bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-centre prospective cohort study of diaphragmatic defect phenotype and repair in neonates with congenital diaphragmatic hernia: ‘The Defect Study’
Authors:   Paediatric Surgery Trainee Research Network (PSTRN) Organisation and Writing Group, Eastwood Mary Patrice , Harwood Rachel , Rhodes Hannah , Bethell George Stephen , Bradnock Timothy J , Hall Nigel J ,   ‘The Defect Study’ Lead Team
Published: February 2022

Abstract
Defect size and closure technique in neonates with congenital diaphragmatic hernia (CDH) has long-term consequences for morbidity in survivors. Although subjective operative reporting of the defect size has been standardized, objective evaluation is lacking. There is no reported optimum closure technique related to the size and position of the diaphragmatic defect. We aim to objectively describe diaphragmatic defects and repair methods, at the time of neonatal CDH repair, through a prospective multi-centre service evaluation project. We will evaluate all neonates born with CDH surviving to diaphragmatic repair. All specialist paediatric surgical centres in the UK, Ireland and New Zealand will be invited to participate. Non-identifiable patient data will be collected over a 24-month period using a REDCap database. Diaphragmatic defects and hemidiaphragm measurements will be recorded intra-operatively alongside standardized defect reporting. Closure technique and 1-year outcomes will be captured. Demographics and peri-operative data will be reported as median (interquartile range), mean (standard deviation) or categorical variables. Defect measurement will be calculated as an ellipse with area displayed as a histogram. Patch usage will be compared to the defect area using univariate logistic regression analysis. Univariate logistic regression analysis will also be used to assess for the association between peri-operative variables and complications. Where possible, a multi-variate regression analysis will be performed. Centres will register the project as service evaluation at each participating hospital site. The results will be submitted to an international peer reviewed journal and will be disseminated via appropriate international forums and through patient support networks (CDH-UK).
Clustering with general photo-z uncertainties: application to Baryon Acoustic Oscillations
Authors: Chan Kwan Chuen , Ferrero Ismael , Avila Santiago , Ross Ashley J , Crocce Martin , Gaztañaga Enrique 
Published: February 2022

ABSTRACT
Photometric data can be analysed using the 3D correlation function ξp to extract cosmological information via e.g. measurement of the Baryon Acoustic Oscillations (BAO). Previous studies modeled ξp assuming a Gaussian photo-z approximation. In this work we improve the modeling by incorporating realistic photo-z distribution. We show that the position of the BAO scale in ξp is determined by the photo-z distribution and the Jacobian of the transformation. The latter diverges at the transverse scale of the separation s⊥, and it explains why ξp traces the underlying correlation function at s⊥, rather than s, when the photo-z uncertainty σz/(1+ z) ≳ 0.02. We also obtain the Gaussian covariance for ξp. Due to photo-z mixing, the covariance of ξp shows strong off-diagonal elements. The high correlation of the data causes some issues to the data fitting. None the less, we find that either it can be solved by suppressing the largest eigenvalues of the covariance or it is not directly related to the BAO. We test our BAO fitting pipeline using a set of mock catalogs. The data set is dedicated for Dark Energy Survey Year 3 (DES Y3) BAO analyses and includes realistic photo-z distributions. The theory template is in good agreement with mock measurement. Based on the DES Y3 mocks, ξp statistic is forecast to constrain the BAO shift parameter α to be 1.001 ± 0.023, which is well consistent with the corresponding constraint derived from the angular correlation function measurements. Thus, ξp offers a competitive alternative for the photometric data analyses.
MUSE sneaks a peek at extreme ram-pressure stripping events – V. Towards a complete view of the galaxy cluster A1367
Authors: Pedrini Alex , Fossati Matteo , Gavazzi Giuseppe , Fumagalli Michele , Boselli Alessandro , Consolandi Guido , Sun Ming , Yagi Masafumi , Yoshida Michitoshi 
Published: February 2022

ABSTRACT
We present an analysis of the kinematics and ionization conditions in a sample composed of seven star-forming galaxies undergoing ram-pressure stripping in the A1367 cluster, and the galaxy ESO137–001 in the Norma cluster. MUSE observations of two new galaxies in this sample, CGCG097–073 and CGCG097–079, are also presented. This sample is characterized by homogeneous integral field spectroscopy with MUSE and by a consistent selection based on the presence of ionized gas tails. The ratio [O i]/H α is consistently elevated in the tails of these objects compared to what observed in unperturbed galaxy discs, an ubiquitous feature which we attribute to shocks or turbulent phenomena in the stripped gas. Compact star-forming regions are observed in only $\approx 50 {{\ \rm per\ cent}}$ of the tails, implying that specific (currently unknown) conditions are needed to trigger star formation inside the stripped gas. Focusing on the interface regions between the interstellar and intracluster medium, we observe different line ratios that we associate to different stages of the stripping process, with galaxies at an early stage of perturbation showing more prominent signatures of elevated star formation. Our analysis, thus, demonstrates the power of a well selected and homogeneous sample to infer general properties arising from ram-pressure stripping inside local clusters.
The first X-ray spectrum of the high-mass X-ray binary XTE J1855−026 during the compact object eclipse
Authors: Sanjurjo-Ferrín G , Torrejón J M , Rodes-Roca J J 
Published: February 2022

ABSTRACT
We present the first XMM–Newton observation of the classical supergiant high-mass X-ray binary XTE J1855−026 taken entirely during the eclipse of the neutron star (NS), covering the orbital phases ϕ = 0.00–0.11. The analysis of the data allows us to (a) compare with the parameters obtained during the existing pre-eclipse observation and (b) explore the back-illuminated stellar wind of the B0I-type donor. The blackbody component, used to describe the soft excess during pre-eclipse, is not observed during eclipse. It must be then produced near the NS or along the donor–NS line. The 0.3–10 keV luminosity during eclipse (∼1034 erg s−1) is 70 times lower than pre-eclipse. The intensity of the Fe Kα line, in the average eclipse spectrum, is ∼7.4 times lower than the one measured during pre-eclipse. Since Kα photons cannot be resonantly scattered in the wind, the vast majority of Fe Kα emission must come from distances within 1R* from the NS. The eclipse spectrum is successfully modelled through the addition of two photoionized plasmas, one with low ionization (log ξ1,cold = 0.36) and high emission measure (EM1,cold ≈ 3 × 1059 cm−3) and another with high ionization (log ξ2,hot = 3.7) and low emission measure (EM2,hot ≈ 2 × 1056 cm−3). Assuming that the cold and hot gas phases are the clumps and the interclump medium of the stellar wind, respectively, and a clump volume filling factor of ≈0.04–0.05, typical for massive stars, a density contrast between clumps and the interclump medium of nc/ni ≈ 180 is deduced, in agreement with theoretical expectations and optical–ultraviolet observations of massive star winds.
Low-mass members of nearby young stellar moving groups from Gaia EDR3
Authors: Lee Jinhee , Song Inseok , Murphy Simon J 
Published: February 2022

ABSTRACT
Gaia EDR3 offers greatly improved kinematics for nearby objects, including members of nearby young stellar moving groups (NYMGs). In this study, we aim to identify low-mass NYMG members (spectral types of M0 to mid-L) in Gaia EDR3. We calculated spatio-kinematic membership probabilities by utilizing a Bayesian membership probability calculation scheme developed in our previous study. We evaluated stellar youth primarily based on colour–magnitude diagram positions. Combining spatio-kinematic membership assessment and youth evaluation, we identified ∼2900 low-mass NYMG candidate members, including ∼700 previously claimed members. In the set of ∼2200 new candidate members, ∼550 appear to be young based on NUV brightness. Our pilot spectroscopic study with Wide Field Spectrograph (WiFeS) on the ANU 2.3-m telescope observed 78 candidates, with 79 per cent confirmed as members. Using our new member sample, we estimated an isochronal age of the β Pictoris Moving Group. The mean age (∼10 Myr), which is around half the age of recent estimates, suggests either a truly younger age of the β Pictoris Moving Group or inaccuracies in contemporary isochrones. As the main results of this study, we provide lists of newly confirmed and candidate low-mass NYMG members.
Spatially Resolved Chandra Spectroscopy of Supernova Remnant DEM L71 in the Large Magellanic Cloud
Authors: Alan N , Bilir S 
Published: February 2022

ABSTRACT
We present a detailed X-ray spectroscopic study of the supernova remnant (SNR) DEM L71 in the Large Magellanic Cloud. Based on deep ∼103 ks archival Chandra data, we perform a detailed spatially resolved spectral analysis of DEM L71. We analyse regional spectra extracted from thin-sliced regions along several different azimuthal directions of the SNR to construct radial profiles of elemental abundances for O, Ne, Mg, Si, and Fe. Our elemental abundance measurements reveal an asymmetrical spatial distribution of metal-rich ejecta gas. Especially the asymmetry in the western part of the central Fe distribution is remarkable. While the location of the contact discontinuity is generally at ∼5 pc from the geometric center of the X-ray emission of DEM L71, it is uncertain in the western part of the remnant. Fe is enhanced in the ejecta while O and Ne abundances are generally negligible. This finding confirms the Type Ia origin of DEM L71. We estimate an upper limit on the Sedov age of ∼6660 ± 770 yr and explosion energy of ∼1.74 ± 0.35 × 1051 erg for the remnant. This explosion energy estimate is consistent with a canonical explosion of a type Ia SNR.
Effects of the refractive index of the X-ray corona on the emission lines in AGNs
Authors: Chainakun P , Watcharangkool A , Young A J 
Published: February 2022

ABSTRACT
X-ray reflection from an accretion disc produces characteristic emission lines allowing us to probe the innermost regions in active galactic nuclei. We investigate these emission lines under a framework of Riemannian geometrical optics where the corona has a refractive index of n ≠ 1. The empty space outside is a vacuum with n = 1. The Kerr metric is modified to trace the light rays that are bent due to not only the gravity of the black hole but also the effects of coronal plasma dependent on n. The choice of n alters the null geodesics, producing the effect which is analogous to the light deflection. For the corona with n &gt; 1, the disc on the far side within the corona covers a larger area on the observer’s sky, enhancing the blue wing of the line and producing more flux difference between the blue peak and extended red tail. The inverse effects are seen when n &lt; 1. Moreover, the corona with n &gt; 1 and n &lt; 1 could induce extra shifts in the blue wing (Δgmax) to higher and lower energy, respectively. These effects are more prominent when the inclination angle is ≳60° and the corona extends to ≳5rg. To obtain the deviation of the line shift of Δgmax ≳ 0.01, the difference between the refractive index of the corona and that of the empty space must be $\Delta n \gtrsim 0.5{{\ \rm per\ cent}}$. Finally, the lensing corona can influence the arrival time of photons that may affect the observed variability of these emission lines.
Colchicine as rescue treatment in two pediatric patients with chronic recurrent multifocal osteomyelitis (CRMO)
Authors: Quintana-Ortega Cristian , Prieto-Moreno Pfeifer Ana , Palomino Lozano Laura , Lancharro Ángel , Saavedra Lozano Jesús , Villa-García Ángel José , Seoane-Reula Elena 
Published: February 2022

ABSTRACT
Chronic recurrent multifocal osteomyelitis (CRMO) is a rare idiopathic autoinflammatory bone disease characterised by noninfective inflammation of bones. Diagnostic approach is challenging and requires exclusion of other causes such as malignancies or infections. Nonsteroidal anti-inflammatory drugs (NSAIDs) and corticosteroids are usually applied as first-line therapy in CRMO patients; however, some cases require more intensive therapy with second-line agents to control disease activity. We hereby describe the use of colchicine as a nonconventional second-line disease-modifying antirheumatic drug in two pediatric patients with CRMO refractory to NSAIDs and corticosteroids. Our data indicate that colchicine might prove an important area for future research as a potential therapeutic option with easy administration, low cost, and a good safety profile in CRMO patients refractory to first-line therapy.
Engineered Sleeping Beauty transposase redirects transposon integration away from genes
Authors: Miskey Csaba , Kesselring Lisa , Querques Irma , Abrusán György , Barabas Orsolya , Ivics Zoltán 
Published: February 2022

Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
A tRNA modifying enzyme as a tunable regulatory nexus for bacterial stress responses and virulence
Authors: Fleming Brittany A , Blango Matthew G , Rousek Alexis A , Kincannon William M , Tran Alexander , Lewis Adam J , Russell Colin W , Zhou Qin , Baird Lisa M , Barber Amelia E , Brannon John R , Beebout Connor J , Bandarian Vahe , Hadjifrangiskou Maria , Howard Michael T , Mulvey Matthew A 
Published: February 2022

Abstract
Post-transcriptional modifications can impact the stability and functionality of many different classes of RNA molecules and are an especially important aspect of tRNA regulation. It is hypothesized that cells can orchestrate rapid responses to changing environmental conditions by adjusting the specific types and levels of tRNA modifications. We uncovered strong evidence in support of this tRNA global regulation hypothesis by examining effects of the well-conserved tRNA modifying enzyme MiaA in extraintestinal pathogenic Escherichia coli (ExPEC), a major cause of urinary tract and bloodstream infections. MiaA mediates the prenylation of adenosine-37 within tRNAs that decode UNN codons, and we found it to be crucial to the fitness and virulence of ExPEC. MiaA levels shifted in response to stress via a post-transcriptional mechanism, resulting in marked changes in the amounts of fully modified MiaA substrates. Both ablation and forced overproduction of MiaA stimulated translational frameshifting and profoundly altered the ExPEC proteome, with variable effects attributable to UNN content, changes in the catalytic activity of MiaA, or availability of metabolic precursors. Cumulatively, these data indicate that balanced input from MiaA is critical for optimizing cellular responses, with MiaA acting much like a rheostat that can be used to realign global protein expression patterns.
A transcriptional roadblock protects yeast centromeres
Authors: Hedouin Sabrine , Logsdon Glennis A , Underwood Jason G , Biggins Sue 
Published: February 2022

Abstract
Centromeres are the chromosomal loci essential for faithful chromosome segregation during cell division. Although centromeres are transcribed and produce non-coding RNAs (cenRNAs) that affect centromere function, we still lack a mechanistic understanding of how centromere transcription is regulated. Here, using a targeted RNA isoform sequencing approach, we identified the transcriptional landscape at and surrounding all centromeres in budding yeast. Overall, cenRNAs are derived from transcription readthrough of pericentromeric regions but rarely span the entire centromere and are a complex mixture of molecules that are heterogeneous in abundance, orientation, and sequence. While most pericentromeres are transcribed throughout the cell cycle, centromere accessibility to the transcription machinery is restricted to S-phase. This temporal restriction is dependent on Cbf1, a centromere-binding transcription factor, that we demonstrate acts locally as a transcriptional roadblock. Cbf1 deletion leads to an accumulation of cenRNAs at all phases of the cell cycle which correlates with increased chromosome mis-segregation that is partially rescued when the roadblock activity is restored. We propose that a Cbf1-mediated transcriptional roadblock protects yeast centromeres from untimely transcription to ensure genomic stability.
Virus-specific editing identification approach reveals the landscape of A-to-I editing and its impacts on SARS-CoV-2 characteristics and evolution
Authors: Song Yulong , He Xiuju , Yang Wenbing , Wu Yaoxing , Cui Jun , Tang Tian , Zhang Rui 
Published: February 2022

Abstract
Upon SARS-CoV-2 infection, viral intermediates specifically activate the IFN response through MDA5-mediated sensing and accordingly induce ADAR1 p150 expression, which might lead to viral A-to-I RNA editing. Here, we developed an RNA virus-specific editing identification pipeline, surveyed 7622 RNA-seq data from diverse types of samples infected with SARS-CoV-2, and constructed an atlas of A-to-I RNA editing sites in SARS-CoV-2. We found that A-to-I editing was dynamically regulated, varied between tissue and cell types, and was correlated with the intensity of innate immune response. On average, 91 editing events were deposited at viral dsRNA intermediates per sample. Moreover, editing hotspots were observed, including recoding sites in the spike gene that affect viral infectivity and antigenicity. Finally, we provided evidence that RNA editing accelerated SARS-CoV-2 evolution in humans during the epidemic. Our study highlights the ability of SARS-CoV-2 to hijack components of the host antiviral machinery to edit its genome and fuel its evolution, and also provides a framework and resource for studying viral RNA editing.
Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice
Authors: Ma Xing , Feng Yilong , Yang Ying , Li Xin , Shi Yining , Tao Shentong , Cheng Xuejiao , Huang Jian , Wang Xiu-e , Chen Caiyan , Monchaud David , Zhang Wenli 
Published: February 2022

Abstract
I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic DNA regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions are now suspected in key cellular processes in human cells such as genome stability and regulation of gene transcription. In plants, their biological relevance is still largely unknown. Here, we characterized PiMFSs with high potential for i-motif formation in the rice genome by developing and applying a protocol hinging on an iMab antibody-based immunoprecipitation (IP) coupled with high-throughput sequencing (seq), consequently termed iM-IP-seq. We found that PiMFSs had intrinsic subgenomic distributions, cis-regulatory functions and an intricate relationship with DNA methylation. We indeed found that the coordination of PiMFSs with DNA methylation may affect dynamics of transposable elements (TEs) among different cultivated Oryza subpopulations or during evolution of wild rice species. Collectively, our study provides first and unique insights into the biology of iMs in plants, with potential applications in plant biotechnology for improving important agronomic rice traits.
Tobacco Control in Bolivia: Transnational Civil Society Efforts in Securing a Comprehensive Law
Authors: Crosbie Eric , Perez Sara , Copa Pamela Cortez , Monje Alejandra Karina Garron , Machin Nina , Lopez Gabrielle , Sebrié Ernesto M 
Published: February 2022

Abstract

Introduction
To document the adoption of a comprehensive tobacco control law in Bolivia, a low-income country in South America.

Aims and Methods
Analysis of the Bolivian case study by reviewing news sources, tobacco control legislation, industry websites, and advocacy reports. Application of the Policy Dystopia Model to analyze tobacco industry and health advocacy arguments and action-based strategies.

Results
For decades tobacco control progress in Bolivia remained relatively stagnant due to industry interference. In the 2000s and 2010s, Bolivia ratified the WHO Framework Convention on Tobacco Control (FCTC) and implemented a couple of laws that began restricting smoking in public places and tobacco advertising. In 2015, tobacco control civil society emerged with the creation of Fundación InterAmericana del Corazón (FIC) Bolivia, which began coordinating efforts to counter industry interference. Between 2016 and 2020, FIC Bolivia with financial and technical support from international health groups proactively coordinated interministerial meetings, identified and met with key policymakers, and held public educational socialization events to introduce and support a FCTC-based tobacco control bill. Tobacco companies argued to policymakers and the media the bill would result in lost sales/jobs, increase illicit trade and help smugglers profit but only secured minimal changes. In February 2020, Bolivia passed Law 1280, which established 100% smoke-free environments, banned tobacco advertising (except at the point-of-sale), required 60% pictorial health warnings, among others.

Conclusions
International financial and technical support combined with proactive advocacy strategies, including identifying and engaging key policymakers, coordinating interministerial meetings, and educating the public can help pass strong tobacco control laws, especially in low-income countries.

Implications
Low- and middle-income countries struggle to adopt comprehensive tobacco control legislation due to weak state capacity, limited resources, and aggressive tobacco industry interference. This is one of a handful of studies to examine the adoption of a comprehensive tobacco control law in a low-income country, Bolivia. Proactive health advocacy strategies, including identifying and engaging key political allies, helping coordinate interministerial meetings, and aggressively educating and engaging the public can help pass strong tobacco control laws, especially in low-income countries.