bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radio eclipses of exoplanets by the winds of their host stars
Authors: Kavanagh R D , Vidotto A A 
Published: February 2020

ABSTRACT
The search for exoplanetary radio emission has resulted in zero conclusive detections to date. Various explanations for this have been proposed, from the observed frequency range, telescope sensitivity, to beaming of the emission. In a recent paper, we illustrated that exoplanets can orbit through the radio photosphere of the wind of the host star, a region that is optically thick at a specific frequency, for a large fraction of their orbits. As a result, radio emission originating from the planet could be absorbed or ‘eclipsed’ by the wind of the host star. Here, we investigate how the properties of the stellar wind and orbital parameters affect the fraction of the orbit where the planet is eclipsed by the stellar wind. We show that planets orbiting stars with low-density winds are more favourable for detection in the radio. In terms of the orbital parameters, emission from transiting planets can escape the stellar wind easiest. We apply our model to the τ Boo planetary system, and show that observing the fraction of the planet’s orbit where it is eclipsed by the wind of the host star could be used to constrain the properties of the stellar wind. However, our model developed would need to be used in conjunction with a separate method to disentangle the mass-loss rate and temperature of the stellar wind.
The three causes of low-mass assembly bias
Authors: Mansfield Philip , Kravtsov Andrey V 
Published: February 2020

ABSTRACT
We present a detailed analysis of the physical processes that cause halo assembly bias – the dependence of halo clustering on proxies of halo formation time. We focus on the origin of assembly bias in the mass range corresponding to the hosts of typical galaxies and use halo concentration as our chief proxy of halo formation time. We also repeat our key analyses across a broad range of halo masses and for alternative formation time definitions. We show that splashback subhaloes are responsible for two-thirds of the assembly bias signal, but do not account for the entire effect. After splashback subhaloes have been removed, we find that the remaining assembly bias signal is due to a relatively small fraction ($\lesssim \!10{{\ \rm per\ cent}}$) of haloes in dense regions. We test a number of additional physical processes thought to contribute to assembly bias and demonstrate that the two key processes are the slowing of mass growth by large-scale tidal fields and by the high velocities of ambient matter in sheets and filaments. We also rule out several other proposed physical causes of halo assembly bias. Based on our results, we argue that there are three processes that modify the assembly bias of small-mass haloes arising from the properties of the primordial Gaussian field: large-scale tidal fields, gravitational heating due to the collapse of large-scale structures, and splashback subhaloes located outside the virial radius.
Possible detection of a new cyclotron feature in 4U 1700–37
Authors: Bala Suman , Roy Jayashree , Bhattacharya Dipankar 
Published: February 2020

ABSTRACT
We present a spectral and timing study of the high-mass X-ray binary transient source 4U 1700–37 using NuSTAR and ASTROSAT/LAXPC. The source is observed in two different flux states. A combined spectral analysis of NuSTAR’s focal plane modules A and B shows the possible hint of a cyclotron line feature at ∼16 keV. The line feature is consistently present in different continuum models with at least 3σ confidence level. We do not detect the presence of a previously reported 39 keV cyclotron line in the combined spectra. A ∼16 keV cyclotron feature would suggest that the compact object is a neutron star with a magnetic field strength ∼2.1 × 1012 G in the emission region. We also find the presence of a rare Ni Kα emission line around 7.6 keV in the NuSTAR spectrum. We searched the NuSTAR and ASTROSAT data for coherent or quasi-periodic oscillation signals but found no evidence in the frequency range 0.1 mHz to 103 Hz.
High-resolution spectroscopy of detached solar-type eclipsing binaries observed during the Kepler K2 mission
Authors: Hoyman B , Çakırlı Ö 
Published: February 2020

ABSTRACT
Solar-type stars in eclipsing binaries are proving to be a remarkable resource of knowledge for testing models of stellar evolution, as spectroscopic and photometric studies have opened up a window into their interiors. Until recently, many cases have been worked out with Kepler data. In an ongoing effort to elucidate this research, we examine five detached eclipsing binaries, selected from the Kepler catalogue. There is a well-known stellar parameter discrepancy for low-mass stars, in that the observed radii and masses are often larger and stars overluminous than predicted by theory by several per cent. In our samples, we found five double-lined binaries, with solar-type stars dominating the spectrum. The orbital and light-curve solutions were found for them, and compared with isochrones, in order to estimate absolute physical parameters and evolutionary status of the components. An important aspect of this work is that the calculated stellar radii and masses are consistent with theoretical models within the uncertainties, whereas the estimated temperatures from the disentangled spectra of the components are no different than predicted.
Gravitational potential from small-scale clustering in action space: application to Gaia Data Release 2
Authors: Yang Tianyi , Boruah Supranta S , Afshordi Niayesh 
Published: February 2020

ABSTRACT
Most measurements of mass in astronomy that use kinematics of stars or gas rely on assumptions of equilibrium that are often hard to verify. Instead, we develop a novel idea that uses the clustering in action space, as a probe of the underlying gravitational potential: the correct potential should maximize small-scale clustering in the action space. We provide a first-principle derivation of likelihood using the two-point correlation function in action space, and we test it against simulations of stellar streams. We then apply this method to the second data release of Gaia, and we use it to measure the radial force fraction fh and logarithmic slope α of the dark matter halo profile. We investigate stars within 9–11 kpc and 11.5–15 kpc from the Galactic Centre, and we find (fh, α) = (0.391 ± 0.009, 1.835 ± 0.092) and (0.351 ± 0.012, 1.687 ± 0.079), respectively. We also confirm that the set of parameters that maximize the likelihood function does correspond to the most clustering in the action space. The best-fitting circular velocity curve for the Milky Way potential is consistent with past measurements (although it is ∼5–10 per cent lower than previous methods that use masers or globular clusters). Our work provides a clear demonstration of the full statistical power that lies in the full phase space information, relieving the need for ad hoc assumptions such as virial equilibrium, circular motion or steam-finding algorithms.
Asymmetric accretion and thermal ‘mountains’ in magnetized neutron star crusts
Authors: Singh N , Haskell B , Mukherjee D , Bulik T 
Published: February 2020

ABSTRACT
Accreting neutron stars (NSs) are one of the main targets for continuous gravitational wave searches, as asymmetric accretion may lead to quadrupolar deformations, or ‘mountains’, on the crust of the star, which source gravitational wave (GW) emission at twice the rotation frequency. The GW torque may also impact on the spin evolution of the star, possibly dictating the currently observed spin periods of NSs in low-mass X-ray binaries and leading to the increased spin-down rate observed during accretion in PSR J1023+0038. Previous studies have shown that deformed reaction layers in the crust of the NS lead to thermal and compositional gradients that can lead to GW emission. However, there are no realistic constraints on the level of asymmetry that is expected. In this paper, we consider a natural source of asymmetry, namely the magnetic field, and calculate the density and pressure perturbations that are expected in the crust of accreting NSs. In general, we find that only the outermost reaction layers of the NS are strongly perturbed. The mass quadrupole that we estimate is generally small and cannot explain the increase of spin-down rate of PSR J1023+0038. However, if strong shallow heating sources are present at low densities in the crust, as cooling observations suggest, these layers will be strongly perturbed and the resulting quadrupole could explain the observed spin-down of PSR J1023+0038, and lead to observable GW signals from systems with higher accretion rates.
Characterizing the structure of halo merger trees using a single parameter: the tree entropy
Authors: Obreschkow Danail , Elahi Pascal J , Lagos Claudia del P , Poulton Rhys J J , Ludlow Aaron D 
Published: February 2020

ABSTRACT
Linking the properties of galaxies to the assembly history of their dark matter haloes is a central aim of galaxy evolution theory. This paper introduces a dimensionless parameter s ∈ [0, 1], the ‘tree entropy’, to parametrize the geometry of a halo’s entire mass assembly hierarchy, building on a generalization of Shannon’s information entropy. By construction, the minimum entropy (s = 0) corresponds to smoothly assembled haloes without any mergers. In contrast, the highest entropy (s = 1) represents haloes grown purely by equal-mass binary mergers. Using simulated merger trees extracted from the cosmological N-body simulation SURFS, we compute the natural distribution of s, a skewed bell curve peaking near s = 0.4. This distribution exhibits weak dependences on halo mass M and redshift z, which can be reduced to a single dependence on the relative peak height δc/σ(M, z) in the matter perturbation field. By exploring the correlations between s and global galaxy properties generated by the SHARK semi-analytic model, we find that s contains a significant amount of information on the morphology of galaxies – in fact more information than the spin, concentration, and assembly time of the halo. Therefore, the tree entropy provides an information-rich link between galaxies and their dark matter haloes.
Relativistic SZ temperature scaling relations of groups and clusters derived from the BAHAMAS and MACSIS simulations
Authors: Lee Elizabeth , Chluba Jens , Kay Scott T , Barnes David J 
Published: February 2020

ABSTRACT
The Sunyaev–Zeldovich (SZ) effect has long been recognized as a powerful cosmological probe. Using the BAHAMAS and MACSIS simulations to obtain ${\gt }10\, 000$ simulated galaxy groups and clusters, we compute three temperature measures and quantify the differences between them. The first measure is related to the X-ray emission of the cluster, while the second describes the non-relativistic thermal SZ (tSZ) effect. The third measure determines the lowest order relativistic correction to the tSZ signal, which is seeing increased observational relevance. Our procedure allows us to accurately model the relativistic SZ (rSZ) contribution and we show that a ${\gtrsim}10\!-\!40{{\ \rm per\ cent}}$ underestimation of this rSZ cluster temperature is expected when applying standard X-ray relations. The correction also exhibits significant mass and redshift evolution, as we demonstrate here. We present the mass dependence of each temperature measure alongside their profiles and a short analysis of the temperature dispersion as derived from the aforementioned simulations. We also discuss a new relation connecting the temperature and Compton-y parameter, which can be directly used for rSZ modelling. Simple fits to the obtained scaling relations and profiles are provided. These should be useful for future studies of the rSZ effect and its relevance to cluster cosmology.
Profiling C4N radicals of astrophysical interest
Authors: Bâldea Ioan 
Published: February 2020

ABSTRACT
Based on a theoretical study of neutral, anion, and cation $\text{C}_{4}\text{N}$ chains, we suggest that this molecular species can still be observed in space. We analyse the dependence on n of the enthalpies of formation across the $\text{C}_{{{ n}}}\text{N}$ family and present possible chemical pathways of $\text{C}_{4}\text{N}$ production, which are not only exoenergetic but also barrierless. To further assist astronomical observation, we report estimates obtained at the CCSD(T) level of theory for astrophysically and astrochemically relevant properties. These include structural and chemical data, dipole moments, vibrational frequencies, rotational and centrifugal distortion constants as well as electron affinity, ionization potential, and related chemical reactivity indices. Our results indicate that anion chains can be easily detected in space than neutral chains; $\text{C}_{4}\text{N}^{-}$ possesses a smaller enthalpy of formation and a substantially larger dipole moment than $\text{C}_{4}\text{N}^{\text{0}}$.
Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
Authors: Wisotsky Sadie R , Kosakovsky Pond Sergei L , Shank Stephen D , Muse Spencer V 
Published: February 2020

AbstractMost molecular evolutionary studies of natural selection maintain the decades-old assumption that synonymous substitution rate variation (SRV) across sites within genes occurs at levels that are either nonexistent or negligible. However, numerous studies challenge this assumption from a biological perspective and show that SRV is comparable in magnitude to that of nonsynonymous substitution rate variation. We evaluated the impact of this assumption on methods for inferring selection at the molecular level by incorporating SRV into an existing method (BUSTED) for detecting signatures of episodic diversifying selection in genes. Using simulated data we found that failing to account for even moderate levels of SRV in selection testing is likely to produce intolerably high false positive rates. To evaluate the effect of the SRV assumption on actual inferences we compared results of tests with and without the assumption in an empirical analysis of over 13,000 Euteleostomi (bony vertebrate) gene alignments from the Selectome database. This exercise reveals that close to 50% of positive results (i.e., evidence for selection) in empirical analyses disappear when SRV is modeled as part of the statistical analysis and are thus candidates for being false positives. The results from this work add to a growing literature establishing that tests of selection are much more sensitive to certain model assumptions than previously believed.
Pervasive Suicidal Integrases in Deep-Sea Archaea
Authors: Badel Catherine , Da Cunha Violette , Forterre Patrick , Oberto Jacques 
Published: February 2020

Abstract
Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes.
Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo
Authors: Connelly John C , Cholewa-Waclaw Justyna , Webb Shaun , Steccanella Verdiana , Waclaw Bartlomiej , Bird Adrian 
Published: February 2020

Abstract
MeCP2 is a nuclear protein that binds to sites of cytosine methylation in the genome. While most evidence confirms this epigenetic mark as the primary determinant of DNA binding, MeCP2 is also reported to have an affinity for non-methylated DNA sequences. Here we investigated the molecular basis and in vivo significance of its reported affinity for non-methylated GT-rich sequences. We confirmed this interaction with isolated domains of MeCP2 in vitro and defined a minimal target DNA sequence. Binding depends on pyrimidine 5′ methyl groups provided by thymine and requires adjacent guanines and a correctly orientated A/T-rich flanking sequence. Unexpectedly, full-length MeCP2 protein failed to bind GT-rich sequences in vitro. To test for MeCP2 binding to these motifs in vivo, we analysed human neuronal cells using ChIP-seq and ATAC-seq technologies. While both methods robustly detected DNA methylation-dependent binding of MeCP2 to mCG and mCAC, neither showed evidence of MeCP2 binding to GT-rich motifs. The data suggest that GT binding is an in vitro phenomenon without in vivo relevance. Our findings argue that MeCP2 does not read unadorned DNA sequence and therefore support the notion that its primary role is to interpret epigenetic modifications of DNA.
Deletion of Endonuclease V suppresses chemically induced hepatocellular carcinoma
Authors: Kong Xiang Yi , Vik Erik Sebastian , Nawaz Meh Sameen , Berges Natalia , Dahl Tuva Børresdatter , Vågbø Cathrine , Suganthan Rajikala , Segers Filip , Holm Sverre , Quiles-Jiménez Ana , Gregersen Ida , Fladeby Cathrine , Aukrust Pål , Bjørås Magnar , Klungland Arne , Halvorsen Bente , Alseth Ingrun 
Published: February 2020

AbstractEndonuclease V (EndoV) is a conserved inosine-specific ribonuclease with unknown biological function. Here, we present the first mouse model lacking EndoV, which is viable without visible abnormalities. We show that endogenous murine EndoV cleaves inosine-containing RNA in vitro, nevertheless a series of experiments fails to link an in vivo function to processing of such transcripts. As inosine levels and adenosine-to-inosine editing often are dysregulated in hepatocellular carcinoma (HCC), we chemically induced HCC in mice. All mice developed liver cancer, however, EndoV−/− tumors were significantly fewer and smaller than wild type tumors. Opposed to human HCC, adenosine deaminase mRNA expression and site-specific editing were unaltered in our model. Loss of EndoV did not affect editing levels in liver tumors, however mRNA expression of a selection of cancer related genes were reduced. Inosines are also found in certain tRNAs and tRNAs are cleaved during stress to produce signaling entities. tRNA fragmentation was dysregulated in EndoV−/− livers and apparently, inosine-independent. We speculate that the inosine-ribonuclease activity of EndoV is disabled in vivo, but RNA binding allowed to promote stabilization of transcripts or recruitment of proteins to fine-tune gene expression. The EndoV−/− tumor suppressive phenotype calls for related studies in human HCC.
Decreased kidney function and agricultural work: a cross-sectional study in middle-aged adults from Tierra Blanca, Mexico
Authors: Aguilar-Ramirez Diego , Raña-Custodio Alejandro , Villa Antonio , Rubilar Ximena , Olvera Nadia , Escobar Alejandro , Johnson Richard J , Sanchez-Lozada Laura , Obrador Gregorio T , Madero Magdalena 
Published: February 2020

Abstract

Background
We aimed to determine the prevalence of decreased kidney function in a potential chronic kidney disease (KD) of unknown aetiology hotspot in Mexico, assess its distribution across occupations and examine the associated risk factors.

Methods
A cross-sectional study collected sociodemographic, occupational, medical and biometric data from 616 men and women aged 20–60 years who were residents of three communities within the Tierra Blanca region in Mexico. Kidney function was assessed by standardized serum creatinine and estimated glomerular filtration rate (eGFR) and semi-quantitative albumin-to-creatinine ratio (ACR). To examine the distribution of decreased kidney function within the population, age- and sex-adjusted prevalence of low eGFR (≤60 mL/min/1.73 m2) was estimated for all participants and across occupations. Multivariable logistic regression was used to assess the association of occupation with having low eGFR.

Results
Of the 579 participants analysed (37 excluded due to missing data), the age- and sex-adjusted prevalence of low eGFR was 3.5%. Agriculture was the occupation associated with the highest adjusted prevalence of low eGFR (8.8%), with 1 in every 11 agricultural workers having low eGFR. Working in agriculture was independently associated with more than a 5-fold risk of having low eGFR [odds ratio 5.2 (95% confidence interval 1.1–24.3), P = 0.032], after adjustment for age, sex, diabetes, hypertension, body mass index, ACR and family history of KD. Additionally, a quarter of the population (25%) had either low eGFR or an ACR &gt;30 mg/g, mostly due to albuminuria.

Conclusions
Our work suggests that there is a high prevalence of decreased kidney function in Tierra Blanca, particularly amongst agricultural workers.
MKRN3 regulates the epigenetic switch of mammalian puberty via ubiquitination of MBD3
Authors: Li Chuanyin , Lu Wenli , Yang Liguang , Li Zhengwei , Zhou Xiaoyi , Guo Rong , Wang Junqi , Wu Zhebao , Dong Zhiya , Ning Guang , Shi Yujiang , Gu Yinmin , Chen Peng , Hao Zijian , Han Tianting , Yang Meiqiang , Wang Wei , Huang Xuehui , Li Yixue , Gao Shan , Hu Ronggui 
Published: February 2020

AbstractCentral precocious puberty (CPP) refers to a human syndrome of early puberty initiation with characteristic increase in hypothalamic production and release of gonadotropin-releasing hormone (GnRH). Previously, loss-of-function mutations in human MKRN3, encoding a putative E3 ubiquitin ligase, were found to contribute to about 30% of cases of familial CPP. MKRN3 was thereby suggested to serve as a ‘brake’ of mammalian puberty onset, but the underlying mechanisms remain as yet unknown. Here, we report that genetic ablation of Mkrn3 did accelerate mouse puberty onset with increased production of hypothalamic GnRH1. MKRN3 interacts with and ubiquitinates MBD3, which epigenetically silences GNRH1 through disrupting the MBD3 binding to the GNRH1 promoter and recruitment of DNA demethylase TET2. Our findings have thus delineated a molecular mechanism through which the MKRN3–MBD3 axis controls the epigenetic switch in the onset of mammalian puberty.