bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single fluid versus multifluid: comparison between single-fluid and multifluid dust models for disc–planet interactions
Authors: Chan Kevin , Paardekooper Sijme-Jan 
Published: September 2022

ABSTRACT
Recent observations of substructures such as dust gaps and dust rings in protoplanetary discs have highlighted the importance of including dust into purely gaseous disc models. At the same time, computational difficulties arise with the standard models of simulating the dust and gas separately. These include the cost of accurately simulating the interactions between well-coupled dust and gas and issues of dust concentration in areas below resolution of the gas phase. We test a single-fluid approach that incorporates the terminal velocity approximation valid for small particles, which can overcome these difficulties, through modification of FARGO3D. We compare this single-fluid model with a multifluid model for a variety of planet masses. We find differences in the dust density distribution in all cases. For high-mass, gap-opening planets, we find differences in the amplitude of the resulting dust rings, which we attribute to the failure of the terminal velocity approximation around shocks. For low-mass planets, both models agree everywhere except in the corotation region, where the terminal velocity approximation shows overdense dust lobes. We tentatively interpret these as dusty equivalents of thermal lobes seen in non-isothermal simulations with thermal diffusion, but more work is necessary to confirm this. At the same resolution, the computational time for the terminal velocity approximation model is significantly less than a two-fluid model. We conclude that the terminal velocity approximation is a valuable tool for modelling a protoplanetary disc, but care should be taken when shocks are involved.
Impact of subsurface convective flows on the formation of sunspot magnetic field and energy build-up
Authors: Kaneko Takafumi , Hotta Hideyuki , Toriumi Shin , Kusano Kanya 
Published: September 2022

ABSTRACT
Strong solar flares occur in δ-spots characterized by the opposite-polarity magnetic fluxes in a single penumbra. Sunspot formation via flux emergence from the convection zone to the photosphere can be strongly affected by convective turbulent flows. It has not yet been shown how crucial convective flows are for the formation of δ-spots. The aim of this study is to reveal the impact of convective flows in the convection zone on the formation and evolution of sunspot magnetic fields. We simulated the emergence and transport of magnetic flux tubes in the convection zone using radiative magnetohydrodynamics code r2d2. We carried out 93 simulations by allocating the twisted flux tubes to different positions in the convection zone. As a result, both δ-type and β-type magnetic distributions were reproduced only by the differences in the convective flows surrounding the flux tubes. The δ-spots were formed by the collision of positive and negative magnetic fluxes on the photosphere. The unipolar and bipolar rotations of the δ-spots were driven by magnetic twist and writhe, transporting magnetic helicity from the convection zone to the corona. We detected a strong correlation between the distribution of the non-potential magnetic field in the photosphere and the position of the downflow plume in the convection zone. The correlation could be detected 20–30 h before the flux emergence. The results suggest that high free energy regions in the photosphere can be predicted even before the magnetic flux appears in the photosphere by detecting the downflow profile in the convection zone.
VLT/UVES observation of the SDSS J2357−0048 outflow
Authors: Byun Doyee , Arav Nahum , Hall Patrick B 
Published: September 2022

ABSTRACT
We found a broad absorption line (BAL) outflow in the VLT/UVES spectrum of the quasar SDSS J235702.54−004824.0, in which we identified four subcomponents. We measured the column densities of the ions in one of the subcomponents (v = −1600 km s−1), which include O i and Fe ii. We found the kinetic luminosity of this component to be at most $\sim 2.4{{\ \rm per\ cent}}$ of the quasar’s Eddington luminosity. This is near the amount required to contribute to active galactic nucleus feedback. We also examined the time variability of a C iv mini-BAL found at v = −8700 km s−1, which shows a shallower and narrower absorption feature attached to it in previous SDSS observations from 2000 to 2001, but not in the spectra from 2005 and onwards.
Environmental variation of the low-mass IMF
Authors: Tanvir Tabassum S , Krumholz Mark R , Federrath Christoph 
Published: September 2022

ABSTRACT
We use a series of magnetohydrodynamic simulations including both radiative and protostellar outflow feedback to study environmental variation of the initial mass function (IMF). The simulations represent a carefully-controlled experiment whereby we keep all dimensionless parameters of the flow constant except for those related to feedback. We show that radiation feedback suppresses the formation of lower mass objects more effectively as the surface density increases, but this only partially compensates for the decreasing Jeans mass in denser environments. Similarly, we find that protostellar outflows are more effective at suppressing the formation of massive stars in higher surface density environments. The combined effect of these two trends is towards an IMF with a lower characteristic mass and a narrower overall mass range in high surface density environments. We discuss the implications for these findings for the interpretation of observational evidence of IMF variation in early type galaxies.
The global structure of magnetic fields and gas in simulated Milky Way-analogue galaxies
Authors: Wibking Benjamin D , Krumholz Mark R 
Published: September 2022

ABSTRACTWe simulate an isolated, magnetized Milky Way-like disc galaxy using a self-consistent model of unresolved star formation and feedback, evolving the system until it reaches statistical steady state. We show that the quasi-steady-state structure is distinctly layered in galactocentric height z, with a broken power-law structure in Alfven Mach number and plasma beta. Magnetic pressure exceeds turbulent and thermal pressures after the gas is depleted to levels below that of the present-day Galaxy, but is subdominant at higher gas fractions and star formation rates. We find field strengths, gas surface densities, and star formation rates that agree well with those observed in the Solar neighbourhood. The most significant dynamical effect of magnetic fields on the global properties of the disc is a reduction of the star formation rate by a factor of 1.5–2 with respect to an unmagnetized control simulation. At a fixed star formation rate of approximately $2 \, {\rm M}_{\odot }$ yr−1, there is no significant difference in the mass outflow rates or profiles between the magnetized and non-magnetized simulations. Our results for the global structure of the magnetic field have significant implications for models of cosmic ray-driven winds and cosmic ray propagation in the Galaxy, and can be tested against observations with the forthcoming Square Kilometre Array and other facilities. Finally, we report the discovery of a physical error in the implementation of neutral gas heating and cooling in the popular gizmo code, which may lead to qualitatively incorrect phase structures if not corrected.
On the estimation of frequency residuals in a radio occultation experiment
Authors: Tripathi Keshav R , Choudhary R K , Jayalal Lakshmi 
Published: September 2022

ABSTRACT
In the radio occultation (RO) experiments, the difference between observed and predicted Doppler, called frequency residuals, form basic input data to retrieve the vertical profiles of atmospheric parameters. In this paper, we compare different methods to estimate frequency residuals in a one-way downlink single frequency RO experiment, and propose a suitable method that not only improves the residual estimates but is easy to implement too. We show that the Doppler broadening in the received radio signals, which causes uncertainties in Doppler estimation, is predominantly due to changes in the line of sight velocity between the receiver and transmitter during the sampling period. Coupled with the random noises in the receiving system and fluctuations in plasma medium along the propagation path, the resultant uncertainty in Doppler estimates can become as large as 60 Hz. The expected phase changes due to the ionospheric dispersion/refraction, on the other hand, are of the order of 0.01–2 Hz only. To circumvent the issue, we re-sample the observed radio signals in smaller time packets. After removing DC constant shift, a narrow bandpass filter is applied to suppress small-scale fluctuations and Doppler and power of the received signals are estimated. Using Akatsuki radio signals, tracked at Indian Deep Space Network as test data sets, we compare our results with the residuals provided by the Akatsuki team and using the method used for analysing Cassini RO data. We show that our method provides a better estimate of frequency residuals with lesser standard deviations.
Photometry and astrometry with JWST – I. NIRCam point spread functions and the first JWST colour–magnitude diagrams of a globular cluster
Authors: Nardiello D , Bedin L R , Burgasser A , Salaris M , Cassisi S , Griggio M , Scalco M 
Published: September 2022

ABSTRACT
As the James Webb Space Telescope (JWST) has become fully operational, early release data are now available to begin building the tools and calibrations for precision point-source photometry and astrometry in crowded cluster environments. Here, we present our independent reduction of NIRCam imaging of the metal-poor globular cluster M 92, which were collected under Director’s Discretionary Early Release Science programme ERS-1334. We derived empirical models of the point spread function (PSF) for filters F090W, F150W, F277W, and F444W, and find that these PSFs: (i) are generally undersampled (FWHM ∼ 2 pixel) in F150W and F444W and severely undersampled (FWHM ∼ 1 pixel) in F090W and F277W; (ii) have significant variation across the field of view, up to ∼15–20 per cent; and (iii) have temporal variations of ∼ 3–4 per cent across multi-epoch exposures. We deployed our PSFs to determine the photometric precision of NIRCam for stars in the crowded, central regions of M 92, measured to be at the ∼0.01 mag level. We use these data to construct the first JWST colour–magnitude diagrams of a globular cluster. Employing existing stellar models, we find that the data reach almost the bottom of the M 92 main sequence (∼0.1 M⊙), and reveal 24 white dwarf candidate members of M 92 in the brightest portion of the white dwarf cooling sequence. The latter are confirmed through a cross-match with archival HST UV and optical data. We also detect the presence of multiple stellar populations along the low-mass main sequence of M 92.
Telluric absorption lines in the ALMA spectra of η Car
Authors: Abraham Zulema , Beaklini Pedro P B , Cox Pierre , Falceta-Gonçalves Diego , Nyman Lars-Åke 
Published: September 2022

ABSTRACT
The massive binary system formed by η Car and an unknown companion is a strong source at millimetre and submillimetre wavelengths. Close to the stars, continuum bremsstrahlung and radio recombination lines originate in the massive ionized wind of η Car and in several compact sources of high density plasma. Molecular lines are also detected at these wavelengths, some of them are seen in absorption towards the continuum emission region, many of them revealed by ALMA observations. However, because the ALMA atmospheric calibration is performed in a low spectral resolution mode, telluric lines can still be present in some high-resolution spectra of scientific products, which could lead to a false identification of molecules. In this work, we explore three different sets of ALMA archive data of η Car, including high resolution (0.065 arcsec × 0.043 arcsec) observations recently published by our group, to verify which of these absorption lines are real and discuss their origin. We conclude that some of them truly originate in clouds close to the binary system, while others are artefacts of a faulty elimination of telluric lines during ALMA calibration procedure. We found that these absorption lines are not present in the phase calibrators because they are much weaker than η Car, where the absorption line appears because the high intensity continuum enhances the small individual systematic calibration errors.
Image reconstruction algorithms in radio interferometry: From handcrafted to learned regularization denoisers
Authors: Terris Matthieu , Dabbech Arwa , Tang Chao , Wiaux Yves 
Published: September 2022

ABSTRACTWe introduce a new class of iterative image reconstruction algorithms for radio interferometry, at the interface of convex optimization and deep learning, inspired by plug-and-play methods. The approach consists in learning a prior image model by training a deep neural network (DNN) as a denoiser, and substituting it for the handcrafted proximal regularization operator of an optimization algorithm. The proposed AIRI (‘AI for Regularization in radio-interferometric Imaging’) framework, for imaging complex intensity structure with diffuse and faint emission from visibility data, inherits the robustness and interpretability of optimization, and the learning power and speed of networks. Our approach relies on three steps. First, we design a low dynamic range training data base from optical intensity images. Secondly, we train a DNN denoiser at a noise level inferred from the signal-to-noise ratio of the data. We use training losses enhanced with a non-expansiveness term ensuring algorithm convergence, and including on-the-fly data base dynamic range enhancement via exponentiation. Thirdly, we plug the learned denoiser into the forward–backward optimization algorithm, resulting in a simple iterative structure alternating a denoising step with a gradient-descent data-fidelity step. We have validated AIRI against clean, optimization algorithms of the SARA family, and a DNN trained to reconstruct the image directly from visibility data. Simulation results show that AIRI is competitive in imaging quality with SARA and its unconstrained forward–backward-based version uSARA, while providing significant acceleration. clean remains faster but offers lower quality. The end-to-end DNN offers further acceleration, but with far lower quality than AIRI.
Quantum fluctuations masquerade as haloes: bounds on ultra-light dark matter from quadruply imaged quasars
Authors: Laroche Alexander , Gilman Daniel , Li Xinyu , Bovy Jo , Du Xiaolong 
Published: September 2022

ABSTRACT
Ultra-light dark matter (ULDM) refers to a class of theories, including ultra-light axions, in which particles with mass $m_{\psi } \lt 10^{-20}\, \rm {eV}$ comprise a significant fraction of the dark matter. A galactic scale de Broglie wavelength distinguishes these theories from cold dark matter (CDM), suppressing the overall abundance of structure on sub-galactic scales, and producing wave-like interference phenomena in the density profiles of haloes. With the aim of constraining the particle mass, we analyse the flux ratios in a sample of 11 quadruple-image strong gravitational lenses. We account for the suppression of the halo mass function and concentration–mass relation predicted by ULDM theories, and the wave-like fluctuations in the host halo density profile, calibrating the model for the wave interference against numerical simulations of galactic-scale haloes. We show that the granular structure of halo density profiles, in particular, the amplitude of the fluctuations, significantly impacts image flux ratios, and therefore inferences on the particle mass derived from these data. We infer relative likelihoods of CDM to ULDM of 8:1, 7:1, 6:1, and 4:1 for particle masses $\log _{10}(m_\psi /\rm {eV})\in [-22.5,-22.25], [-22.25,-22.0],[-22.0,-21.75], [-21.75,-21.5]$, respectively. Repeating the analysis and omitting fluctuations associated with the wave interference effects, we obtain relative likelihoods of CDM to ULDM with a particle mass in the same ranges of 98:1, 48:1, 26:1, and 18:1, highlighting the significant perturbation to image flux ratios associated with the fluctuations. Nevertheless, our results disfavour the lightest particle masses with $m_{\psi } \lt 10^{-21.5}\, \rm {eV}$, adding to mounting pressure on ultra-light axions as a viable dark matter candidate.
A pilot biomonitoring study of air pollution in the urban area of Sarajevo, Bosnia and Herzegovina: genotoxicity assessment in buccal cells
Authors: Cetkovic Tamara , Haveric Anja , Behmen Selma , Hadzic Omanovic Maida , Caluk Klacar Lejla , Dzaferspahic Alen , Durmisevic Irma , Mehanovic Mahira , Haveric Sanin 
Published: September 2022

Abstract
Air pollution, recognized as a human carcinogen, is a significant cause of death in industrial and developing countries, and Bosnia and Herzegovina (B&H) is one of the leading countries for air pollution—caused death rate and has the poorest urban air quality in Europe. Despite a population decrease, urban air pollution in B&H has increased due to traffic pollution and still intensive use of solid fuel for heating and cooking. Human biomonitoring studies, regarding the described air pollution, have not been conducted before, and particularly have not been conducted in the region of Sarajevo. Good health, well-being, and environmental protection are part of the 17 defined Sustainable Development Global Goals. Accordingly, this study aimed to determine baseline levels of DNA damage in a group of Sarajevo citizens and to compare seasonal variations in DNA damage in relation to the reported levels of air pollution. From 33 individuals included in the study, samples were collected in the summer and winter seasons. The buccal micronucleus cytome (BMCyt) assay and comet assay in leucocytes isolated from saliva were performed. Mean values and standard deviations of log-transformed tail intensity (%), tail length (µm), and tail moment results in winter were 1.14 ± 0.23, 2.20 ± 0.14, and 1.03 ± 0.29, respectively, while in the summer season those values were 1.19 ± 0.19, 2.25 ± 0.17, and 1.07 ± 0.25, respectively. No significant differences were found for the comet assay parameters. Nevertheless, BMCyt results showed significant increases in micronuclei (P = .008), binuclear cells (P = .04), karyolysis (P = .0003), condensed chromatin (P = .03), and pyknosis (P = .002) in winter. Although the results of comet and BMCyt assays are not in accordance, this study contributes to the human air pollution biomonitoring in Sarajevo, B&H, and based on the genotoxic effects of air pollution evidenced by the BMCyt biomarker further studies of this kind are necessary.
Super-enhancer-controlled positive feedback loop BRD4/ERα–RET–ERα promotes ERα-positive breast cancer
Authors: Zheng Zao-zao , Xia Lin , Hu Guo-sheng , Liu Jun-yi , Hu Ya-hong , Chen Yu-jie , Peng Jia-yin , Zhang Wen-juan , Liu Wen 
Published: September 2022

Abstract
Estrogen and estrogen receptor alpha (ERα)-induced gene transcription is tightly associated with ERα-positive breast carcinogenesis. ERα-occupied enhancers, particularly super-enhancers, have been suggested to play a vital role in regulating such transcriptional events. However, the landscape of ERα-occupied super-enhancers (ERSEs) as well as key ERα-induced target genes associated with ERSEs remain to be fully characterized. Here, we defined the landscape of ERSEs in ERα-positive breast cancer cell lines, and demonstrated that bromodomain protein BRD4 is a master regulator of the transcriptional activation of ERSEs and cognate ERα target genes. RET, a member of the tyrosine protein kinase family of proteins, was identified to be a key ERα target gene of BRD4-regulated ERSEs, which, in turn, is vital for ERα-induced gene transcriptional activation and malignant phenotypes through activating the RAS/RAF/MEK2/ERK/p90RSK/ERα phosphorylation cascade. Combination therapy with BRD4 and RET inhibitors exhibited additive effects on suppressing ERα-positive breast cancer both in vitro and in vivo, comparable with that of standard endocrine therapy tamoxifen. Furthermore, combination therapy re-sensitized a tamoxifen-resistant ERα-positive breast cancer cell line to tamoxifen treatment. Taken together, our data uncovered the critical role of a super-enhancer-associated positive feedback loop constituting BRD4/ERα–RET–ERα in ERα-positive breast cancer, and suggested that targeting components in this loop would provide a new therapeutic avenue for treating ERα-positive breast cancer in the clinic.
PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information
Authors: Hou Chao , Wang Xinxin , Xie Haotai , Chen Taoyu , Zhu Peiyu , Xu Xiaofeng , You Kaiqiang , Li Tingting 
Published: September 2022

Abstract
Phase separation (PS) proteins form droplets to regulate myriad membraneless organelles (MLOs) and cellular pathways such as transcription, signaling transduction and protein degeneration. PS droplets are usually liquid-like and can convert to hydrogel/solid-like under certain conditions. The PS behavior of proteins is regulated by co-PS partners and mutations, modifications, oligomerizations, repeat regions and alternative splicing of the proteins. With growing interest in PS condensates and associated proteins, we established PhaSepDB 1.0, which provided experimentally verified PS proteins and MLO-related proteins. The past few years witnessed a surge in PS-related research works; thus, we kept updating PhaSepDB. The current PhaSepDB contains 1419 PS entries, 770 low-throughput MLO-related entries and 7303 high-throughput MLO-related entries. We provided more detailed annotations of PS proteins, including PS verification experiments, regions used in experiments, phase diagrams of different experimental conditions, droplet states, co-PS partners and PS regulatory information. We believe that researchers can go further in studying PS proteins with the updated PhaSepDB (http://db.phasep.pro/).
Density-based detection of cell transition states to construct disparate and bifurcating trajectories
Authors: Lan Tian , Hutvagner Gyorgy , Zhang Xuan , Liu Tao , Wong Limsoon , Li Jinyan 
Published: September 2022

Abstract
Tree- and linear-shaped cell differentiation trajectories have been widely observed in developmental biologies and can be also inferred through computational methods from single-cell RNA-sequencing datasets. However, trajectories with complicated topologies such as loops, disparate lineages and bifurcating hierarchy remain difficult to infer accurately. Here, we introduce a density-based trajectory inference method capable of constructing diverse shapes of topological patterns including the most intriguing bifurcations. The novelty of our method is a step to exploit overlapping probability distributions to identify transition states of cells for determining connectability between cell clusters, and another step to infer a stable trajectory through a base-topology guided iterative fitting. Our method precisely re-constructed various benchmark reference trajectories. As a case study to demonstrate practical usefulness, our method was tested on single-cell RNA sequencing profiles of blood cells of SARS-CoV-2-infected patients. We not only re-discovered the linear trajectory bridging the transition from IgM plasmablast cells to developing neutrophils, and also found a previously-undiscovered lineage which can be rigorously supported by differentially expressed gene analysis.