bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral and Written Transmission in the Early Jeu-Parti
Authors: Mason Joseph W 
Published: April 2022

ABSTRACT
This article explores the contentious issue of oral and written transmission in thirteenth-century French song by looking at a selection of early jeux-partis that share their melodies with other songs. It argues that acts of contrafacture were sometimes carried out using written exemplars, or when written transmission was occurring. First, it is asserted that melodic variance could result from both written and oral transmission. Second, evidence for ephemeral written exemplars of jeux-partis and their models is discussed. Finally, it is shown that for one contrafact jeu-parti and its model, some of the melodic variants must have resulted from errors in the process of copying the songs. The melodic variants show that scribes and performers continually engaged with the two songs during their reception, indicating that knowledge of contrafacture persisted several decades after the songs were originally composed.
Dynamical state of galaxy clusters evaluated from X-ray images
Authors: Yuan Z S , Han J L , Wen Z L 
Published: April 2022

ABSTRACT
X-ray images of galaxy clusters often show disturbed structures that are indications of cluster mergers. To complement our previous work on the dynamical state of 964 clusters observed by Chandra, we process the X-ray images for 1308 clusters from XMM–Newton archival data, together with the images of 22 clusters newly released by Chandra, and we evaluate their dynamical state from these X-ray images. The concentration index c, the centroid shift ω and the power ratio P3/P0 are calculated in circular regions with a certain radius of 500 kpc, and the morphology index δ is estimated within elliptical regions that can be adapted to the cluster size and shape. In addition, the dynamical parameters for 42 clusters previously estimated from Chandra images are upgraded based on the newly available redshifts. Good consistence is found between dynamical parameters derived from XMM–Newton and Chandra images for the overlapped sample of clusters in the two data sets. The dependence of mass scaling relations on the dynamical state is shown by using the data of 388 clusters. All data and related software are available at http://zmtt.bao.ac.cn/galaxy_clusters/dyXimages/.
Jet-cocoon geometry in the optically dark, very high energy gamma-ray burst 201216C
Authors: Rhodes L , van der Horst A J , Fender R , Aguilera-Dena D R , Bright J S , Vergani S , Williams D R A 
Published: April 2022

ABSTRACT
We present the results of a radio observing campaign on GRB 201216C, combined with publicly available optical and X-ray data. The detection of very high energy (VHE, &gt;100 GeV) emission by MAGIC makes this the fifth VHE GRB at the time of publication. Comparison between the optical and X-ray light curves show that GRB 201216C is a dark GRB, i.e. the optical emission is significantly absorbed and is fainter than expected from the X-ray detections. Our e-MERLIN data also shows evidence of diffractive interstellar scintillation. We can study the column density along the line of sight to the GRB in both the host galaxy, from the damped optical light curve, and the Milky Way, via scintillation studies. We find that the afterglow is best modelled using a jet-cocoon geometry within a stellar wind environment. Fitting the data with a multicomponent model, we estimate that the optical, X-ray, and higher frequency radio data before ∼25 d originates from an ultrarelativistic jet with an isotropic equivalent kinetic energy of (0.6–10) × 1052 erg and an opening angle of ∼1–9°. The lower frequency radio emission detected by MeerKAT, from day 28 onwards, is produced by the cocoon with a kinetic energy that is between two and seven orders of magnitude lower (0.02–50) × 1048 erg. The energies of the two components are comparable to those derived in simulations of such scenarios.
Modulation of pulse profile as a signal for phase transitions in a pulsar core
Authors: Bagchi Partha , Layek Biswanath , Sarkar Anjishnu , Srivastava Ajit M 
Published: April 2022

ABSTRACT
We calculate detailed modification of pulses from a pulsar arising from the effects of phase transition induced density fluctuations on the pulsar moment of inertia. We represent general statistical density fluctuations using a simple model where the initial moment of inertia tensor of the pulsar (taken to be diagonal here) is assumed to get random additional contributions for each of its component which are taken to be Gaussian distributed with certain width characterized by the strength of density fluctuations ϵ. Using sample values of ϵ, (and the pulsar deformation parameter η) we numerically calculate detailed pulse modifications by solving Euler’s equations for the rotational dynamics of the pulsar. We also give analytical estimates which can be used for arbitrary values of ϵ and η. We show that there are very specific patterns in the perturbed pulses which are observable in terms of modulations of pulses over large time periods. In view of the fact that density fluctuations fade away eventually leading to a uniform phase in the interior of pulsar, the off-diagonal components of MI tensor also vanish eventually. Thus, the modification of pulses due to induced wobbling (from the off-diagonal MI components) will also die away eventually. This allows one to distinguish these transient pulse modulations from the effects of any wobbling originally present. Further, the decay of these modulations in time directly relates to relaxation of density fluctuations in the pulsar giving valuable information about the nature of phase transition occurring inside the pulsar.
Coincidence between morphology and star formation activity through cosmic time: the impact of the bulge growth
Authors: Dimauro Paola , Daddi Emanuele , Shankar Francesco , Cattaneo Andrea , Huertas-Company Marc , Bernardi Mariangela , Caro Fernando , Dupke Renato , Häußler Boris , Johnston Evelyn , Cortesi Arianna , Mei Simona , Peletier Reynier 
Published: April 2022

ABSTRACT
The origin of the quenching in galaxies is still highly debated. Different scenarios and processes are proposed. We use multiband (400–1600 nm) bulge–disc decompositions of massive galaxies in the redshift range 0 &lt; z &lt; 2 to explore the distribution and the evolution of galaxies in the $\log \, {\rm SFR-log}\: M_{*}$ plane as a function of the stellar mass weighted bulge-to-total ratio ($B/T_{M_{*}}$) and also for internal galaxy components (bulge/disc) separately. We find evidence of a clear link between the presence of a bulge and the flattening of the main sequence in the high-mass end. All bulgeless galaxies ($B/T_{M_{*}}$ &lt; 0.2) lie on the main sequence, and there is little evidence of a quenching channel without bulge growth. Galaxies with a significant bulge component ($B/T_{M_{*}}$ &gt; 0.2) are equally distributed in number between star forming and passive regions. The vast majority of bulges in the main-sequence galaxies are quiescent, while star formation is localized in the disc component. Our current findings underline a strong correlation between the presence of the bulge and the star formation state of the galaxy. A bulge, if present, is often quiescent, independently of the morphology or the star formation activity of the host galaxy. Additionally, if a galaxy is quiescent, with a large probability, is hosting a bulge. Conversely, if the galaxy has a discy shape is highly probable to be star forming.
Magnetic fields and young stellar objects in cometary cloud L1616
Authors: Saha Piyali , Soam Archana , Baug Tapas , Gopinathan Maheswar , Mondal Soumen , Ghosh Tuhin 
Published: April 2022

ABSTRACT
The Lynds’ Dark Nebula (LDN) 1615/1616 and CB 28 (hereafter L1616) together form a cometary globule located at an angular distance of about 8° west of the Orion OB1 association, aligned roughly along the east–west direction, and showing a distinct head–tail structure. The presence of massive stars in the Orion belt has been considered to be responsible for the radiation-driven implosion mode of star formation in L1616. Based on the latest Gaia Early Data Release 3 (EDR3) measurements of the previously known young stellar objects (YSOs) associated with L1616, we find the distance to this cloud to be 384 ± 5 pc. We present optical polarimetry towards L1616 that maps the plane-of-sky component of the ambient magnetic field (BPOS) geometry. Based on the proper motion of the YSOs associated with L1616, we investigate their plane-of-sky motion relative to the exciting star ϵ Ori. Using the Gaia EDR3 measurements of the distances and proper motions of the YSOs, we find two additional sources comoving with the known YSOs. One comoving source is HD 33056, a B9 star, and the other might be a young pre-main-sequence star not reported in previous studies. The mean direction of BPOS is found to follow the cloud structure. This could be the effect of dragging of the magnetic field lines by the impact of the ionizing radiation from ϵ Ori. Based on the pressure exerted on L1616, and the ages of the associated YSOs, we show that it could possibly be the main source of ionization in L1616, and thus the star formation in it.
Categorize radio interference using component and temporal analysis
Authors: Yuan Mao , Zhu Weiwei , Zhang Haiyan , Huang Shijie , Xue Mengyao , Li Di , Yue Youling , Wang Pei , Niu Jiarui , Hu Yuxuan , Li Chunjiang , Miao Chenchen , Wang Yu , Meng Lingqi , Peng Bo 
Published: April 2022

ABSTRACT
Radio frequency interference (RFI) is a significant challenge faced by today’s radio astronomers. While most past efforts were devoted to cleaning the RFI from the data, we develop a novel method for categorizing and cataloguing RFI for forensic purpose. We present a classifier that categorizes RFI into different types based on features extracted using Principal Component Analysis (PCA) and Fourier analysis. The classifier can identify narrowband non-periodic RFI above 2σ, narrowband periodic RFI above 3σ, and wideband impulsive RFI above 5σ with F1 scores [defined as F1 = (2 · recall × precision)/(recall + precision)] between 0.87 and 0.91 in simulation. This classifier could be used to identify the sources of RFI as well as to clean RFI contamination (particularly in pulsar search). In the long-term analysis of the categorized RFI, we found a special type of drifting periodic RFI that is detrimental to pulsar search. We also found pieces of evidence of an increased rate of impulsive RFI when the telescope is pointing towards the cities. These results demonstrate this classifier’s potential as a forensic tool for RFI environment monitoring of radio telescopes.
An asymmetrical model for high-energy radiation of Cassiopeia A
Authors: Zhan Shihong , Wang Wei , Mou Guobin , Li Zhuo 
Published: April 2022

ABSTRACT
The supernova remnant Cassiopeia A (Cas A) shows strong radiation from radio to gamma-ray bands. The mechanism of gamma-ray radiation in Cas A and its possible contribution to PeV cosmic rays are still under debate. The X-ray imaging reveals an asymmetric profile of Cas A, suggesting the existence of a jet-like structure. In this paper, we propose an asymmetrical model for Cas A, consisting of a fast moving jet-like structure and a slowly expanding isotropic shell. This model can account for the multiwavelength spectra of Cas A, especially for the power-law hard X-ray spectrum from ∼60 to 220 keV. The GeV to TeV emission from Cas A should be contributed by both hadronic and leptonic processes. Moreover, the jet-like structure may produce a gamma-ray flux of $\sim 10^{-13}\rm erg\, cm^{-2}\, s^{-1}$ at ∼100 TeV, to be examined by the Large High Altitude Air Shower Observatory (LHAASO) and the Cherenkov Telescope Array (CTA).
A reliable workflow for improving nanoscale X-ray fluorescence tomographic analysis on nanoparticle-treated HeLa cells
Authors: Luo Yanqi , Paunesku Tatjana , Antipova Olga , Liu Yuzi , Zaluzec Nestor J , Di Zichao , Woloschak Gayle , Chen Si 
Published: April 2022

AbstractScanning X-ray fluorescence (XRF) tomography provides powerful characterization capabilities in evaluating elemental distribution and differentiating their inter- and intra-cellular interactions in a three-dimensional (3D) space. Scanning XRF tomography encounters practical challenges from the sample itself, where the range of rotation angles is limited by geometric constraints, involving sample substrates or nearby features either blocking or converging into the field of view. This study aims to develop a reliable and efficient workflow that can (1) expand the experimental window for nanoscale tomographic analysis of local areas of interest within a laterally extended specimen, and (2) bridge 3D analysis at micrometer and nanoscales on the same specimen. We demonstrate the workflow using a specimen of HeLa cells exposed to iron oxide core and titanium dioxide shell (Fe3O4/TiO2) nanocomposites. The workflow utilizes iterative and multiscale XRF data collection with intermediate sample processing by focused ion beam (FIB) sample preparation between measurements at different length scales. Initial assessment combined with precise sample manipulation via FIB allows direct removal of sample regions that are obstacles to both incident X-ray beam and outgoing XRF signals, which considerably improves the subsequent nanoscale tomography analysis. This multiscale analysis workflow has advanced bio-nanotechnology studies by providing deep insights into the interaction between nanocomposites and single cells at a subcellular level as well as statistical assessments from measuring a population of cells.
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering
Authors: Planas-Iglesias Joan , Opaleny Filip , Ulbrich Pavol , Stourac Jan , Sanusi Zainab , Pinto Gaspar P , Schenkmayerova Andrea , Byska Jan , Damborsky Jiri , Kozlikova Barbora , Bednar David 
Published: April 2022

AbstractThe transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.
Histone H3.3 phosphorylation promotes heterochromatin formation by inhibiting H3K9/K36 histone demethylase
Authors: Udugama Maheshi , Vinod Benjamin , Chan F Lyn , Hii Linda , Garvie Andrew , Collas Philippe , Kalitsis Paul , Steer David , Das Partha P , Tripathi Pratibha , Mann Jeffrey R , Voon Hsiao P J , Wong Lee H 
Published: April 2022

Abstract
Histone H3.3 is an H3 variant which differs from the canonical H3.1/2 at four residues, including a serine residue at position 31 which is evolutionarily conserved. The H3.3 S31 residue is phosphorylated (H3.3 S31Ph) at heterochromatin regions including telomeres and pericentric repeats. However, the role of H3.3 S31Ph in these regions remains unknown. In this study, we find that H3.3 S31Ph regulates heterochromatin accessibility at telomeres during replication through regulation of H3K9/K36 histone demethylase KDM4B. In mouse embryonic stem (ES) cells, substitution of S31 with an alanine residue (H3.3 A31 –phosphorylation null mutant) results in increased KDM4B activity that removes H3K9me3 from telomeres. In contrast, substitution with a glutamic acid (H3.3 E31, mimics S31 phosphorylation) inhibits KDM4B, leading to increased H3K9me3 and DNA damage at telomeres. H3.3 E31 expression also increases damage at other heterochromatin regions including the pericentric heterochromatin and Y chromosome-specific satellite DNA repeats. We propose that H3.3 S31Ph regulation of KDM4B is required to control heterochromatin accessibility of repetitive DNA and preserve chromatin integrity.
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects
Authors: Zuber Jeffrey , Schroeder Susan J , Sun Hongying , Turner Douglas H , Mathews David H 
Published: April 2022

AbstractNearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated 5′GGUC3′ paired to 3′CUGG5′ separately from other 5′GU3′/3′UG5′ stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37°C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.
The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism
Authors: Zhang Haolin , Gong Xuemei , Zhao Qianqian , Mukai Takahito , Vargas-Rodriguez Oscar , Zhang Huiming , Zhang Yuxing , Wassel Paul , Amikura Kazuaki , Maupin-Furlow Julie , Ren Yan , Xu Xun , Wolf Yuri I , Makarova Kira S , Koonin Eugene V , Shen Yue , Söll Dieter , Fu Xian 
Published: April 2022

Abstract
Site-specific incorporation of distinct non-canonical amino acids into proteins via genetic code expansion requires mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. Pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs are ideal for genetic code expansion and have been extensively engineered for developing mutually orthogonal pairs. Here, we identify two novel wild-type PylRS/tRNAPyl pairs simultaneously present in the deep-rooted extremely halophilic euryarchaeal methanogen Candidatus Methanohalarchaeum thermophilum HMET1, and show that both pairs are functional in the model halophilic archaeon Haloferax volcanii. These pairs consist of two different PylRS enzymes and two distinct tRNAs with dissimilar discriminator bases. Surprisingly, these two PylRS/tRNAPyl pairs display mutual orthogonality enabled by two unique features, the A73 discriminator base of tRNAPyl2 and a shorter motif 2 loop in PylRS2. In vivo translation experiments show that tRNAPyl2 charging by PylRS2 is defined by the enzyme's shortened motif 2 loop. Finally, we demonstrate that the two HMET1 PylRS/tRNAPyl pairs can simultaneously decode UAG and UAA codons for incorporation of two distinct noncanonical amino acids into protein. This example of a single base change in a tRNA leading to additional coding capacity suggests that the growth of the genetic code is not yet limited by the number of identity elements fitting into the tRNA structure.
AutozygosityMapper: Identification of disease-mutations in consanguineous families
Authors: Steinhaus Robin , Boschann Felix , Vogel Melanie , Fischer-Zirnsak Björn , Seelow Dominik 
Published: April 2022

Abstract
With the shift from SNP arrays to high-throughput sequencing, most researchers studying diseases in consanguineous families do not rely on linkage analysis any longer, but simply search for deleterious variants which are homozygous in all patients. AutozygosityMapper allows the fast and convenient identification of disease mutations in patients from consanguineous pedigrees by focussing on homozygous segments shared by all patients. Users can upload multi-sample VCF files, including WGS data, without any pre-processing. Genome-wide runs of homozygosity and the underlying genotypes are presented in graphical interfaces. AutozygosityMapper extends the functions of its predecessor, HomozygosityMapper, to the search for autozygous regions, in which all patients share the same homozygous genotype. We provide export of VCF files containing only the variants found in homozygous regions, this usually reduces the number of variants by two orders of magnitude. These regions can also directly be analysed with our disease mutation identification tool MutationDistiller. The application comes with simple and intuitive graphical interfaces for data upload, analysis, and results. We kept the structure of HomozygosityMapper so that previous users will find it easy to switch. With AutozygosityMapper, we provide a fast web-based way to identify disease mutations in consanguineous families. AutozygosityMapper is freely available at https://www.genecascade.org/AutozygosityMapper/.
Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5′ and the 3′ UTRs of barley yellow dwarf virus mRNA
Authors: Powell Paul , Bhardwaj Usha , Goss Dixie 
Published: April 2022

Abstract
Viral mRNAs that lack a 5′ m7GTP cap and a 3′ poly-A tail rely on structural elements in their untranslated regions (UTRs) to form unique RNA-protein complexes that regulate viral translation. Recent studies of the barley yellow dwarf virus (BYDV) have revealed eukaryotic initiation factor 3 (eIF3) plays a significant role in facilitating communication between its 5′ and 3′ UTRs by binding both UTRs simultaneously. This report uses in vitro translation assays, fluorescence anisotropy binding assays, and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting to identify secondary structures that are selectively interacting with eIF3. SHAPE data also show that eIF3 alters its interaction with BYDV structures when another factor crucial for BYDV translation, eIF4F, is introduced by the 3′ BYDV translational enhancer (BTE). The observed BTE and eIF4F-induced shift of eIF3 position on the 5’ UTR and the translational effects of altering eIF3-binding structures (SLC and SLII) support a new model for BYDV translation initiation that requires the reorientation of eIF3 on BYDV UTRs. This eIF3 function in BYDV translation initiation is both reminiscent of and distinct from eIF3–RNA interactions found in other non-canonically translating mRNAs (e.g. HCV). This characterization of a new role in translation initiation expands the known functionality of eIF3 and may be broadly applicable to other non-canonically translating mRNAs.