bluuebunny/crossref_metadata_2025_split huggingface dataset:
sMILES: a library of semi-empirical MILES stellar spectra with variable [α/Fe] abundances
Authors: Knowles Adam T , Sansom A E , Allende Prieto C , Vazdekis A 
Published: April 2021

ABSTRACT
We present a new library of semi-empirical stellar spectra that is based on the empirical Medium resolution Isaac Newton Library of Empirical Spectra (MILES) library. A new, high-resolution library of theoretical stellar spectra is generated that is specifically designed for use in stellar population studies. We test these models across their full wavelength range against other model libraries and find reasonable agreement in their predictions of spectral changes due to atmospheric α-element variations, known as differential corrections. We also test the models against the MILES and MaStar libraries of empirical stellar spectra and also find reasonable agreements, as expected from previous work. We then use the abundance pattern predictions of the new theoretical stellar spectra to differentially correct MILES spectra to create semi-empirical MILES (sMILES) star spectra with abundance patterns that differ from those present in the Milky Way. The final result is five families of 801 sMILES stars with [α/Fe] abundances ranging from −0.20 to 0.60 dex at MILES resolution (FWHM = $2.5\,$Å) and wavelength coverage ($3540.5\!-\!7409.6\,$Å). We make the sMILES library publicly available.
New X-ray observations of the hot subdwarf binary HD 49798/RX J0648.0–4418
Authors: Mereghetti S , Pintore F , Rauch T , La Palombara N , Esposito P , Geier S , Pelisoli I , Rigoselli M , Schaffenroth V , Tiengo A 
Published: April 2021

ABSTRACT
HD 49798/RX J0648.0–4418 is the only confirmed X-ray binary in which the mass donor is a hot subdwarf star of O spectral type and, most likely, it contains a massive white dwarf (1.28 ± 0.05 M⊙) with a very fast spin period of 13.2 s. Here, we report the results of new XMM–Newton pointings of this peculiar binary, carried out in 2018 and in 2020, together with a reanalysis of all the previous observations. The new data indicate that the compact object is still spinning-up at a steady rate of (−2.17 ± 0.01) × 10−15 s s−1, consistent with its interpretation in terms of a young contracting white dwarf. Comparison of observations obtained at similar orbital phases, far from the ecplise, shows evidence for long-term variability of the hard (&gt;0.5 keV) spectral component at a level of ∼(70 ± 20) per cent, suggesting the presence of time-dependent inhomogeneities in the weak stellar wind of the HD 49798 subdwarf. To investigate better the soft spectral component that dominates the X-ray flux from this system, we computed a theoretical model for the thermal emission expected from an atmosphere with element abundances and surface gravity appropriate for this massive white dwarf. This model gives a best fit with effective temperature of Teff = 2.25 × 105 K and an emitting area with a radius of ∼1600 km, larger than that found with blackbody fits. This model also predicts a contribution of the pulsed emission from the white dwarf in the optical band significantly larger than previously thought and possibly relevant for optical variability studies of this system.
A revised SALT2 surface for fitting Type Ia supernova light curves
Authors: Taylor G , Lidman C , Tucker B E , Brout D , Hinton S R , Kessler R 
Published: April 2021

ABSTRACT
We present a revised Spectral Adaptive Light Curve Template (SALT2) surface (SALT2-2021) for fitting the light curves of Type Ia supernovae (SNe Ia), which incorporates new measurements of zero-point calibration offsets and Milky Way extinction. The most notable change in the new surface occurs in the UV region. This new surface alters the distance measurements of SNe Ia, which can be used to investigate the nature of dark energy by probing the expansion history of the Universe. Using the revised SALT2 surface on public data from the first 3 yr of the Dark Energy Survey Supernova Program (combined with an external low-z SNe Ia sample) and combining with cosmic microwave background constraints, we find a change in the dark energy equation-of-state parameter, Δw = 0.015 ± 0.004. This result highlights the continued importance of controlling and reducing systematic uncertainties, particularly with the next generation of supernova analyses aiming to improve constraints on dark energy properties.
Correlation between optical and γ-ray flux variations in BL Lacs
Authors: Rajput Bhoomika , Shah Zahir , Stalin C S , Sahayanathan S , Rakshit Suvendu 
Published: April 2021

ABSTRACT
We report here results of the analysis of correlated flux variations between the optical and GeV γ-ray bands in three bright BL Lac objects, namely AO 0235+164, OJ 287, and PKS 2155−304. This was based on the analysis of about 10 yr of data from the Fermi Gamma-ray Space Telescope covering the period between 2008 August 8 and 2018 August 8 along with optical data covering the same period. For all the sources, during the flares analysed in this work, the optical and γ-ray flux variations are found to be closely correlated. From broad-band spectral energy distribution modelling of different epochs in these sources using the one-zone leptonic emission model, we found that the optical–ultraviolet emission is dominated by synchrotron emission from the jet. The γ-ray emission in the low synchrotron peaked sources AO 0235+164 and OJ 287 is found to be well fitted with external Compton (EC) component, while the γ-ray emission in the high synchrotron peaked source PKS 2155−304 is well fitted with synchrotron self-Compton component. Further, we note that the γ-ray emission during the high-flux state of AO 0235+164 (epochs A and B) requires seed photons from both the dusty torus and broad-line region, while the γ-ray emission in OJ 287 and during epochs C and D of AO 0235+164 can be modelled by EC scattering of infrared photons from the torus.
Explaining the extended GeV gamma-ray emission adjacent to HESS J1825-137
Authors: Collins T , Rowell G , Mitchell A M W , Voisin F , Fukui Y , Sano H , Alsulami R , Einecke S 
Published: April 2021

ABSTRACT
HESS J1825-137 is one of the most powerful and luminous TeV gamma-ray pulsar wind nebulae (PWN). To the south of HESS J1825-137, Fermi-LAT observation revealed a new region of GeV gamma-ray emission with three apparent peaks (termed here, GeV-ABC). This study presents interstellar medium (ISM) data and spectral energy distribution (SED) modelling towards the GeV emission to understand the underlying particle acceleration. We considered several particle accelerator scenarios – the PWN associated with HESS J1825-137, the progenitor SNR also associated with HESS J1825-137, plus the gamma-ray binary system LS 5039. It was found that the progenitor SNR of HESS J1825-137 has insufficient energetics to account for all GeV emission. GeV-ABC may be a reflection of an earlier epoch in the history of the PWN associated with HESS 1825-137, assuming fast diffusion perhaps including advection. LS 5039 cannot meet the required energetics to be the source of particle acceleration. A combination of HESS J1825-137 and LS 5039 could be plausible sources.
Extracting the 21 cm EoR signal using MWA drift scan data
Authors: Patwa Akash Kumar , Sethi Shiv , Dwarakanath K S 
Published: April 2021

ABSTRACT
The detection of redshifted hyperfine line of neutral hydrogen (H i) is the most promising probe of the epoch of reionization (EoR). We report an analysis of 55 h of Murchison Widefield Array (MWA) phase II drift scan EoR data. The data correspond to a central frequency $\nu _0 = 154.24 \, \rm MHz$ (z ≃ 8.2 for the redshifted H i hyperfine line) and bandwidth $B = 10.24 \, \rm MHz$. As one expects greater system stability in a drift scan, we test the system stability by comparing the extracted power spectra from data with noise simulations and show that the power spectra for the cleanest data behave as thermal noise. We compute the H i power spectrum as a function of time in one and two dimensions. The best upper limit on the 1D power spectrum are: $\Delta ^2(k) \simeq (1000~\rm mK)^2$ at k ≃ 0.2h Mpc−1 and at k ≃ 1h Mpc−1. The cleanest modes, which might be the most suited for obtaining the optimal signal to noise, correspond to k ≳ 1h Mpc−1. We also study the time-dependence of the foreground-dominated modes in a drift scan and compare with the expected behaviour.
Topology and obliquity of core magnetic fields in shaping seismic properties of slowly rotating evolved stars
Authors: Loi Shyeh Tjing 
Published: April 2021

ABSTRACT
It is thought that magnetic fields must be present in the interiors of stars to resolve certain discrepancies between theory and observation (e.g. angular momentum transport), but such fields are difficult to detect and characterize. Asteroseismology is a powerful technique for inferring the internal structures of stars by measuring their oscillation frequencies, and succeeds particularly with evolved stars, owing to their mixed modes, which are sensitive to the deep interior. The goal of this work is to present a phenomenological study of the combined effects of rotation and magnetism in evolved stars, where both are assumed weak enough that first-order perturbation theory applies, and we focus on the regime where Coriolis and Lorentz forces are comparable. Axisymmetric ‘twisted-torus’ field configurations are used, which are confined to the core and allowed to be misaligned with respect to the rotation axis. Factors such as the field radius, topology and obliquity are examined. We observe that fields with finer-scale radial structure and/or smaller radial extent produce smaller contributions to the frequency shift. The interplay of rotation and magnetism is shown to be complex: we demonstrate that it is possible for nearly symmetric multiplets of apparently low multiplicity to arise even under a substantial field, which might falsely appear to rule out its presence. Our results suggest that proper modelling of rotation and magnetism, in a simultaneous fashion, may be required to draw robust conclusions about the existence/non-existence of a core magnetic field in any given object.
Towards a better understanding of supernova environments: a study of SNe 2004dg and 2012P in NGC 5806 with HST and MUSE
Authors: Sun Ning-Chen , Maund Justyn R , Crowther Paul A , Fang Xuan , Zapartas Emmanouil 
Published: April 2021

ABSTRACT
Core-collapse supernovae (SNe) are the inevitable fate of most massive stars. Since most stars form in groups, SN progenitors can be constrained with information of their environments. It remains challenging to accurately analyse the various components in the environment and to correctly identify their relationships with the SN progenitors. Using a combined data set of VLT/MUSE spatially resolved integral field unit (IFU) spectroscopy and HST/ACS+WFC3 high-spatial-resolution imaging, we present a detailed investigation of the environment of the Type II-P SN 2004dg and Type IIb SN 2012P. The two SNe occurred in a spiral arm of NGC 5806, where a star-forming complex is apparent with a giant H ii region. By modelling the ionized gas, a compact star cluster and the resolved stars, we derive the ages and extinctions of stellar populations in the vicinity of the SNe. The various components are consistent with a sequence of triggered star formation as the spiral density wave swept through their positions. For SNe 2004dg and 2012P, we identify their host stellar populations and derive initial masses of $10.0^{+0.3}_{-0.2}$ and $15.2^{+2.0}_{-1.0}$ M⊙ for their progenitors, respectively. Both results are consistent with those from pre-explosion images or nebular-phase spectroscopy. SN 2012P is spatially coincident but less likely to be coeval with the star-forming complex. As in this case, star formation bursts on small scales may appear correlated if they are controlled by any physical processes on larger scales; this may lead to a high probability of chance alignment between older SN progenitors and younger stellar populations.
The effect of flanking bases on direct and triplet sensitized cyclobutane pyrimidine dimer formation in DNA depends on the dipyrimidine, wavelength and the photosensitizer
Authors: Lu Chen , Gutierrez-Bayona Natalia Eugenia , Taylor John-Stephen 
Published: April 2021

Abstract
Cyclobutane pyrimidine dimers (CPDs) are the major products of DNA produced by direct absorption of UV light, and result in C to T mutations linked to human skin cancers. Most recently a new pathway to CPDs in melanocytes has been discovered that has been proposed to arise from a chemisensitized pathway involving a triplet sensitizer that increases mutagenesis by increasing the percentage of C-containing CPDs. To investigate how triplet sensitization may differ from direct UV irradiation, CPD formation was quantified in a 129-mer DNA designed to contain all 64 possible NYYN sequences. CPD formation with UVB light varied about 2-fold between dipyrimidines and 12-fold with flanking sequence and was most frequent at YYYR and least frequent for GYYN sites in accord with a charge transfer quenching mechanism. In contrast, photosensitized CPD formation greatly favored TT over C-containing sites, more so for norfloxacin (NFX) than acetone, in accord with their differing triplet energies. While the sequence dependence for photosensitized TT CPD formation was similar to UVB light, there were significant differences, especially between NFX and acetone that could be largely explained by the ability of NFX to intercalate into DNA.
Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations
Authors: Yang Jie , Horton John R , Akdemir Kadir C , Li Jia , Huang Yun , Kumar Janani , Blumenthal Robert M , Zhang Xing , Cheng Xiaodong 
Published: April 2021

Abstract
DNA cytosine methylation in mammals modulates gene expression and chromatin accessibility. It also impacts mutation rates, via spontaneous oxidative deamination of 5-methylcytosine (5mC) to thymine. In most cases the resulting T:G mismatches are repaired, following T excision by one of the thymine DNA glycosylases, TDG or MBD4. We found that C-to-T mutations are enriched in the binding sites of CCAAT/enhancer binding proteins (CEBP). Within a CEBP site, the presence of a T:G mismatch increased CEBPβ binding affinity by a factor of &gt;60 relative to the normal C:G base pair. This enhanced binding to a mismatch inhibits its repair by both TDG and MBD4 in vitro. Furthermore, repair of the deamination product of unmethylated cytosine, which yields a U:G DNA mismatch that is normally repaired via uracil DNA glycosylase, is also inhibited by CEBPβ binding. Passage of a replication fork over either a T:G or U:G mismatch, before repair can occur, results in a C-to-T mutation in one of the daughter duplexes. Our study thus provides a plausible mechanism for accumulation of C-to-T human somatic mutations.
Arena3Dweb: interactive 3D visualization of multilayered networks
Authors: Karatzas Evangelos , Baltoumas Fotis A , Panayiotou Nikolaos A , Schneider Reinhard , Pavlopoulos Georgios A 
Published: April 2021

AbstractEfficient integration and visualization of heterogeneous biomedical information in a single view is a key challenge. In this study, we present Arena3Dweb, the first, fully interactive and dependency-free, web application which allows the visualization of multilayered graphs in 3D space. With Arena3Dweb, users can integrate multiple networks in a single view along with their intra- and inter-layer connections. For clearer and more informative views, users can choose between a plethora of layout algorithms and apply them on a set of selected layers either individually or in combination. Users can align networks and highlight node topological features, whereas each layer as well as the whole scene can be translated, rotated and scaled in 3D space. User-selected edge colors can be used to highlight important paths, while node positioning, coloring and resizing can be adjusted on-the-fly. In its current version, Arena3Dweb supports weighted and unweighted undirected graphs and is written in R, Shiny and JavaScript. We demonstrate the functionality of Arena3Dweb using two different use-case scenarios; one regarding drug repurposing for SARS-CoV-2 and one related to GPCR signaling pathways implicated in melanoma. Arena3Dweb is available at http://bib.fleming.gr:3838/Arena3D or http://bib.fleming.gr/Arena3D.
The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity
Authors: Fergus Claire , Al-qasem Mashael , Cotter Michelle , McDonnell Ciara M , Sorrentino Emiliano , Chevot Franciane , Hokamp Karsten , Senge Mathias O , Southern John M , Connon Stephen J , Kelly Vincent P 
Published: April 2021

Abstract
Base-modification can occur throughout a transfer RNA molecule; however, elaboration is particularly prevalent at position 34 of the anticodon loop (the wobble position), where it functions to influence protein translation. Previously, we demonstrated that the queuosine modification at position 34 can be substituted with an artificial analogue via the queuine tRNA ribosyltransferase enzyme to induce disease recovery in an animal model of multiple sclerosis. Here, we demonstrate that the human enzyme can recognize a very broad range of artificial 7-deazaguanine derivatives for transfer RNA incorporation. By contrast, the enzyme displays strict specificity for transfer RNA species decoding the dual synonymous NAU/C codons, determined using a novel enzyme-RNA capture-release method. Our data highlight the broad scope and therapeutic potential of exploiting the queuosine incorporation pathway to intentionally engineer chemical diversity into the transfer RNA anticodon.
Living with a central nervous system (CNS) tumor: findings on long-term survivorship from the NIH Natural History Study
Authors: Rogers James L , Vera Elizabeth , Acquaye Alvina , Briceno Nicole , Jammula Varna , King Amanda L , Leeper Heather , Quezado Martha M , Gonzalez Alarcon Javier , Boris Lisa , Burton Eric , Celiku Orieta , Choi Anna , Christ Alexa , Crandon Sonja , Grajkowska Ewa , Leggiero Nicole , Lollo Nicole , Penas-Prado Marta , Reyes Jennifer , Siegel Christine , Theeler Brett J , Timmer Michael , Wall Kathleen , Wu Jing , Aldape Kenneth , Gilbert Mark R , Armstrong Terri S 
Published: April 2021

Abstract

Background
Primary central nervous system (CNS) tumors are often associated with high symptom burden and a poor prognosis from the time of diagnosis. The purpose of this study is to describe patient-reported outcomes (PRO) data from long-term survivors (LTS; ≥5-year survival post-diagnosis).

Methods
Clinical/treatment/molecular characteristics and PROs (symptom burden/interference (MDASI-BT/SP), perceived cognition (Neuro-QoL), anxiety/depression (PROMIS), and general health status (EQ-5D-3L)) were collected on 248 adult LTS between 9/2016 and 8/2019. Descriptive statistics and regression analysis were used to report results.

Results
Participants had a median age of 47 years (19-82) and were primarily White (83%) males (51%) with high-grade tumors (59%) and few mutations. Forty-two percent of the 222 brain tumor LTS reported no moderate-to-severe symptoms, whereas 45% reported three or more; most common symptoms were fatigue (40%), difficulty remembering (29%), and drowsiness (28%). Among spine tumor LTS (n = 42), nearly half reported moderate-to-severe weakness, pain, fatigue, and numbness/tingling, with 72% experiencing activity-related interference. Severe anxiety, depression, and cognitive symptoms were reported in up to 23% of the sample. Brain tumor LTS at higher risk for severe symptoms were more likely to be young, unemployed, and have poor KPS (Karnofsky Performance Status), whereas high symptom-risk spinal cord tumor LTS had poor KPS and received any tumor treatment.

Conclusions
Findings indicate LTS fall into distinct cohorts with no significant symptoms or very high symptom burden, regardless of tumor grade or mutational profile. These LTS data demonstrate the need for survivorship care programs and future studies to explore the symptom trajectory of all CNS tumor patients for prevention and early interventions.
R-CHOP Chemotherapy for Disseminated Mycobacterium avium Complex Disease due to Anti-Interferon-Gamma Autoantibodies: A Case Report
Authors: Uno Shunsuke , Uehara Eisuke , Kimura Toshiki , Sakagami Takuro , Namkoong Ho , Uchida Sho , Uwamino Yoshifumi , Hasegawa Naoki 
Published: April 2021

Abstract
A 77-year-old Japanese man with disseminated Mycobacterium avium complex (MAC) disease due to anti-interferon-gamma autoantibodies received rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP) chemotherapy because of non-Hodgkin lymphoma complication. The hepatobiliary nodules due to MAC resolved with R-CHOP and multidrug antimycobacterial treatment. R-CHOP could serve as an alternative adjunctive therapy for patients with anti-interferon-gamma autoantibodies.
Species limits and taxonomy in birds
Authors: Winker Kevin , Rasmussen Pamela C 
Published: April 2021

AbstractDespite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often remain contentious. This is true even among practitioners of a single species concept and is inevitable owing to the continuous nature of the speciation process, our incomplete and changing understanding of individual cases, and differing interpretations of available data. This issue of Ornithology brings together several papers on species limits, some more theoretical and general, and others case studies of specific taxa. These are viewed primarily through the lens of the biological species concept (BSC), by far the most widely adopted species concept in influential ornithological works. The more conceptual contributions focus on the importance of the integrative approach in species delimitation; the importance of considering selection with the increasing use of genomic data; examinations of the effectiveness of the Tobias et al. character-scoring species limits criteria; a review of thorny issues in species delimitation using examples from Australo-Papuan birds; and a review of the process of speciation that addresses how population divergence poses challenges. Case studies include population genomics of the American Kestrel (Falco sparverius); an integrative taxonomic analysis of Graceful Prinia (Prinia gracilis) that suggests two species are involved; and a reevaluation of species limits in Caribbean Sharp-shinned Hawk (Accipiter striatus) taxa.