bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the HERA Phase I receiver system with simulations and its impact on the detectability of the EoR delay power spectrum
Authors: Fagnoni Nicolas , de Lera Acedo Eloy , DeBoer David R , Abdurashidova Zara , Aguirre James E , Alexander Paul , Ali Zaki S , Balfour Yanga , Beardsley Adam P , Bernardi Gianni , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Bull Phil , Burba Jacob , Carilli Chris L , Cheng Carina , Dexter Matt , Dillon Joshua S , Ewall-Wice Aaron , Fritz Randall , Furlanetto Steve R , Gale-Sides Kingsley , Glendenning Brian , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Halday Ziyaad , Hazelton Bryna J , Hewitt Jacqueline N , Hickish Jack , Jacobs Daniel C , Josaitis Alec , Julius Austin , Kern Nicholas S , Kerrigan Joshua , Kim Honggeun , Kittiwisit Piyanat , Kohn Saul A , Kolopanis Matthew , Lanman Adam , Plante Paul La , Lekalake Telalo , Liu Adrian , MacMahon David , Malan Lourence , Malgas Cresshim , Maree Matthys , Martinot Zachary E , Matsetela Eunice , Mena Parra Juan , Mesinger Andrei , Molewa Mathakane , Morales Miguel F , Mosiane Tshegofalang , Neben Abraham R , Nikolic Bojan , Parsons Aaron R , Patra Nipanjana , Pieterse Samantha , Pober Jonathan C , Razavi-Ghods Nima , Robnett James , Rosie Kathryn , Sims Peter , Smith Craig , Syce Angelo , Thyagarajan Nithyanandan , Williams Peter K G , Zheng Haoxuan 
Published: October 2020

ABSTRACT
The detection of the Epoch of Reionization (EoR) delay power spectrum using a ‘foreground avoidance method’ highly depends on the instrument chromaticity. The systematic effects induced by the radio telescope spread the foreground signal in the delay domain, which contaminates the EoR window theoretically observable. Applied to the Hydrogen Epoch of Reionization Array (HERA), this paper combines detailed electromagnetic and electrical simulations in order to model the chromatic effects of the instrument, and quantify its frequency and time responses. In particular, the effects of the analogue receiver, transmission cables, and mutual coupling are included. These simulations are able to accurately predict the intensity of the reflections occurring in the 150-m cable which links the antenna to the backend. They also show that electromagnetic waves can propagate from one dish to another one through large sections of the array due to mutual coupling. The simulated system time response is attenuated by a factor 104 after a characteristic delay which depends on the size of the array and on the antenna position. Ultimately, the system response is attenuated by a factor 105 after 1400 ns because of the reflections in the cable, which corresponds to characterizable k∥-modes above 0.7 $h\,\,\rm {Mpc}^{-1}$ at 150 MHz. Thus, this new study shows that the detection of the EoR signal with HERA Phase I will be more challenging than expected. On the other hand, it improves our understanding of the telescope, which is essential to mitigate the instrument chromaticity.
Determining the systemic redshift of Lyman α emitters with neural networks and improving the measured large-scale clustering
Authors: Gurung-López Siddhartha , Saito Shun , Baugh Carlton M , Bonoli Silvia , Lacey Cedric G , Orsi Álvaro A 
Published: October 2020

ABSTRACT
We explore how to mitigate the clustering distortions in Lyman α emitter (LAE) samples caused by the misidentification of the Lyman α ($\rm {Ly}\,\alpha$) wavelength in their $\rm {Ly}\,\alpha$ line profiles. We use the $\rm {Ly}\,\alpha$ line profiles from our previous LAE theoretical model that includes radiative transfer in the interstellar and intergalactic mediums. We introduce a novel approach to measure the systemic redshift of LAEs from their $\rm {Ly}\,\alpha$ line using neural networks. In detail, we assume that for a fraction of the whole LAE population their systemic redshift is determined precisely through other spectral features. We then use this subset to train a neural network that predicts the $\rm {Ly}\,\alpha$ wavelength given an $\rm {Ly}\,\alpha$ line profile. We test two different training sets: (i) the LAEs are selected homogeneously and (ii) only the brightest LAE is selected. In comparison with previous approaches in the literature, our methodology improves significantly the accuracy in determining the $\rm {Ly}\,\alpha$ wavelength. In fact, after applying our algorithm in ideal $\rm {Ly}\,\alpha$ line profiles, we recover the clustering unperturbed down to $1\, {\rm cMpc}\, h^{-1}$. Then, we test the performance of our methodology in realistic $\rm {Ly}\,\alpha$ line profiles by downgrading their quality. The machine learning technique using the uniform sampling works well even if the $\rm {Ly}\,\alpha$ line profile quality is decreased considerably. We conclude that LAE surveys such as HETDEX would benefit from determining with high accuracy the systemic redshift of a subpopulation and applying our methodology to estimate the systemic redshift of the rest of the galaxy sample.
Detailed studies of IPHAS sources - I. The disrupted late bipolar IPHASX J193718.6+202102
Authors: Sabin L , Guerrero M A , Zavala S , Toalá J A , Ramos-Larios G , Gómez-Llanos V 
Published: October 2020

Abstract
We present a detailed analysis of the new planetary nebula (PN) IPHASX J193718.6+202102 using deep imaging and intermediate- and high resolution spectroscopy that are interpreted through morpho-kinematic and photoionisation modelling. The physical structure of the nebula consists of a fragmented torus and an extremely faint orthogonal bipolar outflow, contrary to the pinched waist PN morphology suggested by its optical image. Our kinematic analysis indicates that the torus is expanding at 25±5 km s−1 and is gradually breaking up. At an estimated distance of 7.1$_{-0.3}^{+0.8}$ kpc, the corresponding kinematic age of ∼26000 years is consistent with a faint and disintegrating PN. The intermediate-resolution spectra reveal an excited PN with chemical abundances typical of Type II PNe. Based on the latter we also estimate an initial mass for the progenitor in the range 2–3 M⊙ and a central star (CSPN) mass MCSPN ∼0.61 M⊙. The Spitzer MIPS 24 μm emission that closely follows the fragmented torus could be attributed to the emission of [O iv] at 25.9 μm rather than to dust emission. All the results coherently point towards an evolved moderately massive bipolar Type II PN on the brink of dissolving into the interstellar medium.
Metallicity and X-ray luminosity variations in NGC 922
Authors: Kouroumpatzakis K , Zezas A , Wolter A , Fruscione A , Anastasopoulou K , Prestwich A 
Published: October 2020

ABSTRACT
We present a systematic study of the metallicity variations within the collisional ring galaxy NGC 922 based on long-slit optical spectroscopic observations. We find a metallicity difference between star-forming regions in the bulge and the ring, with metallicities ranging from almost solar to significantly sub-solar ($\rm {[12+\log (O/H)]\sim 8.2}$). We detect $\rm{He\,{\small I}}$ emission in all the studied regions of the bulge and the ring, indicating ionization from massive stars associated with recent (&lt;10 Myr) star formation, in agreement with the presence of very young star clusters. We find an anticorrelation between the X-ray luminosity and metallicity of the sub-galactic regions of NGC 922. The different regions have similar stellar population ages, leaving metallicity as the main driver of the anticorrelation. The dependence of the X-ray emission of the different regions in NGC 922 on metallicity is in agreement with similar studies of the integrated X-ray output of galaxies and predictions from X-ray binary population models.
Combining ILC and moment expansion techniques for extracting average-sky signals and CMB anisotropies
Authors: Rotti Aditya , Chluba Jens 
Published: October 2020

Abstract
The method of weighted addition of multi-frequency maps, more commonly referred to as Internal Linear Combination (ILC), has been extensively employed in the measurement of cosmic microwave background (CMB) anisotropies and its secondaries along with similar application in 21cm data analysis. Here we argue and demonstrate that ILC methods can also be applied to data from absolutely-calibrated CMB experiments to extract average-sky signals in addition to the conventional CMB anisotropies. The performance of the simple ILC method is, however, limited, but can be significantly improved by adding constraints informed by physics and existing empirical information. In recent work, a moment description has been introduced as a technique of carrying out high precision modeling of foregrounds in the presence of inevitable averaging effects. We combine these two approaches to construct a heavily constrained form of the ILC, dubbed MILC, which can be used to recover tiny monopolar spectral distortion signals in the presence of realistic foregrounds and instrumental noise. This is a first demonstration for measurements of the monopolar and anisotropic spectral distortion signals using ILC and extended moment methods. We also show that CMB anisotropy measurements can be improved, reducing foreground biases and signal uncertainties when using the MILC. While here we focus on CMB spectral distortions, the scope extends to the 21cm monopole signal and B-mode analysis. We briefly discuss augmentations that need further study to reach the full potential of the method.
Evaluating hydrodynamical simulations with green valley galaxies
Authors: Angthopo J , Negri A , Ferreras I , de la Rosa I G , Dalla Vecchia C , Pillepich A 
Published: October 2020

ABSTRACT
We test cosmological hydrodynamical simulations of galaxy formation regarding the properties of the blue cloud (BC), green valley (GV), and red sequence (RS), as measured on the 4000Å break strength versus stellar mass plane at z = 0.1. We analyse the RefL0100N1504 run of EAGLE and the TNG100 run of IllustrisTNG project, by comparing them with the Sloan Digital Sky Survey (SDSS), while taking into account selection bias. Our analysis focuses on the GV, within stellar mass $\log \, \mathrm{{\it M}_\star /M_{\odot }} \simeq 10\!-\!11$, selected from the bimodal distribution of galaxies on the Dn(4000) versus stellar mass plane, following Angthopo et al. methodology. Both simulations match the fraction of AGN in the GV. However, they overproduce quiescent GV galaxies with respect to observations, with IllustrisTNG yielding a higher fraction of quiescent GV galaxies than EAGLE. In both, GV galaxies have older luminosity-weighted ages with respect to the SDSS, while a better match is found for mass-weighted ages. We find EAGLE GV galaxies quench their star formation early, but undergo later episodes of star formation, matching observations. In contrast, IllustrisTNG GV galaxies have a more extended star formation history, and quench more effectively at later cosmic times, producing the excess of quenched galaxies in GV compared with SDSS, based on the 4000Å break strength. These results suggest the AGN feedback subgrid physics, more specifically, the threshold halo mass for black hole input and the black hole seed mass, could be the primary cause of the overproduction of quiescent galaxies found with respect to the observational constraints.
Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences
Authors: Georgakopoulos-Soares Ilias , Mouratidis Ioannis , Parada Guillermo E , Matharu Navneet , Hemberg Martin , Ahituv Nadav 
Published: October 2020

Abstract
DNA strand asymmetries can have a major effect on several biological functions, including replication, transcription and transcription factor binding. As such, DNA strand asymmetries and mutational strand bias can provide information about biological function. However, a versatile tool to explore this does not exist. Here, we present Asymmetron, a user-friendly computational tool that performs statistical analysis and visualizations for the evaluation of strand asymmetries. Asymmetron takes as input DNA features provided with strand annotation and outputs strand asymmetries for consecutive occurrences of a single DNA feature or between pairs of features. We illustrate the use of Asymmetron by identifying transcriptional and replicative strand asymmetries of germline structural variant breakpoints. We also show that the orientation of the binding sites of 45% of human transcription factors analyzed have a significant DNA strand bias in transcribed regions, that is also corroborated in ChIP-seq analyses, and is likely associated with transcription. In summary, we provide a novel tool to assess DNA strand asymmetries and show how it can be used to derive new insights across a variety of biological disciplines.
Viral RNA recognition by LGP2 and MDA5, and activation of signaling through step-by-step conformational changes
Authors: Duic Ivana , Tadakuma Hisashi , Harada Yoshie , Yamaue Ryo , Deguchi Katashi , Suzuki Yuki , Yoshimura Shige H , Kato Hiroki , Takeyasu Kunio , Fujita Takashi 
Published: October 2020

Abstract
Cytoplasmic RIG-I-like receptor (RLR) proteins in mammalian cells recognize viral RNA and initiate an antiviral response that results in IFN-β induction. Melanoma differentiation-associated protein 5 (MDA5) forms fibers along viral dsRNA and propagates an antiviral response via a signaling domain, the tandem CARD. The most enigmatic RLR, laboratory of genetics and physiology (LGP2), lacks the signaling domain but functions in viral sensing through cooperation with MDA5. However, it remains unclear how LGP2 coordinates fiber formation and subsequent MDA5 activation. We utilized biochemical and biophysical approaches to observe fiber formation and the conformation of MDA5. LGP2 facilitated MDA5 fiber assembly. LGP2 was incorporated into the fibers with an average inter-molecular distance of 32 nm, suggesting the formation of hetero-oligomers with MDA5. Furthermore, limited protease digestion revealed that LGP2 induces significant conformational changes on MDA5, promoting exposure of its CARDs. Although the fibers were efficiently dissociated by ATP hydrolysis, MDA5 maintained its active conformation to participate in downstream signaling. Our study demonstrated the coordinated actions of LGP2 and MDA5, where LGP2 acts as an MDA5 nucleator and requisite partner in the conversion of MDA5 to an active conformation. We revealed a mechanistic basis for LGP2-mediated regulation of MDA5 antiviral innate immune responses.
Early versus late acute kidney injury among patients with COVID-19—a multicenter study from Wuhan, China
Authors: Peng Suyuan , Wang Huai-Yu , Sun Xiaoyu , Li Pengfei , Ye Zhanghui , Li Qing , Wang Jinwei , Shi Xuanyu , Liu Liu , Yao Ying , Zeng Rui , He Fan , Li Junhua , Ge Shuwang , Ke Xianjun , Zhou Zhibin , Dong Erdan , Wang Haibo , Xu Gang , Zhang Luxia , Zhao Ming-Hui 
Published: October 2020

Abstract

Background
Acute kidney injury (AKI) is an important complication of coronavirus disease 2019 (COVID-19), which could be caused by both systematic responses from multi-organ dysfunction and direct virus infection. While advanced evidence is needed regarding its clinical features and mechanisms. We aimed to describe two phenotypes of AKI as well as their risk factors and the association with mortality.

Methods
Consecutive hospitalized patients with COVID-19 in tertiary hospitals in Wuhan, China from 1 January 2020 to 23 March 2020 were included. Patients with AKI were classified as AKI-early and AKI-late according to the sequence of organ dysfunction (kidney as the first dysfunctional organ or not). Demographic and clinical features were compared between two AKI groups. Their risk factors and the associations with in-hospital mortality were analyzed.

Results
A total of 4020 cases with laboratory-confirmed COVID-19 were included and 285 (7.09%) of them were identified as AKI. Compared with patients with AKI-early, patients with AKI-late had significantly higher levels of systemic inflammatory markers. Both AKIs were associated with an increased risk of in-hospital mortality, with similar fully adjusted hazard ratios of 2.46 [95% confidence interval (CI) 1.35–4.49] for AKI-early and 3.09 (95% CI 2.17–4.40) for AKI-late. Only hypertension was independently associated with the risk of AKI-early. While age, history of chronic kidney disease and the levels of inflammatory biomarkers were associated with the risk of AKI-late.

Conclusions
AKI among patients with COVID-19 has two clinical phenotypes, which could be due to different mechanisms. Considering the increased risk for mortality for both phenotypes, monitoring for AKI should be emphasized during COVID-19.
Comorbidities and outcomes in South Asian individuals with chronic kidney disease: an observational primary care cohort
Authors: Major Rupert W , Shepherd David , Medcalf James F , Xu Gang , Gray Laura J , Brunskill Nigel J 
Published: October 2020

Abstract

Background
South Asian (SA) individuals are more likely to develop end-stage renal disease (ESRD), but how chronic kidney disease (CKD) differs in relation to demographics, comorbidities and outcomes has not been studied. We aimed to study differences in SA individuals with CKD compared with White individuals.

Methods
This was an observational CKD cohort comparing SA with White individuals. Inclusion criteria were ≥18 years of age and two or more Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) eGFRs &lt;60 mL/min/1.73 m2 &gt;3 months apart. Individuals with ESRD at baseline were excluded. Baseline characteristics, including eGFR formulae [CKD-EPI and CKD-EPI-Pakistan (CKD-EPI-PK)], were compared. Analysis using competing risk regression for cardiovascular (CV) and ESRD events and Cox proportional hazard model for mortality was performed.

Results
From an adult population of 277 248 individuals, 17 248 individuals had CKD, of whom 1990 (11.5%) were of SA ethnicity. Age-adjusted prevalence of CKD was similar between ethnicities. SA individuals were more likely to be male, younger and socioeconomically deprived, and to have diabetes mellitus, CV disease and advanced CKD. Mean CKD-EPI-PK eGFR was 6.5 mL/min/1.73 m2 lower (41.1 versus 47.6, 95% confidence interval for difference 6.47–6.56) than for CKD-EPI. During 5 years of follow-up, 5109 (29.6%) individuals died, 2072 (12.0%) had a CV and 156 (0.90%) an ESRD event. Risk for SA individuals was higher for ESRD, similar to CV events and lower for mortality. Each 1 mL/min/1.73 m2 decrease in CKD-EPI-PK was associated with a 13.1% increased ESRD risk (adjusted subdistribution hazard ratio 0.869, 95% confidence interval 0.841–0.898).

Conclusions
SA individuals with CKD were younger and had more advanced disease than White individuals. Risk of ESRD was higher and CKD-EPI-PK was associated with ESRD risk in SA individuals. Specific CKD interventions, including the use of CKD-EPI-PK, should be considered in SA populations.
Investigating new treatment opportunities for patients with chronic kidney disease in type 2 diabetes: the role of finerenone
Authors: Agarwal Rajiv , Anker Stefan D , Bakris George , Filippatos Gerasimos , Pitt Bertram , Rossing Peter , Ruilope Luis , Gebel Martin , Kolkhof Peter , Nowack Christina , Joseph Amer ,   on behalf of the FIDELIO-DKD and FIGARO-DKD Investigators
Published: October 2020

Abstract
Despite the standard of care, patients with chronic kidney disease (CKD) and type 2 diabetes (T2D) progress to dialysis, are hospitalized for heart failure and die prematurely. Overactivation of the mineralocorticoid receptor (MR) causes inflammation and fibrosis that damages the kidney and heart. Finerenone, a nonsteroidal, selective MR antagonist, confers kidney and heart protection in both animal models and Phase II clinical studies; the effects on serum potassium and kidney function are minimal. Comprising the largest CKD outcomes program to date, FIDELIO-DKD (FInerenone in reducing kiDnEy faiLure and dIsease prOgression in Diabetic Kidney Disease) and FIGARO-DKD (FInerenone in reducinG cArdiovascular moRtality and mOrbidity in Diabetic Kidney Disease) are Phase III trials investigating the efficacy and safety of finerenone on kidney failure and cardiovascular outcomes from early to advanced CKD in T2D. By including echocardiograms and biomarkers, they extend our understanding of pathophysiology; by including quality of life measurements, they provide patient-centered outcomes; and by including understudied yet high-risk cardiorenal subpopulations, they have the potential to widen the scope of therapy in T2D with CKD.
Trial registration number: FIDELIO-DKD (NCT02540993) and FIGARO-DKD (NCT02545049)
Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification
Authors: Xu Wei , Dong Wen-Jie , Fu Ting-Ting , Gao Wei , Lu Chen-Qi , Yan Fang , Wu Yun-He , Jiang Ke , Jin Jie-Qiong , Chen Hong-Man , Zhang Ya-Ping , Hillis David M , Che Jing 
Published: October 2020

Abstract
The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. The Himalayan region is a relatively small area but with exceptional diversity and endemism. One common hypothesis to explain the rich montane diversity is uplift-driven diversification—that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We test this hypothesis in the Himalayan region using amphibians and reptiles, two environmentally sensitive vertebrate groups. In addition, analysis of diversification of the herpetofauna provides an independent source of information to test competing geological hypotheses of Himalayan orogenesis. We conclude that the origins of the Himalayan herpetofauna date to the early Paleocene, but that diversification of most groups was concentrated in the Miocene. There was an increase in both rates and modes of diversification during the early to middle Miocene, together with regional interchange (dispersal) between the Himalaya and adjacent regions. Our analyses support a recently proposed stepwise geological model of Himalayan uplift beginning in the Paleocene, with a subsequent rapid increase of uplifting during the Miocene, finally giving rise to the intensification of the modern South Asian Monsoon.
Capital Accumulation, Supply Networks and the Composition of the Roman Senate, 14–235 ce
Authors: Weisweiler John 
Published: October 2020

Abstract
In the first two centuries ce, the Roman senate transformed from an assembly of Italian landowners into a multi-regional group. The admission of thousands of provincials into Rome’s governing elite is often taken as evidence for the successful integration of subject populations. This article challenges such views of the senate as an inclusive institution. It shows that the overwhelming majority of non-Italian senators came from merely four (out of more than thirty) provinces: Baetica (in southern Spain), Narbonensis (Provence), Africa (the coastlines of Algeria, Tunisia and Libya) and Asia (western Anatolia). The elites of these regions entertained close links to Italy since the second century bce. In the first centuries ce, they acquired enormous wealth through predation, through investments in capital-intensive agriculture and through their ability to exploit state supply networks for their own benefit. The steep rise in the number of provincial senators should thus not be read as evidence for the large-scale participation of conquered groups in the imperial administration. Rather, it chiefly was a product of the new opportunities for wealth accumulation and exploitation generated by Roman imperialism.