bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical dissipation strongly affects the equatorial jet speed in simulations of hot Jupiter atmospheres
Authors: Hammond Mark , Abbot Dorian S 
Published: January 2022

ABSTRACT
Hot Jupiters are tidally locked gaseous exoplanets with atmospheric circulations dominated by a super-rotating equatorial jet. Their global circulation is often studied with simulations in 3D general circulation models (GCMs). Energy builds up at the smallest scales in these models and must be dissipated. Many models use ‘hyperdiffusion’ for this, which applies a tendency to the prognostic variables based on a high-order Laplacian operator. This removes the unrealistic and unstable build-up of energy at small scales, and ideally does not affect the large-scale circulation. In this study, we show that hyperdiffusion can in fact affect the large-scale circulation of simulations of hot Jupiters. These planets have large velocity gradients, so hyperdiffusion can produce a momentum tendency that may affect the largest scales. We analyse four simulations with different hyperdiffusion parameters in the GCM THOR. These show that hyperdiffusion can affect the atmospheric zonal momentum budget as strongly as the physical forcing. The hyperdiffusion slows down and spreads out the jet, reducing its speed by more than $50{{\ \rm per\ cent}}$ at some levels. We analyse simulations from the GCMs MITgcm and Exo-FMS and compare the effects of their different dissipation methods. The drag on the jet due to hyperdiffusion can be reduced by using a weaker hyperdiffusion coefficient, a higher resolution, or higher order diffusion. We aim to provide a basis for a study to investigate the ‘real’ momentum budget and jet speed of hot Jupiters. This study shows the need to examine long-held modelling assumptions when studying novel exoplanets.
Far-ultraviolet investigation into the galactic globular cluster M30 (NGC 7099): I. Photometry and radial distributions
Authors: Mansfield Santana , Dieball Andrea , Kroupa Pavel , Knigge Christian , Zurek David R , Shara Michael , Long Knox S 
Published: January 2022

ABSTRACT
We present a far-ultraviolet (FUV) study of the globular cluster M30 (NGC 7099). The images were obtained using the Advanced Camera for Surveys (ACS/SBC, F150LP, FUV) and the Wide Field Planetary Camera 2 (WFPC2, F300W, UV) which were both onboard the Hubble Space Telescope. The FUV − UV colour–magnitude diagram (CMD) shows a main sequence (MS) turnoff at FUV ≈ 22 mag and $FUV-UV\, \approx 3$ mag. The MS extends 4 mag below the turnoff, and a prominent horizontal branch (HB) and blue straggler (BS) sequence can be seen. A total of 1218 MS stars, 185 red giant branch stars, 47 BS stars, and 41 HB stars are identified, along with 78 sources blueward of the MS which consist of white dwarfs (WDs) and objects in the gap between the WDs and the MS that include potential cataclysmic variable (CV) candidates. The radial distribution of the BS population is concentrated towards the cluster centre, indicating that mass segregation has occurred. The blue and red sub-populations of the double BS sequence appear mixed in the ultraviolet CMD, and no significant central concentration of CV candidates is seen in this cluster.
High-energy neutrinos from fast winds in novae
Authors: Bednarek W , Śmiałkowski A 
Published: January 2022

ABSTRACT
We discuss a scenario in which TeV neutrinos are produced during explosions of novae. It is argued that hadrons are accelerated to very high energies in the inner part of a nova wind, as a result of reconnection of the strong magnetic field of a white dwarf. Hadrons are expected to interact efficiently with a dense matter of the wind, either already during the acceleration process or during their advection with the equatorial wind. We calculate the neutrino spectra and estimate the muon neutrino event rates in the IceCube telescope, in the case of a few novae. In general, those event rates are unlikely to be detected with the present neutrino detectors. However, for a favourable location of the observer, some neutrino events might be detected not only from the class of novae recently detected in the GeV γ-rays by the Fermi-LAT (Large Area Telescope), but also from novae not detected in γ-rays. The GeV γ-ray emission observed from novae cannot originate in terms of the model discussed here, since protons are accelerated within a few stellar radii of the white dwarf, i.e. in the region in which GeV γ-rays are expected to be severely absorbed in the interactions with the radiation field and the matter of the wind.
Exploring the GRB population: robust afterglow modelling
Authors: Aksulu M D , Wijers R A M J , van Eerten H J , van der Horst A J 
Published: January 2022

ABSTRACT
Gamma-ray bursts (GRBs) are ultra-relativistic collimated outflows, which emit synchrotron radiation throughout the entire electromagnetic spectrum when they interact with their environment. This afterglow emission enables us to probe the dynamics of relativistic blast waves, the microphysics of shock acceleration, and environments of GRBs. We perform Bayesian inference on a sample of GRB afterglow data sets consisting of 22 long GRBs and 4 short GRBs, using the afterglow model scalefit, which is based on 2D relativistic hydrodynamic simulations. We make use of Gaussian processes to account for systematic deviations in the data sets, which allows us to obtain robust estimates for the model parameters. We present the inferred parameters for the sample of GRBs and make comparisons between short and long GRBs in constant-density and stellar-wind-like environments. We find that in almost all respects such as energy and opening angle, short, and long GRBs are statistically the same. Short GRBs however have a markedly lower prompt gamma-ray emission efficiency than long GRBs. We also find that for long GRBs in ISM (interstellar medium)-like ambient media there is a significant anticorrelation between the fraction of thermal energy in the magnetic fields, ϵB, and the beaming corrected kinetic energy. Furthermore, we find no evidence that the mass-loss rates of the progenitor stars are lower than those of typical Wolf–Rayet stars.
Viscous energy dissipation of kink waves due to phase mixing in twisted coronal flux tubes
Authors: Ebrahimi Zanyar , Soler Roberto 
Published: January 2022

ABSTRACT
We have studied viscous energy damping of kink Magnetohydrodynamic (MHD) waves in weakly twisted magnetic flux tubes. The flux tube has been modelled as a homogeneous internal region with a straight magnetic field, surrounded by a radially non-uniform and magnetically twisted transitional layer embedded in a homogeneous ambient with a straight field. Using a modal expansion technique, we have solved an initial value problem for the incompressible viscous MHD equations and obtained spatio-temporal behaviour of the perturbations of the kink mode in linear regime. In the transitional layer, the perturbations are subject to phase mixing which enhances the viscous effects in the region. We show that magnetic twist can increase or decrease the efficiency of viscous damping of the phase-mixed perturbations in the non-uniform transitional layer. Using the temporal evolution of the total energy, we have obtained the viscous dissipation time as a power function of the Reynolds number. Our results show that magnetic twist could decrease or increase the viscous dissipation time.
Dust and the intrinsic spectral index of quasar variations: hints of finite stress at the innermost stable circular orbit
Authors: Weaver John R , Horne Keith 
Published: January 2022

ABSTRACT
We present a study of 9 242 spectroscopically confirmed quasars with multiepoch ugriz photometry from the SDSS Southern Survey. By fitting a separable linear model to each quasar’s spectral variations, we decompose their five-band spectral energy distributions into variable (disc) and non-variable (host galaxy) components. In modelling the disc spectra, we include attenuation by dust on the line of sight through the host galaxy to its nucleus. We consider five commonly used attenuation laws, and find that the best description is by dust similar to that of the Small Magellanic Cloud, inferring a lack of carbonaceous grains from the relatively weak 2175-Å absorption feature. We go on to construct a composite spectrum for the quasar variations spanning 700–8000 Å. By varying the assumed power-law Lν ∝ να spectral slope, we find a best-fitting value α = 0.71 ± 0.02, excluding at high confidence the canonical Lν ∝ ν1/3 prediction for a steady-state accretion disc with a T ∝ r−3/4 temperature profile. The bluer spectral index of the observed quasar variations instead supports the model of Agol & Krolik, and Mummery & Balbus, in which a steeper temperature profile, T ∝ r−7/8, develops as a result of finite magnetically induced stress at the innermost stable circular orbit extracting energy and angular momentum from the black hole spin.
Pulsations of microwave emission from a solar flare in a twisted loop caused by intrinsic magnetohydrodynamic oscillations
Authors: Smith Christopher , Gordovskyy M , Browning P K 
Published: January 2022

ABSTRACT
We present results revealing microwave pulsations produced in a model of a flaring twisted solar coronal loop, without any external oscillatory driver. Two types of oscillations are identified: slowly decaying oscillations with a period of about 70–75 s and amplitude of about 5–10 per cent seen in loops both with and without energetic electrons, and oscillations with a period of about 40 s and amplitude of a few tens of per cent observed only in loops with energetic electrons for about 100 s after the onset of fast energy release. We interpret the longer-period oscillations as the result of a standing kink mode modulating the average magnetic field strength in the loop, whilst the short-period intermittent oscillations associated with energetic electrons are likely to be produced by fast variations of the electric field, which produces energetic electrons in this scenario. The slowly decaying oscillations can explain the quasi-periodic pulsations often observed in the flaring corona.
Kaniadakis-holographic dark energy: observational constraints and global dynamics
Authors: Hernández-Almada A , Leon Genly , Magaña Juan , García-Aspeitia Miguel A , Motta V , Saridakis Emmanuel N , Yesmakhanova Kuralay 
Published: January 2022

ABSTRACT
We investigate Kaniadakis-holographic dark energy by confronting it with observations. We perform a Markov Chain Monte Carlo analysis using cosmic chronometers, supernovae type Ia, and Baryon Acoustic Oscillations data. Concerning the Kaniadakis parameter, we find that it is constrained around zero, namely around the value in which Kaniadakis entropy recovers standard Bekenstein-Hawking one. Additionally, for the present matter density parameter $\Omega _m^{(0)}$, we obtain a value slightly smaller compared to ΛCDM scenario. Furthermore, we reconstruct the evolution of the Hubble, deceleration, and jerk parameters extracting the deceleration-acceleration transition redshift as $z_T = 0.86^{+0.21}_{-0.14}$. Finally, performing a detailed local and global dynamical system analysis, we find that the past attractor of the Universe is the matter-dominated solution, while the late-time stable solution is the dark-energy-dominated one.
Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline
Authors: Raman Pravrutha , Rominger Mary C , Young Janet M , Molaro Antoine , Tsukiyama Toshio , Malik Harmit S 
Published: January 2022

Abstract
Histones and their posttranslational modifications facilitate diverse chromatin functions in eukaryotes. Core histones (H2A, H2B, H3, and H4) package genomes after DNA replication. In contrast, variant histones promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance. Previous studies have identified only a few H2B variants in animals; their roles and evolutionary origins remain largely unknown. Here, using phylogenomic analyses, we reveal the presence of five H2B variants broadly present in mammalian genomes. Three of these variants have been previously described: H2B.1, H2B.L (also called subH2B), and H2B.W. In addition, we identify and describe two new variants: H2B.K and H2B.N. Four of these variants originated in mammals, whereas H2B.K arose prior to the last common ancestor of bony vertebrates. We find that though H2B variants are subject to high gene turnover, most are broadly retained in mammals, including humans. Despite an overall signature of purifying selection, H2B variants evolve more rapidly than core H2B with considerable divergence in sequence and length. All five H2B variants are expressed in the germline. H2B.K and H2B.N are predominantly expressed in oocytes, an atypical expression site for mammalian histone variants. Our findings suggest that H2B variants likely encode potentially redundant but vital functions via unusual chromatin packaging or nonchromatin functions in mammalian germline cells. Our discovery of novel histone variants highlights the advantages of comprehensive phylogenomic analyses and provides unique opportunities to study how innovations in chromatin function evolve.
Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes
Authors: Conover Justin L , Wendel Jonathan F 
Published: January 2022

Abstract
Whole-genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1–2 Million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two coresident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g., dN/dS, πN/πS) may be biased when species of different ploidy levels are compared.
Allograft dysfunction after lung transplantation for COPA syndrome: A case report and literature review
Authors: Matsubayashi Tadashi , Yamamoto Masaki , Takayama Saki , Otsuki Yoshiro , Yamadori Ichiro , Honda Yoshitaka , Izawa Kazushi , Nishikomori Ryuta , Oto Takahiro 
Published: January 2022

ABSTRACT
Coatomer subunit alpha (COPA) syndrome is an autoinflammatory disease with autoimmune and autoinflammatory manifestations affecting lungs, joints, and kidneys. COPA syndrome is caused by heterozygous loss-of-function mutations in COPA gene, encoding α subunit of coatmer protein complex I (COP-I) coated vesicles. Mutant COPA induces constitutive activation of stimulator of interferon genes, leading to systemic inflammation and elevated type I interferon response. We have previously reported a Japanese family of COPA syndrome with a novel V242G mutation. Two out of four patients required lung transplantation due to intractable interstitial lung disease and respiratory failure. Both of them deceased after lung transplantation, one due to sepsis and the other due to allograft dysfunction possibly caused by the reccurent interstitial lung disease. The literature review indentified unfavorable outcome of the solid organ transplant in COPA syndrome and its related disease, however, precise clinico-pathological description of these cases has been scarce. Here, we report in detail the clinical course of our cases to clarify the pathophysiology of allograft dysfunction in COPA syndrome and propose potential therapeutic approaches to improve post-transplant graft survival.
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci
Authors: Mohamad Merianne , Nicholson David , Saha Chayan Kumar , Hauryliuk Vasili , Edwards Thomas A , Atkinson Gemma C , Ranson Neil A , O’Neill Alex J 
Published: January 2022

Abstract
The first member of the pleuromutilin (PLM) class suitable for systemic antibacterial chemotherapy in humans recently entered clinical use, underscoring the need to better understand mechanisms of PLM resistance in disease-causing bacterial genera. Of the proteins reported to mediate PLM resistance in staphylococci, the least-well studied to date is Sal(A), a putative ABC-F NTPase that—by analogy to other proteins of this type—may act to protect the ribosome from PLMs. Here, we establish the importance of Sal proteins as a common source of PLM resistance across multiple species of staphylococci. Sal(A) is revealed as but one member of a larger group of Sal-type ABC-F proteins that vary considerably in their ability to mediate resistance to PLMs and other antibiotics. We find that specific sal genes are intrinsic to particular staphylococcal species, and show that this gene family is likely ancestral to the genus Staphylococcus. Finally, we solve the cryo-EM structure of a representative Sal-type protein (Sal(B)) in complex with the staphylococcal 70S ribosome, revealing that Sal-type proteins bind into the E site to mediate target protection, likely by displacing PLMs and other antibiotics via an allosteric mechanism.
Epitranscriptomic regulation of HIV-1 full-length RNA packaging
Authors: Pereira-Montecinos Camila , Toro-Ascuy Daniela , Ananías-Sáez Catarina , Gaete-Argel Aracelly , Rojas-Fuentes Cecilia , Riquelme-Barrios Sebastián , Rojas-Araya Bárbara , García-de-Gracia Francisco , Aguilera-Cortés Paulina , Chnaiderman Jonás , Acevedo Mónica L , Valiente-Echeverría Fernando , Soto-Rifo Ricardo 
Published: January 2022

Abstract
During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that deposition of N6-methyladenosine (m6A) regulates full-length RNA packaging. While m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation promoted the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus and contributes to full-length RNA demethylation. We further identified two highly conserved adenosines within the 5′-UTR that have a crucial functional role in m6A methylation and packaging of the full-length RNA. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the HIV-1 full-length RNA molecules that will be used as viral genomes.
Survival of patients who opt for dialysis versus conservative care: a systematic review and meta-analysis
Authors: Voorend Carlijn G N , van Oevelen Mathijs , Verberne Wouter R , van den Wittenboer Iris D , Dekkers Olaf M , Dekker Friedo , Abrahams Alferso C , van Buren Marjolijn , Mooijaart Simon P , Bos Willem Jan W 
Published: January 2022

ABSTRACTBackgroundNon-dialytic conservative care (CC) has been proposed as a treatment option for patients with kidney failure. This systematic review and meta-analysis aims at comparing survival outcomes between dialysis and CC in studies where patients made an explicit treatment choice.MethodsFive databases were systematically searched from origin through 25 February 2021 for studies comparing survival outcomes among patients choosing dialysis versus CC. Adjusted and unadjusted survival rates were extracted and meta-analysis performed where applicable. Risk of bias analysis was performed according to the Cochrane Risk Of Bias In Non-randomized Studies of Interventions.ResultsA total of 22 cohort studies were included covering 21 344 patients. Most studies were prone to selection bias and confounding. Patients opting for dialysis were generally younger and had fewer comorbid conditions, fewer functional impairments and less frailty than patients who chose CC. The unadjusted median survival from treatment decision or an estimated glomerular filtration rate &lt;15 mL/min/1.73 m2 ranged from 20 and 67 months for dialysis and 6 and 31 months for CC. Meta-analysis of 12 studies that provided adjusted hazard ratios (HRs) for mortality showed a pooled adjusted HR of 0.47 (95% confidence interval 0.39–0.57) for patients choosing dialysis compared with CC. In subgroups of patients with older age or severe comorbidities, the reduction of mortality risk remained statistically significant, although analyses were unadjusted.ConclusionsPatients opting for dialysis have an overall lower mortality risk compared with patients opting for CC. However, a high risk of bias and heterogeneous reporting preclude definitive conclusions and results cannot be translated to an individual level.
Highly stable Co-doped MnO2 nanoarrays as enhanced cathode materials for aqueous zinc-ion batteries
Authors: Yao Jia , Ji Jie , Wan Houzhao , Duan Jinxia , Wang Xunying , Lv Lin , Ma Guokun , Tao Li , Wang Hanbin , Zhang Jun , Wang Hao 
Published: January 2022

ABSTRACT
Aqueous zinc-ion batteries (ZIBs) are a promising battery technology because of low costs and high safety. However, dissolution, self-aggregation and irreversible phase changes during charge and discharge of cathode materials may severely restrict the cycle stability of ZIBs. The main objective of this work was to prepare a more stable cathode material. For this purpose, we successfully prepared transition metal Co-doped MnO2 (Co-MnO2) using a simple one-step potentiostatic electrodeposition method. Co-MnO2 showed a high specific capacity of 237 mAh g−1 at 0.1 A g−1. Even at a high current density of 4 A g−1, the capacity retention was 87 mAh g−1. When returning back to 0.1 A g−1, the capacity retention rate exceeded 100%. Compared with long-cycle performance of the undoped MnO2, the electrochemical performance of the ion-doped electrodes with transition metal was significantly improved. The results indicate that transition metal doped electrode material (here Co-MnO2) can significantly improve the electrochemical performance and structural stability of the electrode material and improve the cycling performance. The results are relevant for the developing advanced cathodes for ZIBs.