bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression and prognostic value of DNA sensors in hepatocellular carcinoma
Authors: Chen Danchun , Ren He , Zhao Na , Hao Jianlei 
Published: May 2023

Abstract
DNA sensor proteins play an important role in transducing DNA signals to induce immune responses that initiate inflammation or clear pathogens. It has been previously shown that several DNA sensors are involved in regulating tumor biology and/or cancer immunology. However, a systemic analysis of DNA sensor expression and its correlation with prognosis has not been conducted. Here, we analyzed messenger RNA expression and protein abundance in liver cancer databases and found that the genes of 5 DNA sensors (POLR3A, PRKDC, DHX9, cGAS, and MRE11) were consistently upregulated in tumor tissue. Moreover, the expression of these DNA sensor genes correlated with patient survival. Using a gene alterations analysis, we discovered that patients with genetically altered DNA sensors had significantly lower survival compared with an unaltered group. Furthermore, receiver-operating characteristic curves confirmed that the signatures of the 5 DNA sensors were independent prognostic factors in hepatocellular carcinoma. Tumor-infiltrating immune cell analysis revealed that expression of all 5 DNA sensors correlated with the amount of B cells, CD8 T cells, CD4 T cells, Tregs, DCs, Mϕs, and neutrophils. Surprisingly, 4 of the DNA sensors (POLR3A, PRKDC, DHX9, and MRE11) were inversely correlated with the amount of γδ T cells. Gene set enrichment analysis showed that all 5 DNA sensor genes were enriched for oxidative phosphorylation and xenobiotic metabolism. These results suggest that expression of these DNA sensors is associated with a unique immune profile and metabolic regulation in hepatocellular carcinoma.
Clinical development of new drugs for adults and children with cancer, 2010-2020
Authors: Arfè Andrea , Narang Claire , DuBois Steven G , Reaman Gregory , Bourgeois Florence T 
Published: May 2023

Abstract

Background
Many new molecular entities enter clinical development to evaluate potential therapeutic benefits for oncology patients. We characterized adult and pediatric development of the set of new molecular entities that started clinical testing in 2010-2015 worldwide.

Methods
We extracted data from AdisInsight, an extensive database of global pharmaceutical development, and the FDA.gov website. We followed the cohort of new molecular entities initiating first-in-human phase I clinical trials in 2010-2015 to the end of 2020. For each new molecular entity, we determined whether it was granted US Food and Drug Administration (FDA) approval, studied in a trial open to pediatric enrollment, or stalled during development. We characterized the cumulative incidence of these endpoints using statistical methods for censored data.

Results
The 572 new molecular entities starting first-in-human studies in 2010-2015 were studied in 6142 trials by the end of 2020. Most new molecular entities were small molecules (n = 316, 55.2%), antibodies (n = 148, 25.9%), or antibody-drug conjugates (n = 44, 7.7%). After a mean follow-up of 8.0 years, 173 new molecular entities did not advance beyond first-in-human trials, and 39 were approved by the FDA. New molecular entities had a 10.4% estimated probability (95% confidence interval = 6.6% to 14.1%) of being approved by the FDA within 10 years of first-in-human trials. After a median of 4.6 years since start of first-in-human trials, 67 (11.7%) new molecular entities were tested in trials open to pediatric patients, and 5 (0.9%) were approved for pediatric indications.

Conclusions
More efficient clinical development strategies are needed to evaluate new cancer therapies, especially for children, and incorporate approaches to ensure knowledge gain from investigational products that stall in development.
Autoregressive optimal transport models
Authors: Zhu Changbo , Müller Hans-Georg 
Published: May 2023

Abstract
Series of univariate distributions indexed by equally spaced time points are ubiquitous in applications and their analysis constitutes one of the challenges of the emerging field of distributional data analysis. To quantify such distributional time series, we propose a class of intrinsic autoregressive models that operate in the space of optimal transport maps. The autoregressive transport models that we introduce here are based on regressing optimal transport maps on each other, where predictors can be transport maps from an overall barycenter to a current distribution or transport maps between past consecutive distributions of the distributional time series. Autoregressive transport models and their associated distributional regression models specify the link between predictor and response transport maps by moving along geodesics in Wasserstein space. These models emerge as natural extensions of the classical autoregressive models in Euclidean space. Unique stationary solutions of autoregressive transport models are shown to exist under a geometric moment contraction condition of Wu & Shao [(2004) Limit theorems for iterated random functions. Journal of Applied Probability 41, 425–436)], using properties of iterated random functions. We also discuss an extension to a varying coefficient model for first-order autoregressive transport models. In addition to simulations, the proposed models are illustrated with distributional time series of house prices across U.S. counties and annual summer temperature distributions.
arepo white dwarf merger simulations resulting in edge-lit detonation and run-away hypervelocity companion
Authors: Burmester Uri Pierre , Ferrario Lilia , Pakmor Rüdiger , Seitenzahl Ivo R , Ruiter Ashley J , Hole Matthew 
Published: May 2023

ABSTRACT
We present a series of high-resolution simulations generated with the moving-mesh code arepo to model the merger of a 1.1-M⊙ carbon-oxygen primary white dwarf (WD) with an outer helium layer and a 0.35-M⊙ secondary helium WD. Our simulations lead to detonations that are consistent with the edge-lit scenario, where a helium detonation is ignited at the base of the helium layer of the primary WD, which triggers an off-centre carbon detonation. This produces an asymmetric ejecta pattern and differences in line-of-sight observables (e.g. mean atomic weight). The ejecta that are flung into space are dominated by 56Ni, 4He, 28Si, and 32S. Our simulations result in a surviving degenerate companion of mass 0.22–0.25 M⊙ moving at &gt;1700 $\mathrm{km}\, \mathrm{s}^{-1}$, consistent with the observational findings of hypervelocity WDs. The secondary’s surface layers are enriched by heavy metals, with 56Ni making up approximately 0.8 per cent of the remaining mass. We also analyse the sensitivity of the outcome on simulation parameters, including the ‘inspiral time’, which defines a period of accelerated angular momentum loss. We find that the choice of ‘inspiral time’ qualitatively influences the simulation result, including the survival of the secondary. We argue that the shorter inspiral cases result in qualitatively and quantitatively similar outcomes. We also investigate the sensitivity of our results on the primary’s chemical profile by comparing simulations using isothermal, constant composition models with the same mass and central composition and characterized by either a bare carbon-oxygen core (no helium) or a carbon-oxygen core enveloped by a thick helium layer.
Probing sub-galactic mass structure with the power spectrum of surface-brightness anomalies in high-resolution observations of galaxy–galaxy strong gravitational lenses. II. Observational constraints on the subgalactic matter power spectrum
Authors: Bayer D , Chatterjee S , Koopmans L V E , Vegetti S , McKean J P , Treu T , Fassnacht C D , Glazebrook K 
Published: May 2023

ABSTRACT
Stringent observational constraints on the subgalactic matter power spectrum would allow one to distinguish between the concordance ΛCDM and the various alternative dark-matter models that predict significantly different properties of mass structure in galactic haloes. Galaxy–galaxy strong gravitational lensing provides a unique opportunity to probe the subgalactic mass structure in lens galaxies beyond the Local Group. Here, we demonstrate the first application of a novel methodology to observationally constrain the subgalactic matter power spectrum in the inner regions of massive elliptical lens galaxies on 1–10 kpc scales from the power spectrum of surface-brightness anomalies in highly magnified galaxy-scale Einstein rings and gravitational arcs. The pilot application of our approach to Hubble Space Telescope (HST/WFC3/F390W) observations of the SLACS lens system SDSS J0252+0039 allows us to place the following observational constraints (at the 99 per cent confidence level) on the dimensionless convergence power spectrum $\Delta ^{2}_{\delta \kappa }$ and the standard deviation in the aperture mass σAM: $\Delta ^{2}_{\delta \kappa }\lt 1$ (σAM &lt; 0.8 × 108 M⊙) on 0.5-kpc scale, $\Delta ^{2}_{\delta \kappa }\lt 0.1$ (σAM &lt; 1 × 108 M⊙) on 1-kpc scale and $\Delta ^{2}_{\delta \kappa }\lt 0.01$ (σAM &lt; 3 × 108 M⊙) on 3-kpc scale. These first upper-limit constraints still considerably exceed the estimated effect of CDM subhaloes. However, future analysis of a larger sample of galaxy–galaxy strong lens systems can substantially narrow down these limits and possibly rule out dark-matter models that predict a significantly higher level of density fluctuations on the critical subgalactic scales.
Probing sub-galactic mass structure with the power spectrum of surface-brightness anomalies in high-resolution observations of galaxy-galaxy strong gravitational lenses – I. Power-spectrum measurement and feasibility study
Authors: Bayer D , Koopmans L V E , McKean J P , Vegetti S , Treu T , Fassnacht C D , Glazebrook K 
Published: May 2023

ABSTRACT
While the direct detection of the dark-matter particle remains very challenging, the nature of dark matter could be possibly constrained by comparing the observed abundance and properties of small-scale sub-galactic mass structures with predictions from the phenomenological dark-matter models, such as cold, warm, or hot dark matter. Galaxy-galaxy strong gravitational lensing provides a unique opportunity to search for tiny surface-brightness anomalies in the extended lensed images (i.e. Einstein rings or gravitational arcs), induced by possible small-scale mass structures in the foreground lens galaxy. In this paper, the first in a series, we introduce and test a methodology to measure the power spectrum of such surface-brightness anomalies from high-resolution Hubble Space Telescope (HST) imaging. In particular, we focus on the observational aspects of this statistical approach, such as the most suitable observational strategy and sample selection, the choice of modelling techniques, and the noise correction. We test the feasibility of the power-spectrum measurement by applying it to a sample of galaxy-galaxy strong gravitational lens systems from the Sloan Lens ACS Survey, with the most extended, bright, high-signal-to-noise-ratio lensed images, observed in the rest-frame ultraviolet. In the companion paper, we present the methodology to relate the measured power spectrum to the statistical properties of the underlying small-scale mass structures in the lens galaxy and infer the first observational constraints on the sub-galactic matter power spectrum in a massive elliptical (lens) galaxy.
Three-dimensional dust stirring by a giant planet embedded in a protoplanetary disc
Authors: Binkert Fabian , Szulágyi Judit , Birnstiel Til 
Published: May 2023

ABSTRACT
The motion of solid particles embedded in gaseous protoplanetary discs is influenced by turbulent fluctuations. Consequently, the dynamics of moderately to weakly coupled solids can be distinctly different from the dynamics of the gas. Additionally, gravitational perturbations from an embedded planet can further impact the dynamics of solids. In this work, we investigate the combined effects of turbulent fluctuations and planetary dust stirring in a protoplanetary disc on three-dimensional dust morphology and on synthetic ALMA continuum observations. We carry out 3D radiative two-fluid (gas + 1-mm-dust) hydrodynamic simulations in which we explicitly model the gravitational perturbation of a Jupiter-mass planet. We derived a new momentum-conserving turbulent diffusion model that introduces a turbulent pressure to the pressureless dust fluid to capture the turbulent transport of dust. The model implicitly captures the effects of orbital oscillations and reproduces the theoretically predicted vertical settling-diffusion equilibrium. We find a Jupiter-mass planet to produce distinct and large-scale three-dimensional flow structures in the mm-sized dust, which vary strongly in space. We quantify these effects by locally measuring an effective vertical diffusivity (equivalent alpha) and find azimuthally averaged values in a range δeff ∼ 5 × 10−3–2 × 10−2 and local peaks at values of up to δeff ∼ 3 × 10−1. In synthetic ALMA continuum observations of inclined discs, we find effects of turbulent diffusion to be observable, especially at disc edges, and effects of planetary dust stirring in edge-on observations.
Timing analysis of Swift J0243.6+6124 with NICER and Fermi/GBM during the decay phase of the 2017–2018 outburst
Authors: Serim M M , Dönmez Ç K , Serim D , Ducci L , Baykal A , Santangelo A 
Published: May 2023

ABSTRACT
We present a timing and noise analysis of the Be/X-ray binary system Swift J0243.6+6124 during its 2017–2018 super-Eddington outburst using NICER/XTI observations. We apply a synthetic pulse timing analysis to enrich the Fermi/GBM spin frequency history of the source with the new measurements from NICER/XTI. We show that the pulse profiles switch from double-peaked to single-peaked when the X-ray luminosity drops below ∼7 × 1036 erg s−1. We suggest that this transitional luminosity is associated with the transition from a pencil beam pattern to a hybrid beam pattern when the Coulomb interactions become ineffective to decelerate the accretion flow, which implies a dipolar magnetic field strength of ∼5 × 1012 G. We also obtained the power density spectra (PDS) of the spin frequency derivative fluctuations. The red noise component of the PDS is found to be steeper (ω−3.36) than the other transient accreting sources. We find significantly high noise strength estimates above the super-Eddington luminosity levels, which may arise from the torque fluctuations due to interactions with the quadrupole fields at such levels.
Primordial non-Gaussianity with angular correlation function: integral constraint and validation for DES
Authors: Riquelme Walter , Avila Santiago , García-Bellido Juan , Porredon Anna , Ferrero Ismael , Chan Kwan Chuen , Rosenfeld Rogerio , Camacho Hugo , Adame Adrian G , Carnero Rosell Aurelio , Crocce Martin , De Vicente Juan , Eifler Tim , Elvin-Poole Jack , Fang Xiao , Krause Elisabeth , Rodriguez Monroy Martin , Ross Ashley J , Sanchez Eusebio , Sevilla Ignacio 
Published: May 2023

ABSTRACT
Local primordial non-Gaussianity (PNG) is a promising observable of the underlying physics of inflation, characterized by $f_{\rm NL}^{\rm loc}$. We present the methodology to measure $f_{\rm NL}^{\rm loc}$ from the Dark Energy Survey (DES) data using the two-point angular correlation function (ACF) with scale-dependent bias. One of the focuses of the work is the integral constraint (IC). This condition appears when estimating the mean number density of galaxies from the data and is key in obtaining unbiased $f_{\rm NL}^{\rm loc}$ constraints. The methods are analysed for two types of simulations: ∼246 goliat-png N-body small area simulations with fNL equal to −100 and 100, and 1952 Gaussian ice-cola mocks with fNL = 0 that follow the DES angular and redshift distribution. We use the ensemble of goliat-png mocks to show the importance of the IC when measuring PNG, where we recover the fiducial values of fNL within the 1σ when including the IC. In contrast, we found a bias of ΔfNL ∼ 100 when not including it. For a DES-like scenario, we forecast a bias of ΔfNL ∼ 23, equivalent to 1.8σ, when not using the IC for a fiducial value of fNL = 100. We use the ice-cola mocks to validate our analysis in a realistic DES-like set-up finding it robust to different analysis choices: best-fitting estimator, the effect of IC, BAO damping, covariance, and scale choices. We forecast a measurement of fNL within σ(fNL) = 31 when using the DES-Y3 BAO sample, with the ACF in the 1 deg &lt; θ &lt; 20 deg range.
The need for a risk-assessment tool among patients with chronic liver diseases interested in intermittent fasting: Ramadan model
Authors: Emara Mohamed H , Abdelaty Abdelaty I , Elbatae Hassan E , Abdelrazik Osama Mostafa , Elgammal Nahla E 
Published: May 2023

Abstract
Liver diseases, especially the chronic type, are a global concern. There is a growing interest in the intermittent fasting model due to its presumed health benefits. Ramadan fasting, although religious fasting, is one of the best examples of intermittent fasting, with some differences, and is observed by more than 1 billion Muslims around the world. This month follows the Arabic Hijri calendar, which is 12 days shorter than the Gregorian calendar; hence, this entire month of fasting may occur in any season of the year. There is evidence that many patients with chronic liver disease are prone to adverse events upon observing this month of continuous intermittent fasting, particularly during the hot summer with prolonged hours of fasting, if they are not adequately addressed and prevented from fasting. There is a need to sound the alarm to develop a risk-assessment tool to omit vulnerable patients with chronic liver disease—who are exempted on religious grounds from observing this pattern of fasting.
The Effects of Polarized Evaluations on Political Participation: Does Hating the Other Side Motivate Voters?
Authors: Ahn Chloe , Mutz Diana C 
Published: May 2023

Abstract
This study examines whether rising polarization in Americans’ partisan judgments has positive implications for political participation. Drawing on cross-sectional and panel survey data, we find evidence that polarized judgments are related to pre-election intent to vote, as well as to post-election self-reported voter turnout. Polarized evaluations also predict greater reporting of participation in campaign activities beyond voting. Polarization in candidate evaluations consistently has more of an impact than affective polarization. However, our results suggest that polarization in evaluations of both parties and candidates includes an expressive component that does not necessarily translate into political action. Roughly one-quarter to one-third of the actual change in turnout can potentially be attributed to polarization in evaluations of Republican and Democratic presidential candidates.
Data structures for photoadsorption within the ExoMol project
Authors: Tennyson Jonathan , Pezzella Marco , Zhang Jingxin , Yurchenko Sergei N 
Published: May 2023

Abstract
The ExoMol data base currently provides comprehensive line lists for modelling the spectroscopic properties of molecules in hot atmospheres. Extending the spectral range of the data provided to ultraviolet (UV) wavelengths brings into play three processes not currently accounted for in the ExoMol data structure, namely photodissociation, which is an important chemical process in its own right, the opacity contribution due to continuum absorption, and predissociation which can lead to significant and observable line-broadening effects. Data structures are proposed which will allow these processes to be correctly captured and the (strong) temperature-dependent effects predicted for UV molecular photoabsorption in general and photodissociation in particular to be represented.
Health-related quality of life in patients with ANCA vasculitides compared to rheumatoid arthritis: a cross-sectional comparative study
Authors: Panagiotopoulos Alexandros , Thomas Konstantinos , Argyriou Evangelia , Chalkia Aglaia , Kapsala Noemin , Koutsianas Christos , Mavrea Evgenia , Petras Dimitrios , Boumpas Dimitrios T , Vassilopoulos Dimitrios 
Published: May 2023

Abstract

Objectives
There are limited data regarding health-related quality of life (HRQoL) in patients with ANCA-associated vasculitides (AAVs). We aimed to evaluate the HRQoL in patients with AAVs and compare it to another chronic inflammatory disease like RA and to healthy controls (HC).

Methods
This was a multicentre, cross-sectional study of patients with AAVs and RA recruited from three tertiary rheumatology clinics. HRQoL was assessed with the Short Form 36 Health Survey, which included the physical and mental component summary scores (PCS and MCS). Data from 1007 HC served as historical controls.

Results
Sixty-six patients with AAVs and 71 with RA were included. Both AAV and RA patients had significantly lower PCS and MCS scores compared with HC (P &lt; 0.05). HRQoL in AAV patients was worse in patients with microscopic polyangiitis compared with granulomatosis with polyangiitis (physical components) and those with high (VDI ≥ 3) vs low (VDI &lt; 3) damage scores while it did not differ between those with active (BVASv3 ≥ 1) vs. inactive (BVASv3 &lt; 1) disease. In contrast, in RA patients, HRQoL correlated both with disease activity (assessed by the DAS28-ESR) and functional impairment/damage (assessed by the HAQ). Although overall patients with RA had similar HRQoL compared with those with AAVs, those with active RA had worse HRQoL compared with those with active AAV.

Conclusions
In patients with AAVs, HRQoL correlated more with organ damage and less with disease activity whereas in RA patients, it correlated with both. These data emphasize the need for AAV therapies aiming at preventing organ damage and thus improving HRQoL.