bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic orbits and dynamical masses of emission-line binaries
Authors: Grant David , Blundell Katherine 
Published: October 2021

ABSTRACT
The observed orbits of emission-line stars may be affected by systematics owing to their broad emission lines being formed in complex and extended environments. This is problematic when orbital parameter probability distributions are estimated assuming radial-velocity data are solely comprised of Keplerian motion plus Gaussian white noise, leading to overconfident and inaccurate orbital solutions, with implications for the inferred dynamical masses and hence evolutionary models. We present a framework in which these systems can be meaningfully analysed. We synthesize benchmark data sets, each with a different and challenging noise formulation, for testing the performance of different algorithms. We make these data sets freely available with the aim of making model validation an easy and standardized practice in this field. Next, we develop an application of Gaussian processes to model the radial-velocity systematics of emission-line binaries, named marginalized $\mathcal {GP}$. We benchmark this algorithm, along with current standardized algorithms, on the synthetic data sets and find our marginalized $\mathcal {GP}$ algorithm performs significantly better than the standard algorithms for data contaminated by systematics. Finally, we apply the marginalized $\mathcal {GP}$ algorithm to four prototypical emission-line binaries: Eta Carinae, GG Carinae, WR 140, and WR 133. We find systematics to be present in several of these case studies; and consequently, the predicted orbital parameter distributions, and dynamical masses, are modified from those previously determined.
The spatial distribution deviation and the power suppression of baryons from dark matter
Authors: Yang Hua-Yu , Wang Yun , He Ping , Zhu Weishan , Feng Long-Long 
Published: October 2021

ABSTRACT
The spatial distribution between dark matter and baryonic matter of the Universe is biased or deviates from each other. In this work, by comparing the results derived from IllustrisTNG and WIGEON simulations, we find that many results obtained from TNG are similar to those from WIGEON data, but differences between the two simulations do exist. For the ratio of density power spectrum between dark matter and baryonic matter, as scales become smaller and smaller, the power spectra for baryons are increasingly suppressed for WIGEON simulations; while for TNG simulations, the suppression stops at $k=15-20\, {h {\rm Mpc}^{-1}}$, and the power spectrum ratios increase when $k\gt 20\, {h {\rm Mpc}^{-1}}$. The suppression of power ratio for WIGEON is also redshift-dependent. From z = 1 to z = 0, the power ratio decreases from about 70 per cent to less than 50 per cent at $k=8\, {h {\rm Mpc}^{-1}}$. For TNG simulation, the suppression of power ratio is enhanced with decreasing redshifts in the scale range $k\gt 4\, {h {\rm Mpc}^{-1}}$, but is nearly unchanged with redshifts in $k\lt 4\, {h {\rm Mpc}^{-1}}$. These results indicate that turbulent heating can also have the consequence to suppress the power ratio between baryons and dark matter. Regarding the power suppression for TNG simulations as the norm, the power suppression by turbulence for WIGEON simulations is roughly estimated to be 45 per cent at $k=2\, {h {\rm Mpc}^{-1}}$, and gradually increases to 69 per cent at $k=8\, {h {\rm Mpc}^{-1}}$, indicating the impact of turbulence on the cosmic baryons are more significant on small scales.
SKAO H i intensity mapping: blind foreground subtraction challenge
Authors: Spinelli Marta , Carucci Isabella P , Cunnington Steven , Harper Stuart E , Irfan Melis O , Fonseca José , Pourtsidou Alkistis , Wolz Laura 
Published: October 2021

ABSTRACT
Neutral Hydrogen Intensity Mapping (H i IM) surveys will be a powerful new probe of cosmology. However, strong astrophysical foregrounds contaminate the signal and their coupling with instrumental systematics further increases the data cleaning complexity. In this work, we simulate a realistic single-dish H i IM survey of a 5000 deg2 patch in the 950–1400 MHz range, with both the MID telescope of the SKA Observatory (SKAO) and MeerKAT, its precursor. We include a state-of-the-art H i simulation and explore different foreground models and instrumental effects such as non-homogeneous thermal noise and beam side lobes. We perform the first Blind Foreground Subtraction Challenge for H i IM on these synthetic data cubes, aiming to characterize the performance of available foreground cleaning methods with no prior knowledge of the sky components and noise level. Nine foreground cleaning pipelines joined the challenge, based on statistical source separation algorithms, blind polynomial fitting, and an astrophysical-informed parametric fit to foregrounds. We devise metrics to compare the pipeline performances quantitatively. In general, they can recover the input maps’ two-point statistics within 20 per cent in the range of scales least affected by the telescope beam. However, spurious artefacts appear in the cleaned maps due to interactions between the foreground structure and the beam side lobes. We conclude that it is fundamental to develop accurate beam deconvolution algorithms and test data post-processing steps carefully before cleaning. This study was performed as part of SKAO preparatory work by the H i IM Focus Group of the SKA Cosmology Science Working Group.
Redshift-space effects in voids and their impact on cosmological tests – II. The void-galaxy cross-correlation function
Authors: Correa Carlos M , Paz Dante J , Padilla Nelson D , Sánchez Ariel G , Ruiz Andrés N , Angulo Raúl E 
Published: October 2021

ABSTRACT
This is the second part of a thorough investigation of the redshift-space effects that affect void properties and the impact they have on cosmological tests. Here, we focus on the void-galaxy cross-correlation function, specifically, on the projected versions that we developed in a previous work. The pillar of the analysis is the one-to-one relationship between real and redshift-space voids above the shot-noise level identified with a spherical void finder. Under this mapping, void properties are affected by three effects: (i) a systematic expansion as a consequence of the distortions induced by galaxy dynamics, (ii) the Alcock–Paczynski volume effect, which manifests as an overall expansion or contraction depending on the fiducial cosmology, and (iii) a systematic off-centring along the line of sight as a consequence of the distortions induced by void dynamics. We found that correlations are also affected by an additional source of distortions: the ellipticity of voids. This is the first time that distortions due to the off-centring and ellipticity effects are detected and quantified. With a simplified test, we verified that the Gaussian streaming model is still robust provided all these effects are taken into account, laying the foundations for improvements in current models in order to obtain unbiased cosmological constraints from spectroscopic surveys. Besides this practical importance, this analysis also encodes key information about the structure and dynamics of the Universe at the largest scales. Furthermore, some of the effects constitute cosmological probes by themselves, as is the case of the void ellipticity.
Simulating the complexity of the dark matter sheet – II. Halo and subhalo mass functions for non-cold dark matter models
Authors: Stücker Jens , Angulo Raul E , Hahn Oliver , White Simon D M 
Published: October 2021

ABSTRACT
We present ‘sheet + release’ simulations that reliably follow the evolution of dark matter structure at and below the dark matter free-streaming scale, where instabilities in traditional N-body simulations create a large population of spurious artificial haloes. Our simulations sample a large range of power-spectrum cutoff functions, parameterized through the half-mode scale khm and a slope parameter β. This parameter space can represent many non-cold dark matter (NCDM) models, including thermal relic warm dark matter, sterile-neutrinos, fuzzy dark matter, and a significant fraction of ETHOS models. Combining these simulations with additional N-body simulations, we find the following results. (1) Even after eliminating spurious haloes, the halo mass function in the strongly suppressed regime ($n_{\rm {X}}/n_{\rm {CDM}} \lt 5 \ \mathrm{ per \, cent}$) remains uncertain because it depends strongly on the definition of a halo. At these mass scales traditional halo finders primarily identify overdensities that are unbound, highly elongated, dominated by tidal fields, or far from virialized. (2) The regime where the suppression is smaller than a factor of 20 is quite robust to these uncertainties, however, and can be inferred reliably from suitable N-body simulations. (3) Parameterizing the suppression in the halo- and subhalo mass functions through the scales where the suppression reaches $20 \ \mathrm{ per \, cent}$, 50 per cent, and $80 \ \mathrm{ per \, cent}$, we provide simple formulae which enable predictions for many NCDM models. (4) The halo mass–concentration relations in our sheet + release simulations agree well with previous results based on N-body simulations. (5) In general, we confirm the validity of previous N-body studies of warm dark matter models, largely eliminating concerns about the effects of artificial haloes.
The 2D metallicity distribution and mixing scales of nearby galaxies
Authors: Williams Thomas G , Kreckel Kathryn , Belfiore Francesco , Groves Brent , Sandstrom Karin , Santoro Francesco , Blanc Guillermo A , Bigiel Frank , Boquien Médéric , Chevance Mélanie , Congiu Enrico , Emsellem Eric , Glover Simon C O , Grasha Kathryn , Klessen Ralf S , Koch Eric , Kruijssen J M Diederik , Leroy Adam K , Liu Daizhong , Meidt Sharon , Pan Hsi-An , Querejeta Miguel , Rosolowsky Erik , Saito Toshiki , Sánchez-Blázquez Patricia , Schinnerer Eva , Schruba Andreas , Watkins Elizabeth J 
Published: October 2021

ABSTRACT
Understanding the spatial distribution of metals within galaxies allows us to study the processes of chemical enrichment and mixing in the interstellar medium. In this work, we map the 2D distribution of metals using a Gaussian Process Regression (GPR) for 19 star-forming galaxies observed with the Very Large Telescope/Multi Unit Spectroscopic Explorer (VLT–MUSE) as a part of the PHANGS–MUSE survey. We find that 12 of our 19 galaxies show significant 2D metallicity variation. Those without significant variations typically have fewer metallicity measurements, indicating this is due to the dearth of ${\rm H\, {\small II}}$ regions in these galaxies, rather than a lack of higher-order variation. After subtracting a linear radial gradient, we see no enrichment in the spiral arms versus the disc. We measure the 50 per cent correlation scale from the two-point correlation function of these radially subtracted maps, finding it to typically be an order of magnitude smaller than the fitted GPR kernel scale length. We study the dependence of the two-point correlation scale length with a number of global galaxy properties. We find no relationship between the 50 per cent correlation scale and the overall gas turbulence, in tension with existing theoretical models. We also find more actively star-forming galaxies, and earlier type galaxies have a larger 50 per cent correlation scale. The size and stellar mass surface density do not appear to correlate with the 50 per cent correlation scale, indicating that perhaps the evolutionary state of the galaxy and its current star formation activity is the strongest indicator of the homogeneity of the metal distribution.
RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids
Authors: Lee Hyunjee , Cho HyeokJin , Kim Jooyoung , Lee Sua , Yoo Jungmin , Park Daeho , Lee Gwangrog 
Published: October 2021

Abstract
RNase H is involved in fundamental cellular processes and is responsible for removing the short stretch of RNA from Okazaki fragments and the long stretch of RNA from R-loops. Defects in RNase H lead to embryo lethality in mice and Aicardi-Goutieres syndrome in humans, suggesting the importance of RNase H. To date, RNase H is known to be a non-sequence-specific endonuclease, but it is not known whether it performs other functions on the structural variants of RNA:DNA hybrids. Here, we used Escherichia coli RNase H as a model, and examined its catalytic mechanism and its substrate recognition modes, using single-molecule FRET. We discovered that RNase H acts as a processive exoribonuclease on the 3′ DNA overhang side but as a distributive non-sequence-specific endonuclease on the 5′ DNA overhang side of RNA:DNA hybrids or on blunt-ended hybrids. The high affinity of previously unidentified double-stranded (ds) and single-stranded (ss) DNA junctions flanking RNA:DNA hybrids may help RNase H find the hybrid substrates in long genomic DNA. Our study provides new insights into the multifunctionality of RNase H, elucidating unprecedented roles of junctions and ssDNA overhang on RNA:DNA hybrids.
Genome-wide mapping of G-quadruplex structures with CUT&Tag
Authors: Lyu Jing , Shao Rui , Kwong Yung Philip Yuk , Elsässer Simon J 
Published: October 2021

Abstract
Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (ESC), observing widespread G4 formation at active promoters, active and poised enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mouse ESCs. Upon differentiation to neural progenitor cells (NPC), enhancer G4s are lost. Further, performing R-loop CUT&Tag, we demonstrate the genome-wide co-occurrence of single-stranded DNA, G4s and R loops at promoters and enhancers. We confirm that G4 structures exist independent of ongoing transcription, suggesting an intricate relationship between transcription and non-canonical DNA structures.
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
Authors: Quaglia Federica , Mészáros Bálint , Salladini Edoardo , Hatos András , Pancsa Rita , Chemes Lucía B , Pajkos Mátyás , Lazar Tamas , Peña-Díaz Samuel , Santos Jaime , Ács Veronika , Farahi Nazanin , Fichó Erzsébet , Aspromonte Maria Cristina , Bassot Claudio , Chasapi Anastasia , Davey Norman E , Davidović Radoslav , Dobson Laszlo , Elofsson Arne , Erdős Gábor , Gaudet Pascale , Giglio Michelle , Glavina Juliana , Iserte Javier , Iglesias Valentín , Kálmán Zsófia , Lambrughi Matteo , Leonardi Emanuela , Longhi Sonia , Macedo-Ribeiro Sandra , Maiani Emiliano , Marchetti Julia , Marino-Buslje Cristina , Mészáros Attila , Monzon Alexander Miguel , Minervini Giovanni , Nadendla Suvarna , Nilsson Juliet F , Novotný Marian , Ouzounis Christos A , Palopoli Nicolás , Papaleo Elena , Pereira Pedro José Barbosa , Pozzati Gabriele , Promponas Vasilis J , Pujols Jordi , Rocha Alma Carolina Sanchez , Salas Martin , Sawicki Luciana Rodriguez , Schad Eva , Shenoy Aditi , Szaniszló Tamás , Tsirigos Konstantinos D , Veljkovic Nevena , Parisi Gustavo , Ventura Salvador , Dosztányi Zsuzsanna , Tompa Peter , Tosatto Silvio C E , Piovesan Damiano 
Published: October 2021

Abstract
The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
The pioneer round of translation ensures proper targeting of ER and mitochondrial proteins
Authors: Park Joori , Chang Jeeyoon , Hwang Hyun Jung , Jeong Kwon , Lee Hyuk-Joon , Ha Hongseok , Park Yeonkyoung , Lim Chunghun , Woo Jae-Sung , Kim Yoon Ki 
Published: October 2021

Abstract
The pioneer (or first) round of translation of newly synthesized mRNAs is largely mediated by a nuclear cap-binding complex (CBC). In a transcriptome-wide analysis of polysome-associated and CBC-bound transcripts, we identify RN7SL1, a noncoding RNA component of a signal recognition particle (SRP), as an interaction partner of the CBC. The direct CBC–SRP interaction safeguards against abnormal expression of polypeptides from a ribosome–nascent chain complex (RNC)–SRP complex until the latter is properly delivered to the endoplasmic reticulum. Failure of this surveillance causes abnormal expression of misfolded proteins at inappropriate intracellular locations, leading to a cytosolic stress response. This surveillance pathway also blocks protein synthesis through RNC–SRP misassembled on an mRNA encoding a mitochondrial protein. Thus, our results reveal a surveillance pathway in which pioneer translation ensures proper targeting of endoplasmic reticulum and mitochondrial proteins.
R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation
Authors: Lin Ruoyao , Zhong Xiaoming , Zhou Yongli , Geng Huichao , Hu Qingxi , Huang Zhihao , Hu Jun , Fu Xiang-Dong , Chen Liang , Chen Jia-Yu 
Published: October 2021

AbstractR-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.
Rituximab plus methotrexate combination as a salvage therapy in persistently active granulomatosis with polyangiitis
Authors: Sorin Boris , Samson Maxime , Durel Cécile-Audrey , Diot Elisabeth , Guichard Isabelle , Grados Aurélie , Limal Nicolas , Régent Alexis , Cohen Pascal , Dion Jérémie , Legendre Paul  , Le Guern Véronique , Mouthon Luc , Guillevin Loïc , Terrier Benjamin ,   the French Vasculitis Study Group (FVSG)
Published: October 2021

Abstract

Objective
The aim of this study was to describe the efficacy and safety of rituximab and MTX (RTX/MTX) combination therapy in ANCA-associated vasculitides (AAV).

Methods
A retrospective French nationwide study was conducted in patients with AAV who received RTX/MTX combination therapy for persistently active disease.

Results
Seventeen patients were included. All patients had granulomatosis with polyangiitis (GPA), with positive ANCA in 76% of them, mainly with PR3-ANCA specificity. Sixteen patients (94%) had priorly failed to achieve remission with RTX and 11 (65%) with CYC. Patients had experienced a median of 3 (2–4) flares. Manifestations requiring RTX/MTX combination therapy were subglottic or bronchial stenosis in 6 patients (35%), orbital mass in 6 (35%), disabling ENT involvement in 2 (12%), and epiduritis and pachymeningitis in 1 case (6%) each. The median follow-up duration for the RTX/MTX combination therapy was 11 months (11–26 months). At 6 months, global response had been achieved in 15 patients (88%), including partial response in 11 (65%) and complete response in 4 (24%). At last evaluation, global response had been achieved in 16 patients (94%). Seven patients (41%) experienced severe adverse events (grade 3 or 4), including infections in 4 (24%) and hepatitis in 2 (12%). Combination therapy was withdrawn in 4 patients (24%), but never for safety concerns. In contrast, the MTX dose was decreased in 2 patients (12%) because of adverse events. One patient died of an unknown cause.

Conclusion
RTX/MTX combination therapy could be an effective salvage therapy to treat persistently active GPA with granulomatous manifestations, with an acceptable safety profile.