bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D MHD simulation of a pulsationally driven MRI decretion disc
Authors: Ressler S M 
Published: October 2021

ABSTRACT
We explore the pulsationally driven orbital mass ejection mechanism for Be star disc formation using isothermal, 3D magnetohydrodynamic (MHD) and hydrodynamic simulations. Non-radial pulsations are added to a star rotating at 95 per cent of critical as an inner boundary condition that feeds gas into the domain. In MHD, the initial magnetic field within the star is weak. The hydrodynamics simulation has limited angular momentum transport, resulting in repeating cycles of mass accumulation into a rotationally supported disc at small radii followed by fall-back on to the star. The MHD simulation, conversely, has efficient (Maxwell αM ∼ 0.04) angular momentum transport provided by both turbulent and coherent magnetic fields: a slowly decreting midplane driven by the magnetorotational instability and a supersonic wind on the surface of the disc driven by global magnetic torques. The angle and time-averaged properties near the midplane agree reasonably well with a 1D viscous decretion disc model with a modified $\tilde{\alpha }=0.5$, in which the gas transitions from a subsonic thin disc to a supersonic spherical wind at the critical point. 1D models, however, cannot capture the multiphase decretion/angular structure seen in our simulations. Our results demonstrate that, at least under certain conditions, non-radial pulsations on the surface of a rapidly rotating, weakly magnetised star can drive a Keplerian disc with the basic properties of the viscous decretion disc paradigm, albeit coupled to a laminar wind away from the midplane. Future modelling of Be star discs should consider the possible existence of such a surface wind.
Exploring the dust content of galactic haloes with Herschel – IV. NGC 3079
Authors: Veilleux S , Meléndez M , Stone M , Cecil G , Hodges-Kluck E , Bland-Hawthorn J , Bregman J , Heitsch F , Martin C L , Mueller T , Rupke D S N , Sturm E , Tanner R , Engelbracht C 
Published: October 2021

ABSTRACT
We present the results from an analysis of deep Herschel far-infrared (far-IR) observations of the edge-on disc galaxy NGC 3079. The point spread function-cleaned Photodetector Array Camera and Spectrometer (PACS) images at 100 and 160 µm display a 25 × 25 kpc2 X-shape structure centred on the nucleus that is similar in extent and orientation to that seen in H α, X-rays, and the far-ultraviolet. One of the dusty filaments making up this structure is detected in the Spectral and Photometric Imaging Receiver 250 µm map out to ∼25 kpc from the nucleus. The match between the far-IR filaments and those detected at other wavelengths suggests that the dusty material has been lifted out of the disc by the same large-scale galactic wind that has produced the other structures in this object. A closer look at the central 10 × 10 kpc2 region provides additional support for this scenario. The dust temperatures traced by the 100–160 µm flux ratios in this region are enhanced within a biconical region centred on the active galactic nucleus, aligned along the minor axis of the galaxy, and coincident with the well-known double-lobed cm-wave radio structure and H α–X-ray nuclear superbubbles. PACS imaging spectroscopy of the inner 6 kpc region reveals broad [C ii] 158 µm emission line profiles and OH 79 µm absorption features along the minor axis of the galaxy with widths well in excess of those expected from beam smearing of the disc rotational motion. This provides compelling evidence that the cool material traced by the [C ii] and OH features directly interacts with the nuclear ionized and relativistic outflows traced by the H α, X-ray, and radio emission.
The NuSTAR extragalactic survey of the James Webb Space Telescope North Ecliptic Pole time-domain field
Authors: Zhao X , Civano F , Fornasini F M , Alexander D M , Cappelluti N , Chen C T , Cohen S H , Elvis M , Gandhi P , Grogin N A , Hickox R C , Jansen R A , Koekemoer A , Lanzuisi G , Maksym W P , Masini A , Rosario D J , Ward M J , Willmer C N A , Windhorst R A 
Published: October 2021

ABSTRACT
We present the NuSTAR extragalactic survey of the James Webb Space Telescope (JWST) North Ecliptic Pole (NEP) Time-Domain Field. The survey covers a ∼0.16 deg2 area with a total exposure of 681 ks acquired in a total of nine observations from three epochs. The survey sensitivities at 20 per cent of the area are 2.39, 1.14, 2.76, 1.52, and 5.20 × 10−14 erg cm−2 s−1 in the 3–24, 3–8, 8–24, 8–16, and 16–24 keV bands, respectively. The NEP survey is one of the most sensitive extragalactic surveys with NuSTAR so far. A total of 33 sources were detected above 95 per cent reliability in at least one of the five bands. We present the number counts, logN-logS, measured in the hard X-ray 8–24 and 8–16 keV bands, uniquely accessible by NuSTAR down to such faint fluxes. We performed source detection on the XMM–Newton and Chandra observations of the same field to search for soft X-ray counterparts of each NuSTAR detection. The soft band positions were used to identify optical and infrared associations. We present the X-ray properties (hardness ratio and luminosity) and optical-to-X-ray properties of the detected sources. The measured fraction of candidate Compton-thick (N$\rm _H\ge 10^{24}\, cm^{-2}$) active galactic nuclei, derived from the hardness ratio, is between 3 and 27 per cent. As this survey was designed to have variability as its primary focus, we present preliminary results on multiepoch flux variability in the 3–24 keV band.
Gravitational waves from GRB core spin-down
Authors: Contopoulos I , Strantzalis A , Papadopoulos D , Kazanas D 
Published: October 2021

ABSTRACT
We investigate long Gamma-Ray Bursts which manifest a sharp linear rise followed by an exponential decay in their γ-ray prompt emission observed with the BAT instrument on board the Swift satellite. We offer a simple electrodynamic model that may account for these particular characteristics. We associate the sharp rise with the winding of the magnetic field by the fast-rotating core that formed in the interior of the stellar precursor. We also associate the subsequent exponential decay with the electromagnetic spin-down of the core following the release of the electromagnetic jet from the stellar interior. Any non-axisymmetric distortion in the rotating core will generate gravitational waves with exponentially decreasing frequency, a so-called ‘down-chirp’. We obtain a detailed estimate of the gravitational-wave profile if the distortion of space–time is due to the winding of a non-axisymmetric component of the magnetic field during that particular phase of the burst. We offer 7 particular time intervals during which one may look into LIGO archival data for the presence of our particular predicted waveforms in order to test our interpretation.
Fundamental parameters and abundance analysis of the components in the SB2 system HD 60803
Authors: Ryabchikova T , Zvyagintsev S , Tkachenko A , Tsymbal V , Pakhomov Yu , Semenko E 
Published: October 2021

ABSTRACT
We perform a detailed spectroscopic study of the SB2 system HD 60803 based on high-resolution spectra obtained with different spectrographs. The analysis was done using two independent methods: a) direct modelling of the observed binary spectrum by a sum of synthetic spectra with a varying set of free parameters and minimizing the difference between the observed and theoretical spectra; and b) spectrum disentangling and independent modelling of the individual components. When applied to binary spectra from different spectrographs, both methods converge to a consistent solution for the fundamental parameters of the HD 60803 components: Teff = 6 055 ± 70 K, log g = 4.08 ± 0.12, ξt = 1.45 ± 0.18 km s−1, [M/H] = 0.03 ± 0.06 (primary), and Teff = 6 069 ± 70 K, log g= 4.14 ± 0.09, ξt = 1.48 ± 0.18 km s−1, [M/H] = 0.03 ± 0.06 (secondary). Differential abundance analysis of the components does not reveal any significant difference in their chemical composition. Apart from Li, both components have solar atmospheric abundances. The Li abundance exceeds the solar value by ∼2 dex, but it agrees with the Li abundance in main-sequence late-F-type stars. Relative-to-solar abundances in both components slightly correlate with the condensation temperature in the same way as that found in the solar analogues with/without detected giant planets. The estimated age of the system is 5.5 ± 0.5 Gyr.
The distribution of [α/Fe] in the Milky Way disc
Authors: Vincenzo Fiorenzo , Weinberg David H , Miglio Andrea , Lane Richard R , Roman-Lopes Alexandre 
Published: October 2021

ABSTRACT
Using a sample of red giant stars from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) Data Release 16, we infer the conditional distribution $p([\alpha /{\rm Fe}]\, |\, [{\rm Fe}/{\rm H}])$ in the Milky Way disk for the α-elements Mg, O, Si, S, and Ca. In each bin of [Fe/H] and Galactocentric radius R, we model p([α/Fe]) as a sum of two Gaussians, representing ‘low-α’ and ‘high-α’ populations with scale heights $z_1=0.45\, {\rm kpc}$ and $z_2=0.95\, {\rm kpc}$, respectively. By accounting for age-dependent and z-dependent selection effects in APOGEE, we infer the [α/Fe] distributions that would be found for a fair sample of long-lived stars covering all z. Near the Solar circle, this distribution is bimodal at sub-solar [Fe/H], with the low-α and high-α peaks clearly separated by a minimum at intermediate [α/Fe]. In agreement with previous results, we find that the high-α population is more prominent at smaller R, lower [Fe/H], and larger |z|, and that the sequence separation is smaller for Si and Ca than for Mg, O, and S. We find significant intrinsic scatter in [α/Fe] at fixed [Fe/H] for both the low-α and high-α populations, typically ∼0.04-dex. The means, dispersions, and relative amplitudes of this two-Gaussian description, and the dependence of these parameters on R, [Fe/H], and α-element, provide a quantitative target for chemical evolution models and a test for hydrodynamic simulations of disk galaxy formation. We argue that explaining the observed bimodality will probably require one or more sharp transitions in the disk’s gas accretion, star formation, or outflow history in addition to radial mixing of stellar populations.
G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities
Authors: He Xiaomei , Yuan Jun , Wang Yinsheng 
Published: October 2021

Abstract
RNA guanine quadruplexes (rG4) assume important roles in post-transcriptional regulations of gene expression, which are often modulated by rG4-binding proteins. Hence, understanding the biological functions of rG4s requires the identification and functional characterizations of rG4-recognition proteins. By employing a bioinformatic approach based on the analysis of overlap between peaks obtained from rG4-seq analysis and those detected in &gt;230 eCLIP-seq datasets for RNA-binding proteins generated from the ENCODE project, we identified a large number of candidate rG4-binding proteins. We showed that one of these proteins, G3BP1, is able to bind directly to rG4 structures with high affinity and selectivity, where the binding entails its C-terminal RGG domain and is further enhanced by its RRM domain. Additionally, our seCLIP-Seq data revealed that pyridostatin, a small-molecule rG4 ligand, could displace G3BP1 from mRNA in cells, with the most pronounced effects being observed for the 3′-untranslated regions (3′-UTR) of mRNAs. Moreover, luciferase reporter assay results showed that G3BP1 positively regulates mRNA stability through its binding with rG4 structures. Together, we identified a number of candidate rG4-binding proteins and validated that G3BP1 can bind directly with rG4 structures and regulate the stabilities of mRNAs.
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database
Authors: Fu Weiwei , Wang Rui , Nanaei Hojjat Asadollahpour , Wang Jinxin , Hu Dexiang , Jiang Yu 
Published: October 2021

Abstract
Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.
VThunter: a database for single-cell screening of virus target cells in the animal kingdom
Authors: Chen Dongsheng , Tan Cong , Ding Peiwen , Luo Lihua , Zhu Jiacheng , Jiang Xiaosen , Ou Zhihua , Ding Xiangning , Lan Tianming , Zhu Yixin , Jia Yi , Wei Yanan , Li Runchu , Qin Qiuyu , Sun Chengcheng , Zhao Wandong , Lv Zhiyuan , Wang Haoyu , Wu Wendi , Yuan Yuting , Pu Mingyi , Li Yuejiao , Zhang Yanan , Chang Ashley , Guo Guoji , Bai Yong , Jin Xin , Liu Huan 
Published: October 2021

Abstract
Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center
Authors: Amos Beatrice , Aurrecoechea Cristina , Barba Matthieu , Barreto Ana , Basenko Evelina Y , Bażant Wojciech , Belnap Robert , Blevins Ann S , Böhme Ulrike , Brestelli John , Brunk Brian P , Caddick Mark , Callan Danielle , Campbell Lahcen , Christensen Mikkel B , Christophides George K , Crouch Kathryn , Davis Kristina , DeBarry Jeremy , Doherty Ryan , Duan Yikun , Dunn Michael , Falke Dave , Fisher Steve , Flicek Paul , Fox Brett , Gajria Bindu , Giraldo-Calderón Gloria I , Harb Omar S , Harper Elizabeth , Hertz-Fowler Christiane , Hickman Mark J , Howington Connor , Hu Sufen , Humphrey Jay , Iodice John , Jones Andrew , Judkins John , Kelly Sarah A , Kissinger Jessica C , Kwon Dae Kun , Lamoureux Kristopher , Lawson Daniel , Li Wei , Lies Kallie , Lodha Disha , Long Jamie , MacCallum Robert M , Maslen Gareth , McDowell Mary Ann , Nabrzyski Jaroslaw , Roos David S , Rund Samuel S C , Schulman Stephanie Wever , Shanmugasundram Achchuthan , Sitnik Vasily , Spruill Drew , Starns David , Stoeckert Christian J , Tomko Sheena Shah , Wang Haiming , Warrenfeltz Susanne , Wieck Robert , Wilkinson Paul A , Xu Lin , Zheng Jie 
Published: October 2021

Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports &gt;500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate &gt;1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
Proteome-pI2.0: proteome isoelectric point database update
Authors: Kozlowski Lukasz Pawel 
Published: October 2021

AbstractProteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. The isoelectric point—the pH at which a particular molecule carries no net electrical charge—is an important parameter for many analytical biochemistry and proteomics techniques. Additionally, it can be obtained directly from the pKa values of individual charged residues of the protein. The Proteome-pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release). The isoelectric point for proteins is predicted by 21 methods, whereas pKa values are inferred by one method. To facilitate bottom-up proteomics analysis, individual proteomes were digested in silico with the five most commonly used proteases (trypsin, chymotrypsin, trypsin + LysC, LysN, ArgC), and the peptides’ isoelectric point and molecular weights were calculated. The database enables the retrieval of virtual 2D-PAGE plots and customized fractions of a proteome based on the isoelectric point and molecular weight. In addition, isoelectric points for proteins in NCBI non-redundant (nr), UniProt, SwissProt, and Protein Data Bank are available in both CSV and FASTA formats. The database can be accessed at http://isoelectricpointdb2.org.
Targeting 3′ and 5′ untranslated regions with antisense oligonucleotides to stabilize frataxin mRNA and increase protein expression
Authors: Li Yanjie , Li Jixue , Wang Jun , Lynch David R , Shen Xiulong , R. Corey David , Parekh Darshan , Bhat Balkrishen , Woo Caroline , Cherry Jonathan J , Napierala Jill S , Napierala Marek 
Published: October 2021

Abstract
Friedreich’s ataxia (FRDA) is a severe multisystem disease caused by transcriptional repression induced by expanded GAA repeats located in intron 1 of the Frataxin (FXN) gene encoding frataxin. FRDA results from decreased levels of frataxin; thus, stabilization of the FXN mRNA already present in patient cells represents an attractive and unexplored therapeutic avenue. In this work, we pursued a novel approach based on oligonucleotide-mediated targeting of FXN mRNA ends to extend its half-life and availability as a template for translation. We demonstrated that oligonucleotides designed to bind to FXN 5′ or 3′ noncoding regions can increase FXN mRNA and protein levels. Simultaneous delivery of oligonucleotides targeting both ends increases efficacy of the treatment. The approach was confirmed in several FRDA fibroblast and induced pluripotent stem cell-derived neuronal progenitor lines. RNA sequencing and single-cell expression analyses confirmed oligonucleotide-mediated FXN mRNA upregulation. Mechanistically, a significant elongation of the FXN mRNA half-life without any changes in chromatin status at the FXN gene was observed upon treatment with end-targeting oligonucleotides, indicating that transcript stabilization is responsible for frataxin upregulation. These results identify a novel approach toward upregulation of steady-state mRNA levels via oligonucleotide-mediated end targeting that may be of significance to any condition resulting from transcription downregulation.
Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8
Authors: Czernecki Dariusz , Hu Haidai , Romoli Filippo , Delarue Marc 
Published: October 2021

Abstract
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
Inferring primase-DNA specific recognition using a data driven approach
Authors: Soffer Adam , Eisdorfer Sarah A , Ifrach Morya , Ilic Stefan , Afek Ariel , Schussheim Hallel , Vilenchik Dan , Akabayov Barak 
Published: October 2021

AbstractDNA–protein interactions play essential roles in all living cells. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is both challenging and important, since it may contribute to finding the means to regulate metabolic pathways involving DNA–protein interactions. Using a massive experimental benchmark dataset of binding scores for DNA sequences and a machine learning workflow, we describe the binding to DNA of T7 primase, as a model system for specific DNA–protein interactions. Effective binding of T7 primase to its specific DNA recognition sequences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.