bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct collapse of exceptionally heavy black holes in the merger-driven scenario
Authors: Zwick Lorenz , Mayer Lucio , Haemmerlé Lionel , Klessen Ralf S 
Published: November 2022

ABSTRACT
We revisit the conditions present in supermassive discs (SMDs) formed by the merger of gas-rich, metal-enriched galaxies at redshift z ∼ 10. We find that SMDs naturally form hydrostatic cores which go through a rapidly accreting supermassive star phase, before directly collapsing into massive black holes via the general relativistic instability. The growth and collapse of the cores occurs within ∼5 × 105 yr from the formation of the SMD, producing bright electromagnetic, neutrino and gravitational wave transients with a typical duration of a few minutes and, respectively, a typical flux and a typical strain amplitude at Earth of ∼10−8 erg s−1 cm−2 and ∼4 × 10−21. We provide a simple fitting formula for the resulting black hole masses, which range from a few 106 to 108 M⊙ depending on the initial SMD configuration. Crucially, our analysis does not require any specific assumption on the thermal properties of the gas, nor on the angular momentum loss mechanisms within the SMD. Led by these findings, we argue that the merger-driven scenario provides a robust pathway for the rapid formation of supermassive black holes at z &gt; 6. It provides an explanation for the origin of the brightest and oldest quasars without the need of a sustained growth phase from a much smaller seed. Its smoking gun signatures can be tested directly via multimessenger observations.
Turbulent diffusion of streaming cosmic rays in compressible, partially ionized plasma
Authors: Sampson Matt L , Beattie James R , Krumholz Mark R , Crocker Roland M , Federrath Christoph , Seta Amit 
Published: November 2022

ABSTRACT
Cosmic rays (CRs) are a dynamically important component of the interstellar medium (ISM) of galaxies. The ∼GeV CRs that carry most CR energy and pressure are likely confined by self-generated turbulence, leading them to stream along magnetic field lines at the ion Alfvén speed. However, the consequences of self-confinement for CR propagation on galaxy scales remain highly uncertain. In this paper, we use a large ensemble of magnetohydrodynamical turbulence simulations to quantify how the basic parameters describing ISM turbulence – the sonic Mach number, $\mathcal {M}$ (plasma compressibility), Alfvén Mach number, $\mathcal {M}_{\text{A0}}$ (strength of the large-scale field with respect to the turbulence), and ionization fraction by mass, χ – affect the transport of streaming CRs. We show that the large-scale transport of CRs whose small-scale motion consists of streaming along field lines is well described as a combination of streaming along the mean field and superdiffusion both along (parallel to) and across (perpendicular to) it; $\mathcal {M}_{\text{A0}}$ drives the level of anisotropy between parallel and perpendicular diffusion and χ modulates the magnitude of the diffusion coefficients, while in our choice of units, $\mathcal {M}$ is unimportant except in the sub-Alfvénic ($\mathcal {M}_{\text{A0}}\lesssim 0.5$) regime. Our finding that superdiffusion is ubiquitous potentially explains the apparent discrepancy between CR diffusion coefficients inferred from measurements close to individual sources compared to those measured on larger, Galactic scales. Finally, we present empirical fits for the diffusion coefficients as a function of plasma parameters that may be used as subgrid recipes for global ISM, galaxy, or cosmological simulations.
Dynamics of stellar disc tilting from satellite mergers
Authors: Dodge Benjamin C , Slone Oren , Lisanti Mariangela , Cohen Timothy 
Published: November 2022

ABSTRACT
The Milky Way’s stellar disc can tilt in response to torques that result from infalling satellite galaxies and their associated tidal debris. In this work, we explore the dynamics of disc tilting by running N-body simulations of mergers in an isolated, isotropic Milky Way-like host galaxy, varying over satellite virial mass, initial position, and orbit. We develop and validate a first-principles understanding of the dynamics that govern how the host galaxy’s stellar disc responds to the satellite’s dark matter (DM) debris. We find that the degree of disc tilting can be large for cosmologically motivated merger histories. In particular, our results suggest that the Galactic disc may still be tilting in response to Gaia-Sausage-Enceladus, one of the most significant recent mergers in the Milky Way’s history. These findings have implications for terrestrial direct detection experiments as disc tilting changes the relative location of the Sun with respect to DM substructure left behind by a merging galaxy.
A local measurement of the growth rate from peculiar velocities and galaxy clustering correlations in the 6dF Galaxy Survey
Authors: Turner Ryan J , Blake Chris , Ruggeri Rossana 
Published: November 2022

ABSTRACT
Galaxy peculiar velocities provide an integral source of cosmological information that can be harnessed to measure the growth rate of large-scale structure and constrain possible extensions to General Relativity. In this work, we present a method for extracting the information contained within galaxy peculiar velocities through an ensemble of direct peculiar velocity and galaxy clustering correlation statistics, including the effects of redshift space distortions, using data from the 6-degree Field Galaxy Survey. Our method compares the auto- and cross-correlation function multipoles of these observables, with respect to the local line of sight, with the predictions of cosmological models. We find that the uncertainty in our measurement is improved when combining these two sources of information in comparison to fitting to either peculiar velocity or clustering information separately. When combining velocity and density statistics in the range $27 \lt s \lt 123 \, h^{-1}$ Mpc we obtain a value for the local growth rate of fσ8 = 0.358 ± 0.075 and for the linear redshift distortion parameter β = 0.298 ± 0.065, recovering both with 20.9 per cent and 21.8 per cent accuracy, respectively. We conclude this work by comparing our measurement with other recent local measurements of the growth rate, spanning different data sets and methodologies. We find that our results are in broad agreement with those in the literature and are fully consistent with ΛCDM cosmology. Our methods can be readily scaled to analyse upcoming large galaxy surveys and achieve accurate tests of the cosmological model.
Planet(esimal)s around stars with TESS (PAST) III: A search for triplet He i in the atmospheres of two 200 Myr-old planets
Authors: Gaidos Eric , Hirano Teruyuki , Lee Rena A , Harakawa Hiroki , Hodapp Klaus , Jacobson Shane , Kotani Takayuki , Kudo Tomoyuki , Kurokawa Takashi , Kuzuhara Masayuki , Nishikawa Jun , Omiya Masashi , Serizawa Takuma , Tamura Motohide , Ueda Akitoshi , Vievard Sebastien 
Published: November 2022

ABSTRACT
We report a search for excess absorption in the 1083.2 nm line of ortho (triplet) helium during transits of TOI-1807b and TOI-2076b, 1.25 and 2.5-R⊕ planets on 0.55- and 10.4-d orbits around nearby ∼200 Myr-old K dwarf stars. We limit the equivalent width of any transit-associated absorption to &lt;4 and &lt;8 mÅ, respectively. We limit the escape of solar-composition atmospheres from TOI-1807b and TOI-2076b to ≲1 and ≲0.1M⊕Gyr−1, respectively, depending on wind temperature. The absence of a H/He signature for TOI-1807b is consistent with a measurement of mass indicating a rocky body and the prediction by a hydrodynamic model that any H-dominated atmosphere would be unstable and already have been lost. Differential spectra obtained during the transit of TOI-2076b contain a He i-like feature, but this closely resembles the stellar line and extends beyond the transit interval. Until additional transits are observed, we suspect this to be the result of variation in the stellar He i line produced by rotation of active regions and/or flaring on the young, active host star. Non-detection of escape could mean that TOI-2076b is more massive than expected, the star is less EUV luminous, the models overestimate escape, or the planet has a H/He-poor atmosphere that is primarily molecules such as H2O. Photochemical models of planetary winds predict a semimajor axis at which triplet He i observations are most sensitive to mass-loss: TOI-2076b orbits near this optimum. Future surveys could use a distance criterion to increase the yield of detections.
Can scallop-shell stars trap dust in their magnetic fields?
Authors: Sanderson H , Jardine M , Collier Cameron A , Morin J , Donati J-F 
Published: November 2022

ABSTRACT
One of the puzzles to have emerged from the Kepler and TESS missions is the existence of unexplained dips in the light curves of a small fraction of rapidly rotating M dwarfs in young open clusters and star-forming regions. We present a theoretical investigation of one possible explanation – that these are caused by dust clouds trapped in the stellar magnetic fields. The depth and duration of the observed dips allow us to estimate directly the linear extent of the dust clouds and their distances from the rotation axis. The dips are found to be between 0.4 and 4.8 per cent. We find that their distance is close to the co-rotation radius: the typical location for stable points where charged particles can be trapped in a stellar magnetosphere. We estimate the charge acquired by a dust particle due to collisions with the coronal gas and hence determine the maximum grain size that can be magnetically supported, the stopping distance due to gas drag, and the time-scale on which dust particles can diffuse out of a stable point. Using the observationally derived magnetic field of the active M dwarf V374 Peg, we model the distribution of these dust clouds and produce synthetic light curves. We find that for 1μm dust grains, the light curves have dips of 1–3 per cent and can support masses of order of 1012 kg. We conclude that magnetically trapped dust clouds (potentially from residual disc accretion or tidally disrupted planetesimal or cometary bodies) are capable of explaining the periodic dips in the Kepler and TESS data.
COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas
Authors: Wang Dapeng , Kumar Vinod , Burnham Katie L , Mentzer Alexander J , Marsden Brian D , Knight Julian C 
Published: November 2022

Abstract
Advances in our understanding of the nature of the immune response to SARS-CoV-2 infection, and how this varies within and between individuals, is important in efforts to develop targeted therapies and precision medicine approaches. Here we present a database for the COvid-19 Multi-omics Blood ATlas (COMBAT) project, COMBATdb (https://db.combat.ox.ac.uk). This enables exploration of multi-modal datasets arising from profiling of patients with different severities of illness admitted to hospital in the first phase of the pandemic in the UK prior to vaccination, compared with community cases, healthy controls, and patients with all-cause sepsis and influenza. These data include whole blood transcriptomics, plasma proteomics, epigenomics, single-cell multi-omics, immune repertoire sequencing, flow and mass cytometry, and cohort metadata. COMBATdb provides access to the processed data in a well-defined framework of samples, cell types and genes/proteins that allows exploration across the assayed modalities, with functionality including browse, search, download, calculation and visualisation via shiny apps. This advances the ability of users to leverage COMBAT datasets to understand the pathogenesis of COVID-19, and the nature of specific and shared features with other infectious diseases.
Internal RNA 2′O-methylation in the HIV-1 genome counteracts ISG20 nuclease-mediated antiviral effect
Authors: El Kazzi Priscila , Rabah Nadia , Chamontin Célia , Poulain Lina , Ferron François , Debart Françoise , Canard Bruno , Missé Dorothée , Coutard Bruno , Nisole Sébastien , Decroly Etienne 
Published: November 2022

AbstractRNA 2′O-methylation is a ‘self’ epitranscriptomic modification allowing discrimination between host and pathogen. Indeed, human immunodeficiency virus 1 (HIV-1) induces 2′O-methylation of its genome by recruiting the cellular FTSJ3 methyltransferase, thereby impairing detection by RIG-like receptors. Here, we show that RNA 2′O-methylations interfere with the antiviral activity of interferon-stimulated gene 20-kDa protein (ISG20). Biochemical experiments showed that ISG20-mediated degradation of 2′O-methylated RNA pauses two nucleotides upstream of and at the methylated residue. Structure-function analysis indicated that this inhibition is due to steric clash between ISG20 R53 and D90 residues and the 2′O-methylated nucleotide. We confirmed that hypomethylated HIV-1 genomes produced in FTSJ3-KO cells were more prone to in vitro degradation by ISG20 than those produced in cells expressing FTSJ3. Finally, we found that reverse-transcription of hypomethylated HIV-1 was impaired in T cells by interferon-induced ISG20, demonstrating the direct antagonist effect of 2′O-methylation on ISG20-mediated antiviral activity.
Small is beautiful: the important role of small copepods in carbon budgets of the southern Benguela upwelling system
Authors: Bode-Dalby Maya , Würth Randi , de Oliveira Lívia Dias Fernandes , Lamont Tarron , Verheye Hans M , Schukat Anna , Hagen Wilhelm , Auel Holger 
Published: November 2022

Abstract
Small copepod genera play an important role in marine food webs and biogeochemical fluxes but have been neglected in many studies. This is the first study determining biomass, carbon consumption and egestion rates of small- (&lt;1 mm prosome length, PL), medium- (1–1.5 mm PL) and large-sized (&gt;2 mm PL) copepods along a cross-shelf transect in the southern Benguela upwelling system. Calanoids contributed on average 55 ± 19% to total copepod abundance and 82 ± 13% to total copepod biomass. Small-sized Oithona spp. (114–119 mg C m−2 d−1) and Clausocalanidae/Paracalanidae (87–263 mg C m−2 d−1) as well as large-sized Calanoides natalis (47–193 mg C m−2 d−1) were the dominant consumers at the most inshore stations. Small- and medium-sized copepodite stages of Metridia lucens were also important, especially towards the continental slope. At offshore stations, Clausocalanidae/Paracalanidae, Oithona spp., Pleuromamma spp., Calanus agulhensis, Acartia spp., C. natalis and M. lucens were dominant consumers. Hence, usually small- and medium-sized copepods dominated total copepod ingestion and egestion, emphasizing that inadequate representation of small copepods will lead to significant underestimations and misinterpretations of the functioning of zooplankton communities and finally to inadequate biogeochemical models.
Type I interferon and neutrophil transcripts in lupus nephritis renal biopsies: clinical and histopathological associations
Authors: Mavragani Clio P , Kirou Kyriakos A , Seshan Surya V , Crow Mary K 
Published: November 2022

Abstract

Objectives
To investigate the expression of type I IFN (IFN-I) and neutrophil transcripts in kidney tissue from patients with different classes of LN and their association with distinct clinical and histopathological features.

Methods
Quantitation of IFN-I, defensin-α3 and formyl peptide receptor-like 1 (FPRL-1) transcripts was performed in kidney biopsy tissue from 24 patients with various classes of LN (6 class III, 14 class IV, 4 class V) and 3 control samples. Patient demographics, glomerular filtration rate (eGFR) and histopathological characteristics, including activity and chronicity indices, were analysed.

Results
IFNα2 and IFNβ transcripts were overexpressed in renal tissues from patients with proliferative forms of LN (III/IV) compared with patients with membranous nephritis and control kidneys. Patients with LN and impaired renal function, attested by eGFR, displayed higher relative expression of IFNα2 transcripts in renal tissues compared with those with normal renal function (23.0 ± 16.2 vs 12.0 ± 14.8, P = 0.04). Defensin-α3, but not FPRL-1, transcripts were overexpressed in LN tissues, particularly those with segmental necrotizing lesions, and were correlated with higher renal pathological activity indices (r = 0.61, P = 0.02), urinary protein levels (r = 0.44, P = 0.048) and IFNα2 expression (r = 0.50, P = 0.01).

Conclusion
IFN-I transcripts are expressed locally in kidneys from patients with proliferative LN and are associated with impaired renal function. Elevated defensin-α3 transcripts, a neutrophil product associated with neutrophil extracellular traps, may identify a driver of local IFN-I expression. These findings provide insights into the mechanisms of proliferative LN and may inform therapeutic decisions regarding selection of IFN-I pathway inhibitors.
New Notations for Better Morphological Distinction of Postaxial Polydactyly of the Foot
Authors: Hirota Yuka , Ueda Koichi , Umeda Chizuru , Yoshida Eriko 
Published: November 2022

Background:
There have been many reports on the classification and treatment of postaxial polydactyly of the foot. However, despite its being a common congenital anomaly, there is no universal notation about its morphology.

Methods:
We performed an analysis of 65 postaxial polydactyly cases from 2004 to 2021. Judgment criteria for deciding the surgical procedure were selected, and the points required for notation were decided. Based on them, we devised a new notation.

Results:
The necessary points required for notation were decided based on the following criteria: (1) the presence and level of syndactyly, (2) bifurcation level of the phalanges, (3) the presence of other deformities, and (4) predominant toes. We came up with a new notation and description method. Different types of syndactyly were represented using a horizontal bar, and predominant toes were represented using equality or inequality symbols. The bifurcation level of the phalanges and accessory deformities were additionally recorded (eg, 4—5>—6, Middle, 5,6: External rotation). From this notation, it is obvious which toe should be resected. Furthermore, syndactyly, accessory deformities, and the condition of the phalanges are also easily understood.

Conclusions:
Our new notation for postaxial polydactyly consists of some related symbols that are each provided a meaning. This system is simple, especially for easily understanding the morphology, and ideal for daily medical use. We conclude that it could become a universal notation method for cases of postaxial polydactyly of the foot.
Effect of Topical 5-Fluorouracil on Lacrimal Drainage System: Histopathological Evidence From Animal Experiments and Potential Clinical Implications
Authors: Singh Swati , Trakos Nikolaos , Ali Mohammad Javed 
Published: November 2022

Purpose:
The purpose of this study is to investigate the histopathological changes in the lacrimal drainage system of rabbits following the application of 1% topical 5-fluorouracil (5-FU) for 4 weeks.

Methods:
Ten eyes of 10 healthy New Zealand white rabbits were subjected to topical instillation of 1% (10 mg/mL) 5-FU, 1 drop 4 times a day for 4 weeks. Rabbits underwent a detailed ocular examination including eyelids, ocular surface, punctal, peri-punctal changes, and nasolacrimal duct patency at baseline and after 4 weeks of 5-FU. The rabbits were then sacrificed, and the eyelid, conjunctiva, lacrimal gland, and the entire lacrimal drainage system were retrieved for histopathological analysis as per standard protocols.

Results:
Clinically demonstrable peripunctal changes and canalicular stenosis were noted in 6 (60%, 6/10) rabbits. Two of these (20%, 2/10) had additional complete regurgitation of clear fluid, indicating a nasolacrimal duct obstruction. The remaining 4 (40%, 4/10) clinically did not demonstrate lacrimal drainage changes and were patent on irrigation. The conjunctiva showed focal loss of goblet cells in several areas. Significant changes were noted in the canalicular, lacrimal sac, and the nasolacrimal duct tissues in the form of epithelial hyperplasia, subepithelial inflammation, edema, dilated and congested vessels, and fibrosis. The lacrimal gland, eyelid tissue (excluding tarsal conjunctiva), and cornea showed no significant histopathological changes.

Conclusions:
Clinical and histopathological changes were noted in the lacrimal drainage system of rabbits subjected to topical 5-FU application. These findings can have potential clinical implications for patients receiving 5-FU therapy.
Comorbidities in older adults with opioid use disorders
Authors: Baumann Steven L. , Samuels William Ellery 
Published: November 2022

Background:
There is a growing number of opioid use disorders (OUDs) and overdose deaths in older adults. In addition, older adults with OUD routinely receive lower-quality preventive and chronic care that result in poorer overall health.

Purpose:
The purpose of this study was to identify older patients with OUD at the study site and determine the prevalence of medical and psychiatric comorbidities.

Methodology:
This retrospective study used a computer algorithm employed by a network of Federally Qualified Health Center primary care clinics in lower New York state. With the approval from institutional review board, the IT department of the organization captured data about older adults with an OUD diagnosis. The IT department identified 664 patients and provided anonymized demographic and medical history data of these patients for analysis.

Results:
Patients with OUD had 2–3 times more medical and psychiatric co-occurring conditions than national sample of older adults with no OUD of similar age and income. The most frequent co-occurring medical conditions in the patients were heart or circulatory disorders, movement disorders, respiratory disorders, pain disorders, nutritional disorders, and metabolic disorders. The most common co-occurring psychiatric conditions were anxiety disorders, major depressive disorder, post-traumatic stress disorder (PTSD), and bipolar disorder.

Conclusions:
Older adults with OUD often have complex health care needs that often include one or more chronic medical and psychiatric conditions.

Implications:
Providers should be aware of the multiple needs of older adults with OUD so that appropriate and comprehensive care can be offered to the patients.