bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capturing the Zeitgeist: Dvořák’s Prague Debut and the Politics of Patriotism
Authors: Branda Eva 
Published: April 2021

Abstract
While Dvořák’s Hymnus: Heirs of the White Mountain (1872) for chorus and orchestra is largely unknown today, its Prague premiere in 1873 was a landmark event in Dvořák’s career. This study shows that the work’s success at its first performance depended on cultural expectations and political circumstances that were particular to Prague in the 1870s. Audiences were accustomed to choral concerts of modest proportions, and the spectacle delivered by the Hlahol choral society on this occasion caught the public by surprise, as did Dvořák’s seemingly sudden emergence onto the scene. The performance also came in the midst of heated debates on the nature of Czech music, and Hymnus was harnessed in the service of certain critical agendas. Moreover, the work explores the aftermath of a crucial seventeenth-century Czech military defeat; this reference was timely in 1873, as Czech politicians had recently waged and lost their own battle in the Austrian parliament, leading audiences to relate in a unique way to Hymnus.
AstroSat/UVIT observations of IC 4329A: constraining the accretion disc inner radius
Authors: Dewangan Gulab C , Tripathi P , Papadakis I E , Singh K P 
Published: April 2021

ABSTRACT
We present a study of far- and near ultraviolet (UV) emission from the accretion disc in a powerful Seyfert 1 galaxy IC 4329A using observations performed with the Ultraviolet Imaging Telescope (UVIT) onboard AstroSat. These data provide the highest spatial resolution and deepest images of IC 4329A in the far- and near UV bands acquired to date. The excellent spatial resolution of the UVIT data has allowed us to accurately separate the extended emission from the host galaxy and the AGN emission in the far- and near UV bands. We derive the intrinsic AGN flux after correcting for the Galactic and internal reddening, as well as for the contribution of emission lines from the broad and narrow-line regions. The intrinsic UV continuum emission shows a marked deficit compared to that expected from the ‘standard’ models of the accretion disc around an estimated black hole mass of $1-2\times 10^8\, {\rm M}_{\odot }$ when the disc extends to the innermost stable circular orbit. We find that the intrinsic UV continuum is fully consistent with the standard disc models, but only if the disc emits from distances larger than ∼80–150 gravitational radii.
Rapid modification of neutron star surface magnetic field: a proposed mechanism for explaining radio emission state changes in pulsars
Authors: Geppert U , Basu R , Mitra D , Melikidze G I , Szkudlarek M 
Published: April 2021

ABSTRACT
The radio emission in many pulsars shows sudden changes, usually within a period, that cannot be related to the steady state processes within the inner acceleration region (IAR) above the polar cap. These changes are often quasi-periodic in nature, where regular transitions between two or more stable emission states are seen. The durations of these states show a wide variety ranging from several seconds to hours at a time. There are strong, small-scale magnetic field structures and huge temperature gradients present at the polar cap surface. We have considered several processes that can cause temporal modifications of the local magnetic field structure and strength at the surface of the polar cap. Using different magnetic field strengths and scales, and also assuming realistic scales of the temperature gradients, the evolutionary time-scales of different phenomena affecting the surface magnetic field were estimated. We find that the Hall drift results in faster changes in comparison to both Ohmic decay and thermoelectric effects. A mechanism based on the partially screened gap (PSG) model of the IAR has been proposed, where the Hall and thermoelectric oscillations perturb the polar cap magnetic field to alter the sparking process in the PSG. This is likely to affect the observed radio emission resulting in the observed state changes.
The peculiar WAT NGC 2329 with Seyfert/FR I-like radio lobes
Authors: Das S , Kharb P , Morganti R , Nandi S 
Published: April 2021

ABSTRACT
We report the complex radio properties of the radio galaxy NGC 2329 that resides in the centre of the galaxy cluster Abell 569. For this study, we have used archival data from the Very Large Array (VLA) at various resolutions and frequencies, as well as the Very Long Baseline Array (VLBA). While the wide-angle tailed (WAT) Fanaroff–Riley type I (FR I) radio morphology of the source has been discussed widely in the literature, the nature of the inner lobes has not been as widely discussed. In particular, we note that the inner lobes resemble the bubble-like radio structures observed in Seyfert galaxies. Polarization-sensitive data from the VLA clearly show magnetic field structures consistent with FR Is for the outer lobes and Seyferts for the inner lobes in NGC 2329. FR Is are classified as radio-loud (RL) active galactic nuclei (AGN) and Seyferts as radio-quiet (RQ) AGN, making this source unique. The VLBA shows a one-sided radio jet suggesting a relativistic pc-scale outflow, leading into the inner lobes. Electron lifetime estimates suggest that the outer FR I-like lobes are nearly twice as old (∼45 Myr) as the inner Seyfert-like lobes (∼25 Myr). Gas inflow in this merging cluster seems to have rejuvenated the AGN about ∼25 Myr ago, and may have caused a change in the accretion disc state. The complex composite radio morphology of NGC 2329 suggests that the RL/RQ dichotomy is a function of time in the lifecycle of an AGN.
Observational constraints to the dynamics of dust particles in the coma of comet 67P/Churyumov–Gerasimenko
Authors: Frattin E , Bertini I , Ivanovski S L , Marzari F , Fulle M , Zakharov V V , Moreno F , Naletto G , Lazzarin M , Cambianica P , Cremonese G , Ferrari S , Ferri F , Güttler C , La Forgia F , Lucchetti A , Pajola M , Penasa L , Rotundi A , Sierks H , Tubiana C 
Published: April 2021

ABSTRACT
In this work, we aim to characterize the dust motion in the inner coma of comet 67P/Churyumov–Gerasimenko to provide constraints for theoretical 3D coma models. The OSIRIS camera on-board the Rosetta mission was able for the first time to acquire images of single dust particles from inside the cometary coma, very close to the nucleus. We analyse a large number of particles, performing a significant statistic of their behaviour during the post-perihelion period, when the spacecraft covered distances from the nucleus ranging between 80 and 400 km. We describe the particle trajectories, investigating their orientation and finding highly radial motion with respect to the nucleus. Then, from the particle brightness profiles, we derive a particle rotational frequency of ν &lt; 3.6 Hz, revealing that they are slow rotators and do not undergo fragmentation. We use scattering models to compare the observed spectral radiance of the particles with the simulated ones in order to estimate their size, finding values that range from millimetres up to centimetres. The statistics performed in this paper provide useful parameters to constrain the cometary coma dynamical models.
Recovering the wedge modes lost to 21-cm foregrounds
Authors: Gagnon-Hartman Samuel , Cui Yue , Liu Adrian , Ravanbakhsh Siamak 
Published: April 2021

ABSTRACT
One of the critical challenges facing imaging studies of the 21-cm signal at the Epoch of Reionization (EoR) is the separation of astrophysical foreground contamination. These foregrounds are known to lie in a wedge-shaped region of (k⊥, k∥) Fourier space. Removing these Fourier modes excises the foregrounds at grave expense to image fidelity, since the cosmological information at these modes is also removed by the wedge filter. However, the 21-cm EoR signal is non-Gaussian, meaning that the lost wedge modes are correlated to the surviving modes by some covariance matrix. We have developed a machine learning-based method that exploits this information to identify ionized regions within a wedge-filtered image. Our method reliably identifies the largest ionized regions and can reconstruct their shape, size, and location within an image. We further demonstrate that our method remains viable when instrumental effects are accounted for, using the Hydrogen EoR Array and the Square Kilometre Array as fiducial instruments. The ability to recover spatial information from wedge-filtered images unlocks the potential for imaging studies using current- and next-generation instruments without relying on detailed models of the astrophysical foregrounds themselves.
Isocyanic acid (HNCO) in the hot molecular core G331.512-0.103: observations and chemical modelling
Authors: Canelo Carla M , Bronfman Leonardo , Mendoza Edgar , Duronea Nicolas , Merello Manuel , Carvajal Miguel , Friaça Amâncio C S , Lepine Jacques 
Published: April 2021

ABSTRACT
Isocyanic acid (HNCO) is a simple molecule with a potential to form prebiotic and complex organic species. Using a spectral survey collected with the Atacama Pathfinder EXperiment, in this work we report the detection of 42 transitions of HNCO in the hot molecular core/outflow G331.512-0.103 (hereafter G331). The spectral lines were observed in the frequency interval ∼160–355 GHz. By means of Local Thermodynamic Equilibrium analyses, applying the rotational diagram method, we studied the excitation conditions of HNCO. The excitation temperature and column density are estimated to be Tex= 58.8 ± 2.7 K and N = (3.7 ± 0.5) × 1015 cm−2, considering beam dilution effects. The derived relative abundance is between (3.8 ± 0.5) × 10−9 and (1.4 ± 0.2) × 10−8. In comparison with other hot molecular cores, our column densities and abundances are in agreement. An update of the internal partition functions of the four CHNO isomers: HNCO; cyanic acid, HOCN; fulminic acid, HCNO; and isofulminic acid, HONC is provided. We also used the astrochemical code Nautilus to model and discuss HNCO abundances. The simulations could reproduce the abundances with a simple zero-dimensional model at a temperature of 60 K and for a chemical age of ∼105 yr, which is larger than the estimated dynamical age for G331. This result could suggest the need for a more robust model and even the revision of chemical reactions associated with HNCO.
A spectral survey of WASP-19b with ESPRESSO
Authors: Sedaghati Elyar , MacDonald Ryan J , Casasayas-Barris Núria , Hoeijmakers H Jens , Boffin Henri M J , Rodler Florian , Brahm Rafael , Jones Matías , Sánchez-López Alejandro , Carleo Ilaria , Figueira Pedro , Mehner Andrea , López-Puertas Manuel 
Published: April 2021

ABSTRACT
High-resolution precision spectroscopy provides a multitude of robust techniques for probing exoplanetary atmospheres. We present multiple VLT/ESPRESSO transit observations of the hot-Jupiter exoplanet WASP-19b with previously published but disputed atmospheric features from low resolution studies. Through spectral synthesis and modelling of the Rossiter–McLaughlin (RM) effect we calculate stellar, orbital and physical parameters for the system. From narrow-band spectroscopy we do not detect any of H i, Fe i, Mg i, Ca i, Na i, and K i neutral species, placing upper limits on their line contrasts. Through cross-correlation analyses with atmospheric models, we do not detect Fe i and place a 3σ upper limit of $\log \, (X_{\textrm {Fe}}/X_\odot) \approx -1.83\, \pm \, 0.11$ on its mass fraction, from injection and retrieval. We show the inability to detect the presence of H2O for known abundances, owing to lack of strong absorption bands, as well as relatively low S/N ratio. We detect a barely significant peak (3.02 ± 0.15 σ) in the cross-correlation map for TiO, consistent with the sub-solar abundance previously reported. This is merely a hint for the presence of TiO and does not constitute a confirmation. However, we do confirm the presence of previously observed enhanced scattering towards blue wavelengths, through chromatic RM measurements, pointing to a hazy atmosphere. We finally present a reanalysis of low-resolution transmission spectra of this exoplanet, concluding that unocculted starspots alone cannot explain previously detected features. Our reanalysis of the FORS2 spectra of WASP-19b finds a ∼100× sub-solar TiO abundance, precisely constrained to $\log \, X_{\textrm {TiO}} \approx -7.52 \pm 0.38$, consistent with the TiO hint from ESPRESSO. We present plausible paths to reconciliation with other seemingly contradicting results.
Statistical exploration of halo anisotropic clustering and intrinsic alignments with the mass-Peak Patch algorithm
Authors: Regaldo-Saint Blancard Bruno , Codis Sandrine , Bond J Richard , Stein George 
Published: April 2021

ABSTRACT
The anisotropy or triaxiality of massive dark matter haloes largely defines the structure of the cosmic web, in particular the filaments that join the haloes together. Here, we investigate such oriented correlations in mass-Peak Patch halo catalogues by using the initial strain tensor of spherical proto-halo regions to orient the haloes. To go beyond the spherically averaged two-point correlation function of haloes, we use oriented stacks to compute oriented two-point correlations: we explicitly break isotropy by imposing a local frame set by the strain tensor of the reference halo before stacking neighbouring haloes. Beyond the exclusion zone of the reference halo, clustering is found to be strongly enhanced along the major direction of the strain tensor as expected. This anisotropic clustering of haloes along filaments is further quantified by using a spherical harmonics decomposition. Furthermore, we compute the evolution of cluster-scale halo principal directions relative to those of their neighbours and show that there are strong correlations extending up to very large scales. In order to provide calculations more suitable to observational confrontations, we also utilize 2D projected versions of some equivalent correlation functions. Finally, we show that the multipole structure of the mass-peak patch halo’s anisotropic clustering can be qualitatively captured in an analytic treatment based on peak theory. Though highly informative, giving the same qualitative features as the oriented correlations found from the simulation catalogue, analytic evaluation involves extensive use of Monte Carlo methods, which is also what the simulated catalogue uses, taking into account as they do the adaptive nature of the mass-peak patch mass hierarchy and all non-local complexities associated with the exclusion of smaller haloes overlapping with larger ones: there is no substitute for the mass-Peak Patch simulation-based determination of oriented and anisotropic correlations.
Cosmological cross-correlations and nearest neighbour distributions
Authors: Banerjee Arka , Abel Tom 
Published: April 2021

ABSTRACT
Cross-correlations between data sets are used in many different contexts in cosmological analyses. Recently, k-nearest neighbour cumulative distribution functions (kNN-CDF) were shown to be sensitive probes of cosmological (auto) clustering. In this paper, we extend the framework of NN measurements to describe joint distributions of, and correlations between, two data sets. We describe the measurement of joint kNN-CDFs, and show that these measurements are sensitive to all possible connected N-point functions that can be defined in terms of the two data sets. We describe how the cross-correlations can be isolated by combining measurements of the joint kNN-CDFs and those measured from individual data sets. We demonstrate the application of these measurements in the context of Gaussian density fields, as well as for fully non-linear cosmological data sets. Using a Fisher analysis, we show that measurements of the halo-matter cross-correlations, as measured through NN measurements are more sensitive to the underlying cosmological parameters, compared to traditional two-point cross-correlation measurements over the same range of scales. Finally, we demonstrate how the NN cross-correlations can robustly detect cross-correlations between sparse samples – the same regime where the two-point cross-correlation measurements are dominated by noise.
Molecular and morphological evidence for a unified, inclusiveSinotaia quadrata(Caenogastropoda: Viviparidae: Bellamyinae)
Authors: Ye Bin , Hirano Takahiro , Saito Takumi , Dong Zhengzhong , Do Van Tu , Chiba Satoshi 
Published: April 2021

ABSTRACTThe taxonomy of species in the caenogastropod genus Sinotaia (Viviparidae: Bellamyinae) has been a complex and controversial issue since the 19th century. Sinotaia quadrata, the type species of Sinotaia, comprises many named forms and transitions between them, and the taxonomic validity of some species similar to S. quadrata also requires clarification. To clarify relationships in this common and significant member of the freshwater benthos, we reconstructed a phylogeny for species related to S. quadrata based on the 16S rRNA and cytochrome c oxidase subunit I genes to test which classifications are robust using modern data and interpretation. We also compared the shell outline morphology of type material of most species in the genus Sinotaia from the original literature. The combination of phylogenetic and shape variance data suggests that seven currently recognized species of Sinotaia should be synonymized with S. quadrata. We used microsatellite markers and landmark-based geometric morphometric analysis to examine the genetic differentiation and shell shape variation of S. quadrata populations in both China and Japan. Genetic and shape variations were not congruent, suggesting that minor variations in shell shape do not indicate distinct Sinotaia species. Shell shape variation shows no clear separations and shows environmental plasticity. Using data on molecular phylogenetics, genetic diversity and shell morphology, we provide a more inclusive species concept for S. quadrata. This provides a basis to formally revise this taxon and the seven closely related nominal species that are widely distributed in China and East Asia.
PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
Authors: Hwang Gue-Ho , Jeong You Kyeong , Habib Omer , Hong Sung-Ah , Lim Kayeong , Kim Jin-Soo , Bae Sangsu 
Published: April 2021

AbstractPrime editing technology is capable of generating targeted insertions, deletions, and base conversions. However, the process of designing prime editing guide RNAs (pegRNAs), which contain a primer binding site and a reverse-transcription template at the 3′ end, is more complex than that for the single guide RNAs used with CRISPR nucleases or base editors. Furthermore, the assessment of high-throughput sequencing data after prime editors (PEs) have been employed should consider the unique feature of PEs; thus, pre-existing assessment tools cannot directly be adopted for PEs. Here, we present two user-friendly web-based tools for PEs, named PE-Designer and PE-Analyzer. PE-Designer, a dedicated tool for pegRNA selection, provides all possible target sequences, pegRNA extension sequences, and nicking guide RNA sequences together with useful information, and displays the results in an interactive image. PE-Analyzer, a dedicated tool for PE outcome analysis, accepts high-throughput sequencing data, summarizes mutation-related information in a table, and provides interactive graphs. PE-Analyzer was mainly written using JavaScript so that it can analyze several data sets without requiring that huge sequencing data (&gt;100MB) be uploaded to the server, reducing analysis time and increasing personal security. PE-Designer and PE-Analyzer are freely available at http://www.rgenome.net/pe-designer/ and http://www.rgenome.net/pe-analyzer/ without a login process.
LitSuggest: a web-based system for literature recommendation and curation using machine learning
Authors: Allot Alexis , Lee Kyubum , Chen Qingyu , Luo Ling , Lu Zhiyong 
Published: April 2021

Abstract
Searching and reading relevant literature is a routine practice in biomedical research. However, it is challenging for a user to design optimal search queries using all the keywords related to a given topic. As such, existing search systems such as PubMed often return suboptimal results. Several computational methods have been proposed as an effective alternative to keyword-based query methods for literature recommendation. However, those methods require specialized knowledge in machine learning and natural language processing, which can make them difficult for biologists to utilize. In this paper, we propose LitSuggest, a web server that provides an all-in-one literature recommendation and curation service to help biomedical researchers stay up to date with scientific literature. LitSuggest combines advanced machine learning techniques for suggesting relevant PubMed articles with high accuracy. In addition to innovative text-processing methods, LitSuggest offers multiple advantages over existing tools. First, LitSuggest allows users to curate, organize, and download classification results in a single interface. Second, users can easily fine-tune LitSuggest results by updating the training corpus. Third, results can be readily shared, enabling collaborative analysis and curation of scientific literature. Finally, LitSuggest provides an automated personalized weekly digest of newly published articles for each user's project. LitSuggest is publicly available at https://www.ncbi.nlm.nih.gov/research/litsuggest.
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
Authors: Dieckmann Marius Alfred , Beyvers Sebastian , Nkouamedjo-Fankep Rudel Christian , Hanel Patrick Harald Georg , Jelonek Lukas , Blom Jochen , Goesmann Alexander 
Published: April 2021

AbstractThe EDGAR platform, a web server providing databases of precomputed orthology data for thousands of microbial genomes, is one of the most established tools in the field of comparative genomics and phylogenomics. Based on precomputed gene alignments, EDGAR allows quick identification of the differential gene content, i.e. the pan genome, the core genome, or singleton genes. Furthermore, EDGAR features a wide range of analyses and visualizations like Venn diagrams, synteny plots, phylogenetic trees, as well as Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI) matrices. During the last few years, the average number of genomes analyzed in an EDGAR project increased by two orders of magnitude. To handle this massive increase, a completely new technical backend infrastructure for the EDGAR platform was designed and launched as EDGAR3.0. For the calculation of new EDGAR3.0 projects, we are now using a scalable Kubernetes cluster running in a cloud environment. A new storage infrastructure was developed using a file-based high-performance storage backend which ensures timely data handling and efficient access. The new data backend guarantees a memory efficient calculation of orthologs, and parallelization has led to drastically reduced processing times. Based on the advanced technical infrastructure new analysis features could be implemented including POCP and FastANI genomes similarity indices, UpSet intersecting set visualization, and circular genome plots. Also the public database section of EDGAR was largely updated and now offers access to 24,317 genomes in 749 free-to-use projects. In summary, EDGAR 3.0 provides a new, scalable infrastructure for comprehensive microbial comparative gene content analysis. The web server is accessible at http://edgar3.computational.bio.