bluuebunny/crossref_metadata_2025_split huggingface dataset:
TLDR: time lag/delay reconstructor
Authors: Anderson M D , Baron F , Bentz M C 
Published: May 2021

ABSTRACT
We present the time lag/delay reconstructor (TLDR), an algorithm for reconstructing velocity delay maps in the maximum a posteriori framework for reverberation mapping. Reverberation mapping is a tomographical method for studying the kinematics and geometry of the broad-line region of active galactic nuclei at high spatial resolution. Leveraging modern image reconstruction techniques, including total variation and compressed sensing, TLDR applies multiple regularization schemes to reconstruct velocity delay maps using the alternating direction method of multipliers. Along with the detailed description of the TLDR algorithm we present test reconstructions from TLDR applied to synthetic reverberation mapping spectra as well as a preliminary reconstruction of the Hβ feature of Arp 151 from the 2008 Lick Active Galactic Nuclei Monitoring Project.
Morphological classification of compact and extended radio galaxies using convolutional neural networks and data augmentation techniques
Authors: Maslej-Krešňáková Viera , El Bouchefry Khadija , Butka Peter 
Published: May 2021

ABSTRACT
Machine-learning techniques have been increasingly used in astronomical applications and have proven to successfully classify objects in image data with high accuracy. The current work uses archival data from the Faint Images of the Radio Sky at Twenty Centimeters (FIRST) to classify radio galaxies into four classes: Fanaroff–Riley Class I (FRI), Fanaroff–Riley Class II (FRII), Bent-Tailed (BENT), and Compact (COMPT). The model presented in this work is based on Convolutional Neural Networks (CNNs). The proposed architecture comprises three parallel blocks of convolutional layers combined and processed for final classification by two feed-forward layers. Our model classified selected classes of radio galaxy sources on an independent testing subset with an average of 96 per cent for precision, recall, and F1 score. The best selected augmentation techniques were rotations, horizontal or vertical flips, and increase of brightness. Shifts, zoom, and decrease of brightness worsened the performance of the model. The current results show that model developed in this work is able to identify different morphological classes of radio galaxies with a high efficiency and performance.
Local Volume Late-Type Galaxies with an Extreme Ratio of Hα-to-FUV Star-Formation Rates
Authors: Karachentsev I D , Kaisina E I , Kaisin S S 
Published: May 2021

Abstract
Using a currently most representative sample of 477 late-type galaxies within 11 Mpc of the Milky Way with measured star-formation rates (SFRs) from the far ultraviolet (FUV) and Hα emission line fluxes, we select galaxies with the extreme ratios: SFR(Hα)/SFR(FUV) &gt; 2 and SFR(Hα)/SFR(FUV) &lt; 1/20. Each subsample amounts to ∼5% of the total number and consists of dwarf galaxies with the stellar masses M*/M⊙ = (5.5 − 9.5) dex. In spite of a huge difference in their SFR(Hα) activity on a scale of ∼10 Myr, the temporarily “excited” and temporarily “quiescent” galaxies follow one and the same relation between SFR(FUV) and M* on a scale of ∼100 Myr. Their average specific star-formation rate log [SFR(FUV)/M*] = −10.1 ± 0.1 (yr−1) coinsides with the Hubble parameter log (H0) = −10.14 (yr−1). On a scale of t ∼ 10 Myr, variations of SFR have a moderate flash amplitude of less than 1 order above the main-sequence and a fading amplitude to 2 orders below the average level. In general, both temporarily excited and temporarily quiescent galaxies have almost similar gas fractions as normal main-sequence galaxies, being able to maintain the current rate of star-formation on another Hubble time scale. Ranging the galaxies according to the density contrast produced by the nearest massive neighbor exhibits only a low average excess of SFR caused by tidal interactions.
Modeling of two CoRoT solar analogues constrained by seismic and spectroscopic analysis
Authors: Castro M , Baudin F , Benomar O , Samadi R , Morel T , Barban C , do Nascimento J D , Lebreton Y , Boumier P , Marques J P , da Costa J S 
Published: May 2021

ABSTRACT
Solar analogues are important stars to study for understanding the properties of the Sun. Combined with seismic and spectroscopic analysis, evolutionary modelling becomes a powerful method to characterize stellar intrinsic parameters, such as mass, radius, metallicity and age. However, these characteristics, relevant for other aspects of astrophysics or exoplanetary system physics, for example, are difficult to obtain with high precision and/or accuracy. The goal of this study is to characterize the two solar analogues, HD 42618 and HD 43587, observed by CoRoT. In particular, we aim to infer their precise mass, radius and age, using evolutionary modelling constrained by spectroscopic, photometric and seismic analysis. These stars show evidence of being older than the Sun but with a relatively large lithium abundance. We present the seismic analysis of HD 42618, and the modelling of the two solar analogues, HD 42618 and HD 43587 using the cestam stellar evolution code. Models were computed to reproduce the spectroscopic (effective temperature and metallicity) and seismic (mode frequency) data, and the luminosity of the stars, based on Gaia parallaxes. We infer very similar values of mass and radius for both stars compared with the literature, within the uncertainties, and we reproduce correctly the seismic constraints. The modelling shows that HD 42618 is slightly less massive and older than the Sun, and that HD 43587 is more massive and older than the Sun, in agreement with previous results. The use of chemical clocks improves the reliability of our age estimates.
The origin of the orbital parameter distribution of merging haloes
Authors: Benson Andrew J 
Published: May 2021

ABSTRACT
We describe a simple model that explains the qualitative and (approximate) quantitative features of the distribution of orbital velocities of merging pairs of dark matter haloes. Our model considers a primary dark matter halo as a perturber in a background of secondary haloes with velocities described by linear theory. By evaluating the ensemble of secondary haloes on orbits within the perturbing halo’s ‘loss cone’ we derive the distribution of orbital parameters of these captured haloes. This model is able provide qualitative explanations for the features of this distribution as measured from N-body simulations, and is in approximate quantitative agreement with those measurements. As the velocity dispersion of the background haloes is larger on smaller scales our model predicts an overall increase in the characteristic velocities of merging haloes, relative to the virial velocities of those haloes, in lower mass systems. Our model also provides a simple explanation for the measured independence of the orbital velocity distribution function on redshift when considered at fixed peak height. By connecting the orbital parameter distribution to the underlying power spectrum our model also allows for estimates to be made of the effect of modifying that power spectrum, for example by including a truncation at large wavenumber. For plausible warm dark matter models, we find that this truncation has only a small effect on the predicted distributions.
Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions
Authors: Yu Dan , Horton John R , Yang Jie , Hajian Taraneh , Vedadi Masoud , Sagum Cari A , Bedford Mark T , Blumenthal Robert M , Zhang Xing , Cheng Xiaodong 
Published: May 2021

Abstract
MettL3-MettL14 methyltransferase complex has been studied widely for its role in RNA adenine methylation. This complex is also recruited to UV- and X-ray exposed DNA damaged sites, and its methyltransfer activity is required for subsequent DNA repair, though in theory this could result from RNA methylation of short transcripts made at the site of damage. We report here that MettL3-MettL14 is active in vitro on double-stranded DNA containing a cyclopyrimidine dimer – a major lesion of UV radiation-induced products – or an abasic site or mismatches. Furthermore, N6-methyladenine (N6mA) decreases misincorporation of 8-oxo-guanine (8-oxoG) opposite to N6mA by repair DNA polymerases. When 8-oxoG is nevertheless incorporated opposite N6mA, the methylation inhibits N6mA excision from the template (correct) strand by the adenine DNA glycosylase (MYH), implying that the methylation decreases inappropriate misrepair. Finally, we observed that the N6mA reader domain of YTHDC1, which is also recruited to sites of DNA damage, binds N6mA that is located across from a single-base gap between two canonical DNA helices. This YTHDC1 complex with a gapped duplex is structurally similar to DNA complexes with FEN1 and GEN1 – two members of the nuclease family that act in nucleotide excision repair, mismatch repair and homologous recombination, and which incise distinct non-B DNA structures. Together, the parts of our study provide a plausible mechanism for N6mA writer and reader proteins acting directly on lesion-containing DNA, and suggest in vivo experiments to test the mechanisms involving methylation of adenine.
Borrowing in Music
Authors: Sallis Friedemann 
Published: May 2021

Abstract
This text examines the idea and practice of musical borrowing in the composition of art music in two distinct historical contexts: the age of music conceived as oration (ca. 1600–1800) and the age of the strong work concept (ca. 1800 to the present). It shows that the idea of musical borrowing is an evolving, historical concept that needs to be examined contextually in order to understand what it meant in the period within which the music in question was composed, as well as for the specific composer. The text also briefly examines related topics: authorship, plagiarism, imitation vs. emulation, music conceived as oration, and the strong work concept.
People With Hematological Malignancies Treated With Bone Marrow Transplantation Have Improved Function, Quality of Life, and Fatigue Following Exercise Intervention: A Systematic Review and Meta-Analysis
Authors: Abo Shaza , Denehy Linda , Ritchie David , Lin Kuan-Yin , Edbrooke Lara , McDonald Cassie , Granger Catherine L 
Published: May 2021

Abstract

Objective
For people with hematological malignancies treated with bone marrow transplantation (BMT), this systematic review aimed to identify, evaluate, and synthesize the evidence examining the effect of exercise training on the outcomes of exercise capacity, health-related quality of life (HRQoL), and hospital length of stay (LOS) and to identify any difference in the effect on people treated with allogeneic versus autologous transplantation.

Methods
Five electronic databases were systematically searched from inception to December 5, 2020. Prospective studies with a comparator group, with or without randomization, were included if they investigated the effects of an exercise intervention compared with usual care or another intervention in adults who had a hematological malignancy and were undergoing BMT. Primary outcomes of interest were functional exercise capacity and HRQoL; secondary outcomes included strength, fatigue, hospital LOS, and feasibility. Only randomized controlled trials were included in the meta-analyses. Risk of bias was evaluated using the Physiotherapy Evidence Database or Newcastle-Ottawa Scale; the quality of evidence for meta-analyses was assessed using the Grading of Recommendations Assessment, Development and Evaluation approach.

Results
Twenty-four randomized controlled trials and 3 prospective nonrandomized experimental trials were included (n = 2432). There was moderate-quality evidence that exercise improves functional exercise capacity (mean difference [MD] = 29 m; 95% CI = 12.59 to 45.4), global HRQoL (MD = 3.38 points; 95% CI = 0.37 to 6.39), and fatigue (MD = 2.52 points; 95% CI = 0.42 to 4.63) and low-quality evidence for reduced hospital LOS (MD = 2.07 days; 95% CI = 0.43 to 3.72). These effects were more pronounced in recipients of allogeneic transplantation. No serious adverse events were associated directly with exercise in the included studies.

Conclusion
Exercise is safe and improves outcomes, including functional exercise capacity, HRQoL, and hospital LOS in adults undergoing BMT.

Impact
The results of this systematic review support the implementation of exercise programs in adults undergoing BMT, particularly recipients of allogeneic transplantation.
The role of TNFRSF11B in development of osteoarthritic cartilage
Authors: Rodríguez Ruiz Alejandro , Tuerlings Margo , Das Ankita , Coutinho de Almeida Rodrigo , Suchiman H Eka D , Nelissen Rob G H H , Ramos Yolande F M , Meulenbelt Ingrid 
Published: May 2021

Abstract

Objectives
OA is a complex genetic disease with different risk factors contributing to its development. One of the genes, TNFRSF11B, previously identified with gain-of-function mutation in a family with early-onset OA with chondrocalcinosis, is among the highest upregulated genes in lesioned OA cartilage (RAAK-study). Here, we determined the role of TNFRSF11B overexpression in development of OA.

Methods
Human primary articular chondrocytes (9 donors RAAK study) were transduced using lentiviral particles with or without TNFRSF11B. Cells were cultured for 1 week in a 3 D in-vitro chondrogenic model. TNFRSF11B overexpression was confirmed by RT-qPCR, immunohistochemistry and ELISA. Effects of TNFRSF11B overexpression on cartilage matrix deposition, matrix mineralization, and genes highly correlated to TNFRSF11B in RNA-sequencing dataset (r &gt;0.75) were determined by RT-qPCR. Additionally, glycosaminoglycans and collagen deposition were visualized with Alcian blue staining and immunohistochemistry (COL1 and COL2).

Results
Overexpression of TNFRSF11B resulted in strong upregulation of MMP13, COL2A1 and COL1A1. Likewise, mineralization and osteoblast characteristic markers RUNX2, ASPN and OGN showed a consistent increase. Among 30 genes highly correlated to TNFRSF11B, expression of only eight changed significantly, with BMP6 showing the highest increase (9-fold) while expression of RANK and RANKL remained unchanged indicating previously unknown downstream pathways of TNFRSF11B in cartilage.

Conclusion
Results of our 3D in vitro chondrogenesis model indicate that upregulation of TNFRSF11B in lesioned OA cartilage may act as a direct driving factor for chondrocyte to osteoblast transition observed in OA pathophysiology. This transition does not appear to act via the OPG/RANK/RANKL triad common in bone remodeling.
Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden
Authors: Jönsson Elias , Ljung Lotta , Norrman Eva , Freyhult Eva , Ärlestig Lisbeth , Dahlqvist Johanna , Rantapää-Dahlqvist Solbritt 
Published: May 2021

Abstract

Objectives
Pulmonary manifestations in RA are common comorbidities. Interstitial lung disease (ILD), both idiopathic and in RA, has been associated with several genetic variants. We assessed pulmonary fibrosis (PF) in an inception cohort of RA patients in relation to genetic variants and disease-related factors.

Methods
A total of 1466 early RA patients were consecutively included and followed prospectively from the index date until death or 31 December 2016. Clinical and laboratory data and treatment were continuously registered according to the Swedish Rheumatology Quality Register. DNA was available from 1184 patients and 571 151 genome-wide single-nucleotide polymorphisms (SNPs) were analysed. Thirteen identified genetic variants were extracted. At follow-up, the patients answered a questionnaire regarding disease progression and lung involvement that was validated by reviewing medical records and analysing radiological examinations.

Results
The prevalence of PF was 5.6% and the annualized incidence rate was 5.0/1000 (95% CI 3.80, 6.54). Four SNPs were associated with PF in RA: rs35705950 [MUC5B; OR 2.5 (95% CI 1.5, 4.0), adjusted P-value = 0.00016, q-value = 0.0021]; rs111521887 [TOLLIP; OR 1.9 (95% CI 1.3, 2.8), adjusted P-value = 0.0014, q-value = 0.0092]; rs2609255 [FAM13A; OR 1.7 (95% CI 1.1, 2.5), adjusted P-value = 0.013, q-value = 0.055] and rs2736100 [TERT; OR 1.5 (95% CI 1.0, 2.2), adjusted P-value = 0.046, q-value = 0.15]. Older age and RF positivity were associated with increased risk, while MTX treatment was associated with a lower risk of PF.

Conclusions
Development of PF in an inception cohort of RA patients was associated with 4 of 12 ILD risk genes. RA-related factors except for age at diagnosis and RF positivity were of limited importance in PF development.
Evaluating the Interrater Agreement and Acceptability of a New Reference Tool for Assessing Respiratory Rate in Children under Five with Cough and/or Difficulty Breathing
Authors: Stratil Ann-Sophie , Ward Charlotte , Habte Tedila , Maurel Alice , Antson Max , Naydenova Elina , Baker Kevin 
Published: May 2021

Abstract

Background
Manual assessment of respiratory rate (RR) in children is unreliable, but remains the main method to diagnose pneumonia in low-resource settings. While automated RR counters offer a potential solution, there is currently no gold standard to validate these diagnostic aids. A video-based reference tool is proposed that allows users to annotate breaths and distortions including movement periods, allowing the exclusion of distortions from the computation of RR measures similar to how new diagnostic aids account for distortions automatically. This study evaluated the interrater agreement and acceptability of the new reference tool.

Methods
Annotations were based on previously recorded reference videos of children under five years old with cough and/or difficulty breathing (n = 50). Five randomly selected medical experts from a panel of ten annotated each video. RR measures (breaths per minute, bpm) were computed as the number of annotated certain breaths divided by the length of calm periods after removing annotated distorted periods.

Results
Reviewers showed good interrater agreement on continuous RR {standard error of measurement (SEM) [4.8 (95%CI 4.4–5.3)]} and substantial agreement on classification of fast breathing (Fleiss kappa, κ 0.71). Agreement was lowest in the youngest age group [&lt; 2 months: SEM 6.2 (5.4–7.4) bpm, κ 0.48; 2–11 months: 4.7 (4.0–5.8) bpm, κ 0.84; 12–59 months: 2.6 (2.2–3.1) bpm, κ 0.8]. Reviewers found the functionalities of the tool helpful in annotating breaths, but remained uncertain about the validity of their annotations.

Conclusions
Before the new tool can be considered a reference standard for RR assessments, interrater agreement in children younger than 2 months must be improved.
Seeing Complexity: Cultural Historical Activity Theory (CHAT) As a Lens for Shared Decision Making
Authors: Witkop Catherine T. , Maggio Lauren A. , Harvey Emily J. , Torre Dario M. 
Published: May 2021

Shared decision making, a collaborative approach between patient and provider that considers the patient’s values and preferences in addition to the scientific evidence, is a complex clinical activity that has not realized its full potential. Gaps in education and training have been cited as barriers to shared decision making, and evidence is inconsistent on effective educational interventions. Because individual agents with their own social and behavioral contexts co-construct a shared decision, the educational approach may need to consider the role of patient agency and sociocultural influences.
To address the inherent complexity in shared decision making, the authors identified cultural historical activity theory (CHAT) as a framework for analysis. Although certainly not the only relevant theory, CHAT offers an appropriate lens through which the multivoiced nature of shared decision making can be more clearly appreciated. In this article, the authors demonstrate the application of CHAT as a lens for researchers and educators to examine the complexity of shared decision making.
The fictitious case presented in this article describes the use of CHAT with a patient who experiences 2 clinical encounters; during the second, shared decision making takes place. Elements of the case are threaded through the article, demonstrating a sample analysis of the interacting activity systems of the patient and physician and highlighting inherent tensions and contradictions. The authors propose CHAT as a tool for future research around the role of agency in shared decision making and other complex topics and as a framework for design of novel instructional strategies. Although not applicable to all topics and settings, CHAT has significant potential within health professions education.
Perinatal OUD Treatment Provider Understandings of Rural Patients’ Experiences
Authors: Leiner Catherine , Antono Brian , Ostrach Bayla 
Published: May 2021

Objectives:
To present perspectives of substance use treatment providers offering perinatal opioid use disorder (OUD) treatment in a largely rural, Appalachian region. To demonstrate the extent to which providers sought to understand their patients’ experiences accessing treatment and how this understanding informed providers’ approach to offering patient-centered care.

Methods:
A qualitative study combining semi-structured interviews and participant-observation with perinatal substance use treatment providers, conducted within a comprehensive program. Using purposive and opportunistic sampling with key informants (n = 10), a saturation sample was achieved. Data were analyzed using modified Grounded Theory.

Results:
Perinatal substance use treatment providers had a good understanding of their patients’ experiences seeking treatment for opioid use disorder, including being aware of obstacles patients encountered. This understanding allowed providers to better address patients’ needs in and out of the clinic.

Conclusions:
Participants demonstrated a good understanding of what their largely rural, Appalachian patients experienced when attempting to access perinatal OUD treatment. This understanding may enable more patient-centered care.
Intraparenchymal Neuromonitoring of Cerebral Fat Embolism Syndrome
Authors: Hoiland Ryan Leo , Griesdale Donald E. , Gooderham Peter , Sekhon Mypinder S. 
Published: May 2021

Objectives:
We aimed to characterize the cerebrovascular physiology of cerebral fat embolism using invasive multimodal neuromonitoring.

Data Sources:
ICU, Vancouver General Hospital, Vancouver, BC, Canada.

Study Selection:
Case report.

Data Extraction:
Patient monitoring software (ICM+, Cambridge, United Kingdom), clinical records, and surgical records.

Data Synthesis:
None.

Conclusions:
Our integrated assessment of the cerebrovascular physiology of fat embolism syndrome provides a physiologic basis to investigate the importance of augmenting mean arterial pressure to optimize cerebral oxygen delivery for the mitigation of long-term neurologic ischemic sequelae of cerebral fat embolism.