bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radio/X-ray correlations and variability in the X-ray binary LS I +61°303
Authors: Sharma R , Massi M , Chernyakova M , Malyshev D , Perrott Y C , Kraus A , Dzib S A , Jaron F , Cantwell T M 
Published: November 2020

ABSTRACT
The high-mass X-ray binary LS I +61°303 exhibits variability in its radio and X-ray emissions, ranging from minute to hour time-scales. At such short time-scales, not much is known about the possible correlations between these two emissions from this source, which might offer hints to their origin. Here, we study the relationship between these emissions using simultaneous X-ray and radio monitoring. We present new radio observations using the Arcminute Microkelvin Imager Large Array telescope at two frequency bands, 13–15.5 and 15.5–18 GHz. We also describe new X-ray observations performed using the XMM–Newton telescope. These X-ray and radio observations overlapped for five hours. We find for the first time that the radio and X-ray emission are correlated up to 81${{\ \rm per\ cent}}$ with their few per cent variability correlated up to 40 ${{\ \rm per\ cent}}$. We discuss possible physical scenarios that produces the observed correlations and variability in the radio and X-ray emission of LS I +61°303.
The dual nature of blazar fast variability: Space and ground observations of S5 0716+714
Authors: Raiteri C M , Villata M , Carosati D , Benítez E , Kurtanidze S O , Gupta A C , Mirzaqulov D O , D’Ammando F , Larionov V M , Pursimo T , Acosta-Pulido J A , Baida G V , Balmaverde B , Bonnoli G , Borman G A , Carnerero M I , Chen W-P , Dhiman V , Di Maggio A , Ehgamberdiev S A , Hiriart D , Kimeridze G N , Kurtanidze O M , Lin C S , Lopez J M , Marchini A , Matsumoto K , Mujica R , Nakamura M , Nikiforova A A , Nikolashvili M G , Okhmat D N , Otero-Santos J , Rizzi N , Sakamoto T , Semkov E , Sigua L A , Stiaccini L , Troitsky I S , Tsai A L , Vasilyev A A , Zhovtan A V 
Published: November 2020

ABSTRACT
Blazar S5 0716+714 is well-known for its short-term variability, down to intraday time-scales. We here present the 2-min cadence optical light curve obtained by the TESS space telescope in 2019 December–2020 January and analyse the object fast variability with unprecedented sampling. Supporting observations by the Whole Earth Blazar Telescope Collaboration in B, V, R, and I bands allow us to investigate the spectral variability during the TESS pointing. The spectral analysis is further extended in frequency to the UV and X-ray bands with data from the Neil Gehrels Swift Observatory. We develop a new method to unveil the shortest optical variability time-scales. This is based on progressive de-trending of the TESS light curve by means of cubic spline interpolations through the binned fluxes, with decreasing time bins. The de-trended light curves are then analysed with classical tools for time-series analysis (periodogram, autocorrelation, and structure functions). The results show that below 3 d there are significant characteristic variability time-scales of about 1.7, 0.5, and 0.2 d. Variability on time-scales $\lesssim 0.2$ d is strongly chromatic and must be ascribed to intrinsic energetic processes involving emitting regions, likely jet substructures, with dimension less than about 10−3 pc. In contrast, flux changes on time-scales $\gtrsim 0.5$ d are quasi-achromatic and are probably due to Doppler factor changes of geometric origin.
Sparse Bayesian mass-mapping with uncertainties: Full sky observations on the celestial sphere
Authors: Price M A , McEwen J D , Pratley L , Kitching T D 
Published: November 2020

ABSTRACT
To date weak gravitational lensing surveys have typically been restricted to small fields of view, such that the flat-sky approximation has been sufficiently satisfied. However, with Stage IV surveys (e.g. LSST and Euclid) imminent, extending mass-mapping techniques to the sphere is a fundamental necessity. As such, we extend the sparse hierarchical Bayesian mass-mapping formalism presented in previous work to the spherical sky. For the first time, this allows us to construct maximum a posteriori spherical weak lensing dark-matter mass-maps, with principled Bayesian uncertainties, without imposing or assuming Gaussianty. We solve the spherical mass-mapping inverse problem in the analysis setting adopting a sparsity promoting Laplace-type wavelet prior, though this theoretical framework supports all log-concave posteriors. Our spherical mass-mapping formalism facilitates principled statistical interpretation of reconstructions. We apply our framework to convergence reconstruction on high resolution N-body simulations with pseudo-Euclid masking, polluted with a variety of realistic noise levels, and show a significant increase in reconstruction fidelity compared to standard approaches. Furthermore, we perform the largest joint reconstruction to date of the majority of publicly available shear observational data sets (combining DESY1, KiDS450, and CFHTLens) and find that our formalism recovers a convergence map with significantly enhanced small-scale detail. Within our Bayesian framework we validate, in a statistically rigorous manner, the community’s intuition regarding the need to smooth spherical Kaiser-Squires estimates to provide physically meaningful convergence maps. Such approaches cannot reveal the small-scale physical structures that we recover within our framework.
dbCNS: A New Database for Conserved Noncoding Sequences
Authors: Inoue Jun , Saitou Naruya 
Published: November 2020

Abstract
We developed dbCNS (http://yamasati.nig.ac.jp/dbcns), a new database for conserved noncoding sequences (CNSs). CNSs exist in many eukaryotes and are assumed to be involved in protein expression control. Version 1 of dbCNS, introduced here, includes a powerful and precise CNS identification pipeline for multiple vertebrate genomes. Mutations in CNSs may induce morphological changes and cause genetic diseases. For this reason, many vertebrate CNSs have been identified, with special reference to primate genomes. We integrated ∼6.9 million CNSs from many vertebrate genomes into dbCNS, which allows users to extract CNSs near genes of interest using keyword searches. In addition to CNSs, dbCNS contains published genome sequences of 161 species. With purposeful taxonomic sampling of genomes, users can employ CNSs as queries to reconstruct CNS alignments and phylogenetic trees, to evaluate CNS modifications, acquisitions, and losses, and to roughly identify species with CNSs having accelerated substitution rates. dbCNS also produces links to dbSNP for searching pathogenic single-nucleotide polymorphisms in human CNSs. Thus, dbCNS connects morphological changes with genetic diseases. A test analysis using 38 gnathostome genomes was accomplished within 30 s. dbCNS results can evaluate CNSs identified by other stand-alone programs using genome-scale data.
UniPath: a uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles
Authors: Chawla Smriti , Samydurai Sudhagar , Kong Say Li , Wu Zhengwei , Wang Zhenxun , TAM Wai Leong , Sengupta Debarka , Kumar Vibhor 
Published: November 2020

Abstract
Recent advances in single-cell open-chromatin and transcriptome profiling have created a challenge of exploring novel applications with a meaningful transformation of read-counts, which often have high variability in noise and drop-out among cells. Here, we introduce UniPath, for representing single-cells using pathway and gene-set enrichment scores by a transformation of their open-chromatin or gene-expression profiles. The robust statistical approach of UniPath provides high accuracy, consistency and scalability in estimating gene-set enrichment scores for every cell. Its framework provides an easy solution for handling variability in drop-out rate, which can sometimes create artefact due to systematic patterns. UniPath provides an alternative approach of dimension reduction of single-cell open-chromatin profiles. UniPath's approach of predicting temporal-order of single-cells using their pathway enrichment scores enables suppression of covariates to achieve correct order of cells. Analysis of mouse cell atlas using our approach yielded surprising, albeit biologically-meaningful co-clustering of cell-types from distant organs. By enabling an unconventional method of exploiting pathway co-occurrence to compare two groups of cells, our approach also proves to be useful in inferring context-specific regulations in cancer cells. Available at https://reggenlab.github.io/UniPathWeb/.
High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19
Authors: Pandey Utsav , Yee Rebecca , Shen Lishuang , Judkins Alexander R , Bootwalla Moiz , Ryutov Alex , Maglinte Dennis T , Ostrow Dejerianne , Precit Mimi , Biegel Jaclyn A , Bender Jeffrey M , Gai Xiaowu , Dien Bard Jennifer 
Published: November 2020

AbstractBackgroundThe full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children.MethodsWhole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity.ResultsHigher viral load was detected in symptomatic patients (P = .0007) and in children &lt;5 years old (P = .0004). Genomic analysis revealed a mean pairwise difference of 10.8 single nucleotide variants (SNVs), and the majority (55.4%) of SNVs led to an amino acid change in the viral proteins. The D614G mutation in the spike protein was present in 99.3% of the isolates. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. Phylogenetic clade 20C was associated with severe cases of COVID-19 (odds ratio, 6.95; P = .0467). Epidemiological investigation revealed major representation of 3 of 5 major Nextstrain clades (20A, 20B, and 20C) consistent with multiple introductions of SARS-CoV-2 in Southern California.ConclusionsGenomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.
The Gender Earnings Gap in the Gig Economy: Evidence from over a Million Rideshare Drivers
Authors: Cook Cody , Diamond Rebecca , Hall Jonathan V , List John A , Oyer Paul 
Published: November 2020

Abstract
The growth of the “gig” economy generates worker flexibility that, some have speculated, will favour women. We explore this by examining labour supply choices and earnings among more than a million rideshare drivers on Uber in the U.S. We document a roughly 7% gender earnings gap amongst drivers. We show that this gap can be entirely attributed to three factors: experience on the platform (learning-by-doing), preferences and constraints over where to work (driven largely by where drivers live and, to a lesser extent, safety), and preferences for driving speed. We do not find that men and women are differentially affected by a taste for specific hours, a return to within-week work intensity, or customer discrimination. Our results suggest that, in a “gig” economy setting with no gender discrimination and highly flexible labour markets, women’s relatively high opportunity cost of non-paid-work time and gender-based differences in preferences and constraints can sustain a gender pay gap.
Significance of PR3-ANCA positivity in eosinophilic granulomatosis with polyangiitis (Churg-Strauss)
Authors: Papo Matthias , Sinico Renato A. , Teixeira Vítor , Venhoff Nils , Urban Maria-Letizia , Iudici Michele , Mahrhold Juliane , Locatelli Francesco , Cassone Giulia , Schiavon Franco , Seeliger Benjamin , Neumann Thomas , Kroegel Claus , Groh Matthieu , Marvisi Chiara , Samson Maxime , Barba Thomas , Jayne David , Troilo Arianna , Thiel Jens , Hellmich Bernhard , Monti Sara , Montecucco Carlomaurizio , Salvarani Carlo , Kahn Jean-Emmanuel , Bonnotte Bernard , Durel Cécile-Audrey , Puéchal Xavier , Mouthon Luc , Guillevin Loïc , Emmi Giacomo , Vaglio Augusto , Terrier Benjamin ,   the French Vasculitis Study Group and the EGPA European Study Group
Published: November 2020

Abstract

Objectives
Only a third of patients with eosinophilic granulomatosis with polyangiitis (EGPA) are ANCA-positive, mainly directed against MPO. ANCA directed against PR3 are rarely found in EGPA. We aimed to examine the significance of PR3-ANCA in EGPA.

Methods
We set up a retrospective European multicentre cohort including 845 patients. Baseline characteristics and outcomes were analysed and compared according to ANCA status.

Results
ANCA status was available for 734 patients: 508 (69.2%) ANCA-negative, 210 (28.6%) MPO-ANCA and 16 (2.2%) PR3-ANCA. At baseline, PR3-ANCA patients, compared with those with MPO-ANCA and ANCA-negative, less frequently had active asthma (69% vs 91% and 93%, P = 0.003, respectively) and peripheral neuropathy (31% vs 71% and 47%, P &lt; 0.0001), more frequently had cutaneous manifestations (63% vs 38% and 34%, P = 0.03) and pulmonary nodules (25% vs 10% and 8%, P = 0.046), and lower median eosinophil count (1450 vs 5400 and 3224/mm3, P &lt; 0.0001). Vasculitis relapse-free survival was shorter for PR3-ANCA (hazard ratio 6.05, P = 0.005) and MPO-ANCA patients (hazard ratio 1.88, P = 0.0002) compared with ANCA-negative patients.

Conclusion
PR3-ANCA EGPA patients differ from those with MPO-ANCA and negative ANCA, and share clinical features with granulomatosis with polyangiitis. This suggests that PR3-ANCA EGPA could be a particular form of PR3-ANCA-associated vasculitis.
Corporate Transfers for Dual-Career Couples: From GenderedTenkinto Gender-Equal Negotiations?
Authors: FUJITA Noriko 
Published: November 2020

AbstractThis qualitative-research-based article discusses corporate transfers of dual-career couples in large Japanese firms. In Japan’s internal labour market, inter-regional transfers, or tenkin, are de rigueur in many companies for purposes of training and promotion of long-term employees. Their implementation is often taken for granted because of the gendered assumption that only men are subject to tenkin. Women, who take responsibility in domestic roles, are not able to accept tenkin. Rather, they are either exempted from tenkin regardless of their wishes or forced to remain in secondary positions that require no tenkin. This gendered division of labour in tenkin has hampered women’s promotion in Japanese workplaces and hindered dual-career couples from achieving dual careers through tenkin. Using Acker’s (1990) theory of gendered organisations and Nemoto’s (2016) study of gendered practices in Japanese firms, this article elucidates the processes by which these cultural, gendered corporate transfers (a) reproduce gendered organisations, (b) are changing from dictates to negotiations in some companies where female workers are given more opportunities alongside intensification of the firms’ global competition, but (c) nevertheless continue to be in tension with dual-career families in contemporary Japan. To make a dual-career-couple model mainstream, the labour market structure that views corporate transfers as an absolute necessity needs radical change.
Automatic COVID-19 Detection from chest radiographic images using Convolutional Neural Network
Authors: Asif Sohaib , Amjad Kamran 
Published: November 2020

AbstractThe global pandemic of the novel coronavirus that started in Wuhan, China has affected more than 50 million people worldwide and caused more than 1263,787 tragic deaths. To date, the COVID-19 virus is still spreading and affecting thousands of people. The main problem with testing for COVID-19 is that there are very few test kits available for a large number of affected or suspicious individuals. This leads to the need for automatic detection systems that use artificial intelligence. Deep learning is one of the most powerful AI tools available, so we recommend creating a convolutional neural network to detect COVID-19 positive patients from chest radiographs. According to previous studies, lung X-rays of COVID-19-positive patients show obvious characteristics, so this is a reliable method for testing patients, because X-ray examination of suspicious patients is easier than rt-PCR. Our model has been trained with 820 chest radiographic images (excluding data augmentation) collected from 3 databases, with a classification accuracy of 99.45% (training accuracy of 99.70%), sensitivity of 99.30% and specificity of 99.40 %, proved that our model has become a reliable COVID-19 detector.
Multifaceted Brain Age Measures Reveal Premature Brain Aging and Associations with Clinical Manifestations in Schizophrenia
Authors: Chen Chang-Le , Hwang Tzung-Jeng , Tung Yu-Hung , Yang Li-Ying , Hsu Yung-Chin , Liu Chih-Min , Hwu Hai-Gwo , Lin Yi-Tin , Hsieh Ming-Hsien , Liu Chen-Chung , Chien Yi-Ling , Isaac Tseng Wen-Yih 
Published: November 2020

AbstractSchizophrenia is a mental disorder with extensive alterations of cerebral gray matter (GM) and white matter (WM) and is known to have advanced brain aging. However, how the structural alterations contribute to brain aging and how brain aging is related to clinical manifestations remain unclear. Here, we estimated the bias-free multifaceted brain age measures in patients with schizophrenia (N=147) using structural and diffusion magnetic resonance imaging data. We calculated feature importance to estimate regional contributions to advanced brain aging in schizophrenia. Furthermore, regression analyses were conducted to test the associations of brain age with illness duration, onset age, symptom severity, and intelligence quotient. The patients with schizophrenia manifested significantly old-appearing brain age (P<.001) in both GM and WM compared with the healthy norm. The GM and WM structures contributing to the advanced brain aging were mostly located in the frontal and temporal lobes. Among the features, the GM volume and mean diffusivity of WM were most sensitive to the neuropathological changes in schizophrenia. The WM brain age index was associated with a negative symptom score (P=.006), and the WM and multimodal brain age indices demonstrated negative associations with the intelligence quotient (P=.037; P=.040, respectively). Moreover, brain age exhibited associations with the onset age (P=.006) but no associations with the illness duration, which may support the early-hit non-progression hypothesis. In conclusion, our study reveals the structural underpinnings of premature brain aging in schizophrenia and its clinical significance. The brain age measures might be a potentially informative biomarker for stratification and prognostication of patients with schizophrenia.
Predictors of adverse outcome in patients with suspected COVID-19 managed in a ‘virtual hospital’ setting: a cohort study
Authors: Francis Nick A , Stuart Beth , Knight Matthew , Vancheeswaran Rama , Oliver Charles , Willcox Merlin , Barlow Andrew , Moore Michael 
Published: November 2020

ABSTRACTObjectiveIdentify predictors of adverse outcome in a Virtual Hospital (VH) setting for COVID 19.DesignReal-world prospective observational study.SettingVirtual hospital remote assessment service in West Hertfordshire NHS Trust, UK.ParticipantsPatients with suspected COVID-19 illness enrolled directly from the community (post-accident and emergency (A&E) or medical intake assessment) or post-inpatient admission.Main outcome measureDeath or (re-)admission to inpatient hospital care over 28 days.Results900 patients with a clinical diagnosis of COVID-19 (455 referred from A&E or medical intake and 445 post-inpatient) were included in the analysis. 76 (8.4%) of these experienced an adverse outcome (15 deaths in admitted patients, 3 deaths in patients not admitted, and 58 additional inpatient admissions). Predictors of adverse outcome were increase in age (OR 1.04 [95%CI: 1.02, 1.06] per year of age), history of cancer (OR 2.87 [95%CI: 1.41, 5.82]), history of mental health problems (OR 1.76 [95%CI: 1.02, 3.04]), severely impaired renal function (OR for eGFR <30 = 9.09 [95%CI: 2.01, 41.09]) and having a positive SARS-CoV-2 PCR result (OR 2.0 [95% CI: 1.11, 3.60]).ConclusionsThese predictors may help direct intensity of monitoring for patients with suspected or confirmed COVID-19 who are being remotely monitored by primary or secondary care services. Further research is needed to identify the reasons for increased risk of adverse outcome associated with cancer and mental health problems.ARTICLE SUMMARYStrengths and limitations of this studyThe study uses anonymised data from all patients registered for the virtual hospital between 17/03/20 and 17/05/20, and therefore selection bias is not an issue.At the time of this study, this was the only service providing remote follow-up for patients with suspected COVID-19 in the area, and therefore our findings are likely to be relevant to primary care patients receiving remote follow-up.We were able to collect reliable data on a wide range of clinical and demographic features, and reliably follow all patients for the primary outcome for at least two weeks following their discharge from the VH.We were not able to extract detailed symptom or clinical examination data, and there were significant amounts of missing data for some variables.Our study is likely underpowered to detect all predictors, especially in the analysis of our two sub-groups
Changes in sexual behavior, PrEP adherence, and access to sexual health services due to the COVID-19 pandemic among a cohort of PrEP-using MSM in the South
Authors: Pampati Sanjana , Emrick Kayla , Siegler Aaron J. , Jones Jeb 
Published: November 2020

AbstractBackgroundThe COVID-19 pandemic has had unforeseen consequences on the delivery of HIV and STD prevention services. However, little is known about how the pandemic has impacted PrEP-using men who have sex with men (MSM).MethodsData come from an online cohort of PrEP-using MSM in the Southern United States from October 2019 to July 2020. Participants were administered ten surveys in total, including one ad hoc survey specifically on COVID-19. We conducted a cross-sectional analysis of this ad hoc survey (n=56) and present changes in sexual behaviors and utilization of and access to sexual health services. Using linear mixed-effects regression models, we also analyzed data from the larger cohort (n=78) and document how sexual behaviors and PrEP use varied longitudinally focusing on three months: February (pre-pandemic), April (early pandemic), and June (later in the pandemic).ResultsA fifth of participants discontinued or changed how often they take PrEP because of COVID-19. A quarter of the cohort documented challenges when attempting to access PrEP, HIV testing, or STD testing. For all sexual behaviors examined longitudinally—number of male sexual partners, anal sex acts, condomless anal sex, oral sex (all measured in the past 2 weeks)—there was a significant decrease from February to April followed by a significant increase from April to June.DiscussionOur findings suggest reduced access to and utilization of STD and HIV services coupled with a continuation of behaviors which confer STD/HIV risk. Ensuring appropriate delivery of STD/HIV prevention services during this pandemic is imperative.