bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rare case of a digital papillary carcinoma of the hand with secondary conservative management
Authors: Khan Rabeet , Irri Renu , Katsarma Effie 
Published: December 2019

Abstract
A digital papillary carcinoma (DPC) is a cancer of the sweat glands which develops on the digits of the hands and feet. With an incidence of 0.08 per 1 000 000 people/year, it is often initially misdiagnosed as a simple ganglion although it has a significant risk of metastasis. Histological analysis is beneficial in the formal diagnosis of DPCs. In this report, we present a rare case of DPC affecting the palm of the hand, rather than the more commonly reported DPC of the digits. We discuss the management strategy utilized in this case and the various prognostic considerations taken into account when deciding on an amputation versus local excision surgical approach. All cases of DPC require regular follow up imaging for early detection of recurrence or new metastases to maximize prognosis.
Freeing Ahasuerus, Haman, and Mordechai: Liberating the Oppressor in the Book of Esther
Authors: Flanders Denise 
Published: December 2019

Abstract
The approach taken in this essay proceeds from the assumption that the biblical text of Esther reflects a patriarchal ideology and it is largely the males in the story who wield the power. However, instead of examining the negative consequences for the female characters and how the patriarchal system forces them to operate, I look to the male characters to see how they fare in the system of patriarchy which they undoubtedly inhabit. In the first part of the essay, I consider the call issued by womanist and liberation theologians from traditionally marginalized communities for the need for liberation of both the oppressed and the oppressors from systems of oppression. In the second part of the essay, I respond to this call via an analysis of the book of Esther. First, I examine four different actions or attitudes that characterize the men in the story. Second, I observe some places where their power clearly brings them loss. Third, I argue that the destructive attitudes, actions, and relationships of the men in the story demonstrate their own need for liberation from the oppressive system of patriarchy from which they supposedly benefit.
The Radio Scream from black holes at Cosmic Dawn: a semi-analytic model for the impact of radio-loud black holes on the 21 cm global signal
Authors: Ewall-Wice Aaron , Chang Tzu-Ching , Lazio T Joseph W 
Published: December 2019

ABSTRACT
We use a semi-analytic model to explore the potential impact of a brief and violent period of radio-loud accretion on to black holes (The Radio Scream) during the Cosmic Dawn on the H i hyperfine 21 cm signal. We find that radio emission from supermassive black hole seeds can impact the global 21 cm signal at the level of tens to hundreds of per cent provided that they were as radio loud as $z$ ≈ 1 black holes and obscured by gas with column depths of NH ≳ 1023 cm−2. We determine plausible sets of parameters that reproduce some of the striking features of the EDGES absorption feature including its depth, timing, and side steepness while producing radio/X-ray backgrounds and source counts that are consistent with published limits. Scenarios yielding a dramatic 21 cm signature also predict large populations of ∼$\mu$Jy point sources that will be detectable in future deep surveys from the Square Kilometer Array (SKA). Thus, 21 cm measurements, complemented by deep point-source surveys, have the potential to constrain optimistic scenarios where supermassive black hole progenitors were radio loud.
Pulsar candidate selection using pseudo-nearest centroid neighbour classifier
Authors: Xiao Jiangping , Li Xiangru , Lin Haitao , Qiu Kaibin 
Published: December 2019

ABSTRACT
A typical characteristic of the pulsar candidate classification task is the class imbalance between true pulsars and false candidates. This imbalance has negative effects on traditional classification methods. In this study, we introduce a strategy using a scatter matrix-based class separability measure to estimate the harmfulness of class imbalance on pulsar candidate classification. The measure quantitatively describes the damage of the imbalanced situations on the pulsar candidate classification problem and provides some priori information to guide us to select an appropriate data processing method and to construct an effective classifier. After that, we present a non-parametric data exploration technique, a pseudo-nearest centroid neighbour classifier (PNCN), to identify credible pulsar candidates from pulsar survey data sets. The PNCN algorithm can effectively resolve the class imbalance problem and is applicable to data streams. The proposed algorithm is tested on High Time Resolution Universe Pulsar Survey (HTRU) 2 (obtained by an analysis of HTRU Medium Latitude data) and LOTAAS 1 (obtained from the LOFAR Tied-Array All-Sky Survey). The experimental results show that the proposed classifier can excellently identify the pulsars with high performance: the precision and the recall on HTRU 2 are 92.3 per cent and 83.1 per cent, and those on LOTAAS 1 are 97.4 per cent and 95.6 per cent, respectively; the false positive rate (FPR) on HTRU 2 is 0.7 per cent, on LOTAAS 1 is 0.03 per cent, which is an order of magnitude lower than the corresponding FPR obtained in Lyon et al. (2016) and Tan et al. (2018).
The importance of Hall effect on the magnetized thin accretion disc
Authors: Ghasemnezhad Maryam 
Published: December 2019

ABSTRACT
To study the role of Hall effect on the structure of accretion disc, we have considered a toroidal magnetic field in our paper. To study the vertical structure of the disc, we have written a set of magnetohydrodynamic (MHD) equations in the spherical coordinates (r, θ, ϕ) based on the two assumptions of axisymmetric and steady state. Also, we employed the self-similar solutions in the radial direction to obtain the structure of the disc in the θ-direction. We have solved a set of ordinary differential equations in the θ-coordinate with symmetrical boundary conditions in the equatorial plane. In order to describe the behaviour of Hall effect, we introduced the ΛH parameter that was called the dimensionless Hall Elsasser number. The strength of the Hall effect is measured by the inverse of dimensionless Hall Elsasser number. We have shown that the strong Hall effect decreases the accretion rate or infall velocity and size of inflow part. It has also been found the Hall effect is maximum in the equatorial plane and gets the value close to zero near the boundary, and it has the antidiffusive nature. The results display that the strong Hall effect makes the standard accretion sub-Keplerian disc becomes thinner. Our solutions have shown the Hall effect leads to transport magnetic flux outward in the upper layer of the disc and it produces outflows in the surface of the disc.
The EDGE–CALIFA survey: using optical extinction to probe the spatially resolved distribution of gas in nearby galaxies
Authors: Barrera-Ballesteros Jorge K , Utomo Dyas , Bolatto Alberto D , Sánchez Sebastián F , Vogel Stuart N , Wong Tony , Levy Rebecca C , Colombo Dario , Kalinova Veselina , Teuben Peter , García-Benito Rubén , Husemann Bernd , Mast Damián , Blitz Leo 
Published: December 2019

ABSTRACT
We present an empirical relation between the cold gas surface density (Σgas) and the optical extinction (AV) in a sample of 103 galaxies from the Extragalactic Database for Galaxy Evolution (EDGE) survey. This survey provides CARMA interferometric CO observations for 126 galaxies included in the Calar Alto Legacy Integral Field Area (CALIFA) survey. The matched, spatially resolved nature of these data sets allows us to derive the Σgas–AV relation on global, radial, and kpc (spaxel) scales. We determine AV from the Balmer decrement (H α/H β). We find that the best fit for this relation is $\Sigma _{\rm gas}\,(\rm {M_\odot \,pc}^{-2}) \sim 26 \times {\rm \mathit{ A}_\mathit{ V}} \,(\rm mag)$, and that it does not depend on the spatial scale used for the fit. However, the scatter in the fits increases as we probe smaller spatial scales, reflecting the complex relative spatial distributions of stars, gas, and dust. We investigate the Σgas/AV ratio on radial and spaxel scales as a function of $\mathrm{EW(H\,\alpha)}$. We find that at larger values of $\mathrm{EW({H\,\alpha })}$ (i.e. actively star-forming regions) this ratio tends to converge to twice the value expected for a foreground dust screen geometry (∼30 $\mathrm{M_{\odot } \, pc^{-2} \, mag^{-1}}$). On radial scales, we do not find a significant relation between the Σgas/AV ratio and the ionized gas metallicity. We contrast our estimates of Σgas using AV with compilations in the literature of the gas fraction on global and radial scales as well as with well-known scaling relations such as the radial star formation law and the Σgas–Σ* relation. These tests show that optical extinction is a reliable proxy for estimating Σgas in the absence of direct sub/millimeter observations of the cold gas.
magritte, a modern software library for 3D radiative transfer: I. Non-LTE atomic and molecular line modelling
Authors: De Ceuster Frederik , Homan Ward , Yates Jeremy , Decin Leen , Boyle Peter , Hetherington James 
Published: December 2019

ABSTRACT
Radiative transfer is a key component in almost all astrophysical and cosmological simulations. We present magritte: a modern open-source software library for 3D radiative transfer. It uses a deterministic ray-tracer and formal solver, i.e. it computes the radiation field by tracing rays through the model and solving the radiative transfer equation in its second-order form along a fixed set of rays originating from each point. magritte can handle structured and unstructured input meshes, as well as smoothed-particle hydrodynamics (SPH) particle data. In this first paper, we describe the numerical implementation, semi-analytic tests and cross-code benchmarks for the non-LTE line radiative transfer module of magritte. This module uses the radiative transfer solver to self-consistently determine the populations of the quantized energy levels of atoms and molecules using an accelerated Lambda iteration (ALI) scheme. We compare magritte with the established radiative transfer solvers ratran (1D) and lime (3D) on the van Zadelhoff benchmark and present a first application to a simple Keplerian disc model. Comparing with lime, we conclude that magritte produces more accurate and more precise results, especially at high optical depth, and that it is faster.
Amino acetaldehyde conformers: structure and spectroscopic properties
Authors: Redondo Pilar , Sanz-Novo Miguel , Largo Antonio , Barrientos Carmen 
Published: December 2019

ABSTRACT
We present a computational study of the different conformers of amino acetaldehyde. This molecule is a precursor of glycine and also an isomer of the detected molecules acetaldehyde and methylformamide. In addition, a previous theoretical result shows that amino acetaldehyde could be formed from the gas phase reaction of formamide with CH$_{5}^{+}$. Different computational approaches, going from density functional theory (DFT) to coupled cluster (CC) calculations, are employed for the characterization of the amino acetaldehyde conformers. We locate four low-lying conformation on the singlet potential energy surface (PES), two with a synperiplanar arrangement of the carboxylic oxygen atom and the NH2 group, and the other two conformers with an anticlinal disposition. All levels of theory predict the conformer with a synperiplanar arrangement and the H atoms of the NH2 group pointing in the direction of the oxygen, denoted as in-sp-amino acetaldehyde, as the most stable. The viability of the interconversion processes between the four conformers in space is analysed. Relevant spectroscopic parameters to rotational spectroscopy with ‘spectroscopic’ accuracy at the composite level are reported. Vibrational frequencies and infrared intensities are also computed at the CC with single and double excitations (CCSD) level including anharmonic corrections. This information could help in the experimental characterization of amino acetaldehyde that could be considered as a good candidate molecule to be searched for in space.
On the survival of cool clouds in the circumgalactic medium
Authors: Li Zhihui , Hopkins Philip F , Squire Jonathan , Hummels Cameron 
Published: December 2019

ABSTRACT
We explore the survival of cool clouds in multiphase circumgalactic media. We revisit the ‘cloud-crushing problem’ in a large survey of simulations including radiative cooling, self-shielding, self-gravity, magnetic fields, and anisotropic Braginskii conduction and viscosity (with saturation). We explore a wide range of parameters including cloud size, velocity, ambient temperature and density, and a variety of magnetic field configurations and cloud turbulence. We find that realistic magnetic fields and turbulence have weaker effects on cloud survival; the most important physics is radiative cooling and conduction. Self-gravity and self-shielding are important for clouds that are initially Jeans-unstable, but largely irrelevant otherwise. Non-self-gravitating, realistically magnetized clouds separate into four regimes: (1) at low column densities, clouds evaporate rapidly via conduction; (2) a ‘failed pressure confinement’ regime, where the ambient hot gas cools too rapidly to provide pressure confinement for the cloud; (3) an ‘infinitely long-lived’ regime, in which the cloud lifetime becomes longer than the cooling time of gas swept up in the leading bow shock, so the cloud begins to accrete and grow; and (4) a ‘classical cloud destruction’ regime, where clouds are eventually destroyed by instabilities. In the final regime, the cloud lifetime can exceed the naive cloud-crushing time owing to conduction-induced compression. However, small and/or slow-moving clouds can also evaporate more rapidly than the cloud-crushing time. We develop simple analytic models that explain the simulated cloud destruction times in this regime.
Determining the primordial helium abundance and UV background using fluorescent emission in star-free dark matter haloes
Authors: Sykes Calvin , Fumagalli Michele , Cooke Ryan , Theuns Tom 
Published: December 2019

ABSTRACT
Observational measures of the primordial helium mass fraction, YP, are of interest for cosmology and fundamental particle physics. Current measures obtained from ${\text{H}\, \small {II}}$ regions agree with the Standard Model prediction to approximately 1 per cent precision, although these determinations may be affected by systematic uncertainties. This possibility can only be tested by independently measuring the helium abundance in new ways. Here, we propose a novel method to obtain a measurement of YP using hydrogen and helium recombination line emission from REionization-Limited HI Clouds (RELHICs): pristine, gas-rich but star-free low-mass dark matter haloes whose existence is predicted by hydrodynamical simulations. Although expected to be uncommon and intrinsically faint in emission, the primordial composition and simple physical properties of these objects make them an ideal laboratory to determine YP. We present radiative transfer simulations to demonstrate the effectiveness of this approach, finding that a comparison of the emission in H and He lines, either via their volumetric emissivities, or integrated properties such as the surface brightness and total flux, may be used to infer YP. Furthermore, we show that RELHICs can be used to provide an entirely novel constraint on the spectral slope of the ultraviolet background, and discuss the possibility of measuring this slope and the primordial helium abundance simultaneously.
Disentangling sRNA-Seq data to study RNA communication between species
Authors: Bermúdez-Barrientos José Roberto , Ramírez-Sánchez Obed , Chow Franklin Wang-Ngai , Buck Amy H , Abreu-Goodger Cei 
Published: December 2019

Abstract
Many organisms exchange small RNAs (sRNAs) during their interactions, that can target or bolster defense strategies in host–pathogen systems. Current sRNA-Seq technology can determine the sRNAs present in any symbiotic system, but there are very few bioinformatic tools available to interpret the results. We show that one of the biggest challenges comes from sequences that map equally well to the genomes of both interacting organisms. This arises due to the small size of the sRNAs compared to large genomes, and because a large portion of sequenced sRNAs come from genomic regions that encode highly conserved miRNAs, rRNAs or tRNAs. Here, we present strategies to disentangle sRNA-Seq data from samples of communicating organisms, developed using diverse plant and animal species that are known to receive or exchange RNA with their symbionts. We show that sequence assembly, both de novo and genome-guided, can be used for these sRNA-Seq data, greatly reducing the ambiguity of mapping reads. Even confidently mapped sequences can be misleading, so we further demonstrate the use of differential expression strategies to determine true parasite-derived sRNAs within host cells. We validate our methods on new experiments designed to probe the nature of the extracellular vesicle sRNAs from the parasitic nematode Heligmosomoides bakeri that get into mouse intestinal epithelial cells.
Reassembling green fluorescent protein for in vitro evaluation of trans-translation
Authors: Guyomar Charlotte , Thépaut Marion , Nonin-Lecomte Sylvie , Méreau Agnès , Goude Renan , Gillet Reynald 
Published: December 2019

AbstractIn order to discover new antibiotics with improved activity and selectivity, we created a reliable in vitro reporter system to detect trans-translation activity, the main mechanism for recycling ribosomes stalled on problematic messenger RNA (mRNA) in bacteria. This system is based on an engineered tmRNA variant that reassembles the green fluorescent protein (GFP) when trans-translation is active. Our system is adapted for high-throughput screening of chemical compounds by fluorescence.
Integrative network analysis identifies cell-specific trans regulators of m6A
Authors: An Sanqi , Huang Wanxu , Huang Xiang , Cun Yixian , Cheng Weisheng , Sun Xiang , Ren Zhijun , Chen Yaxin , Chen Wenfang , Wang Jinkai 
Published: December 2019

Abstract
N6-methyladenosine (m6A) is a reversible and dynamic RNA modification in eukaryotes. However, how cells establish cell-specific m6A methylomes is still poorly understood. Here, we developed a computational framework to systematically identify cell-specific trans regulators of m6A through integrating gene expressions, binding targets and binding motifs of large number of RNA binding proteins (RBPs) with a co-methylation network constructed using large-scale m6A methylomes across diverse cell states. We applied the framework and successfully identified 32 high-confidence m6A regulators that modulated the variable m6A sites away from stop codons in a cell-specific manner. To validate them, we knocked down three regulators respectively and found two of them (TRA2A and CAPRIN1) selectively promoted the methylations of the m6A sites co-localized with their binding targets on RNAs through physical interactions with the m6A writers. Knockdown of TRA2A increased the stabilities of the RNAs with TRA2A bound near the m6A sites and decreased the viability of cells. The successful identification of m6A regulators demonstrates a powerful and widely applicable strategy to elucidate the cell-specific m6A regulators. Additionally, our discovery of pervasive trans-acting regulating of m6A provides novel insights into the mechanisms by which spatial and temporal dynamics of m6A methylomes are established.
iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains
Authors: Gräwe Alexander , Ranglack Jan , Weyrich Anastasia , Stein Viktor 
Published: December 2019

Abstract
Recent years have witnessed increasing efforts to engineer artificial biological functions through recombination of modular-organized toolboxes of protein scaffolds and parts. A critical, yet frequently neglected aspect concerns the identity of peptide linkers or spacers connecting individual domains which remain poorly understood and challenging to assemble. Addressing these limitations, iFlinkC comprises a highly scalable DNA assembly process that facilitates the combinatorial recombination of functional domains with linkers of varying length and flexibility, thereby overcoming challenges with high GC-content and the repeat nature of linker elements. The capacity of iFLinkC is demonstrated in the construction of synthetic protease switches featuring PDZ-FN3-based affinity clamps and single-chain FKBP12-FRB receptors as allosteric inputs. Library screening experiments demonstrate that linker space is highly plastic as the induction of allosterically regulated protease switches can vary from &gt;150-fold switch-ON to &gt;13-fold switch-OFF solely depending on the identity of the connecting linkers and relative orientation of functional domains. In addition, Pro-rich linkers yield the most potent switches contradicting the conventional use of flexible Gly-Ser linkers. Given the ease and efficiency how functional domains can be readily recombined with any type of linker, iFLinkC is anticipated to be widely applicable to the assembly of any type of fusion protein.
Electron-hole hybridization in bilayer graphene
Authors: Wang Siqi , Zhao Mervin , Zhang Changjian , Yang Sui , Wang Yuan , Watanabe Kenji , Taniguchi Takashi , Hone James , Zhang Xiang 
Published: December 2019

Abstract
Band structure determines the motion of electrons in a solid, giving rise to exotic phenomena when properly engineered. Drawing an analogy between electrons and photons, artificially designed optical lattices indicate the possibility of a similar band modulation effect in graphene systems. Yet due to the fermionic nature of electrons, modulated electronic systems promise far richer categories of behaviors than those found in optical lattices. Here, we uncovered a strong modulation of electronic states in bilayer graphene subject to periodic potentials. We observed for the first time the hybridization of electron and hole sub-bands, resulting in local band gaps at both primary and secondary charge neutrality points. Such hybridization leads to the formation of flat bands, enabling the study of correlated effects in graphene systems. This work may provide a novel way to manipulate electronic states in layered systems, which is important to both fundamental research and application.