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At least 1,171 records · Page 65

Radiation transfer of models of massive star formation. III. The evolutionary sequence

We present radiation transfer simulations of evolutionary sequences of massive protostars forming from massive dense cores in environments of high mass surface densities, based on the Turbulent Core Model. The protostellar evolution is calculated with a multi-zone numerical model, with the accretion rate regulated by feedback from an evolving disk wind outflow cavity. The disk evolution is calculated assuming a fixed ratio of disk to protostellar mass, while the core envelope evolution assumes an inside-out collapse of the core with a fixed outer radius. In this framework, an evolutionary track is determined by three environmental initial conditions: the core mass M{sub c} , the mass surface density of the ambient clump Σ{sub cl}, and the ratio of the core's initial rotational to gravitational energy β {sub c}. Evolutionary sequences with various M{sub c} , Σ{sub cl}, and β {sub c} are constructed. We find that in a fiducial model with M{sub c} = 60 M {sub ☉}, Σ{sub cl} = 1 g cm{sup –2}, and β {sub c} = 0.02, the final mass of the protostar reaches at least ∼26 M {sub ☉}, making the final star formation efficiency ≳ 0.43. For each of the evolutionary tracks, radiation transfer simulations are performed at selected stages, with temperature profiles, spectral energy distributions (SEDs), and multiwavelength images produced. At a given stage, the envelope temperature depends strongly on Σ{sub cl}, with higher temperatures in a higher Σ{sub cl} core, but only weakly on M{sub c} . The SED and MIR images depend sensitively on the evolving outflow cavity, which gradually widens as the protostar grows. The fluxes at ≲ 100 μm increase dramatically, and the far-IR peaks move to shorter wavelengths. The influence of Σ{sub cl} and β {sub c} (which determines disk size) are discussed. We find that, despite scatter caused by different M{sub c} , Σ{sub cl}, β {sub c}, and inclinations, sources at a given evolutionary stage appear in similar regions of color-color diagrams, especially when using colors with fluxes at ≳ 70 μm, where scatter due to inclination is minimized, implying that such diagrams can be useful diagnostic tools for identifying the evolutionary stages of massive protostars. We discuss how intensity profiles along or perpendicular to the outflow axis are affected by environmental conditions and source evolution and can thus act as additional diagnostics of the massive star formation process.

79 ASTRONOMY AND ASTROPHYSICS↗

The shock-induced star formation sequence resulting from a constant spiral pattern speed

We utilize a suite of multiwavelength data of nine nearby spirals to analyze the shock-induced star formation sequence that may result from a constant spiral pattern speed. The sequence involves tracers as the H I, CO 24 μm, and FUV, where the spiral arms were analyzed with Fourier techniques in order to obtain their azimuthal phases as a function of radius. It was found that only two of the objects, NGC 628 and NGC 5194, present coherent phases resembling the theoretical expectations, as indicated by the phase shifts of CO- 24 μm. The evidence is more clear for NGC 5194 and moderate for NGC 628. It was also found that the phase shifts are different for the two spiral arms. With the exception on NGC 3627, a two-dimensional Fourier analysis showed that the rest of the objects do not exhibit bi-symmetric spiral structures of stellar mass, i.e., grand-design spirals. A phase order inversion indicates a corotation radius of ∼89'' for NGC 628 and ∼202'' for NGC 5194. For these two objects, the CO-Hα phase shifts corroborate the CO-24 μm azimuthal offsets. Also for NGC 5194, the CO-70 μm, CO-140 μm, and CO-250 μm phase shifts indicate a corotation region.

79 ASTRONOMY AND ASTROPHYSICS↗

First detection of the white dwarf cooling sequence of the galactic bulge

We present Hubble Space Telescope data of the low-reddening Sagittarius window in the Galactic bulge. The Sagittarius Window Eclipsing Extrasolar Planet Search field (∼3'× 3'), together with three more Advanced Camera for Surveys and eight Wide-Field Camera 3 fields, were observed in the F606W and F814W filters, approximately every two weeks for 2 yr, with the principal aim of detecting a hidden population of isolated black holes and neutron stars through astrometric microlensing. Proper motions were measured with an accuracy of ≈0.1 mas yr{sup –1} (≈4 km s{sup –1}) at F606W ≈ 25.5 mag, and better than ≈0.5 mas yr{sup –1} (≈20 km s{sup –1}) at F606W ≈ 28 mag, in both axes. Proper-motion measurements allowed us to separate disk and bulge stars and obtain a clean bulge color-magnitude diagram. We then identified for the first time a white dwarf (WD) cooling sequence in the Galactic bulge, together with a dozen candidate extreme horizontal branch stars. The comparison between theory and observations shows that a substantial fraction of the WDs (≈30%) are systematically redder than the cooling tracks for CO-core H-rich and He-rich envelope WDs. This evidence would suggest the presence of a significant number of low-mass WDs and WD-main-sequence binaries in the bulge. This hypothesis is further supported by the finding of two dwarf novae in outburst, two short-period (P ≲ 1 day) ellipsoidal variables, and a few candidate cataclysmic variables in the same field.

79 ASTRONOMY AND ASTROPHYSICS↗

Constraining the low-mass Slope of the star formation sequence at 0.5 < z < 2.5

We constrain the slope of the star formation rate (SFR; log Ψ) to stellar mass (log M {sub *}) relation down to log (M {sub *}/M {sub ☉}) = 8.4 (log (M {sub *}/M {sub ☉}) = 9.2) at z = 0.5 (z = 2.5) with a mass-complete sample of 39,106 star-forming galaxies selected from the 3D-HST photometric catalogs, using deep photometry in the CANDELS fields. For the first time, we find that the slope is dependent on stellar mass, such that it is steeper at low masses (log Ψ∝log M {sub *}) than at high masses (log Ψ∝(0.3-0.6)log M {sub *}). These steeper low-mass slopes are found for three different star formation indicators: the combination of the ultraviolet (UV) and infrared (IR), calibrated from a stacking analysis of Spitzer/MIPS 24 μm imaging; β-corrected UV SFRs; and Hα SFRs. The normalization of the sequence evolves differently in distinct mass regimes as well: for galaxies less massive than log (M {sub *}/M {sub ☉}) < 10 the specific SFR (Ψ/M {sub *}) is observed to be roughly self-similar with Ψ/M {sub *}∝(1 + z){sup 1.9}, whereas more massive galaxies show a stronger evolution with Ψ/M {sub *}∝(1 + z){sup 2.2-3.5} for log (M {sub *}/M {sub ☉}) = 10.2-11.2. The fact that we find a steep slope of the star formation sequence for the lower mass galaxies will help reconcile theoretical galaxy formation models with the observations.

79 ASTRONOMY AND ASTROPHYSICS↗

A far-infrared spectral sequence of galaxies: trends and models

We present a framework for the interpretation of the far-infrared spectra of galaxies in which we have expanded the model parameters compared with previous work by varying the ionization parameter U, column density N(H), and gas density at the cloud face n(H{sup +}) for a central starburst or active galactic nucleus (AGN). We compare these models carried out with the Cloudy spectral synthesis code to trends in line-to-total far-infrared luminosity ratios, far-infrared fine-structure line ratios, IRAS colors, and OH and H{sub 2}O column densities found in the well-studied sample of 10 nearby galaxies from the IRAS Bright Galaxy Sample with infrared luminosities greater than 10{sup 10} L {sub ☉} and IRAS 60 μm fluxes equal to or greater than that of the nearby ultraluminous infrared galaxy (ULIRG) Arp 220. We find that the spectral sequence extending from normal starburst-type emission-line-dominated spectra to ULIRG-type absorption-dominated spectra with significant absorption from excited levels can be best explained by simultaneously increasing the hydrogen column density, from as low as 10{sup 21} cm{sup –2} to as high as 10{sup 24.8} cm{sup –2} or greater, and the ionization parameter, from as low as 10{sup –4} to as high as 1. The starburst models best reproduce most of the sequence, while AGN models are somewhat better able to produce the high OH and H{sub 2}O column densities in Arp 220. Our results suggest that the molecular interstellar medium in ULIRG-like, molecular-absorption-dominated systems is located close to and at least partially obscures the source of power throughout much of the far-infrared, which must be taken into account in order to properly interpret diagnostics of both their sources of power and of feedback.

79 ASTRONOMY AND ASTROPHYSICS↗

CONSTRUCTING A ONE-SOLAR-MASS EVOLUTIONARY SEQUENCE USING ASTEROSEISMIC DATA FROM KEPLER

Asteroseismology of solar-type stars has entered a new era of large surveys with the success of the NASA Kepler mission, which is providing exquisite data on oscillations of stars across the Hertzsprung-Russell diagram. From the time-series photometry, the two seismic parameters that can be most readily extracted are the large frequency separation ({Delta}{nu}) and the frequency of maximum oscillation power ({nu}{sub max}). After the survey phase, these quantities are available for hundreds of solar-type stars. By scaling from solar values, we use these two asteroseismic observables to identify for the first time an evolutionary sequence of 1 M{sub sun} field stars, without the need for further information from stellar models. Comparison of our determinations with the few available spectroscopic results shows an excellent level of agreement. We discuss the potential of the method for differential analysis throughout the main-sequence evolution and the possibility of detecting twins of very well-known stars.

79 ASTRONOMY AND ASTROPHYSICS↗

THE STAR FORMATION MASS SEQUENCE OUT TO z = 2.5

We study the star formation rate (SFR)-stellar mass (M{sub *}) relation in a self-consistent manner from 0 < z < 2.5 with 22,816 star-forming galaxies selected from the NEWFIRM Medium-Band Survey. We find a significant nonlinear slope of the relation, SFR{proportional_to}M {sup 0.6}{sub *}, and a constant observed scatter of 0.34 dex, independent of redshift and M{sub *}. However, if we select only blue galaxies we find a linear relation SFR{proportional_to}M{sub *}, similar to previous results at z = 0 by Peng et al. This selection excludes red, dusty, star-forming galaxies with higher masses, which brings down the slope. By selecting on L{sub IR}/L{sub UV} (a proxy for dust obscuration) and the rest-frame U - V colors, we show that star-forming galaxies fall in three distinct regions of the log(SFR)-log(M{sub *}) plane: (1) actively star-forming galaxies with 'normal' dust obscuration and associated colors (54% for log (M{sub *}) > 10 at 1 < z < 1.5), (2) red star-forming galaxies with low levels of dust obscuration and low-specific SFRs (11%), and (3) dusty, blue star-forming galaxies with high-specific SFRs (7%). The remaining 28% comprises quiescent galaxies. Galaxies on the 'normal' star formation sequence show strong trends of increasing dust attenuation with stellar mass and a decreasing specific SFR, with an observed scatter of 0.25 dex. The dusty, blue galaxies reside in the upper envelope of the star formation sequence with remarkably similar spectral shapes at all masses, suggesting that the same physical process is dominating the stellar light. The red, low-dust star-forming galaxies may be in the process of shutting off and migrating to the quiescent population.

79 ASTRONOMY AND ASTROPHYSICS↗

LINEAR RELATION FOR WIND-BLOWN BUBBLE SIZES OF MAIN-SEQUENCE OB STARS IN A MOLECULAR ENVIRONMENT AND IMPLICATION FOR SUPERNOVA PROGENITORS

We find a linear relationship between the size of a massive star's main-sequence bubble in a molecular environment and the star's initial mass: R{sub b} Almost-Equal-To 1.22 M/M{sub Sun} - 9.16 pc, assuming a constant interclump pressure. Since stars in the mass range of 8 to 25-30 M{sub Sun} will end their evolution in the red supergiant phase without launching a Wolf-Rayet wind, the main-sequence wind-blown bubbles are mainly responsible for the extent of molecular gas cavities, while the effect of the photoionization is comparatively small. This linear relation can thus be used to infer the masses of the massive star progenitors of supernova remnants (SNRs) that are discovered to evolve in molecular cavities, while few other means are available for inferring the properties of SNR progenitors. We have used this method to estimate the initial masses of the progenitors of eight SNRs: Kes 69, Kes 75, Kes 78, 3C 396, 3C 397, HC 40, Vela, and RX J1713-3946.

79 ASTRONOMY AND ASTROPHYSICS↗

NEW ASPECTS OF A LID-REMOVAL MECHANISM IN THE ONSET OF AN ERUPTION SEQUENCE THAT PRODUCED A LARGE SOLAR ENERGETIC PARTICLE (SEP) EVENT

We examine a sequence of two ejective eruptions from a single active region on 2012 January 23, using magnetograms and EUV images from the Solar Dynamics Observatory's (SDO) Helioseismic and Magnetic Imager (HMI) and Atmospheric and Imaging Assembly (AIA), and EUV images from STEREO/EUVI. This sequence produced two coronal mass ejections (CMEs) and a strong solar energetic particle event (SEP); here we focus on the magnetic onset of this important space weather episode. Cheng et al. showed that the first eruption's ({sup E}ruption 1{sup )} flux rope was apparent only in ''hotter'' AIA channels, and that it removed overlying field that allowed the second eruption ({sup E}ruption 2{sup )} to begin via ideal MHD instability; here we say that Eruption 2 began via a ''lid removal'' mechanism. We show that during Eruption 1's onset, its flux rope underwent a ''tether weakening'' (TW) reconnection with field that arched from the eruption-source active region to an adjacent active region. Standard flare loops from Eruption 1 developed over Eruption 2's flux rope and enclosed filament, but these overarching new loops were unable to confine that flux rope/filament. Eruption 1's flare loops, from both TW reconnection and standard-flare-model internal reconnection, were much cooler than Eruption 2's flare loops (GOES thermal temperatures of ∼7.5 MK and 9 MK, compared to ∼14 MK). The corresponding three sequential GOES flares were, respectively, due to TW reconnection plus earlier phase Eruption 1 tether-cutting reconnection, Eruption 1 later-phase tether-cutting reconnection, and Eruption 2 tether-cutting reconnection.

79 ASTRONOMY AND ASTROPHYSICS↗

EVOLUTION OF COLD STREAMS AND THE EMERGENCE OF THE HUBBLE SEQUENCE

A new physical framework for the emergence of the Hubble sequence is outlined, based on novel analyses performed to quantify the evolution of cold streams of a large sample of galaxies from a state-of-the-art ultra-high resolution, large-scale adaptive mesh-refinement hydrodynamic simulation in a fully cosmological setting. It is found that the following three key physical variables of galactic cold inflows crossing the virial sphere substantially decrease with decreasing redshift: the number of streams N {sub 90} that make up 90% of concurrent inflow mass flux, average inflow rate per stream M-dot {sub 90} and mean (mass flux weighted) gas density in the streams n {sub gas}. Another key variable, the stream dimensionless angular momentum parameter λ, is found to instead increase with decreasing redshift. Assimilating these trends and others naturally leads to a physically coherent scenario for the emergence of the Hubble sequence, including the following expectations: (1) the predominance of a mixture of disproportionately small irregular and complex disk galaxies at z ≥ 2 when most galaxies have multiple concurrent streams, (2) the beginning of the appearance of flocculent spirals at z ∼ 1-2 when the number of concurrent streams are about 2-3, (3) the grand-design spiral galaxies appear at z ≤ 1 when galaxies with only one major cold stream significantly emerge. These expected general trends are in good accord with observations. Early-type galaxies are those that have entered a perennial state of zero cold gas stream, with their abundance increasing with decreasing redshift.

79 ASTRONOMY AND ASTROPHYSICS↗

Persistent minimal sequences of SARS-CoV-2

Abstract Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis and therapeutics are of great importance. Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein coding sequence. This protein is fundamental for binding in human ACE2 and further use as an entry receptor to invade target cells. Applying protein structural prediction, we localized this PmRAW at the surface of the Spike protein, providing a potential targeted vector for diagnostics and therapeutics. In addition, we show a new pattern of relative absent words (RAWs), characterized by the progressive increase of GC content (Guanine and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host genome distributions. New analysis shows the same property during the Ebola virus outbreak. At a computational level, we improved the alignment-free method to identify pathogen-specific signatures in balance with GC measures and removed previous size limitations. Availability and implementation https://github.com/cobilab/eagle. Supplementary information Supplementary data are available at Bioinformatics online.

Pratas, Diogo↗

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗

Identification and removal of ribosomal RNA sequences from metatranscriptomes

Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.

59 BASIC BIOLOGICAL SCIENCES↗

CDvist: A webserver for identification and visualization of conserved domains in protein sequences

Identification of domains in protein sequences allows their assigning to biological functions. Several webservers exist for identification of protein domains using similarity searches against various databases of protein domain models. However, none of them provides comprehensive domain coverage while allowing bulk querying and their visualization schemes can be improved. To address these issues, we developed CDvist (a comprehensive domain visualization tool), which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models using high-specificity tools and only then unmatched segments are subjected to more sensitive algorithms resulting in a best possible comprehensive coverage. In conclusion, bulk querying and rich visualization and download options provide improved functionality to domain architecture analysis.

59 BASIC BIOLOGICAL SCIENCES↗

The EVcouplings Python framework for coevolutionary sequence analysis

Coevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein complexes. We present the EVcouplings framework, a fully integrated open-source application and Python package for coevolutionary analysis. The framework enables generation of sequence alignments, calculation and evaluation of evolutionary couplings (ECs), and de novo prediction of structure and mutation effects. The combination of an easy to use, flexible command line interface and an underlying modular Python package makes the full power of coevolutionary analyses available to entry-level and advanced users.

59 BASIC BIOLOGICAL SCIENCES↗

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs

Abstract Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.

Environmental Sciences & Ecology↗

The first sequenced Sphaerotilus natans bacteriophage– characterization and potential to control its filamentous bacterium host

ABSTRACT Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.

Ferreira, Rute↗

Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance

Decades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field cannot be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an interspecies hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here, we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.

59 BASIC BIOLOGICAL SCIENCES↗