bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the extreme luminosity of DES14X2fna
Authors: Grayling M , Gutiérrez C P , Sullivan M , Wiseman P , Vincenzi M , González-Gaitán S , Tucker B E , Galbany L , Kelsey L , Lidman C , Swann E , Smith M , Frohmaier C , Carollo D , Glazebrook K , Lewis G F , Möller A , Hinton S R , Uddin S A , Abbott T M C , Aguena M , Avila S , Bertin E , Bhargava S , Brooks D , Carnero Rosell A , Carrasco Kind M , Carretero J , Costanzi M , da Costa L N , De Vicente J , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hoyle B , Kuehn K , Kuropatkin N , Lima M , MacCrann N , Marshall J L , Martini P , Miquel R , Morgan R , Palmese A , Paz-Chinchón F , Plazas A A , Romer A K , Sánchez C , Sanchez E , Scarpine V , Serrano S , Sevilla-Noarbe I , Soares-Santos M , Suchyta E , Tarle G , Thomas D , To C , Varga T N , Walker A R , Wilkinson R D ,   (DES Collaboration)
Published: May 2021

ABSTRACT
We present DES14X2fna, a high-luminosity, fast-declining Type IIb supernova (SN IIb) at redshift z = 0.0453, detected by the Dark Energy Survey (DES). DES14X2fna is an unusual member of its class, with a light curve showing a broad, luminous peak reaching Mr ≃ −19.3 mag 20 d after explosion. This object does not show a linear decline tail in the light curve until ≃60 d after explosion, after which it declines very rapidly (4.30 ± 0.10 mag 100 d−1 in the r band). By fitting semi-analytic models to the photometry of DES14X2fna, we find that its light curve cannot be explained by a standard 56Ni decay model as this is unable to fit the peak and fast tail decline observed. Inclusion of either interaction with surrounding circumstellar material or a rapidly-rotating neutron star (magnetar) significantly increases the quality of the model fit. We also investigate the possibility for an object similar to DES14X2fna to act as a contaminant in photometric samples of SNe Ia for cosmology, finding that a similar simulated object is misclassified by a recurrent neural network (RNN)-based photometric classifier as an SN Ia in ∼1.1–2.4 per cent of cases in DES, depending on the probability threshold used for a positive classification.
Tree-based solvers for adaptive mesh refinement code flash – II: radiation transport module TreeRay
Authors: Wünsch Richard , Walch Stefanie , Dinnbier František , Seifried Daniel , Haid Sebastian , Klepitko Andre , Whitworth Anthony P , Palouš Jan 
Published: May 2021

ABSTRACT
The treatment of radiative transfer with multiple radiation sources is a critical challenge in simulations of star formation and the interstellar medium (ISM). In this paper, we present the novel TreeRay method for solving general radiative transfer problems, based on reverse ray-tracing combined with tree-based accelerated integration. We implement TreeRay in the adaptive mesh refinement code flash, as a module of the tree solver developed by Wünsch et al. However, the method itself is independent of the host code and can be implemented in any grid-based or particle-based hydrodynamics code. A key advantage of TreeRay is that its computational cost is independent of the number of sources, making it suitable for simulations with many point sources (e.g. massive star clusters) as well as simulations where diffuse emission is important. A very efficient communication and tree-walk strategy enable TreeRay to achieve almost ideal parallel scalings. TreeRay can easily be extended with sub-modules to treat radiative transfer at different wavelengths and to implement related physical processes. Here, we focus on ionizing radiation and use the on-the-spot approximation to test the method and its parameters. The ability to set the tree solver time-step independently enables the speedy calculation of radiative transfer in a multiphase ISM, where the hydrodynamic time-step is typically limited by the sound speed of the hot gas produced in stellar wind bubbles or supernova remnants. We show that complicated simulations of star clusters with feedback from multiple massive stars become feasible with TreeRay.
Repeated pattern of gamma-ray flares in the light curve of the blazar 3C 279
Authors: Blinov D , Jorstad S G , Larionov V M , MacDonald N R , Grishina T , Kopatskaya E , Larionova E , Larionova L , Morozova D , Nikiforova A , Savchenko S , Troitskaya Y , Troitsky I 
Published: May 2021

ABSTRACT
The optical polarization plane of some blazars occasionally exhibits smooth hundred degree long rotations. Multiple theoretical models have been proposed to explain the nature of such events. A deterministic origin of these rotations, however, remains uncertain. We aim to find repeating patterns of flares in gamma-ray light curves of blazars, which accompany optical polarization plane rotations. Such patterns have been predicted to occur by one of the models explaining this phenomenon. For the blazar 3C 279, where multiple polarization plane rotations have been reported in the literature, we obtain the Fermi-LAT gamma-ray light curve and analyse its intervals adjacent to polarization plane rotations. We find a complex characteristic pattern of flares in the gamma-ray light curve that is repeated during periods adjacent to three large amplitude EVPA rotation events in 3C 279. We discover a ‘hidden EVPA rotation’, which can only be seen in the relative Stokes parameters plane and that occurred simultaneously with the fourth repetition of the pattern. This finding strongly favours the hypothesis of emission features propagating in the jet as the reason of optical polarization plane rotations. Furthermore, it is compatible with the hypothesis of a sheath in the jet comprised of more slowly propagating emission features.
s-process enrichment of ultrafaint dwarf galaxies
Authors: Tarumi Yuta , Suda Takuma , van de Voort Freeke , Inoue Shigeki , Yoshida Naoki , Frebel Anna 
Published: May 2021

ABSTRACT
We study the production of barium (Ba) and strontium (Sr) in ultrafaint dwarf (UFDs) galaxies. Both r- and s- processes produce these elements, and one can infer the contribution of the r-process from the characteristic r-process abundance pattern, whereas the s-process contribution remains largely unknown. We show that the current s-process yield from asymptotic giant branch (AGB) stars is not sufficient to explain the Ba and Sr abundances observed in UFDs. Production of these elements would need to be efficient from the beginning of star formation in the galaxies. The discrepancy of nearly or more than 1 dex is not reconciled even if we consider s-process in super-AGB stars. We consider a possible resolution by assuming rotating massive stars (RMSs) and electron-capture supernovae (ECSNe) as additional contributors. We find that the RMSs could be the origin of Ba in UFDs if ∼10 per cent of massive stars are rotating at 300 km s−1. As for ECSNe, we argue that their fraction is less than 2 per cent of core-collapse supernova. It narrows the progenitor mass-range to ${\lesssim}0.1\, \mathrm{M}_\odot$ at −3 ≲ [Fe/H] ≲ −2. We also explore another resolution by modifying the stellar initial mass function (IMF) in UFDs and find a top-light IMF model that reproduces the observed level of Ba-enrichment. Future observations that determine or tightly constrain the europium and nitrogen abundances are crucial to identify the origin of Ba and Sr in UFDs.
The Gaia view of the Cepheus flare
Authors: Szilágyi Máté , Kun Mária , Ábrahám Péter 
Published: May 2021

ABSTRACT
We present a new census of candidate pre-main-sequence stars in the Cepheus flare star-forming region, based on Gaia EDR3 parallaxes, proper motions, and colour–magnitude diagrams. We identified new candidate members of the previously known young stellar groups associated with NGC 7023, L1177, L1217/L1219, L1228, L1235, and L1251. We studied the 3D structure of the star-forming complex and the distribution of tangential velocities of the young stars. The young stellar groups are located between 330 and 368 pc from the Sun, divided into three kinematic subgroups, and have ages between 1 and 5 million yr. The results confirm the scenario of propagating star formation, suggested by previous studies. In addition to the bulk pre-main-sequence star population between 330 and 370 pc, there is a scattered and more evolved pre-main-sequence population around 150–180 pc. We found new candidate members of the nearby Cepheus Association, and identified a new moving group of 46, 15–20 million yr old pre-main-sequence stars located at a distance of 178 pc, around the A0-type star HD 190833. A few pre-main-sequence stars are located at 800–900 pc, indicative of star-forming regions associated with the Galactic local arm above the Galactic latitude of +10°.
Modelling low charge ions in the solar atmosphere
Authors: Dufresne R P , Del Zanna G , Storey P J 
Published: May 2021

ABSTRACT
Extensions have been made recently to the coronal approximation for the purpose of modelling line emission from carbon and oxygen in the lower solar atmosphere. The same modelling is used here for other elements routinely observed in the solar transition region: N, Ne, Mg, Si, and S. The modelling includes the effects of higher densities suppressing dielectronic recombination and populating long lived, metastable levels; the presence of metastable levels typically causes effective ionization rates to increase and recombination rates to decrease. Processes induced by the radiation field, namely photoionization and photoexcitation, have been included, along with charge transfer, which occurs when electrons are exchanged during atom–ion and ion–ion collisions. The resulting ion balances are shown, and indicate significant changes compared to the frequently employed coronal approximation. The effect on level populations within ions caused by photoexcitation is also assessed. To give an illustration of how line emission could be altered by these processes, selected line contribution functions are presented at the end.
Adaptive Proteome Diversification by Nonsynonymous A-to-I RNA Editing in Coleoid Cephalopods
Authors: Shoshan Yoav , Liscovitch-Brauer Noa , Rosenthal Joshua J C , Eisenberg Eli 
Published: May 2021

Abstract
RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
Bacterial Evolutionary Precursors of Eukaryotic Copper–Zinc Superoxide Dismutases
Authors: Wright Gareth S A 
Published: May 2021

Abstract
Internalization of a bacteria by an archaeal cell expedited eukaryotic evolution. An important feature of the species that diversified into the great variety of eukaryotic life visible today was the ability to combat oxidative stress with a copper–zinc superoxide dismutase (CuZnSOD) enzyme activated by a specific, high-affinity copper chaperone. Adoption of a single protein interface that facilitates homodimerization and heterodimerization was essential; however, its evolution has been difficult to rationalize given the structural differences between bacterial and eukaryotic enzymes. In contrast, no consistent strategy for the maturation of periplasmic bacterial CuZnSODs has emerged. Here, 34 CuZnSODs are described that closely resemble the eukaryotic form but originate predominantly from aquatic bacteria. Crystal structures of a Bacteroidetes bacterium CuZnSOD portray both prokaryotic and eukaryotic characteristics and propose a mechanism for self-catalyzed disulfide maturation. Unification of a bacterial but eukaryotic-like CuZnSOD along with a ferredoxin-fold MXCXXC copper-binding domain within a single polypeptide created the advanced copper delivery system for CuZnSODs exemplified by the human copper chaperone for superoxide dismutase-1. The development of this system facilitated evolution of large and compartmentalized cells following endosymbiotic eukaryogenesis.
Litocranius walleri(Artiodactyla: Bovidae)
Authors: Bärmann Eva V , Klappert Ariana N , Chen Augustin 
Published: May 2021

AbstractLitocranius walleri (Brooke, 1878) is a bovid commonly called the gerenuk. It is a medium-sized antelope closely related to gazelles and springbok, but unlike these it has low-crowned teeth. L. walleri is the only species in the genus Litocranius. It is commonly found in dry thornbush savannah in northeastern Africa, where it feeds almost exclusively on thorny shrubs and trees while frequently using a bipedal stance. L. walleri is classified as “Near Threatened” (NT) by the International Union for Conservation of Nature and Natural Resources (IUCN) because its population trends are decreasing.
Overview of approved and upcoming vaccines for SARS-CoV-2: a living review
Authors: Alderson Jennifer , Batchelor Vicky , O’Hanlon Miriam , Cifuentes Liliana , Richter Felix Clemens , Kopycinski Jakub ,   The Oxford-Cardiff COVID-19 Literature Consortium
Published: May 2021

Abstract
The rapid design and implementation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines is testament to a successfully coordinated global research effort. While employing a variety of different technologies, some of which have been used for the first time, all approved vaccines demonstrate high levels of efficacy with excellent safety profiles. Despite this, there remains an urgent global demand for coronavirus disease 2019 vaccines that require further candidates to pass phase 3 clinical trials. In the expectation of SARS-CoV-2 becoming endemic, researchers are looking to adjust the vaccine constructs to tackle emerging variants. In this review, we outline different platforms used for approved vaccines and summarize latest research data with regards to immunogenicity, dosing regimens and efficiency against emerging variants.
Tools for Assessing Cell-Cycle Progression in Plants
Authors: Echevarría Clara , Gutierrez Crisanto , Desvoyes Bénédicte 
Published: May 2021

AbstractEstimation of cell-cycle parameters is crucial for understanding the developmental programs established during the formation of an organism. A number of complementary approaches have been developed and adapted to plants to assess the cell-cycle status in different proliferative tissues. The most classical methods relying on metabolic labeling are still very much employed and give valuable information on cell-cycle progression in fixed tissues. However, the growing knowledge of plant cell-cycle regulators with defined expression pattern together with the development of fluorescent proteins technology enabled the generation of fusion proteins that function individually or in conjunction as cell-cycle reporters. Together with the improvement of imaging techniques, in vivo live imaging to monitor plant cell-cycle progression in normal growth conditions or in response to different stimuli has been possible. Here, we review these tools and their specific outputs for plant cell-cycle analysis.
A Three-Dimensional Scanning System for Digital Archiving and Quantitative Evaluation of Arabidopsis Plant Architectures
Authors: Kunita Itsuki , Morita Miyo Terao , Toda Masashi , Higaki Takumi 
Published: May 2021

Abstract
A plant’s architecture contributes to its ability to acquire resources and reduce mechanical load. Arabidopsis thaliana is the most common model plant in molecular biology, and there are several mutants and transgenic lines with modified plant architecture regulation, such as lazy1 mutants, which have reversed angles of lateral branches. Although some phenotyping methods have been used in larger agricultural plants, limited suitable methods are available for three-dimensional reconstruction of Arabidopsis, which is smaller and has more uniform surface textures and structures. An inexpensive, easily adopted three-dimensional reconstruction system that can be used for Arabidopsis is needed so that researchers can view and quantify morphological changes over time. We developed a three-dimensional reconstruction system for A. thaliana using the visual volume intersection method, which uses a fixed camera to capture plant images from multiple directions while the plant slowly rotates. We then developed a script to autogenerate stack images from the obtained input movie and visualized the plant architecture by rendering the output stack image using the general bioimage analysis software. We successfully three-dimensionally and time-sequentially scanned wild-type and lazy1 mutant A. thaliana plants and measured the angles of the lateral branches. This non-contact, non-destructive method requires no specialized equipment and is space efficient, inexpensive and easily adopted by Arabidopsis researchers. Consequently, this system will promote three- and four-dimensional phenotyping of this model plant, and it can be used in combination with molecular genetics to further elucidate the molecular mechanisms that regulate Arabidopsis architecture.
Secondary Nummular Headache: A New Case Series and Review of the Literature
Authors: García-Iglesias Cristina , Martínez-Badillo Cristina , García-Azorín David , Trigo-López Javier , Martínez-Pías Enrique , Guerrero-Peral Ángel Luis 
Published: May 2021

Abstract

Background
Nummular headache (NH) is defined in the International Classification of Headache Disorders (ICHD) by the presence of localized pain circumscribed to a small round area of the scalp, not better accounted by any other diagnosis. As in many other primary headache disorders, secondary cases might occur. To date, 13 secondary cases have been published. We aim to present a long series of secondary NH and review the literature of symptomatic NH.

Patients and methods
Retrospective analysis of an observational prospective cohort in a headache unit located in a tertiary hospital. We included patients that fulfilled ICHD criteria and were attributed to a secondary cause. We describe the clinical characteristics, the underlying causes, and the response to treatment.

Results
We included 274 NH patients; eight of them (2.9%) were considered secondary. In one patient the underlying cause was subcutaneous, as for six cases the lesion was located in the bone (two hemangiomas, one osteoma, three different types of cysts), and in one was intracranial but closely related with internal diploe (cavernoma). Among our patients with secondary NH, a preventive therapy was not always needed and, when required, gabapentin or onabotulinumtoxinA were used with positive response.

Conclusions
Secondary NH phenotype overlaps primary NH. Therefore, we recommend routine imaging study in every NH patient. Concerning treatment, it was not necessary to remove the underlying lesion to control the pain and many cases responded to the same prophylactics as primary NH cases.
ON THE POSSIBILITY TO RESOLVE GADOLINIUM- AND CERIUM-BASED CONTRAST AGENTS FROM THEIR CT NUMBERS IN DUAL-ENERGY COMPUTED TOMOGRAPHY
Authors: Malusek Alexandr , Henriksson Lilian , Eriksson Peter , Dahlström Nils , Carlsson Tedgren Åsa , Uvdal Kajsa 
Published: May 2021

Abstract
Cerium oxide nanoparticles with integrated gadolinium have been proved to be useful as contrast agents in magnetic resonance imaging. Of question is their performance in dual-energy computed tomography. The aims of this work are to determine (1) the relation between the computed tomography number and the concentration of the I, Gd or Ce contrast agent and (2) under what conditions it is possible to resolve the type of contrast agent. Hounsfield values of iodoacetic acid, gadolinium acetate and cerium acetate dissolved in water at molar concentrations of 10, 50 and 100 mM were measured in a water phantom using the Siemens SOMATOM Definition Force scanner; gadolinium- and cerium acetate were used as substitutes for the gadolinium-integrated cerium oxide nanoparticles. The relation between the molar concentration of the I, Gd or Ce contrast agent and the Hounsfield value was linear. Concentrations had to be sufficiently high to resolve the contrast agents.
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies
Authors: Talavera Gerard , Lukhtanov Vladimir , Pierce Naomi E , Vila Roger 
Published: May 2021

Abstract
Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy]