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CoverM: read alignment statistics for metagenomics

SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results. AVAILABILITY AND IMPLEMENTATION: CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.

Aroney, Samuel T N↗

Publishing Environmental Assessment and Management Science: Crossing the Hurdles

Benefits accrue to scientists, resource managers, companies, and policymakers when environmental scientists publish in peer-reviewed journals. However, environmental scientists and practitioners face challenges, including the sometimes low value placed on journal articles, institutional vested interests in outcomes, and the changing priorities of employers and project sponsors. Confidentiality agreements can also lead scientists to assume publication is not an option. Case studies may be viewed by potential authors as too routine for peer-reviewed journals. On the basis of 30 years of experience, we suggest that publishing hurdles can be overcome and that environmental scientists have a range of options. The topics of manuscripts can include not only results from case studies and perspectives based on them but also byproducts of assessments, including definitions, plans, monitoring methods and models, and decision frameworks. Environmental scientists have unique opportunities to move science forward with their practical knowledge if they can move across the institutional, logistical, data-related, and content-related hurdles.

54 ENVIRONMENTAL SCIENCES↗

Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features

Abstract Alterations in RNA-splicing are a molecular hallmark of several neurological diseases, including muscular dystrophies, where mutations in genes involved in RNA metabolism or characterized by alterations in RNA splicing have been described. Here, we present five patients from two unrelated families with a limb-girdle muscular dystrophy (LGMD) phenotype carrying a biallelic variant in SNUPN gene. Snurportin-1, the protein encoded by SNUPN, plays an important role in the nuclear transport of small nuclear ribonucleoproteins (snRNPs), essential components of the spliceosome. We combine deep phenotyping, including clinical features, histopathology and muscle MRI, with functional studies in patient-derived cells and muscle biopsies to demonstrate that variants in SNUPN are the cause of a new type of LGMD according to current definition. Moreover, an in vivo model in Drosophila melanogaster further supports the relevance of Snurportin-1 in muscle. SNUPN patients show a similar phenotype characterized by proximal weakness starting in childhood, restrictive respiratory dysfunction and prominent contractures, although inter-individual variability in terms of severity even in individuals from the same family was found. Muscle biopsy showed myofibrillar-like features consisting of myotilin deposits and Z-disc disorganization. MRI showed predominant impairment of paravertebral, vasti, sartorius, gracilis, peroneal and medial gastrocnemius muscles. Conservation and structural analyses of Snurportin-1 p.Ile309Ser variant suggest an effect in nuclear-cytosol snRNP trafficking. In patient-derived fibroblasts and muscle, cytoplasmic accumulation of snRNP components is observed, while total expression of Snurportin-1 and snRNPs remains unchanged, which demonstrates a functional impact of SNUPN variant in snRNP metabolism. Furthermore, RNA-splicing analysis in patients’ muscle showed widespread splicing deregulation, in particular in genes relevant for muscle development and splicing factors that participate in the early steps of spliceosome assembly. In conclusion, we report that SNUPN variants are a new cause of limb girdle muscular dystrophy with specific clinical, histopathological and imaging features, supporting SNUPN as a new gene to be included in genetic testing of myopathies. These results further support the relevance of splicing-related proteins in muscle disorders.

Iruzubieta, Pablo (ORCID:0000000303316222)↗

Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize

Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4–40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.

60 APPLIED LIFE SCIENCES↗

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗

Quantification of spatial and seasonal trends in the atmosphere and construction of statistical models for infrasonic propagation

SUMMARY Infrasonic waves are influenced by variations in the density, pressure and temperature as well as the ambient winds. Modelling infrasonic propagation can be challenging due to the dynamic nature of the atmosphere as well as the sparseness of measurements which result in variability and notable uncertainty. A framework is presented to quantify spatial and seasonal trends in atmospheric structure via analysis of the effective sound speed profile and identification of temporal trends in the middle atmospheric waveguide produced by the circumpolar vortex winds. Seasonal definitions identifying typical atmospheric structures during the summer, winter and spring/fall transition periods are identified using atmospheric data from 2010 through 2020. Seasonal trend analysis is conducted for a number of locations across the contiguous United States to quantify spatial variations in atmospheric structure that impact infrasonic propagation. For each season and location, empirical orthogonal function analysis is used to reduce the historical archive of atmospheric data into a smaller representative set that can be analysed using numerical tools more efficiently. Infrasonic ray tracing and finite-frequency modal propagation analyses are applied to construct propagation path geometry and transmission loss statistics which are useful in localization and yield estimation for infrasonic sources, respectively. An example application is detailed in which transmission loss statistics are combined with an explosive source model and noise statistics to quantify the capability of a network to detect nearby sources.

58 GEOSCIENCES↗

A deep learning approach to identify missing is-a relations in SNOMED CT

Abstract Objective SNOMED CT is the largest clinical terminology worldwide. Quality assurance of SNOMED CT is of utmost importance to ensure that it provides accurate domain knowledge to various SNOMED CT-based applications. In this work, we introduce a deep learning-based approach to uncover missing is-a relations in SNOMED CT. Materials and Methods Our focus is to identify missing is-a relations between concept-pairs exhibiting a containment pattern (ie, the set of words of one concept being a proper subset of that of the other concept). We use hierarchically related containment concept-pairs as positive instances and hierarchically unrelated containment concept-pairs as negative instances to train a model predicting whether an is-a relation exists between 2 concepts with containment pattern. The model is a binary classifier leveraging concept name features, hierarchical features, enriched lexical attribute features, and logical definition features. We introduce a cross-validation inspired approach to identify missing is-a relations among all hierarchically unrelated containment concept-pairs. Results We trained and applied our model on the Clinical finding subhierarchy of SNOMED CT (September 2019 US edition). Our model (based on the validation sets) achieved a precision of 0.8164, recall of 0.8397, and F1 score of 0.8279. Applying the model to predict actual missing is-a relations, we obtained a total of 1661 potential candidates. Domain experts performed evaluation on randomly selected 230 samples and verified that 192 (83.48%) are valid. Conclusions The results showed that our deep learning approach is effective in uncovering missing is-a relations between containment concept-pairs in SNOMED CT.

97 MATHEMATICS AND COMPUTING↗

Survey of Gravitationally lensed Objects in HSC Imaging (SuGOHI) – V. Group-to-cluster scale lens search from the HSC–SSP Survey

ABSTRACT We report the largest sample of candidate strong gravitational lenses belonging to the Survey of Gravitationally lensed Objects in HSC Imaging for group-to-cluster scale (SuGOHI-c) systems. These candidates are compiled from the S18A data release of the Hyper Suprime-Cam Subaru Strategic Program (HSC–SSP) Survey. We visually inspect ∼39 500 galaxy clusters, selected from several catalogues, overlapping with the Wide, Deep, and UltraDeep fields, spanning the cluster redshift range of 0.05 < zcl < 1.38. We discover 641 candidate lens systems, of which 536 are new. From the full sample, 47 are almost certainly bona fide lenses, 181 of them are highly probable lenses, and 413 are possible lens systems. Additionally, we present 131 lens candidates at galaxy scale serendipitously discovered during the inspection. We obtained spectroscopic follow-up of 10 candidates using the X-shooter. With this follow-up, we confirm eight systems as strong gravitational lenses. Of the remaining two, one of the sources is too faint to detect any emission, and the other has a tentative redshift close to the lens redshift, but additional arcs in this system are yet to be observed spectroscopically. Since the HSC–SSP is an ongoing survey, we expect to find ∼600 definite or probable lenses using this procedure and even more if combined with other lens finding methods.

Jaelani, Anton T.↗

Validation of emission-line galaxies target selection algorithms for the Dark Energy Spectroscopic Instrument using the MMT Binospec

ABSTRACT The forthcoming Dark Energy Spectroscopic Instrument (DESI) experiment plans to measure the effects of dark energy on the expansion of the Universe and create a 3D map of the Universe using galaxies up to z ∼ 1.6 and QSOs up to z ∼ 3.5. In order to create this map, DESI will obtain spectroscopic redshifts of over 30 million objects; among them, a majority are [O ii] emitting star-forming galaxies known as emission-line galaxies (ELGs). These ELG targets will be pre-selected by drawing a selection region on the g − r versus r − z colour–colour plot, where high-redshift ELGs form a separate locus from the lower redshift ELGs and interlopers. In this paper, we study the efficiency of three ELG target selection algorithms – the Final Design Report (FDR) cut based on the DEEP2 photometry, Number Density Modelling (NDM) and Random Forest – to determine how the combination of these three algorithms can be best used to yield a simple selection boundary that will be best suited to meet DESI’s science goals. To do this, we selected 17 small patches in the DESI footprint where we run the three target selection algorithms to pre-select ELGs based on their photometry. We observed the pre-selected ELGs using the MMT Binospec, which is similar in functionality to the DESI instrument, to obtain their spectroscopic redshifts and fluxes of 1054 ELGs. By analysing the redshift and fluxing distribution of these galaxies, we find that although NDM performed the best, simple changes in the FDR definition would also yield sufficient performance.

79 ASTRONOMY AND ASTROPHYSICS↗

Dark Energy Survey Year 1 results: the lensing imprint of cosmic voids on the cosmic microwave background

ABSTRACT Cosmic voids gravitationally lens the cosmic microwave background (CMB) radiation, resulting in a distinct imprint on degree scales. We use the simulated CMB lensing convergence map from the Marenostrum Institut de Ciencias de l’Espai (MICE) N-body simulation to calibrate our detection strategy for a given void definition and galaxy tracer density. We then identify cosmic voids in Dark Energy Survey (DES) Year 1 data and stack the Planck 2015 lensing convergence map on their locations, probing the consistency of simulated and observed void lensing signals. When fixing the shape of the stacked convergence profile to that calibrated from simulations, we find imprints at the 3σ significance level for various analysis choices. The best measurement strategies based on the MICE calibration process yield S/N ≈ 4 for DES Y1, and the best-fitting amplitude recovered from the data is consistent with expectations from MICE (A ≈ 1). Given these results as well as the agreement between them and N-body simulations, we conclude that the previously reported excess integrated Sachs–Wolfe (ISW) signal associated with cosmic voids in DES Y1 has no counterpart in the Planck CMB lensing map.

79 ASTRONOMY AND ASTROPHYSICS↗

Model-independent discovery prospects for primordial black holes at LIGO

ABSTRACT Primordial black holes may encode the conditions of the early Universe, and may even constitute a significant fraction of cosmological dark matter. Their existence has yet to be established. However, black holes with masses below ${\sim}{1}{\, \mathrm{M}_\odot }$ cannot form as an endpoint of stellar evolution, so the detection of even one such object would be a smoking gun for new physics, and would constitute evidence that at least a fraction of the dark matter consists of primordial black holes. Gravitational wave detectors are capable of making a definitive discovery of this kind by detecting mergers of light black holes. But since the merger rate depends strongly on the shape of the black hole mass function, it is difficult to determine the potential for discovery or constraint as a function of the overall abundance of black holes. Here, we directly maximize and minimize the merger rate to connect observational results to the actual abundance of observable objects. We show that LIGO can discover mergers of light primordial black holes within the next decade even if such black holes constitute only a very small fraction of dark matter. A single merger event involving such an object would (i) provide conclusive evidence of new physics, (ii) establish the nature of some fraction of dark matter, and (iii) probe cosmological history at scales far beyond those observable today.

79 ASTRONOMY AND ASTROPHYSICS↗

Dissipation measures in weakly collisional plasmas

ABSTRACT The physical foundations of the dissipation of energy and the associated heating in weakly collisional plasmas are poorly understood. Here, we compare and contrast several measures that have been used to characterize energy dissipation and kinetic-scale conversion in plasmas by means of a suite of kinetic numerical simulations describing both magnetic reconnection and decaying plasma turbulence. We adopt three different numerical codes that can also include interparticle collisions: the fully kinetic particle-in-cell vpic, the fully kinetic continuum Gkeyll, and the Eulerian Hybrid Vlasov–Maxwell (HVM) code. We differentiate between (i) four energy-based parameters, whose definition is related to energy transfer in a fluid description of a plasma, and (ii) four distribution function-based parameters, requiring knowledge of the particle velocity distribution function. There is an overall agreement between the dissipation measures obtained in the PIC and continuum reconnection simulations, with slight differences due to the presence/absence of secondary islands in the two simulations. There are also many qualitative similarities between the signatures in the reconnection simulations and the self-consistent current sheets that form in turbulence, although the latter exhibits significant variations compared to the reconnection results. All the parameters confirm that dissipation occurs close to regions of intense magnetic stresses, thus exhibiting local correlation. The distribution function-based measures show a broader width compared to energy-based proxies, suggesting that energy transfer is co-localized at coherent structures, but can affect the particle distribution function in wider regions. The effect of interparticle collisions on these parameters is finally discussed.

79 ASTRONOMY AND ASTROPHYSICS↗

Dark Energy Survey Year 3 results: galaxy sample for BAO measurement

Here, we present and validate the galaxy sample used for the analysis of the baryon acoustic oscillation (BAO) signal in the Dark Energy Survey (DES) Y3 data. The definition is based on a colour and redshift-dependent magnitude cut optimized to select galaxies at redshifts higher than 0.5, while ensuring a high-quality determination. The sample covers ~ 4100 square degrees to a depth of i = 22.3 (AB) at 10σ. It contains 7,031,993 galaxies in the redshift range from z = 0.6 to 1.1, with a mean effective redshift of 0.835. Redshifts are estimated with the machine learning algorithm DNF, and are validated using the VIPERS PDR2 sample. We find a mean redshift bias of z bias ~ 0.01 and a mean uncertainty, in units of 1 + z, of σ 68 ~ 0.03$. We evaluate the galaxy population of the sample, showing it is mostly built upon Elliptical to Sbc types. Furthermore, we find a low level of stellar contamination of ≲ 4 %. We present the method used to mitigate the effect of spurious clustering coming from observing conditions and other large-scale systematics. We apply it to the BAO sample and calculate weights that are used to get a robust estimate of the galaxy clustering signal. This paper is one of a series dedicated to the analysis of the BAO signal in DES Y3. In the companion papers, we present the galaxy mock catalogues used to calibrate the analysis and the angular diameter distance constraints obtained through the fitting to the BAO scale.

79 ASTRONOMY AND ASTROPHYSICS↗

The DESI N -body simulation project – I. Testing the robustness of simulations for the DESI dark time survey

ABSTRACT Analysis of large galaxy surveys requires confidence in the robustness of numerical simulation methods. The simulations are used to construct mock galaxy catalogues to validate data analysis pipelines and identify potential systematics. We compare three N-body simulation codes, abacus, gadget-2, and swift, to investigate the regimes in which their results agree. We run N-body simulations at three different mass resolutions, 6.25 × 108, 2.11 × 109, and 5.00 × 109 h−1 M⊙, matching phases to reduce the noise within the comparisons. We find systematic errors in the halo clustering between different codes are smaller than the Dark Energy Spectroscopic Instrument (DESI) statistical error for $s\ \gt\ 20\ h^{-1}$ Mpc in the correlation function in redshift space. Through the resolution comparison we find that simulations run with a mass resolution of 2.1 × 109 h−1 M⊙ are sufficiently converged for systematic effects in the halo clustering to be smaller than the DESI statistical error at scales larger than $20\ h^{-1}$ Mpc. These findings show that the simulations are robust for extracting cosmological information from large scales which is the key goal of the DESI survey. Comparing matter power spectra, we find the codes agree to within 1 per cent for k ≤ 10 h Mpc−1. We also run a comparison of three initial condition generation codes and find good agreement. In addition, we include a quasi-N-body code, FastPM, since we plan use it for certain DESI analyses. The impact of the halo definition and galaxy–halo relation will be presented in a follow-up study.

79 ASTRONOMY AND ASTROPHYSICS↗

Red Dragon: a redshift-evolving Gaussian mixture model for galaxies

ABSTRACT Precision-era optical cluster cosmology calls for a precise definition of the red sequence (RS), consistent across redshift. To this end, we present the Red Dragon algorithm: an error-corrected multivariate Gaussian mixture model (GMM). Simultaneous use of multiple colours and smooth evolution of GMM parameters result in a continuous RS and blue cloud (BC) characterization across redshift, avoiding the discontinuities of red fraction inherent in swapping RS selection colours. Based on a mid-redshift spectroscopic sample of SDSS galaxies, an RS defined by Red Dragon selects quiescent galaxies (low specific star formation rate) with a balanced accuracy of over $90{{\ \rm per\ cent}}$. This approach to galaxy population assignment gives more natural separations between RS and BC galaxies than hard cuts in colour–magnitude or colour–colour spaces. The Red Dragon algorithm is publicly available at bitbucket.org/wkblack/red-dragon-gamma/.

79 ASTRONOMY AND ASTROPHYSICS↗

Image feature extraction and galaxy classification: a novel and efficient approach with automated machine learning

ABSTRACT In this work, we explore the possibility of applying machine learning methods designed for 1D problems to the task of galaxy image classification. The algorithms used for image classification typically rely on multiple costly steps, such as the point spread function deconvolution and the training and application of complex Convolutional Neural Networks of thousands or even millions of parameters. In our approach, we extract features from the galaxy images by analysing the elliptical isophotes in their light distribution and collect the information in a sequence. The sequences obtained with this method present definite features allowing a direct distinction between galaxy types. Then, we train and classify the sequences with machine learning algorithms, designed through the platform Modulos AutoML. As a demonstration of this method, we use the second public release of the Dark Energy Survey (DES DR2). We show that we are able to successfully distinguish between early-type and late-type galaxies, for images with signal-to-noise ratio greater than 300. This yields an accuracy of $86{{\ \rm per\ cent}}$ for the early-type galaxies and $93{{\ \rm per\ cent}}$ for the late-type galaxies, which is on par with most contemporary automated image classification approaches. The data dimensionality reduction of our novel method implies a significant lowering in computational cost of classification. In the perspective of future data sets obtained with e.g. Euclid and the Vera Rubin Observatory, this work represents a path towards using a well-tested and widely used platform from industry in efficiently tackling galaxy classification problems at the peta-byte scale.

79 ASTRONOMY AND ASTROPHYSICS↗

The impact and mitigation of broad-absorption-line quasars in Lyman α forest correlations

ABSTRACT Correlations in and with the flux transmission of the Lyman α (Ly α) forest in the spectra of high-redshift quasars are powerful cosmological tools, yet these measurements can be compromised if the intrinsic quasar continuum is significantly uncertain. One particularly problematic case is broad-absorption-line (BAL) quasars, which exhibit blueshifted absorption associated with many spectral features that are consistent with outflows of up to ∼0.1c. As these absorption features can both fall in the forest region and be difficult to distinguish from Ly α absorption, cosmological analyses eliminate the ∼12–16 per cent of quasars that exhibit BALs. In this paper, we explore an alternate approach that includes BALs in the Ly α autocorrelation function, with the exception of the expected locations of the BAL absorption troughs. This procedure returns over 95 per cent of the path-length that is lost by the exclusion of BALs, as well as increasing the density of sightlines. We show that including BAL quasars reduces the fractional uncertainty in the covariance matrix and correlation function by 12 per cent and does not significantly change the shape of the correlation function relative to analyses that exclude BAL quasars. We also evaluate different definitions of BALs, masking strategies, and potential differences in the quasar continuum in the forest region for BALs with different amounts of absorption.

79 ASTRONOMY AND ASTROPHYSICS↗

Cuspy dark matter density profiles in massive dwarf galaxies

ABSTRACT Rotation curves of galaxies probe their total mass distributions, including dark matter. Dwarf galaxies are excellent systems to investigate the dark matter density distribution, as they tend to have larger fractions of dark matter compared to higher mass systems. The core-cusp problem describes the discrepancy found in the slope of the dark matter density profile in the centres of galaxies (β*) between observations of dwarf galaxies (shallower cores) and dark matter-only simulations (steeper cusps). We investigate β* in six nearby spiral dwarf galaxies for which high-resolution CO J = 1–0 data were obtained with ALMA (Atacama Large Millimeter/submillimeter Array). We derive rotation curves and decompose the mass profile of the dark matter using our CO rotation curves as a tracer of the total potential and 4.5 $\mu$m photometry to define the stellar mass distribution. We find 〈β*〉 = 0.6 with a standard deviation of ±0.1 among the galaxies in this sample, in agreement with previous measurements in this mass range. The galaxies studied are on the high stellar mass end of dwarf galaxies and have cuspier profiles than lower mass dwarfs, in agreement with other observations. When the same definition of the slope is used, we observe steeper slopes than predicted by the FIRE and NIHAO simulations. This may signal that these relatively massive dwarfs underwent stronger gas inflows towards their centres than predicted by these simulations, that these simulations overpredict the frequency of accretion or feedback events, or that a combination of these or other effects are at work.

Cooke, Lauren H. (ORCID:0000000284337553)↗