bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protostellar collapse simulations in spherical geometry with dust coagulation and fragmentation
Authors: Lebreuilly Ugo , Vallucci-Goy Valentin , Guillet Vincent , Lombart Maxime , Marchand Pierre 
Published: November 2022

ABSTRACT
We model the coagulation and fragmentation of dust grains during the protostellar collapse with our newly developed shark code. It solves the gas-dust hydrodynamics in a spherical geometry and the coagulation/fragmentation equation. It also computes the ionization state of the cloud and the Ohmic, ambipolar, and Hall resistivities. We find that the dust size distribution evolves significantly during the collapse, large grain formation being controlled by the turbulent differential velocity. When turbulence is included, only ambipolar diffusion remains efficient at removing the small grains from the distribution, brownian motion is only efficient as a standalone process. The macroscopic gas-dust drift is negligible for grain growth and only dynamically significant near the first Larson core. At high density, we find that the coagulated distribution is unaffected by the initial choice of dust distribution. Strong magnetic fields are found to enhance the small grains depletion, causing an important increase of the ambipolar diffusion. This hints that the magnetic field strength could be regulated by the small grain population during the protostellar collapse. Fragmentation could be effective for bare silicates, but its modeling relies on the choice of ill-constrained parameters. It is also found to be negligible for icy grains. When fragmentation occurs, it strongly affects the magnetic resistivities profiles. Dust coagulation is a critical process that needs to be fully taken into account during the protostellar collapse. The onset and feedback of fragmentation remains uncertain and its modeling should be further investigated.
Dynamical mass measurements of two protoplanetary discs
Authors: Lodato G , Rampinelli L , Viscardi E , Longarini C , Izquierdo A , Paneque-Carreño T , Testi L , Facchini S , Miotello A , Veronesi B , Hall C 
Published: November 2022

ABSTRACT
ALMA observations of line emission from planet forming discs have demonstrated to be an excellent tool to probe the internal disc kinematics, often revealing subtle effects related to important dynamical processes occurring in them, such as turbulence, or the presence of planets, that can be inferred from pressure bumps perturbing the gas motion, or from the detection of the planetary wake. In particular, we have recently shown for the case of the massive disc in Elias 2-27 as how one can use such kind of observations to measure deviations from Keplerianity induced by the disc self-gravity, thus constraining the total disc mass with good accuracy and independently on mass conversion factors between the tracer used and the total mass. Here, we refine our methodology and extend it to two additional sources, GM Aur and IM Lup, for which archival line observations are available for both the 12CO and the 13CO line. For IM Lup, we are able to obtain a consistent disc mass of $M_{\rm disc}=0.1 \, \mathrm{M}_{\odot }$, implying a disc-star mass ratio of 0.1 (consistent with the observed spiral structure in the continuum emission) and a gas/dust ratio of ∼65 (consistent with standard assumptions), with a systematic uncertainty by a factor of ≃ 2 due to the different methods to extract the rotation curve. For GM Aur, the two lines we use provide slightly inconsistent rotation curves that cannot be attributed only to a difference in the height of the emitting layer, nor to a vertical temperature stratification. Our best-fitting disc mass measurement is $M_{\rm disc}=0.26 \, \mathrm{M}_{\odot }$, implying a disc-star mass ratio of ∼0.35 and a gas/dust ratio of ∼130. Given the complex kinematics in the outer disc of GM Aur and its interaction with the infalling cloud, the CO lines might not well trace the rotation curve and our results for this source should then be considered with some caution.
Sensitivity of modelled cometary gas production on the properties of the surface layer of the nucleus
Authors: Skorov Yu , Reshetnyk V , Küppers M , Bentley M S , Besse S , Hartogh P 
Published: November 2022

ABSTRACT
Explanation of the observed gas activity based on the parameters of the comet’s nucleus is not an obvious matter. Solutions based on certain thermal models can be obtained, but the use of arbitrary values for poorly known model parameters is always required. In this work, we carry out a study of the dependence of gas activity on these parameters and assess the importance of each of them. We consider model porous dust layers of diverse structures. Solid state and gas thermal conductivities are examined to estimate the possible range of effective thermal conductivity. The simulation results are embedded in a thermal model, explicitly including a radiative thermal conductivity and a resistance of the dust layer against the gas flow. Sublimation of water ice and supervolatiles (CO2 and CO) is tested at different heliocentric distances. It is shown that when sublimation is the main energy sink, the role of uncertainties in the structure of the layer is small. As the relative contribution of sublimation decreases, the scatter of solutions reaches tens of per cent. The expected large uncertainties in the effective thermal conductivity can also significantly change the gas production. The analysis performed shows that, in spite of the parameter range having been narrowed down by results from the Rosetta mission, the unavoidable uncertainty in the values of some model parameters (e.g. thermal conductivity) blurs the theoretical simulation estimates. Instead of presenting a narrow set of specific solutions, it is desirable to analyse the entire range of possible solutions.
Gaia DR3 and nearby galaxies: where do foregrounds matter?
Authors: Barmby P 
Published: November 2022

ABSTRACT
Nearby galaxies provide populations of stellar and non-stellar sources at a common distance and in quantifiable environments. All are observed through the Milky Way foreground, with varying degrees of contamination that depend on observed Galactic latitude and the distance and size of the target galaxy. This work uses Gaia Data Release 3 (DR3) to identify foreground sources via astrometric measurements and thus quantify foreground contamination for a large sample of nearby galaxies. There are approximately half a million Gaia sources in the directions of 1401 galaxies listed in the Local Volume Galaxy catalogue (D &lt; 11 Mpc), excluding the largest Local Group galaxies. About two-thirds of the Gaia sources have astrometric properties consistent with foreground sources; these sources are brighter, redder, and less centrally concentrated than non-foreground sources. Averaged over galaxies, foreground sources make up 50 per cent of Gaia sources at projected radius r50 = 1.06a26, where a26 is the angular diameter at the B = 26.5 isophote. Foreground sources make up 50 per cent of Gaia sources at apparent magnitude mG, 50 = 20.50. This limit corresponds to the tip of the red giant branch absolute magnitude at D = 450 kpc, and to the globular cluster luminosity function peak absolute magnitude at 5 Mpc. Gaia data provide a powerful tool for removing foreground contamination in stellar population studies of nearby galaxies, although Gaia foreground removal will be incomplete beyond distances of 5 Mpc.
Triage of theGaiaDR3 astrometric orbits – I. A sample of binaries with probable compact companions
Authors: Shahaf S , Bashi D , Mazeh T , Faigler S , Arenou F , El-Badry K , Rix H W 
Published: November 2022

AbstractIn preparation for the release of the astrometric orbits of Gaia, Shahaf et al. (2019) proposed a triage technique to identify astrometric binaries with compact companions based on their astrometric semimajor axis, parallax, and primary mass. The technique requires the knowledge of the appropriate mass–luminosity relation to rule out single or close-binary main-sequence companions. The recent publication of the Gaia DR3 astrometric orbits used a schematic version of this approach, identifying 735 astrometric binaries that might have compact companions. In this communication, we return to the triage of the DR3 astrometric binaries with more careful analysis, estimating the probability for its astrometric secondary to be a compact object or a main-sequence close binary. We compile a sample of 177 systems with highly probable non-luminous massive companions, which is smaller but cleaner than the sample reported in Gaia DR3. The new sample includes eight candidates to be black-hole systems with compact-object masses larger than 2.4 M⊙. The orbital–eccentricity–secondary–mass diagram of the other 169 systems suggests a tentative separation between the white-dwarf and the neutron-star binaries. Most white-dwarf binaries are characterized by small eccentricities of about 0.1 and masses of 0.6 M⊙, while the neutron star binaries display typical eccentricities of 0.4 and masses of 1.3 M⊙.
Dynamical history of the Galilean satellites for a fast migration of Callisto
Authors: Lari Giacomo , Saillenfest Melaine , Grassi Clara 
Published: November 2022

Abstract
The dynamics of the innermost Galilean satellites (Io, Europa, and Ganymede) is characterized by a chain of mean motion resonances, called Laplace resonance, and by a strong tidal dissipation that causes wide variations of their semimajor axes over large time-scales. The precise history of energy dissipation in the Jovian system is not known, but several theories have been proposed. Tidal resonance locking states that big outer moons can also migrate fast. If this is the case for Callisto, then it should have crossed the 2:1 mean motion resonance with Ganymede in the past, affecting the motion of all four Galilean satellites. Therefore, we aim to determine whether a fast migration for Callisto is compatible with the current orbital configuration of the system. Due to the chaotic nature of the resonant crossing, different outcomes are possible. A small portion of our simulations shows that Callisto can cross the 2:1 resonance with Ganymede without being captured and preserving the Laplace resonance. However, in most cases, we found that Callisto is captured into resonance, despite its divergent migration. As Callisto continues to migrate fast outwards, the moons depart substantially from the exact 8:4:2:1 commensurability, while still maintaining the resonant chain. Callisto can eventually escape it by crossing a high-order mean motion resonance with Ganymede. Afterwards, the moons’ system is able to relax to its current configuration for suitable dissipation parameters of the satellites. Therefore, it is possible, although challenging, to build a self-consistent picture of the past history of the Galilean satellites for a fast migration of Callisto.
Isochrone fitting of Galactic globular clusters – IV. NGC 6362 and NGC 6723
Authors: Gontcharov George A , Khovritchev Maxim Yu , Mosenkov Aleksandr V , Il’in Vladimir B , Marchuk Alexander A , Poliakov Denis M , Ryutina Olga S , Savchenko Sergey S , Smirnov Anton A , Usachev Pavel A , Lee Jae-Woo , Camacho Conner , Hebdon Noah 
Published: November 2022

Abstract
We present new isochrone fits to the colour–magnitude diagrams of the Galactic globular clusters NGC 6362 and NGC 6723. We utilize 22 and 26 photometric filters for NGC 6362 and NGC 6723, respectively, from the ultraviolet to mid-infrared using data sets from Hubble Space Telescope, Gaia, unWISE, and other photometric sources. We use models and isochrones from the Dartmouth Stellar Evolution Database (DSED) and Bag of Stellar Tracks and Isochrones (BaSTI) for α-enhanced [α/Fe] = +0.4 and different helium abundances. The metallicities [Fe/H] = −1.04 ± 0.07 and −1.09 ± 0.06 are derived from the red giant branch slopes in our fitting for NGC 6362 and NGC 6723, respectively. They agree with spectroscopic estimates from the literature. We find a differential reddening up to ΔE(B − V) = 0.13 mag in the NGC 6723 field due to the adjacent Corona Australis cloud complex. We derive the following for NGC 6362 and NGC 6723, respectively: distances 7.75 ± 0.03 ± 0.15 (statistic and systematic error) and 8.15 ± 0.04 ± 0.15 kpc; ages 12.0 ± 0.1 ± 0.8 and 12.4 ± 0.1 ± 0.8 Gyr; extinctions AV = 0.19 ± 0.04 ± 0.06 and 0.24 ± 0.03 ± 0.06 mag; reddenings E(B − V) = 0.056 ± 0.01 ± 0.02 and 0.068 ± 0.01 ± 0.02 mag. DSED provides systematically lower [Fe/H] and higher reddenings than BaSTI. However, the models agree in their relative estimates: NGC 6723 is 0.44 ± 0.04 kpc further, 0.5 ± 0.1 Gyr older, ΔE(B − V) = 0.007 ± 0.002 more reddened, and with 0.05 ± 0.01 dex lower [Fe/H] than NGC 6362. The lower metallicity and greater age of NGC 6723 with respect to NGC 6362 explain their horizontal branch morphology difference. This confirms age as the second parameter for these clusters. We provide lists of the cluster members from the Gaia Data Release 3.
The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence
Authors: Raad Nicole , Tandon Disha , Hapfelmeier Siegfried , Polacek Norbert 
Published: November 2022

AbstractBacterial pathogens employ a plethora of virulence factors for host invasion, and their use is tightly regulated to maximize infection efficiency and manage resources in a nutrient-limited environment. Here we show that during Escherichia coli stationary phase the 3′ UTR-derived small non-coding RNA FimR2 regulates fimbrial and flagellar biosynthesis at the post-transcriptional level, leading to biofilm formation as the dominant mode of survival under conditions of nutrient depletion. FimR2 interacts with the translational regulator CsrA, antagonizing its functions and firmly tightening control over motility and biofilm formation. Generated through RNase E cleavage, FimR2 regulates stationary phase biology by fine-tuning target mRNA levels independently of the chaperones Hfq and ProQ. The Salmonella enterica orthologue of FimR2 induces effector protein secretion by the type III secretion system and stimulates infection, thus linking the sRNA to virulence. This work reveals the importance of bacterial sRNAs in modulating various aspects of bacterial physiology including stationary phase and virulence.
Increased chromatin accessibility facilitates intron retention in specific cell differentiation states
Authors: Petrova Veronika , Song Renhua ,   DEEP Consortium, Nordström Karl J V , Walter Jörn , Wong Justin J L , Armstrong Nicola J , Rasko John E J , Schmitz Ulf 
Published: November 2022

Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
Guard Cell Transcriptome Reveals Membrane Transport, Stomatal Development and Cell Wall Modifications as Key Traits Involved in Salinity Tolerance in HalophyticChenopodium quinoa
Authors: Rasouli Fatemeh , Kiani-Pouya Ali , Movahedi Ali , Wang Yuan , Li Leiting , Yu Min , Pourkheirandish Mohammad , Zhou Meixue , Chen Zhonghua , Zhang Heng , Shabala Sergey 
Published: November 2022

AbstractA comparative investigation was conducted to evaluate transcriptional changes in guard cells (GCs) of closely related halophytic (Chenopodium quinoa) and glycophytic (Spinacia oleracea) species. Plants were exposed to 3 weeks of 250 mM sodium chloride treatment, and GC-enriched epidermal fragments were mechanically prepared. In both species, salt-responsive genes were mainly related to categories of protein metabolism, secondary metabolites, signal transduction and transport systems. Genes related to abscisic acid (ABA) signaling and ABA biosynthesis were strongly induced in quinoa but not in spinach GCs. Also, expression of the genes encoding transporters of amino acids, proline, sugars, sucrose and potassium increased in quinoa GCs under salinity stress. Analysis of cell-wall-related genes suggests that genes involved in lignin synthesis (e.g. lignin biosynthesis LACCASE 4) were highly upregulated by salt in spinach GCs. In contrast, transcripts related to cell wall plasticity Pectin methylesterase3 (PME3) were highly induced in quinoa. Faster stomatal response to light and dark measured by observing kinetics of changes in stomatal conductance in quinoa might be associated with higher plasticity of the cell wall regulated by PME3 Furthermore, genes involved in the inhibition of stomatal development and differentiation were highly expressed by salt in quinoa, but not in spinach. These changes correlated with reduced stomatal density and index in quinoa, thus improving its water use efficiency. The fine modulation of transporters, cell wall modification and controlling stomatal development in GCs of quinoa may have resulted in high K+/Na+ ratio, lower stomatal conductance and higher stomatal speed for better adaptation to salinity stress in quinoa.
Amputation for Complex Regional Pain Syndrome: Meta-Analysis and Validation of a Histopathology Scoring System
Authors: Howard Emily L , Singleton Michael , Soulakvelidze Irakli 
Published: November 2022

AbstractObjectivePathology can provide crucial insights into the etiology of disease. The goal of this review is to evaluate the rigor of histopathology reports of Complex Regional Pain Syndrome (CRPS).MethodsA systematic search of multiple databases identified papers that described amputation for CRPS with pathology findings. Control pathology articles were randomly chosen from the same journals. Landmark articles in Surgical Pathology were previously identified. Papers were categorized by the use of histology: Anatomic (microscopic description), Diagnostic (binary result), and Substrate (special studies only). A novel Histopathology Score assigned 1 point for each of 10 History elements and 15 Pathology elements. All articles were scored and analyzed by appropriate statistics.ResultsThe search identified 22 CRPS, 50 Control and 50 Landmark articles. Multivariable analysis of the Pathology Score showed a significantly higher score for Anatomic vs Non-Anatomic papers (Incidence Rate Ratio (IRR) 1.54, P &lt; .001) and Landmark vs CRPS articles (IRR 1.39, P value .003). CRPS papers reported some elements infrequently: diagnostic criteria (31.8%), routine stain (50%), any clinic-pathologic correlation (40.9%), and sample size &gt;2 (27.3%).ConclusionsThe Pathology Score is a useful quality assessment tool to evaluate studies. As expected, Anatomic papers scored significantly higher than Non-Anatomic papers. CRPS papers had small sample sizes (median 1) and infrequent reporting of diagnostic criteria, routine stain, any clinical pathologic correlation. These particular elements are crucial for analyzing and reviewing pathologic features. The analysis explains why it is quite difficult to write a meaningful systematic review of CRPS histology at this time.
IMPACT OF THE ENDF/B-VIII.0 LIBRARY ON MCNP6.2-COMPUTED AMBIENT AND PERSONAL DOSE EQUIVALENT CONVERSION COEFFICIENTS
Authors: McHale Stephen R , Millett Marshall , Prince Madeline I 
Published: November 2022

Abstract
The 2018 release of the Evaluated Nuclear Data File (ENDF)/B-VIII.0 library initiated several examinations of the impact of the revised nuclear data on Monte Carlo models. This study used version 6.2 of the Monte Carlo N-Particle® code (MCNP6.2) with the ENDF/B-VI and ENDF/B-VIII.0 libraries to compute conversion coefficients for fluence-to-ambient and fluence-to-personal dose equivalent from neutron energy groups described by an International Atomic Energy Agency 53-bin structure and 47 monoenergetic neutron sources listed in International Commission on Radiological Protection (ICRP) 74. The MCNP6.2 models with ENDF/B-VI data were validated against results published in 2005 by Veinot and Hertel. Conversion coefficients computed with MCNP6.2 and ENDF/B-VIII.0 slightly underestimated the ICRP 74 values but were within ICRP-specified tolerances and do not justify revising the ICRP coefficients. Conversion coefficients for personal dose equivalent were computed with MCNP6.2 and ENDF/B-VIII.0 at four angles of incidence greater than those available in ICRP 74. These new coefficients are relevant to radiation protection studies of interest to US defence-focused organisations.
Making sense of transdisciplinarity: Interpreting science policy in a biotechnology centre
Authors: Hesjedal Maria Bårdsen , Åm Heidrun 
Published: November 2022

AbstractTransdisciplinarity is a much-used concept in research policy to emphasize a need for new collaborations beyond scientific disciplines to solve societal challenges. However, how do scientists interpret transdisciplinarity and what do transdisciplinarity policies mean for their work? This paper focuses on researchers’ definitions of transdisciplinarity. It is based on an empirical study of a Norwegian biotechnology centre founded to stimulate a transition in biotechnology research towards transdisciplinarity. Drawing on interpretive methods, we identify three interpretations of transdisciplinarity. In our case, the science policy idea of ‘transdisciplinarity’ faded away in practice in terms of collaboration with non-academic actors, but boosted the establishment of new interdisciplinary teams. By pointing to the multiplicity of ways in which policy recipients can interpret science policy, this study contributes to scholarship analysing the relation between transdisciplinarity in policy and practice.