bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal instability in the CGM of L⋆ galaxies: testing ‘precipitation’ models with the FIRE simulations
Authors: Esmerian Clarke J , Kravtsov Andrey V , Hafen Zachary , Faucher-Giguère Claude-André , Quataert Eliot , Stern Jonathan , Kereš Dušan , Wetzel Andrew 
Published: May 2021

ABSTRACT
We examine the thermodynamic state and cooling of the low-z circumgalactic medium (CGM) in five FIRE-2 galaxy formation simulations of Milky Way-mass galaxies. We find that the CGM in these simulations is generally multiphase and dynamic, with a wide spectrum of largely non-linear density perturbations sourced by the accretion of gas from the intergalactic medium (IGM) and outflows from both the central and satellite galaxies. We investigate the origin of the multiphase structure of the CGM with a particle-tracking analysis and find that most of the low-entropy gas has cooled from the hot halo as a result of thermal instability triggered by these perturbations. The ratio of cooling to free-fall time-scales tcool/tff in the hot component of the CGM spans a wide range of ∼1−100 at a given radius but exhibits approximately constant median values of ∼5−20 at all radii 0.1Rvir &lt; r &lt; Rvir. These are similar to the ≈10−20 value typically adopted as the thermal instability threshold in ‘precipitation’ models of the ICM. Consequently, a one-dimensional model based on the assumption of a constant tcool/tff and hydrostatic equilibrium approximately reproduces the number density and entropy profiles of each simulation but only if it assumes the metallicity profile and temperature boundary condition taken directly from the simulation. We explicitly show that the tcool/tff value of a gas parcel in the hot component of the CGM does not predict its probability of subsequently accreting on to the central galaxy. This suggests that the value of tcool/tff is a poor predictor of thermal stability in gaseous haloes in which large-amplitude density perturbations are prevalent.
The H i and stellar mass bivariate distribution of centrals and satellites for all, late-, and early-type local galaxies
Authors: Calette A R , Avila-Reese Vladimir , Rodríguez-Puebla Aldo , Lagos Claudia del P , Catinella Barbara 
Published: May 2021

ABSTRACT
We characterize the conditional distributions of the H i gas-to-stellar mass ratio, $\mbox{$R_{\rm H\,\rm{i}}$}\equiv \mbox{$M_{\rm H\,\rm{i}}$}/\mbox{$M_{\ast }$}$, given the stellar mass, M*, of local galaxies from M* ∼ 107–1012 M⊙ separated into centrals and satellites as well as into late- and early-type galaxies (LTGs and ETGs, respectively). To do so, we use (1) the homogeneous ‘eXtended GALEX Arecibo SDSS Survey’, xGASS (Catinella et al. 2018), by re-estimating their upper limits and taking into account them in our statistical analysis; and (2) the results from a large compilation of H i data reported in Calette et al. (2018). We use the $R_{\rm H\,\rm{i}}$ conditional distributions combined with the Galaxy Stellar Mass Function to infer the bivariate $M_{\rm H\,\rm{i}}$ and M* distribution of all galaxies as well of the late/early-type and central/satellite subsamples and their combinations. Satellites are on average less H i gas-rich than centrals at low and intermediate masses, with differences being larger for ETGs than LTGs; at M* &gt; 3−5 × 1010 M⊙ the differences are negligible. The differences in the H i gas content are much larger between LTGs and ETGs than between centrals and satellites. Our empirical H i Mass Function is strongly dominated by central galaxies at all masses. The empirically constrained bivariate $M_{\rm H\,\rm{i}}$ and M* distributions presented here can be used to compare and constrain theoretical predictions as well as to generate galaxy mock catalogues.
Black hole magnetic fields and their imprint on circular polarization images
Authors: Ricarte Angelo , Qiu Richard , Narayan Ramesh 
Published: May 2021

ABSTRACT
The circular polarization of black hole accretion flows can encode properties of the underlying magnetic field structure. Using general relativistic magnetohydrodynamic (GRMHD) simulations, we study the imprint of magnetic field geometry on circular polarization images potentially observable by the Event Horizon Telescope (EHT). We decompose images into the different mechanisms that generate circular polarization in these models that are sensitive to both the line-of-sight direction and twist of the magnetic field. In these models, a stable sign of the circular polarization over time, as observed for several sources, can be attributed to a stability of these properties. We illustrate how different aspects of a generic helical magnetic field geometry become imprinted on a circular polarization image. We also identify novel effects of light bending that affect the circular polarization image on event horizon scales. One consequence is the sign flipping of successive photon rings in face-on systems, which if observable and uncorrupted by Faraday rotation, can directly encode the handedness of the approaching magnetic field.
A scaling relation for the molecular cloud lifetime in Milky Way-like galaxies
Authors: Jeffreson Sarah M R , Keller Benjamin W , Winter Andrew J , Chevance Mélanie , Kruijssen J M Diederik , Krumholz Mark R , Fujimoto Yusuke 
Published: May 2021

ABSTRACTWe study the time evolution of molecular clouds across three Milky Way-like isolated disc galaxy simulations at a temporal resolution of 1 Myr and at a range of spatial resolutions spanning two orders of magnitude in spatial scale from ∼10 pc up to ∼1 kpc. The cloud evolution networks generated at the highest spatial resolution contain a cumulative total of ∼80 000 separate molecular clouds in different galactic–dynamical environments. We find that clouds undergo mergers at a rate proportional to the crossing time between their centroids, but that their physical properties are largely insensitive to these interactions. Below the gas–disc scale height, the cloud lifetime τlife obeys a scaling relation of the form τlife∝ℓ−0.3 with the cloud size ℓ, consistent with over-densities that collapse, form stars, and are dispersed by stellar feedback. Above the disc scale height, these self-gravitating regions are no longer resolved, so the scaling relation flattens to a constant value of ∼13 Myr, consistent with the turbulent crossing time of the gas disc, as observed in nearby disc galaxies.
The interplay between ambipolar diffusion and Hall effect on magnetic field decoupling and protostellar disc formation
Authors: Zhao Bo , Caselli Paola , Li Zhi-Yun , Krasnopolsky Ruben , Shang Hsien , Lam Ka Ho 
Published: May 2021

ABSTRACT
Non-ideal magnetohydrodynamic (MHD) effects have been shown recently as a robust mechanism of averting the magnetic braking ‘catastrophe’ and promoting protostellar disc formation. However, the magnetic diffusivities that determine the efficiency of non-ideal MHD effects are highly sensitive to microphysics. We carry out non-ideal MHD simulations to explore the role of microphysics on disc formation and the interplay between ambipolar diffusion (AD) and Hall effect during the protostellar collapse. We find that removing the smallest grain population (≲10 nm) from the standard MRN size distribution is sufficient for enabling disc formation. Further varying the grain sizes can result in either a Hall-dominated or an AD-dominated collapse; both form discs of tens of au in size regardless of the magnetic field polarity. The direction of disc rotation is bimodal in the Hall-dominated collapse but unimodal in the AD-dominated collapse. We also find that AD and Hall effect can operate either with or against each other in both radial and azimuthal directions, yet the combined effect of AD and Hall is to move the magnetic field radially outward relative to the infalling envelope matter. In addition, microphysics and magnetic field polarity can leave profound imprints both on observables (e.g. outflow morphology, disc to stellar mass ratio) and on the magnetic field characteristics of protoplanetary discs. Including Hall effect relaxes the requirements on microphysics for disc formation, so that prestellar cores with cosmic ray ionization rate of ≲2–3 × 10−16 s−1 can still form small discs of ≲10 au radius. We conclude that disc formation should be relatively common for typical prestellar core conditions, and that microphysics in the protostellar envelope is essential to not only disc formation, but also protoplanetary disc evolution.
Kepler’s Goat Herd: An exact solution to Kepler’s equation for elliptical orbits
Authors: Philcox Oliver H E , Goodman Jeremy , Slepian Zachary 
Published: May 2021

ABSTRACT
A fundamental relation in celestial mechanics is Kepler’s equation, linking an orbit’s mean anomaly to its eccentric anomaly and eccentricity. Being transcendental, the equation cannot be directly solved for eccentric anomaly by conventional treatments; much work has been devoted to approximate methods. Here, we give an explicit integral solution, utilizing methods recently applied to the ‘geometric goat problem’ and to the dynamics of spherical collapse. The solution is given as a ratio of contour integrals; these can be efficiently computed via numerical integration for arbitrary eccentricities. The method is found to be highly accurate in practice, with our C++ implementation outperforming conventional root-finding and series approaches by a factor greater than two.
Mammals with Small Populations Do Not Exhibit Larger Genomes
Authors: Roddy Adam B , Alvarez-Ponce David , Roy Scott W 
Published: May 2021

AbstractGenome size in cellular organisms varies by six orders of magnitude, yet the cause of this large variation remains unexplained. The influential Drift-Barrier Hypothesis proposes that large genomes tend to evolve in small populations due to inefficient selection. However, to our knowledge no explicit tests of the Drift-Barrier Hypothesis have been reported. We performed the first explicit test, by comparing estimated census population size and genome size in mammals while incorporating potential covariates and the effect of shared evolutionary history. We found a lack of correlation between census population size and genome size among 199 species of mammals. These results suggest that population size is not the predominant factor influencing genome size and that the Drift-Barrier Hypothesis should be considered provisional.
Population Structure Limits Parallel Evolution in Sticklebacks
Authors: Fang Bohao , Kemppainen Petri , Momigliano Paolo , Merilä Juha 
Published: May 2021

AbstractPopulation genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.
Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex
Authors: Chen Ying , Khazina Elena , Izaurralde Elisa , Weichenrieder Oliver 
Published: May 2021

Abstract
The CCR4 and CAF1 deadenylases physically interact to form the CCR4-CAF1 complex and function as the catalytic core of the larger CCR4-NOT complex. Together, they are responsible for the eventual removal of the 3′-poly(A) tail from essentially all cellular mRNAs and consequently play a central role in the posttranscriptional regulation of gene expression. The individual properties of CCR4 and CAF1, however, and their respective contributions in different organisms and cellular environments are incompletely understood. Here, we determined the crystal structure of a human CCR4-CAF1 complex and characterized its enzymatic and substrate recognition properties. The structure reveals specific molecular details affecting RNA binding and hydrolysis, and confirms the CCR4 nuclease domain to be tethered flexibly with a considerable distance between both enzyme active sites. CCR4 and CAF1 sense nucleotide identity on both sides of the 3′-terminal phosphate, efficiently differentiating between single and consecutive non-A residues. In comparison to CCR4, CAF1 emerges as a surprisingly tunable enzyme, highly sensitive to pH, magnesium and zinc ions, and possibly allowing distinct reaction geometries. Our results support a picture of CAF1 as a primordial deadenylase, which gets assisted by CCR4 for better efficiency and by the assembled NOT proteins for selective mRNA targeting and regulation.
CPA: a web-based platform for consensus pathway analysis and interactive visualization
Authors: Nguyen Hung , Tran Duc , Galazka Jonathan M , Costes Sylvain V , Beheshti Afshin , Petereit Juli , Draghici Sorin , Nguyen Tin 
Published: May 2021

AbstractIn molecular biology and genetics, there is a large gap between the ease of data collection and our ability to extract knowledge from these data. Contributing to this gap is the fact that living organisms are complex systems whose emerging phenotypes are the results of multiple complex interactions taking place on various pathways. This demands powerful yet user-friendly pathway analysis tools to translate the now abundant high-throughput data into a better understanding of the underlying biological phenomena. Here we introduce Consensus Pathway Analysis (CPA), a web-based platform that allows researchers to (i) perform pathway analysis using eight established methods (GSEA, GSA, FGSEA, PADOG, Impact Analysis, ORA/Webgestalt, KS-test, Wilcox-test), (ii) perform meta-analysis of multiple datasets, (iii) combine methods and datasets to accurately identify the impacted pathways underlying the studied condition and (iv) interactively explore impacted pathways, and browse relationships between pathways and genes. The platform supports three types of input: (i) a list of differentially expressed genes, (ii) genes and fold changes and (iii) an expression matrix. It also allows users to import data from NCBI GEO. The CPA platform currently supports the analysis of multiple organisms using KEGG and Gene Ontology, and it is freely available at http://cpa.tinnguyen-lab.com.
b2bTools: online predictions for protein biophysical features and their conservation
Authors: Kagami Luciano Porto , Orlando Gabriele , Raimondi Daniele , Ancien Francois , Dixit Bhawna , Gavaldá-García Jose , Ramasamy Pathmanaban , Roca-Martínez Joel , Tzavella Konstantina , Vranken Wim 
Published: May 2021

AbstractWe provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata β-sheet aggregation. These predictions, several of which were previously not available online, capture ‘emergent’ properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.
Oocyte meiosis-coupled poly(A) polymerase α phosphorylation and activation trigger maternal mRNA translation in mice
Authors: Jiang Jun-Chao , Zhang Hua , Cao Lan-Rui , Dai Xing-Xing , Zhao Long-Wen , Liu Hong-Bin , Fan Heng-Yu 
Published: May 2021

AbstractMammalian oocyte maturation is driven by strictly regulated polyadenylation and translational activation of maternal mRNA stored in the cytoplasm. However, the poly(A) polymerase (PAP) that directly mediates cytoplasmic polyadenylation in mammalian oocytes has not been determined. In this study, we identified PAPα as the elusive enzyme that catalyzes cytoplasmic mRNA polyadenylation implicated in mouse oocyte maturation. PAPα was mainly localized in the germinal vesicle (GV) of fully grown oocytes but was distributed to the ooplasm after GV breakdown. Inhibition of PAPα activity impaired cytoplasmic polyadenylation and translation of maternal transcripts, thus blocking meiotic cell cycle progression. Once an oocyte resumes meiosis, activated CDK1 and ERK1/2 cooperatively mediate the phosphorylation of three serine residues of PAPα, 537, 545 and 558, thereby leading to increased activity. This mechanism is responsible for translational activation of transcripts lacking cytoplasmic polyadenylation elements in their 3′-untranslated region (3′-UTR). In turn, activated PAPα stimulated polyadenylation and translation of the mRNA encoding its own (Papola) through a positive feedback circuit. ERK1/2 promoted Papola mRNA translation in a 3′-UTR polyadenylation signal-dependent manner. Through these mechanisms, PAPα activity and levels were significantly amplified, improving the levels of global mRNA polyadenylation and translation, thus, benefiting meiotic cell cycle progression.
ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs
Authors: Zhang Yuwei , Bu Dechao , Huo Peipei , Wang Zhihao , Rong Hao , Li Yanguo , Liu Jingjia , Ye Meng , Wu Yang , Jiang Zheng , Liao Qi , Zhao Yi 
Published: May 2021

Abstract
Increasing evidence proves the essential regulatory roles of non-coding RNAs (ncRNAs) in biological processes. However, characterizing the specific functions of ncRNAs remains a challenging task, owing to the intensive consumption of the experimental approaches. Here, we present an online platform ncFANs v2.0 that is a significantly enhanced version of our previous ncFANs to provide multiple computational methods for ncRNA functional annotation. Specifically, ncFANs v2.0 was updated to embed three functional modules, including ncFANs-NET, ncFANs-eLnc and ncFANs-CHIP. ncFANs-NET is a new module designed for data-free functional annotation based on four kinds of pre-built networks, including the co-expression network, co-methylation network, long non-coding RNA (lncRNA)-centric regulatory network and random forest-based network. ncFANs-eLnc enables the one-stop identification of enhancer-derived lncRNAs from the de novo assembled transcriptome based on the user-defined or our pre-annotated enhancers. Moreover, ncFANs-CHIP inherits the original functions for microarray data-based functional annotation and supports more chip types. We believe that our ncFANs v2.0 carries sufficient convenience and practicability for biological researchers and facilitates unraveling the regulatory mechanisms of ncRNAs. The ncFANs v2.0 server is freely available at http://bioinfo.org/ncfans or http://ncfans.gene.ac.
Light signals generated by vegetation shade facilitate acclimation to low light in shade-avoider plants
Authors: Morelli Luca , Paulišić Sandi , Qin Wenting , Iglesias-Sanchez Ariadna , Roig-Villanova Irma , Florez-Sarasa Igor , Rodriguez-Concepcion Manuel , Martinez-Garcia Jaime F 
Published: May 2021

Abstract
When growing in search for light, plants can experience continuous or occasional shading by other plants. Plant proximity causes a decrease in the ratio of R to far-red light (low R:FR) due to the preferential absorbance of R light and reflection of FR light by photosynthetic tissues of neighboring plants. This signal is often perceived before actual shading causes a reduction in photosynthetically active radiation (low PAR). Here, we investigated how several Brassicaceae species from different habitats respond to low R:FR and low PAR in terms of elongation, photosynthesis, and photoacclimation. Shade-tolerant plants such as hairy bittercress (Cardamine hirsuta) displayed a good adaptation to low PAR but a poor or null response to low R:FR exposure. In contrast, shade-avoider species, such as Arabidopsis (Arabidopsis thaliana), showed a weak photosynthetic performance under low PAR but they strongly elongated when exposed to low R:FR. These responses could be genetically uncoupled. Most interestingly, exposure to low R:FR of shade-avoider (but not shade-tolerant) plants improved their photoacclimation to low PAR by triggering changes in photosynthesis-related gene expression, pigment accumulation, and chloroplast ultrastructure. These results indicate that low R:FR signaling unleashes molecular, metabolic, and developmental responses that allow shade-avoider plants (including most crops) to adjust their photosynthetic capacity in anticipation of eventual shading by nearby plants.
Skilled Labor Risk and Corporate Policies
Authors: Qiu Yue , Wang Tracy Yue 
Published: May 2021

Abstract
We measure U.S. listed companies’ skilled labor risk—that is, the potential failure in attracting and retaining skilled labor, by the intensity of discussions on this issue in 10-K filings. We show that this measure effectively captures firm risk due to the mobility of skilled labor. We find that an increase from the 25th to the 75th percentile in the skilled labor risk would increase the skilled labor wage by 22% (or $15,593) and also lead to higher equity-based incentive pay. The skilled labor risk also interacts with other corporate policies such as financial leverage, cash holdings, and M&As. (JEL G30, G32, G34, H20, J20, J24, J40, J41)
Received September 28, 2020; editorial decision March 12, 2021 by Editor Andrew Ellul.