bluuebunny/crossref_metadata_2025_split huggingface dataset:
High time resolution and polarization properties of ASKAP-localized fast radio bursts
Authors: Day Cherie K , Deller Adam T , Shannon Ryan M , Qiu(邱昊) Hao , Bannister Keith W , Bhandari Shivani , Ekers Ron , Flynn Chris , James Clancy W , Macquart Jean-Pierre , Mahony Elizabeth K , Phillips Chris J , Xavier Prochaska J 
Published: July 2020

ABSTRACT
Combining high time and frequency resolution full-polarization spectra of fast radio bursts (FRBs) with knowledge of their host galaxy properties provides an opportunity to study both the emission mechanism generating them and the impact of their propagation through their local environment, host galaxy, and the intergalactic medium. The Australian Square Kilometre Array Pathfinder (ASKAP) telescope has provided the first ensemble of bursts with this information. In this paper, we present the high time and spectral resolution, full polarization observations of five localized FRBs to complement the results published for the previously studied ASKAP FRB 181112. We find that every FRB is highly polarized, with polarization fractions ranging from 80 to 100 per cent, and that they are generally dominated by linear polarization. While some FRBs in our sample exhibit properties associated with an emerging archetype (i.e. repeating or apparently non-repeating), others exhibit characteristic features of both, implying the existence of a continuum of FRB properties. When examined at high time resolution, we find that all FRBs in our sample have evidence for multiple subcomponents and for scattering at a level greater than expected from the Milky Way. We find no correlation between the diverse range of FRB properties (e.g. scattering time, intrinsic width, and rotation measure) and any global property of their host galaxy. The most heavily scattered bursts reside in the outskirts of their host galaxies, suggesting that the source-local environment rather than the host interstellar medium is likely the dominant origin of the scattering in our sample.
The cosmic evolution of the stellar mass–velocity dispersion relation of early-type galaxies
Authors: Cannarozzo Carlo , Sonnenfeld Alessandro , Nipoti Carlo 
Published: July 2020

ABSTRACTWe study the evolution of the observed correlation between central stellar velocity dispersion σe and stellar mass M* of massive ($M_*\gtrsim 3\times 10^{10}\, \mathrm{M_\odot}$) early-type galaxies (ETGs) out to redshift z ≈ 2.5, taking advantage of a Bayesian hierarchical inference formalism. Collecting ETGs from state-of-the-art literature samples, we build a fiducial sample (0 ≲ z ≲ 1), which is obtained with homogeneous selection criteria, but also a less homogeneous extended sample (0 ≲ z ≲ 2.5). Based on the fiducial sample, we find that at z ≲ 1 the M*–σe relation is well represented by $\sigma _{\mathrm{e}}\propto M_*^{\beta }(1+z)^{\zeta}$, with β ≃ 0.18 independent of redshift and ζ ≃ 0.4 (at a given M*, σe decreases for decreasing z, for instance by a factor of ≈1.3 from z = 1 to z = 0). When the slope β is allowed to evolve, we find it increasing with redshift: β(z) ≃ 0.16 + 0.26log (1 + z) describes the data as well as constant β ≃ 0.18. The intrinsic scatter of the M*–σe relation is ≃0.08 dex in σe at given M*, independent of redshift. Our results suggest that, on average, the velocity dispersion of individual massive (M* ≳ 3 × 1011M⊙) ETGs decreases with time while they evolve from z ≈ 1 to z ≈ 0. The analysis of the extended sample, over the wider redshift range 0 ≲ z ≲ 2.5, leads to results similar to that of the fiducial sample, with slightly stronger redshift dependence of the normalization (ζ ≃ 0.5) and weaker redshift dependence of the slope (dβ/dlog (1 + z) ≃ 0.18) when β varies with time. At z = 2 ETGs with $M_*\approx 10^{11}\, \mathrm{M_\odot}$ have, on average, ≈1.7 higher σe than ETGs of similar stellar mass at z = 0.
Multimessenger observations of counterparts to IceCube-190331A
Authors: Krauß Felicia , Calamari Emily , Keivani Azadeh , Coleiro Alexis , Evans Phil A , Fox Derek B , Kennea Jamie A , Mészáros Peter , Murase Kohta , Russell Thomas D , Santander Marcos , Tohuvavohu Aaron 
Published: July 2020

ABSTRACT
High-energy neutrinos are a promising tool for identifying astrophysical sources of high and ultra-high energy cosmic rays (UHECRs). Prospects of detecting neutrinos at high energies (≳TeV) from blazars have been boosted after the recent association of IceCube-170922A and TXS 0506+056. We investigate the high-energy neutrino, IceCube-190331A, a high-energy starting event (HESE) with a high likelihood of being astrophysical in origin. We initiated a Swift/XRT and UVOT tiling mosaic of the neutrino localization and followed up with ATCA radio observations, compiling a multiwavelength spectral energy distribution (SED) for the most likely source of origin. NuSTAR observations of the neutrino location and a nearby X-ray source were also performed. We find two promising counterpart in the 90 per cent confidence localization region and identify the brightest as the most likely counterpart. However, no Fermi/LAT γ-ray source and no prompt Swift/BAT source is consistent with the neutrino event. At this point, it is unclear whether any of the counterparts produced IceCube-190331A. We note that the Helix Nebula is also consistent with the position of the neutrino event and we calculate that associated particle acceleration processes cannot produce the required energies to generate a high-energy HESE neutrino.
Bi-abundance photoionization models of planetary nebulae: determining the amount of oxygen in the metal-rich component
Authors: Gómez-Llanos V , Morisset C 
Published: July 2020

ABSTRACT
We study the hypothesis of high-metallicity clumps being responsible for the abundance discrepancy found in planetary nebulae between the values obtained from recombination and collisionally excited lines. We generate grids of photoionization models combining cold metal-rich clumps emitting the heavy element recombination lines, embedded in a normal metallicity region responsible for the forbidden lines. The two running parameters of the grid are the metallicity of the clumps and its volume fraction relative to the whole nebula. We determine the density and temperatures (from the Balmer jump and the [O iii] 5007/4363 Å line ratio) and the ionic abundances from the collisional and recombination lines, as an observer would do. The metallicity of the near-to-solar region is recovered, while the metallicity of the clumps is systematically underestimated by up to two orders of magnitude. This is mainly because most of the Hβ emission is coming from the ‘normal’ region, and only the small contribution emitted by the metal-rich clumps should be used. We find that a given ADF(O++) can be reproduced by a small amount of rich clumps, or a bigger amount of less rich clumps. Finally, comparing with the observations of NGC 6153, we find two models that reproduce its ADF(O++) and the observed electron temperatures. We determine the fraction of oxygen embedded in the metal-rich region (with a fraction of volume less than 1 per cent) to be roughly between 25 per cent and 60 per cent of the total amount of oxygen in the nebula (a few 10−3M⊙).
An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life
Authors: Kuhl Heiner , Frankl-Vilches Carolina , Bakker Antje , Mayr Gerald , Nikolaus Gerhard , Boerno Stefan T , Klages Sven , Timmermann Bernd , Gahr Manfred 
Published: July 2020

Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes
Authors: Bayona-Serrano Juan David , Viala Vincent Louis , Rautsaw Rhett M , Schramer Tristan D , Barros-Carvalho Gesiele A , Nishiyama Milton Yutaka , Freitas-de-Sousa Luciana A , Moura-da-Silva Ana Maria , Parkinson Christopher L , Grazziotin Felipe Gobbi , Junqueira-de-Azevedo Inácio L M 
Published: July 2020

Abstract
Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an “SVMP-like” function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.
Microcephaly family protein MCPH1 stabilizes RAD51 filaments
Authors: Chang Hao-Yen , Lee Chia-Yi , Lu Chih-Hao , Lee Wei , Yang Han-Lin , Yeh Hsin-Yi , Li Hung-Wen , Chi Peter 
Published: July 2020

Abstract
Microcephalin 1 (MCPH1) was identified from genetic mutations in patients with primary autosomal recessive microcephaly. In response to DNA double-strand breaks (DSBs), MCPH1 forms damage-induced foci and recruits BRCA2–RAD51 complex, a key component of the DSB repair machinery for homologous recombination (HR), to damage sites. Accordingly, the efficiency of HR is significantly attenuated upon depletion of MCPH1. The biochemical characteristics of MCPH1 and its functional interaction with the HR machinery had remained unclear due to lack of highly purified MCPH1 recombinant protein for functional study. Here, we established a mammalian expression system to express and purify MCPH1 protein. We show that MCPH1 is a bona fide DNA-binding protein and provide direct biochemical analysis of this MCPH family protein. Furthermore, we reveal that MCPH1 directly interacts with RAD51 at multiple contact points, providing evidence for how MCPH1 physically engages with the HR machinery. Importantly, we demonstrate that MCPH1 enhances the stability of RAD51 on single-strand DNA, a prerequisite step for RAD51-mediated recombination. Single-molecule tethered particle motion analysis showed a ∼2-fold increase in the lifetime of RAD51–ssDNA filaments in the presence of MCPH1. Thus, our study demonstrates direct crosstalk between microcephaly protein MCPH1 and the recombination component RAD51 for DSB repair.
Canonical non-homologous end-joining promotes genome mutagenesis and translocations induced by transcription-associated DNA topoisomerase 2 activity
Authors: Olmedo-Pelayo Joaquín , Rubio-Contreras Diana , Gómez-Herreros Fernando 
Published: July 2020

Abstract
DNA topoisomerase II (TOP2) is a major DNA metabolic enzyme, with important roles in replication, transcription, chromosome segregation and spatial organisation of the genome. TOP2 is the target of a class of anticancer drugs that poison the DNA-TOP2 transient complex to generate TOP2-linked DNA double-strand breaks (DSBs). The accumulation of DSBs kills tumour cells but can also result in genome instability. The way in which topoisomerase activity contributes to transcription remains unclear. In this work we have investigated how transcription contributes to TOP2-dependent DSB formation, genome instability and cell death. Our results demonstrate that gene transcription is an important source of abortive TOP2 activity. However, transcription does not contribute significantly to apoptosis or cell death promoted by TOP2-induced DSBs. On the contrary: transcription-dependent breaks greatly contribute to deleterious mutations and translocations, and can promote oncogenic rearrangements. Importantly, we show that TOP2-induced genome instability is mediated by mutagenic canonical non-homologous end joining whereas homologous recombination protects cells against these insults. Collectively, these results uncover mechanisms behind deleterious effects of TOP2 abortive activity during transcription, with relevant implications for chemotherapy.
Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei
Authors: Smith Jr. Joseph T , Doleželová Eva , Tylec Brianna , Bard Jonathan E , Chen Runpu , Sun Yijun , Zíková Alena , Read Laurie K 
Published: July 2020

AbstractTrypanosoma brucei is a parasitic protozoan that undergoes a complex life cycle involving insect and mammalian hosts that present dramatically different nutritional environments. Mitochondrial metabolism and gene expression are highly regulated to accommodate these environmental changes, including regulation of mRNAs that require extensive uridine insertion/deletion (U-indel) editing for their maturation. Here, we use high throughput sequencing and a method for promoting life cycle changes in vitro to assess the mechanisms and timing of developmentally regulated edited mRNA expression. We show that edited CYb mRNA is downregulated in mammalian bloodstream forms (BSF) at the level of editing initiation and/or edited mRNA stability. In contrast, edited COIII mRNAs are depleted in BSF by inhibition of editing progression. We identify cell line-specific differences in the mechanisms abrogating COIII mRNA editing, including the possible utilization of terminator gRNAs that preclude the 3′ to 5′ progression of editing. By examining the developmental timing of altered mitochondrial mRNA levels, we also reveal transcript-specific developmental checkpoints in epimastigote (EMF), metacyclic (MCF), and BSF. These studies represent the first analysis of the mechanisms governing edited mRNA levels during T. brucei development and the first to interrogate U-indel editing in EMF and MCF life cycle stages.
Bone evaluation in paediatric chronic kidney disease: clinical practice points from the European Society for Paediatric Nephrology CKD-MBD and Dialysis working groups and CKD-MBD working group of the ERA-EDTA
Authors: Bakkaloglu Sevcan A , Bacchetta Justine , Lalayiannis Alexander D , Leifheit-Nestler Maren , Stabouli Stella , Haarhaus Mathias , Reusz George , Groothoff Jaap , Schmitt Claus Peter , Evenepoel Pieter , Shroff Rukshana , Haffner Dieter ,   the European Society for Paediatric Nephrology (ESPN) Chronic Kidney Disease Mineral and Bone Disorder (CKD-MBD) and Dialysis working groups and CKD-MBD working group of the European Renal Association–European Dialysis and Transplant Association (ERA-EDTA)
Published: July 2020

AbstractMineral and bone disorder (MBD) is widely prevalent in children with chronic kidney disease (CKD) and is associated with significant morbidity. CKD may cause disturbances in bone remodelling/modelling, which are more pronounced in the growing skeleton, manifesting as short stature, bone pain and deformities, fractures, slipped epiphyses and ectopic calcifications. Although assessment of bone health is a key element in the clinical care of children with CKD, it remains a major challenge for physicians. On the one hand, bone biopsy with histomorphometry is the gold standard for assessing bone health, but it is expensive, invasive and requires expertise in the interpretation of bone histology. On the other hand, currently available non-invasive measures, including dual-energy X-ray absorptiometry and biomarkers of bone formation/resorption, are affected by growth and pubertal status and have limited sensitivity and specificity in predicting changes in bone turnover and mineralization. In the absence of high-quality evidence, there are wide variations in clinical practice in the diagnosis and management of CKD-MBD in childhood. We present clinical practice points (CPPs) on the assessment of bone disease in children with CKD Stages 2–5 and on dialysis based on the best available evidence and consensus of experts from the CKD-MBD and Dialysis working groups of the European Society for Paediatric Nephrology and the CKD-MBD working group of the European Renal Association–European Dialysis and Transplant Association. These CPPs should be carefully considered by treating physicians and adapted to individual patients’ needs as appropriate. Further areas for research are suggested.
Haematological disorders following kidney transplantation
Authors: Malyszko Jolanta , Basak Grzegorz , Batko Krzysztof , Capasso Giavambatista , Capasso Anna , Drozd-Sokolowska Joanna , Krzanowska Katarzyna , Kulicki Pawel , Matuszkiewicz-Rowinska Joanna , Soler Maria Jose , Sprangers Ben , Malyszko Jacek 
Published: July 2020

Abstract
Transplantation offers cure for some haematological cancers, end-stage organ failure, but at the cost of long-term complications. Renal transplantation is the best-known kidney replacement therapy and it can prolong end-stage renal disease patient lives for decades. However, patients after renal transplantation are at a higher risk of developing different complications connected not only with surgical procedure but also with immunosuppressive treatment, chronic kidney disease progression and rejection processes. Various blood disorders can develop in post-transplant patients ranging from relatively benign anaemia through cytopenias to therapy-related myelodysplasia and acute myeloid leukaemia (AML) and post-transplant lymphoproliferative disorders followed by a rare and fatal condition of thrombotic microangiopathy and haemophagocytic syndrome. So far literature mainly focused on the post-transplant lymphoproliferative disease. In this review, a variety of haematological problems after transplantation ranging from rare disorders such as myelodysplasia and AML to relatively common conditions such as anaemia and iron deficiency are presented with up-to-date diagnosis and management.
New Philosophy, Clinical Pearls, and Methods for Intraoperative Cognition Mapping and Monitoring “à la carte” in Brain Tumor Patients
Authors: Duffau Hugues 
Published: July 2020

Abstract
The purpose of surgery for brain tumors involving eloquent neural circuits is to maximize the extent of resection while preserving an optimal quality of life. To this end, especially in diffuse glioma, the goal is to remove the cerebral parenchyma invaded by the neoplasm up to the individual cortico-subcortical networks critical for brain functions. Intraoperative mapping combined with real-time cognitive monitoring throughout the resection in awake patient is thus highly recommended to resume a normal life. Indeed, beyond avoiding hemiplegia or aphasia, enjoying a familial, social, and professional life implies that motor and language mapping is not sufficient. Identifying and sparing neural networks that subserve cognition (movement control, visuospatial cognition, executive functions, multimodal semantics, metacognition) and mentalizing (theory of mind, which plays a key role for social cognition) is essential to preserve an adapted behavior.
Here, the aim is to review when and how to map these critical functions, which have nonetheless been neglected for many decades by neurosurgeons. In fact, the disorders generated by surgical injuries of circuits underpinning nonmotor and nonspeech functions are usually not immediately visible on postoperative standard clinical examination, leading the physician to believe that the patient has no deficit. Yet, cognitive or emotional disturbances may subsequently prevent to resume an active life, as to work full time. Therefore, a systematic neuropsychological assessment should be performed before, during, and after mapping-guided surgery, regardless of the tumor location, to preserve the functional connectome intraoperatively and to plan a postoperative tailored cognitive rehabilitation according to the patient's needs.
Measles or Not Measles? That is the Question!
Authors: Ibraheim Marina Kristy , Awadh Hesham , Allana Ambreen , Ostrosky-Zeichner Luis , Arias Cesar A 
Published: July 2020

Abstract
We present a diagnostically challenging case of a patient who presented with fever and rash during a measles outbreak. The diagnosis was complicated by the interpretation of the results of serological tests, which resulted in implementation of major preventive measures in the hospital. The patient was later confirmed to have murine typhus.