bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining the evolution of [C ii] intensity through the end stages of reionization
Authors: Padmanabhan Hamsa 
Published: July 2019

ABSTRACT
We combine available constraints on the local [C ii] 158 $\mu$m line luminosity function from galaxy observations (Hemmati et al. 2017), with the evolution of the star formation rate density and the recent [C ii] intensity mapping measurement in Pullen et al. (2018, assuming detection), to derive the evolution of the [C ii] luminosity–halo mass relation over z ∼ 0–6. We develop convenient fitting forms for the evolution of the [C ii] luminosity–halo mass relation and forecast constraints on the [C ii] intensity mapping power spectrum and its associated uncertainty across redshifts. We predict the sensitivities to detect the power spectrum for upcoming PIXIE-, STARFIRE-, EXCLAIM-, CONCERTO-, TIME-, and CCAT-p-like surveys, as well as possible future intensity mapping observations with the ALMA (Atacama Large Millimetre Array) facility.
Assessing the effect of lens mass model in cosmological application with updated galaxy-scale strong gravitational lensing sample
Authors: Chen Yun , Li Ran , Shu Yiping , Cao Xiaoyue 
Published: July 2019

ABSTRACT
By comparing the dynamical and lensing masses of early-type lens galaxies, one can constrain both the cosmological parameters and the density profiles of galaxies. We explore the constraining power on cosmological parameters and the effect of the lens mass model in this method with 161 galaxy-scale strong lensing systems, which is currently the largest sample with both high-resolution imaging and stellar dynamical data. We assume a power-law mass model for the lenses, and consider three different parametrizations for γ (i.e. the slope of the total mass density profile) to include the effect of the dependence of γ on redshift and surface mass density. When treating δ (i.e. the slope of the luminosity density profile) as a universal parameter for all lens galaxies, we find the limits on the cosmological parameter Ωm are quite weak and biased, and also heavily dependent on the lens mass model in the scenarios of parametrizing γ with three different forms. When treating δ as an observable for each lens, the unbiased estimate of Ωm can be obtained only in the scenario of including the dependence of γ on both the redshift and the surface mass density, that is $\Omega _\mathrm{ m} = 0.381^{+0.185}_{-0.154}$ at 68 per cent confidence level in the framework of a flat ΛCDM model. We conclude that the significant dependencies of γ on both the redshift and the surface mass density, as well as the intrinsic scatter of δ among the lenses, need to be properly taken into account in this method.
Constraints on the interacting vacuum–geodesic CDM scenario
Authors: Martinelli Matteo , Hogg Natalie B , Peirone Simone , Bruni Marco , Wands David 
Published: July 2019

Abstract
We investigate an interacting dark sector scenario in which the vacuum energy is free to interact with cold dark matter (CDM), which itself is assumed to cluster under the sole action of gravity, i.e. it is in freefall (geodesic), as in ΛCDM. The interaction is characterized by a dimensionless coupling qV(z), in general a function of redshift. Aiming to reconstruct the evolution of the coupling, we use cosmic microwave background data from Planck 2015, along with baryon acoustic oscillation, redshift space distortion, and Type Ia supernova measurements to constrain various parametrizations of qV(z). We present the full linear perturbation theory of this interacting scenario and use Monte Carlo Markov Chains (MCMC) sampling to study five different cases: two cases in which we have ΛCDM evolution in the distant past, until a set redshift ztrans, below which the interaction switches on and qV is the single-sampled parameter, with ztrans fixed at ztrans = 3000 and 0.9, respectively; a case where we allow this transition redshift to vary along with qV; a case in which the vacuum energy is zero for z &gt; ztrans and then begins to grow once the interaction switches on; and the final case in which we bin qV(z) in four redshift bins to investigate the possibility of a dynamical interaction, reconstructing the redshift evolution of the function using Gaussian processes. We find that, in all cases where the high-redshift evolution is not modified, the results are compatible with a vanishing coupling, thus finding no significant deviation from ΛCDM.
Metallicity gradients in small and nearby spiral galaxies
Authors: Bresolin Fabio 
Published: July 2019

ABSTRACT
Spectra of H ii regions obtained with Gemini/GMOS are used to derive the radial metallicity gradients of four small, low-mass spiral galaxies. The analysis of the outer disc of one of them, NGC 1058, uncovers the characteristic flattening found in similar extended disc galaxies. After combining these data with published long-slit observations of nearby spiral galaxies, no evidence for a dependence of the disc scale length-normalized metallicity gradients with stellar mass is found, down to log (M⋆/M⊙) ∼ 8.5. The abundance gradients derived from these observations are compared to predictions from recent cosmological simulations of galaxy evolution, finding that in several cases the simulations fail to reproduce the mean steepening of the gradients, expressed in dex kpc−1, with decreasing stellar mass for present-day galaxies, or do not extend to sufficiently small stellar masses for a meaningful comparison. The mean steepening of the abundance gradients (in dex kpc−1) with decreasing disc scale length is in qualitative agreement with predictions from the inside-out model of Boissier & Prantzos, although the predicted slopes are systematically steeper than observed. This indicates the necessity of including processes such as outflows and radial mixing in similar models of galactic chemical evolution. Published spatially resolved metallicity and photometric data of dwarf irregular galaxies suggest that significant, but transitory, metallicity gradients can develop for systems that have experienced recent (t &lt; 100 Myr) enhanced star formation in their inner discs.
2PBC J0658.0–1746: a hard X-ray eclipsing polar in the orbital period gap
Authors: Bernardini F , de Martino D , Mukai K , Falanga M , Masetti N 
Published: July 2019

Abstract
The hard X-ray source 2PBC J0658.0–1746 was proposed as an eclipsing magnetic cataclysmic variable of the polar type, based on optical follow-ups. We present the first spectral and timing analysis at X-ray energies with XMM–Newton, complemented with archival X-ray, optical, infrared (IR) photometry, and spectroscopy. The X-ray emission shows bright and faint phases and total eclipses recurring every 2.38 h, consistent with optical properties. This firmly identifies 2PBC J0658.0–1746 as an eclipsing polar, the second hard X-ray selected in the orbital period gap. The X-ray orbital modulation changes from cycle-to-cycle and the X-ray flux is strongly variable over the years, implying a non-stationary mass accretion rate both on short and long time-scales. The X-ray eclipses allow to refine the orbital ephemeris with period 0.09913398(4) d, and to constrain the binary inclination $79^{\circ}\lesssim i \lesssim 90^{\circ}$ and the mass ratio 0.18$\lt M_2/M_{\mathrm{ WD}}\lt $0.40. A companion mass M$_{2}=0.2-0.25\rm \, M_{\odot }$ with a radius R$_{2}=0.24-0.26\rm \, R_{\odot }$ and spectral type ∼M4, at D$=209^{+3}_{-2}\rm \, pc$, is derived. A lower limit to the white dwarf mass of $\sim 0.6\, \rm \, M_{\odot }$ is obtained from the X-ray spectrum. An upper limit to the magnetic colatitude, $\beta \lesssim 50^{\circ}$, and a shift in azimuth, $\psi \sim 14^{\circ}$, of the main accreting pole are also estimated. The optical/IR spectral energy distribution shows large excess in the mid-IR due to lower harmonics of cyclotron emission. A high-state mass accretion rate $\rm \, \sim 0.4-1\times 10^{-10}\, M_{\odot }\, yr^{-1}$, lower than that of cataclysmic variables above the gap and close to that of systems below it, is estimated. With 2PBC J0658.0–1746, the number of hard X-ray-selected polars increases to 13 members, suggesting that they are not as rare as previously believed.
Simulating radial velocity observations of trappist-1 with SPIRou
Authors: Klein Baptiste , Donati J-F 
Published: July 2019

ABSTRACT
We simulate a radial velocity (RV) follow-up of the TRAPPIST-1 system, a faithful representative of M dwarfs hosting transiting Earth-sized exoplanets to be observed with SPIRou in the months to come. We generate an RV curve containing the signature of the seven transiting TRAPPIST-1 planets and a realistic stellar activity curve statistically compatible with the light curve obtained with the K2 mission. We find a ±5 m s−1 stellar activity signal comparable in amplitude with the planet signal. Using various sampling schemes and white noise levels, we create time-series from which we estimate the masses of the seven planets. We find that the precision on the mass estimates is dominated by (i) the white noise level for planets c, f, and e and (ii) the stellar activity signal for planets b, d, and h. In particular, the activity signal completely outshines the RV signatures of planets d and h that remain undetected regardless of the RV curve sampling and level of white noise in the data set. We find that an RV follow-up of TRAPPIST-1 using SPIRou alone would likely result in an insufficient coverage of the rapidly evolving activity signal of the star, especially with bright-time observations only, making statistical methods such as Gaussian Process Regression hardly capable of firmly detecting planet f and accurately recovering the mass of planet g. In contrast, we show that using bi-site observations with good longitudinal complementary would allow for a more accurate filtering of the stellar activity RV signal.
The estrogen-regulated lncRNA H19/miR-216a-5p axis alters stromal cell invasion and migration via ACTA2 in endometriosis
Authors: Xu Zhen , Zhang Liping , Yu Qian , Zhang Yanan , Yan Lei , Chen Zi-Jiang 
Published: July 2019

AbstractFibrotic tissue may contribute to the origin of some endometriosis-related symptoms, such as chronic pelvic pain and infertility. Alterations in the H19/miR-216a-5p/ACTA2 pathway may mediate the regulation of eutopic endometrial stromal cell (euESC) invasion and migration and may represent a potential mechanism underlying fibrous tissue formation or fibrosis in women with endometriosis. In this study, we aimed to determine the expression of H19 and ACTA2 in endometrial tissues of women with endometriosis. Two groups of 23 infertile women with endometriosis and 23 matched infertile women without endometriosis were investigated. Primary cultured cells of endometrial tissues were analyzed using RT-PCR and western blotting (WB) to determine expression of H19 and ACTA2. 5-Ethyl-2′-deoxyuridine, CCK8 and Transwell assays were used to study the functions of H19 and ACTA2. Human embryonic kidney 293 cells were used for luciferase assays to study miR-216a-5p binding sites with H19 and ACTA2. We found that H19 and ACTA2 levels were significantly higher in endometriosis euESCs than in control euESCs (P < 0.05) and were positively correlated in endometriosis euESCs. Luciferase assays indicated that H19 regulates ACTA2 expression via competition for inhibitory miR-216a-5p binding sites. Our results indicate that alterations in the estrogen/H19/miR-216a-5p/ACTA2 pathway regulated endometriosis euESC invasion and migration. Downregulation of H19 or ACTA2 inhibited endometriosis euESC invasion and migration; however, estrogen promoted endometriosis euESC invasion and migration via H19. The main limitation of our study was that experiments were conducted in vitro and further in vivo studies are required in the future. However, our study showed that primary cultured cells represented endometriosis cells more clearly than cell lines.
ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast
Authors: Mondeel Thierry D G A , Holland Petter , Nielsen Jens , Barberis Matteo 
Published: July 2019

AbstractThe understanding of the multi-scale nature of molecular networks represents a major challenge. For example, regulation of a timely cell cycle must be coordinated with growth, during which changes in metabolism occur, and integrate information from the extracellular environment, e.g. signal transduction. Forkhead transcription factors are evolutionarily conserved among eukaryotes, and coordinate a timely cell cycle progression in budding yeast. Specifically, Fkh1 and Fkh2 are expressed during a lengthy window of the cell cycle, thus are potentially able to function as hubs in the multi-scale cellular environment that interlocks various biochemical networks. Here we report on a novel ChIP-exo dataset for Fkh1 and Fkh2 in both logarithmic and stationary phases, which is analyzed by novel and existing software tools. Our analysis confirms known Forkhead targets from available ChIP-chip studies and highlights novel ones involved in the cell cycle, metabolism and signal transduction. Target genes are analyzed with respect to their function, temporal expression during the cell cycle, correlation with Fkh1 and Fkh2 as well as signaling and metabolic pathways they occur in. Furthermore, differences in targets between Fkh1 and Fkh2 are presented. Our work highlights Forkhead transcription factors as hubs that integrate multi-scale networks to achieve proper timing of cell division in budding yeast.
The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112
Authors: van Tran Nhan , Ernst Felix G M , Hawley Ben R , Zorbas Christiane , Ulryck Nathalie , Hackert Philipp , Bohnsack Katherine E , Bohnsack Markus T , Jaffrey Samie R , Graille Marc , Lafontaine Denis L J 
Published: July 2019

Abstract
N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here, we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5–TRMT112, supporting that its RNA-binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5–TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.
DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging
Authors: Kim Daehyung , Rashid Fahad , Cho Yeonmo , Zaher Manal S , Cho I I Hwan , Hamdan Samir M , Jeong Cherlhyun , Lee Jong-Bong 
Published: July 2019

Abstract
Real-time visualization of single-proteins or -complexes on nucleic acid substrates is an essential tool for characterizing nucleic acid binding proteins. Here, we present a novel surface-condition independent and high-throughput single-molecule optical imaging platform called ‘DNA skybridge’. The DNA skybridge is constructed in a 3D structure with 4 μm-high thin quartz barriers in a quartz slide. Each DNA end is attached to the top of the adjacent barrier, resulting in the extension and immobilization of DNA. In this 3D structure, the bottom surface is out-of-focus when the target molecules on the DNA are imaged. Moreover, the DNA skybridge itself creates a thin Gaussian light sheet beam parallel to the immobilized DNA. This dual property allows for imaging a single probe-tagged molecule moving on DNA while effectively suppressing interference with the surface and background signals from the surface.
Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs
Authors: Mino Takashi , Iwai Noriki , Endo Masayuki , Inoue Kentaro , Akaki Kotaro , Hia Fabian , Uehata Takuya , Emura Tomoko , Hidaka Kumi , Suzuki Yutaka , Standley Daron M , Okada-Hatakeyama Mariko , Ohno Shigeo , Sugiyama Hiroshi , Yamashita Akio , Takeuchi Osamu 
Published: July 2019

AbstractRegnase-1-mediated mRNA decay (RMD), in which inflammatory mRNAs harboring specific stem–loop structures are degraded, is a critical part of proper immune homeostasis. Prior to initial translation, Regnase-1 associates with target stem–loops but does not carry out endoribonucleolytic cleavage. Single molecule imaging revealed that UPF1 is required to first unwind the stem–loops, thus licensing Regnase-1 to proceed with RNA degradation. Following translation, Regnase-1 physically associates with UPF1 using two distinct points of interaction: The Regnase-1 RNase domain binds to SMG1-phosphorylated residue T28 in UPF1; in addition, an intrinsically disordered segment in Regnase-1 binds to the UPF1 RecA domain, enhancing the helicase activity of UPF1. The SMG1-UPF1–Regnase-1 axis targets pioneer rounds of translation and is critical for rapid resolution of inflammation through restriction of the number of proteins translated by a given mRNA. Furthermore, small-molecule inhibition of SMG1 prevents RNA unwinding in dendritic cells, allowing post-transcriptional control of innate immune responses.
Hallmarks of ribosomopathies
Authors: Kampen Kim R , Sulima Sergey O , Vereecke Stijn , De Keersmaecker Kim 
Published: July 2019

Abstract
Ribosomopathies are diseases caused by defects in ribosomal constituents or in factors with a role in ribosome assembly. Intriguingly, congenital ribosomopathies display a paradoxical transition from early symptoms due to cellular hypo-proliferation to an elevated cancer risk later in life. Another association between ribosome defects and cancer came into view after the recent discovery of somatic mutations in ribosomal proteins and rDNA copy number changes in a variety of tumor types, giving rise to somatic ribosomopathies. Despite these clear connections between ribosome defects and cancer, the molecular mechanisms by which defects in this essential cellular machinery are oncogenic only start to emerge. In this review, the impact of ribosomal defects on the cellular function and their mechanisms of promoting oncogenesis are described. In particular, we discuss the emerging hallmarks of ribosomopathies such as the appearance of ‘onco-ribosomes’ that are specialized in translating oncoproteins, dysregulation of translation-independent extra-ribosomal functions of ribosomal proteins, rewired cellular protein and energy metabolism, and extensive oxidative stress leading to DNA damage. We end by integrating these findings in a model that can provide an explanation how ribosomopathies could lead to the transition from hypo- to hyper-proliferation in bone marrow failure syndromes with elevated cancer risk.
Treatment of Anterior Circulation Aneurysms in the Internal Carotid Artery With Flow Diverters
Authors: Vakharia Kunal , Munich Stephan A , Waqas Muhammad , Levy Elad I , Siddiqui Adnan H 
Published: July 2019

Abstract
Several studies have shown the efficacy and feasibility of flow diversion for the endovascular treatment of wide-necked and otherwise anatomically challenging intracranial aneurysms (IA). Technological advances have led to successful long-term occlusion rates and a safety profile for flow-diverter stents that parallels other endovascular and open surgical options for these lesions. With growing indications for use of the Pipeline Embolization Device (PED, Medtronic, Dublin, Ireland) to include IAs up to the internal carotid artery (ICA) terminus, understanding the nuances of this technology is increasingly relevant. Furthermore, there is a growing body of literature on the use of flow diversion to treat distal (up to A2, M2, and P2), ruptured, and posterior circulation aneurysms, although these applications are “off-label” at present. In this manuscript, we discuss the expanding role of flow diversion in the ICA and compare this technique with other endovascular options for the treatment of ICA IAs. We also discuss technical nuances of the deployment of flow diverters for the treatment of challenging lesions and in difficult and tortuous anatomy.
Experience with tofacitinib in Canada: patient characteristics and treatment patterns in rheumatoid arthritis over 3 years
Authors: Pope Janet , Bessette Louis , Jones Niall , Fallon Lara , Woolcott John , Gruben David , Crooks Michael , Gold David , Haraoui Boulos 
Published: July 2019

Abstract

Objectives
To describe characteristics, treatment patterns and persistence in patients with RA treated with tofacitinib, an oral Janus kinase inhibitor, in Canadian clinical practice between 1 June 2014 and 31 May 2017.

Methods
Data were obtained from the tofacitinib eXel support programme. Baseline demographics and medication history were collected via patient report/special authorization forms; reasons for discontinuation were captured by patient report. Treatment persistence was estimated using Kaplan–Meier methods, with data censored at last follow-up. Cox regression was applied to analyse baseline characteristics associated with treatment discontinuation.

Results
The number of patients with RA enrolled from 2014 to 2017 was 4276; tofacitinib utilization increased during that period, as did the proportion of biologic (b) DMARD-naïve patients prescribed tofacitinib. Of patients who initiated tofacitinib, 1226/3678 (33.3%) discontinued, mostly from lack of efficacy (35.7%) and adverse events (26.9%). Persistence was 62.7% and 49.6% after 1 and 2 years of treatment, respectively. Prior bDMARD experience predicted increased tofacitinib discontinuation (vs bDMARD-naïve, P < 0.001). Increased retention was associated with older age (56–65 years and >65 years vs ⩽45 years; P < 0.05), and time since diagnosis of 15 to <20 years (vs <5 years; P < 0.01). In bDMARD-naïve, post-1 bDMARD, post-2 bDMARD and post-⩾3 bDMARD patients, median survival was >730, 613, 667 and 592 days, respectively.

Conclusion
Since 2014, tofacitinib use in Canadian patients with RA increased, especially among bDMARD-naïve/post-1 bDMARD patients. Median drug survival was ∼2 years. Likelihood of persistence increased for bDMARD-naïve (vs bDMARD-experienced) patients and those aged ⩾56 (vs ⩽45) years.