bluuebunny/crossref_metadata_2025 huggingface dataset:
Searching for orbital decay in a heartbeat star system KIC 3766353
Authors: Ou Jian-Wen , Yu Cong , Jiang Chen , Yang Ming , Niu Hubiao
Published: September 2021

Theory suggests that the orbits of a large fraction of binary systems, including planet–star binary systems, shrink by a few orders of magnitude after formation. But so far, only one hot Jupiter with tidally driven orbital decay has been found by transit timing variations. We propose to search for orbital decay companions in heartbeat star systems because the orbital angular momentum is effectively transferred to the host star, causing tidal dissipation. KIC 3766353 is one of the heartbeat stars with tidally excited oscillations. We acquired the primary and the secondary eclipse time variations from the Kepler photometric light curves. Timing analysis shows that KIC 3766353 is a hierarchical triple system with a hidden third body and a red dwarf (mass 0.35 M⊙, radius 0.34 R⊙) in its inner orbit. The minimum mass of the third body is ∼0.26 M⊙, and the distance from the inner orbital is ∼111.4 R⊙. The period decay rate of the red dwarf is approximately 358 ms yr−1. The combined effects of the light-traveltime and the orbital decay lead to the observed timing variations. Future monitoring with long-time baseline observations is required to delve into the contributions of these two effects.
Decomposition of the CO stretching vibration band of laboratory H2O–CO ices irradiated by heavy ions
Authors: Seperuelo Duarte E , de Barros A L F , da Silveira E F , Domaracka A , Boduch P , Rothard H
Published: September 2021

H2O and CO molecules are the main constituents of the interstellar dust grain ice mantles. Infrared spectra of the ices in line of sights of young stellar objects and background stars have shown that the CO stretching vibration band can be decomposed into three main components: 2143, 2139, and 2136 cm−1, assigned to CO in different environment sites. The relative strengths between the components have been associated with an evolutionary track of the interstellar molecular clouds. H2O:CO (3:2) and (10:1) ice samples were irradiated by 0.79 MeV/u 58Ni13+ ions to simulate the effects produced by heavy ion cosmic rays in typical interstellar ice mixtures. The CO stretching vibration band is decomposed into six Gaussian functions (2150, 2144, 2141, 2138, 2136, and 2133 cm−1) and their integrated absorbances were measured as a function of fluence. The results show that, at the final fluence, the component 2138 cm−1 is the main component of the CO stretching vibration band. The component 2150 cm−1 disappears at the beginning of irradiation. Based on the present and previous results, a time-scale for the components in the interstellar ices is proposed. For H2O:CO ices in the interstellar medium, it is predicted that, after 1 Ma, the main components of the CO stretching vibration band are the 2138 and 2141 cm−1, due to the CO monomers and dimers, respectively.
Modons on tidally synchronized extrasolar planets
Authors: Skinner J W , Cho J Y-K
Published: September 2021

We investigate modons on tidally synchronized extrasolar planet atmospheres. Modons are dynamic, coherent flow structures composed of a pair of storms with opposite signs of vorticity. Modons are important because they can divert flows and lead to recognizable weather patterns. On synchronized planets, powered by the intense irradiation from the host star, large modons reach planetary-scale in size and exhibit quasi-periodic life-cycles – chaotically moving around the planet, breaking and reforming many times over long durations (e.g. thousands of planet days). Additionally, the modons transport and mix planetary-scale patches of hot and cold air around the planet, leading to high-amplitude and quasi-periodic signatures in the disc-averaged temperature flux. Hence, they induce variations of the ‘hotspot’ longitude to either side of the planet’s substellar point – consistent with observations at different epochs. The variability behaviour in our simulations broadly underscores the importance of accurately capturing vortex dynamics in extrasolar planet atmosphere modelling, particularly in understanding current observations.
Measuring cosmic density of neutral hydrogen via stacking the DINGO-VLA data
Authors: Chen Qingxiang , Meyer Martin , Popping Attila , Staveley-Smith Lister , Bryant Julia , Delhaize Jacinta , Holwerda B W , Cluver M E , Loveday J , Lopez-Sanchez Angel R , Zwaan Martin , Taylor E N , Hopkins A M , Wright Angus , Driver Simon , Brough S
Published: September 2021

We use the 21-cm emission-line data from the Deep Investigation of Neutral Gas Origin-Very Large Array (DINGO-VLA) project to study the atomic hydrogen gas H i of the Universe at redshifts z < 0.1. Results are obtained using a stacking analysis, combining the H i signals from 3622 galaxies extracted from 267 VLA pointings in the G09 field of the Galaxy and Mass Assembly Survey (GAMA). Rather than using a traditional one-dimensional spectral stacking method, a three-dimensional cubelet stacking method is used to enable deconvolution and the accurate recovery of average galaxy fluxes from this high-resolution interferometric data set. By probing down to galactic scales, this experiment also overcomes confusion corrections that have been necessary to include in previous single-dish studies. After stacking and deconvolution, we obtain a 30σ H i mass measurement from the stacked spectrum, indicating an average H i mass of ${\rm{M_{\rm{{H}\,\small{I}}}}}=(1.67\pm 0.18)\times 10^{9}~{\rm{{\rm M}_{\odot }}}$. The corresponding cosmic density of neutral atomic hydrogen is ${\rm{\Omega _{\rm{{H}\,\small{I}}}}}=(0.38\pm 0.04)\times 10^{-3}$ at redshift of z = 0.051. These values are in good agreement with earlier results, implying there is no significant evolution of $\Omega _{\rm{{H}\,\small{I}}}$ at lower redshifts.
Spin-based removal of instrumental systematics in 21 cm intensity mapping surveys
Authors: McCallum Nialh , Thomas Daniel B , Bull Philip , Brown Michael L
Published: September 2021

Upcoming cosmological intensity mapping surveys will open new windows on the Universe, but they must first overcome a number of significant systematic effects, including polarization leakage. We present a formalism that uses scan strategy information to model the effect of different instrumental systematics on the recovered cosmological intensity signal for ‘single-dish’ (autocorrelation) surveys. This modelling classifies different systematics according to their spin symmetry, making it particularly relevant for dealing with polarization leakage. We show how to use this formalism to calculate the expected contamination from different systematics as a function of the scanning strategy. Most importantly, we show how systematics can be disentangled from the intensity signal based on their spin properties via map-making. We illustrate this, using a set of toy models, for some simple instrumental systematics, demonstrating the ability to significantly reduce the contamination to the observed intensity signal. Crucially, unlike existing foreground removal techniques, this approach works for signals that are non-smooth in frequency, e.g. polarized foregrounds. These map-making approaches are simple to apply and represent an orthogonal and complementary approach to existing techniques for removing systematics from upcoming 21 cm intensity mapping surveys.
On the impact of the numerical method on magnetic reconnection and particle acceleration – I. The MHD case
Authors: Puzzoni E , Mignone A , Bodo G
Published: September 2021

We present 2D magnetohydrodynamics numerical simulations of tearing-unstable current sheets coupled to a population of non-thermal test particles, in order to address the problem of numerical convergence with respect to grid resolution, numerical method, and physical resistivity. Numerical simulations are performed with the pluto code for astrophysical fluid dynamics through different combinations of Riemann solvers, reconstruction methods, and grid resolutions at various Lundquist numbers. The constrained transport method is employed to control the divergence-free condition of magnetic field. Our results indicate that the reconnection rate of the background tearing-unstable plasma converges only for finite values of the Lundquist number and for sufficiently large grid resolutions. In general, it is found that (for a second-order scheme) the minimum threshold for numerical convergence during the linear phases requires the number of computational zones covering the initial current sheet width to scale roughly as $\sim \sqrt{\bar{S}}$, where $\bar{S}$ is the Lundquist number defined on the current sheet width. On the other hand, the process of particle acceleration is found to be nearly independent of the underlying numerical details inasmuch as the system becomes tearing-unstable and enters in its non-linear stages. In the limit of large $\bar{S}$, the ensuing power-law index quickly converge to p ≈ 1.7, consistently with the fast reconnection regime.
The origin of a universal filament width in molecular clouds
Authors: Priestley F D , Whitworth A P
Published: September 2021

Filamentary structures identified in far-infrared observations of molecular clouds are typically found to have full widths at half-maximum $\sim 0.1\, {\rm pc}$. However, the physical explanation for this phenomenon is currently uncertain. We use hydrodynamic simulations of cylindrically symmetric converging flows to show that the full width at half-maximum of the resulting filament’s surface density profile, $\rm{\small FWHM}{_\Sigma }$, is closely related to the location of the accretion shock, where the inflow meets the boundary of the filament. For inflow Mach number, ${\cal M}$, between 1 and 5, filament $\rm{\small FWHM}{_\Sigma }$s fall in the range $0.03\, {\rm pc}\lesssim \rm{\small FWHM}{_\Sigma }\lesssim 0.3\, {\rm pc}$, with higher ${\cal M}$ resulting in narrower filaments. A large sample of filaments, seen at different evolutionary stages and with different values of ${\cal M}$, naturally results in a peaked distribution of $\rm{\small FWHM}{_\Sigma }$s similar in shape to that obtained from far-infrared observations of molecular clouds. However, unless the converging flows are limited to ${\cal M} \lesssim 3$, the peak of the distribution of $\rm{\small FWHM}{_\Sigma }$s is below the observed $\sim 0.1 \, {\rm pc}$.
Fast estimation of aperture-mass statistics – II. Detectability of higher order statistics in current and future surveys
Authors: Porth Lucas , Smith Robert E
Published: September 2021

We explore an alternative method to the usual shear correlation function approach for the estimation of aperture mass statistics in weak-lensing survey data. Our approach builds on the direct estimator method. In this paper, we extend our analysis to statistics of arbitrary order and to the multiscale aperture mass statistics. We show that there always exists a linear order algorithm to retrieve any of these generalized aperture mass statistics from shape catalogues when the direct estimator approach is adopted. We validate our approach through application to a large number of Gaussian mock-lensing surveys where the true answer is known and we do this up to 10th-order statistics. We then apply our estimators to an ensemble of real-world mock catalogues obtained from N-body simulations – the SLICS mocks, and show that one can expect to retrieve detections of higher order clustering up to fourth order in a KiDS-1000 like survey. We expect that these methods will be of most utility for future wide-field surveys like Euclid and the Rubin Telescope.
A comment on the properties of the matter flow through the first Langrangian point
Authors: Ziółkowski Janusz , Zdziarski Andrzej A
Published: September 2021

We analyse properties of the mass outflow from the Roche lobe filling component of a semi-detached binary system. We follow the approaches published by Paczyński & Sienkiewicz and by Lubow & Shu, which we compare with other simplified approaches. We find that the density of the flow at L1 is orders of magnitude lower than the density on the same equipotential but away from L1. Furthermore, the effective cross-section of the flow, after averaging over its profile of the momentum density, is much lower than some published estimates done without accounting for the averaging. Thus, the use of some simplified formulae for the density and the flow cross-section can lead to overestimates of the accretion rate and of the mass contained in the L1 regions by very large factors unless they are supported by simultaneous integrations of the equations of stellar structure for the outer layers of the donor.
Nucleosynthesis signatures of neutrino-driven winds from proto-neutron stars: a perspective from chemical evolution models
Authors: Vincenzo Fiorenzo , Thompson Todd A , Weinberg David H , Griffith Emily J , Johnson James W , Johnson Jennifer A
Published: September 2021

We test the hypothesis that the observed first-peak (Sr, Y, Zr) and second-peak (Ba) s-process elemental abundances in low-metallicity Milky Way stars, and the abundances of the elements Mo and Ru, can be explained by a pervasive r-process contribution originating in neutrino-driven winds from highly magnetic and rapidly rotating proto-neutron stars (proto-NSs). We construct chemical evolution models that incorporate recent calculations of proto-NS yields in addition to contributions from asymptotic giant branch stars, Type Ia supernovae, and two alternative sets of yields for massive star winds and core-collapse supernovae. For non-rotating massive star yields from either set, models without proto-NS winds underpredict the observed s-process peak abundances by 0.3–$1\, \text{dex}$ at low metallicity, and they severely underpredict Mo and Ru at all metallicities. Models incorporating wind yields from proto-NSs with spin periods P ∼ 2–$5\, \text{ms}$ fit the observed trends for all these elements well. Alternatively, models omitting proto-NS winds but adopting yields of rapidly rotating massive stars, with vrot between 150 and $300\, \text{km}\, \text{s}^{-1}$, can explain the observed abundance levels reasonably well for [Fe/H] < −2. These models overpredict [Sr/Fe] and [Mo/Fe] at higher metallicities, but with a tuned dependence of vrot on stellar metallicity they might achieve an acceptable fit at all [Fe/H]. If many proto-NSs are born with strong magnetic fields and short spin periods, then their neutrino-driven winds provide a natural source for Sr, Y, Zr, Mo, Ru, and Ba in low-metallicity stellar populations. Conversely, spherical winds from unmagnetized proto-NSs overproduce the observed Sr, Y, and Zr abundances by a large factor.
Diffusivity in force-free simulations of global magnetospheres
Authors: Mahlmann J F , Aloy M A
Published: September 2021

Assuming that the numerical diffusivity triggered by violations of the force-free electrodynamics constraints is a proxy for the physical resistivity, we examine its impact on the overall dynamics of force-free aligned pulsar magnetospheres endowed with an equatorial current sheet (ECS). We assess the constraint violations as a diffusivity source. The effects of modifications on electric fields used to restore force-free conditions are not confined to the ECS, but modify the magnetospheric dynamics on time-scales shorter than the pulsar rotational period. These corrections propagate especially via a channel that was unexplored, namely, changes induced to the electric charge density, ρ. We quantify the global consequences of diffusivity by comparing different techniques to model ρ. By default, we combine a conservative ρ-evolution with hyperbolic/parabolic cleaning of inaccuracies in the Maxwell equations. As an alternative, we enforce a constrained evolution, where ρ is directly computed as the electric field divergence. The conservative approach reduces the Poynting flux dissipated in the ECS by an order of magnitude, along with an increase of the pulsar luminosity driven by a shift of the Y-point location. The luminosity changes according to LY ∝ α0.11, where α is the ratio of diffusion to advection time-scales, controlling the amount of (numerical) diffusivity. Our models suggest interpreting the luminosity dependence on the Y-point location as differences in resistivities encountered at the ECS. Alternatively, they could be interpreted in terms of the pair formation multiplicity, κ, smaller diffusion being consistent with κ ≫ 1.
M dwarf spectral indices at moderate resolution: accurate Teff and [Fe/H] for 178 southern stars
Authors: Costa-Almeida Ellen , de Mello Gustavo F Porto , Giribaldi Riano E , Lorenzo-Oliveira Diego , Ubaldo-Melo Maria L
Published: September 2021

We present a spectroscopic and photometric calibration to derive effective temperatures Teff and metallicities [Fe/H] for M dwarfs, based on a principal component analysis (PCA) of 147 spectral indices measured off moderate resolution (R∼11 000), high S/N (>100) spectra in the λλ 8390–8834 region, plus the J−H colour. Internal uncertainties, estimated by the residuals, are 81 K and 0.12 dex, respectively, for Teff and [Fe/H], the calibrations being valid for 3050 K < T$_\text{eff}\, \lt $ 4100 K and −0.45 < [Fe/H] $\lt \, +$0.50 dex. The PCA calibration is a competitive model-independent method to derive Teff and [Fe/H] for large samples of M dwarfs, well suited to the available database of far-red spectra. The median uncertainties are 105 K and 0.23 dex for Teff and [Fe/H], respectively, estimated by Monte Carlo simulations. We compare our values to other works based on photometric and spectroscopic techniques and find median differences 75 ± 273 K and 0.02 ± 0.31 dex for Teff and [Fe/H], respectively, achieving good accuracy but relatively low precision. We find considerable disagreement in the literature between atmospheric parameters for stars in common. We use the new calibration to derive Teff and [Fe/H] for 178 K7-M5 dwarfs, many previously unstudied. Our metallicity distribution function for nearby M dwarfs peaks at [Fe/H]∼−0.10 dex, in good agreement with the RAVE distribution for GK dwarfs. We present radial velocities (internal precision 1.4 km s−1) for 99 objects without previous measurements. The kinematics of the sample shows it to be fully dominated by thin/thick disc stars, excepting the well-known high-velocity Kapteyn’s star.
Bayesian analysis of quasar light curves with a running optimal average: new time delay measurements of COSMOGRAIL gravitationally lensed quasars
Authors: Donnan Fergus R , Horne Keith , Hernández Santisteban Juan V
Published: September 2021

We present a new method of modelling time-series data based on the running optimal average (ROA). By identifying the effective number of parameters for the ROA model, in terms of the shape and width of its window function and the times and accuracies of the data, we enable a Bayesian analysis, optimizing the ROA width, along with other model parameters, by minimizing the Bayesian information criterion (BIC) and sampling joint posterior parameter distributions using MCMC methods. For analysis of quasar light curves, our implementation of ROA modelling can measure time delays among light curves at different wavelengths or from different images of a lensed quasar and, in future work, be used to inter-calibrate light-curve data from different telescopes and estimate the shape and thus the power-density spectrum of the light curve. Our noise model implements a robust treatment of outliers and error-bar adjustments to account for additional variance or poorly quantified uncertainties. Tests with simulated data validate the parameter uncertainty estimates. We compare ROA delay measurements with results from cross-correlation and from javelin, which models light curves with a prior on the power-density spectrum. We analyse published COSMOGRAIL light curves of multilensed quasar light curves and present the resulting measurements of the inter-image time delays and detection of microlensing effects.
Broad-band time-resolved spectroscopy of thermonuclear X-ray bursts from 4U 1636−536 using AstroSat
Authors: Kashyap Unnati , Ram Biki , Güver Tolga , Chakraborty Manoneeta
Published: September 2021

Broad-band spectral studies of type I X-ray bursts can put strong constraints on the physics of burst spectra as well as their interaction with the environment. We present the results obtained from the broad-band time-resolved spectroscopy of 15 thermonuclear bursts detected simultaneously from the neutron star atoll source 4U 1636−536 using the Large Area X-ray Proportional Counter (LAXPC) and Soft X-ray Telescope (SXT) onboard AstroSat. During the observations with AstroSat, the low-mass X-ray binary 4U 1636−536 is observed to show a modest spectral evolution within the island state. The broad-band burst spectra are observed to show an excess in addition to the thermal emission from the neutron star surface near the peak of the bursts. We investigate the interpretation of the excess observed near the peak of the burst as re-emission/reprocessing of the photons by the accretion disc/corona or scattering of the photons in the neutron star atmosphere or the enhanced persistent emission due to the Poynting–Robertson drag. This is the first reported broad-band simultaneous study of type I bursts using LAXPC and SXT onboard AstroSat. This kind of study may provide a better understanding of the burst–accretion interaction and how the bursts influence the overall accretion process contributed by the accretion disc as well as the corona.
Detection of periodic signals in AGN red noise light curves: empirical tests on the Auto-Correlation Function and Phase Dispersion Minimization
Authors: Krishnan S , Markowitz A G , Schwarzenberg-Czerny A , Middleton M J
Published: September 2021

Active galactic nucleus (AGN) emission is dominated by stochastic, aperiodic variability which overwhelms any periodic/quasi-periodic signal (QPO) if one is present. The Auto-Correlation Function (ACF) and Phase Dispersion Minimization (PDM) techniques have been used previously to claim detections of QPOs in AGN light curves. In this paper, we perform Monte Carlo simulations to empirically test QPO detection feasibility in the presence of red noise. Given the community’s access to large data bases of monitoring light curves via large-area monitoring programmes, our goal is to provide guidance to those searching for QPOs via data trawls. We simulate evenly sampled pure red noise light curves to estimate false alarm probabilities; false positives in both tools tend to occur towards time-scales longer than (very roughly) one-third of the light-curve duration. We simulate QPOs mixed with pure red noise and determine the true-positive detection sensitivity; in both tools, it depends strongly on the relative strength of the QPO against the red noise and on the steepness of the red noise PSD slope. We find that extremely large values of peak QPO power relative to red noise (typically ∼104−5) are needed for a 99.7 per cent true-positive detection rate. Given that the true-positive detections using the ACF or PDM are generally rare to obtain, we conclude that period searches based on the ACF or PDM must be treated with extreme caution when the data quality is not good. We consider the feasibility of QPO detection in the context of highly inclined, periodically self-lensing supermassive black hole binaries.
The ultra-steep diffuse radio emission observed in the cool-core cluster RX J1720.1+2638 with LOFAR at 54 MHz
Authors: Biava N , de Gasperin F , Bonafede A , Edler H W , Giacintucci S , Mazzotta P , Brunetti G , Botteon A , Brüggen M , Cassano R , Drabent A , Edge A C , Enßlin T , Gastaldello F , Riseley C J , Rossetti M , Rottgering H J A , Shimwell T W , Tasse C , van Weeren R J
Published: September 2021

Diffuse radio emission at the centre of galaxy clusters has been observed both in merging clusters on scales of Mpc, called giant radio haloes, and in relaxed systems with a cool-core on smaller scales, named mini haloes. Giant radio haloes and mini haloes are thought to be distinct classes of sources. However, recent observations have revealed the presence of diffuse radio emission on Mpc scales in clusters that do not show strong dynamical activity. RX J1720.1+2638 is a cool-core cluster, presenting both a bright central mini halo and a fainter diffuse, steep-spectrum emission extending beyond the cluster core that resembles giant radio halo emission. In this paper, we present new observations performed with the LOw Frequency ARray Low Band Antennas (LBA) at 54 MHz. These observations, combined with data at higher frequencies, allow us to constrain the spectral properties of the radio emission. The large-scale emission presents an ultrasteep spectrum with $\alpha _{54}^{144}\sim 3.2$. The radio emission inside and outside the cluster core have strictly different properties, as there is a net change in spectral index and they follow different radio-X-ray surface brightness correlations. We argue that the large-scale diffuse emission is generated by particles re-acceleration after a minor merger. While for the central mini halo, we suggest that it could be generated by secondary electrons and positrons from hadronic interactions of relativistic nuclei with the dense cool-core gas, as an alternative to re-acceleration models.
Radiatively driven, time dependent bipolar outflows
Authors: Joshi Raj Kishor , Chattopadhyay Indranil , Yadav Lallan
Published: September 2021

We study the radiatively driven fluid jets around a non-rotating black hole. The radiation arising from the inner compact corona and outer sub-Keplerian part of the disc accelerates the jets. We obtain the steady state, semi-analytical, radiatively driven outflow solutions. The thermodynamics of the outflow is described by a variable adiabatic index equation of state. We develop a total variation diminishing (TVD) routine to investigate the time dependent behaviour of the radiatively driven bipolar outflow. We inject with flow variables from the steady state outflow solutions in the TVD code and allow the code to settle into steady state and match the numerical results with the steady state solution. The radiation arising out of the accretion disc can provide a wide range of jet solutions, depending upon parameters like the intensity of disc, location of the inner corona etc. We induce the time dependence of the radiation field by inducing oscillation of the inner corona of the accretion disc. The radiation field then makes the bipolar outflow time dependent. We show that a non-steady radiation field arising out of disc oscillations can generate the internal shocks closer to the jet base. Depending on the disc geometry, there might be transient shocks in the jet and there might be multiple non-stationary shocks in the jet, which are of much interest in jet physics.
The Pristine survey – XIV. Chemical analysis of two ultra-metal-poor stars
Authors: Lardo C , Mashonkina L , Jablonka P , Bonifacio P , Caffau E , Aguado D S , González Hernández J I , Sestito F , Kielty C L , Venn K A , Hill V , Starkenburg E , Martin N F , Sitnova T , Arentsen A , Carlberg R G , Navarro J F , Kordopatis G
Published: September 2021

Elemental abundances of the most metal-poor stars reflect the conditions in the early Galaxy and the properties of the first stars. We present a spectroscopic follow-up of two ultra-metal-poor stars ([Fe/H] < −4.0) identified by the survey Pristine: Pristine 221.8781+9.7844 and Pristine 237.8588+12.5660 (hereafter Pr 221 and Pr 237, respectively). Combining data with earlier observations, we find a radial velocity of −149.25 ± 0.27 and −3.18 ± 0.19 km s−1 for Pr 221  and Pr 237, respectively, with no evidence of variability between 2018 and 2020. From a one-dimensional (1D) local thermodynamic equilibrium (LTE) analysis, we measure [Fe/H]LTE = −4.79 ± 0.14 for Pr 221 and −4.22 ± 0.12 for Pr 237, in good agreement with previous studies. Abundances of Li, Na, Mg, Al, Si, Ca, Ti, Fe, and Sr were derived based on the non-LTE (NLTE) line formation calculations. When NLTE effects are included, we measure slightly higher metallicities: [Fe/H]NLTE = −4.40 ± 0.13 and −3.93 ± 0.12, for Pr 221 and Pr 237, respectively. Analysis of the G band yields [C/Fe]1D-LTE ≤ +2.3 and [C/Fe]1D-LTE ≤ +2.0 for Pr 221 and Pr 237. Both stars belong to the low-carbon band. Upper limits on nitrogen abundances are also derived. Abundances for other elements exhibit good agreement with those of stars with similar parameters. Finally, to get insight into the properties of their progenitors, we compare NLTE abundances to theoretical yields of zero-metallicity supernovae (SNe). This suggests that the SNe progenitors had masses ranging from 10.6 to 14.4 M⊙ and low-energy explosions with (0.3–1.2) × 1051 erg.
A timing-based estimate of the spin of the black hole in MAXI J1820+070
Authors: Bhargava Yash , Belloni Tomaso , Bhattacharya Dipankar , Motta Sara , Ponti. Gabriele
Published: September 2021

MAXI J1820+070 (ASSASN-18ey) is a black hole (BH) X-ray binary discovered in 2018. The brightness of the source triggered multi-wavelength campaigns of this source from different observatories. We analyse the power density spectra (PDS) obtained from NICER high cadence observations of the source in the hard state. We obtain the evolution of the characteristic frequencies by modelling the PDS. We interpret the characteristic frequencies of various PDS components (both QPOs and broad-band noise components) as variability occurring at a particular radius, and explain them in the context of the Relativistic Precession Model (RPM). We estimate the dimensionless spin of the BH at $0.799^{+0.016}_{-0.015}$ by fitting the RPM.
Dynamical modelling of the twisted galaxy PGC 046832
Authors: den Brok Mark , Krajnović Davor , Emsellem Eric , Brinchmann Jarle , Maseda Michael
Published: September 2021

We analyse VLT/MUSE observations of PGC 046832, the brightest cluster galaxy of Abell 3556. The velocity structure of this galaxy is startling and shows two reversals in sign along the minor axis, and one along the major axis. We use triaxial Schwarzschild models to infer the intrinsic shape, central black hole mass, and orbit distribution of this galaxy. The shape determination suggests that the galaxy is highly triaxial in the centre (almost prolate) but has a low triaxiality (almost oblate) in the outer parts. The orbit distribution of the best-fitting Schwarzschild model shows that the kinematic reversal along the projected minor axis is driven by a slight asymmetry in the distribution and amount of long axis tubes in the inner parts. The kinematic reversals along the projected major axis are driven by a high fraction of counter-rotating orbits at intermediate radii in the galaxy. Using chemical tagging of orbits in the Schwarzschild model, we do not find evidence for any association of these orbits with specific stellar population parameters. Although the inner part of the galaxy almost certainty formed through one or more dry mergers producing the prolate shape, the outer parts are consistent with both accretion and in situ formation. While axisymmetric models suggests the presence of a supermassive black hole with mass ∼6 × 109 and ∼1010 M⊙(with Schwarzschild and Jeans modelling, respectively), triaxial Schwarzschild models provide only an upper limit of ∼2 × 109  M⊙.
Vertical settling of pebbles in turbulent circumbinary discs and the in situ formation of circumbinary planets
Authors: Pierens Arnaud , Nelson Richard P , McNally Colin P
Published: September 2021

The inner-most regions of circumbinary discs are unstable to a parametric instability whose non-linear evolution is hydrodynamical turbulence. This results in significant particle stirring, impacting on planetary growth processes such as the streaming instability or pebble accretion. In this paper, we present the results of three-dimensional, inviscid global hydrodynamical simulations of circumbinary discs with embedded particles of 1 cm size. Hydrodynamical turbulence develops in the disc, and we examine the effect of the particle back-reaction on vertical dust. We find that higher solid-to-gas ratios lead to smaller gas vertical velocity fluctuations, and therefore to smaller dust scale heights. For a metallicity Z = 0.1, the dust scale height near the edge of the tidally truncated cavity is $\sim 80{{\ \rm per\ cent}}$ of the gas scale height, such that growing a Ceres-mass object to a 10 M⊕ core via pebble accretion would take longer than the disc lifetime. Collision velocities for small particles are also higher than the critical velocity for fragmentation, which precludes grain growth and the possibility of forming a massive planetesimal seed for pebble accretion. At larger distances from the binary, turbulence is weak enough to enable not only efficient pebble accretion but also grain growth to sizes required to trigger the streaming instability. In these regions, an in situ formation scenario of circumbinary planets involving the streaming instability to form a massive planetesimal followed by pebble accretion on to this core is viable. In that case, planetary migration has to be invoked to explain the presence of circumbinary planets at their observed locations.
Cleaning foregrounds from single-dish 21 cm intensity maps with Kernel principal component analysis
Authors: Irfan Melis O , Bull Philip
Published: September 2021

The high dynamic range between contaminating foreground emission and the fluctuating 21 cm brightness temperature field is one of the most problematic characteristics of 21 cm intensity mapping data. While these components would ordinarily have distinctive frequency spectra, making it relatively easy to separate them, instrumental effects and calibration errors further complicate matters by modulating and mixing them together. A popular class of foreground cleaning method are unsupervised techniques related to principal component analysis (PCA), which exploit the different shapes and amplitudes of each component’s contribution to the covariance of the data in order to segregate the signals. These methods have been shown to be effective at removing foregrounds, while also unavoidably filtering out some of the 21 cm signal too. In this paper we examine, for the first time in the context of 21 cm intensity mapping, a generalized method called Kernel PCA, which instead operates on the covariance of non-linear transformations of the data. This allows more flexible functional bases to be constructed, in principle allowing a cleaner separation between foregrounds and the 21 cm signal to be found. We show that Kernel PCA is effective when applied to simulated single-dish (auto-correlation) 21 cm data under a variety of assumptions about foregrounds models, instrumental effects etc. It presents a different set of behaviours to PCA, e.g. in terms of sensitivity to the data resolution and smoothing scale, outperforming it on intermediate to large scales in most scenarios.
Dietary, Cultural, and Pathogens-Related Selective Pressures Shaped Differential Adaptive Evolution among Native Mexican Populations
Authors: Ojeda-Granados Claudia , Abondio Paolo , Setti Alice , Sarno Stefania , Gnecchi-Ruscone Guido Alberto , González-Orozco Eduardo , De Fanti Sara , Jiménez-Kaufmann Andres , Rangel-Villalobos Héctor , Moreno-Estrada Andrés , Sazzini Marco
Published: September 2021

Native American genetic ancestry has been remarkably implicated with increased risk of diverse health issues in several Mexican populations, especially in relation to the dramatic changes in environmental, dietary, and cultural settings they have recently undergone. In particular, the effects of these ecological transitions and Westernization of lifestyles have been investigated so far predominantly on Mestizo individuals. Nevertheless, indigenous groups, rather than admixed Mexicans, have plausibly retained the highest proportions of genetic components shaped by natural selection in response to the ancient milieu experienced by Mexican ancestors during their pre-Columbian evolutionary history. These formerly adaptive variants have the potential to represent the genetic determinants of some biological traits that are peculiar to Mexican people, as well as a reservoir of loci with possible biomedical relevance. To test such a hypothesis, we used genome-wide genotype data to infer the unique adaptive evolution of Native Mexican groups selected as reasonable descendants of the main pre-Columbian Mexican civilizations. A combination of haplotype-based and gene-network analyses enabled us to detect genomic signatures ascribable to polygenic adaptive traits plausibly evolved by the main genetic clusters of Mexican indigenous populations to cope with local environmental and/or cultural conditions. Some of these adaptations were found to play a role in modulating the susceptibility/resistance of these groups to certain pathological conditions, thus providing new evidence that diverse selective pressures have contributed to shape the current biological and disease-risk patterns of present-day Native and Mestizo Mexican populations.
Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation
Authors: Khamis Hadeel , Rudnizky Sergei , Melamed Philippa , Kaplan Ariel
Published: September 2021

The interaction of transcription factors with their response elements in DNA is emerging as a highly complex process, whose characterization requires measuring the full distribution of binding and dissociation times in a well-controlled assay. Here, we present a single-molecule assay that exploits the thermal fluctuations of a DNA hairpin to detect the association and dissociation of individual, unlabeled transcription factors. We demonstrate this new approach by following the binding of Egr1 to its consensus motif and the three binding sites found in the promoter of the Lhb gene, and find that both association and dissociation are modulated by the 9 bp core motif and the sequences around it. In addition, CpG methylation modulates the dissociation kinetics in a sequence and position-dependent manner, which can both stabilize or destabilize the complex. Together, our findings show how variations in sequence and methylation patterns synergistically extend the spectrum of a protein's binding properties, and demonstrate how the proposed approach can provide new insights on the function of transcription factors.
Calling large indels in 1047 Arabidopsis with IndelEnsembler
Authors: Liu Dong-Xu , Rajaby Ramesh , Wei Lu-Lu , Zhang Lei , Yang Zhi-Quan , Yang Qing-Yong , Sung Wing-Kin
Published: September 2021

Large indels greatly impact the observable phenotypes in different organisms including plants and human. Hence, extracting large indels with high precision and sensitivity is important. Here, we developed IndelEnsembler to detect large indels in 1047 Arabidopsis whole-genome sequencing data. IndelEnsembler identified 34 093 deletions, 12 913 tandem duplications and 9773 insertions. Our large indel dataset was more comprehensive and accurate compared with the previous dataset of AthCNV (1). We captured nearly twice of the ground truth deletions and on average 27% more ground truth duplications compared with AthCNV, though our dataset has less number of large indels compared with AthCNV. Our large indels were positively correlated with transposon elements across the Arabidopsis genome. The non-homologous recombination events were the major formation mechanism of deletions in Arabidopsis genome. The Neighbor joining (NJ) tree constructed based on IndelEnsembler's deletions clearly divided the geographic subgroups of 1047 Arabidopsis. More importantly, our large indels represent a previously unassessed source of genetic variation. Approximately 49% of the deletions have low linkage disequilibrium (LD) with surrounding single nucleotide polymorphisms. Some of them could affect trait performance. For instance, using deletion-based genome-wide association study (DEL-GWAS), the accessions containing a 182-bp deletion in AT1G11520 had delayed flowering time and all accessions in north Sweden had the 182-bp deletion. We also found the accessions with 65-bp deletion in the first exon of AT4G00650 (FRI) flowered earlier than those without it. These two deletions cannot be detected in AthCNV and, interestingly, they do not co-occur in any Arabidopsis thaliana accession. By SNP-GWAS, surrounding SNPs of these two deletions do not correlate with flowering time. This example demonstrated that existing large indel datasets miss phenotypic variations and our large indel dataset filled in the gap.
dNTPpoolDB: a manually curated database of experimentally determined dNTP pools and pool changes in biological samples
Authors: Pancsa Rita , Fichó Erzsébet , Molnár Dániel , Surányi Éva Viola , Trombitás Tamás , Füzesi Dóra , Lóczi Hanna , Szijjártó Péter , Hirmondó Rita , Szabó Judit E , Tóth Judit
Published: September 2021

Stimulated by the growing interest in the role of dNTP pools in physiological and malignant processes, we established dNTPpoolDB, the database that offers access to quantitative data on dNTP pools from a wide range of species, experimental and developmental conditions (https://dntppool.org/). The database includes measured absolute or relative cellular levels of the four canonical building blocks of DNA and of exotic dNTPs, as well. In addition to the measured quantity, dNTPpoolDB contains ample information on sample source, dNTP quantitation methods and experimental conditions including any treatments and genetic manipulations. Functions such as the advanced search offering multiple choices from custom-built controlled vocabularies in 15 categories in parallel, the pairwise comparison of any chosen pools, and control-treatment correlations provide users with the possibility to quickly recognize and graphically analyse changes in the dNTP pools in function of a chosen parameter. Unbalanced dNTP pools, as well as the balanced accumulation or depletion of all four dNTPs result in genomic instability. Accordingly, key roles of dNTP pool homeostasis have been demonstrated in cancer progression, development, ageing and viral infections among others. dNTPpoolDB is designated to promote research in these fields and fills a longstanding gap in genome metabolism research.
LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes
Authors: Jia Lihua , Li Yang , Huang Fangfang , Jiang Yingru , Li Haoran , Wang Zhizhan , Chen Tiantian , Li Jiaming , Zhang Zhang , Yao Wen
Published: September 2021

Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.
NPCDR: natural product-based drug combination and its disease-specific molecular regulation
Authors: Sun Xueni , Zhang Yintao , Zhou Ying , Lian Xichen , Yan Lili , Pan Ting , Jin Ting , Xie Han , Liang Zimao , Qiu Wenqi , Wang Jianxin , Li Zhaorong , Zhu Feng , Sui Xinbing
Published: September 2021

Natural product (NP) has a long history in promoting modern drug discovery, which has derived or inspired a large number of currently prescribed drugs. Recently, the NPs have emerged as the ideal candidates to combine with other therapeutic strategies to deal with the persistent challenge of conventional therapy, and the molecular regulation mechanism underlying these combinations is crucial for the related communities. Thus, it is urgently demanded to comprehensively provide the disease-specific molecular regulation data for various NP-based drug combinations. However, no database has been developed yet to describe such valuable information. In this study, a newly developed database entitled ‘Natural Product-based Drug Combination and Its Disease-specific Molecular Regulation (NPCDR)’ was thus introduced. This database was unique in (a) providing the comprehensive information of NP-based drug combinations & describing their clinically or experimentally validated therapeutic effect, (b) giving the disease-specific molecular regulation data for a number of NP-based drug combinations, (c) fully referencing all NPs, drugs, regulated molecules/pathways by cross-linking them to the available databases describing their biological or pharmaceutical characteristics. Therefore, NPCDR is expected to have great implications for the future practice of network pharmacology, medical biochemistry, drug design, and medicinal chemistry. This database is now freely accessible without any login requirement at both official (https://idrblab.org/npcdr/) and mirror (http://npcdr.idrblab.net/) sites.
Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip
Authors: Novotný Aleš , Novotný Jan , Kejnovská Iva , Vorlíčková Michaela , Fiala Radovan , Marek Radek
Published: September 2021

Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence–structure–stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.