bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of recombining plasma inside the extended gamma-ray supernova remnant HB9
Authors: Sezer A , Ergin T , Yamazaki R , Sano H , Fukui Y 
Published: September 2019

ABSTRACT
We present the results from the Suzaku X-ray Imaging Spectrometer observation of the mixed-morphology supernova remnant (SNR) HB9 (G160.9+2.6). We discovered recombining plasma (RP) in the western Suzaku observation region and the spectra here are well described by a model having collisional ionization equilibrium (CIE) and RP components. On the other hand, the X-ray spectra from the eastern Suzaku observation region are best reproduced by the CIE and non-equilibrium ionization model. We discuss possible scenarios to explain the origin of the RP emission based on the observational properties and concluded that the rarefaction scenario is a possible explanation for the existence of RP. In addition, the gamma-ray emission morphology and spectrum within the energy range of 0.2–300 GeV are investigated using 10 yr of data from the Fermi Large Area Telescope (LAT). The gamma-ray morphology of HB9 is best described by the spatial template of radio continuum emission. The spectrum is well fit to a log-parabola function and its detection significance was found to be 25σ. Moreover, a new gamma-ray point source located just outside the south-east region of the SNR’s shell was detected with a significance of 6σ. We also investigated the archival H i and CO data and detected an expanding shell structure in the velocity range of $-10.5$ and $+1.8$ km s−1 that is coinciding with a region of gamma-ray enhancement at the southern rim of the HB9 shell.
The amplitude of the kilohertz quasi-periodic oscillations in 4U 1636–53 in the frequency-energy space
Authors: Ribeiro Evandro M , Méndez Mariano , de Avellar Marcio G B , Zhang Guobao , Karpouzas Konstantinos 
Published: September 2019

ABSTRACT
We present for the neutron-star low-mass X-ray binary 4U 1636–53, and for the first time for any source of kilohertz quasi-periodic oscillations (kHz QPOs), the two-dimensional behaviour of the fractional rms amplitude of the kHz QPOs in the parameter space defined by QPO frequency and photon energy. We find that the rms amplitude of the lower kHz QPO increases with energy up to $\sim \!\!12$ keV and then decreases at higher energies, while the rms amplitude of the upper kHz QPO either continues increasing or levels off at high energies. The rms amplitude of the lower kHz QPO increases and then decreases with frequency, peaking at $\sim \!\!760$ Hz, while the amplitude of the upper kHz QPO decreases with frequency, with a local maximum at around $\sim \!\!770$ Hz, and is consistent with becoming zero at the same QPO frequency, $\sim \!\!1400$ Hz, in all energy bands, thus constraining the neutron-star mass at $M_{NS} \le 1.6 \, \mathrm{M}_{\odot }$, under the assumption that this QPO reflects the Keplerian frequency at the inner edge of the accretion disc. We show that the slope of the rms energy spectrum is connected to the changing properties of the kHz QPOs in different energy bands as its frequencies change. Finally, we discuss a possible mechanism responsible for the radiative properties of the kHz QPOs and, based on a model in which the QPO arises from oscillations in a Comptonizing cloud of hot electrons, we show that the properties of the kHz QPOs can constrain the thermodynamic properties of the inner accretion flow.
Orphaned exomoons: Tidal detachment and evaporation following an exoplanet–star collision
Authors: Martinez Miguel A S , Stone Nicholas C , Metzger Brian D 
Published: September 2019

ABSTRACT
Gravitational perturbations on an exoplanet from a massive outer body, such as the Kozai–Lidov mechanism, can pump the exoplanet’s eccentricity up to values that will destroy it via a collision or strong interaction with its parent star. During the final stages of this process, any exomoons orbiting the exoplanet will be detached by the star’s tidal force and placed into orbit around the star. Using ensembles of three- and four-body simulations, we demonstrate that while most of these detached bodies either collide with their star or are ejected from the system, a substantial fraction, $\sim 10{{\ \rm per\ cent}}$, of such ‘orphaned’ exomoons (with initial properties similar to those of the Galilean satellites in our own Solar system) will outlive their parent exoplanet. The detached exomoons generally orbit inside the ice line, so that strong radiative heating will evaporate any volatile-rich layers, producing a strong outgassing of gas and dust, analogous to a comet’s perihelion passage. Small dust grains ejected from the exomoon may help generate an opaque cloud surrounding the orbiting body but are quickly removed by radiation blow-out. By contrast, larger solid particles inherit the orbital properties of the parent exomoon, feeding an eccentric disc of solids that drains more gradually on to the star via Poynting–Robertson drag, and which could result in longer time-scale dimming of the star. For characteristic exomoon evaporation times of ∼105–106 yr, attenuation of the stellar light arising from one or more out-gassing exomoons provides a promising explanation for both the dipping and secular dimming behaviour observed from KIC 8462852  (Boyajian’s Star).
Collision excitation of sodium cyanide molecule by helium at low temperature
Authors: Gharbi C , Ajili Y , Ben Abdallah D , Mogren Al Mogren M , Hochlaf M 
Published: September 2019

ABSTRACT
Cyanides/isocyanides are the most common metal-containing molecules in interstellar medium. In this work, quantum scattering calculations were carried out to determine the rotational (de-)excitation cross-sections of the most stable form of the sodium cyanide molecule, t-NaCN, in collision with the helium atom. Rate coefficients for the first 43 rotational levels (up to ${j_{{K_a}{K_c}}}$ = 63,3) of NaCN were determined for kinetic temperatures ranging from 1 to 30 K. Prior to that, we constructed a new three-dimensional potential energy surface (3D-PES) for the t-NaCN–He interacting system. These electronic structure computations are done at the CCSD(T)-F12/aug-cc-pVTZ level of theory. Computations show the dominance of Δj = ΔKc = −1 transitions, which is related to the dissymmetric shape of the t-NaCN–He 3D-PES. The NaCN–He rate coefficients are of the same order of magnitude (∼10−11 cm3.s−1) as those of other metal CN-containing molecules such as MgCN and AlCN in collision with He. This work is a contribution for understanding and modelling the abundances and chemistry of nitriles in astrophysical media.
Diffuse ionized gas and its effects on nebular metallicity estimates of star-forming galaxies
Authors: Vale Asari N , Couto G S , Cid Fernandes R , Stasińska G , de Amorim A L , Ruschel-Dutra D , Werle A , Florido T Z 
Published: September 2019

ABSTRACT
We investigate the impact of the diffuse ionized gas (DIG) on abundance determinations in star-forming (SF) galaxies. The DIG is characterized using the H α equivalent width (WH α). From a set of 1 409 SF galaxies from the Mapping Nearby Galaxies at APO (MaNGA) survey, we calculate the fractional contribution of the DIG to several emission lines using high-S/N data from SF spaxels (instead of using noisy emission-lines in DIG-dominated spaxels). Our method is applicable to spectra with observed WH α ≳ 10 Å (which are not dominated by DIG emission). Since the DIG contribution depends on galactocentric distance, we provide DIG-correction formulae for both entire galaxies and single aperture spectra. Applying those to a sample of $\, \gt 90\, 000$ SF galaxies from the Sloan Digital Sky Survey, we find the following. (1) The effect of the DIG on strong-line abundances depends on the index used. It is negligible for the ([O iii]/H β)/([N ii]/H α) index, but reaches ∼0.1 dex at the high-metallicity end for [N ii]/H α. (2) This result is based on the ∼kpc MaNGA resolution, so the real effect of the DIG is likely greater. (3) We revisit the mass–metallicity–star formation rate (SFR) relation by correcting for the DIG contribution in both abundances and SFR. The effect of DIG removal is more prominent at higher stellar masses. Using the [N ii]/Hα index, O/H increases with SFR at high stellar mass, contrary to previous claims.
The origin of parity changes in the solar cycle
Authors: Hazra Soumitra , Nandy Dibyendu 
Published: September 2019

ABSTRACT
Although sunspots have been systematically observed on the Sun’s surface over the last four centuries, their magnetic properties have been revealed and documented only since the early 1900s. Sunspots typically appear in pairs of opposite magnetic polarities which have a systematic orientation. This polarity orientation is opposite across the equator – a trend that has persisted over the last century. Taken together with the configuration of the global poloidal field of the Sun – this phenomena is consistent with the dipolar parity state of an underlying magnetohydrodynamic dynamo. Although transient hemispheric asymmetry in sunspot emergence is observed, a global parity shift has never been observed. We simulate hemispheric asymmetry through introduction of random fluctuations in a computational dynamo model of the solar cycle and demonstrate that changes in parity are indeed possible in long-term simulations covering thousands of years. Quadrupolar modes are found to exist over significant fraction of the simulated time. In particular, we find that a parity shift in the underlying nature of the sunspot cycle is more likely to occur when sunspot activity dominates in any one hemisphere for a time which is significantly longer than the cycle period. We establish causal pathways connecting hemispheric asymmetry to parity flips mediated via a decoupling of the dynamo cycle period across the two solar hemispheres. Our findings indicate that the solar cycle may have resided in quadrupolar parity states in the past, and provides a possible pathway for predicting parity flips in the future.
Soft X-ray heating as a mechanism of optical continuum generation in solar-type star superflares
Authors: Nizamov Bulat A 
Published: September 2019

ABSTRACT
Superflares on the solar-type stars observed by Kepler demonstrate the contrast in the optical continuum of the order 0.1–1 per cent. The mechanism of formation of this radiation is not firmly established. We consider a model where the stellar atmosphere is irradiated by the soft X-rays emitted from the flaring loop filled with the hot plasma. This radiation heats a large area beneath the loop. Subsequent cooling due to h− and hydrogen free–bound emission can contribute to the observed enhanced continuum. We solve the equations of radiative transfer, statistical equilibrium, ionization balance, and radiative equilibrium in the model atmosphere illuminated by the soft X-rays; compute the temperature and the electron density in the atmosphere; and find the emergent radiation. We found that a flare loop of the length ∼1010 cm and plasma density 1012 cm−3 at the temperature T = 20 MK can provide the contrast in the Kepler bandpass of 0.1 and 0.8 per cent if the heated region covers ∼1 and 10 per cent of the visible stellar surface, respectively. The required emission measure is of the order of 1055 cm−3.
Magnetic field, activity, and companions of V410 Tau
Authors: Yu L , Donati J-F , Grankin K , Collier Cameron A , Moutou C , Hussain G , Baruteau C , Jouve L , MaTYSSE collaboration the 
Published: September 2019

ABSTRACT
We report the analysis, conducted as part of the MaTYSSE programme, of a spectropolarimetric monitoring of the ∼0.8 Myr, ∼1.4 M⊙ disc-less weak-line T Tauri star V410 Tau with the ESPaDOnS instrument at the Canada–France–Hawaii Telescope and NARVAL at the Télescope Bernard Lyot, between 2008 and 2016. With Zeeman-Doppler Imaging, we reconstruct the surface brightness and magnetic field of V410 Tau, and show that the star is heavily spotted and possesses a ∼550 G relatively toroidal magnetic field. We find that V410 Tau features a weak level of surface differential rotation between the equator and pole ∼5 times weaker than the solar differential rotation. The spectropolarimetric data exhibit intrinsic variability, beyond differential rotation, which points towards a dynamo-generated field rather than a fossil field. Long-term variations in the photometric data suggest that spots appear at increasing latitudes over the span of our data set, implying that, if V410 Tau has a magnetic cycle, it would have a period of more than 8 yr. Having derived raw radial velocities (RVs) from our spectra, we filter out the stellar activity jitter, modelled either from our Doppler maps or using Gaussian process regression. Thus filtered, our RVs exclude the presence of a hot Jupiter-mass companion below ∼0.1 au, which is suggestive that hot Jupiter formation may be inhibited by the early depletion of the circumstellar disc, which for V410 Tau may have been caused by the close (few tens of au) M dwarf stellar companion.
Gas accretion as fuel for residual star formation in Galaxy Zoo elliptical galaxies
Authors: Davis Timothy A , Young Lisa M 
Published: September 2019

ABSTRACT
In this letter we construct a large sample of early-type galaxies (ETGs) with measured gas-phase metallicities from the Sloan Digital Sky Survey and Galaxy Zoo in order to investigate the origin of the gas that fuels their residual star formation. We use this sample to show that star-forming elliptical galaxies have a substantially different gas-phase metallicity distribution from spiral galaxies, with ≈7.4 per cent having a very low gas-phase metallicity for their mass. These systems typically have fewer metals in the gas phase than they do in their stellar photospheres, which strongly suggests that the material fuelling their recent star formation was accreted from an external source. We use a chemical evolution model to show that the enrichment time-scale for low-metallicity gas is very short, and thus that cosmological accretion and minor mergers are likely to supply the gas in ≳ 37 per cent of star-forming ETGs, in good agreement with estimates derived from other independent techniques.
METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis
Authors: Haute Lindsey Van , Hendrick Alan G , D’Souza Aaron R , Powell Christopher A , Rebelo-Guiomar Pedro , Harbour Michael E , Ding Shujing , Fearnley Ian M , Andrews Byron , Minczuk Michal 
Published: September 2019

Abstract
Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m4C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m4C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.
The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination
Authors: Martino Julieta , Brunette Gregory J , Barroso-González Jonathan , Moiseeva Tatiana N , Smith Chelsea M , Bakkenist Christopher J , O’Sullivan Roderick J , Bernstein Kara A 
Published: September 2019

AbstractRAD51 plays a central role in homologous recombination during double-strand break repair and in replication fork dynamics. Misregulation of RAD51 is associated with genetic instability and cancer. RAD51 is regulated by many accessory proteins including the highly conserved Shu complex. Here, we report the function of the human Shu complex during replication to regulate RAD51 recruitment to DNA repair foci and, secondly, during replication fork restart following replication fork stalling. Deletion of the Shu complex members, SWS1 and SWSAP1, using CRISPR/Cas9, renders cells specifically sensitive to the replication fork stalling and collapse caused by methyl methanesulfonate and mitomycin C exposure, a delayed and reduced RAD51 response, and fewer sister chromatid exchanges. Our additional analysis identified SPIDR and PDS5B as novel Shu complex interacting partners and genetically function in the same pathway upon DNA damage. Collectively, our study uncovers a protein complex, which consists of SWS1, SWSAP1, SPIDR and PDS5B, involved in DNA repair and provides insight into Shu complex function and composition.
HIF-transcribed p53 chaperones HIF-1α
Authors: Madan Esha , Parker Taylor M , Pelham Christopher J , Palma Antonio M , Peixoto Maria L , Nagane Masaki , Chandaria Aliya , Tomás Ana R , Canas-Marques Rita , Henriques Vanessa , Galzerano Antonio , Cabral-Teixeira Joaquim , Selvendiran Karuppaiyah , Kuppusamy Periannan , Carvalho Carlos , Beltran Antonio , Moreno Eduardo , Pati Uttam K , Gogna Rajan 
Published: September 2019

AbstractChronic hypoxia is associated with a variety of physiological conditions such as rheumatoid arthritis, ischemia/reperfusion injury, stroke, diabetic vasculopathy, epilepsy and cancer. At the molecular level, hypoxia manifests its effects via activation of HIF-dependent transcription. On the other hand, an important transcription factor p53, which controls a myriad of biological functions, is rendered transcriptionally inactive under hypoxic conditions. p53 and HIF-1α are known to share a mysterious relationship and play an ambiguous role in the regulation of hypoxia-induced cellular changes. Here we demonstrate a novel pathway where HIF-1α transcriptionally upregulates both WT and MT p53 by binding to five response elements in p53 promoter. In hypoxic cells, this HIF-1α-induced p53 is transcriptionally inefficient but is abundantly available for protein-protein interactions. Further, both WT and MT p53 proteins bind and chaperone HIF-1α to stabilize its binding at its downstream DNA response elements. This p53-induced chaperoning of HIF-1α increases synthesis of HIF-regulated genes and thus the efficiency of hypoxia-induced molecular changes. This basic biology finding has important implications not only in the design of anti-cancer strategies but also for other physiological conditions where hypoxia results in disease manifestation.
Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution
Authors: Ekesan Şölen , York Darrin M 
Published: September 2019

Abstract
We perform molecular dynamics simulations, based on recent crystallographic data, on the 8–17 DNAzyme at four states along the reaction pathway to determine the dynamical ensemble for the active state and transition state mimic in solution. A striking finding is the diverse roles played by Na+ and Pb2+ ions in the electrostatically strained active site that impact all four fundamental catalytic strategies, and share commonality with some features recently inferred for naturally occurring hammerhead and pistol ribozymes. The active site Pb2+ ion helps to stabilize in-line nucleophilic attack, provides direct electrostatic transition state stabilization, and facilitates leaving group departure. A conserved guanine residue is positioned to act as the general base, and is assisted by a bridging Na+ ion that tunes the pKa and facilitates in-line fitness. The present work provides insight into how DNA molecules are able to solve the RNA-cleavage problem, and establishes functional relationships between the mechanism of these engineered DNA enzymes with their naturally evolved RNA counterparts. This adds valuable information to our growing body of knowledge on general mechanisms of phosphoryl transfer reactions catalyzed by RNA, proteins and DNA.
The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex
Authors: Karakkat Jimsheena V , Kaimala Suneesh , Sreedharan Sreejisha P , Jayaprakash Princy , Adeghate Ernest A , Ansari Suraiya A , Guccione Ernesto , Mensah-Brown Eric P K , Starling Emerald Bright 
Published: September 2019

AbstractThe metabolic sensor Per-Arnt-Sim (Pas) domain-containing serine/threonine kinase (PASK) is expressed predominantly in the cytoplasm of different cell types, although a small percentage is also expressed in the nucleus. Herein, we show that the nuclear PASK associates with the mammalian H3K4 MLL2 methyltransferase complex and enhances H3K4 di- and tri-methylation. We also show that PASK is a histone kinase that phosphorylates H3 at T3, T6, S10 and T11. Taken together, these results suggest that PASK regulates two different H3 tail modifications involving H3K4 methylation and H3 phosphorylation. Using muscle satellite cell differentiation and functional analysis after loss or gain of Pask expression using the CRISPR/Cas9 system, we provide evidence that some of the regulatory functions of PASK during development and differentiation may occur through the regulation of these histone modifications.
Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis
Authors: Nousch Marco , Yeroslaviz Assa , Eckmann Christian R 
Published: September 2019

AbstractRNA-modifying enzymes targeting mRNA poly(A) tails are universal regulators of post-transcriptional gene expression programs. Current data suggest that an RNA-binding protein (RBP) directed tug-of-war between tail shortening and re-elongating enzymes operates in the cytoplasm to repress or activate specific mRNA targets. While this concept is widely accepted, it was primarily described in the final meiotic stages of frog oogenesis and relies molecularly on a single class of RBPs, i.e. CPEBs, the deadenylase PARN and cytoplasmic poly(A) polymerase GLD-2. Using the spatial and temporal resolution of female gametogenesis in the nematode C. elegans, we determined the distinct roles of known deadenylases throughout germ cell development and discovered that the Ccr4–Not complex is the main antagonist to GLD-2-mediated mRNA regulation. We find that the Ccr4–Not/GLD-2 balance is critical for essentially all steps of oocyte production and reiteratively employed by various classes of RBPs. Interestingly, its two deadenylase subunits appear to affect mRNAs stage specifically: while a Caf1/GLD-2 antagonism regulates mRNA abundance during all stages of oocyte production, a Ccr4/GLD-2 antagonism regulates oogenesis in an mRNA abundance independent manner. Our combined data suggests that the Ccr4–Not complex represents the evolutionarily conserved molecular opponent to GLD-2 providing an antagonistic framework of gene-specific poly(A)-tail regulation.