bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamical evolution of two-planet systems and its connection with white dwarf atmospheric pollution
Authors: Maldonado R F , Villaver E , Mustill A J , Chavez M , Bertone E 
Published: August 2020

ABSTRACT
Asteroid material is detected in white dwarfs (WDs) as atmospheric pollution by metals, in the form of gas/dust discs, or in photometric transits. Within the current paradigm, minor bodies need to be scattered, most likely by planets, into highly eccentric orbits where the material gets disrupted by tidal forces and then accreted on to the star. This can occur through a planet–planet scattering process triggered by the stellar mass-loss during the post main-sequence (MS) evolution of planetary systems. So far, studies of the N-body dynamics of this process have used artificial planetary system architectures built ad hoc. In this work, we attempt to go a step further and study the dynamical instability provided by more restrictive systems that, at the same time, allow us an exploration of a wider parameter space: the hundreds of multiple planetary systems found around MS stars. We find that most of our simulated systems remain stable during the MS, Red, and Asymptotic Giant Branch and for several Gyr into the WD phases of the host star. Overall, only ≈2.3 ${{\ \rm per\ cent}}$ of the simulated systems lose a planet on the WD as a result of dynamical instability. If the instabilities take place during the WD phase most of them result in planet ejections with just five planetary configurations ending as a collision of a planet with the WD. Finally 3.2 ${{\ \rm per\ cent}}$ of the simulated systems experience some form of orbital scattering or orbit crossing that could contribute to the pollution at a sustained rate if planetesimals are present in the same system.
The BAHAMAS project: effects of dynamical dark energy on large-scale structure
Authors: Pfeifer Simon , McCarthy Ian G , Stafford Sam G , Brown Shaun T , Font Andreea S , Kwan Juliana , Salcido Jaime , Schaye Joop 
Published: August 2020

ABSTRACT
In this work, we consider the impact of spatially uniform but time-varying dark energy (or ‘dynamical dark energy’, DDE) on large-scale structure in a spatially flat universe, using large cosmological hydrodynamical simulations that form part of the BAHAMAS project. As DDE changes the expansion history of the universe, it impacts the growth of structure. We explore variations in DDE that are constrained to be consistent with the cosmic microwave background. We find that DDE can affect the clustering of matter and haloes at the $\sim 10{{\ \rm per\ cent}}$ level (suppressing it for so-called freezing models, while enhancing it for thawing models), which should be distinguishable with upcoming large-scale structure surveys. DDE cosmologies can also enhance or suppress the halo mass function (with respect to Lambda cold dark matter) over a wide range of halo masses. The internal properties of haloes are minimally affected by changes in DDE, however. Finally, we show that the impact of baryons and associated feedback processes is largely independent of the change in cosmology and that these processes can be modelled separately to typically better than a few per cent accuracy.
Discovery of optical outflows and inflows in the black hole candidate GRS 1716−249
Authors: Cúneo V A , Muñoz-Darias T , Sánchez-Sierras J , Jiménez-Ibarra F , Armas Padilla M , Buckley D A H , Casares J , Charles P , Corral-Santana J M , Fender R , Fernández-Ontiveros J A , Mata Sánchez D , Panizo-Espinar G , Ponti G , Torres M A P 
Published: August 2020

ABSTRACT
We present optical spectroscopy obtained with the GTC, VLT, and SALT telescopes during the decline of the 2016–2017 outburst of the black hole candidate GRS 1716−249 (Nova Oph 1993). Our 18-epoch data set spans 6 months and reveals that the observational properties of the main emission lines are very variable, even on time-scales of a few hours. Several epochs are characterized by P-Cyg (as well as flat-top and asymmetric) profiles in the  Hα,  Hβ, and He  ii (λ4686) emission lines, implying the presence of an accretion disc wind, which is likely hot and dense. The wind’s terminal velocity (∼2000 km s−1) is similar to that observed in other black hole X-ray transients. These lines also show transient and sharp red-shifted absorptions, taking the form of inverted P-Cyg profiles. We argue that these profiles can be explained by the presence of infalling material at ∼1300 km s−1. We propose a failed wind scenario to explain this inflow and discuss other alternatives, such as obscuration produced by an accretion-related structure (e.g. the gas stream) in a high inclination system.
How do different spiral arm models impact the ISM and GMC population?
Authors: Pettitt Alex R , Dobbs Clare L , Baba Junichi , Colombo Dario , Duarte-Cabral Ana , Egusa Fumi , Habe Asao 
Published: August 2020

ABSTRACT
The nature of galactic spiral arms in disc galaxies remains elusive. Regardless of the spiral model, arms are expected to play a role in sculpting the star-forming interstellar medium (ISM). As such, different arm models may result in differences in the structure of the ISM and molecular cloud properties. In this study, we present simulations of galactic discs subject to spiral arm perturbations of different natures. We find very little difference in how the cloud population or gas kinematics vary between the different grand design spirals, indicating that the ISM on cloud scales cares little about where spiral arms come from. We do, however, see a difference in the interarm/arm mass spectra, and minor differences in tails of the distributions of cloud properties (as well as radial variations in the stellar/gaseous velocity dispersions). These features can be attributed to differences in the radial dependence of the pattern speeds between the different spiral models, and could act as a metric of the nature of spiral structure in observational studies.
K2: Background Survey – the search for undiscovered transients in Kepler/K2 data
Authors: Ridden-Harper R , Tucker B E , Gully-Santiago M , Barentsen G , Rest A , Garnavich P , Shaya E 
Published: August 2020

ABSTRACT
The K2 mission of the Kepler Space Telescope offers a unique possibility to examine sources of both Galactic and extragalactic origin with high-cadence photometry. Alongside the multitude of supernovae and quasars detected within targeted galaxies, it is likely that Kepler has serendipitously observed many transients throughout K2. Such events will likely have occurred in background pixels, coincidentally surrounding science targets. Analysing the background pixels presents the possibility to conduct a high-cadence survey with areas of a few square degrees per campaign. We demonstrate the capacity to independently recover key K2 transients such as KSN 2015K and SN 2018oh. With this survey, we expect to detect numerous transients and determine the first comprehensive rates for transients with lifetimes of ≤1 d.
Galactic inflow and wind recycling rates in the eagle simulations
Authors: Mitchell Peter D , Schaye Joop , Bower Richard G 
Published: August 2020

ABSTRACT
The role of galactic wind recycling represents one of the largest unknowns in galaxy evolution, as any contribution of recycling to galaxy growth is largely degenerate with the inflow rates of first-time infalling material, and the rates with which outflowing gas and metals are driven from galaxies. We present measurements of the efficiency of wind recycling from the eagle cosmological simulation project, leveraging the statistical power of large-volume simulations that reproduce a realistic galaxy population. We study wind recycling at the halo scale, i.e. gas that has been ejected beyond the halo virial radius, and at the galaxy scale, i.e. gas that has been ejected from the interstellar medium to at least $\approx 10 \, {{\ \rm per\ cent}}$ of the virial radius. Galaxy-scale wind recycling is generally inefficient, with a characteristic return time-scale that is comparable to or longer than a Hubble time, and with an efficiency that clearly peaks at the characteristic halo mass of $M_{200} = 10^{12} \, \mathrm{M_\odot }$. Correspondingly, the majority of gas being accreted on to galaxies in eagle is infalling for the first time. Recycling is more efficient at the halo scale, with values that differ by orders of magnitude from those assumed by semi-analytical galaxy formation models. Differences in the efficiency of wind recycling with other hydrodynamical simulations are currently difficult to assess, but are likely smaller. We find that cumulative first-time gas accretion rates at the virial radius are reduced relative to the expectation from dark matter accretion for haloes with mass $M_{200} \lt 10^{12} \, \mathrm{M_\odot }$, indicating efficient preventative feedback on halo scales.
Magnetic field fluctuations in anisotropic, supersonic turbulence
Authors: Beattie James R , Federrath Christoph , Seta Amit 
Published: August 2020

ABSTRACTThe rich structure that we observe in molecular clouds is due to the interplay between strong magnetic fields and supersonic (turbulent) velocity fluctuations. The velocity fluctuations interact with the magnetic field, causing it too to fluctuate. Using numerical simulations, we explore the nature of such magnetic field fluctuations, $\delta \mathrm{{\boldsymbol {\mathit {B}}}}$, over a wide range of turbulent Mach numbers, $\operatorname{\mathcal {M}}= 2\!-\!20$ (i.e. from weak to strong compressibility), and Alfvén Mach numbers, $\operatorname{\mathcal {M}_{\text{A0}}}= 0.1\!-\!100$ (i.e. from strong to weak magnetic mean fields, B0). We derive a compressible quasi-static fluctuation model from the magnetohydrodynamical (MHD) equations and show that velocity gradients parallel to the mean magnetic field give rise to compressible modes in sub-Alfvénic flows, which prevents the flow from becoming two dimensional, as is the case in incompressible MHD turbulence. We then generalize an analytical model for the magnitude of the magnetic fluctuations to include $\operatorname{\mathcal {M}}$, and find $|\delta \mathrm{{\boldsymbol {\mathit {B}}}}| = \delta B = c_{\rm s}\sqrt{\pi \rho _0}\operatorname{\mathcal {M}}\operatorname{\mathcal {M}_{\text{A0}}}$, where cs is the sound speed and ρ0 is the mean density of gas. This new relation fits well in the strong B-field regime. We go on to study the anisotropy between the perpendicular (B⊥) and parallel (B∥) fluctuations and the mean-normalized fluctuations, which we find follow universal scaling relations, invariant of $\operatorname{\mathcal {M}}$. We provide a detailed analysis of the morphology for the δB⊥ and δB∥ probability density functions and find that eddies aligned with B0 cause parallel fluctuations that reduce B∥ in the most anisotropic simulations. We discuss broadly the implications of our fluctuation models for magnetized gases in the interstellar medium.
The Genomic Selfing Syndrome Accompanies the Evolutionary Breakdown of Heterostyly
Authors: Wang Xin-Jia , Barrett Spencer C H , Zhong Li , Wu Zhi-Kun , Li De-Zhu , Wang Hong , Zhou Wei 
Published: August 2020

AbstractThe evolutionary transition from outcrossing to selfing can have important genomic consequences. Decreased effective population size and the reduced efficacy of selection are predicted to play an important role in the molecular evolution of the genomes of selfing species. We investigated evidence for molecular signatures of the genomic selfing syndrome using 66 species of Primula including distylous (outcrossing) and derived homostylous (selfing) taxa. We complemented our comparative analysis with a microevolutionary study of P. chungensis, which is polymorphic for mating system and consists of both distylous and homostylous populations. We generated chloroplast and nuclear genomic data sets for distylous, homostylous, and distylous–homostylous species and identified patterns of nonsynonymous to synonymous divergence (dN/dS) and polymorphism (πN/πS) in species or lineages with contrasting mating systems. Our analysis of coding sequence divergence and polymorphism detected strongly reduced genetic diversity and heterozygosity, decreased efficacy of purifying selection, purging of large-effect deleterious mutations, and lower rates of adaptive evolution in samples from homostylous compared with distylous populations, consistent with theoretical expectations of the genomic selfing syndrome. Our results demonstrate that self-fertilization is a major driver of molecular evolutionary processes with genomic signatures of selfing evident in both old and relatively young homostylous populations.
Single molecule mass photometry of nucleic acids
Authors: Li Yiwen , Struwe Weston B , Kukura Philipp 
Published: August 2020

Abstract
Mass photometry is a recently developed methodology capable of measuring the mass of individual proteins under solution conditions. Here, we show that this approach is equally applicable to nucleic acids, enabling their facile, rapid and accurate detection and quantification using sub-picomoles of sample. The ability to count individual molecules directly measures relative concentrations in complex mixtures without need for separation. Using a dsDNA ladder, we find a linear relationship between the number of bases per molecule and the associated imaging contrast for up to 1200 bp, enabling us to quantify dsDNA length with up to 2 bp accuracy. These results introduce mass photometry as an accurate, rapid and label-free single molecule method complementary to existing DNA characterization techniques.
The oncofetal RNA-binding protein IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression in cancer
Authors: Müller Simon , Bley Nadine , Busch Bianca , Glaß Markus , Lederer Marcell , Misiak Claudia , Fuchs Tommy , Wedler Alice , Haase Jacob , Bertoldo Jean Borges , Michl Patrick , Hüttelmaier Stefan 
Published: August 2020

AbstractThe IGF2 mRNA-binding protein 1 (IGF2BP1) is a non-catalytic post-transcriptional enhancer of tumor growth upregulated and associated with adverse prognosis in solid cancers. However, conserved effector pathway(s) and the feasibility of targeting IGF2BP1 in cancer remained elusive. We reveal that IGF2BP1 is a post-transcriptional enhancer of the E2F-driven hallmark in solid cancers. IGF2BP1 promotes G1/S cell cycle transition by stabilizing mRNAs encoding positive regulators of this checkpoint like E2F1. This IGF2BP1-driven shortening of the G1 cell cycle phase relies on 3′UTR-, miRNA- and m6A-dependent regulation and suggests enhancement of cell cycle progression by m6A-modifications across cancers. In addition to E2F transcription factors, IGF2BP1 also stabilizes E2F-driven transcripts directly indicating post-transcriptional ‘super’-enhancer role of the protein in E2F-driven gene expression in cancer. The small molecule BTYNB disrupts this enhancer function by impairing IGF2BP1-RNA association. Consistently, BTYNB interferes with E2F-driven gene expression and tumor growth in experimental mouse tumor models.
The Sac10b homolog from Sulfolobus islandicus is an RNA chaperone
Authors: Zhang Ningning , Guo Li , Huang Li 
Published: August 2020

AbstractNucleic acid-binding proteins of the Sac10b family, also known as Alba, are widely distributed in Archaea. However, the physiological roles of these proteins have yet to be clarified. Here, we show that Sis10b, a member of the Sac10b family from the hyperthermophilic archaeon Sulfolobus islandicus, was active in RNA strand exchange, duplex RNA unwinding in vitro and RNA unfolding in a heterologous host cell. This protein exhibited temperature-dependent binding preference for ssRNA over dsRNA and was more efficient in RNA unwinding and RNA unfolding at elevated temperatures. Notably, alanine substitution of a highly conserved basic residue (K) at position 17 in Sis10b drastically reduced the ability of this protein to catalyse RNA strand exchange and RNA unwinding. Additionally, the preferential binding of Sis10b to ssRNA also depended on the presence of K17 or R17. Furthermore, normal growth was restored to a slow-growing Sis10b knockdown mutant by overproducing wild-type Sis10b but not by overproducing K17A in this mutant strain. Our results indicate that Sis10b is an RNA chaperone that likely functions most efficiently at temperatures optimal for the growth of S. islandicus, and K17 is essential for the chaperone activity of the protein.
The nucleic acid chaperone activity of the HIV-1 Gag polyprotein is boosted by its cellular partner RPL7: a kinetic study
Authors: Karnib Hassan , Nadeem Muhammad F , Humbert Nicolas , Sharma Kamal K , Grytsyk Natalia , Tisné Carine , Boutant Emmanuel , Lequeu Thiebault , Réal Eleonore , Boudier Christian , de Rocquigny Hugues , Mély Yves 
Published: August 2020

AbstractThe HIV-1 Gag protein playing a key role in HIV-1 viral assembly has recently been shown to interact through its nucleocapsid domain with the ribosomal protein L7 (RPL7) that acts as a cellular co-factor promoting Gag's nucleic acid (NA) chaperone activity. To further understand how the two proteins act together, we examined their mechanism individually and in concert to promote the annealing between dTAR, the DNA version of the viral transactivation element and its complementary cTAR sequence, taken as model HIV-1 sequences. Gag alone or complexed with RPL7 was found to act as a NA chaperone that destabilizes cTAR stem-loop and promotes its annealing with dTAR through the stem ends via a two-step pathway. In contrast, RPL7 alone acts as a NA annealer that through its NA aggregating properties promotes cTAR/dTAR annealing via two parallel pathways. Remarkably, in contrast to the isolated proteins, their complex promoted efficiently the annealing of cTAR with highly stable dTAR mutants. This was confirmed by the RPL7-promoted boost of the physiologically relevant Gag-chaperoned annealing of (+)PBS RNA to the highly stable tRNALys3 primer, favoring the notion that Gag recruits RPL7 to overcome major roadblocks in viral assembly.
Location specific annealing of miR-122 and other small RNAs defines an Hepatitis C Virus 5′ UTR regulatory element with distinct impacts on virus translation and genome stability
Authors: Kunden Rasika D , Ghezelbash Sarah , Khan Juveriya Q , Wilson Joyce A 
Published: August 2020

Abstract
Hepatitis C virus (HCV) replication requires annealing of a liver specific small-RNA, miR-122 to 2 sites on 5′ untranslated region (UTR). Annealing has been reported to (a) stabilize the genome, (b) stimulate translation and (c) promote the formation of translationally active Internal Ribosome Entry Site (IRES) RNA structure. In this report, we map the RNA element to which small RNA annealing promotes HCV to nucleotides 1–44 and identify the relative impact of small RNA annealing on virus translation promotion and genome stabilization. We mapped the optimal region on the HCV genome to which small RNA annealing promotes virus replication to nucleotides 19–37 and found the efficiency of viral RNA accumulation decreased as annealing moved away from this region. Then, by using a panel of small RNAs that promote replication with varying efficiencies we link the efficiency of lifecycle promotion with translation stimulation. By contrast small RNA annealing stabilized the viral genome even if they did not promote virus replication. Thus, we propose that miR-122 annealing promotes HCV replication by annealing to an RNA element that activates the HCV IRES and stimulates translation, and that miR-122 induced HCV genome stabilization is insufficient alone but enhances virus replication.
Aberrant mucosal immunoreaction to tonsillar microbiota in immunoglobulin A nephropathy
Authors: Yamaguchi Hiroki , Goto Shin , Takahashi Nao , Tsuchida Masafumi , Watanabe Hirofumi , Yamamoto Suguru , Kaneko Yoshikatsu , Higashi Koichi , Mori Hiroshi , Nakamura Yukio , Horii Arata , Kurokawa Ken , Narita Ichiei 
Published: August 2020

Abstract

Background
Immunoglobulin A nephropathy (IgAN) is the most common glomerulonephritis worldwide, characterized by mesangial polymeric IgA1 deposition. IgAN is believed to develop owing to aberrant mucosal immunoreaction against commensals in the tonsils. However, the exact interrelation between pathogenic IgA and mucosal microbiota in IgAN patients is unclear.

Methods
Biopsy-proven IgAN or recurrent tonsillitis (RT) patients who had undergone tonsillectomy were enrolled. We used 16S ribosomal RNA gene amplicon sequencing with a flow cytometry-based bacterial cell sorting technique) and immunoglobulin repertoire sequencing of the IgA heavy chain to characterize IgA-coated bacteria of the tonsillar microbiota (IgA-SEQ) and their corresponding IgA repertoire. Furthermore, we fractionated patient serum using gel-filtration chromatography and performed flow cytometry-based analysis of IgA binding to bacteria cultured from incised tonsils.

Results
Tonsillar proliferation-inducing ligand and B-cell activating factor levels were significantly higher in IgAN than in RT patients. IgA-SEQ for tonsillar microbiota revealed the preferential binding ability of IgA to Bacteroidetes in IgAN tonsils compared with those from RT patients. Expression of immunoglobulin heavy (IGH) constant alpha 1 with IGH variable 3–30 was significantly higher in IgAN than that in RT, and positively correlated with the IgA-coated enrichment score of Bacteroidetes. Serum polymeric IgA, comprising high levels of GdIgA1, exhibited considerable binding to Bacteroidetes strains cultured from the tonsils of IgAN patients.

Conclusions
These findings provide evidence that aberrant mucosal immune responses to tonsillar anaerobic microbiota, primarily consisting of members of the phylum Bacteroidetes, are involved in IgAN pathophysiology.
Neuropathology of Surgically Managed Epilepsy Specimens
Authors: Thomas Diana L , Pierson Christopher R 
Published: August 2020

Abstract
Epilepsy is characterized as recurrent seizures, and it is one of the most prevalent disorders of the human nervous system. A large and diverse profile of different syndromes and conditions can cause perturbations in neural networks that are associated with epilepsy. Advances in neuroimaging and electrophysiological monitoring have enhanced our ability to localize the neuropathological lesions that alter the neural networks giving rise to epilepsy, whereas advances in surgical management have resulted in excellent seizure control in many patients following resections. Histopathologic study using a variety of special stains, molecular analysis, and functional studies of these resected tissues has facilitated the neuropathological characterization of these lesions. Here, we review the neuropathology of common structural lesions that cause epilepsy and are amenable to neurosurgical resection, such as hippocampal sclerosis, focal cortical dysplasia, and its associated principal lesions, including long-term epilepsy-associated tumors, as well as other malformations of cortical development and Rasmussen encephalitis.