bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core-collapse supernova neutrino emission and detection informed by state-of-the-art three-dimensional numerical models
Authors: Nagakura Hiroki , Burrows Adam , Vartanyan David , Radice David 
Published: October 2020

ABSTRACT
Based on our recent three-dimensional core-collapse supernova (CCSN) simulations including both exploding and non-exploding models, we study the detailed neutrino signals in representative terrestrial neutrino observatories, namely Super-Kamiokande (Hyper-Kamiokande), DUNE, JUNO, and IceCube. We find that the physical origin of difference in the neutrino signals between 1D and 3D is mainly proto-neutron-star convection. We study the temporal and angular variations of the neutrino signals and discuss the detectability of the time variations driven by the spiral standing accretion shock instability (spiral SASI) when it emerges for non-exploding models. In addition, we determine that there can be a large angular asymmetry in the event rate (${\gtrsim} 50 {{\ \rm per\ cent}}$), but the time-integrated signal has a relatively modest asymmetry (${\lesssim} 20 {{\ \rm per\ cent}}$). Both features are associated with the lepton-number emission self-sustained asymmetry and the spiral SASI. Moreover, our analysis suggests that there is an interesting correlation between the total neutrino energy (TONE) and the cumulative number of neutrino events in each detector, a correlation that can facilitate data analyses of real observations. We demonstrate the retrieval of neutrino energy spectra for all flavours of neutrino by applying a novel spectrum reconstruction technique to the data from multiple detectors. We find that this new method is capable of estimating the TONE within the error of ∼20 per cent if the distance to the CCSN is ≲6 kpc.
Double-peaked Lyman α emission at z = 6.803: a reionization-era galaxy self-ionizing its local H ii bubble
Authors: Meyer Romain A , Laporte Nicolas , Ellis Richard S , Verhamme Anne , Garel Thibault 
Published: October 2020

ABSTRACT
We report the discovery of a double-peaked Lyman α profile in a galaxy at z = 6.803, A370p_z1, in the parallel Frontier Field of Abell 370. The velocity separation between the blue and red peaks of the Lyman α profile ($\Delta v=101_{-19}^{+38} (\pm 48)\, \rm km\, \rm s^{-1}$) suggests an extremely high escape fraction of ionizing photons $\gt 59(51){{\ \rm per\ cent}} (2\sigma)$. The spectral energy distribution indicates a young (50 Myr), star-forming ($12\pm 6 \, \rm {M}_\odot \rm {yr}^{-1}$) galaxy with an IRAC excess implying strong [O iii] + H β emission. On the basis of the high escape fraction measured, we demonstrate that A370p_z1 was solely capable of creating an ionized bubble sufficiently large to account for the blue component of its Lyman α profile. We discuss whether A370p_z1 may be representative of a larger population of luminous z ≃ 7 double-peaked Lyman α emitting sources with high escape fractions that self-ionized their surroundings without contributions from associated ultraviolet-fainter sources.
Calibration schemes with O(N log N) scaling for large-N radio interferometers built on a regular grid
Authors: Gorthi Deepthi B , Parsons Aaron R , Dillon Joshua S 
Published: October 2020

ABSTRACT
Future generations of radio interferometers targeting the 21 cm signal at cosmological distances with N ≫ 1000 antennas could face a significant computational challenge in building correlators with the traditional architecture, whose computational resource requirement scales as $\mathcal {O}(N^2)$ with array size. The fundamental output of such correlators is the cross-correlation products of all antenna pairs in the array. The FFT-correlator architecture reduces the computational resources scaling to $\mathcal {O}(N\log {N})$ by computing cross-correlation products through a spatial Fourier transform. However, the output of the FFT-correlator is meaningful only when the input antenna voltages are gain- and phase-calibrated. Traditionally, interferometric calibration has used the $\mathcal {O}(N^2)$ cross-correlations produced by a standard correlator. This paper proposes two real-time calibration schemes that could work in parallel with an FFT-correlator as a self-contained $\mathcal {O}(N\log {N})$ correlator system that can be scaled to large-N redundant arrays. We compare the performance and scalability of these two calibration schemes and find that they result in antenna gains whose variance decreases as 1/log N with increase in the size of the array.
AzTEC survey of the central molecular zone: increasing spectral index of dust with density
Authors: Tang Yuping , Wang Q Daniel , Wilson Grant W 
Published: October 2020

ABSTRACT
The central molecular zone (CMZ) of our Galaxy hosts an extreme environment analogous to that found in typical starburst galaxies in the distant Universe. In order to understand dust properties in environments like our CMZ, we present results from a joint spectral energy distribution analysis of our AzTEC/Large Millimeter Telescope survey, together with existing Herschel far-IR data on the CMZ, from a wavelength range of 160 $\mu {\rm m}$ to 1.1 mm. We include global foreground and background contributions in a novel Bayesian modelling that incorporates the point spread functions of the different maps, which enables the full utilization of our high-resolution (10.5 arcsec) map at 1.1 mm and reveals unprecedentedly detailed information on the spatial distribution of dusty gas across the CMZ. There is a remarkable trend of increasing dust spectral index β, from 2.0 to 2.4, towards dense peaks in the CMZ, indicating a deficiency of large grains or a fundamental change in dust optical properties. This environmental dependence of β could have a significant impact on the determination of dust temperature in other studies. Depending on how the optical properties of dust deviate from the conventional model, dust temperatures could be underestimated by $10\!-\!50{{\ \rm per\ cent}}$ in particularly dense regions.
Constraining the cross-section of dark matter with giant radial arcs in galaxy clusters
Authors: Vega-Ferrero J , Dana J M , Diego J M , Yepes G , Cui W , Meneghetti M 
Published: October 2020

ABSTRACT
We compare the statistics and morphology of giant arcs in galaxy clusters using N-body and non-radiative SPH simulations within the standard cold dark matter (CDM) model and simulations where dark matter (DM) has a non-negligible probability of interaction (parametrized by its cross-section), i.e self-interacting dark matter (SIDM). We use a ray-tracing technique to produce a statistically large number of arcs around six simulated galaxy clusters at different redshifts. Since DM is more likely to interact in colliding clusters than in relaxed clusters, and this probability of interaction is largest in denser regions, we focus our analysis on radial arcs (which trace the lensing potential in the central region better than tangential arcs) in galaxy clusters that underwent (or are undergoing) a major merger. We find that SIDM produces fewer radial arcs than standard CDM but they are on average more magnified. We also appreciate differences in the arc morphology that could be used to statistically favour one model versus the other.
Simulations of common envelope evolution in triple systems: circumstellar case
Authors: Glanz Hila , Perets Hagai B 
Published: October 2020

ABSTRACT
The dynamical evolution of triple stellar systems could induce the formation of compact binaries and binary mergers. Common envelope (CE) evolution, which plays a major role in the evolution of compact binary systems, can similarly play a key role in the evolution of triples. Here, we use hydrodynamical simulations coupled with few-body dynamics to provide the first detailed models of the triple common envelope (TCE) evolution. We focus on the circumstellar case, where the envelope of an evolved giant engulfs a compact binary orbiting the giant, which then in-spirals into the core of the evolved star. Through our exploratory modelling, we find several possible outcomes of such TCE: the merger of the binary inside the third star’s envelope; the disruption of the in-spiralling binary following its plunge, leading to a chaotic triple dynamics of the stellar core and the two components of the former disrupted binary. The chaotic evolution typically leads to the in-spiral and merger of at least one of the former binary components with the core, and sometimes to the ejection of the second, or alternatively its further now-binary CE evolution. The in-spiral in TCE leads to overall slower in-spiral, larger mass ejection, and the production of more aspherical remnant, compared with a corresponding binary case of similar masses, due to the energy/momentum extraction from the inner-binary. We expect TCE to play a key role in producing various types of stellar-mergers and unique compact binary systems, and potentially induce transient electromagnetic and gravitational wave sources.
Self-modulation of fast radio bursts
Authors: Sobacchi Emanuele , Lyubarsky Yuri , Beloborodov Andrei M , Sironi Lorenzo 
Published: October 2020

ABSTRACT
Fast radio bursts (FRBs) are extreme astrophysical phenomena entering the realm of non-linear optics, a field developed in laser physics. A classical non-linear effect is self-modulation. We examine the propagation of FRBs through the circumburst environment using the idealized setup of a monochromatic linearly polarized GHz wave propagating through a uniform plasma slab of density N at distance R from the source. We find that self-modulation occurs if the slab is located within a critical radius Rcrit ∼ 1017(N/102 cm−3)(L/1042 erg s−1) cm, where L is the isotropic equivalent of the FRB luminosity. Self-modulation breaks the burst into pancakes transverse to the radial direction. When R ≲ Rcrit, the transverse size of the pancakes is smaller than the Fresnel scale. The pancakes are strongly diffracted as the burst exits the slab, and interference between the pancakes produces a frequency modulation of the observed intensity with a sub-GHz bandwidth. When R ∼ Rcrit, the transverse size of the pancakes becomes comparable with the Fresnel scale, and the effect of diffraction is weaker. The observed intensity is modulated on a time-scale of 10 µm, which corresponds to the radial width of the pancakes. Our results suggest that self-modulation may cause the temporal and frequency structure observed in FRBs.
Light and colour variations of Mira variables in the Small Magellanic Cloud
Authors: Ita Yoshifusa , Menzies John W , Whitelock Patricia A , Matsunaga Noriyuki , Takayama Masaki , Nakada Yoshikazu , Tanabé Toshihiko , Feast Michael W , Nagayama Takahiro 
Published: October 2020

ABSTRACT
The goal of this paper is to characterize the light variation properties of Mira variables in the Small Magellanic Cloud. We have investigated a combined optical and near-infrared multi-epoch data set of Mira variables based on our monitoring data obtained over 15 yr. Bolometric correction relations are formulated for various near-infrared colours. We find that the same bolometric correction equation holds for both the bolometricly brightest and faintest pulsation phases. Period–bolometric magnitude relations and period–colour relations were derived using time-averaged values. Phase lags between bolometric phase and optical and near-infrared phases were detected from the O-rich (the surface C/O number ratio is below unity) Mira variables, while no significant systematic lags were observed in most of the C-rich (the C/O ratio is over unity) ones. Some Miras show colour phase inversions, e.g. H–Ks at its bluest while J–H and J–Ks are at their reddest values at about the bolometricly brightest phase. Their occurrence conditions were studied but no clear direct or indirect trigger was found. A large NIR colour change unassociated with stellar pulsation was observed in Miras with long secondary periods, and its possible explanation is described.
Radical Empiricism, Neutral Monism, and the Elements of Mind
Authors: Wishon Donovan 
Published: October 2020

AbstractNeutral monism is the view that both ‘mind’ and ‘matter’ are grounded in a more fundamental form of reality that is intrinsically neither mental nor material. It has often been treated as an odd fringe theory deserving of at most a footnote in the broader philosophical debates. Yet such attitudes do a grave disservice to its sophistications and significance for late nineteenth and early twentieth-century philosophy of mind and psychology. This paper sheds light on this neglected view by situating it within broader historical monist debates about the mind and bringing attention to one of its central internal disputes regarding ‘mental chemistry’. By taking a closer look at how Ernst Mach, William James, and Bertrand Russell address the question of whether and how our mental episodes are composed of more basic elements, it highlights deep differences among their conceptions of the fundamental ‘neutral stuff’ and its relations to ‘mind’ and ‘matter’.
Epigenome engineering: new technologies for precision medicine
Authors: Sgro Agustin , Blancafort Pilar 
Published: October 2020

AbstractChromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more ‘normal-like state’, having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
The Transporter Classification Database (TCDB): 2021 update
Authors: Saier Milton H , Reddy Vamsee S , Moreno-Hagelsieb Gabriel , Hendargo Kevin J , Zhang Yichi , Iddamsetty Vasu , Lam Katie Jing Kay , Tian Nuo , Russum Steven , Wang Jianing , Medrano-Soto Arturo 
Published: October 2020

Abstract
The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB) and now (October 1, 2020) consists of 20 653 proteins classified in 15 528 non-redundant transport systems with 1567 tabulated 3D structures, 18 336 reference citations describing 1536 transporter families, of which 26% are members of 82 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. This comprehensive update of the database contents and features include (i) adoption of a chemical ontology for substrates of transporters, (ii) inclusion of new superfamilies, (iii) a domain-based characterization of transporter families for the identification of new members as well as functional and evolutionary relationships between families, (iv) development of novel software to facilitate curation and use of the database, (v) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators and (vi) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment
Authors: Sun Dongqing , Wang Jin , Han Ya , Dong Xin , Ge Jun , Zheng Rongbin , Shi Xiaoying , Wang Binbin , Li Ziyi , Ren Pengfei , Sun Liangdong , Yan Yilv , Zhang Peng , Zhang Fan , Li Taiwen , Wang Chenfei 
Published: October 2020

Abstract
Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy. Here, we present Tumor Immune Single Cell Hub (TISCH, http://tisch.comp-genomics.org), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.
Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding
Authors: Chen Hao , Egger Michaela , Xu Xiaochen , Flemmich Laurin , Krasheninina Olga , Sun Aiai , Micura Ronald , Ren Aiming 
Published: October 2020

Abstract
Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD+. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD+ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg2+-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2).
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes
Authors: Brunet Marie A , Lucier Jean-François , Levesque Maxime , Leblanc Sébastien , Jacques Jean-Francois , Al-Saedi Hassan R H , Guilloy Noé , Grenier Frederic , Avino Mariano , Fournier Isabelle , Salzet Michel , Ouangraoua Aïda , Scott Michelle S , Boisvert François-Michel , Roucou Xavier 
Published: October 2020

AbstractOpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one’s bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.
A phase II study of dose-dense temozolomide and lapatinib for recurrent low-grade and anaplastic supratentorial, infratentorial, and spinal cord ependymoma
Authors: Gilbert Mark R , Yuan Ying , Wu Jimin , Mendoza Tito , Vera Elizabeth , Omuro Antonio , Lieberman Frank , Robins H Ian , Gerstner Elizabeth R , Wu Jing , Wen Patrick Y , Mikkelsen Tom , Aldape Kenneth , Armstrong Terri S 
Published: October 2020

AbstractBackgroundNo standard medical treatment exists for adult patients with recurrent ependymoma, and prospective clinical trials in this population have not succeeded because of its rarity and challenges in accruing patients. The Collaborative Ependymoma Research Network conducted a prospective phase II clinical trial of dose-dense temozolomide (TMZ) and lapatinib, targeting the unmethylated O6-methylguanine-DNA methyltransferase (MGMT) promoter status and increased expression of ErbB2 (human epidermal growth factor receptor 2) and ErbB1 (epidermal growth factor receptor) in ependymomas.MethodsPatients age 18 or older with histologically proven and progressive ependymoma or anaplastic ependymoma were eligible and received dose-dense TMZ and daily lapatinib. The primary outcome measure was median progression-free survival (PFS). Landmark 6- and 12-month PFS and objective response were measured. Serial assessments of symptom burden using the MD Anderson Symptom Inventory Brain Tumor (MDASI-BT)/MDASI–Spine Tumor modules were collected.ResultsThe 50 patients enrolled had a median age of 43.5 years, median Karnofsky performance status of 90, and a median of 2 prior relapses. Twenty patients had grade III, 16 grade II, and 8 grade I ependymoma. Half had spinal cord tumors; 15 had a supratentorial tumor, 8 infratentorial, and 2 had disseminated disease. Treatment was well tolerated. The median PFS was 7.8 months (95% CI: 5.5,12.2); the 6- and 12-month PFS rates were 55% and 38%, with 2 complete and 6 partial responses. Measures of symptom burden showed reduction in moderate-severe pain and other disease-related symptoms in most patients.ConclusionsThis treatment, with demonstrated clinical activity with objective responses and prolonged disease control associated with disease-related symptom improvements, is an option as a salvage regimen for adult patients with recurrent ependymoma.