bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Modified Tumor-Node-Metastasis Classification for Primary Operable Colorectal Cancer
Authors: Zhang Chundong , Mei Zubing , Pei Junpeng , Abe Masanobu , Zeng Xiantao , Huang Qiao , Nishiyama Kazuhiro , Akimoto Naohiko , Haruki Koichiro , Nan Hongmei , Meyerhardt Jeffrey A , Zhang Rui , Li Xinxiang , Ogino Shuji , Ugai Tomotaka 
Published: October 2020

Abstract

Background
The American Joint Committee on Cancer (AJCC) 8th tumor-node-metastasis (TNM) classification for colorectal cancer (CRC) has limited ability to predict prognosis.

Methods
We included 45 379 eligible stage I-III CRC patients from the Surveillance, Epidemiology, and End Results Program. Patients were randomly assigned individually to a training (n = 31 772) or an internal validation cohort (n = 13 607). External validation was performed in 10 902 additional patients. Patients were divided according to T and N stage permutations. Survival analyses were conducted by a Cox proportional hazard model and Kaplan-Meier analysis, with T1N0 as the reference. Area under receiver operating characteristic curve and Akaike information criteria were applied for prognostic discrimination and model fitting, respectively. Clinical benefits were further assessed by decision curve analyses.

Results
We created a modified TNM (mTNM) classification: stages I (T1-2N0-1a); IIA (T1N1b, T2N1b, T3N0); IIB (T1-2N2a-2b, T3N1a-1b, T4aN0); IIC (T3N2a, T4aN1a-2a, T4bN0); IIIA (T3N2b, T4bN1a); IIIB (T4aN2b, T4bN1b); and IIIC (T4bN2a-2b). In the internal validation cohort, compared with the AJCC 8th TNM classification, the mTNM classification showed superior prognostic discrimination (area under receiver operating characteristic curve = 0.675 vs 0.667, respectively; 2-sided P &lt; .001) and better model fitting (Akaike information criteria = 70 937 vs 71 238, respectively). Similar findings were obtained in the external validation cohort. Decision curve analyses revealed that the mTNM had superior net benefits over the AJCC 8th TNM classification in the internal and external validation cohorts.

Conclusions
The mTNM classification provides better prognostic discrimination than AJCC 8th TNM classification, with good applicability in various populations and settings, to help better stratify stage I-III CRC patients into prognostic groups.
Bayesian model predicts the aboveground biomass of Caragana microphylla in sandy lands better than OLS regression models
Authors: Tang Yi , Ali Arshad , Feng Li-Huan 
Published: October 2020

Abstract

Aims
In forest ecosystems, different types of regression models have been frequently used for the estimation of aboveground biomass, where Ordinary Least Squares (OLS) regression models are the most common prediction models. Yet, the relative performance of Bayesian and OLS models in predicting aboveground biomass of shrubs, especially multi-stem shrubs, has relatively been less studied in forests.

Methods
In this study, we developed the biomass prediction models for Caragana microphylla Lam. which is a widely distributed multi-stems shrub, and contributes to the decrease of wind erosion and the fixation of sand dunes in the Horqin Sand Land, one of the largest sand lands in China. We developed six types of formulations under the framework of the regression models, and then, selected the best model based on specific criteria. Consequently, we estimated the parameters of the best model with OLS and Bayesian methods with training and test data under different sample sizes with the bootstrap method. Lastly, we compared the performance of the OLS and Bayesian models in predicting the aboveground biomass of C. microphylla.

Important Findings
The performance of the allometric equation (power = 1) was best among six types of equations, even though all of those models were significant. The results showed that mean squared error of test data with non-informative prior Bayesian method and the informative prior Bayesian method was lower than with the OLS method. Among the tested predictors (i.e. plant height and basal diameter), we found that basal diameter was not a significant predictor either in OLS or Bayesian methods, indicating that suitable predictors and well-fitted models should be seriously considered. This study highlights that Bayesian methods, the bootstrap method and the type of allometric equation could help to improve the model accuracy in predicting shrub biomass in sandy lands.
A rare case of fat embolism syndrome secondary to abdominal liposuction and gluteal fat infiltration
Authors: Recinos Salvador , Barillas Sabrina , Rodas Alejandra , Ardebol Javier 
Published: October 2020

Abstract
Fat embolism syndrome (FES) is a rare, life-threatening condition habitually associated with traumatic events such as fractures and, less commonly, burns, liposuction and bone marrow harvesting and transplant [ 1]. The biochemical theory for this condition suggests that fat droplets embolize and convert into fatty acids, eventually leading to toxic injury and inflammation, which results in increased vascular permeability, edema and hemorrhage [ 2]. FES may have an asymptomatic interval lasting 12–72 hours after the insult; however, in some cases, signs have also been seen intraoperatively. Pulmonary signs and symptoms are customarily the earliest and manifest in 75% of patients. Nevertheless, neurologic and dermatologic manifestations are also characteristic, and most severe cases could perhaps present with disseminated intravascular coagulation, right ventricular dysfunction, shock or death. The following case consists of a 37-year-old patient that presented with fat embolism syndrome during liposuction and gluteal fat infiltration.
A First Description of Arabic on The South Coast of Iran: The Arabic Dialect of Bandar Moqām, Hormozgan
Authors: Leitner Bettina , Anonby Erik , Taheri-Ardali Mortaza , Zarka Dina El , Moqami Ali 
Published: October 2020

Abstract
Arabic has been spoken as a mother tongue in Iran since pre-Islamic times, but a number of the Arabic dialect groups scattered across the country have not been documented. In this study, we provide a first account of Arabic on Iran's southern coast, with a description of the dialect of Bandar Moqām in western Hormozgan Province. Using the Atlas of the Languages of Iran (ALI) linguistic data questionnaire as well as supplementary elicitation and oral texts, we have documented salient elements of its lexicon, phonology and morphosyntax. Our analysis confirms that Bandar Moqām Arabic fits into the wider Gulf Arabic dialect area, yet is internally heterogenous. On the one hand, it shares many features with the regionally dominant ‘Bedouin’ type Gulf Arabic koine, but it also aligns with distinctive structures—both retentions and innovations—in the more ancient ‘Sedentary’ Gulf dialects that originated in southern Arabia. Further, it exhibits a series of structures in common with Mesopotamian Arabic and its descendants that reached as far as Central Asia during the Arab con-quest of greater Persia and are still spoken there today.
Newly discovered viruses
Authors: Froude Susannah J.A. , Hughes Harriet C. 
Published: October 2020

Abstract
Although humans are affected by an enormous range of microorganisms, almost all newly discovered emerging pathogens are viruses that are often zoonotic or vector-borne. These emerging viruses often have high baseline mutation rates, allowing them to adapt relatively easily to new hosts and enabling them to take advantage of new epidemiological opportunities provided by the changing environment. A range of apparently new human viral pathogens has been reported increasingly in international outbreak information over the last few years, most recently SARS-CoV-2 as the cause of the COVID-19 pandemic that started in Wuhan (China) in December 2019 and has now spread worldwide with devastating consequences. In addition to respiratory coronaviruses, emerging viruses that might be of particular global public health importance includeZika virus and severe fever and thrombocytopenia syndrome virus. Other emerging viruses of importance include bocavirus, Bufavirus, PARV4, human parechovirus, Itaya, Heartland, and Bourbon virus. The human pathogenicity of other emerging viruses is less certain.
The imprint of dark subhaloes on the circumgalactic medium
Authors: McCarthy Ian G , Font Andreea S 
Published: October 2020

ABSTRACT
The standard model of cosmology, the Λ cold dark matter (ΛCDM) model, robustly predicts the existence of a multitude of dark matter ‘subhaloes’ around galaxies like the Milky Way. A wide variety of observations have been proposed to look for the gravitational effects such subhaloes would induce in observable matter. Most of these approaches pertain to the stellar or cool gaseous phases of matter. Here we propose a new approach, which is to search for the perturbations that such dark subhaloes would source in the warm/hot circumgalactic medium (CGM) around normal galaxies. With a combination of analytic theory, carefully controlled high-resolution idealized simulations, and full cosmological hydrodynamical simulations (the artemis simulations), we calculate the expected signal and how it depends on important physical parameters (subhalo mass, CGM temperature, and relative velocity). We find that dark subhaloes enhance both the local CGM temperature and density and, therefore, also the pressure. For the pressure and density, the fluctuations can vary in magnitude from tens of per cent (for subhaloes with Msub = 1010 M⊙) to a few per cent (for subhaloes with Msub = 108 M⊙), although this depends strongly on the CGM temperature. The subhaloes also induce fluctuations in the velocity field ranging in magnitude from a few km s−1 up to 25 km s−1. We propose that X-ray, Sunyaev–Zel’dovich effect, radio dispersion measure, and quasar absorption line observations can be used to measure these fluctuations and place constraints on the abundance and distribution of dark subhaloes, thereby placing constraints on the nature of dark matter.
simba: the average properties of the circumgalactic medium of 2 ≤ z ≤ 3 quasars are determined primarily by stellar feedback
Authors: Sorini Daniele , Davé Romeel , Anglés-Alcázar Daniel 
Published: October 2020

ABSTRACT
We use the simba cosmological hydrodynamic simulation suite to explore the impact of feedback on the circumgalactic medium (CGM) and intergalactic medium (IGM) around 2 ≤ z ≤ 3 quasars. We identify quasars in simba as the most rapidly accreting black holes, and show that they are well matched in bolometric luminosity and correlation strength to real quasars. We extract Lyα absorption in spectra passing at different transverse distances ($10 \, \mathrm{kpc} \lesssim b \lesssim 10 \, \rm Mpc$) around those quasars, and compare to observations of the mean Lyα absorption profile. The observations are well reproduced, except within $100 \, \, \rm kpc$ from the foreground quasar, where simba overproduces absorption; this could potentially be mitigated by including ionization from the quasar itself. By comparing runs with different feedback modules activated, we find that (mechanical) AGN feedback has little impact on the surrounding CGM even around these most highly luminous black holes, while stellar feedback has a significant impact. By further investigating thermodynamic and kinematic properties of CGM gas, we find that stellar feedback, and not AGN feedback, is the primary physical driver in determining the average properties of the CGM around z ∼ 2–3 quasars. We also compare our results with previous works, and find that simba predicts much more absorption within $100 \, \rm kpc$ than the nyx and illustris simulations, showing that the Lyα absorption profile can be a powerful constraint on simulations. Instruments such as VLT-MUSE and upcoming surveys (e.g. WEAVE and DESI) promise to further improve such constraints.
emerge – empirical constraints on the formation of passive galaxies
Authors: Moster Benjamin P , Naab Thorsten , White Simon D M 
Published: October 2020

ABSTRACT
We present constraints on the emergence and evolution of passive galaxies with the empirical model emerge, which reproduces the evolution of stellar mass functions (SMFs), specific and cosmic star formation rates since $z$ ≈ 10, ‘quenched’ galaxy fractions, and correlation functions. At fixed halo mass, present-day passive galaxies are more massive than active galaxies, whereas at fixed stellar mass passive galaxies populate more massive haloes in agreement with observations. This effect naturally results from the shape and scatter of the stellar-to-halo mass relation. The stellar mass assembly of present-day passive galaxies is dominated by ‘in situ’ star formation below ∼3 × 1011 M⊙ and by merging and accretion of ‘ex situ’ formed stars at higher mass. The mass dependence is in tension with current cosmological simulations. Lower mass passive galaxies show extended star formation towards low redshift in agreement with IFU surveys. All passive galaxies have main progenitors on the ‘main sequence of star formation’ with the ‘red sequence’ appearing at $z$ ≈ 2. Above this redshift, over 95 per cent of the progenitors of passive galaxies are active. More than 90 per cent of $z$ ≈ 2 ‘main sequence’ galaxies with m* &gt; 1010 M⊙ evolve into present-day passive galaxies. Above redshift 6, more than 80 per cent of the observed SMFs above 109 M⊙ can be accounted for by progenitors of passive galaxies with m* &gt; 1010 M⊙. This implies that high-redshift observations mainly probe the birth of present-day passive galaxies. emerge is available at github.com/bmoster/emerge.
3D hydrodynamic simulations of large-scale precessing jets: radio morphology
Authors: Horton Maya A , Krause Martin G H , Hardcastle Martin J 
Published: October 2020

ABSTRACT
The prospect of relativistic jets exhibiting complex morphologies as a consequence of geodetic precession has long been hypothesized. We have carried out a 3D hydrodynamics simulation study varying the precession cone angle, jet injection speed, and number of turns per simulation time. Using proxies for the radio emission we project the sources with different inclinations to the line of sight to the observer. We find that a number of different precession combinations result in characteristic ‘X’ shaped sources which are frequently observed in radio data, and some precessing jet morphologies may mimic the morphological signatures of restarting radio sources. We look at jets ranging in scale from tens to hundreds of kiloparsecs and develop tools for identifying known precession indicators of point symmetry, curvature, and jet misalignment from the lobe axis and show that, based on our simulation sample of precessing and non-precessing jets, a radio source that displays any of these indicators has a 98 per cent chance of being a precessing source.
Analysis of eclipsing binaries in multiple stellar systems: the case of V1200 Centauri
Authors: Marcadon F , Hełminiak K G , Marques J P , Pawłaszek R , Sybilski P , Kozłowski S K , Ratajczak M , Konacki M 
Published: October 2020

ABSTRACT
We present a new analysis of the multiple-star V1200 Centauri based on the most recent observations for this system. We used the photometric observations from the Solaris network and the Transiting Exoplanet Survey Satellite telescope, combined with the new radial velocities from the CHIRON spectrograph and those published in the literature. We confirmed that V1200 Cen consists of a 2.5-d eclipsing binary orbited by a third body. We derived the parameters of the eclipsing components, which are $M_{\mathrm{ Aa}} = 1.393\pm 0.018\,$M⊙, $R_{\mathrm{ Aa}} = 1.407\pm 0.014\,$R⊙, and $T_{{\rm eff},\mathrm{ Aa}} = 6588\pm 58\,$K for the primary, and $M_{\mathrm{ Ab}} = 0.8633\pm 0.0081\,$M⊙, $R_{\mathrm{ Ab}} = 1.154\pm 0.014\,$R⊙, and $T_{{\rm eff},\mathrm{ Ab}} = 4475\pm 68\,$K for the secondary. Regarding the third body, we obtained significantly different results than those previously published. The period of the outer orbit is found to be 180.4 d, implying a minimum mass of $M_\mathrm{ B} = 0.871\pm 0.020\,$M⊙. Thus, we argue that V1200 Cen is a quadruple system with a secondary pair composed of two low-mass stars. Finally, we determined the ages of each eclipsing component using two evolution codes, namely mesa and cestam. We obtained ages of 16–18.5 and 5.5–7 Myr for the primary and the secondary, respectively. In particular, the secondary appears larger and hotter than that predicted at the age of the primary. We concluded that dynamical and tidal interactions occurring in multiples may alter the stellar properties and explain the apparent non-coevality of V1200 Centauri.
Planet formation and disc mass dependence in a pebble-driven scenario for low-mass stars
Authors: Dash Spandan , Miguel Yamila 
Published: October 2020

ABSTRACT
Measured disc masses seem to be too low to form the observed population of planetary systems. In this context, we develop a population synthesis code in the pebble accretion scenario, to analyse the disc mass dependence on planet formation around low-mass stars. We base our model on the analytical sequential model presented by Ormel, Liu, and Schoonenberg and analyse the populations resulting from varying initial disc mass distributions. Starting out with seeds the mass of Ceres formed by streaming instability inside the ice-line, we grow the planets using the pebble accretion process and migrate them inwards using type I migration. The next planets are formed sequentially after the previous planet crosses the ice line. We explore different initial distributions of disc masses to show the dependence of this parameter with the final planetary population. Our results show that compact close-in resonant systems can be pretty common around M dwarfs between 0.09 and 0.2 M⊙ only when the discs considered are more massive than what is being observed by sub-mm disc surveys. The minimum disc mass to form a Mars-like planet is found to be about 2 × 10−3 M⊙. Small variations in the disc mass distribution also manifest in the simulated planet distribution. The paradox of disc masses might be caused by an underestimation of the disc masses in observations, by a rapid depletion of mass in discs by planets growing within 1 million years, or by deficiencies in our current planet formation picture.
Simple recipes for compact remnant masses and natal kicks
Authors: Mandel Ilya , Müller Bernhard 
Published: October 2020

ABSTRACT
Based on recent results from three-dimensional supernova simulations and semi-analytical parametrized models, we develop analytical prescriptions for the dependence of the mass of neutron stars and black holes and the natal kicks, if any, on the pre-supernova carbon–oxygen core and helium shell masses. Our recipes are probabilistic rather than deterministic in order to account for the intrinsic stochasticity of stellar evolution and supernovae. We anticipate that these recipes will be particularly useful for rapid population synthesis, and we illustrate their application to distributions of remnant masses and kicks for a population of single stars.
Periodic brightening of Kepler light curves: investigating the possibility of forward scattering due to dust clouds
Authors: van Kooten M A M , Kenworthy M , Doelman N 
Published: October 2020

ABSTRACT
Dedicated transiting surveys, such as the Kepler space telescope, have provided the astronomy community with a rich data set resulting in many new discoveries. In this paper, we look at eight Kepler objects identified by Wheeler & Kipping with a periodic, broad increase in flux, that look distinctly different from intrinsic star variability. We consider two physical phenomena as explanations for these observed Kepler light curves; the first being the classical explanation while the second being an alternative scenario: (i) tidal interactions in a binary star system, and (ii) forward scattering from an optically thin cloud around an exoplanet. We investigate the likelihood of each model by modelling and fitting to the observed data. The binary system qualitatively does a good job of reproducing the shape of the observed light curves due to the tidal interaction of the two stars. We do, however, see a mismatch in flux right before or after the peak brightness. We find that six out of the eight systems require an F-type primary star with a K-type companion with large eccentricities. At the same time, we find that optically thin discs, modelled using a Henyey–Greenstein phase function are also able to generate these broad brightening events. Five of the eight observed objects can be described with this new hypothesis in the absence of RV observations. As the other three are not well-described by the disc model, we conclude that they are indeed heartbeat stars.
A robust CRISPR–Cas9-based fluorescent reporter assay for the detection and quantification of DNA double-strand break repair
Authors: Eki Rebeka , She Jane , Parlak Mahmut , Benamar Mouadh , Du Kang-Ping , Kumar Pankaj , Abbas Tarek 
Published: October 2020

AbstractDNA double-strand breaks (DSBs) are highly cytotoxic lesions that can lead to chromosome rearrangements, genomic instability and cell death. Consequently, cells have evolved multiple mechanisms to efficiently repair DSBs to preserve genomic integrity. We have developed a DSB repair assay system, designated CDDR (CRISPR–Cas9-based Dual-fluorescent DSB Repair), that enables the detection and quantification of DSB repair outcomes in mammalian cells with high precision. CDDR is based on the introduction and subsequent resolution of one or two DSB(s) in an intrachromosomal fluorescent reporter following the expression of Cas9 and sgRNAs targeting the reporter. CDDR can discriminate between high-fidelity (HF) and error-prone non-homologous end-joining (NHEJ), as well as between proximal and distal NHEJ repair. Furthermore, CDDR can detect homology-directed repair (HDR) with high sensitivity. Using CDDR, we found HF-NHEJ to be strictly dependent on DNA Ligase IV, XRCC4 and XLF, members of the canonical branch of NHEJ pathway (c-NHEJ). Loss of these genes also stimulated HDR, and promoted error-prone distal end-joining. Deletion of the DNA repair kinase ATM, on the other hand, stimulated HF-NHEJ and suppressed HDR. These findings demonstrate the utility of CDDR in characterizing the effect of repair factors and in elucidating the balance between competing DSB repair pathways.
CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo
Authors: Martín Adrián López , Mounir Mohamed , Meyer Irmtraud M 
Published: October 2020

Abstract
RNA structure formation in vivo happens co-transcriptionally while the transcript is being made. The corresponding co-transcriptional folding pathway typically involves transient RNA structure features that are not part of the final, functional RNA structure. These transient features can play important functional roles of their own and also influence the formation of the final RNA structure in vivo. We here present CoBold, a computational method for identifying different functional classes of transient RNA structure features that can either aid or hinder the formation of a known reference RNA structure. Our method takes as input either a single RNA or a corresponding multiple-sequence alignment as well as a known reference RNA secondary structure and identifies different classes of transient RNA structure features that could aid or prevent the formation of the given RNA structure. We make CoBold available via a web-server which includes dedicated data visualisation.