bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface manifestation of stochastically excited internal gravity waves
Authors: Lecoanet Daniel , Cantiello Matteo , Anders Evan H , Quataert Eliot , Couston Louis-Alexandre , Bouffard Mathieu , Favier Benjamin , Le Bars Michael 
Published: September 2021

ABSTRACT
Recent photometric observations of massive stars show ubiquitous low-frequency ‘red noise’ variability, which has been interpreted as internal gravity waves (IGWs). Simulations of IGWs generated by convection show smooth surface wave spectra, qualitatively matching the observed red noise. Theoretical calculations using linear wave theory by Shiode et al. and Lecoanet et al. predict IGWs should manifest at the surface as regularly spaced peaks associated with standing g modes. In light of the apparent discrepancy between these theories and simulations/observations, we test the theories with simplified 2D numerical simulations of wave generation by convection. The simulations agree with the transfer function calculations presented in Lecoanet et al., demonstrating that the transfer function correctly models linear wave propagation. However, there are differences between our simulations and the g-mode amplitude predictions of Shiode et al. This is because that work did not take into account the finite width of the g-mode peaks; after correcting for this finite width, we again find good agreement between theory and simulations. This paper verifies the theoretical approach of Lecoanet et al. and strengthens their conclusion that IGWs generated by core convection do not have a surface manifestation consistent with observed low-frequency variability of massive stars.
Fragmentation of ring galaxies and transformation to clumpy galaxies
Authors: Inoue Shigeki , Yoshida Naoki , Hernquist Lars 
Published: September 2021

ABSTRACT
We study the fragmentation of collisional ring galaxies (CRGs) using a linear perturbation analysis that computes the physical conditions of gravitational instability, as determined by the balance of self-gravity of the ring against pressure and Coriolis forces. We adopt our formalism to simulations of CRGs and show that the analysis can accurately characterize the stability and onset of fragmentation, although the linear theory appears to underpredict the number of fragments of an unstable CRG by a factor of 2. In addition, since the orthodox ‘density-wave’ model is inapplicable to such self-gravitating rings, we devise a simple approach that describes the rings propagating as material waves. We find that the toy model can predict whether the simulated CRGs fragment or not using information from their pre-collision states. We also apply our instability analysis to a CRG discovered at a high redshift, z = 2.19. We find that a quite high-velocity dispersion is required for the stability of the ring, and therefore the CRG should be unstable to ring fragmentation. CRGs are rarely observed at high redshifts, and this may be because CRGs are usually too faint. Since the fragmentation can induce active star formation and make the ring bright enough to observe, the instability could explain this rarity. An unstable CRG fragments into massive clumps retaining the initial disc rotation, and thus it would evolve into a clumpy galaxy with a low surface density in an interclump region.
Profile changes associated with dispersion measure events in PSR J1713+0747
Authors: Lin Fang Xi , Lin Hsiu-Hsien , Luo Jing , Main Robert , McKee James , Pen Ue-Li , Simard Dana , van Kerkwijk Marten H 
Published: September 2021

ABSTRACT
Propagation effects in the interstellar medium and intrinsic profile changes can cause variability in the timing of pulsars, which limits the accuracy of fundamental science done via pulsar timing. One of the best timing pulsars, PSR J1713+0747, has gone through two ‘dip’ events in its dispersion measure (DM) time series. If these events reflect real changes in electron column density, they should lead to multiple imaging. We show that the events are well fitted by an underdense corrugated sheet model, and look for associated variability in the pulse profile using principal component analysis. We find that there are transient pulse profile variations, but they vary in concert with the DM, unlike what is expected from lensing due to a corrugated sheet. The change is consistent in shape across profiles from both the Green Bank and Arecibo radio observatories, and its amplitude appears to be achromatic across the 820-MHz, 1.4-GHz, and 2.3-GHz bands, again unlike expected from interference between lensed images. This result is puzzling. We note that some of the predicted lensing effects would need higher time and frequency resolution data than used in this analysis. Future events appear likely, and storing baseband data or keeping multiple time–frequency resolutions will allow more in-depth study of propagation effects and hence improvements to pulsar timing accuracy.
NuSTAR monitoring of MAXI J1348−630: evidence of high density disc reflection
Authors: Chakraborty Sudip , Ratheesh Ajay , Bhattacharyya Sudip , Tomsick John A , Tombesi Francesco , Fukumura Keigo , Jaisawal Gaurava K 
Published: September 2021

ABSTRACT
We present the broad-band spectral analysis of all the six hard, intermediate, and soft state NuSTAR observations of the recently discovered transient black hole X-ray binary MAXI J1348−630 during its first outburst in 2019. We first model the data with a combination of a multicolour disc and a relativistic blurred reflection, and, whenever needed, a distant reflection. We find that this simple model scheme is inadequate in explaining the spectra, resulting in a very high iron abundance. We therefore explore the possibility of reflection from a high-density disc. We use two different sets of models to describe the high-density disc reflection: relxill-based reflection models, and reflionx-based ones. The reflionx-based high-density disc reflection models bring down the iron abundance to around the solar value, while the density is found to be $10^{20.3-21.4}\, \rm cm^{-3}$. We also find evidence of a high-velocity outflow in the form of ∼7.3 keV absorption lines. The consistency between the best-fitting parameters for different epochs and the statistical significance of the corresponding model indicates the existence of high-density disc reflection in MAXI J1348−630.
SCSS-Net: solar corona structures segmentation by deep learning
Authors: Mackovjak Šimon , Harman Martin , Maslej-Krešňáková Viera , Butka Peter 
Published: September 2021

ABSTRACT
Structures in the solar corona are the main drivers of space weather processes that might directly or indirectly affect the Earth. Thanks to the most recent space-based solar observatories, with capabilities to acquire high-resolution images continuously, the structures in the solar corona can be monitored over the years with a time resolution of minutes. For this purpose, we have developed a method for automatic segmentation of solar corona structures observed in the EUV spectrum that is based on a deep-learning approach utilizing convolutional neural networks. The available input data sets have been examined together with our own data set based on the manual annotation of the target structures. Indeed, the input data set is the main limitation of the developed model’s performance. Our SCSS-Net model provides results for coronal holes and active regions that could be compared with other generally used methods for automatic segmentation. Even more, it provides a universal procedure to identify structures in the solar corona with the help of the transfer learning technique. The outputs of the model can be then used for further statistical studies of connections between solar activity and the influence of space weather on Earth.
The role of scatter and satellites in shaping the large-scale clustering of X-ray AGN as a function of host galaxy stellar mass
Authors: Viitanen A , Allevato V , Finoguenov A , Shankar F , Marsden C 
Published: September 2021

ABSTRACT
The co-evolution between central supermassive black holes (BHs), their host galaxies, and dark matter haloes is still a matter of intense debate. Present theoretical models suffer from large uncertainties and degeneracies, for example, between the fraction of accreting sources and their characteristic accretion rate. In recent work, we showed that active galactic nuclei (AGNs) clustering represents a powerful tool to break degeneracies when analysed in terms of mean BH mass, and that AGN bias at fixed stellar mass is largely independent of most of the input parameters, such as the AGN duty cycle and the mean scaling between BH mass and host galaxy stellar mass. In this paper, we take advantage of our improved semi-empirical methodology and recent clustering data derived from large AGN samples at z ∼ 1.2, demonstrate that the AGN bias as a function of host galaxy stellar mass is a crucial diagnostic of the BH–galaxy connection, and is highly dependent on the scatter around the BH mass–galaxy mass scaling relation and on the relative fraction of satellite and central active BHs. Current data at z ∼ 1.2 favour relatively high values of AGN in satellites, pointing to a major role of disc instabilities in triggering AGN, unless a high minimum host halo mass is assumed. The data are not decisive on the magnitude/covariance of the BH–galaxy scatter at z ∼ 1.2 and intermediate host masses $M_\mathrm{star} \lesssim 10^{11} \, \mathrm{M}_\mathrm{star}$. However, future surveys like Euclid/LSST will be pivotal in shedding light on the BH–galaxy co-evolution.
FAST early pulsar discoveries: Effelsberg follow-up
Authors: Cruces M , Champion D J , Li (李 菂) D , Kramer M , Zhu W W , Wang P , Cameron A D , Chen Y T , Hobbs G , Freire P C C , Graikou E , Krco M , Liu Z J , Miao C C , Niu J , Pan Z C , Qian L , Xue M Y , Xie X Y , You S P , Yu X H , Yuan M , Yue Y L , Zhu Y ,   CRAFTS collaboration, Lackeos K , Porayko N , Wongphecauxon J , Main R 
Published: September 2021

ABSTRACT
We report the follow-up of 10 pulsars discovered by the Five-hundred-metre Aperture Spherical radio-Telescope (FAST) during its commissioning. The pulsars were discovered at a frequency of 500-MHz using the ultrawide-band (UWB) receiver in drift-scan mode, as part of the Commensal Radio Astronomy FAST Survey (CRAFTS). We carried out the timing campaign with the 100-m Effelsberg radio-telescope at L-band around 1.36 GHz. Along with 11 FAST pulsars previously reported, FAST seems to be uncovering a population of older pulsars, bordering and/or even across the pulsar death-lines. We report here two sources with notable characteristics. PSR J1951+4724 is a young and energetic pulsar with nearly 100 per cent of linearly polarized flux density and visible up to an observing frequency of 8 GHz. PSR J2338+4818, a mildly recycled pulsar in a 95.2-d orbit with a Carbon–Oxygen white dwarf (WD) companion of $\gtrsim 1\, \rm {M}_{\odot }$, based on estimates from the mass function. This system is the widest WD binary with the most massive companion known to-date. Conspicuous discrepancy was found between estimations based on NE2001 and YMW16 electron density models, which can be attributed to underrepresentation of pulsars in the sky region between Galactic longitudes 70° &lt; l &lt; 100°. This work represents one of the early CRAFTS results, which start to show potential to substantially enrich the pulsar sample and refine the Galactic electron density model.
Host galaxy line diagnostics for the candidate tidal disruption events XMMSL1 J111527.3+180638 and PTF09axc
Authors: Inkenhaag Anne , Jonker Peter G , Cannizzaro Giacomo , Mata Sánchez Daniel , Saxton Richard D 
Published: September 2021

ABSTRACT
We present results of our analysis of spectra of the host galaxies of the candidate tidal disruption events (TDEs) XMMSL1 J111527.3+180638 and PTF09axc to determine the nature of these transients. We subtract the starlight component from the host galaxy spectra to determine the origin of the nuclear emission lines. Using a Baldwin–Phillips–Terlevich (BPT) diagram, we conclude that the host galaxy of XMMSL1 J111527.3+180638 is classified as a Seyfert galaxy, suggesting this transient is likely to be caused by (extreme) variability in the active galactic nucleus. We find that the host of PTF09axc falls in the ‘star-forming’ region of the BPT diagram, implying that the transient is a strong TDE candidate. For both galaxies, we find a WISE colour difference of W1 − W2 &lt; 0.8, which means there is no indication of a dusty torus and therefore an active galactic nucleus, seemingly contradicting our BPT finding for the host of XMMSL1 J111527.3+180638. We discuss possible reasons for the discrepant results obtained through these two methods.
High-dispersion spectroscopy of AE Aquarii – II. Evidence of material orbiting the primary star
Authors: Ramírez S H , Echevarría J 
Published: September 2021

ABSTRACT
We present a second paper related to the analyses of high-dispersion spectroscopic observations of the magnetic cataclysmic variable AE Aquarii. We focus our efforts on the study of the emission lines and their radial velocities. We detect a sinusoidal behaviour, in several of the observing runs, with variable amplitudes. Of those runs presented, the velocity curve of 2000 August shows less instability in the emission material. In this case, we obtain K1 = 114 ± 8 km s−1, which we take as our best value for the radial velocity of the primary. This result is consistent within 2σ with previously published values obtained using indirect methods. We interpret this consistency as observational evidence of material orbiting the rapidly rotating primary star. We present a Doppler tomography study, which shows that the H α emission is primarily concentrated within a blob in the lower left quadrant, a structure similar to that predicted by the propeller model. However, for 2000 August, we find the emission centred around the position of the white dwarf, which supports the possibility of the K1 value of this run of being a valid approximation of the orbital motion of the white dwarf.
Numerical convergence of pre-initial conditions on dark matter halo properties
Authors: Zhang Tianchi , Liao Shihong , Li Ming , Zhang Jiajun 
Published: September 2021

ABSTRACT
Generating pre-initial conditions (or particle loads) is the very first step to set up a cosmological N-body simulation. In this work, we revisit the numerical convergence of pre-initial conditions on dark matter halo properties using a set of simulations which only differs in initial particle loads, i.e. grid, glass, and the newly introduced capacity constrained Voronoi tessellation (CCVT). We find that the median halo properties agree fairly well (i.e. within a convergence level of a few per cent) among simulations running from different initial loads. We also notice that for some individual haloes cross-matched among different simulations, the relative difference of their properties sometimes can be several tens of per cent. By looking at the evolution history of these poorly converged haloes, we find that they are usually merging haloes or haloes have experienced recent merger events, and their merging processes in different simulations are out-of-sync, making the convergence of halo properties become poor temporarily. We show that, comparing to the simulation starting with an anisotropic grid load, the simulation with an isotropic CCVT load converges slightly better to the simulation with a glass load, which is also isotropic. Among simulations with different pre-initial conditions, haloes in higher density environments tend to have their properties converged slightly better. Our results confirm that CCVT loads behave as well as the widely used grid and glass loads at small scales, and for the first time we quantify the convergence of two independent isotropic particle loads (i.e. glass and CCVT) on halo properties.
A pathogenic DMC1 frameshift mutation causes nonobstructive azoospermia but not primary ovarian insufficiency in humans
Authors: Cao Dandan , Shi Fu , Guo Chenxi , Liu Ye , Lin Zexiong , Zhang Juanhui , Li Raymond Hang Wun , Yao Yuanqing , Liu Kui , Ng Ernest Hung Yu , Yeung William Shu Biu , Wang Tianren 
Published: September 2021

Abstract
Nonobstructive azoospermia (NOA) and diminished ovarian reserve (DOR) are two disorders that can lead to infertility in males and females. Genetic factors have been identified to contribute to NOA and DOR. However, the same genetic factor that can cause both NOA and DOR remains largely unknown. To explore the candidate pathogenic gene that causes both NOA and DOR, we conducted whole-exome sequencing (WES) in a non-consanguineous family with two daughters with DOR and a son with NOA. We detected one pathogenic frameshift variant (NM_007068:c.28delG, p. Glu10Asnfs*31) following a recessive inheritance mode in a meiosis gene DMC1 (DNA meiotic recombinase 1). Clinical analysis showed reduced antral follicle number in both daughters with DOR, but metaphase II oocytes could be retrieved from one of them. For the son with NOA, no spermatozoa were found after microsurgical testicular sperm extraction. A further homozygous Dmc1 knockout mice study demonstrated total failure of follicle development and spermatogenesis. These results revealed a discrepancy of DMC1 action between mice and humans. In humans, DMC1 is required for spermatogenesis but is dispensable for oogenesis, although the loss of function of this gene may lead to DOR. To our knowledge, this is the first report on the homozygous frameshift mutation as causative for both NOA and DOR and demonstrating that DMC1 is dispensable in human oogenesis.
A Grid in Flux: Sound and Timing in Electronic Dance Music
Authors: Brøvig-Hanssen Ragnhild , Sandvik Bjørnar , Aareskjold-Drecker Jon Marius , Danielsen Anne 
Published: September 2021

AbstractResearchers have argued that temporal microdeviations from the metric grid, such as those produced by musicians in performance, are crucial to making a musical rhythm groovy and danceable. It is curious, then, that the music currently dominating the dance floor, “electronic dance music” or EDM, is typically characterized by grid-based rhythms. But is such a “mechanistic,” grid-based aesthetic necessarily devoid of microrhythmic nuance? In this article, we aim to show that the microrhythmic component of an engaging groove involves the manipulation of more than simply the onset locations of rhythmic events—the sonic features fundamentally contribute to shaping the groove as well. In particular, we seek to demonstrate that EDM producers, with their preference for a grid-based microtiming aesthetic, are very sensitive to and adept at manipulating such sonic features for expressive effect. Drawing on interviews with EDM producers, we show that producers are often concerned with both sonic and temporal features, as well as their interactions. We argue that sonic features are crucial to shaping groove and feel at the micro level of rhythm. Moreover, such features also tend to introduce an indirect microtiming aspect to the grid-based aesthetic of EDM through the ways in which they shape timing at the perceptual level.
Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
Authors: Jun Hyungmin , Wang Xiao , Parsons Molly F , Bricker William P , John Torsten , Li Shanshan , Jackson Steve , Chiu Wah , Bathe Mark 
Published: September 2021

Abstract
Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.
Theoretical basis for stabilizing messenger RNA through secondary structure design
Authors: Wayment-Steele Hannah K , Kim Do Soon , Choe Christian A , Nicol John J , Wellington-Oguri Roger , Watkins Andrew M , Parra Sperberg R Andres , Huang Po-Ssu , Participants Eterna , Das Rhiju 
Published: September 2021

AbstractRNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term ‘superfolder’ mRNAs. These designs exhibit a wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity. Furthermore, their folding is robust to temperature, computer modeling method, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1 and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.