bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpreting correlated observations of cosmic rays and gamma-rays from Centaurus A with a proton blazar inspired model
Authors: Banik Prabir , Bhadra Arunava , Bhattacharyya Abhijit 
Published: October 2020

ABSTRACT
The nearest active radio galaxy Centaurus (Cen) A is a gamma-ray emitter in GeV–TeV energy scale. The high energy stereoscopic system (HESS) and non-simultaneous Fermi–Large Area Telescope observation indicate an unusual spectral hardening above few GeV energies in the gamma-ray spectrum of Cen A. Very recently the HESS observatory resolved the kilo parsec (kpc)-scale jets in Centaurus A at TeV energies. On the other hand, the Pierre Auger Observatory (PAO) detects a few ultrahigh energy cosmic ray (UHECR) events from Cen-A. The proton blazar inspired model, which considers acceleration of both electrons and hadronic cosmic rays in active galactic nuclei (AGN) jet, can explain the observed coincident high-energy neutrinos and gamma-rays from Ice-cube detected AGN jets. Here, we have employed the proton blazar inspired model to explain the observed GeV–TeV gamma-ray spectrum features including the spectrum hardening at GeV energies along with the PAO observation on cosmic rays from Cen-A. Our findings suggest that the model can explain consistently the observed electromagnetic spectrum in combination with the appropriate number of UHECRs from Cen A.
A new lepto-hadronic model applied to the first simultaneous multiwavelength data set for Cygnus X–1
Authors: Kantzas D , Markoff S , Beuchert T , Lucchini M , Chhotray A , Ceccobello C , Tetarenko A J , Miller-Jones J C A , Bremer M , Garcia J A , Grinberg V , Uttley P , Wilms J 
Published: October 2020

ABSTRACTCygnus X–1 is the first Galactic source confirmed to host an accreting black hole. It has been detected across the entire electromagnetic spectrum from radio to GeV gamma-rays. The source’s radio through mid-infrared radiation is thought to originate from the relativistic jets. The observed high degree of linear polarization in the MeV X-rays suggests that the relativistic jets dominate in this regime as well, whereas a hot accretion flow dominates the soft X-ray band. The origin of the GeV non-thermal emission is still debated, with both leptonic and hadronic scenarios deemed to be viable. In this work, we present results from a new semi-analytical, multizone jet model applied to the broad-band spectral energy distribution of Cygnus X–1 for both leptonic and hadronic scenarios. We try to break this degeneracy by fitting the first-ever high-quality, simultaneous multiwavelength data set obtained from the CHOCBOX campaign (Cygnus X–1 Hard state Observations of a Complete Binary Orbit in X-rays). Our model parametrizes dynamical properties, such as the jet velocity profile, the magnetic field, and the energy density. Moreover, the model combines these dynamical properties with a self-consistent radiative transfer calculation including secondary cascades, both of leptonic and hadronic origin. We conclude that sensitive TeV gamma-ray telescopes like Cherenkov Telescope Array (CTA) will definitively answer the question of whether hadronic processes occur inside the relativistic jets of Cygnus X–1.
Modelling long-period variables – II. Fundamental mode pulsation in the non-linear regime
Authors: Trabucchi Michele , Wood Peter R , Mowlavi Nami , Pastorelli Giada , Marigo Paola , Girardi Léo , Lebzelter Thomas 
Published: October 2020

ABSTRACT
Long-period variability in luminous red giants has several promising applications, all of which require models able to accurately predict pulsation periods. Linear pulsation models have proven successful in reproducing the observed periods of overtone modes in evolved red giants, but they fail to accurately predict their fundamental mode (FM) periods. Here, we use a 1D hydrodynamic code to investigate the long-period variability of M-type asymptotic giant branch stars in the non-linear regime. We examine the period and stability of low-order radial pulsation modes as a function of mass and radius, and find overtone mode periods in complete agreement with predictions from linear pulsation models. In contrast, non-linear models predict an earlier onset of dominant FM pulsation, and shorter periods at large radii. Both features lead to a substantially better agreement with observations that we verify against OGLE and Gaia data for the Magellanic Clouds. We provide simple analytical relations describing the non-linear FM period–mass–radius relation. Differences with respect to linear predictions originate from the readjustment of the envelope structure induced by large-amplitude pulsation. We investigate the impact of turbulent viscosity on linear and non-linear pulsation, and probe possible effects of varying metallicity and carbon abundance.
Black widow formation by pulsar irradiation and sustained magnetic braking
Authors: Ginzburg Sivan , Quataert Eliot 
Published: October 2020

ABSTRACT
Black widows are millisecond pulsars with low-mass companions, a few per cent the mass of the sun, on orbits of several hours. These companions are presumably the remnants of main-sequence stars that lost their mass through a combination of Roche lobe overflow and ablation by the host pulsar’s high-energy radiation. While ablation itself is too weak to significantly reduce the mass of the companion star, the ablated wind couples to its magnetic field, removes orbital angular momentum, and thus maintains stable Roche lobe overflow. We use the mesa stellar evolution code, complemented by analytical estimates, to track initially main-sequence companions as they are reduced to a fraction of their original mass by this ablation-driven magnetic braking. We argue that magnetic braking remains effective even for low-mass companions. A key ingredient of our model is that the irradiating luminosity of the pulsar Lirr deposits energy in the companion’s atmosphere and thereby slows down its Kelvin–Helmholtz cooling. We find that the high-energy luminosities measured by Fermi $L_{\rm irr}=0.1\rm {-}3$ L⊙ can explain the span of black widow orbital periods. The same Lirr range reproduces the companions’ night-side temperatures, which cluster around 3000 K, as inferred from optical light curves.
First Light And Reionization Epoch Simulations (FLARES) – I. Environmental dependence of high-redshift galaxy evolution
Authors: Lovell Christopher C , Vijayan Aswin P , Thomas Peter A , Wilkins Stephen M , Barnes David J , Irodotou Dimitrios , Roper Will 
Published: October 2020

ABSTRACT
We introduce the First Light And Reionisation Epoch Simulations (FLARES), a suite of zoom simulations using the EAGLE model. We resimulate a range of overdensities during the Epoch of Reionization (EoR) in order to build composite distribution functions, as well as explore the environmental dependence of galaxy formation and evolution during this critical period of galaxy assembly. The regions are selected from a large $(3.2 \, \mathrm{cGpc})^{3}$ parent volume, based on their overdensity within a sphere of radius 14 h−1 cMpc. We then resimulate with full hydrodynamics, and employ a novel weighting scheme that allows the construction of composite distribution functions that are representative of the full parent volume. This significantly extends the dynamic range compared to smaller volume periodic simulations. We present an analysis of the galaxy stellar mass function (GSMF), the star formation rate distribution function (SFRF), and the star-forming sequence (SFS) predicted by FLARES, and compare to a number of observational and model constraints. We also analyse the environmental dependence over an unprecedented range of overdensity. Both the GSMF and the SFRF exhibit a clear double-Schechter form, up to the highest redshifts (z = 10). We also find no environmental dependence of the SFS normalization. The increased dynamic range probed by FLARES will allow us to make predictions for a number of large area surveys that will probe the EoR in coming years, carried out on new observatories such as Roman and Euclid.
Resolving the outer ring of HD 38206 using ALMA and constraining limits on planets in the system
Authors: Booth Mark , Schulz Michael , Krivov Alexander V , Marino Sebastián , Pearce Tim D , Launhardt Ralf 
Published: October 2020

ABSTRACT
HD 38206 is an A0V star in the Columba association, hosting a debris disc first discovered by IRAS. Further observations by Spitzer and Herschel showed that the disc has two components, likely analogous to the asteroid and Kuiper belts of the Solar system. The young age of this star makes it a prime target for direct imaging planet searches. Possible planets in the system can be constrained using the debris disc. Here, we present the first ALMA observations of the system’s Kuiper belt and fit them using a forward modelling MCMC approach. We detect an extended disc of dust peaking at around 180 au with a width of 140 au. The disc is close to edge on and shows tentative signs of an asymmetry best fit by an eccentricity of $0.25^{+0.10}_{-0.09}$. We use the fitted parameters to determine limits on the masses of planets interior to the cold belt. We determine that a minimum of four planets are required, each with a minimum mass of 0.64 MJ, in order to clear the gap between the asteroid and Kuiper belts of the system. If we make the assumption that the outermost planet is responsible for the stirring of the disc, the location of its inner edge and the eccentricity of the disc, then we can more tightly predict its eccentricity, mass, and semimajor axis to be $e_{\rm {p}}=0.34^{+0.20}_{-0.13}$, $m_{\rm {p}}=0.7^{+0.5}_{-0.3}\, \rm {\it M}_{\rm {J}}$, and $a_{\rm {p}}=76^{+12}_{-13}\, \rm {au}$.
canSAR: update to the cancer translational research and drug discovery knowledgebase
Authors: Mitsopoulos Costas , Di Micco Patrizio , Fernandez Eloy Villasclaras , Dolciami Daniela , Holt Esty , Mica Ioan L , Coker Elizabeth A , Tym Joseph E , Campbell James , Che Ka Hing , Ozer Bugra , Kannas Christos , Antolin Albert A , Workman Paul , Al-Lazikani Bissan 
Published: October 2020

AbstractcanSAR (http://cansar.icr.ac.uk) is the largest, public, freely available, integrative translational research and drug discovery knowledgebase for oncology. canSAR integrates vast multidisciplinary data from across genomic, protein, pharmacological, drug and chemical data with structural biology, protein networks and more. It also provides unique data, curation and annotation and crucially, AI-informed target assessment for drug discovery. canSAR is widely used internationally by academia and industry. Here we describe significant developments and enhancements to the data, web interface and infrastructure of canSAR in the form of the new implementation of the system: canSARblack. We demonstrate new functionality in aiding translation hypothesis generation and experimental design, and show how canSAR can be adapted and utilised outside oncology.
CONQUER: an interactive toolbox to understand functional consequences of GWAS hits
Authors: Bouland Gerard A , Beulens Joline W J , Nap Joey , van der Slik Arno R , Zaldumbide Arnaud , ’t Hart Leen M , Slieker Roderick C 
Published: October 2020

Abstract
Numerous large genome-wide association studies have been performed to understand the influence of genetics on traits. Many identified risk loci are in non-coding and intergenic regions, which complicates understanding how genes and their downstream pathways are influenced. An integrative data approach is required to understand the mechanism and consequences of identified risk loci. Here, we developed the R-package CONQUER. Data for SNPs of interest are acquired from static- and dynamic repositories (build GRCh38/hg38), including GTExPortal, Epigenomics Project, 4D genome database and genome browsers. All visualizations are fully interactive so that the user can immediately access the underlying data. CONQUER is a user-friendly tool to perform an integrative approach on multiple SNPs where risk loci are not seen as individual risk factors but rather as a network of risk factors.
aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs
Authors: Bossanyi Marc-André , Carpentier Valentin , Glouzon Jean-Pierre S , Ouangraoua Aïda , Anselmetti Yoann 
Published: October 2020

AbstractPredicting RNA structure is crucial for understanding RNA’s mechanism of action. Comparative approaches for the prediction of RNA structures can be classified into four main strategies. The three first—align-and-fold, align-then-fold and fold-then-align—exploit multiple sequence alignments to improve the accuracy of conserved RNA-structure prediction. Align-and-fold methods perform generally better, but are also typically slower than the other alignment-based methods. The fourth strategy—alignment-free—consists in predicting the conserved RNA structure without relying on sequence alignment. This strategy has the advantage of being the faster, while predicting accurate structures through the use of latent representations of the candidate structures for each sequence. This paper presents aliFreeFoldMulti, an extension of the aliFreeFold algorithm. This algorithm predicts a representative secondary structure of multiple RNA homologs by using a vector representation of their suboptimal structures. aliFreeFoldMulti improves on aliFreeFold by additionally computing the conserved structure for each sequence. aliFreeFoldMulti is assessed by comparing its prediction performance and time efficiency with a set of leading RNA-structure prediction methods. aliFreeFoldMulti has the lowest computing times and the highest maximum accuracy scores. It achieves comparable average structure prediction accuracy as other methods, except TurboFoldII which is the best in terms of average accuracy but with the highest computing times. We present aliFreeFoldMulti as an illustration of the potential of alignment-free approaches to provide fast and accurate RNA-structure prediction methods.
Second series by the Italian Association of Pediatric Hematology and Oncology of children and adolescents with intracranial ependymoma: an integrated molecular and clinical characterization with a long-term follow-up
Authors: Massimino Maura , Barretta Francesco , Modena Piergiorgio , Witt Hendrik , Minasi Simone , Pfister Stefan M , Pajtler Kristian W , Antonelli Manila , Gandola Lorenza , Luisa Garrè Maria , Bertin Daniele , Mastronuzzi Angela , Mascarin Maurizio , Quaglietta Lucia , Viscardi Elisabetta , Sardi Iacopo , Ruggiero Antonio , Pollo Bianca , Buccoliero Annamaria , Boschetti Luna , Schiavello Elisabetta , Chiapparini Luisa , Erbetta Alessandra , Morra Isabella , Gessi Marco , Donofrio Vittoria , Patriarca Carlo , Giangaspero Felice , Johann Pascal , Buttarelli Francesca Romana 
Published: October 2020

AbstractBackgroundA prospective 2002–2014 study stratified 160 patients by resection extent and histological grade, reporting results in 2016. We re-analyzed the series after a median of 119 months, adding retrospectively patients’ molecular features.MethodsFollow-up of all patients was updated. DNA copy number analysis and gene-fusion detection could be completed for 94/160 patients, methylation classification for 68.ResultsProgression-free survival (PFS) and overall survival (OS) at 5/10 years were 66/58%, and 80/73%. Ten patients had late relapses (range 66–126 mo), surviving after relapse no longer than those relapsing earlier (0–5 y). On multivariable analysis a better PFS was associated with grade II tumor and complete surgery at diagnosis and/or at radiotherapy; female sex and complete resection showed a positive association with OS. Posterior fossa (PF) tumors scoring ≥0.80 on DNA methylation analysis were classified as PFA (n = 41) and PFB (n = 9). PFB patients had better PFS and OS. Eighteen/32 supratentorial tumors were classified as RELA, and 3 as other molecular entities (anaplastic PXA, LGG MYB, HGNET). RELA had no prognostic impact. Patients with 1q gain or cyclin-dependent kinase inhibitor 2A (CDKN2A) loss had worse outcomes, included significantly more patients &gt;3 years old (P = 0.050) and cases of dissemination at relapse (P = 0.007).ConclusionsPreviously described prognostic factors were confirmed at 10-year follow-up. Late relapses occurred in 6.2% of patients. Specific molecular features may affect outcome: PFB patients had a very good prognosis; 1q gain and CDKN2A loss were associated with dissemination. To draw reliable conclusions, modern ependymoma trials need to combine diagnostics with molecular risk stratification and long-term follow-up.
Changing landscapes of death and burial practices: public health response in time of COVID-19 pandemic
Authors: Sarmiento Philip Joseph D 
Published: October 2020

Abstract
In a recent correspondence published in this journal, the author calls for spiritual interventions for the living and the dead that be considered by the medical community especially in the time of COVID-19. This paper further elaborates on the need to consider the death and burial practices of bereaved families of patients who died of COVID-19 with strict observance of health protocols. Death and burial practices are significant moments in finding meaning for bereaved families in accepting the demise of their loved ones during this pandemic.
Intellectual Property Protection and Financial Markets: Patenting versus Secrecy*
Authors: Dass Nishant , Nanda Vikram , Park Haemin Dennis , Xiao Steven Chong 
Published: October 2020

AbstractFirms rely on patenting and trade secrecy to protect their intellectual property. We study how changes in the trade-off between patenting and secrecy affect firms’ stock liquidity and financing outcomes. We show that an international trade agreement (TRIPS) that strengthened patent protection led to a 10.2% increase in patenting, accompanied by a 14.0%–27.1% improvement in stock liquidity for firms in patent-reliant industries. This in turn allows the affected firms to increase equity financing by 1.9% and reduce leverage by 5.9%. Our results suggest that policies that promote use of patenting over secrecy can reduce informational frictions in equity markets.
Black Healers, Surgeons and ‘Witches’: Medicine, Mobility and Knowledge Exchange in Swedish St Barthélemy 1785–1815
Authors: Thomasson Fredrik 
Published: October 2020

Summary
When Swedish civil servants took possession of the Caribbean island of St Barthélemy in 1785, they discovered a complex medical landscape in which Black healers played important roles. They competed with white physicians for patients and formed an itinerant community—both voluntary and forced in nature—which travelled throughout the archipelago exchanging remedies and practices. The healers’ work was not associated to revolt and rebellion as in many other Caribbean territories and the Swedish court of law treated them with less cruelty than in many other colonies. The healers’ activities cannot be simply reduced to acts of resistance to slavery; many of them gained the trust of large parts of both Black and white communities. Their interactions with people on the surrounding islands show how Caribbean colonial historiography gains from a wider geographical contextualisation, allowing a better understanding of the Black population’s role in healing and medicine.
Age-associated trends of vulvar cancer in the US
Authors: Khadraoui Hanaa , Thappa Sarah , Smith Marianne , Davidov Adi , Castellanos Mario R. 
Published: October 2020

Abstract

Objective:
Medical societies have over the years moved away from recommending routine pelvic examinations in older, asymptomatic women above age 65. Consequently, vulvar examination is a largely neglected component of the physical examination, unless sent to a specialist for gynecological evaluation. In recognition of these recommendations, we analyzed US trends in vulvar cancer incidence, age, and stage at diagnosis, survival, and association with human papillomavirus (HPV).

Methods:
Cases of vulvar and cervical cancer from 1992 to 2014 were extracted from the National Cancer Institute's Surveillance, Epidemiology, and End Results and Centers for Disease Control's data on age at diagnosis, stage of disease, and HPV-association were analyzed and compared. Incidence and mortality rates were extracted and calculated.

Results:
From 1992-2014, there was a 14.3% increase in vulvar cancer rates. The absolute average incidence rate was 2.25, with HPV still being seen in vulvar carcinomas in women 65 years and above. Cervical cancer mortality rates declined by 34.2%, while vulvar cancer death rates were unchanged. We show increased intervals for cervical cancer screening is associated with later stage vulvar cancer detection. The proportion of vulvar cancer cases diagnosed in women age <50 steadily decreased, from 42.05% of cases in 1992-1996 to 19.75% of total cases in 2012-2015. Meanwhile, vulvar cancer cases diagnosed in women > 65 yo increased from 36.62% of cases in 1992-1996 to 49.82% of cases in 2012-2015.

Conclusion:
The incidence of vulvar cancer increases with age, with the median age of diagnosis 67 years, with HPV (+) tumors occurring into 70's and 80's. Though medical societies do not routinely recommend an external genital examination in women 65 years and above, we show this is a missed opportunity to improve cancer outcomes in some older females.

Video Summary:

http://links.lww.com/MENO/A678.
Altered trigeminal pain processing on brainstem level in persistent idiopathic facial pain
Authors: Ziegeler Christian , Schulte Laura H. , May Arne 
Published: October 2020

Abstract
Persistent idiopathic facial pain (PIFP) is a poorly understood chronic pain syndrome of the face, formerly known as atypical facial pain. It is characterized by a constant painful sensation without neurological abnormalities and without clinically objectifiable cause. Similarities to neuropathic pain conditions have been discussed and are currently thought to be relevant for the pathophysiology of this disease. In this study, we aim to characterize the trigeminal pain processing in PIFP using functional magnetic resonance imaging of the brainstem. Twenty-five patients suffering from PIFP and 25 healthy controls underwent a standardized and well-established paradigm of painful stimulation of the trigeminal nerve using gaseous ammonia. Functional images were acquired within a 3T magnetic resonance imaging scanner using an optimized protocol for high-resolution echo planar brainstem imaging. Patients with PIFP show exclusively a stronger activation to painful stimulation in the spinal trigeminal nucleus when contrasted against healthy controls. Our data suggest that abnormal central pain processing plays a role in the pathophysiology of PIFP. An integration of these findings into neuropathic pain models might help to gain a better general understanding of the pathophysiology of PIFP.