cosmology with second- and third-order shear statistics for the Dark Energy Survey: Methods and simulated analysis

We present a new pipeline designed for the robust inference of cosmological parameters using both second- and third-order shear statistics. We build a theoretical model for rapid evaluation of three-point correlations using our fastnc code and integrate it into the cosmosis framework. We measure the two-point functions 𝜉 ± and the full configuration-dependent three-point shear correlation functions across all auto- and cross-redshift bins. We compress the three-point functions into the mass aperture statistic ⟨ℳ$^{3}_{ap}$⟩ for a set of 796 simulated shear maps designed to model the Dark Energy Survey Year 3 data. We estimate from it the full covariance matrix and model the effects of intrinsic alignments, shear calibration biases and photometric redshift uncertainties. We apply scale cuts to minimize the contamination from the baryonic signal as modeled through hydrodynamical simulations. We find a significant improvement of 83% on the figure of merit in the Ω m − 𝑆 8 plane when we add the ⟨ℳ$^{3}_{ap}$⟩ data to 𝜉 ± . Here, we present our findings for all relevant cosmological and systematic uncertainty parameters and discuss the complementarity of third-order and second-order statistics.

79 ASTRONOMY AND ASTROPHYSICS↗

Open-Source Data Analysis Tool for Spectral Small-Angle X-ray Scattering Using Spectroscopic Photon-Counting Detector

Spectral small-angle X-ray scattering (sSAXS) is a powerful technique for material characterization from thicker samples by capturing elastic X-ray scattering data in angle- and energy-dispersive modes at small angles. This approach is enabled by the use of a 2D spectroscopic photon-counting detector that provides energy and position information of scattered photons when a sample is irradiated by a polychromatic X-ray beam. Here, we describe an open-source tool with a graphical interface for analyzing sSAXS data obtained from a 2D spectroscopic photon-counting detector with a large number of energy bins. The tool takes system geometry parameters and raw detector data to output 1D scattering patterns and a 2D spatially-resolved scattering map in the energy range of interest. We validated these features using data from samples of caffeine powder with well-known scattering peaks. This open-source tool will facilitate sSAXS data analysis for various material characterization applications.

Chemistry↗

Dark Energy Survey Year 6 Results: Redshift Calibration of the Weak Lensing Source Galaxies

Determining the distribution of redshifts for galaxies in wide-field photometric surveys is essential for robust cosmological studies of weak gravitational lensing. We present the methodology, calibrated redshift distributions, and uncertainties of the final Dark Energy Survey Year 6 (Y6) weak lensing galaxy data, divided into four redshift bins centered at $\langle z \rangle = [0.414, 0.538, 0.846, 1.157]$. We combine independent information from two methods on the full shape of redshift distributions: optical and near-infrared photometry within an improved Self-Organizing Map $p(z)$ (SOMPZ) framework, and cross-correlations with spectroscopic galaxy clustering measurements (WZ), which we demonstrate to be consistent both in terms of the redshift calibration itself and in terms of resulting cosmological constraints within 0.1$σ$. We describe the process used to produce an ensemble of redshift distributions that account for several known sources of uncertainty. Among these, imperfection in the calibration sample due to the lack of faint, representative spectra is the dominant factor. The final uncertainty on mean redshift in each bin is $σ_{\langle z\rangle} = [0.012, 0.008,0.009, 0.024]$. We ensure the robustness of the redshift distributions by leveraging new image simulations and a cross-check with galaxy shape information via the shear ratio (SR) method.

Yin, B. [Duke U.] (ORCID:0009000656049980)↗

Crowdsourcing Felt Reports Using the MyShake Smartphone App

MyShake is a free citizen science smartphone app that provides a range of features related to earthquakes. Features available globally include rapid postearthquake notifications, live maps of earthquake damage as reported by MyShake users, safety tips, and various educational features. The app also uses the accelerometer in the mobile device to detect earthquake shaking, and to record and submit waveforms to a central archive. In addition, MyShake delivers earthquake early warning alerts in California, Oregon, and Washington. Here, in this study, we compare the felt shaking reports provided by MyShake users in California with the U.S. Geological Survey’s (USGSs) “Did You Feel It?” intensity reports. The MyShake app simply asks, “What strength of shaking did you feel?” and users report on a five-level scale. When the MyShake reports are averaged in spatial or time bins, we find strong correlation with the Modified Mercalli Intensity scale values reported by the USGS based on the DYFI surveys. The MyShake felt reports can therefore contribute to the creation of shaking intensity maps.

58 GEOSCIENCES↗

Measuring the X-ray luminosities of DESI groups from eROSITA Final Equatorial-Depth Survey – I. X-ray luminosity–halo mass scaling relation

ABSTRACT We use the eROSITA Final Equatorial-Depth Survey (eFEDS) to measure the rest-frame 0.1–2.4 keV band X-ray luminosities of ∼600 000 DESI groups using two different algorithms in the overlap region of the two observations. These groups span a large redshift range of 0.0 ≤ zg ≤ 1.0 and group mass range of $10^{10.76}\, h^{-1}\, \mathrm{M}_{\odot } \le M_h \le 10^{15.0}\, h^{-1}\, \mathrm{M}_{\odot }$. (1) Using the blind detection pipeline of eFEDS, we find that 10932 X-ray emission peaks can be cross-matched with our groups, ∼38 per cent of which have a signal-to-noise ratio $\rm {S}/\rm {N} \ge 3$ in X-ray detection. Comparing to the numbers reported in previous studies, this matched sample size is a factor of ∼6 larger. (2) By stacking X-ray maps around groups with similar masses and redshifts, we measure the average X-ray luminosity of groups as a function of halo mass in five redshift bins. We find that in a wide halo mass range, the X-ray luminosity, LX, is roughly linearly proportional to Mh and quite independent to the redshift of the groups. (3) We use a Poisson distribution to model the X-ray luminosities obtained using two different algorithms and obtain the best-fit $L_{\rm X}=10^{28.46\pm 0.03}M_{\rm h}^{1.024\pm 0.002}$ and $L_{\rm X}=10^{26.73 \pm 0.04}M_{\rm h}^{1.140 \pm 0.003}$ scaling relations, respectively. The best-fit slopes are flatter than the results previously obtained but closer to a self-similar prediction.

Astronomy & Astrophysics↗

Evolution of structure growth during dark energy domination: Insights from the cross-correlation of DESI galaxies with CMB lensing and galaxy magnification

We use a hybrid effective field theory (HEFT) model to constrain the evolution of low-redshift (z≲0.4) matter fluctuations by cross-correlating DESI Bright Galaxy Survey (BGS) legacy imaging with the latest cosmic microwave background (CMB) lensing maps from Planck and Atacama cosmology telescope. Our tomographic BGS analysis finds that the evolution and amplitude of matter fluctuations align with CMB-conditioned Λ cold dark matter predictions. When including DESI baryon acoustic oscillation (BAO) measurements we obtain σ8=0.876-0.067+0.051 from BGS alone. Jointly analyzing BGS and luminous red galaxy (LRG) cross-correlations with the same CMB lensing maps yields σ8=0.791±0.021. As a complementary approach we isolate the galaxy magnification signal from the cross-correlation of nonoverlapping BGS and LRG photometric redshift bins, ruling out the null-magnification hypothesis at 11σ. For the first time, we constrain quasilinear structure growth from the (finite-difference calibrated) galaxy magnification signal and find σ8=0.720±0.047(stat)±0.050(sys) assuming a linear bias model and including BAO data.

Sailer, Noah↗

Map-level baryonification: unified treatment of weak lensing two-point and higher-order statistics

Precision cosmology benefits from extracting maximal information from cosmic structures, motivating the use of higher-order statistics (HOS) at small spatial scales. However, predicting how baryonic processes modify matter statistics at these scales has been challenging. The baryonic correction model (BCM) addresses this by modifying dark-matter-only simulations to mimic baryonic effects, providing a flexible, simulation-based framework for predicting both two-point and HOS. We show that a 3-parameter version of the BCM can jointly fit weak lensing maps' two-point statistics, wavelet phase harmonics coefficients, scattering coefficients, and the third and fourth moments to within 2% accuracy across all scales ℓ < 2000 and tomographic bins for a DES-Y3-like redshift distribution ( z ≲ 2), using the FLAMINGO simulations. These results demonstrate the viability of BCM-assisted, simulation-based weak lensing inference of two-point and HOS, paving the way for robust cosmological constraints that fully exploit non-Gaussian information on small spatial scales.

79 ASTRONOMY AND ASTROPHYSICS↗

Sparse Data Machine Learning Integration with Theory, Experiment and Uncertainty Quantification: Process-Structure-Property-Performance of Friction Deformation Processing

Computer vision and deep learning tools that advance the ability to establish processing-structure-property-performance (PSPP) relations are presented. The Bayesian binning method for image segmentation enables quantitative analysis of microstructural features in an automated way, while the analysis of shapes and relative orientation of these features reveals local deformation maps indicative of both, material flow and residual stresses due to materials processing. The deep learning method leads to the previous knowledge agnostic mapping of empirically observed microstructural zones in friction stir welding (FSW) process and synthetic microstructure generation capability that is statistically equivalent to experimentally collected data.

97 MATHEMATICS AND COMPUTING↗