bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamical Simulations of Misaligned Accretion Discs in Binary Systems: Companions tear discs
Authors: Doğan S. , Nixon C. J. , King A. R. , Pringle J. E. , Price D. 
Published: January 2023

AbstractAccretion discs appear in many astrophysical systems. In most cases, these discs are probably not completely axisymmetric. Discs in binary systems are often found to be misaligned with respect to the binary orbit. In this case, the gravitational torque from a companion induces nodal precession in misaligned rings of gas. We first calculate whether this precession is strong enough to overcome the internal disc torques communicating angular momentum. For typical parameters, precession torque wins. To check this result, we perform numerical simulations using the Smoothed Particle Hydrodynamics code, PHANTOM, and confirm that sufficiently thin and sufficiently inclined discs can break into distinct planes that precess effectively independently. Disc tearing is widespread and severely changes the disc structure. It enhances dissipation and promotes stronger accretion onto the central object. We also perform a stability analysis on isolated warped discs to understand the physics of disc breaking and tearing observed in numerical simulations. The instability appears in the form of viscous anti-diffusion of the warp amplitude and the surface density. The discovery of disc breaking and tearing has revealed new physical processes that dramatically change the evolution of accretion discs, with obvious implications for observed systems.
From evolved Long-Period-Variable stars to the evolution of M31
Authors: Torki Maryam , Navabi Mahdieh , Javadi Atefeh , Saremi Elham , van Loon Jacco Th , Ghaziasgar Sepideh 
Published: January 2023

AbstractOne of the ways to understand the genesis and evolution of the universe is to know how galaxies have formed and evolved. In this regard, the study of star formation history (SFH) plays an important role in the accurate understanding of galaxies. In this paper, we used long-period variable stars (LPVs) for estimating the SFH in the Andromeda galaxy (M31). These cool stars reach their peak luminosity in the final stage of their evolution also their birth mass is directly related to their luminosity. Therefore, using stellar evolution models, we construct the mass function and hence the star formation history.
Stellar Population Photometric Synthesis with AI of S-PLUS galaxies
Authors: Cernic Vitor ,   for the S-PLUS collaboration
Published: January 2023

AbstractWe trained a Neural Network that can obtain selected STARLIGHT parameters directly from S-PLUS photometry. The training set consisted of over 55 thousand galaxies with their stellar population parameters obtained from a STARLIGHT application by Cid Fernandes et al. (2005). These galaxies were crossmatched with the S-PLUS iDR 3 database, thus, recovering the photometry for the 12 band filters for 55803 objects. We also considered the spectroscopic redshift for each object which was obtained from the SDSS. Finally, we trained a fully connected Neural Network with the 12-band photometry + redshift as features, and targeted some of the STARLIGHT parameters, such as stellar mass and mean stellar age. The model performed very well for some parameters, for example, the stellar mass, with an error of 0.23 dex. In the future, we aim to apply the model to all S-PLUS galaxies, obtaining never-before-seen photometric synthesis for most objects in the catalogue.
Early structure formation in the THESAN radiation-magneto-hydrodynamics simulations
Authors: Garaldi E. , Kannan R. , Smith A. , Springel V. , Pakmor R. , Vogelsberger M. , Hernquist L. 
Published: January 2023

AbstractThe formation of the first galaxies in the Universe is the new frontier of both galaxy formation and reionization studies. This creates a fierce new challenge, i.e. to simultaneously understand in a unique and coherent picture the processes of galaxy formation and reionization, and – crucially – their connection. To this end, we present the thesan suite of cosmological radiation-magneto-hydrodynamical simulations. They are unique since they: (i) cover a very broad range of spatial and temporal scales; (ii) include an unprecedentedly-broad range of physical processes for simulations of such scales and resolution; (iii) exploit knowledge accumulated at low redshift to minimize the number of free parameters in the physical model; (iv) use a variance-suppression technique in the production of initial conditions to increase their statistical fidelity. Finally, the thesan suite includes multiple runs of the same initial conditions, exploring current unknowns in the physics of dark matter and ionizing sources.
The complex evolution of supermassive black holes in cosmological simulations
Authors: Johansson Peter H. , Mannerkoski Matias , Rantala Antti , Liao Shihong , Rawlings Alexander , Irodotou Dimitrios , Rizzuto Francesco 
Published: January 2023

AbstractWe present here self-consistent zoom-in simulations of massive galaxies forming in a full cosmological setting. The simulations are run with an updated version of the KETJU code, which is able to resolve the gravitational dynamics of their supermassive black holes, while simultaneously modelling the large-scale astrophysical processes in the surrounding galaxies, such as gas cooling, star formation and stellar and AGN feedback. The KETJU code is able to accurately model the complex behaviour of multiple SMBHs, including dynamical friction, stellar scattering and gravitational wave emission, and also to resolve Lidov–Kozai oscillations that naturally occur in hierarchical triplet SMBH systems. In general most of the SMBH binaries form at moderately high eccentricities, with typical values in the range of , meaning that the circular binary models that are commonly used in the literature are insufficient for capturing the typical binary evolution.
Studying Magnetic Field Amplification in Interacting Galaxies Using Numerical Simulations
Authors: Selg Simon , Schmidt Wolfram 
Published: January 2023

AbstractThere are indications that the magnetic field evolution in galaxies might be massively shaped by tidal interactions and mergers between galaxies. The details of the connection between the evolution of magnetic fields and that of their host galaxies is still a field of research.We use a combined approach of magnetohydrodynamics for the baryons and an N-body scheme for the dark matter to investigate magnetic field amplification and evolution in interacting galaxies.We find that, for two colliding equal-mass galaxies and for varying initial relative spatial orientations, magnetic fields are amplified during interactions, yet cannot be sustained. Furthermore, we find clues for an active mean-field dynamo.
Modeling protoplanetary disk evolution in young star forming regions
Authors: Wilhelm Martijn J. C. , Portegies Zwart Simon , Cournoyer-Cloutier Claude , Lewis Sean , Polak Brooke , Tran Aaron , Mac Low Mordecai-Mark , McMillan Stephen L. W. 
Published: January 2023

AbstractStars form in clusters, while planets form in gaseous disks around young stars. Cluster dissolution occurs on longer time scales than disk dispersal. Planet formation thus typically takes place while the host star is still inside the cluster. We explore how the presence of other stars affects the evolution of circumstellar disks. Our numerical approach requires multi-scale and multi-physics simulations where the relevant components and their interactions are resolved. The simulations start with the collapse of a turbulent cloud, from which stars with disks form, which are able to influence each other. We focus on the effect of extinction due to residual cloud gas on the early evolution of circumstellar disks. We find that this extinction protects circumstellar disks against external photoevaporation, but these disks then become vulnerable to dynamic truncation by passing stars. We conclude that circumstellar disk evolution is heavily affected by the early evolution of the cluster.
Toward Realistic Models of Core Collapse Supernovae: A Brief Review
Authors: Mezzacappa Anthony 
Published: January 2023

AbstractMotivated by their role as the direct or indirect source of many of the elements in the Universe, numerical modeling of core collapse supernovae began more than five decades ago. Progress toward ascertaining the explosion mechanism(s) has been realized through increasingly sophisticated models, as physics and dimensionality have been added, as physics and numerical modeling have improved, and as the leading computational resources available to modelers have become far more capable. The past five to ten years have witnessed the emergence of a consensus across the core collapse supernova modeling community that had not existed in the four decades prior. For the majority of progenitors – i.e., slowly rotating progenitors – the efficacy of the delayed shock mechanism, where the stalled supernova shock wave is revived by neutrino heating by neutrinos emanating from the proto-neutron star, has been demonstrated by all core collapse supernova modeling groups, across progenitor mass and metallicity. With this momentum, and now with a far deeper understanding of the dynamics of these events, the path forward is clear. While much progress has been made, much work remains to be done, but at this time we have every reason to be optimistic we are on track to answer one of the most important outstanding questions in astrophysics: How do massive stars end their lives?
Kinetic modeling of auroral events at solar and extrasolar planets
Authors: Shematovich Valery I. , Bisikalo Dmitry V. 
Published: January 2023

AbstractAuroral events are the prominent manifestation of solar/stellar forcing on planetary atmospheres and are closely related to the energy deposition by and evolution of planetary atmospheres. Observations of auroras are widely used to analyze the composition, structure, and chemistry of the atmosphere under study, as well as charged particle and energy fluxes that affect the atmosphere. Numerical kinetic Monte Carlo models had been developed allowing us to study the processes of precipitation of high-energy electrons, protons and hydrogen atoms into the planetary atmospheres on molecular level of description, taking into account the stochastic nature of collisional scattering at high kinetic energies. Such models are used to study auroras at both magnetized and non-magnetized planets in the Solar and extrasolar planetary systems. The current status of the kinetic model is illustrated in application to the auroral events at Mars.
Look Up: Probing the Vertical Profile of New Particle Formation and Growth in the Planetary Boundary Layer With Models and Observations
Authors: O’Donnell Samuel E. , Akherati Ali , He Yicong , Hodshire Anna L. , Shilling John E. , Kuang Chongai , Fast Jerome D. , Mei Fan , Schobesberger Siegfried , Thornton Joel A. , Smith James N. , Jathar Shantanu H. , Pierce Jeffrey R. 
Published: January 2023

AbstractThe processes of new particle formation (NPF) and growth are important contributors to cloud condensation nuclei (CCN) concentrations, and CCN are important for climate from their impact on planetary radiative forcing. While the general ubiquity and importance of NPF is understood, the vertical extent and governing mechanisms of NPF and growth in the lower troposphere are uncertain. We present an analysis of four NPF events and two non‐NPF events during the HI‐SCALE field campaign at the Southern Great Plains observatory in Oklahoma, USA. First, we analyzed airborne and ground‐based observations of aerosol and gas‐phase properties. Second, we used a column aerosol chemistry and microphysics model to probe factors that influence the vertical profile of NPF. During HI‐SCALE, we found several instances of enhanced NPF occurring several hundred meters above the surface; however, the spatio‐temporal characteristics of the observed NPF made comparisons between airborne‐ and ground‐based observations difficult. The model represented the observed NPF (or lack of NPF) and particle growth at the surface to final diameters within 10 nm. The model predicted enhanced NPF rates in the upper mixed layer, and this enhancement is primarily due to the temperature dependence in the NPF schemes, but this was also dependent on the vertical profile of gas‐phase precursors measured during HI‐SCALE. We found vertical mixing in the model either enhanced or suppressed NPF rates, aerosol number concentrations, and particle growth rates at the surface. Finally, our analysis provides insights for future field campaigns and modeling efforts investigating the vertical profile of NPF.
Lower and Upper Plate Controls on Crustal Seismicity in the Southern Central and Patagonian Andes
Authors: Correa‐Otto Sebastian , Gianni Guido M. 
Published: January 2023

AbstractWe analyze crustal seismological records to assess the origin of the variable seismic activity along the southern Central and Patagonian Andes (30°–55°S), an area associated with latitudinal changes in the lower‐plate geometry, upper‐plate deformation, and topography. We carried out a statistical analysis of the seismicity records at crustal depths of 0–50 km from an updated earthquake catalog. Studying the seismicity by its area covered, depth, latitude, and time, this analysis reveals a consistent and drastic decrease in the number of earthquakes south of 38.5°S. We note that the low seismicity area is spatially correlated with a thin, hot, and weak (at least in the forearc region) upper plate and the subduction of a young/warm lower plate with short slab depths (∼150–400 km) beneath Patagonia. Notably, the reduced upper plate seismicity is mimicked at depth by a similar decrease in lower plate seismicity associated with the presence of relatively shallow slabs south of 38.5°S. This observation allows us to suspect a genetic connection between lower plate properties and the striking reduction in the upper‐plate seismicity. We tentatively suggest that the young/warm and short Nazca and Antarctic subducting plates, left after Neogene slab detachments, modified the thermomechanical upper plate structure, triggering the drastic decrease in crustal earthquakes. This process was likely aided by an inherited thin continental margin. This study reveals that slab detachment in non‐collisional settings can impact upper‐plate seismicity.
Two‐Dimensional Modeling of Colloid‐Facilitated Contaminant Transport in Groundwater Flow Systems With Stagnant Zones
Authors: Paswan Akhilesh , Sharma Pramod Kumar 
Published: January 2023

AbstractA mathematical model has been developed for the contaminant transport with colloids in groundwater flow systems with stagnant zones to investigate the effect of stagnant zones on the transport of contaminants with colloids. In the present study, colloids and contaminants are supposed to drift via two coexisting homogeneous regions. The critical limitation of the mobile‐immobile (MIM) model is to deal with the number of parameters used upon application to larger scales for both mobile and immobile regions when a series of transport mechanisms are involved. Therefore, the present model is the first attempt model of the equilibrium approach for mobile‐immobile regions to avoid complexities in the model. The present study includes the effect of the stagnant zone on the plume movement in mobile regions for steady‐state flow conditions, and it is discerned that the plume moves faster in the presence of immobile regions. However, when dispersion, velocity, and pulse duration are decreased, tailing is noticed in the breakthrough profiles. Stagnant regions enhance the transport of contaminants in the porous media and produce augmented breakthrough curves by increasing the velocity in the mobile regions where colloids and contaminants migrate simultaneously. The transport of contaminants can be enhanced in the presence of colloids. However, sensitivity analyses indicate that the combination of different distribution coefficients controls the mobility of contaminants even in the presence of colloids. The proposed model has been validated using experimental data of the single‐porosity model in the presence of colloids and the MIM model in the absence of colloids.
Recent advances in CGG repeat diseases and a proposal of fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, and oculophryngodistal myopathy (FNOP) spectrum disorder
Authors: Ishiura Hiroyuki , Tsuji Shoji , Toda Tatsushi 
Published: January 2023

AbstractWhile whole genome sequencing and long-read sequencing have become widely available, more and more focuses are on noncoding expanded repeats. Indeed, more than half of noncoding repeat expansions related to diseases have been identified in the five years. An exciting aspect of the progress in this field is an identification of a phenomenon called repeat motif–phenotype correlation. Repeat motif–phenotype correlation in noncoding repeat expansion diseases is first found in benign adult familial myoclonus epilepsy. The concept is extended in the research of CGG repeat expansion diseases. In this review, we focus on newly identified CGG repeat expansion diseases, update the concept of repeat motif–phenotype correlation in CGG repeat expansion diseases, and propose a clinical concept of FNOP (fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, and oculopharyngodistal myopathy)-spectrum disorder, which shares clinical features and thus probably share some common disease pathophysiology, to further facilitate discussion and progress in this field.
Aldehyde dehydrogenase 2 alleviates mitochondrial dysfunction by promoting PGC-1α-mediated biogenesis in acute kidney injury
Authors: Li Jiaying , Shi Xiaoxiao , Chen Zhixin , Xu Jiatong , Zhao Ruohuan , Liu Yuhao , Wen Yubing , Chen Limeng 
Published: January 2023

AbstractRenal tubular epithelial cells are one of the high energy-consuming cell types, which mainly depend on mitochondrial energy supply. Aldehyde dehydrogenase 2 (ALDH2) is a key enzyme that is involved in alcohol metabolism and mitochondrial oxidative ATP production; however, its function in mitochondrial homoeostasis in acute kidney injury (AKI) is unclear. Here, we found that ALDH2 expression was predominantly decreased in cisplatin or maleic acid (MA) models both in vivo and in vitro. ALDH2 knockout (KO) mice exhibited exacerbated kidney impairment and apoptosis of tubular epithelial cells after cisplatin injection. In contrast, ALDH2 activation alleviated AKI and tubular cell apoptosis in both cisplatin- and MA-induced models. RNA sequencing revealed that the oxidative phosphorylation pathway was positively enriched in the renal tissues after Alda-1 pre-treatment in MA-induced mice. ALDH2 activation restored mitochondrial structure, mitochondrial membrane potential, and respiration rate, but downregulated glycolysis in MA-induced mice and human renal proximal tubular epithelial (HK-2) cells. Mechanistically, co-immunoprecipitation assays revealed that ALDH2 interacts with peroxisomal proliferator-γ coactivator-1α (PGC-1α), a master regulator of mitochondrial biogenesis, and advanced its nuclear translocation. Subsequently, PGC-1α knockdown almost abolished the improvement of ALDH2 activation on MA-induced tubular epithelial cells damage. Thus, our study revealed that ALDH2 activation alleviated mitochondrial dysfunction in AKI by enhancing PGC-1α-mediated mitochondrial biogenesis. Hence, ALDH2 may act as a potential therapeutic target to prevent AKI progression.
PHB2 promotes colorectal cancer cell proliferation and tumorigenesis through NDUFS1-mediated oxidative phosphorylation
Authors: Ren Lin , Meng Li , Gao Jing , Lu Mingdian , Guo Chengyu , Li Yunyun , Rong Ziye , Ye Yan 
Published: January 2023

AbstractThe alteration of cellular energy metabolism is a hallmark of colorectal cancer (CRC). Accumulating evidence has suggested oxidative phosphorylation (OXPHOS) is upregulated to meet the demand for energy in tumor initiation and development. However, the role of OXPHOS and its regulatory mechanism in CRC tumorigenesis and progression remain unclear. Here, we reveal that Prohibitin 2 (PHB2) expression is elevated in precancerous adenomas and CRC, which promotes cell proliferation and tumorigenesis of CRC. Additionally, knockdown of PHB2 significantly reduces mitochondrial OXPHOS levels in CRC cells. Meanwhile, NADH:ubiquinone oxidoreductase core subunit S1 (NDUFS1), as a PHB2 binding partner, is screened and identified by co-immunoprecipitation and mass spectrometry. Furthermore, PHB2 directly interacts with NDUFS1 and they co-localize in mitochondria, which facilitates NDUFS1 binding to NADH:ubiquinone oxidoreductase core subunit V1 (NDUFV1), regulating the activity of complex I. Consistently, partial inhibition of complex I activity also abrogates the increased cell proliferation induced by overexpression of PHB2 in normal human intestinal epithelial cells and CRC cells. Collectively, these results indicate that increased PHB2 directly interacts with NDUFS1 to stabilize mitochondrial complex I and enhance its activity, leading to upregulated OXPHOS levels, thereby promoting cell proliferation and tumorigenesis of CRC. Our findings provide a new perspective for understanding CRC energy metabolism, as well as novel intervention strategies for CRC therapeutics.
Structural insights into DNA N6-adenine methylation by the MTA1 complex
Authors: Yan Junjun , Liu Feiqing , Guan Zeyuan , Yan Xuhui , Jin Xiaohuan , Wang Qiang , Wang Zican , Yan Junjie , Zhang Delin , Liu Zhu , Wu Shan , Yin Ping 
Published: January 2023

AbstractN6-methyldeoxyadenine (6mA) has recently been reported as a prevalent DNA modification in eukaryotes. The Tetrahymena thermophila MTA1 complex consisting of four subunits, namely MTA1, MTA9, p1, and p2, is the first identified eukaryotic 6mA methyltransferase (MTase) complex. Unlike the prokaryotic 6mA MTases which have been biochemically and structurally characterized, the operation mode of the MTA1 complex remains largely elusive. Here, we report the cryogenic electron microscopy structures of the quaternary MTA1 complex in S-adenosyl methionine (SAM)-bound (2.6 Å) and S-adenosyl homocysteine (SAH)-bound (2.8 Å) states. Using an AI-empowered integrative approach based on AlphaFold prediction and chemical cross-linking mass spectrometry, we further modeled a near-complete structure of the quaternary complex. Coupled with biochemical characterization, we revealed that MTA1 serves as the catalytic core, MTA1, MTA9, and p1 likely accommodate the substrate DNA, and p2 may facilitate the stabilization of MTA1. These results together offer insights into the molecular mechanism underpinning methylation by the MTA1 complex and the potential diversification of MTases for N6-adenine methylation.