bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlling outlier contamination in multimessenger time-domain searches for supermasssive binary black holes
Authors: Wang Qiaohong , Taylor Stephen R 
Published: September 2022

ABSTRACT
Time-domain data sets of many varieties can be prone to statistical outliers that result from instrumental or astrophysical anomalies. These can impair searches for signals within the time series and lead to biased parameter estimation. Versatile outlier mitigation methods tuned toward multimessenger time-domain searches for supermassive binary black holes have yet to be fully explored. In an effort to perform robust outlier isolation with low computational costs, we propose a Gibbs sampling scheme. This provides structural simplicity to outlier modelling and isolation, as it requires minimal modifications to adapt to time-domain modelling scenarios with pulsar-timing array or photometric data. We robustly diagnose outliers present in simulated pulsar-timing data sets, and then further apply our methods to pulsar J1909−3744 from the NANOGrav 9-year Data set. We also explore the periodic binary-AGN candidate PG1302−102 using data sets from the Catalina Real-time Transient Survey, All-Sky Automated Survey for Supernovae, and the Lincoln Near-Earth Asteroid Research. We present our findings and outline future work that could improve outlier modelling and isolation for multimessenger time-domain searches.
ASymba: H i global profile asymmetries in the simba simulation
Authors: Glowacki M , Deg N , Blyth S-L , Hank N , Davé R , Elson E , Spekkens K 
Published: September 2022

ABSTRACT
Asymmetry in the spatially integrated, 1D H i global profiles of galaxies can inform us on both internal (e.g. outflows) and external (e.g. mergers, tidal interactions, and ram pressure stripping) processes that shape galaxy evolution. Understanding which of these primarily drive H i profile asymmetry is of particular interest. In the lead-up to SKA pathfinder and SKA H i emission surveys, hydrodynamical simulations have proved to be a useful resource for such studies. Here, we present the methodology behind, as well as first results, of ASymba: Asymmetries in H i of Simba galaxies, the first time this simulation suite has been used for this type of study. We generate mock observations of the H i content of these galaxies and calculate the profile asymmetries using three different methods. We find that $M_{\rm H\, {\small I}}$ has the strongest correlation with all asymmetry measures, with weaker correlations also found with the number of mergers a galaxy has undergone, and gas and galaxy rotation. We also find good agreement with the xGASS sample, in which galaxies with highly asymmetric profiles tend to have lower H i gas fractions than galaxies with symmetric profiles, and additionally find the same holds in sSFR parameter space. For low H i mass galaxies, it is difficult to distinguish between asymmetric and symmetric galaxies, but this becomes achievable in the high H i mass population. These results showcase the potential of ASymba and provide the groundwork for further studies, including comparison to upcoming large H i emission surveys.
A gravitational and dynamical framework of star formation: the Orion nebula
Authors: Kounkel Marina , Stassun Keivan G , Covey Kevin , Hartmann Lee 
Published: September 2022

ABSTRACT
The Orion Nebula Cluster (ONC) is the most massive region of active star formation within a kpc of the Sun. Using Gaia DR3 parallaxes and proper motions, we examine the bulk motions of stars radially and tangentially relative to the cluster centre. We find an age gradient with distance to the stars in the ONC, from 385 pc for the oldest stars, to 395 pc for the younger stars, indicating that the star-forming front is propagating into the cloud. We find an organized signature of rotation of the central cluster, but it is present only in stars younger than 2 Myr. We also observe a net infall of young stars into the centre of the ONC’s deep gravitational potential well. The infalling sources lie preferentially along the filament; on the other hand, outflowing sources are distributed spherically around the cluster, and they have larger velocity dispersion. We further propose a solution to a long-standing question of why the ONC shows a weak signature of expansion even though the cluster is likely bound: much of this expansion may be driven by unstable N-body interactions among stars, resulting in low-velocity ejections. Though analysing signatures imprinted on stellar dynamics across different spatial scales, these observation shed new light on the signatures of formation and evolution of young clusters.
Electron attachment to interstellar grains
Authors: Flower D R 
Published: September 2022

ABSTRACT
We have performed quantum mechanical calculations of cross-sections and rate coefficients for electron attachment to small, neutral, and positively charged grains. In addition to the polarization potential and – for charged grains – the Coulomb potential, we considered the influence of the interaction between the charge of the electron and a possible permanent electric dipole on the grain. We found large discrepancies between the predictions of classical and quantal models of electron scattering on neutral grains at low energies (temperatures) in the absence of a permanent dipole moment, but much closer agreement when a dipole moment was present. The presence of the long-range Coulomb potential also leads to better agreement between classical and quantal models.
Infrared radiation feedback does not regulate star cluster formation
Authors: Menon Shyam H , Federrath Christoph , Krumholz Mark R 
Published: September 2022

ABSTRACT
We present 3D radiation-hydrodynamical (RHD) simulations of star cluster formation and evolution in massive, self-gravitating clouds, whose dust columns are optically thick to infrared (IR) photons. We use VETTAM – a recently developed, novel RHD algorithm, which uses the Variable Eddington Tensor closure – to model the IR radiation transport through the cloud. We also use realistic temperature (T) dependent IR opacities (κ) in our simulations, improving upon earlier works in this area, which used either constant IR opacities or simplified power laws (κ ∝ T2). We investigate the impact of the radiation pressure of these IR photons on the star formation efficiency of the cloud, and its potential to drive dusty winds. We find that IR radiation pressure is unable to regulate star formation or prevent accretion on to the star clusters, even for very high gas surface densities ($\Sigma \gt 10^5 \, \mathrm{M}_{\odot } \, \mathrm{pc}^{-2}$), contrary to recent semi-analytic predictions and simulation results using simplified treatments of the dust opacity. We find that the commonly adopted simplifications of κ ∝ T2 or constant κ for the IR dust opacities leads to this discrepancy, as those approximations overestimate the radiation force. By contrast, with realistic opacities that take into account the microphysics of the dust, we find that the impact of IR radiation pressure on star formation is very mild, even at significantly high dust-to-gas ratios (∼3 times solar), suggesting that it is unlikely to be an important feedback mechanism in controlling star formation in the ISM.
Stability of axially symmetric magnetic fields in stars
Authors: Becerra Laura , Reisenegger Andreas , Valdivia Juan Alejandro , Gusakov Mikhail 
Published: September 2022

Abstract
The magnetic fields observed in Ap stars, white dwarfs, and neutron stars are known to be stable for long times. However, the physical conditions inside the stellar interiors that allow these states are still a matter of research. It has been formally demonstrated that both purely toroidal and purely poloidal magnetic fields develop instabilities at some point in the star. On the other hand, numerical simulations have proved the stability of roughly axisymmetric magnetic field configurations inside stably stratified stars. These configurations consist of mutually stabilizing toroidal and poloidal components in a twisted torus shape. Previous studies have proposed rough upper and lower bounds on the ratio of the magnetic energy in the toroidal and poloidal components of the magnetic field. With the purpose of mapping out the parameter space under which such configurations remain stable, we used the Pencil Code to perform 3D magnetohydrodynamic simulations of the evolution of the magnetic field in non-rotating, non-degenerate stars in which viscosity is the only dissipation mechanism, both for stars with a uniform (barotropic) and radially increasing (stably stratified) specific entropy. Furthermore, we considered different conditions regarding the degree of stable stratification and the magnetic energy in each component, roughly confirming the previously suggested stability boundaries for the magnetic field.
7Be detection in the 2021 outburst of RS Oph
Authors: Molaro P , Izzo L , Selvelli P , Bonifacio P , Aydi E , Cescutti G , Guido E , Harvey E J , Hernanz M , Della Valle M 
Published: September 2022

ABSTRACT
The recurrent nova RS Oph underwent a new outburst on 2021 August 8, reaching a visible brightness of V = 4.8 mag. Observations of the 2021 outburst made with the high-resolution UVES spectrograph at the Kueyen-UT2 telescope at ESO-VLT in Paranal enabled detection of the possible presence of 7Be newly made in the thermonuclear runaway reactions. The 7Be yields can be estimated at N(7Be)/N(H) = 5.7 × 10−6, which are close to the lowest yields measured in classical novae so far. 7Be is short-lived and decays only into 7Li. By means of a spectrum taken during the nebular phase we estimated an ejected mass of ≈ 1.1 × 10−5 M⊙, providing an amount of ≈ 4.4 × 10−10 M⊙ of 7Li created in the 2021 event. Recurrent novae of the RS Oph type may synthesize slightly lower amounts of 7Li per event than classical novae, but occur 103 times more frequently. The recurrent novae fraction is in the range of 10–30 per cent and they could have contributed to the making of the 7Li that we observe today. The detection of 7Be in RS Oph provides further support to the recent suggestion that novae are the most effective source of 7Li in the Galaxy.
The imprint of gas on gravitational waves from LISA intermediate-mass black hole binaries
Authors: Garg Mudit , Derdzinski Andrea , Zwick Lorenz , Capelo Pedro R , Mayer Lucio 
Published: September 2022

ABSTRACT
We study the effect of torques on circular inspirals of intermediate-mass black hole binaries (IMBHBs) embedded in gas discs, wherein both BH masses are in the range 102–105 M⊙, up to redshift z = 10. We focus on how torques impact the detected gravitational wave (GW) waveform in the LISA frequency band when the binary separation is within a few hundred Schwarzschild radii. For a sub-Eddington accretion disc with a viscosity coefficient α = 0.01, surface density Σ ≈ 105 g cm−2, and Mach number $\mathcal {M}_{\rm {a}}\approx 80$, a gap, or a cavity, opens when the binary is in the LISA band. Depending on the torque’s strength, LISA will observe dephasing in the IMBHB’s GW signal up to either z ∼ 5 for high mass ratios (q ≈ 0.1) or to z ∼ 7 for q ≈ 10−3. We study the dependence of the measurable dephasing on variations of BH masses, redshift, and accretion rates. Our results suggest that phase shift is detectable even in high-redshift (z = 10) binaries if they experience super-Eddington accretion episodes. We investigate if the disc-driven torques can result in an observable ‘time-dependent’ chirp mass with a simplified Fisher formalism, finding that, at the expected signal-to-noise ratio, the gas-induced variation of the chirp mass is too small to be detected. This work shows how gas-induced perturbations of vacuum waveforms should be strong enough to be detected by LISA for the IMBHB in the early inspiral phase. These perturbations encode precious information on accretion discs and galactic nuclei astrophysics. High-accuracy waveform models which incorporate these effects will be needed to extract such information.
SWIFT J0503.7-2819: a nearly synchronous intermediate polar below the period gap?
Authors: Rawat Nikita , Pandey J C , Joshi Arti , Scaringi Simone , Yadava Umesh 
Published: September 2022

ABSTRACT
Based on the X-ray observations from XMM–Newton and Swift, and optical observations from Transiting Exoplanet Survey Satellite (TESS) and AAVSO, we present temporal and spectral properties of probable intermediate polar SWIFT J0503.7-2819. The X-ray light curve shows two distinctive features, where possibly the second pole seems to be active during the middle of the XMM–Newton observations. Present analysis confirms and also refines the previously reported orbital period of SWIFT J0503.7-2819 as 81.65 ± 0.04 min. The X-ray and optical variations of this target have been found to occur at the period of ∼65 min, which we propose as the spin period of the white dwarf. The energy-dependent modulation at this period, which are due to the photoelectric absorption in the accretion flow, also assures this conjecture. Two-temperature thermal plasma model well explains the X-ray spectra with temperatures of ∼150 eV and ∼18.5 keV, which is absorbed by a dense material with an average equivalent hydrogen column density of 3.8 × 1022 cm−2 that partially covers ∼27 per cent of the X-ray source. An attempt is made to understand the accretion flow in this system using the present data of SWIFT J0503.7-2819. If the proposed spin period is indeed the actual period, then SWIFT J0503.7-2819 could be the first nearly synchronous intermediate polar below the period gap.
tidy tree: A New Layout for Phylogenetic Trees
Authors: Penel Simon , de Vienne Damien M 
Published: September 2022

AbstractMany layouts exist for visualizing phylogenetic trees, allowing to display the same information (evolutionary relationships) in different ways. For large phylogenies, the choice of the layout is a key element, because the printable area is limited, and because interactive on-screen visualizers can lead to unreadable phylogenetic relationships at high zoom levels. A visual inspection of available layouts for rooted trees reveals large empty areas that one may want to fill in order to use less drawing space and eventually gain readability. This can be achieved by using the nonlayered tidy tree layout algorithm that was proposed earlier but was never used in a phylogenetic context so far. Here, we present its implementation, and we demonstrate its advantages on simulated and biological data (the measles virus phylogeny). Our results call for the integration of this new layout in phylogenetic software. We implemented the nonlayered tidy tree layout in R language as a stand-alone function (available at https://github.com/damiendevienne/non-layered-tidy-trees), as an option in the tree plotting function of the R package ape, and in the recent tool for visualizing reconciled phylogenetic trees thirdkind (https://github.com/simonpenel/thirdkind/wiki).
Recurrent but Short-Lived Duplications of Centromeric Proteins in HolocentricCaenorhabditisSpecies
Authors: Caro Lews , Raman Pravrutha , Steiner Florian A , Ailion Michael , Malik Harmit S 
Published: September 2022

AbstractCentromeric histones (CenH3s) are essential for chromosome inheritance during cell division in most eukaryotes. CenH3 genes have rapidly evolved and undergone repeated gene duplications and diversification in many plant and animal species. In Caenorhabditis species, two independent duplications of CenH3 (named hcp-3 for HoloCentric chromosome-binding Protein 3) were previously identified in C. elegans and C. remanei. Using phylogenomic analyses in 32 Caenorhabditis species, we find strict retention of the ancestral hcp-3 gene and 10 independent duplications. Most hcp-3L (hcp-3-like) paralogs are only found in 1–2 species, are expressed in both males and females/hermaphrodites, and encode histone fold domains with 69–100% identity to ancestral hcp-3. We identified novel N-terminal protein motifs, including putative kinetochore protein-interacting motifs and a potential separase cleavage site, which are well conserved across Caenorhabditis HCP-3 proteins. Other N-terminal motifs vary in their retention across paralogs or species, revealing potential subfunctionalization or functional loss following duplication. An N-terminal extension in the hcp-3L gene of C. afra revealed an unprecedented protein fusion, where hcp-3L fused to duplicated segments from hcp-4 (nematode CENP-C). By extending our analyses beyond CenH3, we found gene duplications of six inner and outer kinetochore genes in Caenorhabditis, which appear to have been retained independent of hcp-3 duplications. Our findings suggest that centromeric protein duplications occur frequently in Caenorhabditis nematodes, are selectively retained for short evolutionary periods, then degenerate or are lost entirely. We hypothesize that unique challenges associated with holocentricity in Caenorhabditis may lead to this rapid “revolving door” of kinetochore protein paralogs.
A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons
Authors: Mikl Martin , Eletto Davide , Nijim Malak , Lee Minkyoung , Lafzi Atefeh , Mhamedi Farah , David Orit , Sain Simona Baghai , Handler Kristina , Moor Andreas E 
Published: September 2022

Abstract
Asymmetric subcellular mRNA localization allows spatial regulation of gene expression and functional compartmentalization. In neurons, localization of specific mRNAs to neurites is essential for cellular functioning. However, it is largely unknown how transcript sorting works in a sequence-specific manner. Here, we combined subcellular transcriptomics and massively parallel reporter assays and tested ∼50 000 sequences for their ability to localize to neurites. Mapping the localization potential of &gt;300 genes revealed two ways neurite targeting can be achieved: focused localization motifs and broadly encoded localization potential. We characterized the interplay between RNA stability and localization and identified motifs able to bias localization towards neurite or soma as well as the trans-acting factors required for their action. Based on our data, we devised machine learning models that were able to predict the localization behavior of novel reporter sequences. Testing this predictor on native mRNA sequencing data showed good agreement between predicted and observed localization potential, suggesting that the rules uncovered by our MPRA also apply to the localization of native full-length transcripts.
Sampling via the aggregation value for data-driven manufacturing
Authors: Liu Xu , Chen Gengxiang , Li Yingguang , Chen Lu , Meng Qinglu , Mehdi-Souzani Charyar 
Published: September 2022

Abstract
Data-driven modelling has shown promising potential in many industrial applications, while the expensive and time-consuming labelling of experimental and simulation data restricts its further development. Preparing a more informative but smaller dataset to reduce labelling efforts has been a vital research problem. Although existing techniques can assess the value of individual data samples, how to represent the value of a sample set remains an open problem. In this research, the aggregation value is defined using a novel representation for the value of a sample set by modelling the invisible redundant information as the overlaps of neighbouring values. The sampling problem is hence converted to the maximisation of the submodular function over the aggregation value. The comprehensive analysis of several manufacturing datasets demonstrates that the proposed method can provide sample sets with superior and stable performance compared with state-of-the-art methods. The research outcome also indicates its appealing potential to reduce labelling efforts for more data-scarcity scenarios.
The Alteration of Tomato Chloroplast Vesiculation Positively Affects Whole-Plant Source–Sink Relations and Fruit Metabolism under Stress Conditions
Authors: Ahouvi Yoav , Haber Zechariah , Zach Yair Yehoshua , Rosental Leah , Toubiana David , Sharma Davinder , Alseekh Saleh , Tajima Hiromi , Fernie Alisdair R , Brotman Yariv , Blumwald Eduardo , Sade Nir 
Published: September 2022

Abstract
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato chloroplast vesiculation (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/CAS9) knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the l-glutamine and l-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
Synergistic chemo-/photothermal therapy based on supercritical technology-assisted chitosan–indocyanine green/luteolin nanocomposites for wound healing
Authors: Xu Pei-Yao , Kankala Ranjith Kumar , Li Yue-Wei , Wang Shi-Bin , Chen Ai-Zheng 
Published: September 2022

Abstract
Despite the success, it is highly challenging to battle against pathogenic biofilms-based chronic bacterial infections by conventional antibiotic therapy. Herein, we report a near-infrared (NIR)/acid-induced nanoplatform based on chitosan (CS)-coated indocyanine green (ICG, photosensitizer)/luteolin (LUT, a natural quorum sensing inhibitor) nanocomposites (ICG/LUT-CS) as antibacterial and antibiofilm agents for skin wound healing. Initially, the ICG/LUT nanoplatforms are prepared by the supercritical antisolvent technology and coated with the CS layer. The obtained ICG/LUT-CS with ultra-high encapsulation efficiency exhibited more favorable photothermal conversion effects and improved NIR laser/acid dual-induced drug release behavior than individual modalities, achieving exceptional bacteria-killing and biofilm elimination effects. Moreover, the ICG/LUT-CS realized the synergetic effects of chemotherapy and photothermal therapy outcomes for wound healing. Together, our findings provided an appealing strategy for the rapid preparation and future translational application of ICG/LUT-CS as an ideal agent for fighting against biofilm infections.